Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009011.1 Hibiscus syriacus cultivar Beakdansim tig00112399_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 579188
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 4
Found at i:158610 original size:12 final size:11
Alignment explanation
Indices: 158589--158646 Score: 77
Period size: 12 Copynumber: 5.4 Consensus size: 11
158579 ACATTAAATC
158589 AATTTAATTCT
1 AATTTAATTCT
158600 AATTCTAATTCT
1 AATT-TAATTCT
158612 AATTCTAATTCT
1 AATT-TAATTCT
158624 AATTTAATT-T
1 AATTTAATTCT
158634 AA-TTAATT-T
1 AATTTAATTCT
158643 AATT
1 AATT
158647 ATCCAATCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.20
10 4 0.09
11 9 0.20
12 23 0.51
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAATTCT
Found at i:158616 original size:18 final size:17
Alignment explanation
Indices: 158589--158646 Score: 86
Period size: 18 Copynumber: 3.5 Consensus size: 17
158579 ACATTAAATC
158589 AATTTAATTCTAATTCT
1 AATTTAATTCTAATTCT
158606 AATTCTAATTCTAATTCT
1 AATT-TAATTCTAATTCT
158624 AATTTAATT-TAA-T-T
1 AATTTAATTCTAATTCT
158638 AATTTAATT
1 AATTTAATT
158647 ATCCAATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 3 0.08
17 9 0.22
18 17 0.43
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTAATTCTAATTCT
Found at i:158641 original size:4 final size:5
Alignment explanation
Indices: 158589--158646 Score: 64
Period size: 6 Copynumber: 10.8 Consensus size: 5
158579 ACATTAAATC
158589 AATTT AATTCT AATTCT AATTCT AATTCT AATTCT AATTT AATTT AA-TT
1 AATTT AATT-T AATT-T AATT-T AATT-T AATT-T AATTT AATTT AATTT
158638 AATTT AATT
1 AATTT AATT
158647 ATCCAATCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.08
5 18 0.35
6 29 0.57
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (5 bp):
AATTT
Found at i:165458 original size:3 final size:3
Alignment explanation
Indices: 165450--165521 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
165440 ATTTTAAAAT
* * * *
165450 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TAA TAA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
165498 TTA ATA -TA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA
165522 CAAAGCCCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:174945 original size:77 final size:76
Alignment explanation
Indices: 174811--174964 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 76
174801 GCAGGTTTCC
174811 TACAGGCATCTAAATATCCAGAATGGGTAGCCAACATTGTTCCGTACCAAAGAAAAAATGGGGAA
1 TACAGGCATCTAAATATCCAGAATGGGTAGCCAACATTGTTCCGTACCAAAGAAAAAAT-GGGAA
174876 AGTTCGAATGTG
65 AGTTCGAATGTG
174888 TACAGGCATCTAAATATCCAGAATGGGTAGCCAACATTGTTCCCGTACCAAAG-AAAAATGGGAA
1 TACAGGCATCTAAATATCCAGAATGGGTAGCCAACATTGTT-CCGTACCAAAGAAAAAATGGGAA
174952 AGTTCGAATGTG
65 AGTTCGAATGTG
174964 T
1 T
174965 GTGGATTACA
Statistics
Matches: 76, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
76 18 0.24
77 47 0.62
78 11 0.14
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (76 bp):
TACAGGCATCTAAATATCCAGAATGGGTAGCCAACATTGTTCCGTACCAAAGAAAAAATGGGAAA
GTTCGAATGTG
Found at i:177884 original size:7 final size:7
Alignment explanation
Indices: 177862--177903 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
177852 ATTATGCTTG
177862 AAGAAGAA
1 AAGAA-AA
177870 AA-AAAA
1 AAGAAAA
177876 AAGAAAA
1 AAGAAAA
177883 AA-AAAA
1 AAGAAAA
177889 AAGAAAA
1 AAGAAAA
177896 AAGAAAA
1 AAGAAAA
177903 A
1 A
177904 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.31
7 20 0.62
8 2 0.06
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:177886 original size:13 final size:13
Alignment explanation
Indices: 177862--177904 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
177852 ATTATGCTTG
177862 AAGAAGAAAAAAAA
1 AAGAA-AAAAAAAA
177876 AAGAAAAAAAAAA
1 AAGAAAAAAAAAA
*
177889 AAGAAAAAAGAAA
1 AAGAAAAAAAAAA
177902 AAG
1 AAG
177905 GGGGTCAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 23 0.82
14 5 0.18
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAAA
Found at i:179745 original size:267 final size:269
Alignment explanation
Indices: 179264--180155 Score: 1340
Period size: 267 Copynumber: 3.3 Consensus size: 269
179254 AACAAATGCC
*
179264 ATGTGTTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-A
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
* *
179321 -AACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTT
66 GAACCAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTT
* * *
179385 ATCTGATCTAGTTTGGTATGAACCACAAAACCCATTATTGAATTTGGAAGAGGAATGGGCTCATA
131 ATCTGATCTGGTTTGG-AT-----A-AAAACCAATTATTGAATTTGGAAGAGGAATGTGCTCATA
*
179450 GCATCTTCTAAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTAT
189 GCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTAT
*
179515 TGAATTTGGAAAAGGA
254 TGAATTTGGAAGAGGA
*
179531 ATGTGCTCATAGCATCTTATAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
* *
179596 GAACCAATTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
66 GAACCAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTT
* * *
179661 ATCTGATCTGGTTTGG-T-AAAACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTT
131 ATCTGATCTGGTTTGGATAAAAACCAATTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTT
179724 CTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTATTGAATTT
196 CTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTATTGAATTT
179789 GGAAGAGGA
261 GGAAGAGGA
*
179798 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGTGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
* *
179863 TAACCAATTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTT
66 GAACCAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTT
*
179928 ATCTGATCTGGTTTGGTATGAACCACAGACCAATTATTGAATTTGGAAGAGGAATGTGCTAATAG
131 ATCTGATCTGGTTTGG-AT-AA--A-A-ACCAATTATTGAATTTGGAAGAGGAATGTGCTCATAG
* * *
179993 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACATAACCAGTTATT
190 CATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTATT
180058 GAATTTGGAAGAGGA
255 GAATTTGGAAGAGGA
* * * *
180073 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGCTATAAAACC-C
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCAC
180137 AGAACCAATCATTGGAATT
65 AGAACCAATCATT-GAATT
180156 AAAAGATGAA
Statistics
Matches: 574, Mismatches: 32, Indels: 29
0.90 0.05 0.05
Matches are distributed among these distances:
267 307 0.53
269 2 0.00
271 1 0.00
273 1 0.00
274 3 0.01
275 176 0.31
276 84 0.15
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (269 bp):
ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
GAACCAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTT
ATCTGATCTGGTTTGGATAAAAACCAATTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTT
CTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTATTGAATTT
GGAAGAGGA
Found at i:179929 original size:359 final size:358
Alignment explanation
Indices: 179264--180155 Score: 1489
Period size: 359 Copynumber: 2.5 Consensus size: 358
179254 AACAAATGCC
* *
179264 ATGTGTTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
179329 ATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
* * *
179394 AGTTTGGTATGAACCACAAAACCCATTATTGAATTTGGAAGAGGAATGGGCTCATAGCATCTTCT
131 GGTTTGGTATGAACCACAGAACCAATTATTGAATTTGGAAGAGGAATGGGCTCATAGCATCTTCT
179459 AAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTATTGAATTTGG
196 AAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTATTGAATTTGG
179524 AAAAGGAATGTGCTCATAGCATCTTATAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG
261 AAAAGGAATGTGCTCATAGCATCTTATAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG
179589 AACCACAGAACCAATTATTGAATTTGGAAGAGGA
326 AACCACAG-ACCAATTATTGAATTTGGAAGAGGA
179623 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
179688 ATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
*
179753 GGTTTGGTATGAACCACAGAACCAATTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCT
131 GGTTTGGTATGAACCACAGAACCAATTATTGAATTTGGAAGAGGAATGGGCTCATAGCATCTTCT
* * *
179818 AGAAGTGTTCTTTGTGTTATCTGATCTGGTTTGGTATGAACCACATAACCAATTATTGAATTTGG
196 AAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTATTGAATTTGG
* *
179883 AAGAGGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG
261 AAAAGGAATGTGCTCATAGCATCTTATAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG
179948 AACCACAGACCAATTATTGAATTTGGAAGAGGA
326 AACCACAGACCAATTATTGAATTTGGAAGAGGA
* *
179981 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AAACCA-A
* * *
180046 TAACCAGTTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
64 T---C----ATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTT
* * * *
180111 ATCTGATTTGGTTTGCTATAAAACC-CAGAACCAATCATTGGAATT
122 ATCTGATCTGGTTTGGTAT-GAACCACAGAACCAATTATT-GAATT
180156 AAAAGATGAA
Statistics
Matches: 502, Mismatches: 20, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
358 80 0.16
359 327 0.65
360 2 0.00
363 1 0.00
367 83 0.17
368 9 0.02
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (358 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
ATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGGTATGAACCACAGAACCAATTATTGAATTTGGAAGAGGAATGGGCTCATAGCATCTTCT
AAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATTATTGAATTTGG
AAAAGGAATGTGCTCATAGCATCTTATAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG
AACCACAGACCAATTATTGAATTTGGAAGAGGA
Found at i:180143 original size:92 final size:92
Alignment explanation
Indices: 179264--180155 Score: 1392
Period size: 92 Copynumber: 9.9 Consensus size: 92
179254 AACAAATGCC
*
179264 ATGTGTTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-A
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
* * *
179321 -AACCAATCATTGAATTTGAAAGATGA
66 GAACCAATTATTGAATTTGGAAGAGGA
*
