Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015335.1 Kokia drynarioides strain JFW-HI SEQ_130382, 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: 733037
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 878 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:439 original size:20 final size:21
Alignment explanation
Indices: 414--458 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
404 CTTACTTATT
*
414 ATTACTGAC-AACAAAATAAA
1 ATTACTAACTAACAAAATAAA
*
434 ATTACTAACTAACAAAATTAA
1 ATTACTAACTAACAAAATAAA
455 ATTA
1 ATTA
459 AAGTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (21 bp):
ATTACTAACTAACAAAATAAA
Found at i:651 original size:18 final size:18
Alignment explanation
Indices: 630--664 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
620 AATTAAATTT
630 AAAATTAACCAAACTTAA
1 AAAATTAACCAAACTTAA
*
648 AAAATTAATCAAACTTA
1 AAAATTAACCAAACTTA
665 TCTTTCTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTAACCAAACTTAA
Found at i:839 original size:4 final size:4
Alignment explanation
Indices: 830--867 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
820 CTTCTTCCCC
* *
830 TTCT TTCT TTCT TTCT TTTT TTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
868 CTTCAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTCT
Found at i:1491 original size:30 final size:30
Alignment explanation
Indices: 1455--1513 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1445 CTTAACAAAT
1455 AAATACCTCTAAAATAATAACAAAATTAAA
1 AAATACCTCTAAAATAATAACAAAATTAAA
*
1485 AAATACCTTTAAAATAATAACAAAATTAA
1 AAATACCTCTAAAATAATAACAAAATTAA
1514 CAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.25
Consensus pattern (30 bp):
AAATACCTCTAAAATAATAACAAAATTAAA
Found at i:1730 original size:30 final size:29
Alignment explanation
Indices: 1689--1751 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
1679 TAAATCTTAT
* *
1689 ATTACTTTATTTATTCTATATAAAAATTAA
1 ATTAATTTATTTATTCTA-AGAAAAATTAA
* *
1719 ATTAATTTATTTATTTTAAGAAATATTAA
1 ATTAATTTATTTATTCTAAGAAAAATTAA
1748 ATTA
1 ATTA
1752 GTCCTAATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (29 bp):
ATTAATTTATTTATTCTAAGAAAAATTAA
Found at i:1814 original size:13 final size:12
Alignment explanation
Indices: 1798--1832 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1788 ATTAGATTTC
1798 TTTTTTAGAATT
1 TTTTTTAGAATT
*
1810 TTTTTTGGTAATT
1 TTTTTTAG-AATT
1823 TTTTTTAGAA
1 TTTTTTAGAA
1833 CCATATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (12 bp):
TTTTTTAGAATT
Found at i:2045 original size:24 final size:22
Alignment explanation
Indices: 2001--2049 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 22
1991 TATGACAAGA
2001 AATTTTAAAATAAAAATATAAT
1 AATTTTAAAATAAAAATATAAT
*
2023 AATTTTAATAATGAAAATAATAAT
1 AATTTTAA-AATAAAAAT-ATAAT
2047 AAT
1 AAT
2050 CAAAAATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.33
23 8 0.33
24 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTTTAAAATAAAAATATAAT
Found at i:4195 original size:22 final size:22
Alignment explanation
Indices: 4150--4189 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
4140 TTATTTAATA
4150 ACTATTTGTTTGAATAATTATG
1 ACTATTTGTTTGAATAATTATG
4172 ACTATTTG-TT-AATAATTA
1 ACTATTTGTTTGAATAATTA
4190 AGTGACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (22 bp):
ACTATTTGTTTGAATAATTATG
Found at i:12211 original size:27 final size:27
Alignment explanation
Indices: 12172--12236 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
12162 CCAATGCTGT
* * * * *
12172 TGATGTTGTTGTTGTTGTTGTTGCAGA
1 TGATGATGATGTTGCTGTTGTTGAAAA
12199 TGATGATGATGTTGCTGTTGTTGAAAA
1 TGATGATGATGTTGCTGTTGTTGAAAA
*
12226 TGATGCTGATG
1 TGATGATGATG
12237 ATGATGATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (27 bp):
TGATGATGATGTTGCTGTTGTTGAAAA
Found at i:12810 original size:5 final size:5
Alignment explanation
Indices: 12800--12825 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12790 TTCATCCTTC
12800 GGGTG GGGTG GGGTG GGGTG GGGTG G
1 GGGTG GGGTG GGGTG GGGTG GGGTG G
12826 AGTTTCGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (5 bp):
GGGTG
Found at i:13557 original size:31 final size:31
Alignment explanation
Indices: 13522--13585 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
13512 ATTTTCCATA
13522 TAAAGGATTGGAGAATGAAATTTCGAGATAT
1 TAAAGGATTGGAGAATGAAATTTCGAGATAT
13553 TAAAGGATTGGAGAATGAAATTTCGAGATAT
1 TAAAGGATTGGAGAATGAAATTTCGAGATAT
13584 TA
1 TA
13586 GGAAAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (31 bp):
TAAAGGATTGGAGAATGAAATTTCGAGATAT
Found at i:14216 original size:31 final size:29
Alignment explanation
Indices: 14173--14267 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 29
14163 TGAACAATTT
14173 AAAAAAATCATAGTTGAGTGACCAAAAAA
1 AAAAAAATCATAGTTGAGTGACCAAAAAA
* *
14202 GAAACAAATCCATAGTTGAGTGACTAAATTAAA
1 -AAAAAAAT-CATAGTTGAGTGACCAAA--AAA
* *
14235 AAAAAGAATTCATAATTGGGTGACCAAAAAA
1 AAAAA-AA-TCATAGTTGAGTGACCAAAAAA
14266 AA
1 AA
14268 TAACCCATAG
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 7 0.13
31 22 0.41
32 4 0.07
33 20 0.37
34 1 0.02
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.20
Consensus pattern (29 bp):
AAAAAAATCATAGTTGAGTGACCAAAAAA
Found at i:19897 original size:16 final size:16
Alignment explanation
Indices: 19837--19897 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
19827 ATTCAACCAA
*
19837 ACAACTAAATTACTGATT
1 ACAACTATATTAC--ATT
* *
19855 ACAACTTTATTCCATT
1 ACAACTATATTACATT
* *
19871 ATAGCTATATTACATT
1 ACAACTATATTACATT
*
19887 ACAACTCTATT
1 ACAACTATATT
19898 CTATTACAGT
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
16 23 0.70
18 10 0.30
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (16 bp):
ACAACTATATTACATT
Found at i:24809 original size:18 final size:19
Alignment explanation
Indices: 24772--24809 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
24762 AAATATAAAT
24772 TAAAAATAAAAAGTATTATA
1 TAAAAATAAAAAG-ATTATA
*
24792 TAAAAATGAAAA-ATTATA
1 TAAAAATAAAAAGATTATA
24810 AAATATGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
TAAAAATAAAAAGATTATA
Found at i:25109 original size:19 final size:21
Alignment explanation
Indices: 25087--25129 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
25077 GTTAAATACC
25087 TTTTTCAATTTT-TAT-ATAT
1 TTTTTCAATTTTGTATAATAT
25106 TTTTTCAATTTTGTATAATAT
1 TTTTTCAATTTTGTATAATAT
25127 TTT
1 TTT
25130 GATTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.55
20 3 0.14
21 7 0.32
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTCAATTTTGTATAATAT
Found at i:25176 original size:15 final size:17
Alignment explanation
Indices: 25143--25185 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
25133 TTTTAAATTT
*
25143 ATATTTATATTTTTTTA
1 ATATTTATATTTTTCTA
25160 ATATTT-TA-TTTTCTA
1 ATATTTATATTTTTCTA
25175 ATGATTTATAT
1 AT-ATTTATAT
25186 ATTATATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
ATATTTATATTTTTCTA
Found at i:26830 original size:9 final size:9
Alignment explanation
Indices: 26818--26850 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
26808 AAATATTAAG
26818 ATTAATCAA
