Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004150.1 Hibiscus syriacus cultivar Beakdansim tig00009078_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: 158864
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:17172 original size:17 final size:18
Alignment explanation
Indices: 17147--17180 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17137 AAAATGGTGT
*
17147 ATTCTTCTTTTTGGTTTG
1 ATTCTTCTTTTAGGTTTG
17165 ATTC-TCTTTTAGGTTT
1 ATTCTTCTTTTAGGTTT
17181 TCAAATAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.09, C:0.12, G:0.15, T:0.65
Consensus pattern (18 bp):
ATTCTTCTTTTAGGTTTG
Found at i:20584 original size:29 final size:29
Alignment explanation
Indices: 20542--20627 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
20532 AGTATTGGCC
20542 GTAGGTCGCCATGCACTCTGGGCGACCTT
1 GTAGGTCGCCATGCACTCTGGGCGACCTT
20571 GTAGGTCGCCATGCACTCCT-GGCGACCTT
1 GTAGGTCGCCATGCACT-CTGGGCGACCTT
* *
20600 GTAGGCCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCTGGGCGACCT
20628 ACCCTTGCTC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.02
29 50 0.94
30 2 0.04
ACGTcount: A:0.14, C:0.35, G:0.30, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCTGGGCGACCTT
Found at i:20765 original size:33 final size:33
Alignment explanation
Indices: 20728--20802 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
20718 CGCTCGGCTT
* * *
20728 CCCTCGGATTCCCTCTCATAGCTCGTTCGGTTG
1 CCCTCGGATGCCCTCACATAGCTCGTTCGGATG
20761 CCCTCGGATGCCCTCACATAGCTCGTTCGGATG
1 CCCTCGGATGCCCTCACATAGCTCGTTCGGATG
*
20794 GCCTCGGAT
1 CCCTCGGAT
20803 CTCTCGGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.12, C:0.36, G:0.24, T:0.28
Consensus pattern (33 bp):
CCCTCGGATGCCCTCACATAGCTCGTTCGGATG
Found at i:20772 original size:10 final size:10
Alignment explanation
Indices: 20754--20839 Score: 57
Period size: 10 Copynumber: 8.4 Consensus size: 10
20744 CATAGCTCGT
*
20754 TCGGTTGCCC
1 TCGGATGCCC
20764 TCGGATGCCC
1 TCGGATGCCC
** *
20774 TCACATAGCTCGT
1 TCGGAT-GC-C-C
*
20787 TCGGATGGCC
1 TCGGATGCCC
*
20797 TCGGAT-CTC
1 TCGGATGCCC
*
20806 TCGGATGGCC
1 TCGGATGCCC
*
20816 TCGGATGCTC
1 TCGGATGCCC
*
20826 TCGGATGGCC
1 TCGGATGCCC
20836 TCGG
1 TCGG
20840 TCGAATGGCC
Statistics
Matches: 56, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
9 7 0.12
10 40 0.71
11 3 0.05
12 2 0.04
13 4 0.07
ACGTcount: A:0.10, C:0.33, G:0.31, T:0.26
Consensus pattern (10 bp):
TCGGATGCCC
Found at i:20811 original size:19 final size:20
Alignment explanation
Indices: 20787--20839 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
20777 CATAGCTCGT
20787 TCGGATGGCCTCGGAT-CTC
1 TCGGATGGCCTCGGATGCTC
20806 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
20826 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
20840 TCGAATGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.09, C:0.30, G:0.36, T:0.25
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:20849 original size:14 final size:14
Alignment explanation
Indices: 20830--20865 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
20820 ATGCTCTCGG
20830 ATGGCCTCGGTCGA
1 ATGGCCTCGGTCGA
*
20844 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGA
20858 ATGGCCTC
1 ATGGCCTC
20866 AGATGCCCAT
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:0.11, C:0.31, G:0.36, T:0.22
Consensus pattern (14 bp):
ATGGCCTCGGTCGA
Found at i:20947 original size:29 final size:29
Alignment explanation
Indices: 20910--20967 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
20900 GCAATCTCTT
*
20910 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
20939 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
20968 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:21183 original size:2 final size:2
Alignment explanation
Indices: 21178--21215 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
21168 CTCGATTTTA
21178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21216 TGTCGCAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21690 original size:10 final size:10
Alignment explanation
Indices: 21675--21699 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
21665 TAAATCAAAG
21675 ATAAAGAAAA
1 ATAAAGAAAA
21685 ATAAAGAAAA
1 ATAAAGAAAA
21695 ATAAA
1 ATAAA
21700 TAATAGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (10 bp):
ATAAAGAAAA
Found at i:21716 original size:15 final size:14
Alignment explanation
Indices: 21662--21718 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
21652 AAATATGAGT
21662 AAATAAATCAAAGATA
1 AAATAAAT-AAAGA-A
*
21678 AAGAAAAATAAAGAA
1 AA-ATAAATAAAGAA
*
21693 AAATAAATAATAGAT
1 AAATAAATAA-AGAA
*
21708 AACTAAATAAA
1 AAATAAATAAA
21719 TAAGATGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 8 0.23
15 15 0.43
16 7 0.20
17 5 0.14
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.18
Consensus pattern (14 bp):
AAATAAATAAAGAA
Found at i:22107 original size:2 final size:2
Alignment explanation
Indices: 22100--22136 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22090 ATAAAATACG
22100 AT AT AT AT AT AT 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 AT AT AT A
22137 AAAAAATAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23514 original size:20 final size:20
Alignment explanation
Indices: 23490--23528 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
23480 ATAAATATAT
*
23490 AATATA-ATT-TATAATATA
1 AATATATATTATATAACATA
23508 AATATATATTATATAACATA
1 AATATATATTATATAACATA
23528 A
1 A
23529 GGACGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATATATTATATAACATA
Found at i:23556 original size:2 final size:2
Alignment explanation
Indices: 23549--23597 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
23539 TAGTGTATTC
23549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23591 AT AT AT A
1 AT AT AT A
23598 ACTCGAGATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24023 original size:23 final size:24
Alignment explanation
Indices: 23979--24023 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
23969 TAAATTAATC
*
23979 GAAAAATAATGTAAACATCTAAAT
1 GAAAAATAATGTAAACAGCTAAAT
24003 GAAAAA-AATGTATAA-AGCTAA
1 GAAAAATAATGTA-AACAGCTAA
24024 TACTAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.22
Consensus pattern (24 bp):
GAAAAATAATGTAAACAGCTAAAT
Found at i:30319 original size:19 final size:19
Alignment explanation
Indices: 30292--30329 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
30282 ACGTTTTTCA
*
30292 AACTCTCGCAACACATTTT
1 AACTATCGCAACACATTTT
30311 AACTATCGCAACACATTTT
1 AACTATCGCAACACATTTT
30330 TCAAAATCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (19 bp):
AACTATCGCAACACATTTT
Found at i:44389 original size:5 final size:5
Alignment explanation
Indices: 44341--44370 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
44331 AAATTGATTG
44341 AAATA AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA
44371 GTGAATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:45269 original size:23 final size:23
Alignment explanation
Indices: 45242--45305 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
45232 CAGCTGCCAC
45242 GTCAGCTGTCACATCATCACCAT