179347 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
* *
179412 AAACCCATTATTGAATTTGGAAGAGGA
66 GAACCAATTATTGAATTTGGAAGAGGA
* *
179439 ATGGGCTCATAGCATCTTCTAAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
*
179504 GAACCAATTATTGAATTTGGAAAAGGA
66 GAACCAATTATTGAATTTGGAAGAGGA
*
179531 ATGTGCTCATAGCATCTTATAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
179596 GAACCAATTATTGAATTTGGAAGAGGA
66 GAACCAATTATTGAATTTGGAAGAGGA
*
179623 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-A
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
* * *
179680 -AACCAATCATTGAATTTGAAAGATGA
66 GAACCAATTATTGAATTTGGAAGAGGA
179706 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
179771 GAACCAATTATTGAATTTGGAAGAGGA
66 GAACCAATTATTGAATTTGGAAGAGGA
*
179798 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGTGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
*
179863 TAACCAATTATTGAATTTGGAAGAGGA
66 GAACCAATTATTGAATTTGGAAGAGGA
179890 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
179955 G-ACCAATTATTGAATTTGGAAGAGGA
66 GAACCAATTATTGAATTTGGAAGAGGA
* *
179981 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
* *
180046 TAACCAGTTATTGAATTTGGAAGAGGA
66 GAACCAATTATTGAATTTGGAAGAGGA
* * * *
180073 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGCTATAAAACC-C
1 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCAC
*
180137 AGAACCAATCATTGGAATT
65 AGAACCAATTATT-GAATT
180156 AAAAGATGAA
Statistics
Matches: 748, Mismatches: 40, Indels: 32
0.91 0.05 0.04
Matches are distributed among these distances:
83 128 0.17
84 1 0.00
85 3 0.00
90 3 0.00
91 90 0.12
92 514 0.69
93 9 0.01
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (92 bp):
ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
GAACCAATTATTGAATTTGGAAGAGGA
Found at i:181051 original size:113 final size:113
Alignment explanation
Indices: 180889--181756 Score: 1409
Period size: 113 Copynumber: 7.7 Consensus size: 113
180879 TGTCAGTTAG
180889 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
180954 AACCTTTTGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAA
181002 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* *
181067 AACATTTTTCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAA
181115 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* *
181180 AACCTTTTGCTCAAATCCATCACTTAATGGATTAGCTTTGCCAGAGAAA
66 AACCTTTTGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAG-AA
181229 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
181294 AACCTTTTGCTCAAATCCATCACTTGATGGATTAACATTGCCAG-GTAG
66 AACCTTTTGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAG-AA
*
181342 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTA
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* * * *
181407 TTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAA
63 TTCAACCTTTTGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAA
181458 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
181523 AACCTTTTGCTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAA
66 AACCTTTTGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAA
181571 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * * *
181636 AACGTTTTGCTCAAATCCATCATCTGATGGATCAGATTTTCCAGAAAA
66 AACCTTTTGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAA
* * ** *
181684 AGTTCATAATGAGAAGAACTCATCTGAAGGA-GAAGAA-AAAGTTCACAATGAGAAGAGCTTATT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTTGTT
181747 CAACCTTTTG
65 CAACCTTTTG
181757 AATGACTCTA
Statistics
Matches: 720, Mismatches: 29, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
111 3 0.00
112 33 0.05
113 472 0.66
114 109 0.15
115 1 0.00
116 102 0.14
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAA
Found at i:181996 original size:3 final size:3
Alignment explanation
Indices: 181988--182038 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
181978 ATTTTAAAAT
* * *
181988 TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
182036 TTA
1 TTA
182039 CAAAGCCCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:183395 original size:21 final size:25
Alignment explanation
Indices: 183369--183418 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 25
183359 TAAATATGAT
183369 AATAATCA-TT-ATATTT-TTT-TC
1 AATAATCATTTAATATTTATTTATC
*
183390 AATAATTATTTAATATTTATTTATC
1 AATAATCATTTAATATTTATTTATC
183415 AATA
1 AATA
183419 TCGAAGAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 2 0.08
23 6 0.25
24 3 0.12
25 6 0.25
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (25 bp):
AATAATCATTTAATATTTATTTATC
Found at i:189225 original size:21 final size:20
Alignment explanation
Indices: 189184--189225 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
189174 TGAGTATCAA
*
189184 ACCCTATGAACAATATTGAT
1 ACCCTATGAACAATATCGAT
*
189204 ACCCTATGAACCTATATCGAT
1 ACCCTATGAA-CAATATCGAT
189225 A
1 A
189226 TTCTCAGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (20 bp):
ACCCTATGAACAATATCGAT
Found at i:195714 original size:331 final size:331
Alignment explanation
Indices: 195110--195758 Score: 1282
Period size: 331 Copynumber: 2.0 Consensus size: 331
195100 ATATGTATCA
195110 TGTGAGGTGAGATAATAACATGATCTCTATTTAGGGGTTAGATTACCTGTCAAACATGCCCAAAG
1 TGTGAGGTGAGATAATAACATGATCTCTATTTAGGGGTTAGATTACCTGTCAAACATGCCCAAAG
195175 GATGGCACTTCTCCAGAAGCTCCTGAACATCTCTCTCATGCAAGGTTCCAGTAACAATCAGAACA
66 GATGGCACTTCTCCAGAAGCTCCTGAACATCTCTCTCATGCAAGGTTCCAGTAACAATCAGAACA
195240 ACATTGTCGATCATGTGACCATACCTAAATGGAACAATCAAAACATTAGGTTTTGTTAGGCTTTC
131 ACATTGTCGATCATGTGACCATACCTAAATGGAACAATCAAAACATTAGGTTTTGTTAGGCTTTC
195305 ACTAAATCCACAACAACCTATTAATCAATCTGCATAACTACACCATCTTAAACAGACAGCTTTCT
196 ACTAAATCCACAACAACCTATTAATCAATCTGCATAACTACACCATCTTAAACAGACAGCTTTCT
195370 GAATATCCTGAGACAACTCATAAAAGCTCAACCAAAGTCCGCTACTTTACAACTAGAGTTTTGTT
261 GAATATCCTGAGACAACTCATAAAAGCTCAACCAAAGTCCGCTACTTTACAACTAGAGTTTTGTT
195435 AGGCTT
326 AGGCTT
195441 TGTGAGGTGAGATAATAACATGATCTCTATTTAGGGGTTAGATTACCTGTCAAACATGCCCAAAG
1 TGTGAGGTGAGATAATAACATGATCTCTATTTAGGGGTTAGATTACCTGTCAAACATGCCCAAAG
195506 GATGGCACTTCTCCAGAAGCTCCTGAACATCTCTCTCATGCAAGGTTCCAGTAACAATCAGAACA
66 GATGGCACTTCTCCAGAAGCTCCTGAACATCTCTCTCATGCAAGGTTCCAGTAACAATCAGAACA
195571 ACATTGTCGATCATGTGACCATACCTAAATGGAACAATCAAAACATTAGGTTTTGTTAGGCTTTC
131 ACATTGTCGATCATGTGACCATACCTAAATGGAACAATCAAAACATTAGGTTTTGTTAGGCTTTC
195636 ACTAAATCCACAACAACCTATTAATCAATCTGCATAACTACACCATCTT-AACAGACAGCTTTCT
196 ACTAAATCCACAACAACCTATTAATCAATCTGCATAACTACACCATCTTAAACAGACAGCTTTCT
195700 GAATATCACTGAGACAACTCATAAAAGCTCAACCAAAGTCCGCTACTTTACAACTAGAG
261 GAATATC-CTGAGACAACTCATAAAAGCTCAACCAAAGTCCGCTACTTTACAACTAGAG
195759 CTTAAGATTG
Statistics
Matches: 317, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
330 22 0.07
331 295 0.93
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (331 bp):
TGTGAGGTGAGATAATAACATGATCTCTATTTAGGGGTTAGATTACCTGTCAAACATGCCCAAAG
GATGGCACTTCTCCAGAAGCTCCTGAACATCTCTCTCATGCAAGGTTCCAGTAACAATCAGAACA
ACATTGTCGATCATGTGACCATACCTAAATGGAACAATCAAAACATTAGGTTTTGTTAGGCTTTC
ACTAAATCCACAACAACCTATTAATCAATCTGCATAACTACACCATCTTAAACAGACAGCTTTCT
GAATATCCTGAGACAACTCATAAAAGCTCAACCAAAGTCCGCTACTTTACAACTAGAGTTTTGTT
AGGCTT
Found at i:197137 original size:14 final size:14
Alignment explanation
Indices: 197118--197166 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
197108 TAGATATTAA
197118 TTTTAATATTAATT
1 TTTTAATATTAATT
197132 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
197142 ATTAAATATTAATT
1 TTTTAATATTAATT
197156 TTTTAATATTA
1 TTTTAATATTA
197167 TATTATAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 6 0.22
13 1 0.04
14 15 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:197242 original size:20 final size:19
Alignment explanation
Indices: 197182--197243 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
197172 TAGATATTTA
*
197182 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
197201 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
197219 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
197239 ATTTT
1 ATTTT
197244 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:197894 original size:31 final size:31
Alignment explanation
Indices: 197857--197916 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
197847 TAGTTGTATG
* *
197857 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
197888 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
197917 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:201230 original size:20 final size:21
Alignment explanation
Indices: 201189--201232 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
201179 ACCAGAGGAG
*
201189 TAGTATTGATACTCCTCCTTA
1 TAGTATTGACACTCCTCCTTA
*
201210 TAGTATTGACACTTC-CCTTA
1 TAGTATTGACACTCCTCCTTA
201230 TAG
1 TAG
201233 GATGCTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (21 bp):
TAGTATTGACACTCCTCCTTA
Found at i:201366 original size:20 final size:20
Alignment explanation
Indices: 201341--201388 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
201331 TTTAATACAC
*
201341 TCTCAAACACCTTGGTTTGA
1 TCTCAAACACCATGGTTTGA
201361 TCTCAAACACCATGGTTTGA
1 TCTCAAACACCATGGTTTGA
201381 TCTCAAAC
1 TCTCAAAC
201389 CATATTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (20 bp):
TCTCAAACACCATGGTTTGA
Found at i:203938 original size:28 final size:28
Alignment explanation
Indices: 203872--203939 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
203862 TTAGTACTTC
*
203872 AAGTATTTATTTTGATAAAAAATATTTT
1 AAGTATTTATTTTGATAAAAAATAATTT
* *
203900 AAATATCTATTTTGATAAAAAATAATTT
1 AAGTATTTATTTTGATAAAAAATAATTT
*
203928 ATGTATTTATTT
1 AAGTATTTATTT
203940 AAAAAAAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (28 bp):
AAGTATTTATTTTGATAAAAAATAATTT