1 ATTAATCAA
26827 ATTAATCAA
1 ATTAATCAA
26836 ATTAATCAA
1 ATTAATCAA
*
26845 ACTAAT
1 ATTAAT
26851 AGCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (9 bp):
ATTAATCAA
Found at i:39302 original size:20 final size:20
Alignment explanation
Indices: 39261--39302 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
39251 TTCTCATAAA
* *
39261 TTTTTAATTTATTTTTTATT
1 TTTTTAATTTAATTATTATT
39281 TTTTTAATTTTAATTATT-TT
1 TTTTTAA-TTTAATTATTATT
39301 TT
1 TT
39303 AATCAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTAATTTAATTATTATT
Found at i:44977 original size:16 final size:18
Alignment explanation
Indices: 44958--44994 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
44948 AATTAGTAAT
44958 TAATTTATA-AAAAAT-G
1 TAATTTATATAAAAATCG
*
44974 TAATTTTTATAAAAATCG
1 TAATTTATATAAAAATCG
44992 TAA
1 TAA
44995 GAAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (18 bp):
TAATTTATATAAAAATCG
Found at i:45226 original size:18 final size:18
Alignment explanation
Indices: 45186--45246 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
45176 ATACATACAT
*
45186 ATTTTATAATTTTCTTATC
1 ATTTTATAATTTT-TTATA
**
45205 ATTTTATAAAATTTTATA
1 ATTTTATAATTTTTTATA
*
45223 ATTTCATAATTTTTTATA
1 ATTTTATAATTTTTTATA
*
45241 TTTTTA
1 ATTTTA
45247 CATATTCTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
18 23 0.68
19 11 0.32
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTATAATTTTTTATA
Found at i:45293 original size:20 final size:20
Alignment explanation
Indices: 45270--45307 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
45260 TCTTTTACGA
45270 AATTTTTATAAT-TTTTTAAT
1 AATTTTTA-AATATTTTTAAT
45290 AATTTTTAAATATTTTTA
1 AATTTTTAAATATTTTTA
45308 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AATTTTTAAATATTTTTAAT
Found at i:51911 original size:12 final size:12
Alignment explanation
Indices: 51894--51921 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
51884 GGAAACATGT
51894 AGAAGAGAAGAG
1 AGAAGAGAAGAG
51906 AGAAGAGAAGAG
1 AGAAGAGAAGAG
51918 AGAA
1 AGAA
51922 AATCCGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
AGAAGAGAAGAG
Found at i:58459 original size:23 final size:24
Alignment explanation
Indices: 58432--58497 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 24
58422 TTTAATGTTC
**
58432 ACGAACATGTTCATTTAAC-TTAA
1 ACGAACATGTTCATCGAACATTAA
*
58455 TCGAACATGTTCA-CGAACATTAA
1 ACGAACATGTTCATCGAACATTAA
58478 ACGAACATGTTCAT-GAACAT
1 ACGAACATGTTCATCGAACAT
58498 ATAATTGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.08
23 34 0.92
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (24 bp):
ACGAACATGTTCATCGAACATTAA
Found at i:58473 original size:12 final size:12
Alignment explanation
Indices: 58456--58497 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
58446 TTAACTTAAT
58456 CGAACATGTTCA
1 CGAACATGTTCA
**
58468 CGAACAT-TAAA
1 CGAACATGTTCA
58479 CGAACATGTTCA
1 CGAACATGTTCA
*
58491 TGAACAT
1 CGAACAT
58498 ATAATTGAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (12 bp):
CGAACATGTTCA
Found at i:59363 original size:29 final size:30
Alignment explanation
Indices: 59310--59368 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
59300 AAATTTGATC
59310 AAATCAAAATTTCATATATAAAATTGCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
* * *
59340 AAATCAAAGTTT-ATGTATATAATTGCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
59369 TTAAACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTGCACA
Found at i:60048 original size:22 final size:24
Alignment explanation
Indices: 60018--60063 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
60008 GAATTGAGAG
*
60018 AATTGAGAGAATAG-A-TGAATAA
1 AATTAAGAGAATAGTATTGAATAA
60040 AATTAAGAGAATAGTATTGAATAA
1 AATTAAGAGAATAGTATTGAATAA
60064 GAAAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 1 0.05
24 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (24 bp):
AATTAAGAGAATAGTATTGAATAA
Found at i:68765 original size:21 final size:22
Alignment explanation
Indices: 68741--68781 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
68731 TCAATCTAAT
68741 TTAATTTGA-TTAATT-GATCAG
1 TTAA-TTGATTTAATTCGATCAG
68762 TTAATTGATTTAATTCGATC
1 TTAATTGATTTAATTCGATC
68782 GAAGGTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (22 bp):
TTAATTGATTTAATTCGATCAG
Found at i:75347 original size:19 final size:20
Alignment explanation
Indices: 75325--75363 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
75315 TATTTCTAGG
75325 AATTAAAAAAC-ATTAAAAT
1 AATTAAAAAACTATTAAAAT
*
75344 AATTTAAAAACTATTAAAAT
1 AATTAAAAAACTATTAAAAT
75364 TATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AATTAAAAAACTATTAAAAT
Found at i:82353 original size:52 final size:52
Alignment explanation
Indices: 82291--82394 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
82281 GACGTGATAT
82291 ATCTGTTTCATTCAATCCTTTCTCTTTAAAGAAGTGCCCACTCTTTCAACCA
1 ATCTGTTTCATTCAATCCTTTCTCTTTAAAGAAGTGCCCACTCTTTCAACCA
*
82343 ATCTGTTTCATTCAATCCTTTCTCTTTAAAGGAGTGCCCACTCTTTCAACCA
1 ATCTGTTTCATTCAATCCTTTCTCTTTAAAGAAGTGCCCACTCTTTCAACCA
82395 CTTCTTCTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (52 bp):
ATCTGTTTCATTCAATCCTTTCTCTTTAAAGAAGTGCCCACTCTTTCAACCA
Found at i:84840 original size:21 final size:20
Alignment explanation
Indices: 84808--84849 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
84798 CATTATTCTG
84808 TAAAAAGTAATAGAAATTTAT
1 TAAAAAGTAATA-AAATTTAT
*
84829 TAAACAAG-AATAAATTTTAT
1 TAAA-AAGTAATAAAATTTAT
84849 T
1 T
84850 TTTTTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 8 0.42
22 3 0.16
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
TAAAAAGTAATAAAATTTAT
Found at i:89256 original size:60 final size:60
Alignment explanation
Indices: 89180--89309 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 60
89170 CCTAAATATA
* * * * *
89180 AAAAAATCAATAAATTT-AGCTCTCAATATTTACAAAACT-TGTCATTTTAGTTC-TAATTCT
1 AAAAAATTAATAAATTTGATC-CTCAACATTTAC-AAACTCTATCATTTTAG-TCATAACTCT
*
89240 AAAAAATTAATAAATTTGATCCTCAACATTTACAAAGTCTATCATTTTAGTCATAACTCT
1 AAAAAATTAATAAATTTGATCCTCAACATTTACAAACTCTATCATTTTAGTCATAACTCT
*
89300 AAAAATTTAA
1 AAAAAATTAA
89310 AAAAAATATT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 6 0.10
60 52 0.87
61 2 0.03
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.38
Consensus pattern (60 bp):
AAAAAATTAATAAATTTGATCCTCAACATTTACAAACTCTATCATTTTAGTCATAACTCT
Found at i:96878 original size:30 final size:31
Alignment explanation
Indices: 96838--96900 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
96828 TGCTTATACC
* *
96838 TTTATTATTTTTAAAGAGTTAAATTA-AATT
1 TTTATCATTTTTAAAGAGTTAAAGTATAATT
* *
96868 TTTATCATTTTTGAAGGGTTAAAGTATAATT
1 TTTATCATTTTTAAAGAGTTAAAGTATAATT
96899 TT
1 TT
96901 ACTATTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (31 bp):
TTTATCATTTTTAAAGAGTTAAAGTATAATT
Found at i:101401 original size:29 final size:30
Alignment explanation
Indices: 101346--101407 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
101336 TACACTTTTG
* * **
101346 TAATTTTTTTTAATTACATAAGTTATT-TA
1 TAATATTTTTTAATTACACAAAATATTATA
*
101375 TAATATTTTTTAATTATACAAAATATTATA
