Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007138.1 Hibiscus syriacus cultivar Beakdansim tig00018671_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: 156351
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:486 original size:20 final size:20
Alignment explanation
Indices: 461--565 Score: 123
Period size: 20 Copynumber: 5.5 Consensus size: 20
451 CTAAAATCGC
*
461 GTTGCGATTTTCATTTTCGT
1 GTTGCGAATTTCATTTTCGT
481 GTTGCG------ATTTTCGT
1 GTTGCGAATTTCATTTTCGT
* *
495 GTTGTGAATTTTATTTTCGT
1 GTTGCGAATTTCATTTTCGT
515 GTTGCGAATTTCATTTTCGT
1 GTTGCGAATTTCATTTTCGT
*
535 ATTGCGAATTTCATTTTCGT
1 GTTGCGAATTTCATTTTCGT
*
555 GTTGCAAATTT
1 GTTGCGAATTT
566 ATGTTTCAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
14 13 0.18
20 60 0.82
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.52
Consensus pattern (20 bp):
GTTGCGAATTTCATTTTCGT
Found at i:925 original size:22 final size:21
Alignment explanation
Indices: 900--956 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
890 GATGTAGATA
900 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAG-TGGG
**
922 GACGGATTTCATCGGAGTGGG
1 GACGGATTTCGCCGGAGTGGG
*
943 GACGGATATCGCCG
1 GACGGATTTCGCCG
957 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (21 bp):
GACGGATTTCGCCGGAGTGGG
Found at i:944 original size:21 final size:22
Alignment explanation
Indices: 900--949 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
890 GATGTAGATA
*
900 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
922 GACGGATTTCATCGGAG-TGGG
1 GACGGATTTCACCGGAGATGGG
943 GACGGAT
1 GACGGAT
950 ATCGCCGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.20, C:0.16, G:0.44, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:1303 original size:2 final size:2
Alignment explanation
Indices: 1296--1343 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1286 CAAATTTTAT
1296 TA TA TA 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 TA TA TA
1338 TA TA TA
1 TA TA TA
1344 GAAACCTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5669 original size:2 final size:2
Alignment explanation
Indices: 5662--5688 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5652 CAGTTGAATC
5662 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 A
5689 GTGGCGGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6363 original size:16 final size:17
Alignment explanation
Indices: 6313--6364 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
6303 AAAATAAAAA
6313 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
6330 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
6345 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
6361 AATT
1 AATT
6365 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:9234 original size:2 final size:2
Alignment explanation
Indices: 9227--9259 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9217 CAGTATTTTA
*
9227 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9260 CACCAAACGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13316 original size:35 final size:33
Alignment explanation
Indices: 13277--13341 Score: 103
Period size: 35 Copynumber: 1.9 Consensus size: 33
13267 TATATAAAAT
*
13277 TTTAGTGAATTCATCTTTATATATATATATATATA
1 TTTAGTGAATTCATCTTT-TATA-AAATATATATA
13312 TTTAGTGAATTCATCTTTTATAAAATATAT
1 TTTAGTGAATTCATCTTTTATAAAATATAT
13342 GTATGAAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 7 0.24
34 4 0.14
35 18 0.62
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (33 bp):
TTTAGTGAATTCATCTTTTATAAAATATATATA
Found at i:29082 original size:21 final size:20
Alignment explanation
Indices: 29058--29124 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
29048 TAAAGGGAGG
29058 TTTTTAAGTTTTTTTTGAAAA
1 TTTTTAAGTTTTTTTT-AAAA
** *
29079 TTTTGGACTTTTTTTT-AAA
1 TTTTTAAGTTTTTTTTAAAA
*
29098 TGTTTTAAAGTTTTTTTTATAA
1 T-TTTT-AAGTTTTTTTTAAAA
29120 TTTTT
1 TTTTT
29125 TTAAAATTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 26 0.72
22 3 0.08
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.66
Consensus pattern (20 bp):
TTTTTAAGTTTTTTTTAAAA
Found at i:29112 original size:22 final size:23
Alignment explanation
Indices: 29087--29129 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29077 AATTTTGGAC
29087 TTTTTTT-TAAATGTTTTAAAGT
1 TTTTTTTATAAATGTTTTAAAGT
* *
29109 TTTTTTTATAATTTTTTTAAA
1 TTTTTTTATAAATGTTTTAAA
29130 ATTACATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TTTTTTTATAAATGTTTTAAAGT
Found at i:29995 original size:3 final size:3
Alignment explanation
Indices: 29987--30048 Score: 108
Period size: 3 Copynumber: 20.7 Consensus size: 3
29977 CAAATTGTCC
29987 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30034 TTA TTA TTA TATA TT
1 TTA TTA TTA T-TA TT
30049 CTAACAAGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31170 original size:31 final size:31
Alignment explanation
Indices: 31098--31177 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
31088 ACTGATTTTT
*
31098 TTGTTTGTGTCCGTTCATTAAGAAATTTAGC
1 TTGTTTGTGTTCGTTCATTAAGAAATTTAGC
*
31129 TTGTTTGTGTTCGTTCATTAATAAATTTAGC
1 TTGTTTGTGTTCGTTCATTAAGAAATTTAGC
* *
31160 TTGTTCGTGTTCATTCAT
1 TTGTTTGTGTTCGTTCAT
31178 GTTCATTCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.50
Consensus pattern (31 bp):
TTGTTTGTGTTCGTTCATTAAGAAATTTAGC
Found at i:31441 original size:18 final size:18
Alignment explanation
Indices: 31418--31458 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
31408 AGAGAACATA
31418 AACGAACA-AAAGGAAACG
1 AACGAACATAAAGG-AACG
*
31436 AACGAACATAAATGAACG
1 AACGAACATAAAGGAACG
31454 AACGA
1 AACGA
31459 GCCTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.59, C:0.17, G:0.20, T:0.05
Consensus pattern (18 bp):
AACGAACATAAAGGAACG
Found at i:33737 original size:20 final size:20
Alignment explanation
Indices: 33673--33737 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
33663 ACGTTGCATT
*
33673 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTG-AAA
** * **
33694 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTT-GAAA
33714 TCGCGTTGCGATAGTTGAAA
1 TCGCGTTGCGATAGTTGAAA
33734 TCGC
1 TCGC
33738 AACGCGATCT
Statistics
Matches: 31, Mismatches: 11, Indels: 5
0.66 0.23 0.11
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
TCGCGTTGCGATAGTTGAAA
Found at i:33786 original size:20 final size:20
Alignment explanation
Indices: 33761--33916 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
33751 CTATCGCAAA
*
33761 TTCGCGTTGCAATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
33781 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
33802 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
33822 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
33843 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
33863 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
*
33884 TTCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
33904 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
33917 AGTCTGCAGT
Statistics
