Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008478.1 Hibiscus syriacus cultivar Beakdansim tig00111309_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: 1476524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:220505 original size:29 final size:30
Alignment explanation
Indices: 220435--220494 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
220425 CAATTTAAGG
220435 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
220466 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
220495 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:220600 original size:21 final size:21
Alignment explanation
Indices: 220574--220672 Score: 105
Period size: 21 Copynumber: 4.7 Consensus size: 21
220564 AGGGTGTCAA
*
220574 AGTGCATCCATACACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
220595 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
220616 AATGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
* *
220637 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
220658 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
220673 TCAAATACCG
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.06
20 13 0.20
21 34 0.52
22 12 0.18
23 3 0.05
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:220878 original size:21 final size:21
Alignment explanation
Indices: 220849--220888 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
220839 TTTTAGTAGA
220849 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCC-AACGGCTCC
*
220871 AAAA-CATCTCCAACGGCT
1 AAAATCATCCCCAACGGCT
220889 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:223514 original size:21 final size:20
Alignment explanation
Indices: 223488--223586 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
223478 AGGGTGTCAA
223488 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
223509 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
223530 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* * *
223551 TAGTGCATCGATGCACCATGT
1 -AGTGCATCCATGCACCCTGC
223572 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
223587 TCAAACACCG
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 35 0.51
22 13 0.19
23 3 0.04
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:223632 original size:20 final size:20
Alignment explanation
Indices: 223607--223694 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
223597 AATGCAATTA
*
223607 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
** *
223627 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC-CTGCT
*
223648 GTGCATCAATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
223668 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
223688 ATGCATC
1 GTGCATC
223695 CATGAACGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 42 0.74
21 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:225458 original size:44 final size:42
Alignment explanation
Indices: 225398--225508 Score: 150
Period size: 44 Copynumber: 2.5 Consensus size: 42
225388 CAGAACCCTT
225398 AGGGGGTATCGATTCCCCTACAGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGTATCGATTCCCCTACAGGGGGAAT-GGTTCCCCTTC-A
* * *
225442 AGGGGGAATCGGTTCCCCTTCAAAGGGGGAATGGTTCCCCTTCA
1 AGGGGGTATCGATTCCCC-T-ACAGGGGGAATGGTTCCCCTTCA
225486 AGGGGGTATCGATTCCCTCTACA
1 AGGGGGTATCGATTCCC-CTACA
225509 CCAAAAATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
43 2 0.03
44 33 0.57
45 13 0.22
46 10 0.17
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (42 bp):
AGGGGGTATCGATTCCCCTACAGGGGGAATGGTTCCCCTTCA
Found at i:225477 original size:22 final size:23
Alignment explanation
Indices: 225398--225502 Score: 137
Period size: 23 Copynumber: 4.7 Consensus size: 23
225388 CAGAACCCTT
* * *
225398 AGGGGGTATCGATTCCCC-T-AC
1 AGGGGGAATCGGTTCCCCTTCAA
225419 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
225442 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
225465 AGGGGGAAT-GGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
225486 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
225503 TCTACACCAA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.33
22 18 0.24
23 33 0.43
ACGTcount: A:0.20, C:0.26, G:0.31, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:232087 original size:83 final size:88
Alignment explanation
Indices: 231986--232206 Score: 256
Period size: 95 Copynumber: 2.5 Consensus size: 88
231976 GGCTAGTTGG
*
231986 ATCCATAAAGCCGGGGCGTTTAACTAATTGCTCTAGAGGGACAGC-TTA-ATAT-GTA-AA-CAC
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTTTATATATAGTATAATCAC
*
232046 CTTTATCAGGCTAGCTGAATCTT
66 CTTTATCAGGCTAGCTGAATATT
* *
232069 ATCCATAAAGTCGGGGCGTTTAACCAATTGC-CTTAGAGGGACAGCTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGG--A---C-AGCTTTA-TATATAGT
* *
232133 ATAATTACCTTTATCAGGCTAGTTGAATATT
58 ATAATCACCTTTATCAGGCTAGCTGAATATT
**
232164 ATCCATAAAGCCGGGATGTTTAACCAATTGCTCTAGAGGGACA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACA
232207 ACTCAAGCTT
Statistics
Matches: 115, Mismatches: 9, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
82 1 0.01
83 36 0.31
85 1 0.01
88 1 0.01
89 4 0.03
90 4 0.03
92 3 0.03
93 4 0.03
94 2 0.02
95 58 0.50
96 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (88 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTTTATATATAGTATAATCAC
CTTTATCAGGCTAGCTGAATATT
Found at i:232212 original size:95 final size:94
Alignment explanation
Indices: 232044--232231 Score: 297
Period size: 95 Copynumber: 2.0 Consensus size: 94
232034 ATATGTAAAC
* * *
232044 ACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGACGTTTAACCAATTGCCTTAGAGGG
*
232109 ACAGCTCAAGCTTTATTGTATAGTATAATT
66 ACAACTCAAGCTTTATTGTATA-TATAATT
* *
232139 ACCTTTATCAGGCTAGTTGAATATTATCCATAAAGCCGGGATGTTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGACGTTTAACCAATTGCCT-TAGAGG
232203 GACAACTCAAGCTTTATTGTATATATAAT
65 GACAACTCAAGCTTTATTGTATATATAAT
232232 ATTATAATCT
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
94 8 0.09
95 78 0.91
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (94 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGACGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATATATAATT
Found at i:235505 original size:7 final size:7
Alignment explanation
Indices: 235493--235525 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
235483 TCTTTAATTG
235493 TAAAAAT
1 TAAAAAT
235500 TAAAAAT
1 TAAAAAT
235507 T-AAAAT
1 TAAAAAT
*
235513 TAAAATT
1 TAAAAAT
235520 TAAAAA
1 TAAAAA
235526 CCCGATTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAAAAT
Found at i:235511 original size:13 final size:13
Alignment explanation
Indices: 235495--235524 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
235485 TTTAATTGTA
235495 AAAATTAAAAATT
1 AAAATTAAAAATT
*
235508 AAAATTAAAATTT
1 AAAATTAAAAATT
235521 AAAA
1 AAAA
235525 ACCCGATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:235854 original size:22 final size:22
Alignment explanation
Indices: 235818--235859 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
235808 AAAATAGAAG
*
235818 TAAAAAAATGCTAATAATAATT
1 TAAAAAAATGATAATAATAATT
*
235840 TAAAAACATGATAATAATAA
1 TAAAAAAATGATAATAATAA
235860 AATAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
TAAAAAAATGATAATAATAATT
Found at i:235865 original size:22 final size:22
Alignment explanation
Indices: 235818--235866 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
235808 AAAATAGAAG
* **
235818 TAAAAAAATGCTAATAATAATT
1 TAAAAAAATGATAATAATAAAA
*
235840 TAAAAACATGATAATAATAAAA
1 TAAAAAAATGATAATAATAAAA
235862 TAAAA
1 TAAAA
235867 TAAAATAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (22 bp):
TAAAAAAATGATAATAATAAAA
Found at i:236961 original size:20 final size:20
Alignment explanation
Indices: 236921--236961 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
236911 TTTGATCATG
*
236921 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
236941 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
236961 A
1 A
236962 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:237208 original size:15 final size:15
Alignment explanation
Indices: 237180--237230 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
237170 CCGTAGGACC
* *
237180 ACTACGTCCTGAAGG
1 ACTACATCCCGAAGG
237195 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
237210 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
237225 ACTACA
1 ACTACA
237231 ATACCCTCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:243831 original size:20 final size:20
Alignment explanation
Indices: 243791--243831 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
243781 TTTGATCATG
*
243791 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
243811 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
243831 A
1 A
243832 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:244070 original size:15 final size:15
Alignment explanation
Indices: 244050--244084 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
244040 CCGTAGGACC
244050 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
244065 ACTACGTCCTGAAGG
1 ACTACGTCCCGAAGG
244080 ACTAC
1 ACTAC
244085 AATACCCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:244727 original size:19 final size:20