1 TAATATTTTTTAATTACACAAAATATTATA
101405 TAA
1 TAA
101408 GTATACAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (30 bp):
TAATATTTTTTAATTACACAAAATATTATA
Found at i:102272 original size:20 final size:21
Alignment explanation
Indices: 102249--102299 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
102239 ATTAATTATT
*
102249 TATAAAATT-TAATTTGAATA
1 TATAAAATTATAATTTAAATA
*
102269 TAT-AAATTATATTTTAAATA
1 TATAAAATTATAATTTAAATA
102289 T-TAAAA-TATAA
1 TATAAAATTATAA
102300 CCAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATAAAATTATAATTTAAATA
Found at i:108731 original size:2 final size:2
Alignment explanation
Indices: 108724--108753 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
108714 ACATTACACA
108724 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
108754 GAGTTTGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124015 original size:18 final size:19
Alignment explanation
Indices: 123971--124015 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
123961 GGTGTCAATT
123971 TCACATTTTATCTTAAAAAA
1 TCACATTTTA-CTTAAAAAA
*
123991 -AAC-TTTTA-TTAAAAAA
1 TCACATTTTACTTAAAAAA
124007 TCACATTTT
1 TCACATTTT
124016 TACATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 6
0.72 0.07 0.21
Matches are distributed among these distances:
16 8 0.38
17 2 0.10
18 9 0.43
19 2 0.10
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (19 bp):
TCACATTTTACTTAAAAAA
Found at i:128429 original size:15 final size:16
Alignment explanation
Indices: 128393--128422 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
128383 ATGTTTTATT
128393 ATAAAATATAATAATA
1 ATAAAATATAATAATA
128409 ATAAAATA-AATAAT
1 ATAAAATATAATAAT
128423 GAAAAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAATATAATAATA
Found at i:129113 original size:24 final size:25
Alignment explanation
Indices: 129068--129114 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
129058 GAAATTATGG
*
129068 AAAACTCTAATTAATTTGAGAAACA
1 AAAACTCTAATAAATTTGAGAAACA
129093 AAAACTCTAA-AAATATT-AGAAA
1 AAAACTCTAATAAAT-TTGAGAAA
129115 AGGGAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (25 bp):
AAAACTCTAATAAATTTGAGAAACA
Found at i:130580 original size:21 final size:22
Alignment explanation
Indices: 130550--130592 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
130540 AATTTATTAT
*
130550 TAAAATTTTAAA-TCTAAAAAG
1 TAAAAATTTAAATTCTAAAAAG
130571 TAAAAATTTAAATTTCTAAAAA
1 TAAAAATTTAAA-TTCTAAAAA
130593 AATATTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAAAATTTAAATTCTAAAAAG
Found at i:137903 original size:46 final size:46
Alignment explanation
Indices: 137851--137938 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
137841 ACTATTAATT
* * ** *
137851 TGTAATATTAGTTATGCACTTGGACGATGTTGTAGTTATCATGTGG
1 TGTAATACTAGTTATACACTTGGAAAATATTGTAGTTATCATGTGG
*
137897 TGTAATACTAGTTATACATTTGGAAAATATTGTAGTTATCAT
1 TGTAATACTAGTTATACACTTGGAAAATATTGTAGTTATCAT
137939 CAATTTGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (46 bp):
TGTAATACTAGTTATACACTTGGAAAATATTGTAGTTATCATGTGG
Found at i:138234 original size:20 final size:20
Alignment explanation
Indices: 138198--138241 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
138188 TCCAAACACC
*
138198 AAAAAATATTAATTTTTTCA
1 AAAAAATATTAATTTTTCCA
*
138218 AAAAAATAATTTA-TTTTCCA
1 AAAAAAT-ATTAATTTTTCCA
138238 AAAA
1 AAAA
138242 TTATTTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATATTAATTTTTCCA
Found at i:142583 original size:84 final size:85
Alignment explanation
Indices: 142490--142648 Score: 243
Period size: 85 Copynumber: 1.9 Consensus size: 85
142480 TTTTCAAATT
* *
142490 TTTTCAAAAAAAGCAATT-AAGCACT-TTTTTTTTACACTCAATTGGGTACTTGAACTT-TCAAA
1 TTTTCAAAAAAA-CAATTAAACCACTACTTTTTTTACACTCAATTGGGTACTTGAA-TTGTCAAA
142552 ATGCATCAAAAAGGCCTTCAAA
64 ATGCATCAAAAAGGCCTTCAAA
* *
142574 TTTTCAAAAAAACAATTAAACCCCTACTTTTTTTGCACTCAATTGGGTACTTGAATTGTCAAAAT
1 TTTTCAAAAAAACAATTAAACCACTACTTTTTTTACACTCAATTGGGTACTTGAATTGTCAAAAT
142639 GCATCAAAAA
66 GCATCAAAAA
142649 AGTCCTTTGA
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
83 5 0.07
84 19 0.28
85 44 0.65
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (85 bp):
TTTTCAAAAAAACAATTAAACCACTACTTTTTTTACACTCAATTGGGTACTTGAATTGTCAAAAT
GCATCAAAAAGGCCTTCAAA
Found at i:142817 original size:20 final size:20
Alignment explanation
Indices: 142785--142823 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
142775 AATAAAAGTT
*
142785 ATAAAATTATTAAA-TTTTA
1 ATAAAAATATTAAAGTTTTA
142804 ATAAAAATATTTAAAGTTTT
1 ATAAAAATA-TTAAAGTTTT
142824 TTAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
ATAAAAATATTAAAGTTTTA
Found at i:142839 original size:10 final size:10
Alignment explanation
Indices: 142826--142891 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
142816 AAAGTTTTTT
142826 AAAAATTAGA
1 AAAAATTAGA
*
142836 AAAAATTA-T
1 AAAAATTAGA
142845 AAAAA-TAGTA
1 AAAAATTAG-A
*
142855 AAAAATTATA
1 AAAAATTAGA
*
142865 AAATATATAG-
1 AAAAAT-TAGA
*
142875 AAATA-TAGA
1 AAAAATTAGA
142884 AAAAATTA
1 AAAAATTA
142892 TAAATTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
8 5 0.11
9 9 0.20
10 26 0.59
11 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (10 bp):
AAAAATTAGA
Found at i:142847 original size:19 final size:19
Alignment explanation
Indices: 142825--142877 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
142815 TAAAGTTTTT
142825 TAAAAATTAGAAAAAATTA
1 TAAAAATTAGAAAAAATTA
142844 TAAAAA-TAGTAAAAAATTA
1 TAAAAATTAG-AAAAAATTA
142863 TAAAATATATAGAAA
1 TAAAA-AT-TAGAAA
142878 TATAGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 20 0.67
20 1 0.03
21 3 0.10
22 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (19 bp):
TAAAAATTAGAAAAAATTA
Found at i:142848 original size:9 final size:9
Alignment explanation
Indices: 142825--142968 Score: 55
Period size: 9 Copynumber: 15.1 Consensus size: 9
142815 TAAAGTTTTT
142825 TAAAAATTA
1 TAAAAATTA
*
142834 GAAAAAATTA
1 -TAAAAATTA
142844 TAAAAA-TA
1 TAAAAATTA
142852 GTAAAAAATTA
1 -T-AAAAATTA
142863 T-AAAATATA
1 TAAAAAT-TA
*
142872 TAGAAATATA
1 TAAAAAT-TA
*
142882 GAAAAAATTA
1 -TAAAAATTA
**
142892 TAAATTTTA
1 TAAAAATTA
*
142901 T-AAACTCGTA
1 TAAAAAT--TA
142911 -ATAAAATTA
1 TA-AAAATTA
* *
142920 TAAAAAATG
1 TAAAAATTA
*
142929 TAAAGAAATA
1 TAAA-AATTA
142939 T-AAAATTCA
1 TAAAAATT-A
142948 TAAAAAAATTA
1 T--AAAAATTA
142959 TAAAAATTA
1 TAAAAATTA
142968 T
1 T
142969 CGTACCAAAA
Statistics
Matches: 103, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
8 13 0.13
9 40 0.39
10 31 0.30
11 13 0.13
12 6 0.06
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:142892 original size:29 final size:29
Alignment explanation
Indices: 142826--142965 Score: 107
Period size: 29 Copynumber: 4.9 Consensus size: 29
142816 AAAGTTTTTT
*
142826 AAAAATTAGAAAAAATTATAAAAATAGTA
1 AAAAATTATAAAAAATTATAAAAATAGTA
*
142855 AAAAATTATAAAATA-TATAGAAATATAG-A
1 AAAAATTATAAAAAATTATA-AAA-ATAGTA
** * *
142884 AAAAATTAT-AAATTTTAT-AAACTCGTA
1 AAAAATTATAAAAAATTATAAAAATAGTA
142911 ATAAAATTATAAAAAATGTA-AAGAAATA-T-
1 A-AAAATTATAAAAAAT-TATAA-AAATAGTA
142940 -AAAATTCATAAAAAAATTATAAAAAT
