Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011238.1 Kokia drynarioides strain JFW-HI SEQ_126216, 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: 114778
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:206 original size:51 final size:52
Alignment explanation
Indices: 142--263 Score: 141
Period size: 50 Copynumber: 2.4 Consensus size: 52
132 ATTTATAATT
142 TTTTTTCTTTTTATTCTTTTCTTTTT-AAAA-AAATA-TATATTAAATATATACAA
1 TTTTTTC-TTTTA-T-TTTTCTTTTTAAAAATAAATATTA-ATTAAATATATACAA
195 TTTTTTC-TTTATTTTTCTTTTTAAAAATAAATATTAATTAAATATA-A-AA
1 TTTTTTCTTTTATTTTTCTTTTTAAAAATAAATATTAATTAAATATATACAA
*
244 TTTATTT-TTTTAATTTTCTT
1 TTT-TTTCTTTTATTTTTCTT
264 AAATTATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 13
0.82 0.01 0.17
Matches are distributed among these distances:
49 15 0.24
50 20 0.32
51 19 0.30
52 2 0.03
53 7 0.11
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (52 bp):
TTTTTTCTTTTATTTTTCTTTTTAAAAATAAATATTAATTAAATATATACAA
Found at i:240 original size:49 final size:50
Alignment explanation
Indices: 158--263 Score: 130
Period size: 49 Copynumber: 2.1 Consensus size: 50
148 CTTTTTATTC
* *
158 TTTTCTTTTTAAAAAAATATATATTAAATATATACAATTT-TTTCTTTAT
1 TTTTCTTTTTAAAAAAATATATATTAAATATATAAAATTTATTTCTTTAA
*
207 TTTTCTTTTTAAAAATAA-ATATTAATT-AA-ATATAAAATTTATTTTTTTAA
1 TTTTCTTTTTAAAAA-AATATA-T-ATTAAATATATAAAATTTATTTCTTTAA
257 TTTTCTT
1 TTTTCTT
264 AAATTATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
49 28 0.56
50 19 0.38
51 3 0.06
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (50 bp):
TTTTCTTTTTAAAAAAATATATATTAAATATATAAAATTTATTTCTTTAA
Found at i:874 original size:11 final size:11
Alignment explanation
Indices: 860--931 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
850 TTTCCATTCC
*
860 ATTTCATTTTA
1 ATTTCATTTAA
*
871 ATTTCATTTCA
1 ATTTCATTTAA
*
882 ATTTCAACTTT-C
1 ATTTC-A-TTTAA
* *
894 ATTTAATTTCA
1 ATTTCATTTAA
*
905 ACTTCTATTTAA
1 ATTTC-ATTTAA
917 ATTTCATTTAA
1 ATTTCATTTAA
928 ATTT
1 ATTT
932 AATCTTTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.06
11 29 0.59
12 14 0.29
13 3 0.06
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTCATTTAA
Found at i:885 original size:6 final size:6
Alignment explanation
Indices: 819--931 Score: 71
Period size: 6 Copynumber: 19.8 Consensus size: 6
809 TGAAATTTGA
* * * *
819 AATTTA AATTTC AAATTTC -ATTT- AATTTG AATTTC CA-TTC CATTTC
1 AATTTC AATTTC -AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC
* *
865 -ATTTT AATTTC -ATTTC AATTTC AACTTTC -ATTT- AATTTC AACTTC
1 AATTTC AATTTC AATTTC AATTTC AA-TTTC AATTTC AATTTC AATTTC
* * *
910 TATTTA AATTTC -ATTTA AATTT
1 AATTTC AATTTC AATTTC AATTT
932 AATCTTTTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
5 33 0.39
6 42 0.49
7 10 0.12
ACGTcount: A:0.32, C:0.14, G:0.01, T:0.53
Consensus pattern (6 bp):
AATTTC
Found at i:927 original size:56 final size:56
Alignment explanation
Indices: 820--931 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 56
810 GAAATTTGAA
* * **
820 ATTTAAATTTCAAATTTCATTTAATTTGAATTTCCATTCCATTTCATTTTAATTTC
1 ATTTAAATTTCAAATTTCATTTAATTTCAACTTCCATTAAATTTCATTTTAATTTC
* * * *
876 ATTTCAATTTCAACTTTCATTTAATTTCAACTTCTATTTAAATTTCATTTAAATTT