1 GTCAGCTGTCACATCATCACCAT
*
45265 GTCAGCTATCACATCATCACCAT
1 GTCAGCTGTCACATCATCACCAT
*
45288 GTCAGCTGCCACATCATC
1 GTCAGCTGTCACATCATC
45306 CGCTGACTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.27, C:0.36, G:0.12, T:0.25
Consensus pattern (23 bp):
GTCAGCTGTCACATCATCACCAT
Found at i:48299 original size:21 final size:20
Alignment explanation
Indices: 48267--48314 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
48257 CGAGTTTCTG
* *
48267 TTTAAATTTAATTGTAAA-TA
1 TTTATATTTAATT-TAAACGA
48287 TTTATATTCTAATTTAAACGA
1 TTTATATT-TAATTTAAACGA
48308 TTTATAT
1 TTTATAT
48315 AATCATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTATATTTAATTTAAACGA
Found at i:50048 original size:29 final size:29
Alignment explanation
Indices: 50007--50072 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
49997 ACTAATGCAT
* * * *
50007 TCTTGATTATGCATGGGATTAAT-TCCCCG
1 TCTTGTTTATGCACGAGATT-ATGTCCCCA
*
50036 TCTTGTTTTTGCACGAGATTATGTCCCCA
1 TCTTGTTTATGCACGAGATTATGTCCCCA
50065 TCTTGTTT
1 TCTTGTTT
50073 CTGTTTGAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.06
29 29 0.94
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (29 bp):
TCTTGTTTATGCACGAGATTATGTCCCCA
Found at i:59869 original size:32 final size:31
Alignment explanation
Indices: 59815--59920 Score: 158
Period size: 32 Copynumber: 3.3 Consensus size: 31
59805 CTTTATTTTG
* *
59815 TTCGGGTCGGTCGGTTTTTTTAAGTGTGATG
1 TTCGGGTCGGTCAGTTTTTTTAAGTGTGATA
59846 TTCGGGTCGAGTCAGTTTTTTTAAGTGTGATA
1 TTCGGGTCG-GTCAGTTTTTTTAAGTGTGATA
*
59878 TTCGGGTCGGATCGATTTTTTTTAAGTGTGATA
1 TTCGGGTCGG-TC-AGTTTTTTTAAGTGTGATA
59911 TTCGGGTCGG
1 TTCGGGTCGG
59921 GTCGGGTCGG
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
31 10 0.14
32 31 0.45
33 28 0.41
ACGTcount: A:0.14, C:0.10, G:0.32, T:0.43
Consensus pattern (31 bp):
TTCGGGTCGGTCAGTTTTTTTAAGTGTGATA
Found at i:59898 original size:33 final size:33
Alignment explanation
Indices: 59815--59920 Score: 157
Period size: 33 Copynumber: 3.3 Consensus size: 33
59805 CTTTATTTTG
*
59815 TTCGGGTCGG-TCG-GTTTTTTTAAGTGTGATG
1 TTCGGGTCGGATCGAGTTTTTTTAAGTGTGATA
59846 TTCGGGTC-GAGTC-AGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGA-TCGAGTTTTTTTAAGTGTGATA
*
59878 TTCGGGTCGGATCGATTTTTTTTAAGTGTGATA
1 TTCGGGTCGGATCGAGTTTTTTTAAGTGTGATA
59911 TTCGGGTCGG
1 TTCGGGTCGG
59921 GTCGGGTCGG
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
30 1 0.01
31 8 0.12
32 29 0.43
33 30 0.44
ACGTcount: A:0.14, C:0.10, G:0.32, T:0.43
Consensus pattern (33 bp):
TTCGGGTCGGATCGAGTTTTTTTAAGTGTGATA
Found at i:62082 original size:2 final size:2
Alignment explanation
Indices: 62075--62103 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62065 ATATGATAAT
62075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62104 GAGTAGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68203 original size:15 final size:16
Alignment explanation
Indices: 68178--68211 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
68168 GACAATGTCT
*
68178 GTTTGGGGTGCTGCTG
1 GTTTGGGGTGCCGCTG
68194 GTTT-GGGTGCCGCTG
1 GTTTGGGGTGCCGCTG
68209 GTT
1 GTT
68212 CCATTGGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.00, C:0.15, G:0.47, T:0.38
Consensus pattern (16 bp):
GTTTGGGGTGCCGCTG
Found at i:74373 original size:3 final size:3
Alignment explanation
Indices: 74367--74391 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
74357 AAATCATCAA
74367 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
74392 TTATTATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:77252 original size:13 final size:13
Alignment explanation
Indices: 77231--77266 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
77221 ACCGGTCATA
*
77231 ACCCGACCCGTTT
1 ACCCGACCCGTTG
*
77244 ACCCAACCCGTTG
1 ACCCGACCCGTTG
77257 ACCCGACCCG
1 ACCCGACCCG
77267 ACCCGTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.50, G:0.17, T:0.14
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:77269 original size:31 final size:31
Alignment explanation
Indices: 77231--77290 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
77221 ACCGGTCATA
*
77231 ACCCGACCCGTTTACCCAACCCGTTGACCCG
1 ACCCGACCCGTTAACCCAACCCGTTGACCCG
*
77262 ACCCGACCCGTTAACCCGACCCGTTGACC
1 ACCCGACCCGTTAACCCAACCCGTTGACC
77291 GTTGACCGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.48, G:0.17, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGTTAACCCAACCCGTTGACCCG
Found at i:77278 original size:13 final size:13
Alignment explanation
Indices: 77229--77286 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 13
77219 TGACCGGTCA
77229 TAACCCGACCCGT
1 TAACCCGACCCGT
* *
77242 TTACCCAACCCGT
1 TAACCCGACCCGT
77255 TGACCCGACCCGACCCGT
1 T-A----ACCCGACCCGT
77273 TAACCCGACCCGT
1 TAACCCGACCCGT
77286 T
1 T
77287 GACCGTTGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
13 24 0.67
17 1 0.03
18 11 0.31
ACGTcount: A:0.21, C:0.47, G:0.16, T:0.17
Consensus pattern (13 bp):
TAACCCGACCCGT
Found at i:77284 original size:18 final size:18
Alignment explanation
Indices: 77244--77284 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
77234 CGACCCGTTT
* *
77244 ACCCAACCCGTTGACCCG
1 ACCCGACCCGTTAACCCG
77262 ACCCGACCCGTTAACCCG
1 ACCCGACCCGTTAACCCG
77280 ACCCG
1 ACCCG
77285 TTGACCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.51, G:0.17, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGTTAACCCG
Found at i:79859 original size:48 final size:48
Alignment explanation
Indices: 79807--79901 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
79797 TTCGATTTAA
*
79807 ATTCTGATCTGATACTTGACATGGATTTTGATATGATATTTGACATGG
1 ATTCTGATCTGATACTTGACATGGATTTTGATATGATACTTGACATGG
* * *
79855 ATTCTGTTCTGATATTTGACCTGGATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATGGATTTTGATATGATACTTGACATG
79902 AATTATGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (48 bp):
ATTCTGATCTGATACTTGACATGGATTTTGATATGATACTTGACATGG
Found at i:79921 original size:24 final size:24
Alignment explanation
Indices: 79811--79901 Score: 119
Period size: 24 Copynumber: 3.8 Consensus size: 24
79801 ATTTAAATTC
* *
79811 TGATCTGATACTTGACATGGATTT
1 TGATATGATATTTGACATGGATTT
*
79835 TGATATGATATTTGACATGGATTC
1 TGATATGATATTTGACATGGATTT
* * *
79859 TGTTCTGATATTTGACCTGGATTT
1 TGATATGATATTTGACATGGATTT
*
79883 TGATATGATACTTGACATG
1 TGATATGATATTTGACATG
79902 AATTATGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (24 bp):
TGATATGATATTTGACATGGATTT
Found at i:79921 original size:48 final size:48
Alignment explanation
Indices: 79814--79921 Score: 153
Period size: 48 Copynumber: 2.2 Consensus size: 48
79804 TAAATTCTGA
* * * *
79814 TCTGATACTTGACATGGATTTTGATATGATATTTGACATGGATTCTGT
1 TCTGATATTTGACATGGATTTTGATATGATACTTGACATGAATTATGT
*
79862 TCTGATATTTGACCTGGATTTTGATATGATACTTGACATGAATTATGT
1 TCTGATATTTGACATGGATTTTGATATGATACTTGACATGAATTATGT
* *
79910 TTTGATTTTTGA
1 TCTGATATTTGA
79922 TATATCCGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.46
Consensus pattern (48 bp):
TCTGATATTTGACATGGATTTTGATATGATACTTGACATGAATTATGT
Found at i:83579 original size:12 final size:12
Alignment explanation
Indices: 83497--83584 Score: 56
Period size: 12 Copynumber: 7.3 Consensus size: 12
