Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 157 of 171
Found at i:46871873 original size:15 final size:15
Alignment explanation
Indices: 46871853--46871883 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46871843 ATGGTGGATG
46871853 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
46871868 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
46871883 G
1 G
46871884 CGGCATAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.55, T:0.19
Consensus pattern (15 bp):
GAGCTGGTGGTGGCA
Found at i:46872090 original size:17 final size:17
Alignment explanation
Indices: 46872068--46872158 Score: 91
Period size: 17 Copynumber: 5.5 Consensus size: 17
46872058 TTTTATTATT
*
46872068 AATTTAAATTTTAATTA
1 AATTTAAATTTAAATTA
**
46872085 AATTTAAATTTAAAGCA
1 AATTTAAATTTAAATTA
46872102 AATTTAAATTT---TTA
1 AATTTAAATTTAAATTA
* *
46872116 CATTTAAATTTAAAATA
1 AATTTAAATTTAAATTA
*
46872133 AATTTAAATTTAACCTT-
1 AATTTAAATTTAA-ATTA
46872150 AATTTAAAT
1 AATTTAAAT
46872159 CTTGTTCAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
14 11 0.18
17 48 0.80
18 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (17 bp):
AATTTAAATTTAAATTA
Found at i:46872091 original size:6 final size:6
Alignment explanation
Indices: 46872068--46872158 Score: 73
Period size: 6 Copynumber: 15.5 Consensus size: 6
46872058 TTTTATTATT
* **
46872068 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA--TTTA
* * **
46872116 CATTTA AATTTA AA-ATA AATTTA AATTTA ACCTT- AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT
46872159 CTTGTTCAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
5 14 0.22
6 46 0.71
8 5 0.08
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:46872667 original size:68 final size:68
Alignment explanation
Indices: 46872492--46873231 Score: 1338
Period size: 68 Copynumber: 10.9 Consensus size: 68
46872482 CTTATTTCAA
* * * * *
46872492 CAATTTCAGAGATAAAGATGTTTTATCCACTCTACTTCAATTCCAAGGGGATGACGTTGCCCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
46872557 CTT
66 CTT
*
46872560 CAATTT-AGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCGCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
46872624 CTT
66 CTT
*
46872627 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCCCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
46872692 CTT
66 CTT
46872695 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
46872760 CTT
66 CTT
* *
46872763 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTTAAGGGGATGACGTTGCTTTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
46872828 CTT
66 CTT
46872831 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTT
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTC-AAGGGGATGACGTTGCTCTT
46872896 ACTT
65 ACTT
*
46872900 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCCATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
46872965 CTT
66 CTT
*
46872968 CAATTTCAGAGATGAAGATGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
46873033 CTT
66 CTT
46873036 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTT
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTC-AAGGGGATGACGTTGCTCTT
46873101 ACTT
65 ACTT
* *
46873105 CAATGTCAGAGATGAAGACGTGTTATCCACTCTACTTCCATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
46873170 CTT
66 CTT
46873173 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
46873232 AGACCTGCAG
Statistics
Matches: 650, Mismatches: 19, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
67 62 0.10
68 456 0.70
69 132 0.20
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (68 bp):
CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
CTT
Found at i:46872977 original size:273 final size:272
Alignment explanation
Indices: 46872492--46873231 Score: 1329
Period size: 273 Copynumber: 2.7 Consensus size: 272
46872482 CTTATTTCAA
* * * ** *
46872492 CAATTTCAGAGATAAAGATGTTTTATCCACTCTACTTCAATTCCAAGGGGATGACGTTGCCCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTAAAGGGGATGACGTTGCTCTTA
*
46872557 CTTCAATTT-AGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCGC
66 CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC
46872621 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
131 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
46872686 CCCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
196 CCCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
46872751 TTGCTCTTACTT
261 TTGCTCTTACTT
* *
46872763 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTTAAGGGGATGACGTTGCTTTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTAAAGGGGATGACGTTGCTCTTA
46872828 CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCT
66 CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTC-AAGGGGATGACGTTGCT
*
46872893 CTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCCATTTCAAGGGGATGACGTT
130 CTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTT
* *
46872958 GCTCTTACTTCAATTTCAGAGATGAAGATGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
195 GCCCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
46873023 GTTGCTCTTACTT
260 GTTGCTCTTACTT
46873036 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTT
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTT-AAAGGGGATGACGTTGCTCTT
* *
46873101 ACTTCAATGTCAGAGATGAAGACGTGTTATCCACTCTACTTCCATTTCAAGGGGATGACGTTGCT
65 ACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCT
46873166 CTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTT
130 CTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTT
46873231 G
195 G
46873232 AGACCTGCAG
Statistics
Matches: 450, Mismatches: 16, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
271 67 0.15
272 37 0.08
273 281 0.62
274 65 0.14
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (272 bp):
CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTAAAGGGGATGACGTTGCTCTTA
CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC
TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
CCCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
TTGCTCTTACTT
Found at i:46872981 original size:205 final size:205
Alignment explanation
Indices: 46872492--46873231 Score: 1349
Period size: 205 Copynumber: 3.6 Consensus size: 205
46872482 CTTATTTCAA
* * * * *
46872492 CAATTTCAGAGATAAAGATGTTTTATCCACTCTACTTCAATTCCAAGGGGATGACGTTGCCCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
*
46872557 CTTCAATTT-AGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCGC
66 CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC
46872621 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTC-AAGGGGATGACGTT
131 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTT
*
46872685 GCCCTTACTT
196 GCTCTTACTT
46872695 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
* *
46872760 CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTTAAGGGGATGACGTTGCTT
66 CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC
46872825 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTT
131 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTT
46872890 GCTCTTACTT
196 GCTCTTACTT
*
46872900 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCCATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
*
46872965 CTTCAATTTCAGAGATGAAGATGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC
66 CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC
46873030 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTT
131 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTT
46873095 GCTCTTACTT
196 GCTCTTACTT
* *
46873105 CAATGTCAGAGATGAAGACGTGTTATCCACTCTACTTCCATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
46873170 CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
66 CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
46873232 AGACCTGCAG
Statistics
Matches: 520, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
203 69 0.13
204 102 0.20
205 349 0.67
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (205 bp):
CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
CTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC
TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTT
GCTCTTACTT
Found at i:46885153 original size:30 final size:29
Alignment explanation
Indices: 46885117--46885270 Score: 156
Period size: 30 Copynumber: 5.2 Consensus size: 29
46885107 ACCCGGGGGC
*
46885117 AAAATGGTAATTTTGGTGTAATCGGGGTT
1 AAAATGGTAATTTTGGTGAAATCGGGGTT
* * *
46885146 AAAAATGG-AATTTTAG-AAAATTCGGGGGGT
1 -AAAATGGTAATTTTGGTGAAA-TC-GGGGTT
46885176 AAAATGGTAATTTTCGGTGAAATCGGGGTT
1 AAAATGGTAATTTT-GGTGAAATCGGGGTT
* *
46885206 AAAATGG-AATTTT-G-AAAGATTCGGGGGT
1 AAAATGGTAATTTTGGTGAA-A-TCGGGGTT
46885234 AAAATGGTAAATTTTGGTGAAATCGGGGTT
1 AAAATGGT-AATTTTGGTGAAATCGGGGTT
46885264 AAAATGG
1 AAAATGG
46885271 GATTTAGGGA
Statistics
Matches: 102, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 16 0.16
29 22 0.22
30 50 0.49
31 5 0.05
32 5 0.05
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.31
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTT
Found at i:46885210 original size:59 final size:57
Alignment explanation
Indices: 46885110--46885305 Score: 261
Period size: 58 Copynumber: 3.4 Consensus size: 57
46885100 TATGGATACC
* *
46885110 CGGGGGCAAAATGGTAATTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAGAAAATT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAAATT
46885168 CGGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAATGGAATTTT-GAAAGATT
1 C-GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAATGGAATTTTAGAAA-ATT
* * *
46885227 CGGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAATGGGA-TTTAGGGAAGTT
1 CGGGGGTAAAATGGT-AATTTTGGTGAAATCGGGGTTAAAATGGAATTTTA-GAAAATT
* *
46885285 TGGGGGTAAAATGATAATTTT
1 CGGGGGTAAAATGGTAATTTT
46885306 TGAAAGTTTT
Statistics
Matches: 125, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
57 9 0.07
58 57 0.46
59 45 0.36
60 14 0.11
ACGTcount: A:0.33, C:0.04, G:0.32, T:0.31
Consensus pattern (57 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAAATT
Found at i:46885319 original size:30 final size:30
Alignment explanation
Indices: 46885280--46885608 Score: 450
Period size: 30 Copynumber: 11.0 Consensus size: 30
46885270 GGATTTAGGG
* *
46885280 AAGTTTGGGGGT-AAAATGATAATTTTTG-A
1 AAGTTTTGGGGTCAAAATG-TAATTTTGGAA
46885309 AAGTTTTGGGGTCAAAATGTAATTTTAGG-A
1 AAGTTTTGGGGTCAAAATGTAATTTT-GGAA
*
46885339 AAGTTTTGGGGTCAAAATGTGATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
46885369 AAGTTTTAGGGTTAAAATGTAATTTTAGG-A
1 AAGTTTTGGGGTCAAAATGTAATTTT-GGAA
* * *
46885399 AAGTTTTAGGGTTAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
46885429 AAGTTTTGGGGTTAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
46885459 AAGTTTTGAGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
46885489 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
46885519 AAGTTTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* * *
46885549 AAGTTTTGGGGTTAAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
46885579 AAGTTTTAGGGTCAAAATGTAATTTCTGGA
1 AAGTTTTGGGGTCAAAATGTAATTT-TGGA
46885609 TAATTTAGGG
Statistics
Matches: 271, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
29 22 0.08
30 244 0.90
31 5 0.02
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAA
Found at i:46886457 original size:23 final size:23
Alignment explanation
Indices: 46886405--46886459 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
46886395 TCTTCGTTTT
*
46886405 ACCAGAACCGGATCTGGTTTTAA