1 ATTTAAATTTCAAATTTCATTTAATTTCAACTTCCA-TTAAATTTCATTTTAATTT
932 AATCTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
56 31 0.66
57 16 0.34
ACGTcount: A:0.31, C:0.14, G:0.01, T:0.54
Consensus pattern (56 bp):
ATTTAAATTTCAAATTTCATTTAATTTCAACTTCCATTAAATTTCATTTTAATTTC
Found at i:1752 original size:36 final size:36
Alignment explanation
Indices: 1710--1787 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
1700 TTGATATTTT
*
1710 AATTAAATTCCATTGTTTAAAT-TAAAAAGCATGGAC
1 AATTAAATTCCAATGTTTAAATAT-AAAAGCATGGAC
*
1746 AATTAAATTTCAATGTTTAAATATAAAAGCATGGAC
1 AATTAAATTCCAATGTTTAAATATAAAAGCATGGAC
1782 AATTAA
1 AATTAA
1788 TGAATAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 38 0.97
37 1 0.03
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.33
Consensus pattern (36 bp):
AATTAAATTCCAATGTTTAAATATAAAAGCATGGAC
Found at i:11680 original size:19 final size:19
Alignment explanation
Indices: 11656--11695 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11646 ATTAATTTTG
11656 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
11675 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
11694 AT
1 AT
11696 ATGGTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:12087 original size:110 final size:110
Alignment explanation
Indices: 11961--12180 Score: 422
Period size: 110 Copynumber: 2.0 Consensus size: 110
11951 TATCTTGATA
*
11961 AATATTATGTTAATTTAATATTAAAGTGATTAAGTTTAATTACAGTTGATCTCTCTAAACTCTTC
1 AATATTATGTTAATTTAATATTAAAGTGATTAAGTTTAATTACAGTTGATCTCTCTAAACTCTCC
12026 TTATATAAAGAGAGTCTTGGGTCATTATTTTCTAAGAAGATACAT
66 TTATATAAAGAGAGTCTTGGGTCATTATTTTCTAAGAAGATACAT
*
12071 AATATTATGTTAATTTAATATTAAAGTGATTAAGTTTAATTACAGTTGATCTCTTTAAACTCTCC
1 AATATTATGTTAATTTAATATTAAAGTGATTAAGTTTAATTACAGTTGATCTCTCTAAACTCTCC
12136 TTATATAAAGAGAGTCTTGGGTCATTATTTTCTAAGAAGATACAT
66 TTATATAAAGAGAGTCTTGGGTCATTATTTTCTAAGAAGATACAT
12181 TTGAATTCAA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (110 bp):
AATATTATGTTAATTTAATATTAAAGTGATTAAGTTTAATTACAGTTGATCTCTCTAAACTCTCC
TTATATAAAGAGAGTCTTGGGTCATTATTTTCTAAGAAGATACAT
Found at i:13999 original size:20 final size:23
Alignment explanation
Indices: 13974--14026 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 23
13964 AGTGGAAGAT
13974 TTTTTTTTTTGTTCAGAG-G-A-
1 TTTTTTTTTTGTTCAGAGAGAAG
*
13994 TTTTTTATTTGTTCAGAGAGAAG
1 TTTTTTTTTTGTTCAGAGAGAAG
14017 TTTTTTTTTT
1 TTTTTTTTTT
14027 AATAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 17 0.61
21 1 0.04
22 1 0.04
23 9 0.32
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.62
Consensus pattern (23 bp):
TTTTTTTTTTGTTCAGAGAGAAG
Found at i:14386 original size:14 final size:15
Alignment explanation
Indices: 14361--14390 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
14351 TAATCCCAAT
14361 TATTTTTATTGTTTA
1 TATTTTTATTGTTTA
14376 TATTTTT-TTGTTTA
1 TATTTTTATTGTTTA
14390 T
1 T
14391 TTTAGCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
TATTTTTATTGTTTA
Found at i:18049 original size:42 final size:42
Alignment explanation
Indices: 18002--18084 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
17992 TTGTGGAATG
*
18002 AAGACACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTA
1 AAGACACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTA
18044 AAGACACCATCCAATCTTTTACCCTAACCAGAGGGCAGATT
1 AAGACACCATCCAATCTTTTACCCTAACCAGAGGGCAGATT
18085 GAAGTTACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (42 bp):
AAGACACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTA
Found at i:18192 original size:102 final size:102
Alignment explanation
Indices: 18009--18196 Score: 297
Period size: 102 Copynumber: 1.8 Consensus size: 102
17999 ATGAAGACAC
*
18009 CATCCAATCTTTTACCCTAATCAGAGGGCAGATTAAAGACACCATCCAATCTTTTACCCTAACCA
1 CATCCAATCTTTTACCCTAATCAGAAGGCAGATTAAAGACACCATCCAATCTTTTACCCTAACCA
18074 GAGGGCAGATTGAAGTTACAAGAGGGCAGATTGAAAT
66 GAGGGCAGATTGAAGTTACAAGAGGGCAGATTGAAAT
* * * * *
18111 CATCTAATCTTTTACCCTAA-CAATAAGGCAGATTGAAGACACCATTCAATCTTTTACCCTAATC
1 CATCCAATCTTTTACCCTAATC-AGAAGGCAGATTAAAGACACCATCCAATCTTTTACCCTAACC
*
18175 AGAGGGCAGATTTAAGTTACAA
65 AGAGGGCAGATTGAAGTTACAA
18197 CACCAAACCT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 1 0.01
102 77 0.99
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (102 bp):
CATCCAATCTTTTACCCTAATCAGAAGGCAGATTAAAGACACCATCCAATCTTTTACCCTAACCA
GAGGGCAGATTGAAGTTACAAGAGGGCAGATTGAAAT
Found at i:18641 original size:22 final size:22
Alignment explanation
Indices: 18609--18654 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
18599 ATGTAAGAGG
18609 GGATTTTTTTTATTTTGTTCAGA
1 GGATTTTTTTTA-TTTGTTCAGA
*
18632 GGATTTTTTTTATTTGTTTAGA
1 GGATTTTTTTTATTTGTTCAGA
18654 G
1 G
18655 AGAAGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.17, C:0.02, G:0.20, T:0.61
Consensus pattern (22 bp):
GGATTTTTTTTATTTGTTCAGA
Found at i:18967 original size:25 final size:26
Alignment explanation
Indices: 18920--18968 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
18910 TTTTATTCTT
18920 ATTTATATTTAGTTGTTTATTTTGAC
1 ATTTATATTTAGTTGTTTATTTTGAC
*
18946 ATTTA-ATTTA-TTGATTTTTTTTG
1 ATTTATATTTAGTTG-TTTATTTTG
18969 TTTATGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.65
Consensus pattern (26 bp):
ATTTATATTTAGTTGTTTATTTTGAC
Found at i:19126 original size:9 final size:10
Alignment explanation
Indices: 19102--19152 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 10
19092 TTCATTCCAT
*
19102 TTTATTGTTA
1 TTTATTTTTA
*
19112 TCT-TTTTTA
1 TTTATTTTTA
19121 TTT-TTTTTA
1 TTTATTTTTA
*
19130 TTTAATTTTCA
1 TTT-ATTTTTA
19141 TTTATTTTTA
1 TTTATTTTTA
19151 TT
1 TT
19153 ATCTTGTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 16 0.47
10 10 0.29
11 8 0.24
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:21244 original size:31 final size:32
Alignment explanation
Indices: 21188--21258 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
21178 GTCACTTAAC
** *
21188 TAAAAATTTACAATTTCGATCACTGAATTATT
1 TAAAAATTTACAATTTAAATCACTGAACTATT
*
21220 TAAAAATTTTC-ATTTAAATCACTGAACTATT
1 TAAAAATTTACAATTTAAATCACTGAACTATT
*
21251 CAAAAATT
1 TAAAAATT
21259 CTTATTTGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (32 bp):
TAAAAATTTACAATTTAAATCACTGAACTATT
Found at i:28825 original size:13 final size:13
Alignment explanation
Indices: 28807--28831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28797 CTCCTTCTAA
28807 ATTTTATATTTTT
1 ATTTTATATTTTT