Alignment explanation
Indices: 244691--244728 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
244681 TTTCATTTAG
244691 GGGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
244711 GGGGGAATCGATACCCCC
1 GGGGGAATCGATACCCCC
244729 TGAACATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCCA
Found at i:245916 original size:4 final size:4
Alignment explanation
Indices: 245907--245951 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
245897 AAAATAAGTG
245907 ATAA ATAA ATAA ATAA AT-A AT-A AT-A AT-A ATAA ATAAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA
245952 TTAGATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 12 0.31
4 23 0.59
5 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:245936 original size:9 final size:10
Alignment explanation
Indices: 245914--245952 Score: 55
Period size: 9 Copynumber: 4.0 Consensus size: 10
245904 GTGATAAATA
245914 AATAAATAAAT
1 AATAAAT-AAT
245925 AAT-AATAAT
1 AATAAATAAT
245934 AATAAATAA-
1 AATAAATAAT
245943 AATAAATAAT
1 AATAAATAAT
245953 TAGATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 15 0.58
10 8 0.31
11 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAAATAAT
Found at i:245937 original size:16 final size:16
Alignment explanation
Indices: 245909--245952 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
245899 AATAAGTGAT
245909 AAATAAATAAATAAATA
1 AAATAAAT-AATAAATA
245926 ATAAT-AATAATAAATA
1 A-AATAAATAATAAATA
245942 AAATAAATAAT
1 AAATAAATAAT
245953 TAGATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 15 0.60
17 4 0.16
18 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAAATAATAAATA
Found at i:246058 original size:37 final size:36
Alignment explanation
Indices: 245971--246072 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
245961 AAAAACGTTC
*
245971 TAAAACTATACAATATATA-TTTTAAAAACTAATTT
1 TAAAACTATATAATATATATTTTTAAAAACTAATTT
*
246006 TCAAAACTATATAATATATATTTTTTTAAAACTAATTT
1 T-AAAACTATATAATATATA-TTTTTAAAAACTAATTT
* * *
246044 TAAAACTATGTAATATATAATTTTGAAAA
1 TAAAACTATATAATATATATTTTTAAAAA
246073 TCGTTTTCTA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
35 1 0.02
36 25 0.42
37 17 0.29
38 16 0.27
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (36 bp):
TAAAACTATATAATATATATTTTTAAAAACTAATTT
Found at i:246085 original size:37 final size:36
Alignment explanation
Indices: 245968--246099 Score: 101
Period size: 36 Copynumber: 3.6 Consensus size: 36
245958 ATAAAAAACG
* *
245968 TTCTAAAACTATACAATATAT-ATTTTAAAAACTAATT
1 TTCTAAAACTATATAATATATAATTTTAAAAA-T-CTT
* *
246005 TTC-AAAACTATATAATATATATTTTTTTAAAA-CTAAT
1 TTCTAAAACTATATAATATATA-ATTTTAAAAATCT--T
* *
246042 TT-TAAAACTATGTAATATATAATTTTGAAAATCGTT
1 TTCTAAAACTATATAATATATAATTTTAAAAATC-TT
* *
246078 TTCTAAAAATTATATATTATAT
1 TTCT-AAAACTATATAATATAT
246100 TACTATATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
35 1 0.01
36 27 0.36
37 25 0.33
38 23 0.30
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (36 bp):
TTCTAAAACTATATAATATATAATTTTAAAAATCTT
Found at i:246108 original size:2 final size:2
Alignment explanation
Indices: 246088--246150 Score: 103
Period size: 2 Copynumber: 32.0 Consensus size: 2
246078 TTCTAAAAAT
246088 TA TA TA T- TA TA T- TA CTA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
246129 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
246151 ATAAAAAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.03
2 54 0.93
3 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:246489 original size:15 final size:15
Alignment explanation
Indices: 246469--246505 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
246459 ATTTTGATCT
246469 GTTTTAATACCTAAA
1 GTTTTAATACCTAAA
246484 GTTTTAATACCTAAA
1 GTTTTAATACCTAAA
246499 GTTTTAA
1 GTTTTAA
246506 CTTTTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (15 bp):
GTTTTAATACCTAAA
Found at i:249332 original size:3 final size:3
Alignment explanation
Indices: 249319--249348 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
249309 TTGAATTCTT
249319 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
249349 ATATTTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:251348 original size:31 final size:31
Alignment explanation
Indices: 251278--251348 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
251268 AACTTAATGT
251278 GCACGAGTCGAGCAACAAGTTTATTTAACGA
1 GCACGAGTCGAGCAACAAGTTTATTTAACGA
** * *
251309 ATATGAGTCGAGCAACAAGTTTTTTTAACGA
1 GCACGAGTCGAGCAACAAGTTTATTTAACGA
251340 GCACGAGTC
1 GCACGAGTC
251349 CAGTACTACC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (31 bp):
GCACGAGTCGAGCAACAAGTTTATTTAACGA
Found at i:254712 original size:16 final size:17
Alignment explanation
Indices: 254672--254712 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
254662 TTTTTTGTCT
*
254672 AAAATAAAATATTGTTA
1 AAAATAAAATATTGTAA
*
254689 GAAA-AAAATATT-TAA
1 AAAATAAAATATTGTAA
254704 AAAATAAAA
1 AAAATAAAA
254713 ATTAAAGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 5 0.25
16 12 0.60
17 3 0.15
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAATAAAATATTGTAA
Found at i:255212 original size:22 final size:21
Alignment explanation
Indices: 255157--255228 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
255147 ATCATCAAAT
*
255157 TTTATAATTTATAAAATAGTA
1 TTTATAATTTATAAAATAATA
*
255178 ATTA-AATTATTATAAAATAATA
1 TTTATAA-T-TTATAAAATAATA
255200 TTTATAAGTTTATAATAAT-ATA
1 TTTATAA-TTTATAA-AATAATA
255222 TTT-TAAT
1 TTTATAAT
255229 GAGTTTTGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
20 3 0.07
21 7 0.16
22 27 0.63
23 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
TTTATAATTTATAAAATAATA
Found at i:255270 original size:26 final size:26
Alignment explanation
Indices: 255241--255292 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
255231 GTTTTGTGAT
255241 TATTTTATAA-TAAATAATAAATTTAA
1 TATTTT-TAATTAAATAATAAATTTAA
**
255267 TATTTTTAATTATTTAATAAATTTAA
1 TATTTTTAATTAAATAATAAATTTAA
255293 GAAACTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTTTAATTAAATAATAAATTTAA
Found at i:256005 original size:20 final size:20
Alignment explanation
Indices: 255980--256025 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
255970 ATCCTCCAAT
255980 GTCGACATTACGTCTTCATA
1 GTCGACATTACGTCTTCATA
256000 GTCGACATTACGTCTTCATA
1 GTCGACATTACGTCTTCATA
256020 GTCGAC
1 GTCGAC
256026 GAGTTACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (20 bp):
GTCGACATTACGTCTTCATA
Found at i:258261 original size:41 final size:40
Alignment explanation
Indices: 258183--258261 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 40
258173 TTCTTTGCAT
* * **
258183 TTTTGCACTGTTCTGTTAGTATGCTTTCCCAGGATTTTGC
1 TTTTGCACTGTTCTGTTAGTATGCTTTACAAAAATTTTGC
* *
258223 TTTTGCACCTGTTTTTTTAGTATGCTTTACAAAAATTTT
1 TTTTGCA-CTGTTCTGTTAGTATGCTTTACAAAAATTTT
258262 ATTTAGTTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 7 0.22
41 25 0.78
ACGTcount: A:0.18, C:0.16, G:0.15, T:0.51
Consensus pattern (40 bp):
TTTTGCACTGTTCTGTTAGTATGCTTTACAAAAATTTTGC
Found at i:264710 original size:72 final size:72
Alignment explanation
Indices: 264624--264764 Score: 264
Period size: 72 Copynumber: 2.0 Consensus size: 72
264614 AGTATTTTAA
*
264624 TGAAAATAAAATTACTCATTTTTATAAAAAATAAAAACTAATAATTTATATAGTGAAATCTTTTT
1 TGAAAATAAAATTACTCATTTTTATAAAAAATAAAAACTAATAATTTATATAGGGAAATCTTTTT
264689 TTTTTCT
66 TTTTTCT
*
264696 TGAAAATAAAATTACTCATTTTTATAAAAATTAAAAACTAATAATTTATATAGGGAAATCTTTTT
1 TGAAAATAAAATTACTCATTTTTATAAAAAATAAAAACTAATAATTTATATAGGGAAATCTTTTT
264761 TTTT
66 TTTT
264765 CTTTAAGTTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (72 bp):
TGAAAATAAAATTACTCATTTTTATAAAAAATAAAAACTAATAATTTATATAGGGAAATCTTTTT
TTTTTCT
Found at i:268419 original size:20 final size:22
Alignment explanation
Indices: 268394--268433 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
268384 TCTTCTGTCA
268394 GTTTAAATTA-AT-TTTTTAAC
1 GTTTAAATTAGATATTTTTAAC
268414 GTTTAAATTAGATATTTTTA
1 GTTTAAATTAGATATTTTTA
268434 TTGTAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (22 bp):
GTTTAAATTAGATATTTTTAAC
Found at i:270496 original size:14 final size:14
Alignment explanation
Indices: 270477--270545 Score: 72
Period size: 14 Copynumber: 4.9 Consensus size: 14
270467 TTTATGTCTA
270477 TATGCAGAGATTAT
1 TATGCAGAGATTAT
270491 TATGCATG-GATTTAT
1 TATGCA-GAGA-TTAT
270506 TA-GCAGAGATTAT
1 TATGCAGAGATTAT
*
270519 TATGCAGGGATTTAT
1 TATGCAGAGA-TTAT
*
270534 TA-GCAGGGATTA
1 TATGCAGAGATTA
270546 CTTCCCATTC
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
13 10 0.20
14 26 0.53
15 13 0.27
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (14 bp):
TATGCAGAGATTAT
Found at i:270520 original size:28 final size:28
Alignment explanation
Indices: 270480--270545 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
270470 ATGTCTATAT
*
270480 GCAGAGATTATTATGCATGGATTTATTA
1 GCAGAGATTATTATGCAGGGATTTATTA
270508 GCAGAGATTATTATGCAGGGATTTATTA
1 GCAGAGATTATTATGCAGGGATTTATTA
*
270536 GCAGGGATTA
1 GCAGAGATTA
270546 CTTCCCATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.35
Consensus pattern (28 bp):
GCAGAGATTATTATGCAGGGATTTATTA
Found at i:270759 original size:3 final size:3
Alignment explanation