Matches: 106, Mismatches: 27, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
20 59 0.56
21 47 0.44
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:33817 original size:41 final size:41
Alignment explanation
Indices: 33758--33941 Score: 307
Period size: 41 Copynumber: 4.5 Consensus size: 41
33748 CCACTATCGC
*
33758 AAATTCGCGTTGCAATTTTCCATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
33799 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
33840 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
*
33881 AAATTCGCATTGCGATTTTCCATTTCGCGTTGCGATAGTCTG
1 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TG
* *
33923 CAGTT-GTCGTTGCGATTTT
1 AAATTCG-CGTTGCGATTTT
33942 TCAAATTCGT
Statistics
Matches: 136, Mismatches: 5, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
41 120 0.88
42 16 0.12
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (41 bp):
AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
Found at i:34030 original size:6 final size:6
Alignment explanation
Indices: 34019--34057 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
34009 ACGTGTCGAA
34019 GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
34058 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.31, C:0.51, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:34551 original size:6 final size:6
Alignment explanation
Indices: 34515--34578 Score: 93
Period size: 6 Copynumber: 11.5 Consensus size: 6
34505 TCTCGTCTCG
34515 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
34558 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
34579 AATACGTGTC
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 25 0.43
6 33 0.57
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:34754 original size:21 final size:21
Alignment explanation
Indices: 34691--34754 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
34681 ACAACTGTAG
*
34691 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
34712 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
34732 ACTATCTCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
34753 AC
1 AC
34755 GCGAATTTGC
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:35998 original size:10 final size:11
Alignment explanation
Indices: 35967--36000 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
35957 GACACGTATT
35967 ACCACGACCACG
1 ACCACGACC-CG
35979 ACCACGACCCG
1 ACCACGACCCG
35990 ACC-CGACCCG
1 ACCACGACCCG
36000 A
1 A
36001 GACGAGACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:36677 original size:21 final size:21
Alignment explanation
Indices: 36653--36703 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
36643 TTACATATTC
36653 GCATTGCGATAATCCAAGTTT
1 GCATTGCGATAATCCAAGTTT
*
36674 GCATTGCGATAATCGAAGTTT
1 GCATTGCGATAATCCAAGTTT
*
36695 GCGTTGCGA
1 GCATTGCGA
36704 ACTTGGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (21 bp):
GCATTGCGATAATCCAAGTTT
Found at i:39966 original size:24 final size:24
Alignment explanation
Indices: 39934--39982 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
39924 ACAGTCTTAA
39934 ATCTGTGTAAAACTAAAGAGTTTT
1 ATCTGTGTAAAACTAAAGAGTTTT
39958 ATCTGTGTAAAACTAAAGAGTTTT
1 ATCTGTGTAAAACTAAAGAGTTTT
39982 A
1 A
39983 CATTATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (24 bp):
ATCTGTGTAAAACTAAAGAGTTTT
Found at i:43986 original size:18 final size:19
Alignment explanation
Indices: 43951--43999 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
43941 ATATTAAAGC
43951 ATTTATTAAAATAGATATA
1 ATTTATTAAAATAGATATA
43970 ATTTA-TAAAAGTA-ATAT-
1 ATTTATTAAAA-TAGATATA
43987 A-TTATTTAAAATA
1 ATTTA-TTAAAATA
44000 TCAGAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.11
17 3 0.11
18 14 0.52
19 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
ATTTATTAAAATAGATATA
Found at i:44259 original size:11 final size:11
Alignment explanation
Indices: 44245--44307 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
44235 GAATAAGATA
44245 AAAATAATAAT
1 AAAATAATAAT
44256 AAAATAATAATT
1 AAAATAATAA-T
**
44268 AAAGCAATAATT
1 AAAATAATAA-T
44280 AAAAT-AT-A-
1 AAAATAATAAT
* *
44288 AAAGTAATGAT
1 AAAATAATAAT
44299 AAAATAATA
1 AAAATAATA
44308 TTGTAAATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 19 0.46
12 14 0.34
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:44259 original size:12 final size:12
Alignment explanation
Indices: 44245--44285 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
44235 GAATAAGATA
44245 AAAATAATAA-T
1 AAAATAATAATT
44256 AAAATAATAATT
1 AAAATAATAATT
**
44268 AAAGCAATAATT
1 AAAATAATAATT
44280 AAAATA
1 AAAATA
44286 TAAAAGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:45728 original size:23 final size:23
Alignment explanation
Indices: 45684--45728 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
45674 TTTTTTTTGT
* *
45684 TGTCTTCTCTCGTTCTTGCTCTG
1 TGTCTCCTCTCGTTCTTCCTCTG
* *
45707 TGTCTCCTCTCTTTTTTCCTCT
1 TGTCTCCTCTCGTTCTTCCTCT
45729 CCTTTTCTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.00, C:0.33, G:0.11, T:0.56
Consensus pattern (23 bp):
TGTCTCCTCTCGTTCTTCCTCTG
Found at i:45978 original size:39 final size:39
Alignment explanation
Indices: 45917--45993 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
45907 ACCTGGCAGT
*
45917 GCTGGAAGCTGCTGCAACTGATGCGTGGAGGGGCTGCTC
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
* *
45956 GCTGGAAGCTGCTGGAAATGATGTGTGGAGGGGCTGCT
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
45994 GGATGGAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.17, C:0.18, G:0.43, T:0.22
Consensus pattern (39 bp):
GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
Found at i:55207 original size:64 final size:64
Alignment explanation
Indices: 55154--55317 Score: 238
Period size: 65 Copynumber: 2.5 Consensus size: 64
55144 CGGTGCACCA
*
55154 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * **
55218 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
55283 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
55318 CAATTAATTC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 33 0.38
65 55 0.62
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:55306 original size:17 final size:19
Alignment explanation
Indices: 55268--55314 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
55258 ATATTCAGAG
55268 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
55287 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
55304 TGCATTCGATG
1 TGCA-TCGATG
55315 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:55337 original size:65 final size:62
Alignment explanation
Indices: 55158--55364 Score: 213
Period size: 65 Copynumber: 3.2 Consensus size: 62
55148 GCACCAAGTG
*
55158 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGATTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGGA--G
55222 -
62 A
* *
55222 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
55286 A
62 A
* * * * *
55287 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