83487 GAATTCTGAT
83497 ATGATACTTGAC
1 ATGATACTTGAC
* *
83509 ATGGATTC-TGAT
1 AT-GATACTTGAC
*
83521 ATGATATTTGAC
1 ATGATACTTGAC
* *
83533 ATGGATTC-TGAT
1 AT-GATACTTGAC
83545 ATGATACTTGAC
1 ATGATACTTGAC
* * *
83557 CTGGAT-TTTGAT
1 AT-GATACTTGAC
83569 ATGATACTTGAC
1 ATGATACTTGAC
83581 ATGA
1 ATGA
83585 ATTATGTTTT
Statistics
Matches: 54, Mismatches: 16, Indels: 12
0.66 0.20 0.15
Matches are distributed among these distances:
11 10 0.19
12 34 0.63
13 10 0.19
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (12 bp):
ATGATACTTGAC
Found at i:83597 original size:24 final size:24
Alignment explanation
Indices: 83489--83583 Score: 163
Period size: 24 Copynumber: 4.0 Consensus size: 24
83479 TTCGATTTGA
83489 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
83513 ATTCTGATATGATATTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
83537 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
83561 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
83584 AATTATGTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:83760 original size:43 final size:43
Alignment explanation
Indices: 83699--83793 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
83689 GGGCCTTACT
* *
83699 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTAGGTGTATGGTTCTGGGAAACCTACACATTA
83742 TGGTGTGTTGGTAGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTAGGTGTATGGTTCTGGGAAACCTACACATTA
83785 TGGTGTGTT
1 TGGTGTGTT
83794 CGGTTGGAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTAGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:89862 original size:6 final size:6
Alignment explanation
Indices: 89853--89877 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
89843 TCGAAGGTTT
89853 TCAACA TCAACA TCAACA TCAACA T
1 TCAACA TCAACA TCAACA TCAACA T
89878 TTGGATCAAC
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:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (6 bp):
TCAACA
Found at i:90928 original size:242 final size:240
Alignment explanation
Indices: 90353--91083 Score: 1079
Period size: 242 Copynumber: 3.0 Consensus size: 240
90343 CTAATTTCCA
* * * * * *
90353 GCCCAATACCTCAATAATTTCACCATTACCACTTAACTAACTAACTAACTTTATCAATACTTGCT
1 GCCCAATACCTCAATAATTCCACCATTACCACTTAAGT--C--ACTAACTTTCTCAATATTTACA
*
90418 ATTTAGTACTCAAACTTTGCCAACTTTCCAAAATAGTCCAATTTCACATTCTAACATTAAATTCA
62 ATTTAGTACTCAAACTTTGCCAACTTCCCAAAATAGTCCAATTTCACATTCTAACATTAAATTCA
* * * **
90483 ACAATCTAACATTAATTTTTAGCATAGTACAATAACTATTTAACAATTACACATCAACCTTATAA
127 ACAATCTAACATTAATTTATAGTATAGTACAACAACTATTTAACAATTACACATCAACCACATAA
** * *
90548 C--TTTAAAATTGTAGAATAGGTCCTCCAACTTTCATAAAATTAAAAATTG
192 CTTTTTAAAATTCCA-AATAGGTCCTCTAACTTTCAT-AAATTACAAATTG
*
90597 GCCCAATACCTCAATAATTCCACCATTACCACTTAAGTCACTAACTTTCTCAATATTTACCATTT
1 GCCCAATACCTCAATAATTCCACCATTACCACTTAAGTCACTAACTTTCTCAATATTTACAATTT
*
90662 AGTACTCAAACTTTGCCAACTTCCCAAAATAGTCCAATTTCACATTCTAACATTAAATTCAACCA
66 AGTACTCAAACTTTGCCAACTTCCCAAAATAGTCCAATTTCACATTCTAACATTAAATTCAACAA
* * * *
90727 TCTAACATTAATTTACAATATGGTACAACAACTATTTAACAATTACACATCAACCCCATAACTTT
131 TCTAACATTAATTTATAGTATAGTACAACAACTATTTAACAATTACACATCAACCACATAACTTT
* *
90792 TTTAAATTACCAAATAGGTTCTCTAACTTTCATAATATTACAAATTG
196 TTAAAATT-CCAAATAGGTCCTCTAACTTTCATAA-ATTACAAATTG
* ** *
90839 GCCTAATACCTTTATAATTCCACCATTACCACTTAAGTCACTAACTTTCTCAATATTTTCAATTT
1 GCCCAATACCTCAATAATTCCACCATTACCACTTAAGTCACTAACTTTCTCAATATTTACAATTT
* *
90904 AGTACTCAAACTTTGCCGACTTCCCAAAATAGTCTAATTTCACATTCTAACATTAAATTCAACAA
66 AGTACTCAAACTTTGCCAACTTCCCAAAATAGTCCAATTTCACATTCTAACATTAAATTCAACAA
* *
90969 TCTAACATTAATTTATAGTATAGTGCACCAACTATTTAACAATTACACATCAACCACATAACTTT
131 TCTAACATTAATTTATAGTATAGTACAACAACTATTTAACAATTACACATCAACCACATAACTTT
91034 TTAAAATTTCCAAATAGGTCCTCTAACTTTCATAAATTACAAATTG
196 TTAAAA-TTCCAAATAGGTCCTCTAACTTTCATAAATTACAAATTG
91080 GCCC
1 GCCC
91084 CAAAATTTTT
Statistics
Matches: 443, Mismatches: 39, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
240 139 0.31
241 16 0.04
242 249 0.56
243 3 0.01
244 36 0.08
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (240 bp):
GCCCAATACCTCAATAATTCCACCATTACCACTTAAGTCACTAACTTTCTCAATATTTACAATTT
AGTACTCAAACTTTGCCAACTTCCCAAAATAGTCCAATTTCACATTCTAACATTAAATTCAACAA
TCTAACATTAATTTATAGTATAGTACAACAACTATTTAACAATTACACATCAACCACATAACTTT
TTAAAATTCCAAATAGGTCCTCTAACTTTCATAAATTACAAATTG
Found at i:92928 original size:2 final size:2
Alignment explanation
Indices: 92921--92992 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
92911 TCTCTTAGAC
92921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92963 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
92993 TCACATGTTC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93345 original size:18 final size:18
Alignment explanation
Indices: 93324--93358 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
93314 TCCCATCTAG
93324 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
93342 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
93359 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:93946 original size:64 final size:66
Alignment explanation
Indices: 93852--93974 Score: 198
Period size: 64 Copynumber: 1.9 Consensus size: 66
93842 ATGAAGGTAT
*
93852 GCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTTAATGGGGA
1 GCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGGGA
93916 A
66 A
*
93917 GCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
1 GCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
93975 ATTCATGCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
63 1 0.02
64 30 0.56
65 23 0.43
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (66 bp):
GCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGGGA
A
Found at i:93985 original size:64 final size:62
Alignment explanation
Indices: 93850--94010 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 62
93840 TAATGAAGGT
* * *
93850 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
* *
93915 AAGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGC
* *
93979 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
94011 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:95793 original size:2 final size:2
Alignment explanation
Indices: 95786--95829 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
95776 CTCCACTTTC
95786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
95828 AT
1 AT
95830 CTTTAACTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97431 original size:23 final size:23
Alignment explanation
Indices: 97405--97449 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
97395 CACCACAGCT
*
97405 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
97428 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
97450 ATATAATAAT
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:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:97696 original size:148 final size:149
Alignment explanation
Indices: 97417--97730 Score: 517
Period size: 148 Copynumber: 2.1 Consensus size: 149
97407 TATAATTGCA
*
97417 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
**
97481 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