Indices: 270751--270778 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
270741 GAATAGAGTT
270751 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
270779 GTTTTTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:271060 original size:14 final size:14
Alignment explanation
Indices: 271041--271081 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
271031 TTTTTGTCTA
*
271041 TATGCAGAGATTAT
1 TATGCAGGGATTAT
271055 TATGCAGGGATTTAT
1 TATGCAGGGA-TTAT
271070 TA-GCAGGGATTA
1 TATGCAGGGATTA
271082 CTTCCTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.64
15 6 0.24
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (14 bp):
TATGCAGGGATTAT
Found at i:271145 original size:4 final size:4
Alignment explanation
Indices: 271136--271166 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
271126 TTCAAATATG
271136 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
271167 ACATGCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:271310 original size:552 final size:548
Alignment explanation
Indices: 270228--271322 Score: 1641
Period size: 552 Copynumber: 2.0 Consensus size: 548
270218 TTAGTGCGGG
270228 TCACTCCTAGGGTGTAACATTATGTCTTCTTTAATGCATTTGTTGTAATTTCTAAGACTTCTACT
1 TCACTCCTAGGGTGTAACATTATGTCTTCTTTAATGCATTTGTTGTAATTTCTAAGACTTCTACT
270293 TTTTATACGTTTCTGTCATTAGAATTAATGAAGGCTTAGACTAGGGTAGGGATTAGTGTTGCTTA
66 TTTTATACGTTTCTGTCATTAGAATTAATGAAGGCTTAGACTAGGGTAGGGATTAGTGTTGCTTA
* *
270358 GTTTAGGTTTAACCCATTTGATTTTATTCCTTCTCGTAGCTTACTATCGTTGACTTCTGTGTATC
131 GTTTAGGTTTAACCCATTTGACTTTATTCATTCTCGTAGCTTACTATCGTTGACTTCTGTGTATC
*
270423 ATTCTCTTCATGTTTCCTCTTTTTAATTTTAGTCGAGTCTTACGTTTATGTCTATATGCAGAGAT
196 ATTCTCTTCATGTTTCCTCTTTTTAATTTTAGTCGAGCCTTACGTTTATGTCTATATGCAGAGAT
* * * *
270488 TATTATGCATGGATTTATTAGCAGAGATTATTATGCAGGGATTTATTAGCAGGGATTACTTCCCA
261 TATTATGCAGGGATTTATTAGCAGAGATTACTATGC---G--CTATTAGCA-GGA-TAC-GCCCA
* * *
270553 TTCCAGAAGTGCATATAAAGACTGTATATGAAGATTGTTCAAATATGTATTTATTTATTTATACA
318 TTCAAGAACTGCATATAAAGACTGTATATGAAGATTATTCAAATATGTATTTATTTATTTATACA
270618 TGCATTGCATTTTATCTTTATTTTTAATTTTCTGACTGCCAGAGGTCTTCCACGGAAGCTGCTCT
383 TGCATTGCATTTTATCTTTATTTTTAATTTTCTGACTGCCAGAGGTCTTCCACGGAAGCTGCTCT
* * * *
270683 CAACCATGCGTTGGGGGCAGCCTACTATCCTATCTCCCTCTTACCCCATTGCATATGGGAATAGA
448 CAACCATGCGTTGGGAGCAGCCTACTACCCTATCTCCCTCTTACCCCATTACATATGAGAATAGA
270748 GTTTTGTTGTTGTTGTTGTTGTTGTTGTTGTGTTTT
513 GTTTTGTTGTTGTTGTTGTTGTTGTTGTTGTGTTTT
* *
270784 TCACATCCATAGGGTGTAACATTTTTGTCTTCTTTTAATGCATTTGTTGTAATTTCTATGACTTC
1 TCAC-TCC-TAGGGTGTAACA-TTATGTCTTC-TTTAATGCATTTGTTGTAATTTCTAAGACTTC
270849 TACTTTTTATACGTTTCTGTCATTAGAATTAATGAAGGCTTAGAACTAGGGTAGCGGATTAGTGT
62 TACTTTTTATACGTTTCTGTCATTAGAATTAATGAAGGCTTAG-ACTAGGGTAG-GGATTAGTGT
270914 TGCCTTAGTTTAGGTTTTAACCCATTTGACTTTATTCATTCTCGTAGCTTACTATCGTTGACTTC
125 TG-CTTAGTTTAGG-TTTAACCCATTTGACTTTATTCATTCTCGTAGCTTACTATCGTTGACTTC
* *
270979 TGTGTATCATTCTCTTCATGTTTCCTCTTTTTAATTTTAGTCGGGCCTTACGTTTTTGTCTATAT
188 TGTGTATCATTCTCTTCATGTTTCCTCTTTTTAATTTTAGTCGAGCCTTACGTTTATGTCTATAT
* *
271044 GCAGAGATTATTATGCAGGGATTTATTAGCAGGGATTACT-T-C-CTATTA-CA-GA-A-GCGCA
253 GCAGAGATTATTATGCAGGGATTTATTAGCAGAGATTACTATGCGCTATTAGCAGGATACGCCCA
* * * * * * * ** *
271102 TATGAAG-ACTGTATATGAAGTCTGTTCAAATATGTA-TTTATTTATTTATTTATTTATTTATTT
318 T-TCAAGAACTGCATATAAAGACTG-T---ATATGAAGATTATTCAAATATGTATTTATTTATTT
* *
271165 ATACATGCATTGCATTTTATCTTTATTTTTTATTTTCTGACTGCCGGAGGTCTTCCACGGAAGCT
378 ATACATGCATTGCATTTTATCTTTATTTTTAATTTTCTGACTGCCAGAGGTCTTCCACGGAAGCT
271230 GCTCTCAACCATGCGTTGGGAGCAGCCTACTACCCTATCTCCCTCTTACCCCATTACATATGAGA
443 GCTCTCAACCATGCGTTGGGAGCAGCCTACTACCCTATCTCCCTCTTACCCCATTACATATGAGA
*
271295 ATAGGGTTTTGTTGTTGTTGTTGTTGTT
508 ATAGAGTTTTGTTGTTGTTGTTGTTGTT
271323 TTACCATCAA
Statistics
Matches: 493, Mismatches: 33, Indels: 30
0.89 0.06 0.05
Matches are distributed among these distances:
549 17 0.03
550 4 0.01
551 1 0.00
552 172 0.35
553 8 0.02
555 2 0.00
556 9 0.02
557 3 0.01
558 12 0.02
559 9 0.02
560 74 0.15
561 10 0.02
562 13 0.03
563 12 0.02
564 147 0.30
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (548 bp):
TCACTCCTAGGGTGTAACATTATGTCTTCTTTAATGCATTTGTTGTAATTTCTAAGACTTCTACT
TTTTATACGTTTCTGTCATTAGAATTAATGAAGGCTTAGACTAGGGTAGGGATTAGTGTTGCTTA
GTTTAGGTTTAACCCATTTGACTTTATTCATTCTCGTAGCTTACTATCGTTGACTTCTGTGTATC
ATTCTCTTCATGTTTCCTCTTTTTAATTTTAGTCGAGCCTTACGTTTATGTCTATATGCAGAGAT
TATTATGCAGGGATTTATTAGCAGAGATTACTATGCGCTATTAGCAGGATACGCCCATTCAAGAA
CTGCATATAAAGACTGTATATGAAGATTATTCAAATATGTATTTATTTATTTATACATGCATTGC
ATTTTATCTTTATTTTTAATTTTCTGACTGCCAGAGGTCTTCCACGGAAGCTGCTCTCAACCATG
CGTTGGGAGCAGCCTACTACCCTATCTCCCTCTTACCCCATTACATATGAGAATAGAGTTTTGTT
GTTGTTGTTGTTGTTGTTGTTGTGTTTT
Found at i:276708 original size:19 final size:19
Alignment explanation
Indices: 276662--276710 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
276652 AAATTTTCCC
*
276662 TTATTTATTTTATTTATGT
1 TTATTTTTTTTATTTATGT
* *
276681 ATATATTTTTTA-TTATTGT
1 TTATTTTTTTTATTTA-TGT
276700 TTATTTTTTTT
1 TTATTTTTTTT
276711 GTTTCTATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (19 bp):
TTATTTTTTTTATTTATGT
Found at i:280279 original size:36 final size:37
Alignment explanation
Indices: 280239--280312 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
280229 AGTAGTGAAT
280239 CTAG-TTTAGGTCAGTTGCTTGGGAATTGAACTCTAA
1 CTAGTTTTAGGTCAGTTGCTTGGGAATTGAACTCTAA
280275 CTAGTTTTAGGTCAGTTGCTTGGGAATTGAACTCTAA
1 CTAGTTTTAGGTCAGTTGCTTGGGAATTGAACTCTAA
280312 C
1 C
280313 GATGAGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 4 0.11
37 33 0.89
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (37 bp):
CTAGTTTTAGGTCAGTTGCTTGGGAATTGAACTCTAA
Found at i:282004 original size:33 final size:34
Alignment explanation
Indices: 281939--282027 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
281929 GTCGCTCTCG
* *
281939 AGACAGTTCTCTTAAAACAATTATGTCTCTCTTA
1 AGACATTTCTCTTAAAACAAATATGTCTCTCTTA
* *
281973 AGACATTTCTTTTAAAACAAAT-TGTCTCTCTTG
1 AGACATTTCTCTTAAAACAAATATGTCTCTCTTA
* *
282006 AGACAGTTTCCCTTGAAACAAA
1 AGACA-TTTCTCTTAAAACAAA
282028 ATCTTTGAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 15 0.32
34 32 0.68
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (34 bp):
AGACATTTCTCTTAAAACAAATATGTCTCTCTTA
Found at i:282211 original size:100 final size:96
Alignment explanation
Indices: 281964--282254 Score: 392
Period size: 96 Copynumber: 3.0 Consensus size: 96
281954 AACAATTATG
* *
281964 TCTCTCTTAAGACA-TTTCTTTTAAAACAAA--TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCCCTTAAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
282026 AAATCTTTGAATCTGTTTTCCTTAAAAAAAT
66 AAATCTTTGAATCTGTTTTCCTTAAAAAAAT
* * *
282057 TCTCCCTTGAGACAGTTTATTTTAAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTCGAAACA
1 TCTCCCTTAAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
* *
282122 AAATCTATGAATCTGTTTTCCTTAAAACAAGTTT
66 AAATCTTTGAATCTGTTTTCCTTAAAA-AA--AT
*
282156 CATCTCCCTT-AGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAA
1 --TCTCCCTTAAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
* * * *
282220 CAAAAATCTTTGAATCTATTTCCCTTGAACAAAT
64 C-AAAATCTTTGAATCTGTTTTCCTTAAAAAAAT
282254 T
1 T
282255 TTGTCTCTTT
Statistics
Matches: 173, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
93 12 0.07
94 15 0.09
96 57 0.33
97 2 0.01
98 1 0.01
99 1 0.01
100 54 0.31
101 31 0.18
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (96 bp):
TCTCCCTTAAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
AAATCTTTGAATCTGTTTTCCTTAAAAAAAT
Found at i:282270 original size:165 final size:163
Alignment explanation
Indices: 282078--282421 Score: 449
Period size: 165 Copynumber: 2.1 Consensus size: 163
282068 ACAGTTTATT
*
282078 TTAAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATCTATGAATCTGTTTTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATCTATGAATCTGTTTTCC
* * * * * *
282143 TTAAAACAAGTTTCATCTCCCTTAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTGAGACGG
66 TT-AAACAAATTTCATCTCCC-GAGACAATTTATCTT-AAA-AAATTTTGTCTCCCTTGAGACGA
282208 TTTCCCTTGAAACA-AAAATCTTTGAATCTATTTCCC
127 TTTCCCTTGAAACACAAAATCTTTGAATCTATTTCCC
* * * * * *
282244 TT-GAACAAATTTTGTCTCTTTTGAGACATTTTCCCTTGAAACAAAATCTTTTAATCTGTTTTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATCTATGAATCTGTTTTCC
* * * * *
282308 TTTAACAAATTTCGTCTCTCGAGACAATTTCTCTTGAAAAATTTTGTCTCCCTTGAGACGATTTC
66 TTAAACAAATTTCATCTCCCGAGACAATTTATCTTAAAAAATTTTGTCTCCCTTGAGACGATTTC
** *
282373 TTTTGAAACACAAAATCTTTGAATTTATTTCCC
131 CCTTGAAACACAAAATCTTTGAATCTATTTCCC
282406 TTAAAACAAATTTTGT
1 TTAAAACAAATTTTGT
282422 TTACCTTATA
Statistics
Matches: 154, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
161 33 0.21
162 25 0.16
163 23 0.15
164 14 0.09
165 57 0.37
166 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.41
Consensus pattern (163 bp):
TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATCTATGAATCTGTTTTCC
TTAAACAAATTTCATCTCCCGAGACAATTTATCTTAAAAAATTTTGTCTCCCTTGAGACGATTTC
CCTTGAAACACAAAATCTTTGAATCTATTTCCC
Found at i:282325 original size:64 final size:65
Alignment explanation
Indices: 282182--282346 Score: 219
Period size: 64 Copynumber: 2.6 Consensus size: 65
282172 TTTATTTTAA
*
282182 AACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAATCTTTGAATCTATTTCCCTTG
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTGAATCTATTTCCCTTG
* * * * * *
282247 AACAAATTTTGTCTCTTTTGAGACATTTTCCCTTGAAAC-AAAATCTTTTAATCTGTTTTCCTTT
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTGAATCTATTTCCCTTG
* * *
282311 AACAAATTTCGTCTCTC--GAGACAATTTCTCTTGAAA
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
282347 AATTTTGTCT
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
62 17 0.19
64 36 0.40
65 36 0.40
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (65 bp):
AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTGAATCTATTTCCCTTG
Found at i:282357 original size:32 final size:33
Alignment explanation
Indices: 282314--282380 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
282304 TTCCTTTAAC
282314 AAATTTCGTCT-CTCGAGACAATTTCTCTTGAA
1 AAATTTCGTCTCCTCGAGACAATTTCTCTTGAA
* * * *
282346 AAATTTTGTCTCCCTTGAGACGATTTCTTTTGAA
1 AAATTTCGTCT-CCTCGAGACAATTTCTCTTGAA
282380 A
1 A
282381 CACAAAATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 10 0.34
34 19 0.66
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (33 bp):
AAATTTCGTCTCCTCGAGACAATTTCTCTTGAA
Found at i:284007 original size:23 final size:22
Alignment explanation
Indices: 283985--284038 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
283975 TGTATATTTA
283985 TTATTTATTATTTTATTTC--T
1 TTATTTATTATTTTATTTCTTT
284005 TTATTTATTATTTTTATTTCTTT
1 TTATTTATTA-TTTTATTTCTTT
*
284028 TTATTCATTAT
1 TTATTTATTAT
284039 ATCATTCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.33
21 9 0.30
22 1 0.03
23 10 0.33
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATTTATTATTTTATTTCTTT
Found at i:284010 original size:20 final size:21
Alignment explanation
Indices: 283985--284027 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
283975 TGTATATTTA
283985 TTATTTATTA-TTTTATTTCT
1 TTATTTATTATTTTTATTTCT
284005 TTATTTATTATTTTTATTTCT
1 TTATTTATTATTTTTATTTCT
284026 TT
1 TT
284028 TTATTCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TTATTTATTATTTTTATTTCT
Found at i:289148 original size:14 final size:15
Alignment explanation
Indices: 289125--289163 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
289115 TCTTTGTGGC
289125 TTATGTTTTTAT-GA
1 TTATGTTTTTATGGA
*
289139 TTATGGTTTT-TGGA
1 TTATGTTTTTATGGA
289153 TTATGTTTTTA
1 TTATGTTTTTA
289164 CCTGGGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (15 bp):
TTATGTTTTTATGGA
Found at i:290671 original size:21 final size:19
Alignment explanation
Indices: 290639--290687 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 19
290629 TAACAAGTTG
290639 AAAAATATTTATATATTTTCTT
1 AAAAA-ATTTATAT-TTTT-TT
*
290661 TAAAAATTTATATTTTTTT
1 AAAAAATTTATATTTTTTT
290680 AAAAAATT
1 AAAAAATT
290688 GAAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 4 0.16
21 8 0.32
22 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
AAAAAATTTATATTTTTTT
Found at i:291563 original size:60 final size:60
Alignment explanation
Indices: 291474--291589 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
291464 AAAGGTAGGC
* * *
291474 TATTGGTTTATTAAGTCCCTCGACTATTAAAAGTTATAAAATGATC-CTCTGACTATAGCA
1 TATTGGTTTATTAAATCCCTCGACAATTAAAAGTTACAAAATGATCACT-TGACTATAGCA
* * * *
291534 TATTGTTTTGTTAAATCCTTCGACAATTAAAATTTACAAAATGATCACTTGACTAT
1 TATTGGTTTATTAAATCCCTCGACAATTAAAAGTTACAAAATGATCACTTGACTAT
291590 TCATTATGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 46 0.96
61 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (60 bp):
TATTGGTTTATTAAATCCCTCGACAATTAAAAGTTACAAAATGATCACTTGACTATAGCA
Found at i:292231 original size:18 final size:19
Alignment explanation
Indices: 292187--292233 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
292177 ATTTATATAG
292187 TAATTTAA-TTAATCAAAT
1 TAATTTAATTTAATCAAAT
*
292205 T-ATTCTAATTTAATC-ATT
1 TAATT-TAATTTAATCAAAT
292223 TAATTTAATTT
1 TAATTTAATTT
292234 CATGAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 13 0.52
19 9 0.36
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATTTAATTTAATCAAAT
Found at i:298921 original size:41 final size:42
Alignment explanation
Indices: 298868--298954 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 42
298858 TCAATTTTGT
298868 AAAAAAATATATATAAATTTTATGAATTTAAATTTTTTAAAG
1 AAAAAAATATATATAAATTTTATGAATTTAAATTTTTTAAAG
298910 AAAAAAA-ATATATAAATTTTATGAATTTAAATTTTTTAAAG
1 AAAAAAATATATATAAATTTTATGAATTTAAATTTTTTAAAG
298951 AAAA
1 AAAA
298955 TATATAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 38 0.84
42 7 0.16
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (42 bp):
AAAAAAATATATATAAATTTTATGAATTTAAATTTTTTAAAG
Found at i:298964 original size:37 final size:37
Alignment explanation
Indices: 298860--298964 Score: 147
Period size: 41 Copynumber: 2.7 Consensus size: 37
298850 TTATCTTTTC
* *
298860 AATTTTGTAAAAAAATATATATAAATTTTATGAATTTA
1 AATTTTTTAAAGAAA-ATATATAAATTTTATGAATTTA
298898 AATTTTTTAAAGAAAAAAAATATATAAATTTTATGAATTTA
1 AATTTTTTAAAG----AAAATATATAAATTTTATGAATTTA
298939 AATTTTTTAAAGAAAATATATAAATT
1 AATTTTTTAAAGAAAATATATAAATT
298965 AATTATAGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
37 14 0.23
38 10 0.16
41 34 0.56
42 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (37 bp):
AATTTTTTAAAGAAAATATATAAATTTTATGAATTTA
Found at i:307387 original size:18 final size:18
Alignment explanation
Indices: 307366--307412 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
307356 GACCCTTATG
*
307366 TCCCGTAGGACCACTACA
1 TCCCGAAGGACCACTACA
307384 TCCCGAAGGACCACTACA
1 TCCCGAAGGACCACTACA
307402 TCCCGAAGGAC
1 TCCCGAAGGAC
307413 TATTATACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.30, C:0.38, G:0.19, T:0.13
Consensus pattern (18 bp):
TCCCGAAGGACCACTACA
Found at i:307542 original size:29 final size:29
Alignment explanation
Indices: 307499--307602 Score: 183
Period size: 29 Copynumber: 3.6 Consensus size: 29
307489 TTTCATATGT
307499 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
307527 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
307556 TCATATAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
307585 TCATGTAGCTCATGTCAT
1 TCATGTAGCTCATGTCAT
307603 GTTTTCATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
28 7 0.10
29 64 0.90
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:307619 original size:58 final size:58
Alignment explanation
Indices: 307506--307619 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
307496 TGTTCATGTA
* * * *
307506 CTCATGTCATTTCTCTTGTGATCATGTAGTTCATGTCATTTCTCTTGTGATCATATAG
1 CTCATGTCATTTCTCTTGTGATCATGTAGCTCATGTCATTTCTCATATCATCATATAG
*
307564 CTCATGTCATTTCTCTTGTGATCATGTAGCTCATGTCATGTTTTCATATCA-CATAT
1 CTCATGTCATTTCTCTTGTGATCATGTAGCTCATGTCAT-TTCTCATATCATCATAT
307620 CATATCACAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 43 0.86
59 7 0.14
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (58 bp):
CTCATGTCATTTCTCTTGTGATCATGTAGCTCATGTCATTTCTCATATCATCATATAG
Found at i:308073 original size:45 final size:45
Alignment explanation
Indices: 308006--308111 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
307996 TGCACTACTT
* * *
308006 GTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATT-AATGG
1 GTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAGA
* *
308050 GATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGA
1 G-TGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
308096 GTGCATCGATGCACTA
1 GTGCATCGATGCACTA
308112 CTTGTGCATC
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
44 1 0.02
45 40 0.75
46 12 0.23
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (45 bp):
GTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:309869 original size:79 final size:79
Alignment explanation
Indices: 309723--309874 Score: 180
Period size: 79 Copynumber: 1.9 Consensus size: 79
309713 ATTCAAACGC
* * * ** *
309723 ATTTTGAAACACAATCACAATTGGTTGTCATGACCAACCCACATATGGACAGTGAGAAGATCGAC
1 ATTTTGAAACACAATCACAAATGGTTGACATGACCAACCCACATATAGACAGACAGAAGATCCAC
309788 TCGTCCAAGCACAT
66 TCGTCCAAGCACAT
* * * * * *
309802 ATTTTGAAGCACAATCATAAATGGTTGACCTGATCAACCCACATATAGACA-ACATAATGTTCCA
1 ATTTTGAAACACAATCACAAATGGTTGACATGACCAACCCACATATAGACAGACAGAA-GATCCA
309866 CTCGTCCAA
65 CTCGTCCAA
309875 ATACACATTC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
78 3 0.05
79 57 0.95
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (79 bp):
ATTTTGAAACACAATCACAAATGGTTGACATGACCAACCCACATATAGACAGACAGAAGATCCAC
TCGTCCAAGCACAT
Found at i:311176 original size:21 final size:22
Alignment explanation
Indices: 311149--311207 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
311139 GATTGATGAG
* *
311149 AGAAAATCAAGAAGAACGGAGT
1 AGAAAATCAAGAAGAAAGGAAT
* *
311171 A-AAAATCAATAACAAAGGAAT
1 AGAAAATCAAGAAGAAAGGAAT
*
311192 AGAAAATGAAGAAGAA
1 AGAAAATCAAGAAGAA
311208 GAGTTTCAGC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.63, C:0.07, G:0.20, T:0.10
Consensus pattern (22 bp):
AGAAAATCAAGAAGAAAGGAAT
Found at i:317158 original size:25 final size:25
Alignment explanation
Indices: 317124--317173 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
317114 ACTTTTAATG
317124 GTTGAGGGACTAAACAAAATAACTT
1 GTTGAGGGACTAAACAAAATAACTT
317149 GTTGAGGGACTAAACAAAATAACTT
1 GTTGAGGGACTAAACAAAATAACTT