Found at i:204214 original size:29 final size:28
Alignment explanation
Indices: 204182--204242 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
204172 CGCCAGGTGG
204182 TCCAAACGAC-TGTGCAGGTCGCCATGCAA
1 TCCAAACGACAT-T-CAGGTCGCCATGCAA
** *
204211 TCCATGCGACATTTAGGTCGCCATGCAA
1 TCCAAACGACATTCAGGTCGCCATGCAA
204239 TCCA
1 TCCA
204243 CGCGACCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.64
29 9 0.32
30 1 0.04
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (28 bp):
TCCAAACGACATTCAGGTCGCCATGCAA
Found at i:204601 original size:13 final size:13
Alignment explanation
Indices: 204568--204619 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
204558 TATGGGGTAA
204568 GAAGAAAGAAAGGG
1 GAAGAAAGAAA-GG
204582 AGAAGAAAGAAAGG
1 -GAAGAAAGAAAGG
204596 GAAGAAAGAAAGG
1 GAAGAAAGAAAGG
*
204609 AAATGAAAGAA
1 GAA-GAAAGAA
204620 GAAAGGGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
13 15 0.43
14 9 0.26
15 11 0.31
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (13 bp):
GAAGAAAGAAAGG
Found at i:204621 original size:17 final size:17
Alignment explanation
Indices: 204566--204625 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 17
204556 GGTATGGGGT
204566 AAGAAGAAA-GAAAGG-
1 AAGAAGAAAGGAAAGGA
* *
204581 GAGAAGAAA-GAAAGGG
1 AAGAAGAAAGGAAAGGA
*
204597 AAGAAAGAAAGGAAATGA
1 AAG-AAGAAAGGAAAGGA
204615 AAGAAGAAAGG
1 AAGAAGAAAGG
204626 GAGAAGAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
15 14 0.37
16 2 0.05
17 14 0.37
18 8 0.21
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (17 bp):
AAGAAGAAAGGAAAGGA
Found at i:204789 original size:34 final size:33
Alignment explanation
Indices: 204715--204790 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
204705 AAATTTAGTT
* * *
204715 AATTAGTTTGTTAGTTTAAGTTATATTATAAAA
1 AATTAGTTTATTAGTTGAAGTTATATTAAAAAA
*
204748 AAGTAGTTTATTAGTTGAAGTTATATTTAAAAAA
1 AATTAGTTTATTAGTTGAAGTTATA-TTAAAAAA
204782 AATTAGTTT
1 AATTAGTTT
204791 TGTTAGTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 22 0.59
34 15 0.41
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (33 bp):
AATTAGTTTATTAGTTGAAGTTATATTAAAAAA
Found at i:205346 original size:12 final size:12
Alignment explanation
Indices: 205329--205354 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
205319 TATCTTCTTG
205329 CCTTCTTCTTCT
1 CCTTCTTCTTCT
205341 CCTTCTTCTTCT
1 CCTTCTTCTTCT
205353 CC
1 CC
205355 CCGTAGGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (12 bp):
CCTTCTTCTTCT
Found at i:207213 original size:12 final size:12
Alignment explanation
Indices: 207196--207227 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
207186 GCATCGGTGC
207196 ACTGTTCACGGT
1 ACTGTTCACGGT
207208 ACTGTTCACGGT
1 ACTGTTCACGGT
*
207220 ATTGTTCA
1 ACTGTTCA
207228 TTAATGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (12 bp):
ACTGTTCACGGT
Found at i:208684 original size:12 final size:12
Alignment explanation
Indices: 208667--208693 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
208657 GATGTCTCAA
208667 AGAGGAAGAGGT
1 AGAGGAAGAGGT
208679 AGAGGAAGAGGT
1 AGAGGAAGAGGT
208691 AGA
1 AGA
208694 AGTCAACCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.48, T:0.07
Consensus pattern (12 bp):
AGAGGAAGAGGT
Found at i:213671 original size:26 final size:26
Alignment explanation
Indices: 213641--213723 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
213631 TTATGAAACA
213641 TGATACGAAATATGTCGATCAAATTT
1 TGATACGAAATATGTCGATCAAATTT
* * * * **
213667 TGATAAGAGCAATATAT-TATGAAA-CA
1 TGATACGA--AATATGTCGATCAAATTT
213693 TGATACGAAATATGTCGATCAAATTT
1 TGATACGAAATATGTCGATCAAATTT
213719 TGATA
1 TGATA
213724 AGAGATTGGA
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
24 6 0.15
25 5 0.12
26 19 0.46
27 5 0.12
28 6 0.15
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (26 bp):
TGATACGAAATATGTCGATCAAATTT
Found at i:213686 original size:52 final size:52
Alignment explanation
Indices: 213624--213727 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
213614 AGGTTTAACA
213624 CAATATATTATGAAACATGATACGAAATATGTCGATCAAATTTTGATAAGAG
1 CAATATATTATGAAACATGATACGAAATATGTCGATCAAATTTTGATAAGAG
213676 CAATATATTATGAAACATGATACGAAATATGTCGATCAAATTTTGATAAGAG
1 CAATATATTATGAAACATGATACGAAATATGTCGATCAAATTTTGATAAGAG
213728 ATTGGAGAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (52 bp):
CAATATATTATGAAACATGATACGAAATATGTCGATCAAATTTTGATAAGAG
Found at i:214394 original size:19 final size:19
Alignment explanation
Indices: 214350--214394 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
214340 GCTTCGTAGA
*
214350 AGTCCAAAGGATCGACCTG
1 AGTCCACAGGATCGACCTG
* *
214369 AGTCCACAGGGTCGACTTG
1 AGTCCACAGGATCGACCTG
214388 AGTCCAC
1 AGTCCAC
214395 TTGTATTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.18
Consensus pattern (19 bp):
AGTCCACAGGATCGACCTG
Found at i:215499 original size:22 final size:21
Alignment explanation
Indices: 215468--215508 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
215458 ATTATTTTAG
*
215468 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGA-TACCCTGCTACA
*
215490 GGGAATCGATACCCTGCTA
1 GGGAACCGATACCCTGCTA
215509 TAGTACTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:216233 original size:21 final size:21
Alignment explanation
Indices: 216207--216263 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
216197 CATACAAAAT
*
216207 TTGTCCCAAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
216228 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
216249 TTGTCCCGAAGGACC
1 TTGTCCCGAAGGACC
216264 TATGAAACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:220329 original size:21 final size:19
Alignment explanation
Indices: 220285--220332 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
220275 ATATATGTTT
* *
220285 TATGAACAGTAAATTACGG
1 TATGAACAGTAAAGTACCG
220304 TATGAACAGTGAACAGTACCG
1 TATGAACAGT-AA-AGTACCG
220325 TATGAACA
1 TATGAACA
220333 TACGTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23
Consensus pattern (19 bp):
TATGAACAGTAAAGTACCG
Found at i:220452 original size:21 final size:22
Alignment explanation
Indices: 220414--220455 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
220404 ATTATAATAG
*
220414 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
220436 GGGAACCGA-TACCCTGCTAC
1 GGGAACCGATTACCCTGCTAC
220456 TATACTGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTACCCTGCTACA
Found at i:223546 original size:16 final size:17
Alignment explanation
Indices: 223518--223549 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
223508 TTATACTTCA
223518 TCCATTCATTTCTTTAT
1 TCCATTCATTTCTTTAT
223535 TCCATT-ATTTCTTTA
1 TCCATTCATTTCTTTA
223550 AAATCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (17 bp):
TCCATTCATTTCTTTAT
Found at i:227302 original size:21 final size:21
Alignment explanation
Indices: 227278--227333 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
227268 CATATGAAAT
* *
227278 TTGTCCTGAATGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
227299 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
227320 TTGTCCCGAAGGAC
1 TTGTCCCGAAGGAC
227334 TTATGAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:230326 original size:18 final size:19
Alignment explanation
Indices: 230291--230327 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
230281 CATTTTTTCG
230291 GGGGGAATCGATACCCCCA
1 GGGGGAATCGATACCCCCA
230310 GGGGGAATCTG-TACCCCC
1 GGGGGAATC-GATACCCCC
230328 TACGTAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.14
Consensus pattern (19 bp):
GGGGGAATCGATACCCCCA
Found at i:232859 original size:21 final size:21
Alignment explanation
Indices: 232835--232878 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
232825 TTTATTATAT
232835 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
*
232856 ATAATTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
232877 AT
1 AT
232879 TTAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:233038 original size:36 final size:36
Alignment explanation
Indices: 232949--233052 Score: 120
Period size: 36 Copynumber: 2.8 Consensus size: 36
232939 CCTTTTCGTC
*
232949 CTACAAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCT-AAAATAGGATAGAATT
* * *
232986 TTGCTAGGATTCAAACTCCTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
**
233022 CTACTATTACTT-AAACTCCTAAAGATAGGAT
1 CTACTAGGA-TTCAAACTCCTAAA-ATAGGAT
233053 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
36 31 0.54
37 26 0.46
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
Found at i:233710 original size:3 final size:3
Alignment explanation
Indices: 233702--233745 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
233692 ATTTTTTCAT
* *
233702 TTA TTA TTA TTA TTA TTA TTA CTA TTA GTA TT- TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
233746 ACATACATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:233718 original size:24 final size:23
Alignment explanation
Indices: 233662--233714 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
233652 TATTTCTATG
*
233662 ATTACTATTTTTTTAGTTAATATT
1 ATTA-TATTTTTTCAGTTAATATT
* *
233686 ATGTATATTTTTTCATTTATTATT
1 AT-TATATTTTTTCAGTTAATATT
233710 ATTAT
1 ATTAT
233715 TATTATTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 3 0.12
24 20 0.80
25 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (23 bp):
ATTATATTTTTTCAGTTAATATT
Found at i:233757 original size:22 final size:21
Alignment explanation
Indices: 233732--233784 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
233722 ACTATTAGTA
233732 TTTTATTATATTATACATACAT
1 TTTTATTAT-TTATACATACAT
* *
233754 TTTTA-TATTTATATATATAT
1 TTTTATTATTTATACATACAT
*
233774 TTTTTTTATTT
1 TTTTATTATTT