1 AAAAATT-AT-AAAAAATTATAAAAAT
142966 TATCGTACCA
Statistics
Matches: 90, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
26 2 0.02
27 11 0.12
28 24 0.27
29 42 0.47
30 8 0.09
31 3 0.03
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAAATTATAAAAAATTATAAAAATAGTA
Found at i:143196 original size:37 final size:37
Alignment explanation
Indices: 143152--143258 Score: 128
Period size: 37 Copynumber: 2.8 Consensus size: 37
143142 TGATGCATTT
*
143152 TATATTTTTTATGATTTTTATAAAATATTAAATTTTC
1 TATATTTTTTATGATTTTTATAAAATATTAAATTTTA
*
143189 TATATTTTTTATGATTTTTATAAAATTTTAATAAATTTTA
1 TATATTTTTTATGATTTTTATAAAA---TATTAAATTTTA
* *
143229 AATATTTTGTAT-ATTTTTATTAAAAT-TTAA
1 TATATTTTTTATGATTTTTA-TAAAATATTAA
143259 TAATGTTTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
36 3 0.05
37 26 0.43
39 7 0.11
40 25 0.41
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (37 bp):
TATATTTTTTATGATTTTTATAAAATATTAAATTTTA
Found at i:153182 original size:16 final size:16
Alignment explanation
Indices: 153158--153195 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
153148 TATAAGCAAG
*
153158 CTAGATGCTTCTATTT
1 CTAGGTGCTTCTATTT
153174 CTAGGTGCTTCTATTT
1 CTAGGTGCTTCTATTT
153190 CTAGGT
1 CTAGGT
153196 ATTGATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.47
Consensus pattern (16 bp):
CTAGGTGCTTCTATTT
Found at i:172225 original size:17 final size:18
Alignment explanation
Indices: 172188--172225 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
172178 TGCAAACTTG
*
172188 TTTTTTTTTGTAATCTGTT
1 TTTTTTTTTATAATC-GTT
172207 TTTTTTTTTATAATC-TT
1 TTTTTTTTTATAATCGTT
172224 TT
1 TT
172226 CACCTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTTTTTTATAATCGTT
Found at i:173203 original size:43 final size:43
Alignment explanation
Indices: 173133--173218 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
173123 TGGGCAAACA
173133 GTTACTGTGGAAGAACATCAGTCTGCAATTTTTAATGGTCTTT
1 GTTACTGTGGAAGAACATCAGTCTGCAATTTTTAATGGTCTTT
* *
173176 GTTACTGTGGAAGAACATTAGTTTGCAATTTTTAATGGTCTTT
1 GTTACTGTGGAAGAACATCAGTCTGCAATTTTTAATGGTCTTT
173219 CACCTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (43 bp):
GTTACTGTGGAAGAACATCAGTCTGCAATTTTTAATGGTCTTT
Found at i:179748 original size:38 final size:38
Alignment explanation
Indices: 179697--179773 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
179687 GGAGTTGAAA
179697 TGAGGTAAAATCCGTTCCACCCGCCCCAAAATAATTAC
1 TGAGGTAAAATCCGTTCCACCCGCCCCAAAATAATTAC
179735 TGAGGTAAAATCCGTTCCACCCGCCCCAAAATAATTAC
1 TGAGGTAAAATCCGTTCCACCCGCCCCAAAATAATTAC
179773 T
1 T
179774 AAAATATCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.22
Consensus pattern (38 bp):
TGAGGTAAAATCCGTTCCACCCGCCCCAAAATAATTAC
Found at i:183791 original size:2 final size:2
Alignment explanation
Indices: 183779--183808 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
183769 GACCCACTTC
183779 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
183809 CAAGTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:185050 original size:6 final size:6
Alignment explanation
Indices: 185039--185100 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
185029 ATAGCTGCAT
185039 CTCACA CTCACA CTCACA CTCACA CTCACA CTCACA CTCACA CTCACA
1 CTCACA CTCACA CTCACA CTCACA CTCACA CTCACA CTCACA CTCACA
185087 CTCACA CTCACA CT
1 CTCACA CTCACA CT
185101 TGAGTCAACG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CTCACA
Found at i:190691 original size:14 final size:14
Alignment explanation
Indices: 190672--190703 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
190662 ATTTTACTAT
190672 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
*
190686 AAAAAAGAAAAAGA
1 AAAAAAAAAAAAGA
190700 AAAA
1 AAAA
190704 CCACACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:193299 original size:8 final size:9
Alignment explanation
Indices: 193283--193369 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
193273 ATTGTTTTAG
193283 AAAATTTTT
1 AAAATTTTT
193292 AAAA-TTTT
1 AAAATTTTT
**
193300 AACTTTCTTT
1 AAAATT-TTT
*
193310 ATATATTTTT
1 A-AAATTTTT
*
193320 -AGATTTTT
1 AAAATTTTT
*
193328 ATAATTTTT
1 AAAATTTTT
*
193337 AAAA-ATTT
1 AAAATTTTT
*
193345 AAATTATTTT
1 AAAAT-TTTT
*
193355 AAAATTTTG
1 AAAATTTTT
193364 AAAATT
1 AAAATT
193370 ATTTTGATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
8 19 0.32
9 23 0.39
10 14 0.24
11 3 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (9 bp):
AAAATTTTT
Found at i:193382 original size:20 final size:20
Alignment explanation
Indices: 193333--193374 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
193323 TTTTTATAAT
*
193333 TTTTAAAAATTT--AAATTA
1 TTTTAAAATTTTGAAAATTA
193351 TTTTAAAATTTTGAAAATTA
1 TTTTAAAATTTTGAAAATTA
193371 TTTT
1 TTTT
193375 GATTTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTAAAATTTTGAAAATTA
Found at i:198807 original size:17 final size:16
Alignment explanation
Indices: 198768--198824 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
198758 TTGGAAATTG
198768 AATTTATTTTAAATTTA
1 AATTTA-TTTAAATTTA
**
198785 TGTTTATTTGAAATTTA
1 AATTTATTT-AAATTTA
*
198802 AATTTATTATAAAATTA
1 AATTTATT-TAAATTTA
198819 AATTTA
1 AATTTA
198825 AAAAAGTCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 3 0.09
17 29 0.88
18 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (16 bp):
AATTTATTTAAATTTA
Found at i:199529 original size:3 final size:3
Alignment explanation
Indices: 199521--199595 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
199511 AGTATTGATT
199521 ATA ATA ATA 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 ATA ATA ATA
* ** * *
199569 ATG GCA TTA ATA ATA ATA TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
199596 GCATAAAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:200609 original size:30 final size:29
Alignment explanation
Indices: 200573--200777 Score: 187
Period size: 30 Copynumber: 6.9 Consensus size: 29
200563 CCTCGAAGGT
*
200573 CCCTAAACTGTCAAAAAATTCCATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
* *
200603 CCCTAAATTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * * *
200633 CTCGAAACTTCCAAAAATTTCATTATTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
200662 CCTTGAAACTTCCAAAAATTCCATTTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
** * *
200692 CCCTAAACTTCCAAAAACACCGTTTTTGAT
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * * *
200722 CCCGAAATTTCTAAAAATTCCATTATTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
** *
200751 CCCCGAA-TGTCTAAAAATTCCATTTTT
1 CCCTAAACT-TCCAAAAATTCCATTTTT
200778 TTTAAAAAAA
Statistics
Matches: 141, Mismatches: 30, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
28 1 0.01
29 62 0.44
30 78 0.55
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:200701 original size:59 final size:59
Alignment explanation
Indices: 200573--200708 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 59
200563 CCTCGAAGGT
* * *
200573 CCCTAAACTGTCAAAAAATTCCATTTTTACCCCTAAATTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACT-TCCAAAAATTCCATTATTACCCCTAAACTTCCAAAAATCCCATTTTTGAC
* * * * *