317174 TCTATAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (25 bp):
GTTGAGGGACTAAACAAAATAACTT
Found at i:321276 original size:19 final size:20
Alignment explanation
Indices: 321249--321290 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
321239 TCTTTATCAG
*
321249 TTCTTTATCTTT-GTTTATC
1 TTCTCTATCTTTCGTTTATC
321268 TTCTCTATCTTTCGTTTATC
1 TTCTCTATCTTTCGTTTATC
321288 TTC
1 TTC
321291 ATTGCTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.10, C:0.21, G:0.05, T:0.64
Consensus pattern (20 bp):
TTCTCTATCTTTCGTTTATC
Found at i:323141 original size:26 final size:26
Alignment explanation
Indices: 323109--323160 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
323099 CCTTCTCGGG
323109 TTAGATCTG-CTTCAGGTCAACTGGGT
1 TTAGATCTGTC-TCAGGTCAACTGGGT
323135 TTAGATCTGTCTCAGGTCAACTGGGT
1 TTAGATCTGTCTCAGGTCAACTGGGT
323161 CAAACCTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (26 bp):
TTAGATCTGTCTCAGGTCAACTGGGT
Found at i:323244 original size:3 final size:3
Alignment explanation
Indices: 323238--323306 Score: 88
Period size: 3 Copynumber: 23.7 Consensus size: 3
323228 TTATTTGTAG
* * *
323238 TAA TAA TAA T-A TAA TTA T-A TAA TAA TAA TAA TAA TAG TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
323284 TAA TAG TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
323307 TTATATAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:324307 original size:23 final size:23
Alignment explanation
Indices: 324281--324325 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
324271 ATATATGGTT
324281 ATATCTATTCATCATGAATAGTC
1 ATATCTATTCATCATGAATAGTC
* *
324304 ATATTTATTCATGATGAATAGT
1 ATATCTATTCATCATGAATAGT
324326 TACATACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (23 bp):
ATATCTATTCATCATGAATAGTC
Found at i:324336 original size:23 final size:23
Alignment explanation
Indices: 324287--324339 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
324277 GGTTATATCT
* **
324287 ATTCATCATGAATAGTCATATTT
1 ATTCATCATGAATAGTCACATAC
* *
324310 ATTCATGATGAATAGTTACATAC
1 ATTCATCATGAATAGTCACATAC
324333 ATTCATC
1 ATTCATC
324340 CTAATACATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTCATCATGAATAGTCACATAC
Found at i:327393 original size:23 final size:22
Alignment explanation
Indices: 327350--327400 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
327340 AAAAAACCGG
*
327350 AAAC-TACCAAAAGGCAAAGAT
1 AAACATACCAAAAGACAAAGAT
*
327371 AAACATACCACAAAGACAGAGAT
1 AAACATACCA-AAAGACAAAGAT
327394 AAACATA
1 AAACATA
327401 TCAGAAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 4 0.15
22 5 0.19
23 17 0.65
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (22 bp):
AAACATACCAAAAGACAAAGAT
Found at i:327892 original size:20 final size:20
Alignment explanation
Indices: 327869--327920 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
327859 AACGCGATCC
327869 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
327889 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
327909 CCAAAATCGCAA
1 CCAGAATCGCAA
327921 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:327937 original size:21 final size:20
Alignment explanation
Indices: 327911--328008 Score: 70
Period size: 21 Copynumber: 4.8 Consensus size: 20
327901 ATCAGTTTCC
327911 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * * *
327932 AAAATCGCGATGCGATAGTAG
1 AAAATCGCAACGCGAT-TTTG
* ** *
327953 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-G
* * *
327974 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
327994 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
328009 ACACATAAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
20 15 0.26
21 42 0.74
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:328050 original size:20 final size:20
Alignment explanation
Indices: 327976--328127 Score: 171
Period size: 20 Copynumber: 7.6 Consensus size: 20
327966 GATTTTCCAT
* ** *
327976 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
327996 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
328016 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
328036 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* **
328056 AATCGCAACACGTATGGGTA
1 AATCGCAACGCGTATCCGTA
* *
328076 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
328096 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
328116 AATCGCAACGCG
1 AATCGCAACGCG
328128 ATATTTAAAG
Statistics
Matches: 109, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
19 1 0.01
20 106 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:328548 original size:33 final size:33
Alignment explanation
Indices: 328509--328579 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
328499 TTCACTTAGA
*
328509 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
328542 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
328575 TTTCA
1 TTTCA
328580 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:328719 original size:14 final size:14
Alignment explanation
Indices: 328700--328754 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
328690 AGAATGACTG
328700 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
328714 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
328733 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
328747 TCGCAACG
1 TCGCAACG
328755 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:328737 original size:33 final size:33
Alignment explanation
Indices: 328700--328770 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
328690 AGAATGACTG
**
328700 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
328733 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
328766 TCGCA
1 TCGCA
328771 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:328788 original size:19 final size:19
Alignment explanation
Indices: 328766--328863 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
328756 GAAACCAAAA
*
328766 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
328785 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
328799 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
328818 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
328832 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
328851 TCGCGTTGCGATT
1 TCGCGTTGCGATT
328864 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:328807 original size:14 final size:14
Alignment explanation
Indices: 328788--328877 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
328778 TTTCATTTCG
328788 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
328802 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
328821 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
328835 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
328852 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
328868 CGTTGCGATT
1 CGTTGCGATT
328878 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:328813 original size:33 final size:33
Alignment explanation
Indices: 328771--328885 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
328761 CAAAATCGCA
328771 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
328804 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
328837 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
328870 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
328886 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:330813 original size:185 final size:186
Alignment explanation
Indices: 330583--331147 Score: 1107
Period size: 185 Copynumber: 3.0 Consensus size: 186
330573 TAGATTGCTT
*
330583 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
330648 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
330713 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
330768 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
330832 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
330897 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
330953 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
331018 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
331083 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
331139 AGTAAATTT
1 AGTAAATTT
331148 ATCCATTCAA
Statistics
Matches: 377, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 92 0.24
185 153 0.41
186 132 0.35
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:330989 original size:93 final size:93
Alignment explanation
Indices: 330583--331147 Score: 1107
Period size: 93 Copynumber: 6.1 Consensus size: 93
330573 TAGATTGCTT
*
330583 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
330648 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
330676 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
330740 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
330768 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
330832 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
330860 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
330925 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
330953 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
331018 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
331046 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
331111 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