97546 CCACAGAATATATATATATC
130 CCAAAGAATATATATATATC
* *
97566 CCGTAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA-
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
97630 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACTAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
*
97694 CCAAAGAATATATATATGTC
130 CCAAAGAATATATATATATC
97714 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
97731 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
148 94 0.61
149 60 0.39
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:98284 original size:2 final size:2
Alignment explanation
Indices: 98277--98320 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
98267 TCTCTTAGAC
98277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98319 AT
1 AT
98321 CACATGTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98671 original size:18 final size:18
Alignment explanation
Indices: 98650--98684 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
98640 TCCCATCTAG
98650 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
98668 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
98685 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:99276 original size:64 final size:66
Alignment explanation
Indices: 99175--99299 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 66
99165 TAATGAAGGT
*
99175 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTTAATGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
99239 G
66 G
* *
99240 ATGCATCGATGCACT-C-CTTATTCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
99300 ATTCATGCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
63 1 0.02
64 29 0.53
65 25 0.45
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (66 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
G
Found at i:99308 original size:64 final size:64
Alignment explanation
Indices: 99175--99335 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
99165 TAATGAAGGT
* *
99175 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
* *
99240 ATGCATCGATGCACT-C-CTTATTCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATG
*
99302 TC
63 GC
* **
99304 ATGCATCGATGCACTGCA-TGTGCATCGATGCA
1 ATGCATCGATGCACTACACCATGCATCGATGCA
99336 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
63 1 0.01
64 56 0.67
65 24 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:102731 original size:23 final size:23
Alignment explanation
Indices: 102705--102749 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
102695 CACCACAGCT
*
102705 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
102728 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
102750 ATATAATAAT
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:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:103005 original size:148 final size:149
Alignment explanation
Indices: 102717--103030 Score: 483
Period size: 148 Copynumber: 2.1 Consensus size: 149
102707 TATAATTGCA
*
102717 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
* **
102781 TTCCTTAAGAATCATATGCATATGCTAGGGATCAAGTATGTATCTTTCAAGACTTCGAACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTATCTCACAAGACTTCGAACATGTT
**
102846 CCACGGAATATATATATATC
130 CCAAAGAATATATATATATC
*
102866 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA-
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
* *
102930 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTC-ACACATGT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTATCTCACAAGACTTCGA-ACATGT
*
102993 TCCAAAGAATATATATATGTC
129 TCCAAAGAATATATATATATC
103014 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
103031 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
147 1 0.01
148 90 0.59
149 61 0.40
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTATCTCACAAGACTTCGAACATGTTC
CAAAGAATATATATATATC
Found at i:103791 original size:2 final size:2
Alignment explanation
Indices: 103784--103819 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
103774 ATTATTTCTT
103784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
103820 ATCTAATCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:103967 original size:18 final size:18
Alignment explanation
Indices: 103946--103980 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
103936 TCCCATCTAG
103946 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
103964 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
103981 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:104573 original size:64 final size:66
Alignment explanation
Indices: 104472--104596 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 66
104462 TAATAAAGGT
*
104472 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTTAATGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
104536 G
66 G
* *
104537 ATGCATCGATGCACT-C-CTTATTCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
104597 ATTCATGCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
63 1 0.02
64 29 0.53
65 25 0.45
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (66 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
G
Found at i:104605 original size:64 final size:64
Alignment explanation
Indices: 104472--104632 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
104462 TAATAAAGGT
* *
104472 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
* *
104537 ATGCATCGATGCACT-C-CTTATTCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATG
*
104599 TC
63 GC
* **
104601 ATGCATCGATGCACTGCA-TGTGCATCGATGCA
1 ATGCATCGATGCACTACACCATGCATCGATGCA
104633 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
63 1 0.01
64 56 0.67
65 24 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:107166 original size:21 final size:21
Alignment explanation
Indices: 107136--107188 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
107126 ATTATGACTA
107136 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
*
107157 TCGCATTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
107178 TCGCAATGCGA
1 TCGCAATGCGA
107189 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
Found at i:107243 original size:20 final size:20
Alignment explanation
Indices: 107218--107307 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
107208 GATTTGGAAA
*
107218 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
107238 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
107259 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
107279 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
107299 TTCGCAACG
1 ATCGCAACG
107308 AGATCGACAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 41 0.68
21 15 0.25
22 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:107772 original size:19 final size:19
Alignment explanation
Indices: 107731--107795 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
107721 GAAATGAAAA
107731 TCGCATTGCGATTTTC--T
1 TCGCATTGCGATTTTCATT
*
107748 T-G--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
107764 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
107783 TTGCATTGCGATT
1 TCGCATTGCGATT
107796 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 2 0.05