1 ACCAGATCCGGATCTGGTTTTAA
46886428 ACCAGATCCGGATCTGGTTTTAA
1 ACCAGATCCGGATCTGGTTTTAA
46886451 ACCAGATCC
1 ACCAGATCC
46886460 AAATGATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (23 bp):
ACCAGATCCGGATCTGGTTTTAA
Found at i:46886731 original size:12 final size:12
Alignment explanation
Indices: 46886711--46886740 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
46886701 GTTATTATTG
46886711 TAATATATTTAT
1 TAATATATTTAT
*
46886723 TAATGTATTTAT
1 TAATATATTTAT
46886735 TAATAT
1 TAATAT
46886741 CATTCACCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
TAATATATTTAT
Found at i:46887438 original size:17 final size:17
Alignment explanation
Indices: 46887416--46887507 Score: 84
Period size: 17 Copynumber: 5.5 Consensus size: 17
46887406 TTTTATTATT
46887416 AATTTAAATTTTAATTA
1 AATTTAAATTTTAATTA
* **
46887433 AATTTAAATTTAAAGCA
1 AATTTAAATTTTAATTA
46887450 AATTTAAA-TTT--TTA
1 AATTTAAATTTTAATTA
* * *
46887464 CATTTAAATTTAAAATA
1 AATTTAAATTTTAATTA
46887481 AATTTAAA-TTTAACCTTA
1 AATTTAAATTTTAA--TTA
46887499 AATTTAAAT
1 AATTTAAAT
46887508 CTTGTTCAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
14 8 0.14
15 2 0.04
16 6 0.11
17 31 0.54
18 10 0.18
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (17 bp):
AATTTAAATTTTAATTA
Found at i:46887439 original size:6 final size:6
Alignment explanation
Indices: 46887416--46887507 Score: 82
Period size: 6 Copynumber: 15.5 Consensus size: 6
46887406 TTTTATTATT
* **
46887416 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA--TTTA
* * **
46887464 CATTTA AATTTA AA-ATA AATTTA AATTTA ACCTTA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT
46887508 CTTGTTCAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
5 11 0.16
6 51 0.76
8 5 0.07
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:46888807 original size:31 final size:28
Alignment explanation
Indices: 46888789--46888863 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 28
46888779 TTAGTATTTT
*
46888789 AATTTAAATTTAAATTTAAATTTAAGGTA
1 AATTTAAATTTAAATTTAAATTT-AGATA
46888818 AATTTAAATAATTAAATTTAAATTTAAGATA
1 AATTTAAAT--TTAAATTTAAATTT-AGATA
46888849 AATTTAAATTTAAAT
1 AATTTAAATTTAAAT
46888864 CAATTTAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 15 0.35
31 28 0.65
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (28 bp):
AATTTAAATTTAAATTTAAATTTAGATA
Found at i:46888812 original size:6 final size:6
Alignment explanation
Indices: 46888772--46888863 Score: 91
Period size: 6 Copynumber: 15.2 Consensus size: 6
46888762 ACTTTTAATG
* * **
46888772 TTTAAA TTTAGTA TTTTAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
46888820 TTTAAA TAATTAAA TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA T
1 TTTAAA T--TTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA T
46888864 CAATTTAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 1 0.01
5 6 0.08
6 53 0.75
7 5 0.07
8 6 0.08
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:46888819 original size:11 final size:11
Alignment explanation
Indices: 46888805--46888855 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
46888795 AATTTAAATT
*
46888805 TAAATTTAAGG
1 TAAATTTAAGA
46888816 TAAATTTAA-A
1 TAAATTTAAGA
* **
46888826 T-AATTAAATT
1 TAAATTTAAGA
46888836 TAAATTTAAGA
1 TAAATTTAAGA
46888847 TAAATTTAA
1 TAAATTTAA
46888856 ATTTAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 24 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:46888819 original size:17 final size:17
Alignment explanation
Indices: 46888799--46888871 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
46888789 AATTTAAATT
*
46888799 TAAATTTAAATTTAAGG
1 TAAATTTAAATTTAAGA
*
46888816 TAAATTTAAA--TAA-T
1 TAAATTTAAATTTAAGA
46888830 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAGA
46888847 TAAATTTAAATTTAA-A
1 TAAATTTAAATTTAAGA
*
46888863 TCAATTTAA
1 TAAATTTAA
46888872 TTCTAAATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 12 0.24
17 25 0.50
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAGA
Found at i:46888833 original size:37 final size:38
Alignment explanation
Indices: 46888792--46888880 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 38
46888782 GTATTTTAAT
*
46888792 TTAAATTTAAATTTAA-ATTTAAGGTAAATTTAAAT-AA
1 TTAAATTTAAATTTAAGA-TAAAGGTAAATTTAAATCAA
**
46888829 TTAAATTTAAATTTAAGATAAATTTAAATTTAAATCAA
1 TTAAATTTAAATTTAAGATAAAGGTAAATTTAAATCAA
*
46888867 TTTAATTCTAAATT
1 TTAAATT-TAAATT
46888881 AGAACAAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
37 30 0.67
38 9 0.20
39 6 0.13
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (38 bp):
TTAAATTTAAATTTAAGATAAAGGTAAATTTAAATCAA
Found at i:46892122 original size:22 final size:21
Alignment explanation
Indices: 46892083--46892132 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
46892073 TATTTCATGC
* *
46892083 TAATTTTTTTTATGATTTTTTA
1 TAATTTTTTTAATGA-TTTTCA
46892105 TAATTTTTTTGAAT-ATTTTCA
1 TAATTTTTTT-AATGATTTTCA
46892126 TAATTTT
1 TAATTTT
46892133 AATTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.48
22 11 0.44
23 2 0.08
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (21 bp):
TAATTTTTTTAATGATTTTCA
Found at i:46902634 original size:53 final size:54
Alignment explanation
Indices: 46902575--46902678 Score: 174
Period size: 55 Copynumber: 1.9 Consensus size: 54
46902565 CTGTTTGGAG
*
46902575 GCACACGGGCGTGTGTCAGGG-TGTGTGTTTACTGTTTGGAGGCACATGGACTA
1 GCACACGGGCGTGTGTCAGGGATGTGTGTATACTGTTTGGAGGCACATGGACTA
*
46902628 GCACACGGGTGTGTGTCAGGGATTGTGTGTATACTGTTTGGAGGCACATGG
1 GCACACGGGCGTGTGTCAGGGA-TGTGTGTATACTGTTTGGAGGCACATGG
46902679 GCATGTGTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 20 0.43
55 27 0.57
ACGTcount: A:0.17, C:0.15, G:0.38, T:0.29
Consensus pattern (54 bp):
GCACACGGGCGTGTGTCAGGGATGTGTGTATACTGTTTGGAGGCACATGGACTA
Found at i:46902643 original size:96 final size:96
Alignment explanation
Indices: 46902543--46902747 Score: 277
Period size: 96 Copynumber: 2.1 Consensus size: 96
46902533 CATACAATCT
* * *
46902543 TGTGTCAAGGTGTATGTGTATACTGTTTGGAGGCACACGGGCGTGTGTCAGGGTGTGTGTTTACT
1 TGTGTCAGGGTGTATGTGTATACTGTTTGGAGGCACACGGGCATGTGTCAGGGTGTGTGTATACT
* * *
46902608 GTTTGGAGGCACATGGACTAGCACACGGGTG
66 GTTTAGAGGCACACGGACTAGCACACGGGCG
* * * *
46902639 TGTGTCAGGGAT-TGTGTGTATACTGTTTGGAGGCACATGGGCATGTGTTAGGGTGTGTGTATGC
1 TGTGTCAGGG-TGTATGTGTATACTGTTTGGAGGCACACGGGCATGTGTCAGGGTGTGTGTATAC
* *
46902703 TGTTTAGAGGCACACGGGCTGGCACACGGGCG
65 TGTTTAGAGGCACACGGACTAGCACACGGGCG
*
46902735 TGTGCCAGGGTGT
1 TGTGTCAGGGTGT
46902748 GTGCATATTG
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
95 1 0.01
96 92 0.98
97 1 0.01
ACGTcount: A:0.17, C:0.15, G:0.39, T:0.30
Consensus pattern (96 bp):
TGTGTCAGGGTGTATGTGTATACTGTTTGGAGGCACACGGGCATGTGTCAGGGTGTGTGTATACT
GTTTAGAGGCACACGGACTAGCACACGGGCG
Found at i:46902675 original size:43 final size:41
Alignment explanation
Indices: 46902628--46902721 Score: 116
Period size: 41 Copynumber: 2.2 Consensus size: 41
46902618 ACATGGACTA
** *
46902628 GCACACGGGTGTGTGTCAGGGATTGTGTGTATACTGTTTGGAG
1 GCACACGGGCATGTGTCAGGG--TGTGTGTATACTGTTTAGAG
* * *
46902671 GCACATGGGCATGTGTTAGGGTGTGTGTATGCTGTTTAGAG
1 GCACACGGGCATGTGTCAGGGTGTGTGTATACTGTTTAGAG
46902712 GCACACGGGC
1 GCACACGGGC
46902722 TGGCACACGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 27 0.61
43 17 0.39
ACGTcount: A:0.17, C:0.14, G:0.39, T:0.30
Consensus pattern (41 bp):
GCACACGGGCATGTGTCAGGGTGTGTGTATACTGTTTAGAG
Found at i:46903221 original size:40 final size:39
Alignment explanation
Indices: 46903177--46903287 Score: 114
Period size: 40 Copynumber: 2.8 Consensus size: 39
46903167 GAGAATATTT
* *
46903177 ACTGAACAAGCAGTGACACTATTAACACTGCAAGATTTCA
1 ACTGAAC-AGCAGTGACACTATAAACACTGCAAGATTACA
* * * *
46903217 ACTGAACCGGCAGTGATACTGTAAACACTACAAGATTACA
1 ACTGAA-CAGCAGTGACACTATAAACACTGCAAGATTACA
* * *
46903257 ACTGATCTGATAGTGACACTATAAACACTGC
1 ACTGAACAG-CAGTGACACTATAAACACTGC
46903288 GATGTGTCAT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
39 2 0.04
40 54 0.95
41 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (39 bp):
ACTGAACAGCAGTGACACTATAAACACTGCAAGATTACA
Found at i:46903423 original size:29 final size:29
Alignment explanation
Indices: 46903386--46903458 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
46903376 TGCCTGCATT
*
46903386 TGTAATTGTATTTATGACATGACTATATC
1 TGTAATTGTATCTATGACATGACTATATC
* * *
46903415 TGTGATTGTATCTGTGTCATGACTATATC
1 TGTAATTGTATCTATGACATGACTATATC
46903444 TGTAATTGTATCTAT
1 TGTAATTGTATCTAT
46903459 ATTATTTCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (29 bp):
TGTAATTGTATCTATGACATGACTATATC
Found at i:46905710 original size:55 final size:53
Alignment explanation
Indices: 46905633--46905878 Score: 233
Period size: 55 Copynumber: 4.5 Consensus size: 53
46905623 ATTATTCAGG
* * * **
46905633 AGGTGTGTGTGCATACTGTTTGGAGGCACACGAGCTGGCACATGGATGTGTGTC
1 AGGT-TGTGTGTATACTATTTGGAGGCACACGGGCTGGCACATGGGCGTGTGTC
* * * *
46905687 AAGGATTATGTGTATACTATTTGGAGGCACACGGGTTGGCATACGGGCGTGTGTC
1 -AGG-TTGTGTGTATACTATTTGGAGGCACACGGGCTGGCACATGGGCGTGTGTC
* *
46905742 AGGGTGTGTGTGTATACTATTTGGAAGCACACGGGCTGACACATGGGCGTGTGTC
1 A-GGT-TGTGTGTATACTATTTGGAGGCACACGGGCTGGCACATGGGCGTGTGTC
* * * ** *
46905797 AGGGTGTGTGTATACTATTCTAG-GGCACATGGGCTGATACATGGGCGCGTGTC
1 AGGTTGTGTGTATACTATT-TGGAGGCACACGGGCTGGCACATGGGCGTGTGTC
* * * * *
46905850 AGGGTGTGTGCATATTATTTTGAGACACA
1 AGGTTGTGTGTATACTATTTGGAGGCACA
46905879 TGGTCTGCAA
Statistics
Matches: 161, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
52 2 0.01
53 63 0.39
54 6 0.04
55 89 0.55
56 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (53 bp):
AGGTTGTGTGTATACTATTTGGAGGCACACGGGCTGGCACATGGGCGTGTGTC
Found at i:46905879 original size:53 final size:53
Alignment explanation
Indices: 46905695--46905881 Score: 189
Period size: 53 Copynumber: 3.5 Consensus size: 53
46905685 TCAAGGATTA
* * * * * * *
46905695 TGTGTATACTATTTGGAGGCACACGGGTTGGCATACGGGCGTGTGTCAGGGTGTG
1 TGTGTATACTATTTTGAGACACATGGGCTGACACATGGGCGTGTGTCA-GG-GTG
* *
46905750 TGTGTATACTATTTGGA-AGCACACGGGCTGACACATGGGCGTGTGTCAGGGTG
1 TGTGTATACTATTTTGAGA-CACATGGGCTGACACATGGGCGTGTGTCAGGGTG
* * * *
46905803 TGTGTATACTATTCT-AGGGCACATGGGCTGATACATGGGCGCGTGTCAGGGTG
1 TGTGTATACTATTTTGA-GACACATGGGCTGACACATGGGCGTGTGTCAGGGTG
* *
46905856 TGTGCATATTATTTTGAGACACATGG
1 TGTGTATACTATTTTGAGACACATGG
46905882 TCTGCAATAA
Statistics
Matches: 113, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
52 1 0.01
53 67 0.59
54 3 0.03
55 42 0.37
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.29
Consensus pattern (53 bp):
TGTGTATACTATTTTGAGACACATGGGCTGACACATGGGCGTGTGTCAGGGTG
Found at i:46906550 original size:29 final size:29
Alignment explanation
Indices: 46906497--46906679 Score: 186
Period size: 29 Copynumber: 6.3 Consensus size: 29
46906487 TCTGCATCTA
* * *
46906497 TAACTGTATTTGTGACTTGATTGTATTTG
1 TAACTGTATCTGTGACATGAATGTATTTG
* * *
46906526 TAACTGTATCTATTACATGACTGTATTTG
1 TAACTGTATCTGTGACATGAATGTATTTG
* * *
46906555 TGACTGTATCTGTGGCATGAATGTATCTG
1 TAACTGTATCTGTGACATGAATGTATTTG
* * * *
46906584 TAACTGTATTTGTGACTTGACTGTACTTG
1 TAACTGTATCTGTGACATGAATGTATTTG
* * *
46906613 TAACTGTATCTATTACATGATTGTATTTG
1 TAACTGTATCTGTGACATGAATGTATTTG
* * * *
46906642 TGACTGTATTTGTGGCATGAATGTATCTG
1 TAACTGTATCTGTGACATGAATGTATTTG
46906671 TAACTGTAT
1 TAACTGTAT
46906680 GTCTTATTTC
Statistics
Matches: 122, Mismatches: 32, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 122 1.00
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.45
Consensus pattern (29 bp):