233785 TATTTATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.52
21 8 0.30
22 5 0.19
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATTATTTATACATACAT
Found at i:233786 original size:22 final size:20
Alignment explanation
Indices: 233689--233815 Score: 64
Period size: 22 Copynumber: 6.2 Consensus size: 20
233679 TAATATTATG
*
233689 TATATTTTTTCA-TTTATTA
1 TATATTTTTTTATTTTATTA
* *
233708 T-TATTATTATTATTACTATTA
1 TATATT-TTTTTATT-TTATTA
* * *
233729 -GTATTTTATTATATTA-TA
1 TATATTTTTTTATTTTATTA
* **
233747 CATACATTTTTATATTTATATA
1 TATATTTTTTTAT-TTTAT-TA
233769 TATATTTTTTTTATTTTATTTA
1 TATA-TTTTTTTATTTTA-TTA
*
233791 TACTATTTATTTATTTTCATTA
1 TA-TATTTTTTTATTTT-ATTA
233813 TAT
1 TAT
233816 TTTAGTTTCT
Statistics
Matches: 82, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
18 6 0.07
19 15 0.18
20 11 0.13
21 10 0.12
22 29 0.35
23 11 0.13
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.65
Consensus pattern (20 bp):
TATATTTTTTTATTTTATTA
Found at i:233797 original size:23 final size:21
Alignment explanation
Indices: 233730--233815 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 21
233720 TTACTATTAG
* * *
233730 TATTTTATTATATTATACATA
1 TATTTTTTTATTTTATATATA
* *
233751 CATTTTTATA-TTTATATATA
1 TATTTTTTTATTTTATATATA
*
233771 TATTTTTTTTATTTTATTTATA
1 TA-TTTTTTTATTTTATATATA
*
233793 CTATTTATTTATTTTCAT-TATA
1 -TATTTTTTTATTTT-ATATATA
233815 T
1 T
233816 TTTAGTTTCT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 9 0.17
21 15 0.29
22 24 0.46
23 4 0.08
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTTTTTATTTTATATATA
Found at i:233925 original size:18 final size:18
Alignment explanation
Indices: 233896--233952 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
233886 ATATTTTATC
*
233896 TTCATTTATTTTATTTTA
1 TTCAATTATTTTATTTTA
*
233914 TTCAATTCTTTT-TTTTCA
1 TTCAATTATTTTATTTT-A
*
233932 TCCAATTATTTTATGTTTA
1 TTCAATTATTTTAT-TTTA
233951 TT
1 TT
233953 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 4 0.13
18 21 0.68
19 3 0.10
20 3 0.10
ACGTcount: A:0.21, C:0.11, G:0.02, T:0.67
Consensus pattern (18 bp):
TTCAATTATTTTATTTTA
Found at i:234726 original size:20 final size:20
Alignment explanation
Indices: 234701--234740 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
234691 TTAAGGGTCT
234701 GGCAAGCCCAAGGGGGCACC
1 GGCAAGCCCAAGGGGGCACC
234721 GGCAAGCCCAAGGGGGCACC
1 GGCAAGCCCAAGGGGGCACC
234741 TACAAGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.35, G:0.40, T:0.00
Consensus pattern (20 bp):
GGCAAGCCCAAGGGGGCACC
Found at i:234746 original size:20 final size:20
Alignment explanation
Indices: 234703--234746 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
234693 AAGGGTCTGG
*
234703 CAAGCCCAAGGGGGCACCGG
1 CAAGCCCAAGGGGGCACCGA
*
234723 CAAGCCCAAGGGGGCACCTA
1 CAAGCCCAAGGGGGCACCGA
234743 CAAG
1 CAAG
234747 GAGAACTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.34, T:0.02
Consensus pattern (20 bp):
CAAGCCCAAGGGGGCACCGA
Found at i:238839 original size:22 final size:22
Alignment explanation
Indices: 238814--238866 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
238804 GCTACCCATC
* *
238814 AACCTTTGAGCATTAAATGTCA
1 AACCTTTGAGCATCAAATGCCA
238836 AACCTTTGAGCATCAAATGCCA
1 AACCTTTGAGCATCAAATGCCA
238858 AACCTTTGA
1 AACCTTTGA
238867 CCAACACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (22 bp):
AACCTTTGAGCATCAAATGCCA
Found at i:239813 original size:106 final size:106
Alignment explanation
Indices: 239452--240548 Score: 1655
Period size: 106 Copynumber: 10.4 Consensus size: 106
239442 TACAGCTTTT
* *
239452 AGAGTCAAGTTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 AGAGCCAA-TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
239517 ACGAAGGGACCGCTGGTTTTCAATAAACAATTTCCCAATTTC
65 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * *
239559 AAAGCCAATTGCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTC-CAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC-G
* *
239623 ACGAAGGGACCACTGGTTGTC-ATAAACAACTT-CCAATTTC
65 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
239663 ATAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
239728 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * *
239769 AGAGCCAATTTTAACTTCACAACAAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
239834 CGAAGGGACCCCTGGTTGTCAACAAAAAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
239875 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
239940 AGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
239981 GGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCGACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
240046 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
240087 GGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
240152 CGAAGGGACTGCTGGTTGTCAACAAATAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
240193 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
240258 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
240299 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTTAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
240364 CGAAGGGACTGTTGGTTGTCAACAAACAATTTCCCAA-TTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * * * * *
240404 GGAGCCAATTTCAACTTCACAACAAAGTATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
240469 CGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
240510 ATAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
240549 GGAACAATGC
Statistics
Matches: 909, Mismatches: 75, Indels: 13
0.91 0.08 0.01
Matches are distributed among these distances:
104 85 0.09
105 118 0.13
106 700 0.77
107 6 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
Found at i:241395 original size:35 final size:36
Alignment explanation
Indices: 241295--241397 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 36
241285 CCTTTTCGTC
241295 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTA-GATTCAAACTCCTAAAAATAGGATAGAATT
* * *
241332 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTA-GATTCAAACTCCTAAAAATAGGATAGAATT
* * *
241369 CTACTA-TTTTAAACTCCTAAAGATAGGAT
1 CTACTAGATTCAAACTCCTAAAAATAGGAT
241398 TCACAAGCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 20 0.34
37 38 0.66
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (36 bp):
CTACTAGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:241865 original size:3 final size:3
Alignment explanation
Indices: 241857--241903 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
241847 CTTTGCGTTA
241857 TAT TAT TAT T-T TAT TAT TAT ATAT ATAT ATAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TAT TAT TAT TAT TAT TAT
241903 T
1 T
241904 TTTTTCTATG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 26 0.63
4 11 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:241873 original size:11 final size:11
Alignment explanation
Indices: 241857--241905 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
241847 CTTTGCGTTA
241857 TATTATTATTT
1 TATTATTATTT
241868 TATTATTATATAT
1 TATTATTAT-T-T
*
241881 ATATATATTATAT
1 -TAT-TATTATTT
241894 TATTATTATTT
1 TATTATTATTT
241905 T
1 T
241906 TTTCTATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 17 0.53
12 4 0.12
13 2 0.06
14 3 0.09
15 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTATTT
Found at i:241881 original size:23 final size:23
Alignment explanation
Indices: 241855--241899 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
241845 TTCTTTGCGT
*
241855 TATAT-TAT-TATTTTATTATTA
1 TATATATATATATTATATTATTA
241876 TATATATATATATTATATTATTA
1 TATATATATATATTATATTATTA
241899 T
1 T
241900 TATTTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 3 0.14
23 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATATATATATATTATATTATTA
Found at i:242112 original size:21 final size:20
Alignment explanation
Indices: 242088--242152 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
242078 ATACATACAA
242088 TTTTATATTTTATATATATAT
1 TTTTATATTTTAT-TATATAT
*
242109 TTTTATTATTTTTTTATACTAT
1 TTTTA-TATTTTATTATA-TAT
*
242131 TTATT-TATTTCATTATAT-T
1 TT-TTATATTTTATTATATAT
242150 TTT
1 TTT
242153 AGTTTCTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 1 0.03
21 19 0.50
22 12 0.32
23 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATATTTTATTATATAT
Found at i:242712 original size:20 final size:20
Alignment explanation
Indices: 242681--242734 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
242671 GGTTGCGACA
242681 CCTTTC-TTCTTCTTCCTTT
1 CCTTTCTTTCTTCTTCCTTT
242700 CCTTTCTTTCTTCTTCCTTT
1 CCTTTCTTTCTTCTTCCTTT
242720 CCTTTCTTTCTTCTT
1 CCTTTCTTTCTTCTT
242735 ACCCCATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 6 0.18
20 28 0.82
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
CCTTTCTTTCTTCTTCCTTT
Found at i:247356 original size:148 final size:150
Alignment explanation
Indices: 247087--247381 Score: 576
Period size: 148 Copynumber: 2.0 Consensus size: 150
247077 TGGACATCAT
247087 TTCCACCAGCTGCTGCTACTAAGTAGAGACTTAAAGGGATACCTCCAATACTGGTCCCTGTCTAA
1 TTCCACCAGCTGCTGCTACTAAGTAGAGACTTAAAGGGATACCTCCAATACTGGTCCCTGTCTAA
247152 GAAAGATTGCCTCAAGTAAATGGATCCAGCAGAGTAATGTTGTTCGTCACTTTTGTGCAG-TACC
66 GAAAGATTGCCTCAAGTAAATGGATCCAGCAGAGTAATGTTGTTCGTCACTTTTGTGCAGATACC
247216 AGTGGACTGAAATTCCCATA
131 AGTGGACTGAAATTCCCATA
247236 TTCCACCAGCTGCTGCTACTAAGTAGAGACTTAAAGGG-TACCTCCAATACTGGTCCCTGTCTAA
1 TTCCACCAGCTGCTGCTACTAAGTAGAGACTTAAAGGGATACCTCCAATACTGGTCCCTGTCTAA
247300 GAAAGATTGCCTCAAGTAAATGGATCCAGCAGAGTAATGTTGTTCGTCACTTTTGTGCAGATACC
66 GAAAGATTGCCTCAAGTAAATGGATCCAGCAGAGTAATGTTGTTCGTCACTTTTGTGCAGATACC
247365 AGTGGACTGAAATTCCC
131 AGTGGACTGAAATTCCC
247382 CAAAAACTAA
Statistics
Matches: 145, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