331139 AGTAAATTT
1 AGTAAATTT
331148 ATCCATTCAA
Statistics
Matches: 470, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 184 0.39
93 286 0.61
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:331231 original size:19 final size:19
Alignment explanation
Indices: 331191--331319 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
331181 TAGTTTACTT
* *
331191 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
331211 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
331230 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
331249 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
331263 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
331282 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
331296 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
331315 TCGCA
1 TCGCA
331320 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:331265 original size:33 final size:32
Alignment explanation
Indices: 331227--331319 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
331217 CGCGAAACCA
**
331227 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
331259 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
331292 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
331320 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:331317 original size:52 final size:52
Alignment explanation
Indices: 331191--331319 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
331181 TAGTTTACTT
* **
331191 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
331243 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
331296 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
331320 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:331337 original size:19 final size:19
Alignment explanation
Indices: 331315--331449 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
331305 GAAACCAAAA
*
331315 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
331334 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
331350 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
331367 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
331383 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
331400 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
331419 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
331439 TCGTGTTGCGA
1 TCGCGTTGCGA
331450 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 11 0.12
19 46 0.49
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:331356 original size:14 final size:14
Alignment explanation
Indices: 331337--331393 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
331327 TTTCATTTCG
331337 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
331351 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
331368 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
331384 CGTTGCGATT
1 CGTTGCGATT
331394 TTAATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:331362 original size:33 final size:33
Alignment explanation
Indices: 331320--331412 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
331310 CAAAATCGCA
*
331320 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
331353 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
331386 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
331413 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:333392 original size:14 final size:14
Alignment explanation
Indices: 333373--333408 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
333363 ATTGTTTAAT
333373 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
333387 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
333401 TGATTTGT
1 TGATTTGT
333409 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:333531 original size:19 final size:19
Alignment explanation
Indices: 333515--333617 Score: 153
Period size: 19 Copynumber: 5.6 Consensus size: 19
333505 AAAAATGACT
333515 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
333534 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
333553 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
333567 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
333586 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
333606 ATCGCAATGCGA
1 ATCGCAATGCGA
333618 TTATAATTTC
Statistics
Matches: 76, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 41 0.54
20 19 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:333635 original size:19 final size:19
Alignment explanation
Indices: 333607--333932 Score: 343
Period size: 19 Copynumber: 18.7 Consensus size: 19
333597 GAAATGAAAA
* * *
333607 TCGCAATGCGATTATAATT
1 TCGCATTGCGATTTTCATT
*
333626 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
333642 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
333659 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
333678 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
333694 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
333711 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
333730 TCGCATTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
333749 TCGCATTGCGA--TTC-TG
1 TCGCATTGCGATTTTCATT
333765 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
333782 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
333801 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
333817 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
333834 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
333853 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
333869 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
333886 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
333904 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
333920 TCGCGTTGCGATT
1 TCGCATTGCGATT
333933 GTATTTTCCG
Statistics
Matches: 262, Mismatches: 14, Indels: 62
0.78 0.04 0.18
Matches are distributed among these distances:
14 41 0.16
16 38 0.15
17 33 0.13
18 3 0.01
19 135 0.52
20 12 0.05
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:333685 original size:52 final size:49
Alignment explanation
Indices: 333607--333932 Score: 285
Period size: 52 Copynumber: 6.3 Consensus size: 49
333597 GAAATGAAAA
* * *
333607 TCGCAATGCGATTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCGTTGCGA-TTTCATT
333659 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGA-T-TTTCGTTGCGA-TTTCATT
** * *
333711 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-T
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT
* * * *
333761 TCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 TC-G-CATTGCGATTTTCATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT
* * * * *
333814 CTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 -TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT
* * *
333866 CTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATT
1 -TCGCATTGCGATTTTCATTT-CGCATTGCGATTTTC--GTTGCGA-TTTCATT
*
333920 TCGCGTTGCGATT
1 TCGCATTGCGATT
333933 GTATTTTCCG
Statistics
Matches: 247, Mismatches: 15, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
50 13 0.05
51 4 0.02
52 187 0.76
53 30 0.12
54 7 0.03
55 6 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (49 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCGTTGCGATTTCATT
Found at i:333720 original size:71 final size:71
Alignment explanation
Indices: 333645--333932 Score: 366
Period size: 71 Copynumber: 4.1 Consensus size: 71
333635 GATTATCTCG
333645 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
333710 TTCGCA
66 TTCGCA
* *
333716 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
333781 TTCGCA
66 TTCGCA
*
333787 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATT
333847 TTCATTTCGCA
61 TTCATTTCGCA
* *
333858 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTTTC--GTTGCGATTTT
*
333916 CATTTCGCG
63 CATTTCGCA
333925 TTGCGATT
1 TTGCGATT
333933 GTATTTTCCG
Statistics
Matches: 193, Mismatches: 9, Indels: 32
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.06
67 27 0.14
68 14 0.07
69 13 0.07
70 2 0.01
71 119 0.62
72 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:333761 original size:123 final size:123
Alignment explanation
Indices: 333607--333865 Score: 473
Period size: 123 Copynumber: 2.1 Consensus size: 123
333597 GAAATGAAAA
*
333607 TCGCAATGCGATTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
*
333672 TTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* * *
333730 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
333795 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
333853 TCGCATTGCGATT
1 TCGCATTGCGATT
333866 CTCTCGTTGC
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 131 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.46
Consensus pattern (123 bp):
TCGCATTGCGATTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:336228 original size:12 final size:12
Alignment explanation
Indices: 336211--336235 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
336201 TCTTCGGGGA
336211 CTTTTTCTTCTT
1 CTTTTTCTTCTT
336223 CTTTTTCTTCTT
1 CTTTTTCTTCTT
336235 C
1 C
336236 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:336444 original size:24 final size:24
Alignment explanation