TAACTGTATCTGTGACATGAATGTATTTG
Found at i:46906614 original size:87 final size:87
Alignment explanation
Indices: 46906492--46906679 Score: 331
Period size: 87 Copynumber: 2.2 Consensus size: 87
46906482 TCATGTCTGC
* * *
46906492 ATCTATAACTGTATTTGTGACTTGATTGTATTTGTAACTGTATCTATTACATGACTGTATTTGTG
1 ATCTGTAACTGTATTTGTGACTTGACTGTACTTGTAACTGTATCTATTACATGACTGTATTTGTG
46906557 ACTGTATCTGTGGCATGAATGT
66 ACTGTATCTGTGGCATGAATGT
*
46906579 ATCTGTAACTGTATTTGTGACTTGACTGTACTTGTAACTGTATCTATTACATGATTGTATTTGTG
1 ATCTGTAACTGTATTTGTGACTTGACTGTACTTGTAACTGTATCTATTACATGACTGTATTTGTG
*
46906644 ACTGTATTTGTGGCATGAATGT
66 ACTGTATCTGTGGCATGAATGT
46906666 ATCTGTAACTGTAT
1 ATCTGTAACTGTAT
46906680 GTCTTATTTC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 96 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.45
Consensus pattern (87 bp):
ATCTGTAACTGTATTTGTGACTTGACTGTACTTGTAACTGTATCTATTACATGACTGTATTTGTG
ACTGTATCTGTGGCATGAATGT
Found at i:46912717 original size:28 final size:28
Alignment explanation
Indices: 46912662--46912732 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
46912652 TATTTTTTAA
* *
46912662 AATATTTATATTATATTATTTTAATATTT
1 AATATTTTTA-TATATTATTTTAATATTG
*
46912691 AATATTTTTATATATT-TTTTATTTATTG
1 AATATTTTTATATATTATTTTA-ATATTG
46912719 AA-ATTTTTTATATA
1 AATA-TTTTTATATA
46912733 GTCATCTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.16
28 22 0.59
29 9 0.24
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (28 bp):
AATATTTTTATATATTATTTTAATATTG
Found at i:46920065 original size:30 final size:30
Alignment explanation
Indices: 46920003--46920245 Score: 303
Period size: 30 Copynumber: 8.2 Consensus size: 30
46919993 GGTAGTTCTC
* * *
46920003 AAACTTTCCTAAAATCATATTTTAA-ACCT
1 AAACTTTCCTAAAATTACATTTTAACCCCT
* *
46920032 AAACTTTTCTAAAATTATATTTTAACCCCT
1 AAACTTTCCTAAAATTACATTTTAACCCCT
* *
46920062 AAACTTTCCTAAAATCATATTTTAACCCCT
1 AAACTTTCCTAAAATTACATTTTAACCCCT
* *
46920092 AAACTTTTCAAAAATTACATTTTAACCCCT
1 AAACTTTCCTAAAATTACATTTTAACCCCT
* *
46920122 AAACTTT-CTAAAAATTACACTTTGACCCCT
1 AAACTTTCCT-AAAATTACATTTTAACCCCT
* * *
46920152 AAACTTTCCAAAAATTACATTTTGACCCTT
1 AAACTTTCCTAAAATTACATTTTAACCCCT
*
46920182 AAACTTTCCAAAAATTACATTTTAACCCCT
1 AAACTTTCCTAAAATTACATTTTAACCCCT
* *
46920212 AAACTTTTCTAAAATCACATTTTAACCCC-
1 AAACTTTCCTAAAATTACATTTTAACCCCT
46920241 AAACT
1 AAACT
46920246 CTTCGAAACT
Statistics
Matches: 191, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
29 29 0.15
30 161 0.84
31 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (30 bp):
AAACTTTCCTAAAATTACATTTTAACCCCT
Found at i:46922548 original size:46 final size:46
Alignment explanation
Indices: 46922475--46922573 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 46
46922465 TGCTCCAACT
* * * *
46922475 ATATTATTATGAGATATTGTTTTTTAGTAATTTGGTTCCTAATAGG
1 ATATTATTATGAGATATTATCTCTTAGTAATTTGATTCCTAATAGG
*
46922521 ATATTATTATGAGATATTATCTCTTAGTAATTTGATTCCTAATGGG
1 ATATTATTATGAGATATTATCTCTTAGTAATTTGATTCCTAATAGG
46922567 ATATTAT
1 ATATTAT
46922574 GATATATTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (46 bp):
ATATTATTATGAGATATTATCTCTTAGTAATTTGATTCCTAATAGG
Found at i:46922590 original size:13 final size:13
Alignment explanation
Indices: 46922572--46922596 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46922562 ATGGGATATT
46922572 ATGATATATTATA
1 ATGATATATTATA
46922585 ATGATATATTAT
1 ATGATATATTAT
46922597 TTTTTAGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
ATGATATATTATA
Found at i:46924060 original size:60 final size:59
Alignment explanation
Indices: 46923930--46924188 Score: 279
Period size: 60 Copynumber: 4.3 Consensus size: 59
46923920 GGGAGTTTAT
* * *
46923930 TTTTCAAAAATTATATTTTAATCTTCGAACTTTTTTAAAAATTATATTTTGATCCAT-AAA
1 TTTTCAAAAATTATATTTTAATCTT--AAATTTTTTAAAAATTATATTTTAACCCATAAAA
* * **
46923990 TTTCTTAAAAATTATATTTTAATCTTCGAATTTTTTAAAAATTATATTTTAACCTTTAAAA
1 TTT-TCAAAAATTATATTTTAATCTT-AAATTTTTTAAAAATTATATTTTAACCCATAAAA
* ** * * *
46924051 TTTTCAAAAATTATGTTTTAACTCTTAAACATTTTAAAAATTATATTTTGACCCCTAAAC
1 TTTTCAAAAATTATATTTTAA-TCTTAAATTTTTTAAAAATTATATTTTAACCCATAAAA
* * * *
46924111 TTTTTAAAAATTATATTTTAACCCTAAATTTTTCT-AAAATTATATTTTAACCCATAAAC
1 TTTTCAAAAATTATATTTTAATCTTAAATTTTT-TAAAAATTATATTTTAACCCATAAAA
* *
46924170 TTTCCCAAAATTATATTTT
1 TTTTCAAAAATTATATTTT
46924189 GACCCTAAAC
Statistics
Matches: 167, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
59 46 0.28
60 90 0.54
61 31 0.19
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (59 bp):
TTTTCAAAAATTATATTTTAATCTTAAATTTTTTAAAAATTATATTTTAACCCATAAAA
Found at i:46924096 original size:90 final size:89
Alignment explanation
Indices: 46923928--46924197 Score: 269
Period size: 90 Copynumber: 3.0 Consensus size: 89
46923918 GAGGGAGTTT
* * * * * * *
46923928 ATTTTTCAAAAATTATATTTTAATCTTCGAACTTTTTTAAAAATTATATTTTGA-TCCATAAATT
1 ATTTTTTAAAAATTATATTTTAACCTT-TAAATTTTTCAAAAATTATATTTTAACT-CATAAACT
* * *
46923992 TCTTAAAAATTATATTTTAA-TCTTCGA
64 T-TTAAAAATTATATTTTAACCCCT-AA
* * *
46924019 ATTTTTTAAAAATTATATTTTAACCTTTAAAATTTTCAAAAATTATGTTTTAACTCTTAAACATT
1 ATTTTTTAAAAATTATATTTTAACCTTTAAATTTTTCAAAAATTATATTTTAACTCATAAAC-TT
*
46924084 TTAAAAATTATATTTTGACCCCTAA
65 TTAAAAATTATATTTTAACCCCTAA
* * * *
46924109 ACTTTTTAAAAATTATATTTTAACC-CTAAATTTTTCTAAAATTATATTTTAACCCATAAACTTT
1 ATTTTTTAAAAATTATATTTTAACCTTTAAATTTTTCAAAAATTATATTTTAACTCATAAACTTT
** *
46924173 CCCAAAATTATATTTTGA-CCCTAA
66 -TAAAAATTATATTTTAACCCCTAA
46924197 A
1 A
46924198 CTCTCTGAAA
Statistics
Matches: 152, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
88 10 0.07
89 45 0.30
90 67 0.44
91 30 0.20
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (89 bp):
ATTTTTTAAAAATTATATTTTAACCTTTAAATTTTTCAAAAATTATATTTTAACTCATAAACTTT
TAAAAATTATATTTTAACCCCTAA
Found at i:46924182 original size:30 final size:29
Alignment explanation
Indices: 46923930--46924199 Score: 229
Period size: 30 Copynumber: 9.0 Consensus size: 29
46923920 GGGAGTTTAT
* * *
46923930 TTTTCAAAAATTATATTTTAATCTTCGAAC
1 TTTTCAAAAATTATATTTTAACCCT-AAAC
* * *
46923960 TTTTTTAAAAATTATATTTTGATCCATAAA-
1 -TTTTCAAAAATTATATTTT-AACCCTAAAC
* * * * *
46923990 TTTCTTAAAAATTATATTTTAATCTTCGAAT
1 TTT-TCAAAAATTATATTTTAACCCT-AAAC
* * *
46924021 TTTTTAAAAATTATATTTTAACCTTTAAAA
1 TTTTCAAAAATTATATTTTAACC-CTAAAC
* *
46924051 TTTTCAAAAATTATGTTTTAACTCTTAAAC
1 TTTTCAAAAATTATATTTTAAC-CCTAAAC
*
46924081 ATTTT-AAAAATTATATTTTGACCCCTAAAC
1 -TTTTCAAAAATTATATTTT-AACCCTAAAC
* *
46924111 TTTTTAAAAATTATATTTTAACCCTAAAT
1 TTTTCAAAAATTATATTTTAACCCTAAAC
*
46924140 TTTTCTAAAATTATATTTTAACCCATAAAC
1 TTTTCAAAAATTATATTTTAACCC-TAAAC
* * *
46924170 TTTCCCAAAATTATATTTTGACCCTAAAC
1 TTTTCAAAAATTATATTTTAACCCTAAAC
46924199 T
1 T
46924200 CTCTGAAACT
Statistics
Matches: 203, Mismatches: 26, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
29 46 0.23
30 122 0.60
31 32 0.16
32 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (29 bp):
TTTTCAAAAATTATATTTTAACCCTAAAC
Found at i:46924299 original size:24 final size:25
Alignment explanation
Indices: 46924257--46924304 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
46924247 CATACATAAA
*
46924257 ATTTAATTATTATTCTTCGTTTTTT
1 ATTTAATTATTATTCTTCGATTTTT
* *
46924282 ATTTAA-TCTTATTTTTCGATTTT
1 ATTTAATTATTATTCTTCGATTTT
46924305 GATCCGCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (25 bp):
ATTTAATTATTATTCTTCGATTTTT
Found at i:46925513 original size:34 final size:34
Alignment explanation
Indices: 46925470--46925593 Score: 144
Period size: 34 Copynumber: 3.6 Consensus size: 34
46925460 TTCCGATCTG
* **
46925470 ATATGACATTTTAACCTGATATATGTTTCTAGAA
1 ATATGACATTTTGATATGATATATGTTTCTAGAA
* *
46925504 ATATGACATTCTGATATGATATA--TTTCTGGAA
1 ATATGACATTTTGATATGATATATGTTTCTAGAA
46925536 ATATGACATTTTGATATGATATATATGTTTCTAGAA
1 ATATGACATTTTGATATG--ATATATGTTTCTAGAA
* * *
46925572 ATATGATATTCTAATATGATAT
1 ATATGACATTTTGATATGATAT
46925594 TTGAATATGT
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
32 25 0.33
34 28 0.37
36 23 0.30
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (34 bp):
ATATGACATTTTGATATGATATATGTTTCTAGAA
Found at i:46925537 original size:32 final size:32
Alignment explanation
Indices: 46925490--46925593 Score: 127
Period size: 32 Copynumber: 3.1 Consensus size: 32
46925480 TTAACCTGAT
*
46925490 ATATGTTTCTAGAAATATGACATTCTGATATG
1 ATATATTTCTAGAAATATGACATTCTGATATG
* *
46925522 ATATATTTCTGGAAATATGACATTTTGATATG
1 ATATATTTCTAGAAATATGACATTCTGATATG
* *
46925554 ATATATATGTTTCTAGAAATATGATATTCTAATATG
1 --ATATA--TTTCTAGAAATATGACATTCTGATATG
46925590 ATAT
1 ATAT
46925594 TTGAATATGT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
32 29 0.48
34 9 0.15
36 23 0.38
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (32 bp):
ATATATTTCTAGAAATATGACATTCTGATATG
Found at i:46925574 original size:36 final size:36
Alignment explanation
Indices: 46925488--46925593 Score: 148
Period size: 36 Copynumber: 3.1 Consensus size: 36
46925478 TTTTAACCTG
46925488 ATATATGTTTCTAGAAATATGACATTCTGATATG--
1 ATATATGTTTCTAGAAATATGACATTCTGATATGAT
* *
46925522 ATATA--TTTCTGGAAATATGACATTTTGATATGAT
1 ATATATGTTTCTAGAAATATGACATTCTGATATGAT
* *
46925556 ATATATGTTTCTAGAAATATGATATTCTAATATGAT
1 ATATATGTTTCTAGAAATATGACATTCTGATATGAT
46925592 AT
1 AT
46925594 TTGAATATGT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
32 25 0.40
34 10 0.16
36 27 0.44
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (36 bp):
ATATATGTTTCTAGAAATATGACATTCTGATATGAT
Found at i:46926062 original size:13 final size:13
Alignment explanation
Indices: 46926046--46926071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46926036 CTAAGTTAGA
46926046 TTTTAAATTAATT
1 TTTTAAATTAATT
46926059 TTTTAAATTAATT
1 TTTTAAATTAATT
46926072 GATGTTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAAATTAATT
Found at i:46930842 original size:24 final size:24
Alignment explanation
Indices: 46930776--46930842 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
46930766 ACATGGTTCA
* * *
46930776 CACATATAGGGTTCACTTACTAGAT
1 CACATA-AGAGTTCACATACTAAAT
*
46930801 CACATAAGAGTTCTCATACTAAAT
1 CACATAAGAGTTCACATACTAAAT
*
46930825 CACATGAG-GATTCACATA
1 CACATAAGAG-TTCACATA
46930843 TACAGGATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 1 0.03
24 28 0.80
25 6 0.17
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (24 bp):
CACATAAGAGTTCACATACTAAAT
Found at i:46930929 original size:24 final size:24
Alignment explanation
Indices: 46930850--46930928 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
46930840 ATATACAGGA
*
46930850 TTCGCATACTAAATCATATG-GGG
1 TTCGCATACTAAATCACATGAGGG
* * *
46930873 TTTGCATACTAATTCACATAAGGG
1 TTCGCATACTAAATCACATGAGGG
** *
46930897 TTCATATATTAAATCACATGAGGG
1 TTCGCATACTAAATCACATGAGGG
46930921 TTCGCATA
1 TTCGCATA
46930929 TAGGGTTCAC
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 16 0.37
24 27 0.63
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (24 bp):
TTCGCATACTAAATCACATGAGGG
Found at i:46930935 original size:13 final size:14
Alignment explanation
Indices: 46930917--46930956 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
46930907 AAATCACATG
46930917 AGGGTTCGCATAT-
1 AGGGTTCGCATATA
* *
46930930 AGGGTTCACACATA
1 AGGGTTCGCATATA
46930944 AGGGTTCGCATAT
1 AGGGTTCGCATAT
46930957 TGAATCCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (14 bp):
AGGGTTCGCATATA
Found at i:46933615 original size:24 final size:24
Alignment explanation
Indices: 46933555--46933615 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