19 25 0.62
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:109366 original size:40 final size:42
Alignment explanation
Indices: 109322--109412 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
109312 CCTCTTCAAC
* *
109322 GATGACAGTGGCCTCTTGAACG-GTGG-GGGGACTCTTGAGG
1 GATGACAGGGGCCTATTGAACGAGTGGAGGGGACTCTTGAGG
* * *
109362 GATGATAGGGGCCTATTGAATGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTATTGAACGAGTGGAGGGGACTCTTGAGG
109404 GATGACAGG
1 GATGACAGG
109413 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 18 0.42
41 3 0.07
42 22 0.51
ACGTcount: A:0.22, C:0.13, G:0.42, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTATTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:109775 original size:20 final size:20
Alignment explanation
Indices: 109750--109788 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
109740 GAAGAATAGT
109750 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
109770 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
109789 ATGACAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:109799 original size:20 final size:20
Alignment explanation
Indices: 109776--109862 Score: 113
Period size: 20 Copynumber: 4.4 Consensus size: 20
109766 AAACTTACTT
*
109776 TCGCAACGCGAAAATGACAA
1 TCGCAACGCGGAAATGACAA
*
109796 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACAA
* *
109816 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACAA
* *
109836 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACAA
109855 TCGCAACG
1 TCGCAACG
109863 ACAAAATCGC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 14 0.24
20 45 0.76
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACAA
Found at i:109800 original size:40 final size:40
Alignment explanation
Indices: 109756--109841 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
109746 TAGTTTACTT
* *
109756 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACAA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACAA
* * * *
109796 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACAA
109836 TCGCAA
1 TCGCAA
109842 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACAA
Found at i:109870 original size:14 final size:14
Alignment explanation
Indices: 109851--109942 Score: 76
Period size: 14 Copynumber: 5.9 Consensus size: 14
109841 ATGCGAAATG
109851 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
109865 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
109884 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
109898 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
109917 AAAATCGCAACGAC
1 AAAATCGCAACGAC
109931 AAAATCGCAACG
1 AAAATCGCAACG
109943 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
14 32 0.50
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.31
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:109958 original size:33 final size:33
Alignment explanation
Indices: 109835--109947 Score: 217
Period size: 33 Copynumber: 3.4 Consensus size: 33
109825 GGAAATGGCT
109835 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
109868 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
109901 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
109934 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
109948 CACAAATCGC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:109976 original size:19 final size:19
Alignment explanation
Indices: 109954--110017 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
109944 GAAACACAAA
109954 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
109973 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
109989 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
110006 TCGCATTGCGAT
1 TCGCATTGCGAT
110018 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 17 0.46
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:110036 original size:20 final size:19
Alignment explanation
Indices: 110002--110056 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
109992 TTGCGATTTT
*
110002 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
110021 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
110041 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
110057 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:110219 original size:18 final size:18
Alignment explanation
Indices: 110196--110245 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
110186 TTTATTAAGC
110196 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
110214 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
110232 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
110246 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:112006 original size:20 final size:20
Alignment explanation
Indices: 111958--112016 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
111948 AATAGTTTCT
* *
111958 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
111978 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
111998 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
112017 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:112306 original size:22 final size:22
Alignment explanation
Indices: 112279--112322 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
112269 GATGGAGATA
112279 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
112301 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
112323 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:112539 original size:20 final size:20
Alignment explanation
Indices: 112489--112583 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
112479 CGCTTTGAAA
*
112489 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
112510 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* *
112530 ATCGCATTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
112551 ATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
112571 ATCGCATTGCGAT
1 ATCGCATTGCGAT
112584 TTTCCAAATT
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
19 5 0.09
20 27 0.47
21 23 0.40
22 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:112549 original size:41 final size:41
Alignment explanation
Indices: 112489--112586 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
112479 CGCTTTGAAA
* *
112489 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
112530 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
112571 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
112587 CCAAATTCGC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.39
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:112602 original size:41 final size:41
Alignment explanation
Indices: 112489--112604 Score: 117
Period size: 41 Copynumber: 2.8 Consensus size: 41
112479 CGCTTTGAAA
* ** * * * *
112489 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCATTGCGATAGTCAGT
** * *
112530 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCATTGCGATAGTCAGT
112571 ATCGCATTGCGATTTTCCAAAT-TCGCATTGCGAT
1 ATCGCATTGCGATTTT-CAAATATCGCATTGCGAT
112605 TTACTTATTC
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 65 0.97
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCAAATATCGCATTGCGATAGTCAGT