148 86 0.59
149 59 0.41
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (150 bp):
TTCCACCAGCTGCTGCTACTAAGTAGAGACTTAAAGGGATACCTCCAATACTGGTCCCTGTCTAA
GAAAGATTGCCTCAAGTAAATGGATCCAGCAGAGTAATGTTGTTCGTCACTTTTGTGCAGATACC
AGTGGACTGAAATTCCCATA
Found at i:249217 original size:2 final size:2
Alignment explanation
Indices: 249210--249279 Score: 117
Period size: 2 Copynumber: 36.0 Consensus size: 2
249200 ATAATATTTA
249210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
249252 AT -T AT A- AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249280 TTTAGTTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 62 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:249989 original size:21 final size:22
Alignment explanation
Indices: 249952--250015 Score: 94
Period size: 21 Copynumber: 2.9 Consensus size: 22
249942 GTCTATAATC
249952 AACAAACTCTAAACATAACATCA
1 AACAAACTC-AAACATAACATCA
*
249975 AACAAACTC-AACATAAAATCA
1 AACAAACTCAAACATAACATCA
249996 AACAAACTCAAAACATAACA
1 AACAAACTC-AAACATAACA
250016 CTTATAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 20 0.54
23 17 0.46
ACGTcount: A:0.61, C:0.25, G:0.00, T:0.14
Consensus pattern (22 bp):
AACAAACTCAAACATAACATCA
Found at i:252950 original size:3 final size:3
Alignment explanation
Indices: 252942--253020 Score: 70
Period size: 3 Copynumber: 26.3 Consensus size: 3
252932 AATTACTTAA
* ** * * * *
252942 ATT ATT ATT TTT AAA ATT ACT ATT ATT ATT -TA AAT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
252989 ATT ATA ATT ATT AATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT A
253021 AATAATTACA
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
2 1 0.02
3 54 0.93
4 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:254342 original size:26 final size:25
Alignment explanation
Indices: 254297--254346 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
254287 GTTTAAATTA
254297 GTATTTTATTTAATTATTTATTCAT
1 GTATTTTATTTAATTATTTATTCAT
* *
254322 GTATTTATATTTAGTTTTTTATTCA
1 GTATTT-TATTTAATTATTTATTCA
254347 CTAATTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (25 bp):
GTATTTTATTTAATTATTTATTCAT
Found at i:254353 original size:26 final size:25
Alignment explanation
Indices: 254299--254355 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
254289 TTAAATTAGT
*
254299 ATTTTATTTAATTATTTATTCATGT
1 ATTTTATTTAATTATTTATTCATGA
* *
254324 ATTTATATTTAGTTTTTTATTCACT-A
1 ATTT-TATTTAATTATTTATTCA-TGA
254350 ATTTTA
1 ATTTTA
254356 CATGAAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 6 0.22
26 20 0.74
27 1 0.04
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (25 bp):
ATTTTATTTAATTATTTATTCATGA
Found at i:254475 original size:16 final size:17
Alignment explanation
Indices: 254432--254479 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
254422 TTTGCTTCGT
254432 TTTTTTTTAA-ATCCTTA
1 TTTTTTTTAATAT-CTTA
*
254449 TATTCTTTTAATAT-TTA
1 T-TTTTTTTAATATCTTA
254466 TTTTTTTTAATATC
1 TTTTTTTTAATATC
254480 AAAGAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 11 0.42
17 5 0.19
18 8 0.31
19 2 0.08
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTTTAATATCTTA
Found at i:256541 original size:43 final size:43
Alignment explanation
Indices: 256477--256561 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
256467 GGCTTTAGAA
* *
256477 AAGTTAGGAGAGAAAGTTATCCCATATATGTAAAATTTTGTTG
1 AAGTTAGGACAGAAAGATATCCCATATATGTAAAATTTTGTTG
* * *
256520 AAGTTAGGACTGAAAGATATCCCCTATATGTAAAGTTTTGTT
1 AAGTTAGGACAGAAAGATATCCCATATATGTAAAATTTTGTT
256562 TAATGCACGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (43 bp):
AAGTTAGGACAGAAAGATATCCCATATATGTAAAATTTTGTTG
Found at i:259304 original size:24 final size:24
Alignment explanation
Indices: 259259--259308 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
259249 ATAAAGAACC
*
259259 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
259283 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
259307 AA
1 AA
259309 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:261646 original size:14 final size:15
Alignment explanation
Indices: 261628--261685 Score: 84
Period size: 15 Copynumber: 4.0 Consensus size: 15
261618 AAAATGATAT
* *
261628 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
261643 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
261657 TAAAAATAAAACAAA
1 TAAAAATAAAACAAA
261672 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
261686 CAAACACTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
14 19 0.47
15 21 0.52
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:261660 original size:29 final size:29
Alignment explanation
Indices: 261628--261685 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
261618 AAAATGATAT
* *
261628 TAAAATTAAAACTAA-AAAAATAAAACAAA
1 TAAAAATAAAACAAATAAAAAT-AAACAAA
261657 TAAAAATAAAACAAATAAAAATAAACAAA
1 TAAAAATAAAACAAATAAAAATAAACAAA
261686 CAAACACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.16
Consensus pattern (29 bp):
TAAAAATAAAACAAATAAAAATAAACAAA
Found at i:264885 original size:24 final size:24
Alignment explanation
Indices: 264840--264889 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
264830 ATAAAGAACC
*
264840 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
264864 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
264888 AA
1 AA
264890 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:266715 original size:10 final size:10
Alignment explanation
Indices: 266700--266746 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
266690 ACTTGAAGAA
266700 GAAAAAAAAG
1 GAAAAAAAAG
266710 G--AAAAAAG
1 GAAAAAAAAG
266718 GAAAAAAAAG
1 GAAAAAAAAG
*
266728 GAAACAAAAG
1 GAAAAAAAAG
266738 GAAAAAAAA
1 GAAAAAAAA
266747 TTGAATCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 8 0.24
10 25 0.76
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAG
Found at i:266757 original size:21 final size:20
Alignment explanation
Indices: 266700--266746 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
266690 ACTTGAAGAA
266700 GAAAAAAAAGG-AA-AAAAG
1 GAAAAAAAAGGAAACAAAAG
266718 GAAAAAAAAGGAAACAAAAG
1 GAAAAAAAAGGAAACAAAAG
266738 GAAAAAAAA
1 GAAAAAAAA
266747 TTGAATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 11 0.41
19 2 0.07
20 14 0.52
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAGGAAACAAAAG
Found at i:272109 original size:45 final size:45
Alignment explanation
Indices: 272058--272463 Score: 634
Period size: 45 Copynumber: 9.0 Consensus size: 45
272048 CTTTTTGATA
*
272058 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* *
272103 TTTTCAAAACCTTTGAGTCATCTGTAAGCCCTTCAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* *
272148 TTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
272193 TTTTCAAAACCTTCGGGTTCATCTGTAAGCCCTTCAGTGCAGGATG
1 TTTTCAAAACCTTCGGG-TCATCTGTAAGCCCTTCAGTGCAGGATG
* *
272239 TTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* *
272284 TTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
*
272329 TTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* * * *
272374 TTTTCAAAGCCTTCAGGTCATCTGTAAGACCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* * *
272419 TTTTCAAACCCTTCGGGTCATCTGTAAGACCTAT-AGTGCAAGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCT-TCAGTGCAGGATG
272464 ATAGGACCTT
Statistics
Matches: 340, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
45 296 0.87
46 44 0.13
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (45 bp):
TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
Found at i:272647 original size:3 final size:3
Alignment explanation
Indices: 272639--272714 Score: 64
Period size: 3 Copynumber: 25.3 Consensus size: 3
272629 AATTACTTAA
* ** * * * *
272639 ATT ATT ATT TTT AAA ATT ACT ATT ATT ATT -TA AAT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
272686 ATT ATA ATT ATT AATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT A
272715 AATAATTACA
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
2 1 0.02
3 51 0.93
4 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:272704 original size:16 final size:16
Alignment explanation
Indices: 272679--272715 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
272669 TAAATATTAG
272679 TATT-ATTATTATAAT
1 TATTAATTATTATAAT
*
272694 TATTAATTATTATTAT
1 TATTAATTATTATAAT
272710 TATTAA
1 TATTAA
272716 ATAATTACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTAATTATTATAAT
Found at i:273027 original size:22 final size:22
Alignment explanation
Indices: 273002--273060 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
272992 ATATCAAGCT
273002 CTATGGTGAGTCACCGCCATAG
1 CTATGGTGAGTCACCGCCATAG
273024 CTATGGTGAGTCACCGCCATAG
1 CTATGGTGAGTCACCGCCATAG
*
273046 CTATGGTGACTCACC
1 CTATGGTGAGTCACC
273061 TAGGCAATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.24
Consensus pattern (22 bp):
CTATGGTGAGTCACCGCCATAG
Found at i:280766 original size:36 final size:36
Alignment explanation
Indices: 280700--280908 Score: 223
Period size: 36 Copynumber: 6.0 Consensus size: 36
280690 AAAAACGAAC
* * * * * *
280700 ACTTGAAACGAAAGTG-CGATACATCTTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
* * *
280735 ACTTAAATCGGAAGTGTCGATGCTTCATTCCGTTCA
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
*
280771 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
* *
280807 ACTTGAATCGGAAGTGCCGATGCCTCCTTTCGTTCA
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
*
280843 ACTTGAATCGGAAATGCCGATG----CTTCC-TTCA
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
* * * *
280874 ACTTGAATCGAAAGTACCGATGCTTTCTTTCGTTC
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTC
280909 TTCTTATTCA
Statistics