200633 CTCGAAACTTCCAAAAATTTCATTATTACCCTTGAAACTTCCAAAAATTCCATTTTT-AC
1 CCCTAAACTTCCAAAAATTCCATTATTACCCCT-AAACTTCCAAAAATCCCATTTTTGAC
200692 CCCTAAACTTCCAAAAA
1 CCCTAAACTTCCAAAAA
200709 CACCGTTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 37 0.57
60 28 0.43
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (59 bp):
CCCTAAACTTCCAAAAATTCCATTATTACCCCTAAACTTCCAAAAATCCCATTTTTGAC
Found at i:200778 original size:89 final size:90
Alignment explanation
Indices: 200577--200777 Score: 268
Period size: 89 Copynumber: 2.3 Consensus size: 90
200567 GAAGGTCCCT
*
200577 AAACTGTCAAAAAATTCCATTTTTACCCCTAAATTTCCAAAAATCCCATTTTTGACCTCGAAACT
1 AAACTGTCAAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCGAAACT
* **
200642 TCCAAAAATTTCATTATTACCCTTG
66 TCCAAAAATTCCATTATTACCCCCG
* *
200667 AAACT-TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAA-CACCGTTTTTGATCC-CGAAA
1 AAACTGTCAAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATC-CCATTTTTGA-CCTCGAAA
* *
200729 TTTCTAAAAATTCCATTATTACCCCCG
64 CTTCCAAAAATTCCATTATTACCCCCG
*
200756 -AA-TGTCTAAAAATTCCATTTTT
1 AAACTGTCAAAAAATTCCATTTTT
200778 TTTAAAAAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
87 1 0.01
88 20 0.20
89 71 0.72
90 7 0.07
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (90 bp):
AAACTGTCAAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCGAAACT
TCCAAAAATTCCATTATTACCCCCG
Found at i:201191 original size:96 final size:96
Alignment explanation
Indices: 201049--201240 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
201039 GAAACTTTAA
* * **
201049 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTCACTAGGTGCAATT
1 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGCGCAACC
*
201114 TTTCCTCAAATCGAAATAATCTAATACCCTT
66 TTTCCTCAAATCGAAATAATCGAATACCCTT
* *
201145 AATCGAGGCAATGTT-TTCTTATCTTCGA--TTCTG-AAATATTGCGCCTTAACTTACTAGGCGC
1 AATCGAGGCAATATTCTT-TTAT-TTCGAGTTTC-GAAAAT-TTGCGCCTTAACTCACTAGGCGC
* * * *
201206 GACCTTTCTTCAAATCGAGATAATCGAATATCCTT
62 AACCTTTCCTCAAATCGAAATAATCGAATACCCTT
201241 TTCTCGAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 9 0.11
96 67 0.83
97 5 0.06
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGCGCAACC
TTTCCTCAAATCGAAATAATCGAATACCCTT
Found at i:203322 original size:21 final size:22
Alignment explanation
Indices: 203296--203336 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
203286 TGAGTTTTTT
203296 TTTTATAG-TATTTTTAAATAA
1 TTTTATAGCTATTTTTAAATAA
* *
203317 TTTTATGGCTTTTTTTAAAT
1 TTTTATAGCTATTTTTAAAT
203337 TACAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTTATAGCTATTTTTAAATAA
Found at i:212149 original size:19 final size:19
Alignment explanation
Indices: 212102--212152 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
212092 TTTTTCTTAA
* *
212102 CAAAAATTAAAAAAAAATT
1 CAAAATTTATAAAAAAATT
212121 CAAAATATTTATAAAAAAATT
1 C-AAA-ATTTATAAAAAAATT
212142 CAAAATTTATA
1 CAAAATTTATA
212153 TATATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.29
20 6 0.21
21 14 0.50
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (19 bp):
CAAAATTTATAAAAAAATT
Found at i:212800 original size:36 final size:36
Alignment explanation
Indices: 212760--212828 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
212750 TAAGAACTTA
*
212760 TTATGAGATGTTGA-AAAAAAAAAAGAAATTATAAAT
1 TTATGAGAT-TTGATAAAAAAAAAACAAATTATAAAT
** *
212796 TTATGTTATTTGATAAAAAAAAAACAATTTATA
1 TTATGAGATTTGATAAAAAAAAAACAAATTATA
212829 CACGTACAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 4 0.14
36 24 0.86
ACGTcount: A:0.55, C:0.01, G:0.10, T:0.33
Consensus pattern (36 bp):
TTATGAGATTTGATAAAAAAAAAACAAATTATAAAT
Found at i:214152 original size:14 final size:14
Alignment explanation
Indices: 214120--214157 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
214110 TCTTATTATA
214120 ATATTTATTTGAAT
1 ATATTTATTTGAAT
*
214134 GTATTTTATTT-AAT
1 ATA-TTTATTTGAAT
214148 ATATTTATTT
1 ATATTTATTT
214158 TTCAAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 7 0.33
14 7 0.33
15 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (14 bp):
ATATTTATTTGAAT
Found at i:214581 original size:2 final size:2
Alignment explanation
Indices: 214574--214599 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
214564 ATATCCAAAG
214574 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
214600 TCTTTTCCAC
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:214910 original size:21 final size:20
Alignment explanation
Indices: 214871--214910 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
214861 ATGTATAATT
*
214871 GAAAAGAATATTATATTTTC
1 GAAAAGAATATAATATTTTC
*
214891 GAAAATAATATAATTATTTT
1 GAAAAGAATATAA-TATTTT
214911 TTTCAATCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (20 bp):
GAAAAGAATATAATATTTTC
Found at i:218907 original size:6 final size:6
Alignment explanation
Indices: 218896--218928 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
218886 CCCCCACAAC
218896 CCTATT CCTATT CCTATT CCTATT CCTATT CCT
1 CCTATT CCTATT CCTATT CCTATT CCTATT CCT
218929 GCTGTAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.36, G:0.00, T:0.48
Consensus pattern (6 bp):
CCTATT
Found at i:222677 original size:19 final size:20
Alignment explanation
Indices: 222640--222679 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
222630 TTTTATCGTA
* *
222640 TAAATTCAATTCAATAATTT
1 TAAATCCAATTCAAAAATTT
222660 TAAATCCAA-TCAAAAATTT
1 TAAATCCAATTCAAAAATTT
222679 T
1 T
222680 GAATTGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATCCAATTCAAAAATTT
Found at i:223443 original size:30 final size:31
Alignment explanation
Indices: 223385--223445 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
223375 CAATGACATG
223385 GAAGGCTTAATTGATTTTTTTAATTATTTTA
1 GAAGGCTTAATTGATTTTTTTAATTATTTTA
223416 GAAGGACTTAATTGA-TTTTTTAA-TATTTTA
1 GAAGG-CTTAATTGATTTTTTTAATTATTTTA
223446 TACTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 7 0.24
31 13 0.45
32 9 0.31
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.52
Consensus pattern (31 bp):
GAAGGCTTAATTGATTTTTTTAATTATTTTA
Found at i:236145 original size:62 final size:62
Alignment explanation
Indices: 236066--236189 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 62
236056 AGTGGTACGA
*
236066 GAATTTCCTGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTTCGGAAAGAGAAGTTGAATT
1 GAATTTCCTGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTCCGGAAAGAGAAGTTGAATT
* *
236128 GAATTTCCTGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTCCTGAAATAGAAGTTGAATT
1 GAATTTCCTGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTCCGGAAAGAGAAGTTGAATT
236190 TGGAATTTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.40
Consensus pattern (62 bp):
GAATTTCCTGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTCCGGAAAGAGAAGTTGAATT
Found at i:237744 original size:30 final size:31
Alignment explanation
Indices: 237708--237776 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
237698 CTAGTCACTC
237708 AATTTTAATATA-A-ACTTATTATATATTTTT
1 AATTTTAATATATATACTTATT-TATATTTTT
* *
237738 AATTTTAATATATATATTTATTTGTATTTTT