55352 TGCATCGGTGCAT
1 TGCATCGATGCAT
55365 CACCTCAAAT
Statistics
Matches: 123, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
63 3 0.02
64 35 0.28
65 78 0.63
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:55557 original size:20 final size:21
Alignment explanation
Indices: 55534--55573 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
55524 GAATCGAATA
55534 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
55554 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
55574 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:61794 original size:22 final size:21
Alignment explanation
Indices: 61752--61791 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61742 GAGTTTGTTT
*
61752 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
61773 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
61792 ACAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:63770 original size:64 final size:64
Alignment explanation
Indices: 63717--63880 Score: 238
Period size: 65 Copynumber: 2.5 Consensus size: 64
63707 CGGTGCACCA
*
63717 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * **
63781 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
63846 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
63881 CAATTAATTC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 33 0.38
65 55 0.62
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:63869 original size:17 final size:19
Alignment explanation
Indices: 63831--63877 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
63821 ATATTCAGAG
63831 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
63850 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
63867 TGCATTCGATG
1 TGCA-TCGATG
63878 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:63900 original size:65 final size:62
Alignment explanation
Indices: 63721--63927 Score: 213
Period size: 65 Copynumber: 3.2 Consensus size: 62
63711 GCACCAAGTG
*
63721 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGATTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGGA--G
63785 -
62 A
* *
63785 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
63849 A
62 A
* * * * *
63850 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
63915 TGCATCGGTGCAT
1 TGCATCGATGCAT
63928 CACCTCAAAT
Statistics
Matches: 123, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
63 3 0.02
64 35 0.28
65 78 0.63
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:64120 original size:20 final size:21
Alignment explanation
Indices: 64097--64136 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
64087 GAATCGAATA
64097 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
64117 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
64137 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:64221 original size:31 final size:30
Alignment explanation
Indices: 64186--64308 Score: 106
Period size: 31 Copynumber: 4.0 Consensus size: 30
64176 ACATAAACTC
64186 TAGATGAAATATCAATTTGACCCTTAAATTT
1 TAGAT-AAATATCAATTTGACCCTTAAATTT
* * *
64217 TAGATAGAATA-CAAATTTGA-TCTCTGAACTT
1 TAGATA-AATATC-AATTTGACCCT-TAAATTT
* * *
64248 TAGATAAAATATCATTTTGACCCCTAAAATT
1 TAGAT-AAATATCAATTTGACCCTTAAATTT
* *
64279 TAGATAAATTATGAATTTGACCTTTAAATT
1 TAGATAAA-TATCAATTTGACCCTTAAATT
64309 CAACCAAAGT
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
30 7 0.10
31 62 0.86
32 3 0.04
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (30 bp):
TAGATAAATATCAATTTGACCCTTAAATTT
Found at i:65356 original size:28 final size:28
Alignment explanation
Indices: 65308--65367 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
65298 ATAACTGCAA
* *
65308 AAAAAATAAAATATTTAAATAAATAATT
1 AAAAAATAAAATATATAAATAAATAAAT
* *
65336 AAAAAATCAAATA-ATACAATAATTAAAT
1 AAAAAATAAAATATATA-AATAAATAAAT
65364 AAAA
1 AAAA
65368 TACTAACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAAAATAAAATATATAAATAAATAAAT
Found at i:65369 original size:13 final size:13
Alignment explanation
Indices: 65311--65369 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
65301 ACTGCAAAAA
*
65311 AAATAAAATATTT
1 AAATAAAATAATT
65324 AAAT-AAATAATT
1 AAATAAAATAATT
*
65336 -AA-AAAATCAAAT
1 AAATAAAAT-AATT
*
65348 -AATACAATAATT
1 AAATAAAATAATT
65360 AAATAAAATA
1 AAATAAAATA
65370 CTAACAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
11 6 0.16
12 15 0.41
13 16 0.43
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:66811 original size:36 final size:36
Alignment explanation
Indices: 66740--66809 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
66730 GATTACTAAA
*
66740 CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTTC
1 CCCGGCCCCGTCCCCGTTTAACATAAACGGTTTTTC
* * *
66776 CCCGGCCCTGTCCCC-TTTAGCATAAACGATTTTT
1 CCCGGCCCCGTCCCCGTTTAACATAAACGGTTTTT
66810 TCTCGTTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.17, C:0.37, G:0.14, T:0.31
Consensus pattern (36 bp):
CCCGGCCCCGTCCCCGTTTAACATAAACGGTTTTTC
Found at i:67970 original size:60 final size:60
Alignment explanation
Indices: 67893--68050 Score: 196
Period size: 60 Copynumber: 2.6 Consensus size: 60
67883 ATTGGTTTTT
* * * * * *
67893 AAACTTTTAAATATTTTAACTTCATCCCTAAACTATGA-CTATTATTCTAAATTAGTCCTCA
1 AAACTTTTGAACATTTTAATTTCATCCCCAAACTATAATCT-TCATTCTAAATTAGTCC-CA
*
67954 AAA-TTTTGAACATTTTAGTTTCATCCCCAAACTATAATCTTCATTCTAAATTAGTCCCA
1 AAACTTTTGAACATTTTAATTTCATCCCCAAACTATAATCTTCATTCTAAATTAGTCCCA
*
68013 AAACTTTTTGAACATTTTAATTTCAT-CCCAAATTATAA
1 AAAC-TTTTGAACATTTTAATTTCATCCCCAAACTATAA
68051 GTATATACTA
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
59 5 0.06
60 55 0.65
61 25 0.29
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.41
Consensus pattern (60 bp):
AAACTTTTGAACATTTTAATTTCATCCCCAAACTATAATCTTCATTCTAAATTAGTCCCA
Found at i:68272 original size:60 final size:59
Alignment explanation
Indices: 68177--68293 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 59
68167 GAATATGGAG
* ** *
68177 ATGAAATTGGAAGATTCAAAAGTTTGGGGATTAATTT-AGAATGAGAGTCATAGTTTGGTT
1 ATGAAATTGAAAGATTCAAAAGTTTAAGGATTAATTTGA-AATAAGA-TCATAGTTTGGTT
*
68237 ATGAAATTGAAATATTCAAAAGTTTAAGG-TCTAATTTGAAATAAGATCATAGTTTGG
1 ATGAAATTGAAAGATTCAAAAGTTTAAGGAT-TAATTTGAAATAAGATCATAGTTTGG
68294 AAACATATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 12 0.24
60 37 0.74
61 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.35
Consensus pattern (59 bp):
ATGAAATTGAAAGATTCAAAAGTTTAAGGATTAATTTGAAATAAGATCATAGTTTGGTT
Found at i:69902 original size:2 final size:2
Alignment explanation
Indices: 69895--69932 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
69885 TGACTCGATC
69895 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
69933 TTTTTATTTT
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:69989 original size:30 final size:29
Alignment explanation
Indices: 69952--70018 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
69942 TTTTTATTAT
*
69952 TAAAATATATT-ATTTAAT-TATTAAAAATA
1 TAAAA-ATATTAATTTAATCAATT-AAAATA
69981 TAAAAATATTAATTTAATCAATTAAAATA