Matches: 148, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
31 23 0.16
32 4 0.03
35 17 0.11
36 104 0.70
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
Found at i:289059 original size:35 final size:35
Alignment explanation
Indices: 289013--289081 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
289003 TTACACAATC
289013 TTCAATTTCATTCTAAA-TCCCAAATTCCAAAATAA
1 TTCAATTTCATTCTAAACT-CCAAATTCCAAAATAA
* * *
289048 TTCAATTTCATTTTAAACTCTAAATTCTAAAATA
1 TTCAATTTCATTCTAAACTCCAAATTCCAAAATA
289082 GGGTTTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (35 bp):
TTCAATTTCATTCTAAACTCCAAATTCCAAAATAA
Found at i:289228 original size:19 final size:19
Alignment explanation
Indices: 289204--289242 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
289194 TTTGAGGTTT
289204 GTTGCATGCACATCCAACG
1 GTTGCATGCACATCCAACG
289223 GTTGCATGCACATCCAACG
1 GTTGCATGCACATCCAACG
289242 G
1 G
289243 CTGCCGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21
Consensus pattern (19 bp):
GTTGCATGCACATCCAACG
Found at i:290833 original size:35 final size:39
Alignment explanation
Indices: 290785--290874 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 39
290775 TAGATTGAAT
* *
290785 GTAATTTAAAATATTAT-TATTT-TAAT-ATTTTTGGTG
1 GTAATTAAAAATATTATATATTTATAATAATTTTAGGTG
* *
290821 G-AATTAAAAATATTATATTTTTATAATAATTTTAGTTG
1 GTAATTAAAAATATTATATATTTATAATAATTTTAGGTG
*
290859 GTAATCAAAAATATTA
1 GTAATTAAAAATATTA
290875 AAATATTACA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
35 14 0.31
36 5 0.11
37 4 0.09
38 9 0.20
39 13 0.29
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (39 bp):
GTAATTAAAAATATTATATATTTATAATAATTTTAGGTG
Found at i:295909 original size:12 final size:12
Alignment explanation
Indices: 295894--295946 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
295884 AGCAGCACAA
*
295894 TCAGCATCATCC
1 TCAGCAACATCC
295906 TCAGCAACAAT-C
1 TCAGCAAC-ATCC
* * *
295918 TCAACAGCACCC
1 TCAGCAACATCC
295930 TCAGCAACATCC
1 TCAGCAACATCC
295942 TCAGC
1 TCAGC
295947 GACAGTTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 1 0.03
12 29 0.91
13 2 0.06
ACGTcount: A:0.32, C:0.42, G:0.09, T:0.17
Consensus pattern (12 bp):
TCAGCAACATCC
Found at i:297181 original size:33 final size:32
Alignment explanation
Indices: 297147--297210 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
297137 TTTTTTAATA
*
297147 AAAAT-CTGACGTGTAAAATTTCACGTCATCAT
1 AAAATACTGACGTG-AAAATTCCACGTCATCAT
*
297179 AAAATAGTGACGTGAAAATTCCACGTCATCAT
1 AAAATACTGACGTGAAAATTCCACGTCATCAT
297211 CAGTGACCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
AAAATACTGACGTGAAAATTCCACGTCATCAT
Found at i:297583 original size:3 final size:3
Alignment explanation
Indices: 297575--297613 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
297565 ATTGTAGCCT
297575 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
297614 GTTACCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:299800 original size:2 final size:2
Alignment explanation
Indices: 299793--299818 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
299783 ACCAATATCA
299793 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
299819 GAATATGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:303681 original size:21 final size:21
Alignment explanation
Indices: 303645--303755 Score: 123
Period size: 21 Copynumber: 5.1 Consensus size: 21
303635 ACCCGACCAA
*
303645 TAATATATATACACTAATATAT
1 TAATA-ATATATACTAATATAT
*
303667 TAATACTATATACTAATATAT
1 TAATAATATATACTAATATAT
* * * *
303688 TAATAATATACATTCATTTAT
1 TAATAATATATACTAATATAT
303709 TAATAATATGTACTACTAATATAT
1 TAATAATA--TA-TACTAATATAT
*
303733 TAATAATATGTACTAATATAT
1 TAATAATATATACTAATATAT
303754 TA
1 TA
303756 GTATATTAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
21 51 0.69
22 6 0.08
23 2 0.03
24 15 0.20
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (21 bp):
TAATAATATATACTAATATAT
Found at i:303710 original size:42 final size:44
Alignment explanation
Indices: 303645--303850 Score: 136
Period size: 42 Copynumber: 4.6 Consensus size: 44
303635 ACCCGACCAA
*
303645 TAATATATATACACTAATATATTAATACTA-TA-TACTAATATAT
1 TAATA-ATATACACTAATATATTAATAATAGTACTACTAATATAT
* * *
303688 TAATAATATACATTCATTTATTAATAATATGTACTACTAATATAT
1 TAATAATATACACTAATATATTAATAATA-GTACTACTAATATAT
** * * *
303733 TAATAATATGTACTAATATATTAGTATATTAATAATATTTACTAACATAT
1 TAATAATATACACTAATATA-T--TA-A-TAATAGTA-CTACTAATATAT
* ** *
303783 TAATTATATGTACTAATATATTGATAATA-TA-TAAC-AATCA-AT
1 TAATAATATACACTAATATATTAATAATAGTACT-ACTAAT-ATAT
* * *
303825 TAATAACATATAATAATATATTAATA
1 TAATAATATACACTAATATATTAATA
303851 TAATCCTTAA
Statistics
Matches: 132, Mismatches: 20, Indels: 23
0.75 0.11 0.13
Matches are distributed among these distances:
42 46 0.35
43 8 0.06
44 4 0.03
45 31 0.23
46 2 0.02
47 1 0.01
48 2 0.02
49 4 0.03
50 34 0.26
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (44 bp):
TAATAATATACACTAATATATTAATAATAGTACTACTAATATAT
Found at i:303761 original size:29 final size:27
Alignment explanation
Indices: 303706--303784 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 27
303696 TACATTCATT
*
303706 TATTAATAATATGTACT-ACTA--ATA
1 TATTAATAATATGTACTAAATATTATA
303730 TATTAATAATATGTACTAATATATTAGTA
1 TATTAATAATATGTACTAA-ATATTA-TA
*
303759 TATTAATAATATTTACTAACATATTA
1 TATTAATAATATGTACTAA-ATATTA
303785 ATTATATGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
24 17 0.36
25 1 0.02
26 2 0.04
28 1 0.02
29 26 0.55
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (27 bp):
TATTAATAATATGTACTAAATATTATA
Found at i:303784 original size:21 final size:21
Alignment explanation
Indices: 303758--303812 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
303748 ATATATTAGT
*
303758 ATATTAATAATATTTACTAAC
1 ATATTAATAATATGTACTAAC
* *
303779 ATATTAATTATATGTACTAAT
1 ATATTAATAATATGTACTAAC
*
303800 ATATTGATAATAT
1 ATATTAATAATAT
303813 ATAACAATCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (21 bp):
ATATTAATAATATGTACTAAC
Found at i:303792 original size:50 final size:52
Alignment explanation
Indices: 303706--303804 Score: 157
Period size: 50 Copynumber: 1.9 Consensus size: 52
303696 TACATTCATT
*
303706 TATTAATAATATGTACTACTAATATATTAATAATATGTACTAATATATTAGTA
1 TATTAATAATATGTA-TACTAACATATTAATAATATGTACTAATATATTAGTA
*
303759 TATTAATAATAT-T-TACTAACATATTAATTATATGTACTAATATATT
1 TATTAATAATATGTATACTAACATATTAATAATATGTACTAATATATT
303805 GATAATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 31 0.70
52 1 0.02
53 12 0.27
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (52 bp):
TATTAATAATATGTATACTAACATATTAATAATATGTACTAATATATTAGTA
Found at i:303830 original size:21 final size:21
Alignment explanation
Indices: 303797--303850 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
303787 TATATGTACT
* *
303797 AATATATTGATAATATATAAC
1 AATATATTAATAACATATAAC
*
303818 AATCA-ATTAATAACATATAAT
1 AAT-ATATTAATAACATATAAC
303839 AATATATTAATA
1 AATATATTAATA
303851 TAATCCTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (21 bp):
AATATATTAATAACATATAAC
Found at i:303969 original size:21 final size:21
Alignment explanation
Indices: 303888--304120 Score: 210
Period size: 21 Copynumber: 11.2 Consensus size: 21
303878 AAACCCTAAT
*
303888 ATATTAATACATATATATAGTAC
1 ATATTATTA-ATATAT-TAGTAC
* *
303911 ATACTATTAATATA-TACTA-
1 ATATTATTAATATATTAGTAC
303930 ATA-TATTAGTATATATTAGTAC
1 ATATTATTA--ATATATTAGTAC
*
303952 ATATTATTAATTTATTAGTAC
1 ATATTATTAATATATTAGTAC
* *
303973 ATACTATTAATATATTAGTAT
1 ATATTATTAATATATTAGTAC
* * *
303994 ACATTATTGATATATTAGTAT
1 ATATTATTAATATATTAGTAC
*
304015 ATATTATTAATATATTGGTAC
1 ATATTATTAATATATTAGTAC
* * *
304036 ATATTATTAATATTTTAATAT
1 ATATTATTAATATATTAGTAC
* *
304057 ATATTCTTAATATA--A-TAT
1 ATATTATTAATATATTAGTAC
* *
304075 ATATTCTTAATATATTAGTAG
1 ATATTATTAATATATTAGTAC
* *
304096 ATATTGTTAATA-ATTAGTAG
1 ATATTATTAATATATTAGTAC
304116 ATATT
1 ATATT
304121 TACTCAAAAA
Statistics
Matches: 179, Mismatches: 23, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
18 22 0.12
19 4 0.02
20 23 0.13
21 110 0.61
22 8 0.04
23 12 0.07
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (21 bp):
ATATTATTAATATATTAGTAC
Found at i:304072 original size:18 final size:18
Alignment explanation
Indices: 304051--304088 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
304041 ATTAATATTT
304051 TAATATATATTCTTAATA
1 TAATATATATTCTTAATA
304069 TAATATATATTCTTAATA
1 TAATATATATTCTTAATA
304087 TA
1 TA
304089 TTAGTAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATATATTCTTAATA
Found at i:307321 original size:21 final size:21
Alignment explanation
Indices: 307295--307647 Score: 214
Period size: 21 Copynumber: 16.8 Consensus size: 21
307285 GCCTAAGATA
307295 ATATTATTAATATATTAGTAC
1 ATATTATTAATATATTAGTAC
* *
307316 ATATTATTAATATATTAATAT
1 ATATTATTAATATATTAGTAC
* *
307337 ATATTATTAGTATAGTAGTAC
1 ATATTATTAATATATTAGTAC
*
307358 ATATTATT-ATATATTATTA-
1 ATATTATTAATATATTAGTAC
* *
307377 ATA-TATTAGTACATATTATTA-
1 ATATTATTA--ATATATTAGTAC
*
307398 ATA-TATTAGTATATATTA-TAA
1 ATATTATTA--ATATATTAGTAC
*
307419 AT-TTATTAGTATATATTATTA-
1 ATATTATTA--ATATATTAGTAC
* *
307440 ATA-TATTAGTATAAATTATTAC
1 ATATTATTA--ATATATTAGTAC
* *
307462 TATATTAGT-ATATATTAATTTTAC
1 -ATATTATTAATATATT-A--GTAC
* * *
307486 AGTAGT-TT-ACA-A-TAGTAT
1 A-TATTATTAATATATTAGTAC
307504 ATATTATTAATATATTAGTAC
1 ATATTATTAATATATTAGTAC
* * * *
307525 ATATTATGAATATAATATTAT
1 ATATTATTAATATATTAGTAC
*
307546 ATATTATTAATATATATTAGTAT
1 ATATTATT-A-ATATATTAGTAC
**
307569 ATATTATTAATATATGGGTAC
1 ATATTATTAATATATTAGTAC
* * *
307590 CTATTATTAATATATTAATAT
1 ATATTATTAATATATTAGTAC
*
307611 ATATTACTAATATATT-GATAC
1 ATATTATTAATATATTAG-TAC
307632 ATATTATTAATATATT
1 ATATTATTAATATATT
307648 TGTAACACTC