46933545 GATTCGCATA
*
46933555 AGGGTTCGCATACTAAATCACATG
1 AGGGTTCGCATATTAAATCACATG
*
46933579 AGGGTTCACATATTAAATCACATG
1 AGGGTTCGCATATTAAATCACATG
*
46933603 AGGGTTTGCATAT
1 AGGGTTCGCATAT
46933616 AGGATTTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (24 bp):
AGGGTTCGCATATTAAATCACATG
Found at i:46933871 original size:15 final size:16
Alignment explanation
Indices: 46933851--46933880 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46933841 GGGTGGTTGC
46933851 ATACAT-AGGGTTCGT
1 ATACATGAGGGTTCGT
46933866 ATACATGAGGGTTCG
1 ATACATGAGGGTTCG
46933881 CCTAACAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (16 bp):
ATACATGAGGGTTCGT
Found at i:46934745 original size:41 final size:41
Alignment explanation
Indices: 46934689--46935097 Score: 383
Period size: 41 Copynumber: 10.1 Consensus size: 41
46934679 AAACGTCGCA
*
46934689 AAAGGT-AGAGCAATAGCGATGCTTATGGAAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCGCCGCT
* * * ** *
46934729 ACAGGTCAGAGCAATAGCGATGCTTTTCCATAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCGCCGCT
* * **
46934770 AAATGTCAGAGCAATAGC-AGCGCTTTTGGGCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGA-CGCTTATGGAAAAGCGCCGCT
* * * *
46934811 AAAGGTCAGAGCAATAGCGGCGCTTACGGGAAAGCGACGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCGCCGCT
* * *
46934852 AAAGGTCAGAGCAATA--G-CGCTT-TTGAGAAAGTGCCACT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGA-AAAGCGCCGCT
* * * *
46934890 AAAGGTTAGAGCAATA--G-CGCTT-TTGAGAAAGTGCCACT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGA-AAAGCGCCGCT
46934928 AAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCGCCGCT
* ** * *
46934969 AAAGGTGAGAGCAATAGCGGTGCTTATGGGAAAGCACCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCGCCGCT
* * * * *
46935010 AAAGGTCAGAACAATAGTGGCG-TTTTTGAGAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGA-AAAGCGCCGCT
* *
46935051 AAAGGTCAGAGCAATAGCGGCGCTTATGTG-AAAGCGCCACT
1 AAAGGTCAGAGCAATAGCGACGCTTATG-GAAAAGCGCCGCT
46935092 AAAGGT
1 AAAGGT
46935098 TAAGTTTTCT
Statistics
Matches: 311, Mismatches: 47, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
37 1 0.00
38 65 0.21
39 1 0.00
40 11 0.04
41 226 0.73
42 6 0.02
43 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.19
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCGCCGCT
Found at i:46934952 original size:158 final size:160
Alignment explanation
Indices: 46934760--46935097 Score: 450
Period size: 158 Copynumber: 2.1 Consensus size: 160
46934750 GCTTTTCCAT
* * * **
46934760 AAGCGCCGCTAAATGTCAGAGCAATAGCAGCGCTTTTGGGCAAGCGCCGCTAAAGGTCAGAGCAA
1 AAGCGCCACTAAAGGTCAGAGCAATAGCAGCGCTTATGGAAAAGCGCCGCTAAAGGTCAGAGCAA
* *
46934825 TAGCGGCGCTTACGGGAAAGCGA-CGCTAAAGGTCAGAGCAATA-GCGCTTTTGAGAAAGTGCCA
66 TAGCGGCGCTTACGGGAAAGC-ACCGCTAAAGGTCAGAACAATAGGCGCTTTTGAGAAAGCGCCA
* *
46934888 CTAAAGGTTAGAGCAATA-GCGCTTTTGAGA
130 CTAAAGGTCAGAGCAATAGGCGCTTATGAGA
* *
46934918 AAGTGCCACTAAAGGTCAGAGCAATAGC-GACGCTTATGGAAAAGCGCCGCTAAAGGTGAGAGCA
1 AAGCGCCACTAAAGGTCAGAGCAATAGCAG-CGCTTATGGAAAAGCGCCGCTAAAGGTCAGAGCA
* * *
46934982 ATAGCGGTGCTTATGGGAAAGCACCGCTAAAGGTCAGAACAATAGTGGCGTTTTTGAGAAAGCGC
65 ATAGCGGCGCTTACGGGAAAGCACCGCTAAAGGTCAGAACAATA--GGCGCTTTTGAGAAAGCGC
* *
46935047 CGCTAAAGGTCAGAGCAATAGCGGCGCTTATGTGA
128 CACTAAAGGTCAGAGCAATA--GGCGCTTATGAGA
46935082 AAGCGCCACTAAAGGT
1 AAGCGCCACTAAAGGT
46935098 TAAGTTTTCT
Statistics
Matches: 155, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
157 2 0.01
158 94 0.61
161 34 0.22
164 25 0.16
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (160 bp):
AAGCGCCACTAAAGGTCAGAGCAATAGCAGCGCTTATGGAAAAGCGCCGCTAAAGGTCAGAGCAA
TAGCGGCGCTTACGGGAAAGCACCGCTAAAGGTCAGAACAATAGGCGCTTTTGAGAAAGCGCCAC
TAAAGGTCAGAGCAATAGGCGCTTATGAGA
Found at i:46937081 original size:20 final size:20
Alignment explanation
Indices: 46937056--46937104 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
46937046 CTTAATGCAT
46937056 AACTTGTGTTTGATATGTTA
1 AACTTGTGTTTGATATGTTA
46937076 AACTTGTGTTTGATATGTTA
1 AACTTGTGTTTGATATGTTA
46937096 AACTTGTGT
1 AACTTGTGT
46937105 CTAGGCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.06, G:0.20, T:0.49
Consensus pattern (20 bp):
AACTTGTGTTTGATATGTTA
Found at i:46943780 original size:49 final size:49
Alignment explanation
Indices: 46943727--46944333 Score: 280
Period size: 49 Copynumber: 12.5 Consensus size: 49
46943717 AATTTATCAC
* * *
46943727 ATCATATCTCTAGGGTATAAGGTTTGCCGTTGTGGCTTTAACCTTTCCT
1 ATCATATCTCTAGGGTATAAGATTCGCCGTTGTGGCTTCAACCTTTCCT
* * * * **
46943776 ATCATATCTCTAAGGTGA-AAGATTCGTCATTTTGGCTTCAATATTTCCCT
1 ATCATATCTCTAGGGT-ATAAGATTCGCCGTTGTGGCTTCAACCTTT-CCT
* ** * * *
46943826 -TCAT-GCTCTAGGGTATAAGATTCGCTATTGTGACTTCAA-TTATTCCC
1 ATCATATCTCTAGGGTATAAGATTCGCCGTTGTGGCTTCAACCT-TTCCT
* * * *** * *
46943873 ATCATATCTCTAGGGTACAAGATTCACCATTACAGCTTCAATCTTTCCC
1 ATCATATCTCTAGGGTATAAGATTCGCCGTTGTGGCTTCAACCTTTCCT
* * * * * * *
46943922 ATCATATTTCTAAGGTACAAGGTTCGTCGTTGCGGCTTCAATCC-TTCCC
1 ATCATATCTCTAGGGTATAAGATTCGCCGTTGTGGCTTCAA-CCTTTCCT
* * * * *
46943971 ATCATATCTCTAGGGTATAAGGTTCGTCGTTATGACTTCAACCTCTCCT
1 ATCATATCTCTAGGGTATAAGATTCGCCGTTGTGGCTTCAACCTTTCCT
* * * * * * * *
46944020 ATTATATCTTTAAGGTACAAAATTCGCCGTTGCGGCATCAATCTTTCCCT
1 ATCATATCTCTAGGGTATAAGATTCGCCGTTGTGGCTTCAACCTTT-CCT
* * * *
46944070 -TCAT-GCTCTAGGGTATAAGGTTCGTCGTTACT-GCTTCAACCTTTCC-
1 ATCATATCTCTAGGGTATAAGATTCGCCGTT-GTGGCTTCAACCTTTCCT
* ** ** *
46944116 ATCTACATCAT-TAGGGTATAAGATTCATCGTTACGGCTTCAATCTTTCCCT
1 ATC-ATATC-TCTAGGGTATAAGATTCGCCGTTGTGGCTTCAACCTTT-CCT
* * * * * * *
46944167 -CCAT-GCTCTAGGGTATAAGGTTTC-TCGTTGCGACTTAAACCTTTCC-
1 ATCATATCTCTAGGGTATAA-GATTCGCCGTTGTGGCTTCAACCTTTCCT
* * * * * * *
46944213 CTC-TA-CATCTAGTGTATAAGAATCGACGTTGCGGTTTCAATCTTTCC-
1 ATCATATC-TCTAGGGTATAAGATTCGCCGTTGTGGCTTCAACCTTTCCT
* * * * *
46944260 CTCAACATCTCTAGGGTATAAGATTCAG-CGTTGCGGCCTCAATCTTTCC-
1 ATC-ATATCTCTAGGGTATAAGATTC-GCCGTTGTGGCTTCAACCTTTCCT
* * *
46944309 CTCAATATCTTTAGGATATAAGATT
1 ATC-ATATCTCTAGGGTATAAGATT
46944334 TAATGTTTCC
Statistics
Matches: 430, Mismatches: 100, Indels: 56
0.73 0.17 0.10
Matches are distributed among these distances:
46 5 0.01
47 43 0.10
48 91 0.21
49 276 0.64
50 15 0.03
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (49 bp):
ATCATATCTCTAGGGTATAAGATTCGCCGTTGTGGCTTCAACCTTTCCT
Found at i:46944109 original size:97 final size:97
Alignment explanation
Indices: 46943932--46944281 Score: 363
Period size: 97 Copynumber: 3.6 Consensus size: 97
46943922 ATCATATTTC
* * * *
46943932 TAAGGTACAAGGTTCGTCGTTGCGGCTTCAATCCTTCCCATCATATCTCTAGGGTATAAGGTTCG
1 TAAGGTACAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCAT-GCTCTAGGGTATAAGGTTCG
* *
46943997 TCGTTATGACTTCAACCTCTCCTAT-TATATCTT
65 TCGTTATGACTTCAACCTCTCC-ATCTACATCAT
* * *
46944030 TAAGGTACAAAATTCGCCGTTGCGGCATCAATCTTTCCCTTCATGCTCTAGGGTATAAGGTTCGT
1 TAAGGTACAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCATGCTCTAGGGTATAAGGTTCGT
*
46944095 CGTTACTG-CTTCAACCTTTCCATCTACATCAT
66 CGTTA-TGACTTCAACCTCTCCATCTACATCAT
* * * * *
46944127 TAGGGTATAAGATTCATCGTTACGGCTTCAATCTTTCCCTCCATGCTCTAGGGTATAAGGTTTC-
1 TAAGGTACAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCATGCTCTAGGGTATAAGG-TTCG
** * * *
46944191 TCGTTGCGACTTAAACCTTTCCCTCTACATC--
65 TCGTTATGACTTCAACCTCTCCATCTACATCAT
* * * * *
46944222 T-AGTGTATAAGAATCGACGTTGCGGTTTCAATCTTTCCCTCAACAT-CTCTAGGGTATAAG
1 TAAG-GTACAAGATTCGTCGTTGCGGCTTCAATCTTTCCCT--TCATGCTCTAGGGTATAAG
46944282 ATTCAGCGTT
Statistics
Matches: 216, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
94 1 0.00
95 32 0.15
96 17 0.08
97 123 0.57
98 43 0.20
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (97 bp):
TAAGGTACAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCATGCTCTAGGGTATAAGGTTCGT
CGTTATGACTTCAACCTCTCCATCTACATCAT
Found at i:46944141 original size:244 final size:244
Alignment explanation
Indices: 46943707--46944165 Score: 572
Period size: 244 Copynumber: 1.9 Consensus size: 244
46943697 AACACACCTA
* * * * * *
46943707 TTGCGGCTTCAATTTATCACATCATATCTCTAGGGTATAAGGTTTGCCGTTGTGGCTTTAACCTT
1 TTGCGGCTTCAATCTATCACATCATATCTCTAGGGTATAAGGTTCGCCGTTATGACTTCAACCTC
* * ** *
46943772 TCCTATCATATCTCTAAGGTGAAAGATTCGTCATTTTGGCTTCAATATTTCCCTTCATGCTCTAG
66 TCCTATCATATCTCTAAGGTGAAAAATTCGCCATTGCGGCATCAATATTTCCCTTCATGCTCTAG
** * *
46943837 GGTATAAGATTCGCTATTGTGACTTCAATTATTCCCATCATATCTCTAGGGTACAAGATTCACCA
131 GGTATAAGATTCGCTATACTGACTTCAACTATTCCCATCACATCTCTAGGGTACAAGATTCACCA
46943902 TTACAGCTTCAATCTTTCCCATCATATTTCTAAGGTACAAGGTTCGTCG
196 TTACAGCTTCAATCTTTCCCATCATATTTCTAAGGTACAAGGTTCGTCG
* *
46943951 TTGCGGCTTCAATCCT-TCCCATCATATCTCTAGGGTATAAGGTTCGTCGTTATGACTTCAACCT
1 TTGCGGCTTCAAT-CTATCACATCATATCTCTAGGGTATAAGGTTCGCCGTTATGACTTCAACCT
* * * *
46944015 CTCCTATTATATCTTTAAGGT-ACAAAATTCGCCGTTGCGGCATCAATCTTTCCCTTCATGCTCT
65 CTCCTATCATATCTCTAAGGTGA-AAAATTCGCCATTGCGGCATCAATATTTCCCTTCATGCTCT
* *
46944079 AGGGTATAAGGTTCGTCGT-TACTG-CTTCAACCT-TT-CCATCTACATCAT-TAGGGTATAAGA
129 AGGGTATAAGATTCG-C-TATACTGACTTCAA-CTATTCCCATC-ACATC-TCTAGGGTACAAGA
* * *
46944139 TTCATCGTTACGGCTTCAATCTTTCCC
189 TTCACCATTACAGCTTCAATCTTTCCC
46944166 TCCATGCTCT
Statistics
Matches: 182, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
243 6 0.03
244 168 0.92
245 7 0.04
246 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (244 bp):
TTGCGGCTTCAATCTATCACATCATATCTCTAGGGTATAAGGTTCGCCGTTATGACTTCAACCTC
TCCTATCATATCTCTAAGGTGAAAAATTCGCCATTGCGGCATCAATATTTCCCTTCATGCTCTAG
GGTATAAGATTCGCTATACTGACTTCAACTATTCCCATCACATCTCTAGGGTACAAGATTCACCA
TTACAGCTTCAATCTTTCCCATCATATTTCTAAGGTACAAGGTTCGTCG
Found at i:46945957 original size:67 final size:67
Alignment explanation
Indices: 46945877--46946020 Score: 191
Period size: 67 Copynumber: 2.1 Consensus size: 67
46945867 TAACTTTTTA
* * * * *
46945877 TTTTTTTTCCTTTT-TTTCTTTTTTCTTTGGGTTTCAATATCCCCTTTACGGGTTTTCATCTCAA
1 TTTTTTTTTCTTTTCTTT-TTCTCTCTTTGGGTTTCAAAATCCCCTTTACGGGTTTCCATCTCAA
46945941 CCC
65 CCC
* * *
46945944 TTTTTTTTTCTTTTCTTTTTCTCTCTTTGGGTTTCAAAATGCCCTTTGCGGGTTTCCATCTCGAC
1 TTTTTTTTTCTTTTCTTTTTCTCTCTTTGGGTTTCAAAATCCCCTTTACGGGTTTCCATCTCAAC
46946009 CC
66 CC
46946011 TCTTTTTTTT
1 T-TTTTTTTT
46946021 AAGATAGCAC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
67 56 0.84
68 11 0.16
ACGTcount: A:0.09, C:0.24, G:0.10, T:0.57
Consensus pattern (67 bp):
TTTTTTTTTCTTTTCTTTTTCTCTCTTTGGGTTTCAAAATCCCCTTTACGGGTTTCCATCTCAAC
CC
Found at i:46958586 original size:3 final size:3
Alignment explanation
Indices: 46958578--46958611 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
46958568 ATTTTTTCTT
46958578 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
46958612 GGAGTAACGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:46959989 original size:72 final size:72
Alignment explanation
Indices: 46959872--46960015 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
46959862 AAAGCAGAAA
46959872 AATGAGAAACTTTGTGTGCTTGGTGTAACACCTCTCACTCGACCTAATTGTCGGGTCTAATTTAC
1 AATGAGAAACTTTGTGTGCTTGGTGTAACACCTCTCACTCGACCTAATTGTCGGGTCTAATTTAC
46959937 AGAATAC
66 AGAATAC
46959944 AATGAGAAACTTTGTGTGCTTGGTGTAACACCTCTCACTCGACCTAATTGTCGGGTCTAATTTAC
1 AATGAGAAACTTTGTGTGCTTGGTGTAACACCTCTCACTCGACCTAATTGTCGGGTCTAATTTAC
46960009 AGAATAC
66 AGAATAC
46960016 TACAGTCGTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (72 bp):
AATGAGAAACTTTGTGTGCTTGGTGTAACACCTCTCACTCGACCTAATTGTCGGGTCTAATTTAC
AGAATAC
Found at i:46968807 original size:56 final size:57
Alignment explanation
Indices: 46968650--46968807 Score: 246
Period size: 57 Copynumber: 2.8 Consensus size: 57