1 TAAAAATATTAATTTAATCAATTAAAATA
70010 TAATAAATA
1 TAA-AAATA
70019 ATTTTAGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 5 0.15
29 21 0.62
30 8 0.24
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAAATATTAATTTAATCAATTAAAATA
Found at i:75388 original size:30 final size:30
Alignment explanation
Indices: 75353--75457 Score: 201
Period size: 30 Copynumber: 3.5 Consensus size: 30
75343 AAGTATTGTC
*
75353 TCAATTAAGCCATTATTTAAAAACTTATGA
1 TCAATTAAGCCATTACTTAAAAACTTATGA
75383 TCAATTAAGCCATTACTTAAAAACTTATGA
1 TCAATTAAGCCATTACTTAAAAACTTATGA
75413 TCAATTAAGCCATTACTTAAAAACTTATGA
1 TCAATTAAGCCATTACTTAAAAACTTATGA
75443 TCAATTAAGCCATTA
1 TCAATTAAGCCATTA
75458 TATAATCAGT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (30 bp):
TCAATTAAGCCATTACTTAAAAACTTATGA
Found at i:76582 original size:20 final size:20
Alignment explanation
Indices: 76557--76602 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
76547 TTAAATCTCT
76557 ATATTTATTGAATAAAAATA
1 ATATTTATTGAATAAAAATA
* * *
76577 ATATTTTTTTAATAAATATA
1 ATATTTATTGAATAAAAATA
*
76597 TTATTT
1 ATATTT
76603 CAGATTGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATTTATTGAATAAAAATA
Found at i:76947 original size:12 final size:12
Alignment explanation
Indices: 76930--76957 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
76920 AAATGTCACC
76930 CACTCTTGGGGA
1 CACTCTTGGGGA
76942 CACTCTTGGGGA
1 CACTCTTGGGGA
76954 CACT
1 CACT
76958 AATGGTCTCT
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:0.18, C:0.29, G:0.29, T:0.25
Consensus pattern (12 bp):
CACTCTTGGGGA
Found at i:78191 original size:183 final size:183
Alignment explanation
Indices: 77833--78201 Score: 607
Period size: 183 Copynumber: 2.0 Consensus size: 183
77823 ATTAAATTTT
* * *
77833 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTAAGCCCAAACAATTTAAAACCCAATTAATAA
*
77898 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAATTTTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
*
77963 ATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTT-AATTAAA
131 ATTTTATAATTATATATTATTTAAATTAATTATAAAC-GTTTTTTTGAATTAAA
* *
78016 AAATATTAAATATATTATATATAACATTTGGACTAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTAAGCCCAAACAATTTAAAACCCAATTAATAA
** *
78081 TTTAAGATCCAATAACTTTTAAATTTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAA-TTATAT-AAATTT
78146 TTATTTTATAATTATATATTATTTAAATTAATTATAAAC-TTTTTTTGAATTAAA
129 TTATTTTATAATTATATATTATTTAAATTAATTATAAACGTTTTTTTGAATTAAA
78200 AA
1 AA
78202 CATTTAATTT
Statistics
Matches: 173, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
183 116 0.67
184 14 0.08
185 43 0.25
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGACTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
ATTTTATAATTATATATTATTTAAATTAATTATAAACGTTTTTTTGAATTAAA
Found at i:86454 original size:20 final size:20
Alignment explanation
Indices: 86431--86497 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
86421 AATCTGTAAA
86431 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
86451 TCGCAACGC-GATAGTAAAAT
1 TCGCAACACAGA-AGTCAAAT
* * *
86471 TTGTAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
86491 TCGCAAC
1 TCGCAAC
86498 GTGAATAGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 2 0.06
20 33 0.92
21 1 0.03
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:86454 original size:40 final size:41
Alignment explanation
Indices: 86410--86517 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 41
86400 AGTTTCCAAT
* *
86410 TTCGCAACGCGAATCTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAAT-AGTAAAATTCGCAACACAAAAGTCAAA
* *
86450 TTCGCAACGCG-ATAGTAAAATTTGTAACACAAAAGTCAAA
1 TTCGCAACGCGAATAGTAAAATTCGCAACACAAAAGTCAAA
* *
86490 TTCGCAACGTGAATAGTAAAAATCGCAA
1 TTCGCAACGCGAATAGTAAAATTCGCAA
86518 TGTGAATAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
38 2 0.04
39 5 0.09
40 37 0.65
41 13 0.23
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (41 bp):
TTCGCAACGCGAATAGTAAAATTCGCAACACAAAAGTCAAA
Found at i:86537 original size:20 final size:21
Alignment explanation
Indices: 86487--86539 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
86477 CACAAAAGTC
86487 AAATTCGCAACGTGAATAGTAA
1 AAATT-GCAACGTGAATAGTAA
* *
86509 AAATCGCAATGTGAATAGT-A
1 AAATTGCAACGTGAATAGTAA
86529 AAATTGCAACG
1 AAATTGCAACG
86540 AATCTATGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (21 bp):
AAATTGCAACGTGAATAGTAA
Found at i:86942 original size:21 final size:21
Alignment explanation
Indices: 86910--86960 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
86900 TAAATTCGCA
86910 TTGCGA-TTTTACTATTCACG
1 TTGCGATTTTTACTATTCACG
86930 TTGCGATTTTTACTATTCACG
1 TTGCGATTTTTACTATTCACG
*
86951 CTGCGATTTT
1 TTGCGATTTT
86961 GAAAACTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.47
Consensus pattern (21 bp):
TTGCGATTTTTACTATTCACG
Found at i:92465 original size:53 final size:53
Alignment explanation
Indices: 92342--92971 Score: 849
Period size: 53 Copynumber: 11.7 Consensus size: 53
92332 TGGGTTCGCT
* * *
92342 CCCTATTTCTTCAGAGGGTATAAGACTTGA-ATCATCTTCAACAAACTT--GTCTG-C
1 CCCTATTTCTTCAGAGAGTATAAGAC-TCACA--ATCTTCATC-AA-TTGCGTCTGCC
* *
92396 CCCTATTTCTTCAGAGAGTATAAGAAC-CATAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCACAATCTTCATCAATTGCGTCTGCC
* * * *
92449 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATTGCGTCTGCC
* * *
92504 CCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
* *
92557 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATTGCGTCTGCC
* *
92612 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGCCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
* *
92665 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
* *
92718 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATTGCGTCTGCC
*
92773 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
*
92826 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
* *
92879 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCA-CGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTT-CATCAATTGCGTCTGCC
* *
92934 CCCTATTTCTTCAGGGAGTATAAGACCCACAATCTTCA
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCA
92972 ACAAATGGGT
Statistics
Matches: 523, Mismatches: 38, Indels: 32
0.88 0.06 0.05
Matches are distributed among these distances:
50 1 0.00
51 2 0.00
52 17 0.03
53 282 0.54
54 24 0.05
55 195 0.37
56 2 0.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.30
Consensus pattern (53 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
Found at i:92553 original size:108 final size:108
Alignment explanation
Indices: 92342--92971 Score: 970
Period size: 108 Copynumber: 5.9 Consensus size: 108
92332 TGGGTTCGCT
* * *
92342 CCCTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTT--GTCTG-CCCCTATT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAAC-GA-TTGCGTCTGCCCCCTATT
* *
92403 TCTTCAGAGAGTATAAGAACCATAATCTTCATCAATCGCGTCTGCC
63 TCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
* * *