Statistics
Matches: 269, Mismatches: 42, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.01
18 9 0.03
19 5 0.02
20 12 0.04
21 199 0.74
22 6 0.02
23 25 0.09
24 10 0.04
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (21 bp):
ATATTATTAATATATTAGTAC
Found at i:307458 original size:94 final size:95
Alignment explanation
Indices: 307295--307647 Score: 306
Period size: 94 Copynumber: 3.6 Consensus size: 95
307285 GCCTAAGATA
* * * * * *
307295 ATATTATTAATATATTAGTACATATTA-TTAATATATTAATATATATTATTAGTATAGTAGTACA
1 ATATTATTAATATATTAGTATATATTACTAAATATATTAGTATATATTATTAATATATTAGTATA
307359 TATTATTATATATTATTAATATATTAGTAC
66 TATTATTATATATTATTAATATATTAGTAC
*
307389 ATATTATTAATATATTAGTATATATTA-TAAATTTATTAGTATATATTATTAATATATTAGTATA
1 ATATTATTAATATATTAGTATATATTACTAAATATATTAGTATATATTATTAATATATTAGTATA
* * *
307453 AATTATTACTATATTAGT-ATATATTAATTTTAC
66 TATTATTA-TATATTATTAATATATT-A--GTAC
* * * * * *
307486 AGTAGTTTACAATAGTATATATTATTAATATATTAGT--ACATATTATGAATATAATATTATATA
1 A-TA--TT--ATTA--ATATATTAGT-ATATATTACTAAATATATTA-GTATATATTATTA-ATA
* * **
307549 TTATTAATATATATTAGTATATATTATTAATATATGGGTAC
56 -TATTAGTATATATTATTATATATTATTAATATATTAGTAC
* * *
307590 CTATTATTAATATATTAATATATATTACT-AATATATT-GATACATATTATTAATATATT
1 ATATTATTAATATATTAGTATATATTACTAAATATATTAG-TATATATTATTAATATATT
307648 TGTAACACTC
Statistics
Matches: 209, Mismatches: 31, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
94 75 0.36
95 13 0.06
96 18 0.09
97 19 0.09
98 2 0.01
99 3 0.01
100 2 0.01
101 2 0.01
102 3 0.01
103 2 0.01
104 18 0.09
105 19 0.09
106 12 0.06
107 21 0.10
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (95 bp):
ATATTATTAATATATTAGTATATATTACTAAATATATTAGTATATATTATTAATATATTAGTATA
TATTATTATATATTATTAATATATTAGTAC
Found at i:307647 original size:42 final size:42
Alignment explanation
Indices: 307295--307647 Score: 312
Period size: 42 Copynumber: 7.9 Consensus size: 42
307285 GCCTAAGATA
* *
307295 ATATTATTAATATATTAGTACATATTATTAATATATTAATATAT
1 ATATTATTAATATATTAGTATATATTATTAATATATT-A-GTAT
* *
307339 ATTATTAGTATAGTAGTACATATTATTATATATTATTAATATATTAGTAC
1 A-TATTA-T-TA--A-T--ATATTAGTATATATTATTAATATATTAGTAT
* *
307389 ATATTATTAATATATTAGTATATATTATAAATTTATTAGTAT
1 ATATTATTAATATATTAGTATATATTATTAATATATTAGTAT
* *
307431 ATATTATTAATATATTAGTATAAATTATTACTATATTAGTAT
1 ATATTATTAATATATTAGTATATATTATTAATATATTAGTAT
* *
307473 ATATTAATTTTACAGTAGTTTACAATAGTATATATTATTAATATATTAGTAC
1 ATATT-A--TTA-A-TA---T--ATTAGTATATATTATTAATATATTAGTAT
* * *
307525 ATATTATGAATATAATATTATATATTATTAATATATATTAGTAT
1 ATATTATTAATATATTAGTATATATTATT-A-ATATATTAGTAT
** ** *
307569 ATATTATTAATATATGGGTACCTATTATTAATATATTAATAT
1 ATATTATTAATATATTAGTATATATTATTAATATATTAGTAT
* *
307611 ATATTACTAATATATT-GATACATATTATTAATATATT
1 ATATTATTAATATATTAG-TATATATTATTAATATATT
307648 TGTAACACTC
Statistics
Matches: 258, Mismatches: 30, Indels: 44
0.78 0.09 0.13
Matches are distributed among these distances:
41 1 0.00
42 128 0.50
43 3 0.01
44 36 0.14
45 9 0.03
46 2 0.01
47 8 0.03
48 2 0.01
49 8 0.03
50 5 0.02
51 2 0.01
52 54 0.21
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (42 bp):
ATATTATTAATATATTAGTATATATTATTAATATATTAGTAT
Found at i:308329 original size:30 final size:31
Alignment explanation
Indices: 308294--308364 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
308284 GAATGACCTA
* *
308294 TCCATATGTTCCGGAGAACATAGCT-AACTG
1 TCCATATGTCCCGAAGAACATAGCTAAACTG
* *
308324 TCCATATGTCCCGAAGTACATAGGTAAACTG
1 TCCATATGTCCCGAAGAACATAGCTAAACTG
308355 TCCATATGTC
1 TCCATATGTC
308365 TCAAAAGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 21 0.58
31 15 0.42
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGCTAAACTG
Found at i:308357 original size:31 final size:30
Alignment explanation
Indices: 308294--308381 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
308284 GAATGACCTA
* * *
308294 TCCATATGTTCCGGAGAACATAGCT-AACTG
1 TCCATATGTCCCGAAG-ACATAGGTAAACTG
308324 TCCATATGTCCCGAAGTACATAGGTAAACTG
1 TCCATATGTCCCGAAG-ACATAGGTAAACTG
**
308355 TCCATATGTCTCAAAAGACATAGGTAA
1 TCCATATGTC-CCGAAGACATAGGTAA
308382 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 21 0.42
31 25 0.50
32 4 0.08
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCGAAGACATAGGTAAACTG
Found at i:308633 original size:6 final size:6
Alignment explanation
Indices: 308622--308647 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
308612 TTTTCGAAAG
308622 ATTCAC ATTCAC ATTCAC ATTCAC AT
1 ATTCAC ATTCAC ATTCAC ATTCAC AT
308648 AGTCATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTCAC
Found at i:309052 original size:17 final size:17
Alignment explanation
Indices: 309015--309053 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
309005 TGTAATATAT
309015 ATATAATCACATATCCTC
1 ATATAATCACATA-CCTC
309033 ATATCAATCACATA-CTC
1 ATAT-AATCACATACCTC
309050 ATAT
1 ATAT
309054 TCATGATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 9 0.45
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAATCACATACCTC
Found at i:313198 original size:57 final size:57
Alignment explanation
Indices: 313077--313188 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 57
313067 AGAGTGCATC
* * *
313077 GATGCATCAAGTGCATTTGATGTTTCAAAATAGCCAGAGTGCATCGATACATGGCTG
1 GATGCATCAAATGCATTAGATGTTTCAAAATAGCCACAGTGCATCGATACATGGCTG
* * *
313134 GATGCATCAAATGCATTAGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGG
1 GATGCATCAAATGCATTAGATG-TTTCA-AAATAGCCACAGTGCATCGATACATGG
313189 TGTGTGCATC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 20 0.43
58 24 0.51
59 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (57 bp):
GATGCATCAAATGCATTAGATGTTTCAAAATAGCCACAGTGCATCGATACATGGCTG
Found at i:313953 original size:14 final size:15
Alignment explanation
Indices: 313934--313962 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
313924 TCAAGCATTT
313934 AACAATCCA-AAACA
1 AACAATCCAGAAACA
313948 AACAATCCAGAAACA
1 AACAATCCAGAAACA
313963 TAAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:322922 original size:31 final size:31
Alignment explanation
Indices: 322871--322972 Score: 136
Period size: 31 Copynumber: 3.3 Consensus size: 31
322861 GTTCCGGAGA
* *
322871 ACATAGGT-AACTGTCTATATGTCCCGAATG
1 ACATAGGTAAACTGTCCATATGTCTCGAATG
* *
322901 ACATAGGTAAACTGCCCATATGTCTCGAAAG
1 ACATAGGTAAACTGTCCATATGTCTCGAATG
*
322932 ACATAGGTAAACTTTCCATATGTCTCGAAAT-
1 ACATAGGTAAACTGTCCATATGTCTCG-AATG
322963 ACATAGGTAA
1 ACATAGGTAA
322973 CCCTTGACTC
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
30 8 0.13
31 53 0.84
32 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
ACATAGGTAAACTGTCCATATGTCTCGAATG
Found at i:329197 original size:51 final size:50
Alignment explanation
Indices: 329142--329400 Score: 193
Period size: 51 Copynumber: 5.3 Consensus size: 50
329132 CAGCCTTTCG
* *
329142 GCCATACCCAGATCCATATCCAGATTCGGATTCCCCATACTCGGGTTTCCT
1 GCCATATCCAGATCCATATCCGGATTCGG-TTCCCCATACTCGGGTTTCCT
* * * *
329193 GCCATATCCGGATCCGTAGT-GGGATTCTTGTTCCCCATACTCGGGTTTCCT
1 GCCATATCCAGATCCATA-TCCGGATTC-GGTTCCCCATACTCGGGTTTCCT
** *
329244 GCCATAT-----T-CGGATCC---TT--GTTCCCCATACCCGGGTTTCCT
1 GCCATATCCAGATCCATATCCGGATTCGGTTCCCCATACTCGGGTTTCCT
* * * * * *
329283 GCCATATCCAGATCCGTATTCGGATCCTTGTTCCACATAATCGGGTTTCCT
1 GCCATATCCAGATCCATATCCGGATTC-GGTTCCCCATACTCGGGTTTCCT
* * *
329334 GCCATATCCAGATCCATATTCGGATCCGTGTTCCCCATACTCAGGTCTTCC-
1 GCCATATCCAGATCCATATCCGGATTCG-GTTCCCCATACTCGGGT-TTCCT
* *
329385 ACCATACCCAGATCCA
1 GCCATATCCAGATCCA
329401 AATTCAGGAG
Statistics
Matches: 169, Mismatches: 22, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
39 28 0.17
42 2 0.01
44 2 0.01
45 8 0.05
46 1 0.01
48 1 0.01
51 121 0.72
52 6 0.04
ACGTcount: A:0.19, C:0.34, G:0.17, T:0.30
Consensus pattern (50 bp):
GCCATATCCAGATCCATATCCGGATTCGGTTCCCCATACTCGGGTTTCCT
Found at i:329249 original size:90 final size:90
Alignment explanation
Indices: 329155--329348 Score: 273
Period size: 90 Copynumber: 2.2 Consensus size: 90
329145 ATACCCAGAT
* * * * *
329155 CCATATCCAGATTC-GGATTCCCCATACTCGGGTTTCCTGCCATATCCGGATCCGTAGTGGGATT
1 CCATATCCAGATCCTGG-TTCCCCATACCCGGGTTTCCTGCCATATCCAGATCCGTAGTCGGATC
* *
329219 CTTGTTCCCCATACTCGGGTTTCCTG
65 CTTGTTCCACATAATCGGGTTTCCTG
* * * *
329245 CCATATTCGGATCCTTGTTCCCCATACCCGGGTTTCCTGCCATATCCAGATCCGTATTCGGATCC
1 CCATATCCAGATCCTGGTTCCCCATACCCGGGTTTCCTGCCATATCCAGATCCGTAGTCGGATCC
329310 TTGTTCCACATAATCGGGTTTCCTG
66 TTGTTCCACATAATCGGGTTTCCTG
329335 CCATATCCAGATCC
1 CCATATCCAGATCC
329349 ATATTCGGAT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 89 0.99
91 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.19, T:0.32
Consensus pattern (90 bp):
CCATATCCAGATCCTGGTTCCCCATACCCGGGTTTCCTGCCATATCCAGATCCGTAGTCGGATCC
TTGTTCCACATAATCGGGTTTCCTG
Found at i:329277 original size:39 final size:39
Alignment explanation
Indices: 329214--329289 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
329204 ATCCGTAGTG
* *
329214 GGATTCTTGTTCCCCATACTCGGGTTTCCTGCCATATTC
1 GGATCCTTGTTCCCCATACCCGGGTTTCCTGCCATATTC
329253 GGATCCTTGTTCCCCATACCCGGGTTTCCTGCCATAT
1 GGATCCTTGTTCCCCATACCCGGGTTTCCTGCCATAT
329290 CCAGATCCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.13, C:0.33, G:0.18, T:0.36
Consensus pattern (39 bp):
GGATCCTTGTTCCCCATACCCGGGTTTCCTGCCATATTC
Found at i:329297 original size:39 final size:39
Alignment explanation
Indices: 329219--329297 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
329209 TAGTGGGATT
* * *
329219 CTTGTTCCCCATACTCGGGTTTCCTGCCATATTCGGATC
1 CTTGTTCCCCATACCCGGGTTTCCTGCCATATCCAGATC
329258 CTTGTTCCCCATACCCGGGTTTCCTGCCATATCCAGATC
1 CTTGTTCCCCATACCCGGGTTTCCTGCCATATCCAGATC
329297 C
1 C
329298 GTATTCGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.14, C:0.37, G:0.16, T:0.33