46968640 TTGTAGTGTC
* * *
46968650 TAAGATTTGGCCCCTCAATAATTACTATATTGTAGCCAAATTGCTTACTGCTATGTT
1 TAAGATTTGGCCCATCAATAATTACTATATTGTAGCCAAATTGCTTACTGCAATCTT
* *
46968707 TAAGATTTGGCCCGTCAATAATTACTATATTGTAGCCAAATTGCTTATTGCAATCTT
1 TAAGATTTGGCCCATCAATAATTACTATATTGTAGCCAAATTGCTTACTGCAATCTT
* *
46968764 TAAGATTTGG-CAATCAATAATTAGTATATTGTAGCCAAATTGCT
1 TAAGATTTGGCCCATCAATAATTACTATATTGTAGCCAAATTGCT
46968808 ATGTTTAGGA
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
56 31 0.33
57 63 0.67
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (57 bp):
TAAGATTTGGCCCATCAATAATTACTATATTGTAGCCAAATTGCTTACTGCAATCTT
Found at i:46969374 original size:22 final size:21
Alignment explanation
Indices: 46969349--46969393 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
46969339 AATAACTTGA
46969349 TTAACTCAATAACTTAAACTAT
1 TTAACTCAA-AACTTAAACTAT
* * *
46969371 TTAATTCAAAATTTAAATTAT
1 TTAACTCAAAACTTAAACTAT
46969392 TT
1 TT
46969394 TTCGAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAACTCAAAACTTAAACTAT
Found at i:46970297 original size:16 final size:16
Alignment explanation
Indices: 46970272--46970302 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46970262 TGAGTTCATG
46970272 TCAAAATTTTTAATAC
1 TCAAAATTTTTAATAC
*
46970288 TCAAATTTTTTAATA
1 TCAAAATTTTTAATA
46970303 ATTTTACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
TCAAAATTTTTAATAC
Found at i:46971147 original size:23 final size:23
Alignment explanation
Indices: 46971121--46971169 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
46971111 GTTACATTGG
*
46971121 AGTAATTAATAATTAACAAATGT
1 AGTAACTAATAATTAACAAATGT
* *
46971144 AGTAACTAATAGTTAATAAATGT
1 AGTAACTAATAATTAACAAATGT
46971167 AGT
1 AGT
46971170 GGTTTAGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (23 bp):
AGTAACTAATAATTAACAAATGT
Found at i:46979579 original size:75 final size:75
Alignment explanation
Indices: 46979456--46979603 Score: 260
Period size: 75 Copynumber: 2.0 Consensus size: 75
46979446 TTAGCTATCC
*
46979456 ATCTAATTCTTTATTATCTATTTTAGTTCTTAAACTTGCGTTGTTTGTCAAAACACCTAAAATGT
1 ATCTAATTCTTTATTATCTATTTTAGTCCTTAAACTTGCGTTGTTTGTCAAAACACCTAAAATGT
46979521 AAGGAAAATT
66 AAGGAAAATT
* *
46979531 ATCTAATTTTTTATTATCTATTTTAGTCCTTAAACTTGCGTTGTTTGTCAGAACACCTAAAATGT
1 ATCTAATTCTTTATTATCTATTTTAGTCCTTAAACTTGCGTTGTTTGTCAAAACACCTAAAATGT
*
46979596 ATGGAAAA
66 AAGGAAAA
46979604 GTTAACGTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (75 bp):
ATCTAATTCTTTATTATCTATTTTAGTCCTTAAACTTGCGTTGTTTGTCAAAACACCTAAAATGT
AAGGAAAATT
Found at i:46979716 original size:21 final size:21
Alignment explanation
Indices: 46979677--46979717 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46979667 TCAACTAATT
46979677 AATTTTTAAAAAATATAAAAA
1 AATTTTTAAAAAATATAAAAA
*
46979698 AATTTATTTAAAAAT-TAAAA
1 AATTT-TTAAAAAATATAAAA
46979718 TTTGGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTTTTAAAAAATATAAAAA
Found at i:46980989 original size:31 final size:31
Alignment explanation
Indices: 46980920--46981010 Score: 112
Period size: 30 Copynumber: 2.9 Consensus size: 31
46980910 TTTATATCAT
*
46980920 TATTTTGGTGCTTTTTTTATTGTTTTGGTTGC
1 TATTTTGGTG-TTTTTTTACTGTTTTGGTTGC
* *
46980952 TATTTTGGT-TTTTTTTACTGGTTTGGTTGT
1 TATTTTGGTGTTTTTTTACTGTTTTGGTTGC
* * *
46980982 TGTTTTTGTGCTTTTTTACTGTTTTGGTT
1 TATTTTGGTGTTTTTTTACTGTTTTGGTT
46981011 CTGTTATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 25 0.49
31 17 0.33
32 9 0.18
ACGTcount: A:0.05, C:0.05, G:0.22, T:0.67
Consensus pattern (31 bp):
TATTTTGGTGTTTTTTTACTGTTTTGGTTGC
Found at i:46981618 original size:19 final size:19
Alignment explanation
Indices: 46981594--46981631 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
46981584 ATGTGCATAC
46981594 ATAATTATTCAAGAATATA
1 ATAATTATTCAAGAATATA
46981613 ATAATTATTCAAGAATATA
1 ATAATTATTCAAGAATATA
46981632 TGTGTCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (19 bp):
ATAATTATTCAAGAATATA
Found at i:46990125 original size:34 final size:34
Alignment explanation
Indices: 46990073--46990138 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
46990063 TATTACGGTA
*
46990073 GCAATTATTATGCTTATAATAG-TTCGATTCAATG
1 GCAATTATTATGCTTATAACAGATT-GATTCAATG
46990107 GCAATTATTATG-TCTATAACAGATTGATTCAA
1 GCAATTATTATGCT-TATAACAGATTGATTCAA
46990139 AAACAAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 1 0.03
34 26 0.90
35 2 0.07
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (34 bp):
GCAATTATTATGCTTATAACAGATTGATTCAATG
Found at i:46994528 original size:24 final size:24
Alignment explanation
Indices: 46994499--46994549 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
46994489 AGAAATAATC
46994499 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
46994523 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
46994547 TTT
1 TTT
46994550 GAGTCAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:46994558 original size:24 final size:24
Alignment explanation
Indices: 46994499--46994561 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
46994489 AGAAATAATC
*
46994499 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATCAAACTCTGTTTAATTG
* *
46994523 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTAATTG
* *
46994547 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
46994562 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTTAATTG
Found at i:46996510 original size:24 final size:24
Alignment explanation
Indices: 46996482--46996544 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
46996472 AGAAATAATC
46996482 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
46996506 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
46996530 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
46996545 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:46999188 original size:57 final size:55
Alignment explanation
Indices: 46999086--46999279 Score: 257
Period size: 60 Copynumber: 3.3 Consensus size: 55
46999076 CCCGAGGACA
46999086 AAATGGTAGATTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGTG
1 AAATGGTA-ATTTT-GTGAAATCGGGG-TAAAAATGGGATTTAGGGAAGTTTG-GGGTG
46999145 AAATGGTAATTTTAGTGAAATCGGGGTAAAAATGGGATTTAGGGAAGTTTGGGGGTG
1 AAATGGTAATTTT-GTGAAATCGGGGTAAAAATGGGATTTAGGGAAGTTT-GGGGTG
*
46999202 AAATGGTAACTTT-TGAAAGTTTCGGGGTAAAAAAATGGGATTTAGGGAAGTTTGGGAGTG
1 AAATGGTAATTTTGTGAAA---TCGGGGT--AAAAATGGGATTTAGGGAAGTTTGGG-GTG
46999262 AAATGGTAATTTT-TGAAA
1 AAATGGTAATTTTGTGAAA
46999280 GTTTTGCGGT
Statistics
Matches: 125, Mismatches: 3, Indels: 13
0.89 0.02 0.09
Matches are distributed among these distances:
55 5 0.04
57 41 0.33
58 25 0.20
59 11 0.09
60 43 0.34
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.31
Consensus pattern (55 bp):
AAATGGTAATTTTGTGAAATCGGGGTAAAAATGGGATTTAGGGAAGTTTGGGGTG
Found at i:46999199 original size:29 final size:29
Alignment explanation
Indices: 46999109--46999257 Score: 101
Period size: 29 Copynumber: 5.1 Consensus size: 29
46999099 TGGTGAAATC
*
46999109 GGGGTTAAAAATGGGATTTAGGGAAGTTT
1 GGGGGTAAAAATGGGATTTAGGGAAGTTT
* * * * *
46999138 GAGGGT-GAAATGGTAATTTTAGTGAA--AT
1 GGGGGTAAAAATGG-GA-TTTAGGGAAGTTT
*
46999166 CGGGGTAAAAATGGGATTTAGGGAAGTTT
1 GGGGGTAAAAATGGGATTTAGGGAAGTTT
* * * *
46999195 GGGGGT-GAAATGGTAACTTT-TGAAAGTTT
1 GGGGGTAAAAATGG-GA-TTTAGGGAAGTTT
*
46999224 CGGGGTAAAAAAATGGGATTTAGGGAAGTTT
1 GGGGGT--AAAAATGGGATTTAGGGAAGTTT
46999255 GGG
1 GGG
46999258 AGTGAAATGG
Statistics
Matches: 86, Mismatches: 23, Indels: 20
0.67 0.18 0.16
Matches are distributed among these distances:
27 8 0.09
28 18 0.21
29 30 0.35
30 14 0.16
31 10 0.12
32 6 0.07
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.30
Consensus pattern (29 bp):
GGGGGTAAAAATGGGATTTAGGGAAGTTT
Found at i:46999252 original size:60 final size:58
Alignment explanation
Indices: 46999107--46999283 Score: 261
Period size: 60 Copynumber: 3.0 Consensus size: 58
46999097 TTTGGTGAAA
*
46999107 TCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGTGAAATGGTAATTTTAGTGAAA---
1 TCGGGG-TAAAAATGGGATTTAGGGAAGTTTGGGGGTGAAATGGTAATTTT--TGAAAGTT
*
46999165 TCGGGGTAAAAATGGGATTTAGGGAAGTTTGGGGGTGAAATGGTAACTTTTGAAAGTT
1 TCGGGGTAAAAATGGGATTTAGGGAAGTTTGGGGGTGAAATGGTAATTTTTGAAAGTT
*
46999223 TCGGGGTAAAAAAATGGGATTTAGGGAAGTTTGGGAGTGAAATGGTAATTTTTGAAAGTT
1 TCGGGGT--AAAAATGGGATTTAGGGAAGTTTGGGGGTGAAATGGTAATTTTTGAAAGTT
46999283 T
1 T
46999284 TGCGGTCAAA
Statistics
Matches: 110, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
55 5 0.05
57 42 0.38
58 13 0.12
60 50 0.45
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.32
Consensus pattern (58 bp):
TCGGGGTAAAAATGGGATTTAGGGAAGTTTGGGGGTGAAATGGTAATTTTTGAAAGTT
Found at i:46999281 original size:29 final size:28
Alignment explanation
Indices: 46999132--46999283 Score: 78
Period size: 29 Copynumber: 5.2 Consensus size: 28
46999122 GGATTTAGGG
46999132 AAGTTTGAGGGTGAAATGGTAATTTTAGTGA
1 AAGTTTG-GGGTGAAATGGTAATTTT--TGA
* * * ** *
46999163 AA--TCGGGGTAAAAATGG-GATTTAGGG
1 AAGTTTGGGGT-GAAATGGTAATTTTTGA
*
46999189 AAGTTTGGGGGTGAAATGGTAACTTTTGA
1 AAGTTT-GGGGTGAAATGGTAATTTTTGA
* * ** *
46999218 AAGTTTCGGGGTAAAAAAATGG-GATTTAGGG
1 AAGTTT-GGGGT---GAAATGGTAATTTTTGA
46999249 AAGTTTGGGAGTGAAATGGTAATTTTTGA
1 AAGTTTGGG-GTGAAATGGTAATTTTTGA
46999278 AAGTTT
1 AAGTTT
46999284 TGCGGTCAAA
Statistics
Matches: 86, Mismatches: 25, Indels: 22
0.65 0.19 0.17
Matches are distributed among these distances:
26 3 0.03
28 21 0.24
29 39 0.45
30 3 0.03
31 14 0.16
32 6 0.07
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.32
Consensus pattern (28 bp):
AAGTTTGGGGTGAAATGGTAATTTTTGA
Found at i:46999326 original size:60 final size:60
Alignment explanation
Indices: 46999262--46999400 Score: 190
Period size: 60 Copynumber: 2.3 Consensus size: 60
46999252 TTTGGGAGTG
46999262 AAATGGTAATTTTTG-AAAGTTTTGCGGTCAAAATATAATTTTCAAAAAGTTTTAGGGTCA
1 AAAT-GTAATTTTTGAAAAGTTTTGCGGTCAAAATATAATTTTCAAAAAGTTTTAGGGTCA
* * * * * *
46999322 AAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTTAGAAAGTTTTGGGGTTA
1 AAATGTAATTTTTGAAAAGTTTTGCGGTCAAAATATAATTTTCAAAAAGTTTTAGGGTCA
*
46999382 AAATTTAATTTTTGGAAAA
1 AAATGTAATTTTT-GAAAA
46999401 TTTAGGGACT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 9 0.13
60 55 0.80
61 5 0.07
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (60 bp):
AAATGTAATTTTTGAAAAGTTTTGCGGTCAAAATATAATTTTCAAAAAGTTTTAGGGTCA
Found at i:46999394 original size:30 final size:30
Alignment explanation
Indices: 46999268--46999399 Score: 160
Period size: 30 Copynumber: 4.4 Consensus size: 30
46999258 AGTGAAATGG
*
46999268 TAATTTTT-GAAAGTTTTGCGGTCAAAATA
1 TAATTTTTAGAAAGTTTTGGGGTCAAAATA
* * * *
46999297 TAATTTTCAAAAAGTTTTAGGGTCAAAATG
1 TAATTTTTAGAAAGTTTTGGGGTCAAAATA
*
46999327 TAA-TTTTGGAAAAGTTTTGGGGTCAAAATA
1 TAATTTTTAG-AAAGTTTTGGGGTCAAAATA
* *
46999357 TAATTTTTAGAAAGTTTTGGGGTTAAAATT
1 TAATTTTTAGAAAGTTTTGGGGTCAAAATA
*
46999387 TAATTTTTGGAAA
1 TAATTTTTAGAAA
46999400 ATTTAGGGAC
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
29 10 0.12
30 71 0.83
31 5 0.06
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (30 bp):
TAATTTTTAGAAAGTTTTGGGGTCAAAATA
Found at i:47001416 original size:6 final size:6
Alignment explanation
Indices: 47001407--47001510 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
47001397 TAATATTATT
* *
47001407 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -GTAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* * *
47001454 TTTAAA TTTAAGA --TAAA TTTAAA TCTAAA -TAAAA TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