92449 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
92514 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
92557 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
* *
92622 TCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGCCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
92665 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
* * * *
92728 TCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
66 TCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
* * *
92773 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
*
92836 TCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
* *
92879 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
*
92944 TCAGGGAGTATAAGACCCACAATCTTCA
66 TCAGAGAGTATAAGACCCACAATCTTCA
92972 ACAAATGGGT
Statistics
Matches: 485, Mismatches: 29, Indels: 17
0.91 0.05 0.03
Matches are distributed among these distances:
105 2 0.00
106 101 0.21
107 46 0.09
108 336 0.69
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.30
Consensus pattern (108 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
Found at i:93008 original size:161 final size:161
Alignment explanation
Indices: 92342--92975 Score: 954
Period size: 161 Copynumber: 3.9 Consensus size: 161
92332 TGGGTTCGCT
* * * **
92342 CCCTATTTCTTCAGAGGGTATAAGACTTGA-ATCATCTTCAACAAACTTGTCTG-CCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAGAC-TCACA--ATCTTCAACAATCGCGTCTGCCCCCTATTTC
* * *
92405 TTCAGAGAGTATAAGAAC-C--ATAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
63 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * * *
92467 TATAAGACTCGAACGATCTTCAACGATTGTGTCTGCC
127 TATAAGAC-C-CACAATCTTCAACAATTGCGTCTGCC
* * *
92504 CCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTC
*
92569 AGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
66 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
* *
92634 AGACCCACAATCTTCATCAATTGCGCCTGCC
131 AGACCCACAATCTTCAACAATTGCGTCTGCC
* *
92665 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTC
*
92730 AGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
66 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
*
92795 AGACCCACAATCTTCATCAATTGCGTCTGCC
131 AGACCCACAATCTTCAACAATTGCGTCTGCC
*
92826 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTC
* *
92891 AGAGAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGCCCCCTATTTCTTCAGGGAGTATA
66 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
92956 AGACCCACAATCTTCAACAA
131 AGACCCACAATCTTCAACAA
92976 ATGGGTTCGC
Statistics
Matches: 436, Mismatches: 31, Indels: 11
0.91 0.06 0.02
Matches are distributed among these distances:
160 18 0.04
161 345 0.79
162 26 0.06
163 47 0.11
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (161 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTC
AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
AGACCCACAATCTTCAACAATTGCGTCTGCC
Found at i:93061 original size:161 final size:160
Alignment explanation
Indices: 92426--93079 Score: 661
Period size: 161 Copynumber: 4.1 Consensus size: 160
92416 TAAGAACCAT
* * * *
92426 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAAC
* * * * * * * *
92491 GATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCG-TCTG
64 AAATGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAC-ATC-TCTTCAAACGGGTTC-G
* * ** *
92555 CCCCCTATTTC-TTCAGAGAGTATAAGACTCGAAC
126 CTCCTTCCTTCTTTAAGAGAGTATAAGACTCGAAC
* *
92589 AATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAA
* * * *
92654 TTGCGCCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACA-ATCTTC-AAC-GATTGCGTCTG
66 ATGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACATCTCTTCAAACGGGTT-CG-CT-
* * *
92716 CC-CCCTATTTCTTCAGAGAGTATAAGACTCGAAC
128 CCTTCCT-TCT-TTAAGAGAGTATAAGACTCGAAC
* *
92750 AATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAA
* * * * *
92815 TTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCG-TCTGCC
66 ATGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAC-ATC-TCTTCAAACGGGTTC-GCT
* ** *
92879 CCCTATTTC-TTCAGAGAGTATAAGACTCGAAC
128 CCTTCCTTCTTTAAGAGAGTATAAGACTCGAAC
* *
92911 AATCTTCCACGATCGCGTCTGCCCCCTATTTCTTCAGGGAGTATAAGACCCACAATCTTCAACAA
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAA
* * *
92976 ATGGGT-TCGCTCCCTATTTC-TCTAGGGAGTAT-AGAACTCGAACATCTCTTCAAACGGGTTCG
66 ATGCGTCT-GCCCCCTATTTCTTC-AGAGAGTATAAG-ACTC--ACATCTCTTCAAACGGGTTCG
93038 CTCCTTCCTTCTTTAAG-GAGTAT-AGAACTCGAAC
126 CTCCTTCCTTCTTTAAGAGAGTATAAG-ACTCGAAC
93072 -ATCTTCAA
1 AATCTTCAA
93080 ACGGGTTCGC
Statistics
Matches: 420, Mismatches: 49, Indels: 47
0.81 0.09 0.09
Matches are distributed among these distances:
157 4 0.01
158 7 0.02
159 3 0.01
160 15 0.04
161 318 0.76
162 11 0.03
163 51 0.12
164 7 0.02
165 4 0.01
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (160 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAA
ATGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACATCTCTTCAAACGGGTTCGCTCCT
TCCTTCTTTAAGAGAGTATAAGACTCGAAC
Found at i:93094 original size:51 final size:51
Alignment explanation
Indices: 92973--93373 Score: 505
Period size: 51 Copynumber: 7.8 Consensus size: 51
92963 CAATCTTCAA
* * * *
92973 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCGAACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATAGAACTCGGACA--TCTT
* * * *
93026 CAAACGGGTTCGCTCCTTCCTTCTTTAAGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATAGAACTCGGACATCTT
* * * * *
93077 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGATTATAGAACTCGCATATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATAGAACTCGGACATCTT
* * *
93128 CACACGGGTTCGCTCCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATAGAACTCGGACATCTT
* * * * * *
93179 TAAACGGTTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATAGAACTCGGACATCTT
* * *
93230 CACACGGGTTCGCTCCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATAGAACTCGGACATCTT
* * *
93281 CAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATAGAACTCGGACATCTT
* * *
93332 CAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 CAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATAGAACTC
93374 AAATAATCTT
Statistics
Matches: 308, Mismatches: 40, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
51 267 0.87
53 41 0.13
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (51 bp):
CAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATAGAACTCGGACATCTT
Found at i:93151 original size:102 final size:102
Alignment explanation
Indices: 92973--93373 Score: 559
Period size: 102 Copynumber: 3.9 Consensus size: 102
92963 CAATCTTCAA
* * * *
92973 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCGAACATCTCTTCAAACGGGTTCG
1 CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCG--CATATCTTCAAACGGGTTCG
* * * *
93038 CTCCTTCCTTCTTTAAGGAGTATAGAACTCGAACATCTT
64 CTCCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
* * * *
93077 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGATTATAGAACTCGCATATCTTCACACGGGTTCGCT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCGCATATCTTCAAACGGGTTCGCT