Found at i:112616 original size:20 final size:21
Alignment explanation
Indices: 112572--112623 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
112562 ATAGTCAGTA
*
112572 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
112593 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
112613 TCGCATTGCGA
1 TCGCATTGCGA
112624 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:113392 original size:30 final size:30
Alignment explanation
Indices: 113356--113443 Score: 151
Period size: 30 Copynumber: 2.9 Consensus size: 30
113346 AGTCTAGCAT
113356 GAAGACGCGTAGCAATCTGTGCGTCTTGTA
1 GAAGACGCGTAGCAATCTGTGCGTCTTGTA
113386 GAAGACGCGTAGCAATCTGTGCGTCTTGTA
1 GAAGACGCGTAGCAATCTGTGCGTCTTGTA
*
113416 GAAGACGCCTAGCAATCTGCT-CGTCTTG
1 GAAGACGCGTAGCAATCTG-TGCGTCTTG
113444 AAGGCAAGAA
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
30 55 0.98
31 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (30 bp):
GAAGACGCGTAGCAATCTGTGCGTCTTGTA
Found at i:113983 original size:12 final size:12
Alignment explanation
Indices: 113966--113990 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
113956 GTCAAATAAT
113966 TTAGGCACCAAA
1 TTAGGCACCAAA
113978 TTAGGCACCAAA
1 TTAGGCACCAAA
113990 T
1 T
113991 GGTGCTTTAT
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:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:117577 original size:21 final size:21
Alignment explanation
Indices: 117553--117602 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
117543 ACAGATATAT
117553 TGTCATATCAACATTATGAAC
1 TGTCATATCAACATTATGAAC
* * * *
117574 TGTCACATTAATATTGTGAAC
1 TGTCATATCAACATTATGAAC
*
117595 TGACATAT
1 TGTCATAT
117603 TATTATTGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (21 bp):
TGTCATATCAACATTATGAAC
Found at i:117604 original size:21 final size:21
Alignment explanation
Indices: 117569--117611 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
117559 ATCAACATTA
*
117569 TGAACTGTCACATTAATATTG
1 TGAACTGACACATTAATATTG
* *
117590 TGAACTGACATATTATTATTG
1 TGAACTGACACATTAATATTG
117611 T
1 T
117612 AACATAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (21 bp):
TGAACTGACACATTAATATTG
Found at i:118311 original size:28 final size:28
Alignment explanation
Indices: 118280--118335 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
118270 TCAATCACAT
*
118280 ATGATTTTAATATAATTTGGGCCAATTC
1 ATGACTTTAATATAATTTGGGCCAATTC
118308 ATGACTTTAATATAATTTGGGCCAATTC
1 ATGACTTTAATATAATTTGGGCCAATTC
118336 GGAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (28 bp):
ATGACTTTAATATAATTTGGGCCAATTC
Found at i:122533 original size:6 final size:6
Alignment explanation
Indices: 122511--122549 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
122501 TTATGAAGGA
* *
122511 AAAAAG GAAAGG AAAAAG AAAAAG AAAAA- AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
122550 GAACAATAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:122537 original size:17 final size:18
Alignment explanation
Indices: 122511--122549 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
122501 TTATGAAGGA
**
122511 AAAAAGGAAAGGAAAAAG
1 AAAAAGGAAAAAAAAAAG
122529 AAAAA-GAAAAAAAAAAG
1 AAAAAGGAAAAAAAAAAG
122546 AAAA
1 AAAA
122550 GAACAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAGGAAAAAAAAAAG
Found at i:123194 original size:4 final size:4
Alignment explanation
Indices: 123185--123209 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
123175 GAAAAATGAT
123185 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
123210 AGTTATGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:124592 original size:23 final size:25
Alignment explanation
Indices: 124543--124592 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 25
124533 CATGATTTCA
*
124543 CCACCATTGCTTTAGGGATTGTGCCT
1 CCACCATTGCTTTA-GGATTGTCCCT
*
124569 CCACCA-TGCTTT-GGTTTGTCCCT
1 CCACCATTGCTTTAGGATTGTCCCT
124592 C
1 C
124593 TTCCCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 10 0.45
25 6 0.27
26 6 0.27
ACGTcount: A:0.12, C:0.32, G:0.20, T:0.36
Consensus pattern (25 bp):
CCACCATTGCTTTAGGATTGTCCCT
Found at i:124833 original size:40 final size:37
Alignment explanation
Indices: 124779--124857 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 37
124769 ACACATACAA
124779 TTTAATTTTTGTTTCATTTTAGTATCCATCCGTTAAAAAT
1 TTTAATTTTTGTTTCATTTTAGTA---ATCCGTTAAAAAT
* *
124819 TTTAGTTTTTGTTTCATTTTAGTAATCCGTTCAAAAT
1 TTTAATTTTTGTTTCATTTTAGTAATCCGTTAAAAAT
124856 TT
1 TT
124858 AACATTAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 14 0.38
40 23 0.62
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.54
Consensus pattern (37 bp):
TTTAATTTTTGTTTCATTTTAGTAATCCGTTAAAAAT
Found at i:126999 original size:6 final size:6
Alignment explanation
Indices: 126988--127548 Score: 972
Period size: 6 Copynumber: 93.7 Consensus size: 6
126978 AGGTAAATTT
126988 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
127036 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
127084 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
127132 TATACA TATACATA TATACA TATACA TATACA TATACA TATACA TATAC-
1 TATACA TATAC--A TATACA TATACA TATACA TATACA TATACA TATACA
127181 -ATACA TATACA TATAC- -ATACA TATACA TATACA TACATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA T--ATACA TATACA
127228 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
127276 TATACA TATACA TATACA TATACA TATAC- -ATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
127322 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
127370 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
127418 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * * *
127466 TATACA TATACA TATACA TATGCA TATGCA TATAAA TATACA TATGCA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * *
127514 TTATGCA TATGCA TATAAA TATACA TATACA TATA
1 -TATACA TATACA TATACA TATACA TATACA TATA
127549 TACGAGGATT
Statistics
Matches: 536, Mismatches: 8, Indels: 22
0.95 0.01 0.04
Matches are distributed among these distances:
4 12 0.02
6 506 0.94
7 6 0.01
8 12 0.02
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:128474 original size:243 final size:244
Alignment explanation
Indices: 128044--128522 Score: 818
Period size: 243 Copynumber: 2.0 Consensus size: 244
128034 TAATATTTTT
** *
128044 TTTAACATTTCCGGTAAAACGTTACCTAAAACATTATTTTTTTTCTACTGAAAATGTTAATATTG
1 TTTAACATTTCCGGTAAAACACTACCTAAAACATTA-TTTTTTTCTACAGAAAATGTTAATATTG
*
128109 GGCGCTACCTAAAATGTTATTTTTTTTTCTACTGAAATTAAGTAGCGAAATTAATATTTCTGGTA
65 GGCGCTACCTAAAATGTTATTTTTTTTTCTACTGAAATTAAGTAGCGAAATTAACATTTCTGGTA
* *
128174 AAAAAAATAATGTTTTAGGTAGCGCTTTACCATAAATGTTAAAAAAATATTAACATTTCCGGTAT
130 AAAAAAATAATATTTTAGGTAGCGCTTTACCATAAACGTTAAAAAAATATTAACATTTCCGGTAT
*
128239 GGTCTTTTCTTAGCCGTATATTAAGGTTGTCATACAACATACCTAAAACG
195 GGTCTTTCCTTAGCCGTATATTAAGGTTGTCATACAACATACCTAAAACG
* *
128289 TTTAACATTTCCGGTAAATCACTACCTAAAATATTA-TTTTTTCTACA-AGAAATGTTAATATTG
1 TTTAACATTTCCGGTAAAACACTACCTAAAACATTATTTTTTTCTACAGA-AAATGTTAATATTG
* *
128352 GGTGTTACCTAAAATGTTATTTTTTTTTCTACTGAAATTAAGTAGCGAAATTAACATTTCTGGTA
65 GGCGCTACCTAAAATGTTATTTTTTTTTCTACTGAAATTAAGTAGCGAAATTAACATTTCTGGTA