47001499 TTTAAA CTTAAA
1 TTTAAA TTTAAA
47001511 AATCAAAGTC
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
4 3 0.04
5 18 0.23
6 50 0.65
7 1 0.01
8 5 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:47001441 original size:17 final size:16
Alignment explanation
Indices: 47001407--47001498 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
47001397 TAATATTATT
*
47001407 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
47001423 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAA-TAAA
47001440 TTTAAA--TAAATAAA
1 TTTAAATTTAAATAAA
47001454 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
*
47001471 TTTAAATCTAAATAAAA
1 TTTAAATTTAAAT-AAA
*
47001488 TTTAAAATTAA
1 TTTAAATTTAA
47001499 TTTAAACTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.15
15 4 0.06
16 16 0.24
17 37 0.55
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:47001510 original size:28 final size:28
Alignment explanation
Indices: 47001409--47001504 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 28
47001399 ATATTATTTT
* *
47001409 TAAATTT-AAT-TAAATTTAAATTTAAAG
1 TAAATTTAAATCTAAA-TAAAATTTAAAA
* * *
47001436 TAAATTTAAATAAATAAATTTAAATTTAAGA
1 TAAATTTAAAT--CTAAA-TAAAATTTAAAA
47001467 TAAATTTAAATCTAAATAAAATTTAAAA
1 TAAATTTAAATCTAAATAAAATTTAAAA
*
47001495 TTAATTTAAA
1 TAAATTTAAA
47001505 CTTAAAAATC
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
27 7 0.12
28 22 0.37
29 4 0.07
31 26 0.44
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (28 bp):
TAAATTTAAATCTAAATAAAATTTAAAA
Found at i:47001988 original size:31 final size:31
Alignment explanation
Indices: 47001947--47002467 Score: 184
Period size: 31 Copynumber: 15.4 Consensus size: 31
47001937 TTATCCACTC
47001947 TACTTCAATTTCAAGAGGATGACATTGCTCT
1 TACTTCAATTTCAAGAGGATGACATTGCTCT
* ** * * *
47001978 TAGTTCAATTTCAGAGATAAAGACATGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGACA---T-TGCTCT
47002014 CTACTTCAATTTCAAGAGGATGACATTGCTCT
1 -TACTTCAATTTCAAGAGGATGACATTGCTCT
** * * * *
47002046 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACT
1 TACTTCAATTTCA-AGAGGATGAC---AT-TGC-TCT
* *
47002083 CTACTTCAATTTCAAGGGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACATTGCTCT
* * *
47002115 TACTTCAATTTCAGAGATGAAGAC-TTGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGACATTG-----CTCT
* *
47002151 CTACTTCAATTTCAAGGGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACATTGCTCT
* * *
47002183 TACTTCAATTTCAAAGATGAAGAC-TTGTTATCCACT
1 TACTTCAATTTC-AAGAGGATGACATTG-----CTCT
* * *
47002219 CAACTTCAATTTCAAGCGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACATTGCTCT
** * * * *
47002251 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGAC---AT-TGCTCT
* *
47002287 CTACTTCAATTTCAAGGGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACATTGCTCT
* ** * * * *
47002319 TACTTCAATTTTAGAGATAAAGACGTGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGAC---AT-TGCTCT
* *
47002355 CTACTTCAATTTCAAGGGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACATTGCTCT
* * *
47002387 TACTTCAATTTCAGAGATGAAGAC-TTGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGACATTG-----CTCT
* *
47002423 CTACTTCAATTTCAAGTGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACATTGCTCT
47002455 TACTTCAATTTCA
1 TACTTCAATTTCA
47002468 GAGATAAAGA
Statistics
Matches: 360, Mismatches: 81, Indels: 98
0.67 0.15 0.18
Matches are distributed among these distances:
31 109 0.30
32 72 0.20
33 5 0.01
34 1 0.00
35 4 0.01
36 65 0.18
37 91 0.25
38 13 0.04
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (31 bp):
TACTTCAATTTCAAGAGGATGACATTGCTCT
Found at i:47002012 original size:68 final size:68
Alignment explanation
Indices: 47001903--47002506 Score: 1028
Period size: 68 Copynumber: 8.9 Consensus size: 68
47001893 GGAAATGATC
* * *
47001903 TTGCTCTTACTTCAAATTCAGAGATAAAGGCGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
47001968 ACA
66 ACG
* * *
47001971 TTGCTCTTAGTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
47002036 ACA
66 ACG
47002039 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
47002104 GACG
65 GACG
* *
47002108 TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
47002173 ACG
66 ACG
* * * * *
47002176 TTGCTCTTACTTCAATTTCAAAGATGAAGACTTGTTATCCACTCAACTTCAATTTCAAGCGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
47002241 ACG
66 ACG
47002244 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
47002309 ACG
66 ACG
*
47002312 TTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
47002377 ACG
66 ACG
* * *
47002380 TTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGTGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
47002445 ACG
66 ACG
47002448 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAG
47002507 CGAATTGGAA
Statistics
Matches: 510, Mismatches: 25, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
68 446 0.87
69 64 0.13
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (68 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
ACG
Found at i:47002291 original size:136 final size:136
Alignment explanation
Indices: 47001828--47002508 Score: 1049
Period size: 136 Copynumber: 4.9 Consensus size: 136
47001818 CTTCATCATA
* * *
47001828 CTCTTACTTCAATTTCAGAGGGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATA
1 CTCTTACTTCAATTTCAGA--GATAAAGACTTGTTATCCA-CTCTACTTCAATTTC-A-AGG---
* *
47001893 GGAAATGATC-TTGCTCTTACTTCAAATTCAGAGATAAAGGCGTGTTATCCACTCTACTTCAATT
58 GG--ATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATT
* *
47001957 TCAAGAGGATGACATTG
120 TCAAGCGGATGACGTTG
* * * *
47001974 CTCTTAGTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACA
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
*
47002039 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
66 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGAT
47002104 GACGTTG
130 GACGTTG
*
47002111 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
* * * *
47002176 TTGCTCTTACTTCAATTTCAAAGATGAAGACTTGTTATCCACTCAACTTCAATTTCAAGCGGATG
66 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGCGGATG
47002241 ACGTTG
131 ACGTTG
*
47002247 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
* *
47002312 TTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
66 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGCGGATG
47002377 ACGTTG
131 ACGTTG
* *
47002383 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGTGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
47002448 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGCG
66 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGCG
47002509 AATTGGAAAT
Statistics
Matches: 500, Mismatches: 33, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
135 1 0.00
136 320 0.64
137 126 0.25
138 2 0.00
141 2 0.00
142 1 0.00
143 15 0.03
144 15 0.03
146 18 0.04
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (136 bp):
CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGCGGATG
ACGTTG
Found at i:47002389 original size:204 final size:204
Alignment explanation
Indices: 47001828--47002506 Score: 1072
Period size: 204 Copynumber: 3.3 Consensus size: 204
47001818 CTTCATCATA
* * * *
47001828 CTCTTACTTCAATTTCAGAGGGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATA
1 CTCTTACTTCAATTTCAGA--GATAAAGACGTGTTATCCA-CTCTACTTCAATTTC-A-AGG---
* *
47001893 GGAAATGATC-TTGCTCTTACTTCAAATTCAGAGATAAAGGCGTGTTATCCACTCTACTTCAATT
58 GG--ATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATT
* * * * *
47001957 TCAAGAGGATGACATTGCTCTTAGTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCA
120 TCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCA
*
47002022 ATTTCAAGAGGATGACATTG
185 ATTTCAAGAGGATGACGTTG
47002042 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGGGGATGAC
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGAC
* *
47002107 GTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGAT
65 GTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
* * *
47002172 GACGTTGCTCTTACTTCAATTTCAAAGATGAAGACTTGTTATCCACTCAACTTCAATTTCAAGCG
130 GACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGAG
47002237 GATGACGTTG
195 GATGACGTTG
47002247 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
*
47002312 TTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
66 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
47002377 ACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGTGG
131 ACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGAGG
47002442 ATGACGTTG
196 ATGACGTTG
47002451 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAG
47002507 CGAATTGGAA
Statistics
Matches: 440, Mismatches: 23, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
204 218 0.50
205 167 0.38
207 2 0.00
210 3 0.01
211 1 0.00
212 29 0.07
213 1 0.00
214 19 0.04
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (204 bp):
CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
ACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGAGG
ATGACGTTG
Found at i:47014304 original size:57 final size:56
Alignment explanation
Indices: 47014201--47014394 Score: 241
Period size: 60 Copynumber: 3.3 Consensus size: 56
47014191 CCCGGGGACA
*
47014201 AAATGGTAGATTTTGGTGAAATCGGGGTCAAAAATGGGATTTAGGGAAGTTTGAGGGTG
1 AAATGGTA-ATTTT-GTGAAATCGGGGTAAAAAATGGGATTTAGGGAAGTTTG-GGGTG
* *
47014260 AAATGATAATTTTAGTGAAATCGGGGT-AAAAATGGGATTTAGGGATGTTTGGTGGTG
1 AAATGGTAATTTT-GTGAAATCGGGGTAAAAAATGGGATTTAGGGAAGTTTGG-GGTG
*
47014317 AAATGGTAACTTT-TGAAAGTTTCGGGGTAAAAAAATGGGATTTAGGGAAGTTTGGGGGTG
1 AAATGGTAATTTTGTGAAA---TCGGGGT-AAAAAATGGGATTTAGGGAAGTTT-GGGGTG
47014377 AAATGGTAATTTT-TGAAA
1 AAATGGTAATTTTGTGAAA
47014395 GTTTTAGGGT
Statistics
Matches: 121, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
55 5 0.04
56 1 0.01
57 38 0.31
58 25 0.21
59 7 0.06
60 43 0.36
61 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.34, T:0.31
Consensus pattern (56 bp):
AAATGGTAATTTTGTGAAATCGGGGTAAAAAATGGGATTTAGGGAAGTTTGGGGTG
Found at i:47014398 original size:29 final size:29
Alignment explanation
Indices: 47014306--47014398 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
47014296 ATTTAGGGAT
* *
47014306 GTTTGGTGGTGAAATGGTAACTTTTGAAA
1 GTTTGGGGGTGAAATGGTAATTTTTGAAA
* * * ** *
47014335 GTTTCGGGGTAAAAAAATGG-GATTTAGGGAA
1 GTTTGGGGGT---GAAATGGTAATTTTTGAAA
47014366 GTTTGGGGGTGAAATGGTAATTTTTGAAA
1 GTTTGGGGGTGAAATGGTAATTTTTGAAA
47014395 GTTT
1 GTTT
47014399 TAGGGTAAAA
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
28 6 0.13
29 19 0.41
31 15 0.33
32 6 0.13
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.35
Consensus pattern (29 bp):
GTTTGGGGGTGAAATGGTAATTTTTGAAA
Found at i:47014431 original size:60 final size:59
Alignment explanation
Indices: 47014367--47014627 Score: 226
Period size: 60 Copynumber: 4.4 Consensus size: 59
47014357 TTTAGGGAAG
*
47014367 TTTGGGGGTGAAATGGTAATTTTTGAAAGTTTTAGGGTAAAAATAT-ATTTTTGCAAAAGT
1 TTTGGGGGTAAAAT-GTAATTTTTGAAAGTTTTAGGGTAAAAATATGATTTTTG-AAAAGT
* * * * *
47014427 TTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATATAATTTTT-AGAAAGT
1 TTTGGGGGTAAAATGTAATTTTTG-AAAGTTTTAGGGTAAAAATATGATTTTTGA-AAAGT
* * * * * *
47014487 TTT-AGGGTCAAAATGTAATTTTGGAAAAGTTTTAAGGTCAAAATATAATTTTGGAAAAG-
1 TTTGGGGGT-AAAATGTAATTTTTG-AAAGTTTTAGGGTAAAAATATGATTTTTGAAAAGT
* * * * *
47014546 TTTAGGGGTCAAAATATAATTTTTAGAAAGTTTTAAGGTCAAAATATAATTTTT-AGAAAGT
1 TTTGGGGGT-AAAATGTAATTTTT-GAAAGTTTTAGGGTAAAAATATGATTTTTGA-AAAGT
* * *
47014607 TTTGGGGTTAGAATTTAATTT
1 TTTGGGGGTAAAATGTAATTT