93142 CCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
66 CCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
* * * * *
93179 TAAACGGTTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTTCACACGGGTTCGCT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCGCATATCTTCAAACGGGTTCGCT
93244 CCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
66 CCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
* * * * * *
93281 CAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCAAACAGGTTCGCT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCGCATATCTTCAAACGGGTTCGCT
* *
93346 CCCTCTTTCTCTAGGGAGTATGGAACTC
66 CCTTCCTTCTCTAGGGAGTATGGAACTC
93374 AAATAATCTT
Statistics
Matches: 269, Mismatches: 28, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
102 232 0.86
104 37 0.14
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (102 bp):
CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCGCATATCTTCAAACGGGTTCGCT
CCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
Found at i:93827 original size:36 final size:36
Alignment explanation
Indices: 93755--93943 Score: 229
Period size: 36 Copynumber: 5.2 Consensus size: 36
93745 ACTCTTCTGA
* * *
93755 GAAGGCTTAAAATGGATCTGCTTCACTACTT-T-TGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * *
93791 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
93827 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
93863 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
93899 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCAGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
93935 GAAGGCTTA
1 GAAGGCTTA
93944 GGATTGACTT
Statistics
Matches: 135, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
34 1 0.01
35 12 0.09
36 122 0.90
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:94942 original size:124 final size:124
Alignment explanation
Indices: 94670--94973 Score: 448
Period size: 124 Copynumber: 2.4 Consensus size: 124
94660 TCAATAATTT
* **
94670 CTTGGTCTGAATCTTTTCATCTCAACATGACGTGGGTTTGGTCTCGCCCCAACATTATCTTACAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCT-GCCCCAACATTATCTTACAC
* * * * *
94735 TGGTAAGGGCCTTCAAAATGCCCCATCACCTCAAATTGTGAGGCTCATTCTTTATGCCTC
65 TGGTAAGGGCCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
* * *
94795 ATTGGTCTGAATATTTTCATCTCAACATGATGTGGGTTCAGTCATGCCCCAACATTATCTTATAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTC-TGCCCCAACATTATCTTACAC
*
94860 TGGTACGGG-CATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
65 TGGTAAGGGCCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
* *
94919 CTTGGTCTGAATCTTGTCTTCTCAACATGATGTGGGTTCAGTCGTGCCCCAACAT
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTC-TGCCCCAACAT
94974 ATCACAACTT
Statistics
Matches: 161, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
124 95 0.59
125 65 0.40
126 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (124 bp):
CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCTGCCCCAACATTATCTTACACT
GGTAAGGGCCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
Found at i:105377 original size:7 final size:7
Alignment explanation
Indices: 105362--105403 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
105352 AATATATATT
105362 ATATATTA
1 ATAT-TTA
*
105370 AAATTTA
1 ATATTTA
105377 ATATTTA
1 ATATTTA
105384 ATATTTA
1 ATATTTA
105391 ATATTTA
1 ATATTTA
105398 ATATTT
1 ATATTT
105404 TCGTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 29 0.91
8 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATATTTA
Found at i:106126 original size:22 final size:22
Alignment explanation
Indices: 106085--106173 Score: 142
Period size: 22 Copynumber: 4.0 Consensus size: 22
106075 CTCGTATAAA
106085 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
106108 TGCACCGAAGTACCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
106130 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
106152 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
106174 GATGTCCATA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
22 52 0.83
23 11 0.17
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:106139 original size:13 final size:13
Alignment explanation
Indices: 106121--106161 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
106111 ACCGAAGTAC
106121 CCGTAGAATTGCA
1 CCGTAGAATTGCA
106134 CCGTAG---TGC-
1 CCGTAGAATTGCA
106143 CCGTAGAATTGCA
1 CCGTAGAATTGCA
106156 CCGTAG
1 CCGTAG
106162 TGCCCGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:107745 original size:21 final size:21
Alignment explanation
Indices: 107721--107765 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
107711 TTCTTGTTCG
* *
107721 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
107742 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
107763 TTG
1 TTG
107766 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:108734 original size:16 final size:17
Alignment explanation
Indices: 108694--108735 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
108684 GCATCAGTTC
*
108694 TTATCACTCAAACTCCT
1 TTATCAATCAAACTCCT
* *
108711 TAATCAATCAAA-TTCT
1 TTATCAATCAAACTCCT
108727 TTATCAATC
1 TTATCAATC
108736 TTTAATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATCAATCAAACTCCT
Found at i:110978 original size:22 final size:22
Alignment explanation
Indices: 110937--111025 Score: 151
Period size: 22 Copynumber: 4.0 Consensus size: 22
110927 CTCGTATAAA
110937 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
110960 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
110982 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
111004 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
111026 GATGTCCATA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 53 0.82
23 12 0.18
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:110991 original size:13 final size:13
Alignment explanation
Indices: 110951--111013 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
110941 CCGAAGTGCC
110951 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
110964 CC---GAAGTGC-
1 CCGTAGAATTGCA
110973 CCGTAGAATTGCA
1 CCGTAGAATTGCA
110986 CCGTAG---TGC-
1 CCGTAGAATTGCA
110995 CCGTAGAATTGCA
1 CCGTAGAATTGCA
111008 CCGTAG
1 CCGTAG
111014 TGCCCGTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 8 0.20
10 9 0.22
12 9 0.22
13 14 0.35
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:112605 original size:21 final size:21
Alignment explanation
Indices: 112581--112625 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
112571 TCTTGTTCGT
* *
112581 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
112602 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
112623 TTG
1 TTG
112626 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:113595 original size:16 final size:17
Alignment explanation
Indices: 113555--113596 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
113545 GCATCAGTTC
*
113555 TTATCACTCAAACTCCT