128417 AAAAAAATAATATTTTAGGTAGCGCTTTACCATAAACGTTAAAAAAATATTAACATTTCCGGTAT
130 AAAAAAATAATATTTTAGGTAGCGCTTTACCATAAACGTTAAAAAAATATTAACATTTCCGGTAT
*
128482 GGTCTTTCCTTAGCCGTATATTAAGGTTGTCATACAGCATA
195 GGTCTTTCCTTAGCCGTATATTAAGGTTGTCATACAACATA
128523 ACTACCCCTT
Statistics
Matches: 221, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
242 1 0.00
243 188 0.85
245 32 0.14
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (244 bp):
TTTAACATTTCCGGTAAAACACTACCTAAAACATTATTTTTTTCTACAGAAAATGTTAATATTGG
GCGCTACCTAAAATGTTATTTTTTTTTCTACTGAAATTAAGTAGCGAAATTAACATTTCTGGTAA
AAAAAATAATATTTTAGGTAGCGCTTTACCATAAACGTTAAAAAAATATTAACATTTCCGGTATG
GTCTTTCCTTAGCCGTATATTAAGGTTGTCATACAACATACCTAAAACG
Found at i:129350 original size:44 final size:43
Alignment explanation
Indices: 129280--129600 Score: 176
Period size: 42 Copynumber: 7.7 Consensus size: 43
129270 ACTATCGCAA
129280 TGCGATT-TTCCAAATT--CGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGCGT
129320 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGA-TTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGCGT
* * * * * *
129364 TACGA-TAGTCGAAGTTCGCGTTGCGATTTATTCTAAGTT--CGT
1 TGCGATTATTCCAAATTCGCGTTGCGA--TAGTCCAAGTTCGCGT
* * * *
129406 TGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGT
1 TGCGATTATTCCAAATTCGCGTTGCGA--TAGTCCAAGTTCGCGT
* * * * *
129448 TGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGT
1 TGCGATTATTCCAAATTCGCGTTGCGA--TAGTCCAAGTTCGCGT
* * *
129490 TGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CGT
1 TGCGATTATTCCAAATTCGCGTTGCGA--TAGTCCAAGTTCGCGT
* * * * *
129532 TGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTTCAAGTT--CGT
1 TGCGATTATTCCAAATTCGCGTTGCGA--TAGTCCAAGTTCGCGT
* * *
129574 TGCGA-TAGTCGAAGTTCGCGTTGCGAT
1 TGCGATTATTCCAAATTCGCGTTGCGAT
129601 CTGGAAACTG
Statistics
Matches: 262, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
40 6 0.02
41 2 0.01
42 217 0.83
44 37 0.14
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (43 bp):
TGCGATTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGCGT
Found at i:129412 original size:42 final size:42
Alignment explanation
Indices: 129336--129600 Score: 444
Period size: 42 Copynumber: 6.3 Consensus size: 42
129326 TTATTCCAAA
* *
129336 TTCGCGTTGCGA--TAGTCCAAGTTCGCGTTACGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGATAGTCGAAG
*
129378 TTCGCGTTGCGATTTATTCTAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
129420 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
129462 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
129504 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
129546 TTCGCGTTGCGATTTATTTCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
129588 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
129601 CTGGAAACTG
Statistics
Matches: 212, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
42 203 0.96
44 9 0.04
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:130942 original size:29 final size:29
Alignment explanation
Indices: 130909--130993 Score: 134
Period size: 29 Copynumber: 2.9 Consensus size: 29
130899 TCCCAACACA
*
130909 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
**
130938 TAGGTCGCCATGCCCTCCTAGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
130967 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
130994 ACCCTCGCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.13, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:131038 original size:33 final size:33
Alignment explanation
Indices: 130997--131090 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
130987 GCGACCTACC
*
130997 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
131030 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * * * *
131063 CTCGTTCGGATGGCCTCGAATGCTCTCG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCG
131091 GATGGCCTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 2 0.04
33 52 0.96
ACGTcount: A:0.10, C:0.38, G:0.26, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:131053 original size:10 final size:10
Alignment explanation
Indices: 131009--131113 Score: 66
Period size: 10 Copynumber: 9.9 Consensus size: 10
130999 CGCTCGGCTT
*
131009 CCCTCGGATT
1 CCCTCGGATG
*
131019 CCCTCGCATAG
1 CCCTCGGAT-G
*
131030 CTCGCTCGGTTG
1 C-C-CTCGGATG
131042 CCCTCGGATG
1 CCCTCGGATG
*
131052 CCCTCGCATAG
1 CCCTCGGAT-G
*
131063 CTCGTTCGGATG
1 C-C-CTCGGATG
* *
131075 GCCTCGAATG
1 CCCTCGGATG
*
131085 CTCTCGGATG
1 CCCTCGGATG
*
131095 GCCTCGGATG
1 CCCTCGGATG
*
131105 CTCTCGGAT
1 CCCTCGGAT
131114 TGCCTCGTTG
Statistics
Matches: 71, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
10 51 0.72
11 5 0.07
12 5 0.07
13 10 0.14
ACGTcount: A:0.11, C:0.35, G:0.28, T:0.26
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:131093 original size:20 final size:20
Alignment explanation
Indices: 131044--131120 Score: 91
Period size: 20 Copynumber: 3.7 Consensus size: 20
131034 CTCGGTTGCC
* *
131044 CTCGGATGCCCTCGCATAGCT
1 CTCGGATGGCCTCGAAT-GCT
131065 CGTTCGGATGGCCTCGAATGCT
1 C--TCGGATGGCCTCGAATGCT
*
131087 CTCGGATGGCCTCGGATGCT
1 CTCGGATGGCCTCGAATGCT
*
131107 CTCGGATTGCCTCG
1 CTCGGATGGCCTCG
131121 TTGGGACGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
20 31 0.62
21 1 0.02
22 4 0.08
23 14 0.28
ACGTcount: A:0.12, C:0.32, G:0.30, T:0.26
Consensus pattern (20 bp):
CTCGGATGGCCTCGAATGCT
Found at i:131797 original size:21 final size:21
Alignment explanation
Indices: 131771--131810 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
131761 CACCGGACTT
131771 CAACACCCTCACCATCTCCCC
1 CAACACCCTCACCATCTCCCC
*
131792 CAACACCCTCACCCTCTCC
1 CAACACCCTCACCATCTCC
131811 GCCGCCGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.62, G:0.00, T:0.15
Consensus pattern (21 bp):
CAACACCCTCACCATCTCCCC
Found at i:134018 original size:4 final size:4
Alignment explanation
Indices: 134009--134034 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
133999 GTACATGTAA
134009 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
134035 GTTAAAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:134792 original size:2 final size:2
Alignment explanation
Indices: 134785--134833 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
134775 AATATTAAAA
134785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
134827 AT A- AT AT
1 AT AT AT AT
134834 TAATTAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:134883 original size:15 final size:16
Alignment explanation
Indices: 134785--134902 Score: 63
Period size: 15 Copynumber: 7.6 Consensus size: 16
134775 AATATTAAAA
*
134785 ATATATATATATATATAT
1 ATATATATA-ATA-ATTT
*
134803 ATATATATATATATATAT
1 ATATATATA-ATA-ATTT
*
134821 ATATATATAAT-ATTA
1 ATATATATAATAATTT
*
134836 AT-TA-AT-TTAATTT
1 ATATATATAATAATTT
* **
134849 AAAT-TA-AATTAAAAT
1 ATATATATAA-TAATTT
134864 ATATATATAAT-ATTT
1 ATATATATAATAATTT
134879 ATATATAT-ATAATTT
1 ATATATATAATAATTT
*
134894 AAATATATA
1 ATATATATA
134903 TACCCGACCC
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
12 1 0.01
13 6 0.08
14 6 0.08
15 32 0.41
16 3 0.04
17 4 0.05