47014628 CTGGAAAATT
Statistics
Matches: 173, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
59 17 0.10
60 141 0.82
61 15 0.09
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (59 bp):
TTTGGGGGTAAAATGTAATTTTTGAAAGTTTTAGGGTAAAAATATGATTTTTGAAAAGT
Found at i:47014434 original size:90 final size:88
Alignment explanation
Indices: 47014327--47014614 Score: 291
Period size: 90 Copynumber: 3.2 Consensus size: 88
47014317 AAATGGTAAC
* * * * * *
47014327 TTTTG-AAAGTTTCGGGGTAAAAAAATGGGATTTAGG-GAAGTTTGGGGGTGAAATGGTAATTTT
1 TTTTGAAAAGTTTTGGGGT-AAAAAAT-GAATTTTGGAAAAGTTTGGGGGTAAAAT-ATAATTTT
*
47014390 T-GAAAGTTTTAGGGTAAAAATATAT
63 TAGAAAGTTTTAGGGTCAAAATATAT
* *
47014415 TTTTGCAAAAGTTTTGGGGT-TAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATATAATTTT
1 TTTTG-AAAAGTTTTGGGGTAAAAAATG-AATTTTGGAAAAG-TTTGGGGGTAAAATATAATTTT
*
47014479 TAGAAAGTTTTAGGGTCAAAATGTAAT
63 TAGAAAGTTTTAGGGTCAAAATAT-AT
* ** * *
47014506 TTTGGAAAAGTTTTAAGGTCAAAATAT-AATTTTGGAAAAGTTTAGGGGTCAAAATATAATTTTT
1 TTTTGAAAAGTTTTGGGGT-AAAAAATGAATTTTGGAAAAGTTTGGGGGT-AAAATATAATTTTT
*
47014570 AGAAAGTTTTAAGGTCAAAATATAAT
64 AGAAAGTTTTAGGGTCAAAATAT-AT
47014596 TTTT-AGAAAGTTTTGGGGT
1 TTTTGA-AAAGTTTTGGGGT
47014615 TAGAATTTAA
Statistics
Matches: 167, Mismatches: 22, Indels: 20
0.80 0.11 0.10
Matches are distributed among these distances:
87 1 0.01
88 16 0.10
89 19 0.11
90 121 0.72
91 6 0.04
92 4 0.02
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (88 bp):
TTTTGAAAAGTTTTGGGGTAAAAAATGAATTTTGGAAAAGTTTGGGGGTAAAATATAATTTTTAG
AAAGTTTTAGGGTCAAAATATAT
Found at i:47014626 original size:90 final size:90
Alignment explanation
Indices: 47014383--47014642 Score: 357
Period size: 90 Copynumber: 2.9 Consensus size: 90
47014373 GGTGAAATGG
* *
47014383 TAATTTTT-GAAAGTTTTAGGGTAAAAATAT-ATTTTTGCAAAAGTTTTGGGGTTAAAATGTAAT
1 TAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTTG-AAAAGTTTTGGGGTTAAAATATAAT
* *
47014446 TTTGGAAAAGTTTTGGGGTTAAAATA
65 TTTGGAAAAGTTTAGGGGTCAAAATA
* * ** *
47014472 TAATTTTTAGAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTAAGGTCAAAATATAATT
1 TAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTTGAAAAGTTTTGGGGTTAAAATATAATT
47014537 TTGGAAAAGTTTAGGGGTCAAAATA
66 TTGGAAAAGTTTAGGGGTCAAAATA
* * *
47014562 TAATTTTTAGAAAGTTTTAAGGTCAAAATATAATTTTT-AGAAAGTTTTGGGGTTAGAATTTAAT
1 TAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTTGA-AAAGTTTTGGGGTTAAAATATAAT
47014626 TTCTGGAAAA-TTTAGGG
65 TT-TGGAAAAGTTTAGGG
47014643 ACTTACAAAG
Statistics
Matches: 150, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
89 9 0.06
90 128 0.85
91 13 0.09
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.40
Consensus pattern (90 bp):
TAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTTGAAAAGTTTTGGGGTTAAAATATAATT
TTGGAAAAGTTTAGGGGTCAAAATA
Found at i:47014627 original size:30 final size:31
Alignment explanation
Indices: 47014383--47014614 Score: 252
Period size: 30 Copynumber: 7.8 Consensus size: 31
47014373 GGTGAAATGG
*
47014383 TAATTTTT-G-AAAGTTTTAGGGTAAAAATA
1 TAATTTTTAGAAAAGTTTTAGGGTCAAAATA
* * *
47014412 T-ATTTTT-GCAAAAGTTTTGGGGTTAAAATG
1 TAATTTTTAG-AAAAGTTTTAGGGTCAAAATA
* * *
47014442 TAA-TTTTGGAAAAGTTTTGGGGTTAAAATA
1 TAATTTTTAGAAAAGTTTTAGGGTCAAAATA
*
47014472 TAATTTTTAG-AAAGTTTTAGGGTCAAAATG
1 TAATTTTTAGAAAAGTTTTAGGGTCAAAATA
* *
47014502 TAA-TTTTGGAAAAGTTTTAAGGTCAAAATA
1 TAATTTTTAGAAAAGTTTTAGGGTCAAAATA
*
47014532 TAA-TTTTGGAAAAG-TTTAGGGGTCAAAATA
1 TAATTTTTAGAAAAGTTTTA-GGGTCAAAATA
*
47014562 TAATTTTTAG-AAAGTTTTAAGGTCAAAATA
1 TAATTTTTAGAAAAGTTTTAGGGTCAAAATA
*
47014592 TAATTTTTAG-AAAGTTTTGGGGT
1 TAATTTTTAGAAAAGTTTTAGGGT
47014615 TAGAATTTAA
Statistics
Matches: 178, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.04
29 10 0.06
30 145 0.81
31 16 0.09
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.40
Consensus pattern (31 bp):
TAATTTTTAGAAAAGTTTTAGGGTCAAAATA
Found at i:47016651 original size:6 final size:6
Alignment explanation
Indices: 47016642--47016745 Score: 69
Period size: 6 Copynumber: 18.0 Consensus size: 6
47016632 TAATATTATT
* * *
47016642 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -GTAAA TTTAAA TAAATAAC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* * *
47016689 TTTAAA TTTAAGA --TAAA TTTAAA TCTAAA -TAAAA TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
47016734 TTTAAA CTTAAA
1 TTTAAA TTTAAA
47016746 AATCAAAGTC
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
4 3 0.04
5 18 0.24
6 49 0.65
7 1 0.01
8 4 0.05
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:47016676 original size:17 final size:16
Alignment explanation
Indices: 47016642--47016733 Score: 107
Period size: 17 Copynumber: 5.7 Consensus size: 16
47016632 TAATATTATT
*
47016642 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
47016658 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAA-TAAA
*
47016675 TTTAAA--TAAATAAC
1 TTTAAATTTAAATAAA
47016689 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
*
47016706 TTTAAATCTAAATAAAA
1 TTTAAATTTAAAT-AAA
*
47016723 TTTAAAATTAA
1 TTTAAATTTAA
47016734 TTTAAACTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
14 9 0.14
15 4 0.06
16 16 0.25
17 36 0.55
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:47016745 original size:28 final size:28
Alignment explanation
Indices: 47016644--47016739 Score: 79
Period size: 31 Copynumber: 3.4 Consensus size: 28
47016634 ATATTATTTT
* *
47016644 TAAATTT-AAT-TAAATTTAAATTTAAAG
1 TAAATTTAAATCTAAA-TAAAATTTAAAA
* * * *
47016671 TAAATTTAAATAAATAACTTTAAATTTAAGA
1 TAAATTTAAAT--CTAA-ATAAAATTTAAAA
47016702 TAAATTTAAATCTAAATAAAATTTAAAA
1 TAAATTTAAATCTAAATAAAATTTAAAA
*
47016730 TTAATTTAAA
1 TAAATTTAAA
47016740 CTTAAAAATC
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
27 7 0.12
28 22 0.39
29 3 0.05
31 24 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
TAAATTTAAATCTAAATAAAATTTAAAA
Found at i:47022267 original size:19 final size:19
Alignment explanation
Indices: 47022240--47022281 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
47022230 TTAAGTTTCC
47022240 ATAAGGTGATAT-AATTTAT
1 ATAAGGTGAT-TCAATTTAT
* *
47022259 ATAATGTGATTCAGTTTAT
1 ATAAGGTGATTCAATTTAT
47022278 ATAA
1 ATAA
47022282 AAATAGGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.43
Consensus pattern (19 bp):
ATAAGGTGATTCAATTTAT
Found at i:47023231 original size:22 final size:22
Alignment explanation
Indices: 47023206--47023268 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 22
47023196 TTTAATTTTT
47023206 TAAAATAATAATTTTAAGGGTC
1 TAAAATAATAATTTTAAGGGTC
**
47023228 T-AAATAAGCA-TTT-----TC
1 TAAAATAATAATTTTAAGGGTC
47023243 TAAAATAATAATTTTAAGGGTC
1 TAAAATAATAATTTTAAGGGTC
47023265 TAAA
1 TAAA
47023269 TAAGTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
15 3 0.10
16 7 0.23
17 3 0.10
20 3 0.10
21 7 0.23
22 7 0.23
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (22 bp):
TAAAATAATAATTTTAAGGGTC
Found at i:47023232 original size:21 final size:21
Alignment explanation
Indices: 47023208--47023271 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
47023198 TAATTTTTTA
47023208 AAATAATAATTTTAAGGGTCT
1 AAATAATAATTTTAAGGGTCT
**
47023229 AAATAAGCA-TTT-----TCT
1 AAATAATAATTTTAAGGGTCT
47023244 AAAATAATAATTTTAAGGGTCT
1 -AAATAATAATTTTAAGGGTCT
47023266 AAATAA
1 AAATAA
47023272 GTTAATTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
15 3 0.09
16 7 0.22
17 3 0.09
20 3 0.09
21 13 0.41
22 3 0.09
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (21 bp):
AAATAATAATTTTAAGGGTCT
Found at i:47023247 original size:37 final size:37
Alignment explanation
Indices: 47023200--47023272 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
47023190 AGAAAATTTA
*
47023200 ATTTTTTAAAATAATAATTTTAAGGGTCTAAATAAGC
1 ATTTTCTAAAATAATAATTTTAAGGGTCTAAATAAGC
47023237 ATTTTCTAAAATAATAATTTTAAGGGTCTAAATAAG
1 ATTTTCTAAAATAATAATTTTAAGGGTCTAAATAAG
47023273 TTAATTAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (37 bp):
ATTTTCTAAAATAATAATTTTAAGGGTCTAAATAAGC
Found at i:47036316 original size:24 final size:24
Alignment explanation
Indices: 47036272--47036317 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
47036262 CCACTAAAAT
**
47036272 TTTTAACAAATCAAAGGAAAATGG
1 TTTTAACAAATCAAAAAAAAATGG
*
47036296 TTTTAACAAATGAAAAAAAAAT
1 TTTTAACAAATCAAAAAAAAAT
47036318 TAATATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.11, T:0.26
Consensus pattern (24 bp):
TTTTAACAAATCAAAAAAAAATGG
Found at i:47038800 original size:23 final size:23
Alignment explanation
Indices: 47038768--47038811 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
47038758 TCCACTAAAA
47038768 TTTTGAACAAATCAAAGAAAATGG
1 TTTTGAACAAATCAAA-AAAATGG
*
47038792 TTTT-AACAAATGAAAAAAAT
1 TTTTGAACAAATCAAAAAAAT
47038812 TAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (23 bp):
TTTTGAACAAATCAAAAAAATGG
Found at i:47044638 original size:29 final size:29
Alignment explanation
Indices: 47044603--47044766 Score: 80
Period size: 29 Copynumber: 5.2 Consensus size: 29
47044593 GCAAAAAGCA
47044603 GTTGCATAGTTGAGCACCAAAAAGTCCTT
1 GTTGCATAGTTGAGCACCAAAAAGTCCTT
* * ***
47044632 GTTGCATTGCT-AGCCAACATTCAACACTCCTCCTT
1 GTTGCATAGTTGAG-C-AC---CAA-A-AAGTCCTT
*
47044667 ATTGCATAGTTGAGCACCAAAAAGTCCTT
1 GTTGCATAGTTGAGCACCAAAAAGTCCTT
* * ***
47044696 GTTGCATTGCT-AGCCAACATTCAACACTCCTCCTT
1 GTTGCATAGTTGAG-C-AC---CAA-A-AAGTCCTT
*
47044731 ATTGCATAGTTGAGCACCAAAAAGTCCTT
1 GTTGCATAGTTGAGCACCAAAAAGTCCTT
47044760 GTTGCAT
1 GTTGCAT
47044767 TGCTAGCCAA
Statistics
Matches: 95, Mismatches: 24, Indels: 32
0.63 0.16 0.21
Matches are distributed among these distances:
28 4 0.04
29 35 0.37
30 6 0.06
31 6 0.06
33 6 0.06
34 6 0.06
35 28 0.29
36 4 0.04
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (29 bp):
GTTGCATAGTTGAGCACCAAAAAGTCCTT
Found at i:47044673 original size:35 final size:35
Alignment explanation
Indices: 47044627--47044737 Score: 101
Period size: 35 Copynumber: 3.3 Consensus size: 35
47044617 CACCAAAAAG
*
47044627 TCCTTGTTGCATTGCTAGCCAACATTCAACACTCC
1 TCCTTATTGCATTGCTAGCCAACATTCAACACTCC
* * ***
47044662 TCCTTATTGCATAGTTGAG-C-AC---CAA-A-AAG
1 TCCTTATTGCATTGCT-AGCCAACATTCAACACTCC
*
47044691 TCCTTGTTGCATTGCTAGCCAACATTCAACACTCC
1 TCCTTATTGCATTGCTAGCCAACATTCAACACTCC
47044726 TCCTTATTGCAT
1 TCCTTATTGCAT
47044738 AGTTGAGCAC
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
28 2 0.04
29 14 0.25
30 3 0.05
31 3 0.05
33 3 0.05
34 3 0.05
35 25 0.45
36 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (35 bp):
TCCTTATTGCATTGCTAGCCAACATTCAACACTCC
Found at i:47044705 original size:64 final size:64
Alignment explanation
Indices: 47044604--47044795 Score: 375
Period size: 64 Copynumber: 3.0 Consensus size: 64
47044594 CAAAAAGCAG
47044604 TTGCATAGTTGAGCACCAAAAAGTCCTTGTTGCATTGCTAGCCAACATTCAACACTCCTCCTTA
1 TTGCATAGTTGAGCACCAAAAAGTCCTTGTTGCATTGCTAGCCAACATTCAACACTCCTCCTTA
47044668 TTGCATAGTTGAGCACCAAAAAGTCCTTGTTGCATTGCTAGCCAACATTCAACACTCCTCCTTA
1 TTGCATAGTTGAGCACCAAAAAGTCCTTGTTGCATTGCTAGCCAACATTCAACACTCCTCCTTA
*
47044732 TTGCATAGTTGAGCACCAAAAAGTCCTTGTTGCATTGCTAGCCAACATTCAACACTCTTCCTTA
1 TTGCATAGTTGAGCACCAAAAAGTCCTTGTTGCATTGCTAGCCAACATTCAACACTCCTCCTTA
47044796 GTTTCTATGC
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 127 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (64 bp):
TTGCATAGTTGAGCACCAAAAAGTCCTTGTTGCATTGCTAGCCAACATTCAACACTCCTCCTTA
Found at i:47054700 original size:15 final size:17
Alignment explanation
Indices: 47054673--47054706 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