1 TTATCAATCAAACTCCT
* *
113572 TAATCAATCAAA-TTCT
1 TTATCAATCAAACTCCT
113588 TTATCAATC
1 TTATCAATC
113597 TTTAATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATCAATCAAACTCCT
Found at i:115836 original size:22 final size:22
Alignment explanation
Indices: 115795--115883 Score: 151
Period size: 22 Copynumber: 4.0 Consensus size: 22
115785 CTCGTATAAA
115795 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
115818 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
115840 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
115862 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
115884 GATGTCCATA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 53 0.82
23 12 0.18
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:115849 original size:13 final size:13
Alignment explanation
Indices: 115809--115871 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
115799 CCGAAGTGCC
115809 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
115822 CC---GAAGTGC-
1 CCGTAGAATTGCA
115831 CCGTAGAATTGCA
1 CCGTAGAATTGCA
115844 CCGTAG---TGC-
1 CCGTAGAATTGCA
115853 CCGTAGAATTGCA
1 CCGTAGAATTGCA
115866 CCGTAG
1 CCGTAG
115872 TGCCCGTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 8 0.20
10 9 0.22
12 9 0.22
13 14 0.35
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:117464 original size:21 final size:21
Alignment explanation
Indices: 117440--117484 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
117430 TCTTGTTCGT
* *
117440 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
117461 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
117482 TTG
1 TTG
117485 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:121451 original size:109 final size:109
Alignment explanation
Indices: 121255--121467 Score: 284
Period size: 109 Copynumber: 2.0 Consensus size: 109
121245 TTATAACGGT
* * * *
121255 GGGGTACTAAAATGAAATAAAAATTAAACGTTAGGTATGATTTTGGATATTTTTTGAAAATTTAG
1 GGGGTACTAAAATAAAACAAAAACTAAACGTTAGGTATGATTTTGGATATTTTTTGAAAATTTAA
* * * * *
121320 GTACTAAAACGGACTAAGACTGATAGTTTATGTACTAAACGTGA
66 GTACTAAAACGGACAAAAACTGATAATTTAGGCACTAAACGTGA
*** * *
121364 GGGGTACTAAAATAAAACAAAAACTAAACGTTAGGTATGATTTTTTTTTTTTTTTGGAAATTTAA
1 GGGGTACTAAAATAAAACAAAAACTAAACGTTAGGTATGATTTTGGATATTTTTTGAAAATTTAA
121429 GTACTAAAGA-GGACAAAAACTGATAATTTAGGCACTAAA
66 GTACTAAA-ACGGACAAAAACTGATAATTTAGGCACTAAA
121468 TGTAAAATTT
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 88 0.99
110 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (109 bp):
GGGGTACTAAAATAAAACAAAAACTAAACGTTAGGTATGATTTTGGATATTTTTTGAAAATTTAA
GTACTAAAACGGACAAAAACTGATAATTTAGGCACTAAACGTGA
Found at i:122054 original size:25 final size:27
Alignment explanation
Indices: 121998--122055 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
121988 ATTGAATTAA
* *
121998 TAAATATAAGTATACAATATATATTTT
1 TAAATATAAATATACAAAATATATTTT
122025 TAAATATAAATAT-CAAAATAT-TTTT
1 TAAATATAAATATACAAAATATATTTT
122050 TAAATA
1 TAAATA
122056 GTTTTATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 10 0.34
26 7 0.24
27 12 0.41
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (27 bp):
TAAATATAAATATACAAAATATATTTT
Found at i:123738 original size:15 final size:15
Alignment explanation
Indices: 123718--123747 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
123708 ATAGTAGTGC
123718 AAGTGTAGCTGTTCA
1 AAGTGTAGCTGTTCA
*
123733 AAGTGTAGTTGTTCA
1 AAGTGTAGCTGTTCA
123748 TCTAGTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (15 bp):
AAGTGTAGCTGTTCA
Found at i:124519 original size:21 final size:21
Alignment explanation
Indices: 124456--124539 Score: 57
Period size: 22 Copynumber: 4.0 Consensus size: 21
124446 ATATTTATTC
*
124456 AAATAT-TTAAAAGATTAAATAT
1 AAATATATTAAAAAATT-AA-AT
* * *
124478 AAAAATACT-AAAAATAAAAATT
1 AAATATATTAAAAAAT-TAAA-T
124500 AAAT-TATTAAAAAATTAAAT
1 AAATATATTAAAAAATTAAAT
* *
124520 ATATATATTATAAAATTAAA
1 AAATATATTAAAAAATTAAA
124540 GTTTTTAGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
20 4 0.08
21 21 0.44
22 22 0.46
23 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
AAATATATTAAAAAATTAAAT
Found at i:126609 original size:36 final size:38
Alignment explanation
Indices: 126564--126652 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 38
126554 TTTGTATAAT
*
126564 ATTACAAATTATAAAATATTTAT-TTATTTTCTTTA-AAA
1 ATTA-AAATTATAAAATATTTATATAATTTT-TTTACAAA
126602 ATT-AAATTCAT--AATATTTATATAATTTTTTTACAAA
1 ATTAAAATT-ATAAAATATTTATATAATTTTTTTACAAA
*
126638 ATTAAAAATATAAAA
1 ATTAAAATTATAAAA
126653 AAAGTTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
35 13 0.30
36 19 0.44
37 6 0.14
38 5 0.12
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (38 bp):
ATTAAAATTATAAAATATTTATATAATTTTTTTACAAA
Found at i:126648 original size:31 final size:31
Alignment explanation
Indices: 126565--126648 Score: 75
Period size: 35 Copynumber: 2.6 Consensus size: 31
126555 TTGTATAATA
*
126565 TTAC-AAATTATAAAATATTTATTTATTTTCT
1 TTACAAAATTA-AAAATATTTATTAATTTTCT
126596 TTA-AAAATTAAATTCATAATATTTATATAATTTT-T
1 TTACAAAATT-AA---A-AATATTTAT-TAATTTTCT
126631 TTACAAAATTAAAAATAT
1 TTACAAAATTAAAAATAT
126649 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
31 14 0.32
32 2 0.05
34 1 0.02
35 15 0.34
36 12 0.27
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (31 bp):
TTACAAAATTAAAAATATTTATTAATTTTCT
Found at i:128482 original size:14 final size:15
Alignment explanation
Indices: 128454--128492 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
128444 ATTTGTTATA
128454 TAAAATATATCTTTT
1 TAAAATATATCTTTT
128469 TAAAA-ATAT-TTTT
1 TAAAATATATCTTTT
128482 TAATAATATAT
1 TAA-AATATAT
128493 AAGTAGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
TAAAATATATCTTTT
Found at i:128605 original size:21 final size:21
Alignment explanation
Indices: 128548--128607 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
128538 AAAAAATAAT
*
128548 ATTTATATTCAATTTTTTAGTA
1 ATTTATATTTAA-TTTTTAGTA
*
128570 ATTTA-ATTTTTATTTTTAGTA
1 ATTTATA-TTTAATTTTTAGTA
*
128591 TTTTATATTTAATTTTT
1 ATTTATATTTAATTTTT
128608 TAAATATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 23 0.72
22 9 0.28
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (21 bp):
ATTTATATTTAATTTTTAGTA
Found at i:128630 original size:16 final size:14
Alignment explanation
Indices: 128544--128633 Score: 67
Period size: 14 Copynumber: 6.1 Consensus size: 14
128534 TTAAAAAAAA
128544 TAATA-TTTATATT
1 TAATATTTTATATT
* *
128557 CAATTTTTTAGTAATT
1 TAATATTTTA-T-ATT
*
128573 TAAT-TTTTATTTT
1 TAATATTTTATATT
*
128586 TAGTATTTTATATT
1 TAATATTTTATATT
*
128600 TAATTTTTTAAATATT
1 TAATATTTT--ATATT
128616 TGAATAATTTTATATT
1 T-AAT-ATTTTATATT
128632 TA
1 TA
128634 TAATTTAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
13 8 0.13
14 20 0.33
15 7 0.12
16 18 0.30
17 3 0.05
18 4 0.07
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (14 bp):
TAATATTTTATATT
Found at i:130077 original size:15 final size:14
Alignment explanation