1 AATTTTAATATATATACTTATTTATATTTTT
*
237769 ACTTTTAA
1 AATTTTAA
237777 AATTTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 12 0.35
31 16 0.47
32 6 0.18
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (31 bp):
AATTTTAATATATATACTTATTTATATTTTT
Found at i:257030 original size:18 final size:18
Alignment explanation
Indices: 257009--257043 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
256999 CTGTTGCTGA
*
257009 TGCTGTTGTTGTTGTTGC
1 TGCTGATGTTGTTGTTGC
257027 TGCTGATGTTGTTGTTG
1 TGCTGATGTTGTTGTTG
257044 AAAGTGCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.09, G:0.34, T:0.54
Consensus pattern (18 bp):
TGCTGATGTTGTTGTTGC
Found at i:259723 original size:24 final size:22
Alignment explanation
Indices: 259691--259740 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
259681 CATTCATCTG
* *
259691 ATATTTTTAAATATTTTTGTATAA
1 ATATATTT-AATATTTTT-TAAAA
259715 ATATATTTAATATTTTTTAAAA
1 ATATATTTAATATTTTTTAAAA
259737 ATAT
1 ATAT
259741 TGATAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 9 0.38
24 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATTTAATATTTTTTAAAA
Found at i:269995 original size:10 final size:11
Alignment explanation
Indices: 269970--270006 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
269960 AAGCTACTTA
269970 TATT-TTAATT
1 TATTATTAATT
269980 TATTATTAATT
1 TATTATTAATT
269991 T-TTATTAATT
1 TATTATTAATT
*
270001 TGTTAT
1 TATTAT
270007 ATACAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TATTATTAATT
Found at i:281675 original size:8 final size:8
Alignment explanation
Indices: 281662--281691 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
281652 AAATTTTTTA
*
281662 TTTAAATT
1 TTTAAAAT
281670 TTTAAAAT
1 TTTAAAAT
281678 TTTAAAAT
1 TTTAAAAT
281686 TTTAAA
1 TTTAAA
281692 TTAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAAAT
Found at i:286514 original size:30 final size:29
Alignment explanation
Indices: 286479--286567 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 29
286469 ATTTTTTTTT
286479 TTTTCCCTCAAAACTTTTATTCTTTCTCAC
1 TTTTCCCT-AAAACTTTTATTCTTTCTCAC
*
286509 TTTTCCGCTAAAACTTTTATTTTTTCTCAC
1 TTTTCC-CTAAAACTTTTATTCTTTCTCAC
* * *
286539 TTTTCCGTTAAAATTTTTACTCTTCTCTC
1 TTTTCC-CTAAAACTTTTATTCTT-TCTC
286568 GTCCCAGTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 46 0.88
31 6 0.12
ACGTcount: A:0.19, C:0.26, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTTCCCTAAAACTTTTATTCTTTCTCAC
Found at i:287160 original size:18 final size:17
Alignment explanation
Indices: 287122--287160 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
287112 TAAAAAAATC
* *
287122 ATATTTTTACATTTAAT
1 ATATTTTTAAATTTAAA
287139 ATATTTTTAAATTTCAAA
1 ATATTTTTAAATTT-AAA
287157 ATAT
1 ATAT
287161 ATAGTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTTTTAAATTTAAA
Found at i:294200 original size:14 final size:14
Alignment explanation
Indices: 294178--294220 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
294168 TTTTTTACAT
294178 AAATAATACAAAAA
1 AAATAATACAAAAA
* *
294192 AAATTATACACCAAA
1 AAATAATACA-AAAA
*
294207 ATATAATACAAAAA
1 AAATAATACAAAAA
294221 TTAAAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAATACAAAAA
Found at i:297568 original size:26 final size:26
Alignment explanation
Indices: 297493--297560 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
297483 TCTGTTTAAA
297493 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAATTTTTATG
297519 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAATTTTTATG
297545 TTTGAATTTATTTAAT
1 TTTGAATTTATTTAAT
297561 GAGGTTTAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (26 bp):
TTTGAATTTATTTAATAATTTTTATG
Found at i:297760 original size:20 final size:20
Alignment explanation
Indices: 297735--297788 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
297725 ATTTAATTGT
*
297735 AAATGAAAAATAATATATAC
1 AAATGAAAAATAAAATATAC
*
297755 AAATGAAAAAAAAAATATAC
1 AAATGAAAAATAAAATATAC
297775 AAATGAAAAATAAA
1 AAATGAAAAATAAA
297789 TTTCAAAGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (20 bp):
AAATGAAAAATAAAATATAC
Found at i:298227 original size:6 final size:6
Alignment explanation
Indices: 298216--298242 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
298206 ATAGTACTAC
298216 GGCTCA GGCTCA GGCTCA GGCTCA GGC
1 GGCTCA GGCTCA GGCTCA GGCTCA GGC
298243 GACTGAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (6 bp):
GGCTCA
Found at i:299586 original size:12 final size:12
Alignment explanation
Indices: 299571--299596 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
299561 CAAATCCAGC
299571 TGCAATCAAGTA
1 TGCAATCAAGTA
299583 TGCAATCAAGTA
1 TGCAATCAAGTA
299595 TG
1 TG
299597 GCATGATGCA
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:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (12 bp):
TGCAATCAAGTA
Found at i:299872 original size:23 final size:25
Alignment explanation
Indices: 299846--299892 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
299836 TTGAGATTAT
299846 CAATTTGT-C-AGAAGTAATTAATA
1 CAATTTGTACTAGAAGTAATTAATA
*
299869 CAATTTTTAACTAGAAGTAATTAA
1 CAATTTGT-ACTAGAAGTAATTAA
299893 AATTCTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
25 1 0.05
26 12 0.60
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (25 bp):
CAATTTGTACTAGAAGTAATTAATA
Found at i:301116 original size:15 final size:17
Alignment explanation
Indices: 301086--301130 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
301076 TTTAAATCCG
* *
301086 TATTAATTTTTTTAAAA
1 TATTTATTTATTTAAAA
301103 T-TTTA-TTATTT-AAA
1 TATTTATTTATTTAAAA
301117 TATTTATTTATTTA
1 TATTTATTTATTTA
301131 CTTAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 9 0.39
17 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTATTTATTTAAAA
Found at i:311993 original size:11 final size:11
Alignment explanation
Indices: 311938--312021 Score: 64
Period size: 11 Copynumber: 7.8 Consensus size: 11
311928 ATATCCAAAT
*
311938 AATAACAATAA
1 AATAATAATAA
311949 AATAATAAT-A
1 AATAATAATAA
* * *
311959 ATTAATTACAA
1 AATAATAATAA
* **
311970 AATGATAGCAA
1 AATAATAATAA
*
311981 AACAATAATAA
1 AATAATAATAA
**
311992 AATAATAGCAA
1 AATAATAATAA
312003 AATAATAA-AA
1 AATAATAATAA
312013 AATAATAAT
1 AATAATAAT
312022 TTTTTTTTTT
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
10 17 0.31
11 38 0.69
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (11 bp):
AATAATAATAA
Found at i:311993 original size:22 final size:21
Alignment explanation
Indices: 311968--312019 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
311958 AATTAATTAC
*
311968 AAAATGATAGCAAAACAATAA
1 AAAATAATAGCAAAACAATAA
*
311989 TAAAATAATAGCAAAATAATAA
1 -AAAATAATAGCAAAACAATAA
312011 AAAATAATA
1 AAAATAATA
312020 ATTTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (21 bp):
AAAATAATAGCAAAACAATAA
Found at i:314190 original size:18 final size:18
Alignment explanation
Indices: 314149--314196 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
314139 TTTGTTGTTT
* **
314149 TAAATTTATTTATTAATT
1 TAAATTTATTTATCAAAA
*
314167 TTAATTTATTTATCAAAA
1 TAAATTTATTTATCAAAA
314185 TAAATTTATTTA