18 27 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATATAATAATTT
Found at i:136419 original size:10 final size:10
Alignment explanation
Indices: 136390--136419 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
136380 ATTTAAATGA
*
136390 TAAACGAACA
1 TAAACGAACG
136400 TAAACGAACG
1 TAAACGAACG
136410 TAAACGAACG
1 TAAACGAACG
136420 AACATAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.17, T:0.10
Consensus pattern (10 bp):
TAAACGAACG
Found at i:136419 original size:14 final size:14
Alignment explanation
Indices: 136392--136437 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
136382 TTAAATGATA
136392 AACGAACATAAACG
1 AACGAACATAAACG
136406 AACG----TAAACG
1 AACGAACATAAACG
136416 AACGAACATAAACG
1 AACGAACATAAACG
136430 AACGAACA
1 AACGAACA
136438 CAAGCAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.36
14 18 0.64
ACGTcount: A:0.57, C:0.22, G:0.15, T:0.07
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:136447 original size:24 final size:24
Alignment explanation
Indices: 136396--136450 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
136386 ATGATAAACG
*
136396 AACATAAACGAACGTAAACGAACG
1 AACATAAACGAACGTAAACGAACA
136420 AACATAAACGAACG-AACAC-AAGCA
1 AACATAAACGAACGTAA-ACGAA-CA
136444 AACATAA
1 AACATAA
136451 TAAACAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.58, C:0.22, G:0.13, T:0.07
Consensus pattern (24 bp):
AACATAAACGAACGTAAACGAACA
Found at i:136489 original size:33 final size:36
Alignment explanation
Indices: 136420--136492 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
136410 TAAACGAACG
*
136420 AACATAAACGAACGAACACAAGCAAACATAATAAACA
1 AACATAAACGAACGAACACAA-CAAACATAAAAAACA
*
136457 AACATAAACGAAC-AACACAA-ACACA-AAAAAACA
1 AACATAAACGAACGAACACAACAAACATAAAAAACA
136490 AAC
1 AAC
136493 TTATTTGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 10 0.29
34 4 0.12
36 7 0.21
37 13 0.38
ACGTcount: A:0.66, C:0.23, G:0.05, T:0.05
Consensus pattern (36 bp):
AACATAAACGAACGAACACAACAAACATAAAAAACA
Found at i:136745 original size:14 final size:14
Alignment explanation
Indices: 136726--136783 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
136716 ACCCTCTGTT
136726 CGAACATAAATGAA
1 CGAACATAAATGAA
*
136740 CGAACAT-AA-GTA
1 CGAACATAAATGAA
136752 --AACATAAATGAA
1 CGAACATAAATGAA
*
136764 CAAACATAAATGAA
1 CGAACATAAATGAA
136778 CGAACA
1 CGAACA
136784 ATCCATTTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 5 0.14
11 2 0.05
12 4 0.11
13 2 0.05
14 24 0.65
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:138122 original size:39 final size:38
Alignment explanation
Indices: 138054--138129 Score: 116
Period size: 39 Copynumber: 2.0 Consensus size: 38
138044 TAGACAACCA
* *
138054 TTAATTTTTAACAAAAAATGACGAGTTATAGTCGGGTG
1 TTAATTTTTAACAAAAAATGACAAATTATAGTCGGGTG
*
138092 TTAATTTTTAAACAAAAAATGATAAATTATAGTCGGGT
1 TTAATTTTT-AACAAAAAATGACAAATTATAGTCGGGT
138130 AATCATTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 9 0.26
39 25 0.74
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (38 bp):
TTAATTTTTAACAAAAAATGACAAATTATAGTCGGGTG
Found at i:141459 original size:27 final size:30
Alignment explanation
Indices: 141406--141461 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
141396 AAATGACAAT
*
141406 ACTCAAACAACCTAATGAAAATTTTCCAACC
1 ACTCAAACAA-CTAATGAAAATGTTCCAACC
141437 ACTCAAACAA-TAAT-AAAA-GTTCCAA
1 ACTCAAACAACTAATGAAAATGTTCCAA
141462 ATTTTCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 4 0.17
29 4 0.17
31 10 0.42
ACGTcount: A:0.50, C:0.25, G:0.04, T:0.21
Consensus pattern (30 bp):
ACTCAAACAACTAATGAAAATGTTCCAACC
Found at i:147280 original size:24 final size:24
Alignment explanation
Indices: 147222--147282 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
147212 TAATATAAAC
* *
147222 AATTATTAAGATATTCAATGAGTTA
1 AATTATTAAAATATTCAA-GAATTA
*
147247 AA-TATAAAAATATTACAA-AATTA
1 AATTATTAAAATATT-CAAGAATTA
147270 AATTATTAAAATA
1 AATTATTAAAATA
147283 AATTAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 6 0.20
24 19 0.63
25 5 0.17
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (24 bp):
AATTATTAAAATATTCAAGAATTA
Found at i:149250 original size:23 final size:23
Alignment explanation
Indices: 149224--149267 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
149214 TTACTAAAAA
149224 TGAATAATAAAAAAAT-AAAAATC
1 TGAATAA-AAAAAAATGAAAAATC
*
149247 TGAATAAAAAATAATGAAAAA
1 TGAATAAAAAAAAATGAAAAA
149268 ATAAATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (23 bp):
TGAATAAAAAAAAATGAAAAATC
Found at i:151465 original size:16 final size:16
Alignment explanation
Indices: 151446--151504 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 16
151436 AAATATAAAG
151446 AAAAATAAATAACCAA
1 AAAAATAAATAACCAA
* * *
151462 AAAAAT-ATTCACCCA
1 AAAAATAAATAACCAA
**
151477 AAAAATAAA-AAGTAA
1 AAAAATAAATAACCAA
151492 ATAAAATAAATAA
1 A-AAAATAAATAA
151505 TAATAAAAGG
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
15 15 0.47
16 15 0.47
17 2 0.06
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAACCAA
Found at i:155969 original size:20 final size:21
Alignment explanation
Indices: 155930--155969 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
155920 CACGCTAAAT
155930 GCTGAATGGTTCAACATTCAAC
1 GCTGAATGGTTC-ACATTCAAC
155952 GCTGAATGGTTC-CATTCA
1 GCTGAATGGTTCACATTCA
155970 GAACCAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (21 bp):
GCTGAATGGTTCACATTCAAC
Found at i:156460 original size:27 final size:27
Alignment explanation
Indices: 156430--156486 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
156420 GATGTCATAA
156430 AATCATATTTTAATGTTGTCTATTGGC
1 AATCATATTTTAATGTTGTCTATTGGC
156457 AATCATATTTTAATGTTGTCTATTGGC
1 AATCATATTTTAATGTTGTCTATTGGC
156484 AAT
1 AAT
156487 GCTGTTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (27 bp):
AATCATATTTTAATGTTGTCTATTGGC
Found at i:157009 original size:17 final size:18
Alignment explanation
Indices: 156976--157015 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
156966 TAATAGTGAG
156976 TTATTATAAAATATATTT
1 TTATTATAAAATATATTT
*
156994 TTATTAT-AATTATATTT
1 TTATTATAAAATATATTT
157011 TTATT
1 TTATT
157016 TATATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATAAAATATATTT
Found at i:157193 original size:48 final size:50
Alignment explanation
Indices: 157017--157215 Score: 260
Period size: 48 Copynumber: 4.0 Consensus size: 50
157007 ATTTTTATTT
* * *
157017 ATATTTTTTATAATTTTATTATAGTTTAAATTGATATAATTAAAATATAATA
1 ATATTTTTT-GAA-TTTATTATAGTTTAAATTGATATGATTCAAATATAATA
* * * *
157069 ATATTTTTTAAAATTTATTATAGTTCAAATTGATAT-ACTCAAATATAATG
1 ATATTTTTT-GAATTTATTATAGTTTAAATTGATATGATTCAAATATAATA
*
157119 ATAACTTTTTGAATTTATTATAGTTTAAATTGATATGATTCAAATATAAT-
1 AT-ATTTTTTGAATTTATTATAGTTTAAATTGATATGATTCAAATATAATA
*
157169 AT-TTTTTTGAATTTATTATAGTTTAAATTGATATGATTCATATATAA
1 ATATTTTTTGAATTTATTATAGTTTAAATTGATATGATTCAAATATAA
157216 GTGTAAATGT
Statistics
Matches: 134, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
48 43 0.32
50 39 0.29
51 40 0.30
52 12 0.09
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (50 bp):
ATATTTTTTGAATTTATTATAGTTTAAATTGATATGATTCAAATATAATA
Done.