Indices: 130034--130104 Score: 58
Period size: 15 Copynumber: 5.0 Consensus size: 14
130024 ATTTCTAAAA
* *
130034 ATTATTTAATATGT
1 ATTATTTAATTTTT
*
130048 A-TATTCAATTTTTT
1 ATTATTTAA-TTTTT
130062 ATTAATTTAATTTTT
1 ATT-ATTTAATTTTT
130077 ATT-TTTAGTATTTTT
1 ATTATTTA--ATTTTT
130092 A-TATTTAATTTTT
1 ATTATTTAATTTTT
130105 TAAATATTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
13 16 0.34
14 6 0.13
15 20 0.43
16 5 0.11
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (14 bp):
ATTATTTAATTTTT
Found at i:131888 original size:21 final size:21
Alignment explanation
Indices: 131850--131889 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
131840 GGTCACTAGT
**
131850 ATAGTTTACCTTTTATTTTAA
1 ATAGTTTACCTTAAATTTTAA
*
131871 ATAGTTTATCTTAAATTTT
1 ATAGTTTACCTTAAATTTT
131890 TTAACTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
ATAGTTTACCTTAAATTTTAA
Found at i:133113 original size:3 final size:3
Alignment explanation
Indices: 133097--133134 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
133087 TATCTGCCTT
*
133097 TTA TTA TT- TT- TTA TTA TTA TTA TTA TCA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
133135 CAAACTAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:133192 original size:24 final size:24
Alignment explanation
Indices: 133165--133212 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
133155 GATCTTGCAG
*
133165 TAATTTTTATCAACTAATTATACC
1 TAATTTTTATCAACAAATTATACC
133189 TAATTTTTATCAACAAATTATACC
1 TAATTTTTATCAACAAATTATACC
133213 ATATTAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATTTTTATCAACAAATTATACC
Found at i:135739 original size:15 final size:14
Alignment explanation
Indices: 135719--135766 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
135709 ATATTCAATT
135719 TTTTTATTAATTTAA
1 TTTTTATT-ATTTAA
135734 TTTTTATT-TTTAGTA
1 TTTTTATTATTTA--A
135749 TTTTTA-TATTTAA
1 TTTTTATTATTTAA
135762 TTTTT
1 TTTTT
135767 TAAATATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.33
14 1 0.03
15 19 0.63
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTTTATTATTTAA
Found at i:138778 original size:3 final size:3
Alignment explanation
Indices: 138761--138799 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
138751 TATCTGCCTT
* *
138761 TTA TTA TT- TTT TTA TTA TTA TTA TTA TCA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
138800 CAAACTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:138857 original size:24 final size:24
Alignment explanation
Indices: 138830--138877 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
138820 GATCTTGCAG
*
138830 TAATTTTTATCAACTAATTATACC
1 TAATTTTTATCAACAAATTATACC
138854 TAATTTTTATCAACAAATTATACC
1 TAATTTTTATCAACAAATTATACC
138878 ATATTAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATTTTTATCAACAAATTATACC
Found at i:148645 original size:2 final size:2
Alignment explanation
Indices: 148638--148671 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
148628 AGATCGCTTG
148638 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
148672 TAAAAATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:149908 original size:25 final size:25
Alignment explanation
Indices: 149875--149922 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
149865 TTTATGTTGT
149875 GTTTATACATTTCTTAATAATTTGC
1 GTTTATACATTTCTTAATAATTTGC
*
149900 GTTTGTACATTTCTTAATAATTT
1 GTTTATACATTTCTTAATAATTT
149923 CATATTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (25 bp):
GTTTATACATTTCTTAATAATTTGC
Found at i:151744 original size:21 final size:23
Alignment explanation
Indices: 151718--151761 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
151708 TAATAAATAG
151718 AACTCATAAT-AAATAAT-TTTT
1 AACTCATAATAAAATAATATTTT
*
151739 AACTCATAGTAAAATAATATTTT
1 AACTCATAATAAAATAATATTTT
151762 TTTCTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (23 bp):
AACTCATAATAAAATAATATTTT
Found at i:151804 original size:21 final size:21
Alignment explanation
Indices: 151778--151860 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
151768 TTAGGGTTAG
*
151778 GATTTAGGCTTTAAGATTTAA
1 GATTTAGGATTTAAGATTTAA
* *
151799 GCTTTAGGATTTAAGGTTTATA
1 GATTTAGGATTTAAGATTTA-A
* *
151821 -ATTTAGGTTTTGAGATTTAA
1 GATTTAGGATTTAAGATTTAA
* * * *
151841 GGTTTTGGGTTTAAGTTTTA
1 GATTTAGGATTTAAGATTTA
151861 GGATAAGGTT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (21 bp):
GATTTAGGATTTAAGATTTAA
Found at i:151818 original size:28 final size:28
Alignment explanation
Indices: 151774--151872 Score: 82
Period size: 28 Copynumber: 3.6 Consensus size: 28
151764 TCTTTTAGGG
151774 TTAGGATTT-AGGCTTTAAGATTTAAGCT
1 TTAGGATTTAAGG-TTTAAGATTTAAGCT
*
151802 TTAGGATTTAAGGTTTATA-ATTT-AGGT
1 TTAGGATTTAAGGTTTA-AGATTTAAGCT
* ** * *
151829 TTTGAGATTTAAGGTTTTGGGTTTAAGTT
1 TTAG-GATTTAAGGTTTAAGATTTAAGCT
151858 TTAGGA--TAAGGTTTA
1 TTAGGATTTAAGGTTTA
151873 CGTTTGAAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
26 8 0.14
27 6 0.10
28 34 0.59
29 10 0.17
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.46
Consensus pattern (28 bp):
TTAGGATTTAAGGTTTAAGATTTAAGCT
Found at i:151853 original size:14 final size:15
Alignment explanation
Indices: 151778--151859 Score: 61
Period size: 14 Copynumber: 5.9 Consensus size: 15
151768 TTAGGGTTAG
* *
151778 GATTT-AGGCTTTAA
1 GATTTAAGGTTTTGA
* *
151792 GATTTAAGCTTTAG-
1 GATTTAAGGTTTTGA
151806 GATTTAAGGTTTAT-A
1 GATTTAAGGTTT-TGA
151821 -ATTT-AGGTTTTGA
1 GATTTAAGGTTTTGA
151834 GATTTAAGGTTTTG-
1 GATTTAAGGTTTTGA
*
151848 GGTTTAA-GTTTT
1 GATTTAAGGTTTT
151860 AGGATAAGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
12 1 0.02
13 12 0.22
14 30 0.55
15 12 0.22
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (15 bp):
GATTTAAGGTTTTGA
Found at i:152037 original size:2 final size:2
Alignment explanation
Indices: 152030--152071 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
152020 ATCCTACCCC
152030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
152071 A
1 A
152072 GTTAGATTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152080 original size:17 final size:17
Alignment explanation
Indices: 152030--152080 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
152020 ATCCTACCCC
*
152030 ATATATATATATATA-T
1 ATATATATATATAGATT
*
152046 ATATATATATATATATT
1 ATATATATATATAGATT
152063 ATATATATAGT-TAGATT
1 ATATATATA-TATAGATT
152080 A
1 A
152081 GCACTTTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 15 0.47
17 16 0.50
18 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
ATATATATATATAGATT
Found at i:153562 original size:29 final size:29
Alignment explanation
Indices: 153483--153562 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
153473 TACCTAACTA
* *
153483 AATTGATGTAAGAAATGACATATTCATCT
1 AATTGATGTAAGCAATGACATCTTCATCT
153512 AATTGATGTAAGCAATGACATCTTCATCT
1 AATTGATGTAAGCAATGACATCTTCATCT
153541 AATTGATGTAAGCAATGACATC
1 AATTGATGTAAGCAATGACATC
153563 AATTTAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (29 bp):
AATTGATGTAAGCAATGACATCTTCATCT
Done.