47054663 TTCTAAATTC
47054673 AATTTTTATAAAA-TAA
1 AATTTTTATAAAATTAA
47054689 AATTTTTA-AAAATTAA
1 AATTTTTATAAAATTAA
47054705 AA
1 AA
47054707 AATTTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTTTATAAAATTAA
Found at i:47057037 original size:7 final size:7
Alignment explanation
Indices: 47057026--47057110 Score: 116
Period size: 7 Copynumber: 12.1 Consensus size: 7
47057016 TGATGCCCAA
*
47057026 TTTAAGA
1 TTTAAGG
47057033 TTTAAGG
1 TTTAAGG
47057040 TTTAAGG
1 TTTAAGG
47057047 TTTAAGG
1 TTTAAGG
47057054 TTTAAGG
1 TTTAAGG
47057061 TTTAAGG
1 TTTAAGG
47057068 TTTAAGG
1 TTTAAGG
*
47057075 TCTAAGG
1 TTTAAGG
*
47057082 TCTAAGG
1 TTTAAGG
*
47057089 TCTAAGG
1 TTTAAGG
*
47057096 TCTAAGG
1 TTTAAGG
*
47057103 TCTAAGG
1 TTTAAGG
47057110 T
1 T
47057111 CTAGGATTTA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 76 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (7 bp):
TTTAAGG
Found at i:47057147 original size:27 final size:26
Alignment explanation
Indices: 47057112--47057175 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
47057102 GTCTAAGGTC
*
47057112 TAGGATTTAGGGTTATATCTTTAGGTTT
1 TAGGTTTTAGGGTTATAT-TTT-GGTTT
*
47057140 T-GGTTTTAGGGTTATGTTTTGGTTT
1 TAGGTTTTAGGGTTATATTTTGGTTT
47057165 TAGGGTTTTAG
1 TA-GGTTTTAG
47057176 TTTTTATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 6 0.19
26 3 0.09
27 22 0.69
28 1 0.03
ACGTcount: A:0.16, C:0.02, G:0.30, T:0.53
Consensus pattern (26 bp):
TAGGTTTTAGGGTTATATTTTGGTTT
Found at i:47057152 original size:14 final size:14
Alignment explanation
Indices: 47057131--47057307 Score: 60
Period size: 14 Copynumber: 12.6 Consensus size: 14
47057121 GGGTTATATC
47057131 TTTA-GGTTTTGGT
1 TTTAGGGTTTTGGT
47057144 TTTAGGGTTATGTTTTGGT
1 TTTAGGG---T-T-TTGGT
*
47057163 TTTAGGGTTTTAGTT
1 TTTAGGGTTTT-GGT
* *
47057178 TTTA-TGTTAT-GT
1 TTTAGGGTTTTGGT
**
47057190 TTTAGGG-TTACGT
1 TTTAGGGTTTTGGT
* * *
47057203 TTTATGATTTTGGG
1 TTTAGGGTTTTGGT
* *
47057217 TTTATGGTTAT-GT
1 TTTAGGGTTTTGGT
*
47057230 TTTAGGGTTTTGGA
1 TTTAGGGTTTTGGT
*** * *
47057244 TTTAATATTTTAGA
1 TTTAGGGTTTTGGT
* * *
47057258 TGTAGGATTAT-GT
1 TTTAGGGTTTTGGT
* *
47057271 TTTAGGGTTCTAGT
1 TTTAGGGTTTTGGT
*
47057285 TTTTGGGTTTTGGT
1 TTTAGGGTTTTGGT
47057299 TTTAGGGTT
1 TTTAGGGTT
47057308 ATATTTTAGG
Statistics
Matches: 118, Mismatches: 34, Indels: 23
0.67 0.19 0.13
Matches are distributed among these distances:
12 6 0.05
13 31 0.26
14 59 0.50
15 7 0.06
16 1 0.01
17 1 0.01
18 1 0.01
19 12 0.10
ACGTcount: A:0.15, C:0.01, G:0.28, T:0.56
Consensus pattern (14 bp):
TTTAGGGTTTTGGT
Found at i:47057173 original size:33 final size:32
Alignment explanation
Indices: 47057131--47057192 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
47057121 GGGTTATATC
47057131 TTTAGGTTTT-GGTTTTAGGGTTATGTTTTGGT
1 TTTAGGTTTTAGGTTTTA-GGTTATGTTTTGGT
* *
47057163 TTTAGGGTTTTAGTTTTTATGTTATGTTTT
1 TTTA-GGTTTTAGGTTTTAGGTTATGTTTT
47057193 AGGGTTACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 4 0.15
33 16 0.62
34 6 0.23
ACGTcount: A:0.11, C:0.00, G:0.26, T:0.63
Consensus pattern (32 bp):
TTTAGGTTTTAGGTTTTAGGTTATGTTTTGGT
Found at i:47057220 original size:27 final size:27
Alignment explanation
Indices: 47057190--47057247 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
47057180 TATGTTATGT
* *
47057190 TTTAGGGTTACGTTTTATGATTTTGGG
1 TTTAGGGTTACGTTTTAGGATTTTGGA
* * *
47057217 TTTATGGTTATGTTTTAGGGTTTTGGA
1 TTTAGGGTTACGTTTTAGGATTTTGGA
47057244 TTTA
1 TTTA
47057248 ATATTTTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.16, C:0.02, G:0.28, T:0.55
Consensus pattern (27 bp):
TTTAGGGTTACGTTTTAGGATTTTGGA
Found at i:47057381 original size:14 final size:14
Alignment explanation
Indices: 47057358--47057460 Score: 73
Period size: 14 Copynumber: 7.2 Consensus size: 14
47057348 CAGTTTAGAA
47057358 TTTAGTTTTTAAGGT
1 TTTAG-TTTTAAGGT
* * *
47057373 TTCACTTTTAAGAT
1 TTTAGTTTTAAGGT
*
47057387 TTTAGTTTTAATGT
1 TTTAGTTTTAAGGT
*
47057401 TTTAGTTTTAGGGT
1 TTTAGTTTTAAGGT
* **
47057415 TTTAATTTTTTGGTGT
1 TTT-AGTTTTAAG-GT
*
47057431 TTTAG-TTTAGGGT
1 TTTAGTTTTAAGGT
* *
47057444 TTTAGTATTAGGGT
1 TTTAGTTTTAAGGT
47057458 TTT
1 TTT
47057461 TTTTGGTGTT
Statistics
Matches: 71, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
13 7 0.10
14 48 0.68
15 11 0.15
16 5 0.07
ACGTcount: A:0.18, C:0.02, G:0.20, T:0.59
Consensus pattern (14 bp):
TTTAGTTTTAAGGT
Found at i:47057403 original size:22 final size:21
Alignment explanation
Indices: 47057386--47057425 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
47057376 ACTTTTAAGA
47057386 TTTTA-GTTTTAATGTTTTAG
1 TTTTAGGTTTTAATGTTTTAG
*
47057406 TTTTAGGGTTTTAATTTTTT
1 TTTTA-GGTTTTAATGTTTT
47057426 GGTGTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (21 bp):
TTTTAGGTTTTAATGTTTTAG
Found at i:47057462 original size:29 final size:30
Alignment explanation
Indices: 47057398--47057462 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
47057388 TTAGTTTTAA
* **
47057398 TGTTTTAGTTTTAGGGTTTTAATTTTTTGG
1 TGTTTTAGTTTTAGGGTTTTAATATTAGGG
*
47057428 TGTTTTAG-TTTAGGGTTTTAGTATTAGGG
1 TGTTTTAGTTTTAGGGTTTTAATATTAGGG
*
47057457 TTTTTT
1 TGTTTT
47057463 TTGGTGTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.14, C:0.00, G:0.25, T:0.62
Consensus pattern (30 bp):
TGTTTTAGTTTTAGGGTTTTAATATTAGGG
Found at i:47057641 original size:40 final size:40
Alignment explanation
Indices: 47057558--47057659 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
47057548 AGGTTTTTGG
* ** **
47057558 TTTAGTGTTACATTTTAGGGTTTTAGATTTATGGTTATGT
1 TTTAGTGTTATATTTTAGGGTTTTAGATTTATGACTACAT
* *
47057598 TTTAGTGTTATATTTTAGGGTTTTGGTTTTATGACTACAT
1 TTTAGTGTTATATTTTAGGGTTTTAGATTTATGACTACAT
*
47057638 TTTAG-GCTTATGTTTTAGGGTT
1 TTTAGTG-TTATATTTTAGGGTT
47057660 ATGCTTTAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.02
40 52 0.98
ACGTcount: A:0.19, C:0.04, G:0.23, T:0.55
Consensus pattern (40 bp):
TTTAGTGTTATATTTTAGGGTTTTAGATTTATGACTACAT
Found at i:47062386 original size:39 final size:40
Alignment explanation
Indices: 47062305--47062389 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
47062295 AAGTCTGTTC
* * * *
47062305 CAAAAGATGTTCATCCAATATGAAAAGGGTTGTGATTTTT
1 CAAAATATGGTCATCCAATATGAAAAGGGTTGTGACTCTT
47062345 CAAAATATGGTCATCCAATATGAAAA-GGTTGTGACTCTT
1 CAAAATATGGTCATCCAATATGAAAAGGGTTGTGACTCTT
47062384 CAAAAT
1 CAAAAT
47062390 GTATTCATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 17 0.41
40 24 0.59
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (40 bp):
CAAAATATGGTCATCCAATATGAAAAGGGTTGTGACTCTT
Found at i:47064127 original size:30 final size:29
Alignment explanation
Indices: 47064093--47064157 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
47064083 GCCCAAAATT
47064093 TTAAAGGAAATATCA-ACAATTTAATAT-CAA
1 TTAAAGGAAATA-CATACAA-TTAATATGC-A
* *
47064123 TTAAAAGTAATACATACAATTAATATGCA
1 TTAAAGGAAATACATACAATTAATATGCA
47064152 TTAAAG
1 TTAAAG
47064158 TTAAAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (29 bp):
TTAAAGGAAATACATACAATTAATATGCA
Found at i:47071253 original size:11 final size:11
Alignment explanation
Indices: 47071233--47071266 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
47071223 TAATTGCTTA
47071233 TATAATTTTTT
1 TATAATTTTTT
* *
47071244 TATGATTTTTA
1 TATAATTTTTT
47071255 TATAATTTTTT
1 TATAATTTTTT
47071266 T
1 T
47071267 CACCTATATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TATAATTTTTT
Found at i:47073873 original size:43 final size:43
Alignment explanation
Indices: 47073812--47073893 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
47073802 AGTTCATTGT
*
47073812 TGAAGCGATTTGACAATGACGAGATTAGAATACAATTATACAA
1 TGAAGCGATTTGACAATGACGAGAATAGAATACAATTATACAA
* * * * *
47073855 TGAAGCGGTTTGGCAATGATGAGAATATAATATAATTAT
1 TGAAGCGATTTGACAATGACGAGAATAGAATACAATTAT
47073894 TAAGGGTTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (43 bp):
TGAAGCGATTTGACAATGACGAGAATAGAATACAATTATACAA
Found at i:47080194 original size:19 final size:19
Alignment explanation
Indices: 47080170--47080211 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
47080160 ACGAGCCCAA
47080170 TATTATATTTATTAAGT-TT
1 TATTAT-TTTATTAAGTATT
*
47080189 TATTATTTTATTATGTATT
1 TATTATTTTATTAAGTATT
47080208 TATT
1 TATT
47080212 CCAAATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TATTATTTTATTAAGTATT
Found at i:47082149 original size:5 final size:5
Alignment explanation
Indices: 47082133--47082163 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
47082123 GATTATTTTG
*
47082133 AGAAA AGTAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
47082164 AGTTTGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (5 bp):
AGAAA
Found at i:47082890 original size:11 final size:11
Alignment explanation
Indices: 47082874--47082898 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
47082864 TGCTATTGTG
47082874 TTTTGTTGTTA
1 TTTTGTTGTTA
47082885 TTTTGTTGTTA
1 TTTTGTTGTTA
47082896 TTT
1 TTT
47082899 CACTATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (11 bp):
TTTTGTTGTTA
Found at i:47084225 original size:22 final size:22
Alignment explanation
Indices: 47084200--47084244 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
47084190 ATTCTTTTAA
*
47084200 AATATTTAT-ATTATATTATTTT
1 AATATTAATAATTATATT-TTTT
*
47084222 AATATTAATAATTTTATTTTTT
1 AATATTAATAATTATATTTTTT
47084244 A
1 A
47084245 TTTACAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATATTAATAATTATATTTTTT
Found at i:47084323 original size:17 final size:18
Alignment explanation
Indices: 47084291--47084325 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
47084281 CACTAGAGTA
47084291 ATATTATATATTTAATAT
1 ATATTATATATTTAATAT
*
47084309 ATATT-TATTTTTAATAT
1 ATATTATATATTTAATAT
47084326 GTTATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTATATATTTAATAT
Found at i:47085183 original size:11 final size:11
Alignment explanation
Indices: 47085142--47085183 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
47085132 CTCATCATTC
47085142 ATAATTTTTT-
1 ATAATTTTTTA
* *
47085152 TTAATTATTTA
1 ATAATTTTTTA
*
47085163 ATAATATTTTA
1 ATAATTTTTTA
47085174 ATAATTTTTT
1 ATAATTTTTT
47085184 CATATCATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATAATTTTTTA
Found at i:47086367 original size:15 final size:16
Alignment explanation
Indices: 47086344--47086377 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
47086334 TCTTTCCATG
47086344 TTTAGTTTTTT-TAGA
1 TTTAGTTTTTTATAGA
*
47086359 TTTATTTTTTTATAGA
1 TTTAGTTTTTTATAGA
47086375 TTT
1 TTT
47086378 TATATAAAAA
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:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (16 bp):
TTTAGTTTTTTATAGA
Found at i:47095295 original size:26 final size:26
Alignment explanation
Indices: 47095266--47095315 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
47095256 GACGTGACTT
47095266 TAGGTGATTTCTTTGCCTCAAATCTG
1 TAGGTGATTTCTTTGCCTCAAATCTG
* * *
47095292 TAGGTTATTTTTTTGCTTCAAATC
1 TAGGTGATTTCTTTGCCTCAAATC
47095316 CATCTAAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (26 bp):
TAGGTGATTTCTTTGCCTCAAATCTG
Found at i:47102496 original size:18 final size:18
Alignment explanation
Indices: 47102473--47102510 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
47102463 TTATTTAAAA
47102473 AATTTAGAT-TTTTTTCAG
1 AATTTAGATATTTTTT-AG
*
47102491 AATTTATATATTTTTTAG
1 AATTTAGATATTTTTTAG
47102509 AA
1 AA
47102511 ATTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (18 bp):
AATTTAGATATTTTTTAG
Done.