1 TAAATTTATTTA
314197 ATTTAAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTTATTTATCAAAA
Found at i:314957 original size:5 final size:6
Alignment explanation
Indices: 314943--314967 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
314933 AGACTAATTT
314943 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
314968 TTTAAGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:318522 original size:16 final size:19
Alignment explanation
Indices: 318487--318521 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
318477 TGAACAATAC
318487 TAAATATTATATTAAAAAA
1 TAAATATTATATTAAAAAA
318506 TAAATA-TA-ATTAAAAA
1 TAAATATTATATTAAAAA
318522 TTATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAATATTATATTAAAAAA
Found at i:318529 original size:18 final size:17
Alignment explanation
Indices: 318497--318535 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
318487 TAAATATTAT
*
318497 ATTAAAAAATAAATATA
1 ATTAAAAAATAAATAAA
*
318514 ATTAAAAATTATAATAAA
1 ATTAAAAAATA-AATAAA
318532 ATTA
1 ATTA
318536 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTAAAAAATAAATAAA
Found at i:318530 original size:16 final size:17
Alignment explanation
Indices: 318487--318535 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
318477 TGAACAATAC
318487 TAAATATTATATTAAAAAA
1 TAAATA-TA-ATTAAAAAA
*
318506 TAAATATAATTAAAAAT
1 TAAATATAATTAAAAAA
*
318523 TATAATAAAATTA
1 TA-AATATAATTA
318536 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 10 0.37
18 11 0.41
19 6 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAATATAATTAAAAAA
Found at i:319772 original size:86 final size:85
Alignment explanation
Indices: 319591--319750 Score: 272
Period size: 86 Copynumber: 1.9 Consensus size: 85
319581 AAATATAAAA
319591 AATTATAAAAAAAATTATTAATTTTTTAGCAAGTAATAATGAAACTTTATTACGAAAGGTCACTA
1 AATTATAAAAAAAATTATTAATTTTTTAGCAAGTAATAATGAAACTTTATTACGAAAGGTCACTA
*
319656 TTTTATATATATATATATAT
66 TTATATATATATATATATAT
*
319676 AATTATAAAAACAATTATTAATTTTTTTAGCAAGTAATAATGAAACTTTATTACGAAAGGT-A-T
1 AATTATAAAAAAAATTATTAA-TTTTTTAGCAAGTAATAATGAAACTTTATTACGAAAGGTCACT
319739 A-TATATATATAT
65 ATTATATATATAT
319751 TTTTTTTTTG
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
83 10 0.14
84 2 0.03
85 21 0.29
86 39 0.54
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (85 bp):
AATTATAAAAAAAATTATTAATTTTTTAGCAAGTAATAATGAAACTTTATTACGAAAGGTCACTA
TTATATATATATATATATAT
Found at i:320286 original size:21 final size:21
Alignment explanation
Indices: 320260--320304 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
320250 TCTGACATTA
*
320260 TTTTTAATAATT-TTAATAAT
1 TTTTTTATAATTCTTAATAAT
*
320280 TTTTTTATAATTCTTAATACT
1 TTTTTTATAATTCTTAATAAT
320301 TTTT
1 TTTT
320305 AAATAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTATAATTCTTAATAAT
Found at i:320289 original size:20 final size:21
Alignment explanation
Indices: 320260--320311 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
320250 TCTGACATTA
320260 TTTTTAATAATT-TTAATAAT
1 TTTTTAATAATTCTTAATAAT
* *
320280 TTTTTTATAATTCTTAATACT
1 TTTTTAATAATTCTTAATAAT
*
320301 TTTTAAATAAT
1 TTTTTAATAAT
320312 CTTCAGCCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTAATAATTCTTAATAAT
Found at i:320310 original size:21 final size:19
Alignment explanation
Indices: 320259--320311 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
320249 TTCTGACATT
320259 ATTTTTAATAATTTTAATA
1 ATTTTTAATAATTTTAATA
*
320278 ATTTTTTTATAATTCTTAATA
1 A-TTTTTAATAATT-TTAATA
*
320299 CTTTTTAAATAAT
1 ATTTTT-AATAAT
320312 CTTCAGCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.04
20 16 0.57
21 11 0.39
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTAATAATTTTAATA
Found at i:320765 original size:5 final size:5
Alignment explanation
Indices: 320757--320784 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
320747 AATTCAATTA
320757 ATTCG ATTCG ATTCG ATTCG ATTCG ATT
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATT
320785 AACCTATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (5 bp):
ATTCG
Found at i:343715 original size:17 final size:17
Alignment explanation
Indices: 343693--343725 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
343683 TTCATCATTA
343693 AAATTAAATACCCAGGG
1 AAATTAAATACCCAGGG
*
343710 AAATTAAATATCCAGG
1 AAATTAAATACCCAGG
343726 AATTTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.21
Consensus pattern (17 bp):
AAATTAAATACCCAGGG
Found at i:347079 original size:5 final size:5
Alignment explanation
Indices: 347069--347094 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
347059 TGTACACCAT
347069 CCTAC CCTAC CCTAC CCTAC CCTAC C
1 CCTAC CCTAC CCTAC CCTAC CCTAC C
347095 ACATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.62, G:0.00, T:0.19
Consensus pattern (5 bp):
CCTAC
Found at i:351384 original size:160 final size:160
Alignment explanation
Indices: 351120--351443 Score: 630
Period size: 160 Copynumber: 2.0 Consensus size: 160
351110 TCAGGTAATC
351120 ACAAGTGTTTTCCCTATAAGACTAAGCACATCACATAATCCCACAAATAATGAGGAATCAAGAAG
1 ACAAGTGTTTTCCCTATAAGACTAAGCACATCACATAATCCCACAAATAATGAGGAATCAAGAAG
*
351185 ACAAGAAACCACAACAATCATTTTAAGGAGAAGGTTAAGGATTACACAAGTATCTAGTTTGAAAG
66 ACAAGAAACCACAACAATCATTTTAAAGAGAAGGTTAAGGATTACACAAGTATCTAGTTTGAAAG
351250 TTAAACACTGCACAGTACAAAACTATTGCT
131 TTAAACACTGCACAGTACAAAACTATTGCT
351280 ACAAGTGTTTTCCCTATAAGACTAAGCACATCACATAATCCCACAAATAATGAGGAATCAAGAAG
1 ACAAGTGTTTTCCCTATAAGACTAAGCACATCACATAATCCCACAAATAATGAGGAATCAAGAAG
351345 ACAAGAAACCACAACAATCATTTTAAAGAGAAGGTTAAGGATTACACAAGTATCTAGTTTGAAAG
66 ACAAGAAACCACAACAATCATTTTAAAGAGAAGGTTAAGGATTACACAAGTATCTAGTTTGAAAG
*
351410 TTAAACACTGCACAGTGCAAAACTATTGCT
131 TTAAACACTGCACAGTACAAAACTATTGCT
351440 ACAA
1 ACAA
351444 TTGAATAATT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (160 bp):
ACAAGTGTTTTCCCTATAAGACTAAGCACATCACATAATCCCACAAATAATGAGGAATCAAGAAG
ACAAGAAACCACAACAATCATTTTAAAGAGAAGGTTAAGGATTACACAAGTATCTAGTTTGAAAG
TTAAACACTGCACAGTACAAAACTATTGCT
Found at i:353888 original size:3 final size:3
Alignment explanation
Indices: 353880--353905 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
353870 TGCAGAGGCA
353880 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
353906 AATTTGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:353996 original size:6 final size:6
Alignment explanation
Indices: 353985--354018 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
353975 GGTGAAAGCA
353985 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGG
1 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGG
354019 GAGGGTGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.00, G:0.53, T:0.32
Consensus pattern (6 bp):
TGGGAT
Found at i:366660 original size:16 final size:16
Alignment explanation
Indices: 366636--366669 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
366626 AAAACTTTAA
366636 TTAAATTAAATCATTT
1 TTAAATTAAATCATTT
* *
366652 TTAATTTAAATTATTT
1 TTAAATTAAATCATTT
366668 TT
1 TT
366670 GTATGATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAATTAAATCATTT
Found at i:370863 original size:24 final size:25