Indices: 336410--336456 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
336400 CTGAAACATC
336410 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
336434 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
336457 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:337167 original size:20 final size:20
Alignment explanation
Indices: 337139--337507 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
337129 AAATTTCAGT
* * * *
337139 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
337159 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
337179 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
337199 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
337219 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
337239 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
337259 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
337279 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
337299 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
337319 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
337339 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
337359 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
337379 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
337399 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
337419 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
337439 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
337459 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
337479 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
337499 GTTGCGATT
1 GTTGCGATT
337508 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:341711 original size:3 final size:3
Alignment explanation
Indices: 341703--341760 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
341693 TAGTAAAATA
341703 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
341751 TAT TAT TAT T
1 TAT TAT TAT T
341761 GTTGTTGTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:342007 original size:20 final size:20
Alignment explanation
Indices: 341982--342030 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
341972 TTTCACATCC
341982 TCCCTCAGCTTATTTACAGT
1 TCCCTCAGCTTATTTACAGT
342002 TCCCTCAGCTTATTTACAGT
1 TCCCTCAGCTTATTTACAGT
*
342022 TACCTCAGC
1 TCCCTCAGC
342031 CGAACAAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (20 bp):
TCCCTCAGCTTATTTACAGT
Found at i:348677 original size:33 final size:33
Alignment explanation
Indices: 348635--348735 Score: 184
Period size: 33 Copynumber: 3.1 Consensus size: 33
348625 ACCTAGTGTA
348635 TATGGTGGACACGACCTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
*
348668 TATGGTGGACACGACCTTATGTGTCATACGAAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
*
348701 TATGGTGGACACGACTTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
348734 TA
1 TA
348736 GCACTACGGT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (33 bp):
TATGGTGGACACGACCTTATGTGTCATACGGAT
Found at i:348698 original size:17 final size:17
Alignment explanation
Indices: 348645--348730 Score: 56
Period size: 17 Copynumber: 5.2 Consensus size: 17
348635 TATGGTGGAC
348645 ACGACCTTATGTGTCAT
1 ACGACCTTATGTGTCAT
* *
348662 ACGGA--TTATG-GTGGAC
1 AC-GACCTTATGTGT-CAT
348678 ACGACCTTATGTGTCAT
1 ACGACCTTATGTGTCAT
* * *
348695 ACGA-ATTATG-GTGGAC
1 ACGACCTTATGTGT-CAT
*
348711 ACGACTTTATGTGTCAT
1 ACGACCTTATGTGTCAT
348728 ACG
1 ACG
348731 GATTAGCACT
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
15 6 0.12
16 18 0.35
17 21 0.41
18 6 0.12
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (17 bp):
ACGACCTTATGTGTCAT
Found at i:348714 original size:16 final size:17
Alignment explanation
Indices: 348635--348721 Score: 56
Period size: 17 Copynumber: 5.2 Consensus size: 17
348625 ACCTAGTGTA
*
348635 TATGGTGGACACGACCT
1 TATGGTGGACACGACAT
* * *
348652 TAT-GTGTCATACG-GAT
1 TATGGTG-GACACGACAT
*
348668 TATGGTGGACACGACCT
1 TATGGTGGACACGACAT
* *
348685 TAT-GTGTCATACGA-AT
1 TATGGTG-GACACGACAT
*
348701 TATGGTGGACACGACTT
1 TATGGTGGACACGACAT
348718 TATG
1 TATG
348722 TGTCATACGG
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
16 23 0.46
17 27 0.54
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (17 bp):
TATGGTGGACACGACAT
Found at i:353603 original size:33 final size:33
Alignment explanation
Indices: 353566--353640 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
353556 GGTAAGAAAT
* * * *
353566 TTATTTTTATGTTAGTAT-TTTTTTAAATAGTTA
1 TTATTTTTATATTAATATATTATGTAAATA-TTA
353599 TTATTTTTATATTAATATATTATGTAAATATTA
1 TTATTTTTATATTAATATATTATGTAAATATTA
353632 TT-TTTTTAT
1 TTATTTTTAT
353641 TAAAATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 7 0.19
33 21 0.57
34 9 0.24
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (33 bp):
TTATTTTTATATTAATATATTATGTAAATATTA
Found at i:353633 original size:30 final size:30
Alignment explanation
Indices: 353597--353670 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
353587 TTTAAATAGT
* *
353597 TATTATTTTTATATTAATATATTATGTAAA
1 TATTATTTTTATATTAAAATAATATGTAAA
* * *
353627 TATTATTTTTTTATTAAAATAATATTTATA
1 TATTATTTTTATATTAAAATAATATGTAAA
353657 TAATTATTATTTAT
1 T-ATTATT-TTTAT
353671 TTAGAATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 26 0.72
31 6 0.17
32 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
TATTATTTTTATATTAAAATAATATGTAAA
Found at i:353835 original size:17 final size:17
Alignment explanation
Indices: 353813--353866 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
353803 AATGTTAATA
353813 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
353830 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
353847 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
353864 TTT
1 TTT
353867 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:355478 original size:21 final size:21
Alignment explanation
Indices: 355448--355520 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
355438 TATGCCATCT
* *
355448 CCGCATGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
355469 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
355490 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
355511 CCGCAGGGTT
1 CCGCAGGGTT
355521 TTATACCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
20 2 0.04
21 43 0.91
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.26, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:356056 original size:28 final size:28
Alignment explanation
Indices: 356024--356118 Score: 109
Period size: 28 Copynumber: 3.2 Consensus size: 28
356014 GATAAATGTT
* *
356024 TTTAAAATACAAATTATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
356052 TTTAAAATAAAAATAATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
*
356080 TTTAAATTTAAAATATAAATTATAGTATTCGAAA
1 TTTAAA-ATAAAA-AT-AA-TAT--TATTCGAAA
356114 TTTAA
1 TTTAA
356119 CATTAAATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
28 32 0.55
29 5 0.09
30 2 0.03
31 2 0.03
32 3 0.05
34 14 0.24
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCGAAA
Found at i:356125 original size:34 final size:32
Alignment explanation
Indices: 356025--356125 Score: 120
Period size: 34 Copynumber: 3.2 Consensus size: 32
356015 ATAAATGTTT
*
356025 TTAAAATACAAATTATATTATTCGAAATTTAAA
1 TTAAAATATAAATTATA-TATTCGAAATTTAAA
*
356058 ATAAAA-AT-AA-TAT-TATTCGAAATTTAAA
1 TTAAAATATAAATTATATATTCGAAATTTAAA
356086 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATATAAATTATA-TATTCGAAATTTAA-A
356121 TTAAA
1 TTAAA
356126 TTTCAACTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
28 15 0.26
29 5 0.09
30 5 0.09
31 4 0.07
32 4 0.07
33 5 0.09
34 19 0.33
35 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (32 bp):
TTAAAATATAAATTATATATTCGAAATTTAAA
Found at i:356995 original size:255 final size:255
Alignment explanation
Indices: 356519--357142 Score: 1035
Period size: 255 Copynumber: 2.5 Consensus size: 255
356509 TTACCTGATT
*
356519 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* * * *** *
356584 TGACAAAATAATGGAAGGCGCCCCCCCGGGAACGTGCCTTCAAGTCCCCT-GAGAAATAATAGGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGT
356648 ACTGATATGAATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTAT
130 ACTGATATGAATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTAT
* * *
356713 GACAAAATAATGGAAGGCGCGCCCCGGGAACGCTCCTTCATGTGAATAGTGAAATAATAGG
195 GACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTAATGTGAATAGTAAAATAATAGG
356774 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
356839 TGACAAAATAATGGAAGGCGCGCCCCC-GGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
* * *
356903 CTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
131 CTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTAT
356967 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTAATGTGAATAGTAAAATAATAGG
195 GACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTAATGTGAATAGTAAAATAATAGG
* *
357029 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
357094 TG---AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
357143 ACTCCGATTA
Statistics
Matches: 349, Mismatches: 16, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
252 22 0.06
253 26 0.07
254 109 0.31
255 192 0.55