Consensus pattern (39 bp):
CTTGTTCCCCATACCCGGGTTTCCTGCCATATCCAGATC
Found at i:329555 original size:51 final size:51
Alignment explanation
Indices: 329413--329556 Score: 148
Period size: 54 Copynumber: 2.8 Consensus size: 51
329403 TTCAGGAGGT
* *
329413 GGAGGCTGCTCGAATTCGGGTTTCCGTCCATAACCGGATCCATAATCCGAT
1 GGAGGCTGCTCGAATTCGGGTTTCCGTCCATAACCAGATCCATAATCCGAA
* * * * * *
329464 TGATGTGAATGCTC-ATATGCGGGTTTCCGGCCATACCCAGATCCATACTCCGAA
1 GGA-G-G-CTGCTCGA-ATTCGGGTTTCCGTCCATAACCAGATCCATAATCCGAA
*
329518 GGAGGCTGCTCGAATTCAGGCTTT-CGTCCATAACCAGAT
1 GGAGGCTGCTCGAATTC-GGGTTTCCGTCCATAACCAGAT
329557 TCGGATTGCT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
51 23 0.32
52 8 0.11
53 3 0.04
54 39 0.53
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (51 bp):
GGAGGCTGCTCGAATTCGGGTTTCCGTCCATAACCAGATCCATAATCCGAA
Found at i:329886 original size:9 final size:9
Alignment explanation
Indices: 329872--329897 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
329862 AGGAGTCGGA
329872 TCGAACTCG
1 TCGAACTCG
329881 TCGAACTCG
1 TCGAACTCG
329890 TCGAACTC
1 TCGAACTC
329898 ATCATCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (9 bp):
TCGAACTCG
Found at i:332134 original size:2 final size:2
Alignment explanation
Indices: 332127--332160 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
332117 CATTTTTGTG
332127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
332161 AGTTTTGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:337926 original size:127 final size:127
Alignment explanation
Indices: 337700--337954 Score: 492
Period size: 127 Copynumber: 2.0 Consensus size: 127
337690 CTTAGAACAA
337700 CAATAAAGGTTAAATCATCCGGCCTGACTTCCTTAATCATCTGCCAGAACATTTCGACCACAACT
1 CAATAAAGGTTAAATCATCCGGCCTGACTTCCTTAATCATCTGCCAGAACATTTCGACCACAACT
337765 CGGCCTCGTCCATGCATAGCTAGTCCACAAAGCATAGCGTTCCATGCCATGACATTACGTTG
66 CGGCCTCGTCCATGCATAGCTAGTCCACAAAGCATAGCGTTCCATGCCATGACATTACGTTG
*
337827 CAATAAAGTTTAAATCATCCGGCCTGACTTCCTTAATCATCTGCCAGAACATTTCGACCACAACT
1 CAATAAAGGTTAAATCATCCGGCCTGACTTCCTTAATCATCTGCCAGAACATTTCGACCACAACT
*
337892 CGGCCTCGTCCATGCATAGCTAGTCCACTAAGCATAGCGTTCCATGCCATGACATTACGTTG
66 CGGCCTCGTCCATGCATAGCTAGTCCACAAAGCATAGCGTTCCATGCCATGACATTACGTTG
337954 C
1 C
337955 GGCATGCACT
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (127 bp):
CAATAAAGGTTAAATCATCCGGCCTGACTTCCTTAATCATCTGCCAGAACATTTCGACCACAACT
CGGCCTCGTCCATGCATAGCTAGTCCACAAAGCATAGCGTTCCATGCCATGACATTACGTTG
Found at i:348492 original size:15 final size:15
Alignment explanation
Indices: 348468--348499 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
348458 GGGGAGTAAT
*
348468 CCCTGTAAATAATTC
1 CCCTGCAAATAATTC
348483 CCCTGCAAATAATTC
1 CCCTGCAAATAATTC
348498 CC
1 CC
348500 TACATAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.34, G:0.06, T:0.28
Consensus pattern (15 bp):
CCCTGCAAATAATTC
Found at i:351505 original size:19 final size:20
Alignment explanation
Indices: 351476--351516 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
351466 TTATCTATAG
351476 TTTAGGGGTTAAATTAATAT
1 TTTAGGGGTTAAATTAATAT
351496 TTTA-GGGTTAAATTAATAT
1 TTTAGGGGTTAAATTAATAT
351515 TT
1 TT
351517 CTCTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (20 bp):
TTTAGGGGTTAAATTAATAT
Found at i:353277 original size:6 final size:6
Alignment explanation
Indices: 353266--353307 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
353256 AACAAGAAAT
353266 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
353308 TTTTCAGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:358506 original size:44 final size:44
Alignment explanation
Indices: 358426--358509 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
358416 ATAACAAAAG
**
358426 CAAAGAGAATATATATTTTAACAAATGCAAGTTTGTGAAGCTTA
1 CAAAGAGAATATATATTTTAACAAATGCAAACTTGTGAAGCTTA
*
358470 CAAAGATAATATATATTTTAACAAA-GACAAACTTGTGAAG
1 CAAAGAGAATATATATTTTAACAAATG-CAAACTTGTGAAG
358510 TTTGCTCACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (44 bp):
CAAAGAGAATATATATTTTAACAAATGCAAACTTGTGAAGCTTA
Found at i:359064 original size:34 final size:34
Alignment explanation
Indices: 359021--359088 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
359011 TTCCAAACTA
*
359021 TATCTATGGGTAGAAGAATCTGGTACAACATGTT
1 TATCTATGGGTAGAAGAATCTAGTACAACATGTT
359055 TATCTATGGGTAGAAGAATCTAGTACAACATGTT
1 TATCTATGGGTAGAAGAATCTAGTACAACATGTT
359089 GCACTCCCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (34 bp):
TATCTATGGGTAGAAGAATCTAGTACAACATGTT
Found at i:364881 original size:21 final size:21
Alignment explanation
Indices: 364828--364891 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
364818 AGGTGGAAAC
364828 ATAGGAGAGAGAAA-GAAG-GA
1 ATAGGAGAGA-AAAGGAAGAGA
*
364848 ATTGTGA-AGGAAAAGGAAGAGA
1 ATAG-GAGA-GAAAAGGAAGAGA
364870 ATAGGAGAGAAAATGGAGAGAG
1 ATAGGAGAGAAAA-GGA-AGAG
364892 GAAGGGCGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
20 7 0.20
21 15 0.43
22 9 0.26
23 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.39, T:0.09
Consensus pattern (21 bp):
ATAGGAGAGAAAAGGAAGAGA
Found at i:365851 original size:20 final size:20
Alignment explanation
Indices: 365826--365865 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
365816 TTATATTTTT
365826 TTTTATCTTT-TTAAATAAAA
1 TTTTAT-TTTATTAAATAAAA
*
365846 TTTTATTTTATTTAATAAAA
1 TTTTATTTTATTAAATAAAA
365866 AATTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATTTTATTAAATAAAA
Found at i:374926 original size:22 final size:20
Alignment explanation
Indices: 374863--374927 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
374853 AATGTTAACC
374863 TGTGATTGTATGCATGAGAG
1 TGTGATTGTATGCATGAGAG
*
374883 TGTGATTGTATACATGAGAG
1 TGTGATTGTATGCATGAGAG
*
374903 TGTGATTGTATGCGTGAGAG
1 TGTGATTGTATGCATGAGAG
*
374923 AGTGA
1 TGTGA
374928 GAGTTGTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.26, C:0.05, G:0.35, T:0.34
Consensus pattern (20 bp):
TGTGATTGTATGCATGAGAG
Found at i:379527 original size:20 final size:20
Alignment explanation
Indices: 379484--379527 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
379474 ATGTCAACCT
* *
379484 GTGATTGTATGCATGAGAGT
1 GTGATTGTATGCATGAAAGA
*
379504 GTGATTGTATGCGTGAAAGA
1 GTGATTGTATGCATGAAAGA
379524 GTGA
1 GTGA
379528 GAGTTGTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.36, T:0.32
Consensus pattern (20 bp):
GTGATTGTATGCATGAAAGA
Found at i:381189 original size:10 final size:10
Alignment explanation
Indices: 381174--381200 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
381164 CTTCGCTCTC
381174 CTCTCTCTAT
1 CTCTCTCTAT
381184 CTCTCTCTAT
1 CTCTCTCTAT
381194 CTCTCTC
1 CTCTCTC
381201 AACCACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.44, G:0.00, T:0.48
Consensus pattern (10 bp):
CTCTCTCTAT
Found at i:382467 original size:55 final size:54
Alignment explanation
Indices: 382396--382780 Score: 320
Period size: 55 Copynumber: 7.1 Consensus size: 54
382386 GGGATAAATG
* * * * ** *
382396 AGACTTGAAAAATCTTCAAATGACGAGTCCACTCCCTTTTTATTCAGGGAGTATA
1 AGACTCGAACAATCTTCAAA-AACGAGTCCACTCCCTATTCGTTCAGAGAGTATA
* * ** * *
382451 AGACTCGCACAATCTTCAGCAAAC-AGGTCTGCTCCCTATTCGTTTAGGGAGTATA
1 AGACTCGAACAATCTTCA-AAAACGA-GTCCACTCCCTATTCGTTCAGAGAGTATA
* *
382506 AGACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATTCGTTCAGAGAGTACA
1 AGACTCGAACAATCTTCAA-AAACGAGTCCACTCCCTATTCGTTCAGAGAGTATA
* * * * * *
382561 TGACTCGATCAATCTTCATAAAACGGGTTCACTCTCTATTCCTTCAGAGAGTATA
1 AGACTCGAACAATCTTCA-AAAACGAGTCCACTCCCTATTCGTTCAGAGAGTATA
* * ** *
382616 AAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGAGTCCACTCCCTATTCGTTCAGAGAGTATA
* * * * *
382671 GGACTCG----ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAATATA
1 AGACTCGAACAATCTTCAA-AAACGAGTCCACTCCCTATTCGTTCAGAGAGTATA
* * *
382722 AGACTCG----ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGAGTCCACTCCCTATTCGTTCAGAGAGTATA
*
382773 GGACTCGA
1 AGACTCGA
382781 TCTTCATAAC
Statistics
Matches: 283, Mismatches: 40, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
51 96 0.34
54 2 0.01
55 182 0.64
56 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (54 bp):
AGACTCGAACAATCTTCAAAAACGAGTCCACTCCCTATTCGTTCAGAGAGTATA
Found at i:382600 original size:110 final size:109
Alignment explanation
Indices: 382396--382782 Score: 407
Period size: 110 Copynumber: 3.6 Consensus size: 109
382386 GGGATAAATG
* * * * * ** * *
382396 AGACTTGAAAAATCTTCAA-ATGACGAGTCCACTCCCTTTTTATTCAGGGAGTATAAGACTCGCA
1 AGACTCGAACAATCTTCAACA-AACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG-A
* * ** * * *
382460 -CAATCTTCAGCAAACAGGTCTGCTCCCTATTCGTTTAGGGAGTATA
64 TC-ATCTTCAACAAACGGGTCCACTCCCTATTCCTTCAGAGAGTATA
* * *
382506 AGACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATTCGTTCAGAGAGTACATGACTCGATC
1 AGACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATC
* *
382571 AATCTTCATA-AAACGGGTTCACTCTCTATTCCTTCAGAGAGTATA
66 -ATCTTCA-ACAAACGGGTCCACTCCCTATTCCTTCAGAGAGTATA
* * *
382616 AAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCG---
1 AGACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATC
* * *
382678 ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAATATA
66 ATCTTCAACAAACGGGTCCACTCCCTATTCCTTCAGAGAGTATA
*
382722 AGACTCG----ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATC
1 AGACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATC
382783 TTCATAACAT
Statistics
Matches: 237, Mismatches: 33, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
102 49 0.21
105 1 0.00
106 43 0.18
109 1 0.00
110 142 0.60
111 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (109 bp):
AGACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATC
ATCTTCAACAAACGGGTCCACTCCCTATTCCTTCAGAGAGTATA
Done.