Alignment explanation
Indices: 370817--370863 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
370807 TTTAAAATTT
*
370817 ATAATTTTTATATAAAATATAAATG
1 ATAATTTTTATAAAAAATATAAATG
370842 ATAA-TTTTATTAAAAAAT-TAAA
1 ATAATTTTTA-TAAAAAATATAAA
370864 AAAAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATAATTTTTATAAAAAATATAAATG
Found at i:373805 original size:11 final size:11
Alignment explanation
Indices: 373789--373818 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
373779 GGCTATATAT
373789 AATACTAATAC
1 AATACTAATAC
373800 AATACTAATAC
1 AATACTAATAC
373811 AATACTAA
1 AATACTAA
373819 AGTATCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (11 bp):
AATACTAATAC
Found at i:378392 original size:16 final size:16
Alignment explanation
Indices: 378348--378397 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
378338 GGCGGAATGG
378348 TAAAATTTT-AATTTA
1 TAAAATTTTAAATTTA
* *
378363 -GATATTTTATAATTTA
1 TAAAATTTTA-AATTTA
*
378379 TAAAATTTTAAATTAA
1 TAAAATTTTAAATTTA
378395 TAA
1 TAA
378398 TGATAAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Found at i:392250 original size:18 final size:18
Alignment explanation
Indices: 392229--392264 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
392219 ACAACATTTG
* *
392229 TATAATATTATTGAAATA
1 TATAAAATTATTAAAATA
392247 TATAAAATTATTAAAATA
1 TATAAAATTATTAAAATA
392265 AAATTTTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TATAAAATTATTAAAATA
Found at i:407783 original size:14 final size:14
Alignment explanation
Indices: 407764--407794 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
407754 ATGTATCAGC
407764 CTTAGTTCCATCAT
1 CTTAGTTCCATCAT
407778 CTTAGTTCCATCAT
1 CTTAGTTCCATCAT
407792 CTT
1 CTT
407795 GCTATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.45
Consensus pattern (14 bp):
CTTAGTTCCATCAT
Found at i:408564 original size:16 final size:17
Alignment explanation
Indices: 408540--408586 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
408530 TATAAATTAC
408540 ATAACATATAAAAATAAT
1 ATAA-ATATAAAAATAAT
*
408558 AT-AATAT-AAAATATT
1 ATAAATATAAAAATAAT
*
408573 ATAAATTTAAAAAT
1 ATAAATATAAAAAT
408587 CAGTTAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 6 0.24
18 2 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAAATATAAAAATAAT
Found at i:411167 original size:6 final size:6
Alignment explanation
Indices: 411156--411194 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
411146 TTTCGATGCA
*
411156 CCATCT CCATCT CCGTCT CCATCT CCATCT CCATCT CCA
1 CCATCT CCATCT CCATCT CCATCT CCATCT CCATCT CCA
411195 ACTTCTCTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.51, G:0.03, T:0.31
Consensus pattern (6 bp):
CCATCT
Found at i:418680 original size:126 final size:126
Alignment explanation
Indices: 418455--418838 Score: 680
Period size: 126 Copynumber: 3.0 Consensus size: 126
418445 ACAAATGCAT
* *
418455 ATTACTCAATTGATAATCCAAAAGCGGGT-AAGCAGGTGAGGCACTTCCCGTATTTGCTGCTAAG
1 ATTACTCAACTGATAATCCAAAGGCGGGTAAAG-AGGTGAGGCACTTCCCGTATTTGCTGCTAAG
418519 GAACTTGTATTGTCTTGCCTGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGGGCTCGGA
65 GAACTTGTATTGTCTTGCCTGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGGGCTCGGA
*
418581 ATTACTCAACTGATTATCCAAAGGCGGGTAAAGAGGTGAGGCACTTCCCGTATTTGCTGCTAAGG
1 ATTACTCAACTGATAATCCAAAGGCGGGTAAAGAGGTGAGGCACTTCCCGTATTTGCTGCTAAGG
418646 AACTTGTATTGTCTTGCCTGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGGGCTCGGA
66 AACTTGTATTGTCTTGCCTGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGGGCTCGGA
*
418707 ATTACTCAACTGATAATCCAAAGGCGGGTAAAGAGGTGAGGCACTTCCCGTATTTGCTGCTAATG
1 ATTACTCAACTGATAATCCAAAGGCGGGTAAAGAGGTGAGGCACTTCCCGTATTTGCTGCTAAGG
* * * *
418772 AACTTGTACTGTCTTGCCGGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGAGCTCAGA
66 AACTTGTATTGTCTTGCCTGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGGGCTCGGA
418833 ATTACT
1 ATTACT
418839 TTCAGGAGGA
Statistics
Matches: 248, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
126 245 0.99
127 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (126 bp):
ATTACTCAACTGATAATCCAAAGGCGGGTAAAGAGGTGAGGCACTTCCCGTATTTGCTGCTAAGG
AACTTGTATTGTCTTGCCTGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGGGCTCGGA
Found at i:420450 original size:15 final size:17
Alignment explanation
Indices: 420420--420451 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
420410 TTTGTGAAAT
420420 TTTTATAATATTTTAAA
1 TTTTATAATATTTTAAA
420437 TTTTAT-AT-TTTTAAA
1 TTTTATAATATTTTAAA
420452 AATGATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTATAATATTTTAAA
Found at i:431285 original size:19 final size:21
Alignment explanation
Indices: 431257--431295 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
431247 ATATGTATAA
431257 AAATTATATATTTAA-AATAT
1 AAATTATATATTTAAGAATAT
431277 AAATT-TATATTTAAGAATA
1 AAATTATATATTTAAGAATA
431296 ACATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
AAATTATATATTTAAGAATAT
Found at i:431382 original size:22 final size:22
Alignment explanation
Indices: 431355--431399 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
431345 ATAAAAAATG
*
431355 TGTATTATTCT-AAGGTTTCATA
1 TGTATTATACTGAA-GTTTCATA
431377 TGTATTATACTGAAGTTTCATA
1 TGTATTATACTGAAGTTTCATA
431399 T
1 T
431400 AAAAACTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (22 bp):
TGTATTATACTGAAGTTTCATA
Found at i:437367 original size:42 final size:42
Alignment explanation
Indices: 437286--437367 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
437276 TTACTTTCAG
* ** *
437286 GAGGAGGATATTGCGCAGGTTTTTGATAAGAGGATGATGACT
1 GAGGAGGATATTGCGCAGGCTGCTGATAAGAGGAGGATGACT
*
437328 GAGGAGGATATTGTGCAGGCTGCTGATAAGTA-GAGGATGA
1 GAGGAGGATATTGCGCAGGCTGCTGATAAG-AGGAGGATGA
437368 TTGCGTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.38, T:0.26
Consensus pattern (42 bp):
GAGGAGGATATTGCGCAGGCTGCTGATAAGAGGAGGATGACT
Found at i:442847 original size:2 final size:2
Alignment explanation
Indices: 442840--442871 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
442830 TTTATTGGCA
442840 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
442872 TATGCTTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:454088 original size:22 final size:22
Alignment explanation
Indices: 454063--454105 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
454053 TCTTTTTGTT
454063 TTGCTACAATTTCACTATTATG
1 TTGCTACAATTTCACTATTATG
* * *
454085 TTGCTACTATTTTACTGTTAT
1 TTGCTACAATTTCACTATTAT
454106 TGTTTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.51
Consensus pattern (22 bp):
TTGCTACAATTTCACTATTATG
Found at i:462991 original size:25 final size:27
Alignment explanation
Indices: 462963--463013 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
462953 AATTTAAAAA
462963 AAATTGTAAT-ATTTT-TTTCTTTCAC
1 AAATTGTAATCATTTTGTTTCTTTCAC
* *
462988 AAATTTTAATCATTTTGTTTTTTTCA
1 AAATTGTAATCATTTTGTTTCTTTCA
463014 TACACTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 5 0.23
27 8 0.36
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.59
Consensus pattern (27 bp):
AAATTGTAATCATTTTGTTTCTTTCAC
Done.