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (255 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
CTGATATGAATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG
ACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTAATGTGAATAGTAAAATAATAGG
Found at i:357091 original size:128 final size:128
Alignment explanation
Indices: 356519--357143 Score: 1023
Period size: 127 Copynumber: 4.9 Consensus size: 128
356509 TTACCTGATT
*
356519 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* * * ***
356584 TGACAAAATAATGGAAGGCGCCCCCCCGGGAACGTGCCTTCAAGTCCCCT-G-AGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTA-AAATAATAGG
* *
356647 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* *
356711 ATGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCTCCTTCATGTGAATAGTGAAATAATAGG
65 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
356774 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
356839 TGACAAAATAATGGAAGGCGCGCCCCC-GGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
*
356901 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
356966 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTAATGTGAATAGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
* *
357029 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
357094 TG---AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTA
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTA
357144 CTCCGATTAT
Statistics
Matches: 472, Mismatches: 19, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
125 47 0.10
126 2 0.00
127 238 0.50
128 184 0.39
129 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
Found at i:357226 original size:8 final size:8
Alignment explanation
Indices: 357213--357253 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
357203 TCACAAGCTT
357213 TCAAATTC
1 TCAAATTC
357221 TCAAATTC
1 TCAAATTC
* *
357229 CCAAACTC
1 TCAAATTC
357237 T-AAATTC
1 TCAAATTC
357244 TCAAATTC
1 TCAAATTC
357252 TC
1 TC
357254 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:362068 original size:29 final size:29
Alignment explanation
Indices: 362014--362127 Score: 106
Period size: 29 Copynumber: 3.9 Consensus size: 29
362004 TTTAAGTCTG
*
362014 AAATATATTTTATTTTTA-CTTCAACTTTA
1 AAATATATTTTATTATTATCTT-AACTTTA
* *
362043 AAATGTATTTTGTTATTATCTTAACTTTAA
1 AAATATATTTTATTATTATCTTAACTTT-A
* * * * *
362073 AAATATATTTTATTCTTTTATTAAATTAA
1 AAATATATTTTATTATTATCTTAACTTTA
* *
362102 AAATGTAGTTT-TTATTATCTTAACTT
1 AAATATATTTTATTATTATCTTAACTT
362128 CAAATAAAAG
Statistics
Matches: 67, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
28 11 0.16
29 31 0.46
30 25 0.37
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (29 bp):
AAATATATTTTATTATTATCTTAACTTTA
Found at i:362078 original size:59 final size:58
Alignment explanation
Indices: 362014--362127 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 58
362004 TTTAAGTCTG
* * *
362014 AAATATATTTTA-T-TTTTACTTCAACTTTAAAATGTATTTTGTTATTATCTTAACTTTAA
1 AAATATATTTTATTCTTTTA-TT-AAATTAAAAATGTAGTTT-TTATTATCTTAACTTTAA
362073 AAATATATTTTATTCTTTTATTAAATTAAAAATGTAGTTTTTATTATCTTAACTT
1 AAATATATTTTATTCTTTTATTAAATTAAAAATGTAGTTTTTATTATCTTAACTT
362128 CAAATAAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 15 0.30
59 27 0.54
60 3 0.06
61 5 0.10
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (58 bp):
AAATATATTTTATTCTTTTATTAAATTAAAAATGTAGTTTTTATTATCTTAACTTTAA
Found at i:362172 original size:29 final size:28
Alignment explanation
Indices: 362140--362259 Score: 102
Period size: 29 Copynumber: 4.1 Consensus size: 28
362130 AATAAAAGAA
*
362140 TTTTAAGTTAATA-AAAGATTAGAATATAT
1 TTTTAAGTTAATATAAA-A-TAAAATATAT
* *
362169 TTTTAAAATTAAGATAAACATAAAATATAT
1 TTTT-AAGTTAATATAAA-ATAAAATATAT
*
362199 TTTAAAGTTAATATAAAAATAAAATATAT
1 TTTTAAGTTAATAT-AAAATAAAATATAT
*
362228 TTAATACA-TTAA-ATGAAAATAAAATATAT
1 TT-TTA-AGTTAATAT-AAAATAAAATATAT
362257 TTT
1 TTT
362260 CTTAAAATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
29 43 0.57
30 27 0.36
31 5 0.07
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (28 bp):
TTTTAAGTTAATATAAAATAAAATATAT
Found at i:362198 original size:30 final size:28
Alignment explanation
Indices: 362162--362274 Score: 113
Period size: 29 Copynumber: 3.8 Consensus size: 28
362152 AAAAGATTAG
362162 AATATATTTTTAAAATTAAGATAAACATAA
1 AATATA-TTTTAAAATTAAGATAAA-ATAA
* *
362192 AATATATTTTAAAGTTAATATAAAAATAA
1 AATATATTTTAAAATTAAGAT-AAAATAA
362221 AATATA-TTTAATACATTAA-ATGAAAATAA
1 AATATATTTTAA-A-ATTAAGAT-AAAATAA
362250 AATATATTTTCTTAAAATTAAGATA
1 AATATA--TT-TTAAAATTAAGATA
362275 TGAATTTAAG
Statistics
Matches: 71, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
28 5 0.07
29 39 0.55
30 13 0.18
31 6 0.08
32 4 0.06
33 4 0.06
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.38
Consensus pattern (28 bp):
AATATATTTTAAAATTAAGATAAAATAA
Found at i:362225 original size:59 final size:57
Alignment explanation
Indices: 362129--362259 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 57
362119 TCTTAACTTC
* * *
362129 AAATAAAAGA-ATTTTAAGTTAATAAAAGATTAGAATATATTTTTAA-A-ATTAAGAT-A
1 AAATAAAATATATTTTAAGTTAATAAAAGAATA-AA-ATATATTTAATACATTAA-ATGA
362185 AACATAAAATATATTTTAAAGTTAATATAAA-AATAAAATATATTTAATACATTAAATGA
1 AA-ATAAAATATATTTT-AAGTTAATA-AAAGAATAAAATATATTTAATACATTAAATGA
362244 AAATAAAATATATTTT
1 AAATAAAATATATTTT
362260 CTTAAAATTA
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
56 2 0.03
57 16 0.25
58 24 0.37
59 20 0.31
60 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (57 bp):
AAATAAAATATATTTTAAGTTAATAAAAGAATAAAATATATTTAATACATTAAATGA
Found at i:362590 original size:16 final size:16
Alignment explanation
Indices: 362569--362655 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 16
362559 TAACCAAAAT
362569 CAACCCGAACTGAAAG
1 CAACCCGAACTGAAAG
* *
362585 CAACCCAAACTGAAAAT
1 CAACCCGAACTG-AAAG
* *
362602 CAACCCGAACCGAAAT
1 CAACCCGAACTGAAAG
*** * *
362618 CAATTAGAACTAAAAA
1 CAACCCGAACTGAAAG
* *
362634 TAACCCGAACTAAAAG
1 CAACCCGAACTGAAAG
362650 CAACCC
1 CAACCC
362656 AAATTTAAGT
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
16 41 0.76
17 13 0.24
ACGTcount: A:0.49, C:0.30, G:0.10, T:0.10
Consensus pattern (16 bp):
CAACCCGAACTGAAAG
Found at i:362606 original size:33 final size:33
Alignment explanation
Indices: 362564--362658 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
362554 TAGTTTAACC
*
362564 AAAATCAACCCGAACTGAAAGCAACCCAAACTG
1 AAAATCAACCCGAACTGAAAGCAACCCAAACTA
* * **
362597 AAAATCAACCCGAACCGAAATCAA-TTAGAACTA
1 AAAATCAACCCGAACTGAAAGCAACCCA-AACTA
*
362630 AAAAT-AACCCGAACTAAAAGCAACCCAAA
1 AAAATCAACCCGAACTGAAAGCAACCCAAA
362659 TTTAAGTTAC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
32 18 0.36
33 32 0.64
ACGTcount: A:0.53, C:0.27, G:0.09, T:0.11
Consensus pattern (33 bp):
AAAATCAACCCGAACTGAAAGCAACCCAAACTA
Found at i:362777 original size:20 final size:20
Alignment explanation
Indices: 362738--362777 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
362728 AACAAATAAT
*
362738 TTATTTATTTATTATTATTA
1 TTATTTATTTATTATAATTA
362758 TTATTTATTT-TTAATAATTA
1 TTATTTATTTATT-ATAATTA
362778 GATAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTATTATAATTA
Found at i:363338 original size:46 final size:46
Alignment explanation
Indices: 363248--363338 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
363238 TAAACAAAAA
* * *
363248 CAACCTGAATTGACCCGAAAATCTAAAGGTTAATCCCAATCGAAAT
1 CAACCCGAATTGACCCGAAAATCTAAAGCTTAATCCCAACCGAAAT
*
363294 CAACCCGAATTGACCCGAAAATCTAAAGCTTGA-CCCGAACCGAAA
1 CAACCCGAATTGACCCGAAAATCTAAAGCTTAATCCC-AACCGAAA
363339 CTAACTGATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 3 0.08
46 37 0.93
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.18
Consensus pattern (46 bp):
CAACCCGAATTGACCCGAAAATCTAAAGCTTAATCCCAACCGAAAT
Found at i:363408 original size:32 final size:31
Alignment explanation
Indices: 363326--363426 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
363316 CTAAAGCTTG
* * * * *
363326 ACCCGAACCGAAACTAACTGATCTGATATTG
1 ACCCGACCCGAAACCAACTGATCCGAGATTA
** *
363357 ACTTGACTCGAAACCAACTGATCCGAGATTA
1 ACCCGACCCGAAACCAACTGATCCGAGATTA
**
363388 ACCCGACCCGAACACCAACTGATCCGATTTTA
1 ACCCGACCCGAA-ACCAACTGATCCGAGATTA
363420 ACCCGAC
1 ACCCGAC
363427 TCGATACCTG
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
31 32 0.57
32 24 0.43
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.20
Consensus pattern (31 bp):
ACCCGACCCGAAACCAACTGATCCGAGATTA
Found at i:364613 original size:20 final size:20
Alignment explanation
Indices: 364568--364613 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
364558 GACCAACAAA
*
364568 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
364588 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
364607 ATCGCAA
1 ATCGCAA
364614 ATCAGTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:364678 original size:21 final size:21
Alignment explanation
Indices: 364648--364700 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
364638 ATTATGACTA
364648 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
*
364669 TCGCATTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
364690 TCGCAATGCGA
1 TCGCAATGCGA
364701 ATAAGTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Done.