28820 ATTTTATATTTT
1 ATTTTATATTTT
28832 CCAAATTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTATATTTTT
Found at i:31552 original size:23 final size:23
Alignment explanation
Indices: 31499--31552 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
31489 AATACCCAGT
*
31499 AAACCCTTATTAACCATTTAACCC
1 AAACCCTTA-TAACCATTAAACCC
31523 AAA-CCTTA-AACCAATTAAACCC
1 AAACCCTTATAACC-ATTAAACCC
31545 AAACCCTT
1 AAACCCTT
31553 TAAAAACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.15
22 11 0.41
23 9 0.33
24 3 0.11
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (23 bp):
AAACCCTTATAACCATTAAACCC
Found at i:31635 original size:20 final size:20
Alignment explanation
Indices: 31610--31647 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31600 TGTGGATCGA
*
31610 TCGACCCGAACCCAATCGGC
1 TCGACCCAAACCCAATCGGC
*
31630 TCGACCCAAACCCGATCG
1 TCGACCCAAACCCAATCG
31648 AATTGACTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.45, G:0.18, T:0.11
Consensus pattern (20 bp):
TCGACCCAAACCCAATCGGC
Found at i:34378 original size:29 final size:26
Alignment explanation
Indices: 34306--34368 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
34296 TGAGTGTGCT
34306 ACTTCAATGCAAATTAGTAATAATGC
1 ACTTCAATGCAAATTAGTAATAATGC
34332 ACTTCAATGCAAATTAGTAATAATGC
1 ACTTCAATGCAAATTAGTAATAATGC
34358 ACTTCAATGCA
1 ACTTCAATGCA
34369 TAGTGTTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (26 bp):
ACTTCAATGCAAATTAGTAATAATGC
Found at i:34660 original size:13 final size:13
Alignment explanation
Indices: 34642--34668 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34632 GTAAGGTTAA
34642 TTCTTGATGTACT
1 TTCTTGATGTACT
34655 TTCTTGATGTACT
1 TTCTTGATGTACT
34668 T
1 T
34669 ACTAAGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (13 bp):
TTCTTGATGTACT
Found at i:38605 original size:191 final size:192
Alignment explanation
Indices: 38338--38701 Score: 527
Period size: 192 Copynumber: 1.9 Consensus size: 192
38328 GTATGGTGTT
* * * *
38338 TGTCAGTAAACTGTTCCCTAACGATGCTACTCACATGAGCTATCTATAATATGCATTTAAGCATA
1 TGTCAGTAAACTGTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATATGCATTTAAGCACA
*
38403 AATCCCAACCATCGTA-GGCCTATAATCCATTTAGGATTCATATATCTTTTTTGACTCACGATGC
66 AATCCCAACCATCGTAGGGCCTATAATCCATTTAGGATTCATATATCTTTTTCGACTCACGATGC
*
38467 TACCCACACGAGCTATCGAGGTCTCACAACATATGCGATACCCTAGCCATCGGTATGATAAC
131 TACCCACACGAGCTATCGAGGACTCACAACATATGCGATACCCTAGCCATCGGTATGATAAC
* * * *
38529 TGTCTGTAAACTG-TCACCTAACGATGCTTCTCACACGAGCTGTCGAGAATATGCATTTTAA-TA
1 TGTCAGTAAACTGTTC-CCTAACGATGCTACTCACACGAGCTATCGAGAATATGCA-TTTAAGCA
* * * *
38592 CAAATCTCAACCATCGTAGGGCCTTTAATCCATTTAGGATTCATATCTCTTTTTCGACTCATGAT
64 CAAATCCCAACCATCGTAGGGCCTATAATCCATTTAGGATTCATATATCTTTTTCGACTCACGAT
* * * *
38657 GCTGCTCACACGAGCTGTCGAGGACTCACAACATATGCGGTACCC
129 GCTACCCACACGAGCTATCGAGGACTCACAACATATGCGATACCC
38702 CACCCTTCAC
Statistics
Matches: 152, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
190 2 0.01
191 63 0.41
192 87 0.57
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (192 bp):
TGTCAGTAAACTGTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATATGCATTTAAGCACA
AATCCCAACCATCGTAGGGCCTATAATCCATTTAGGATTCATATATCTTTTTCGACTCACGATGC
TACCCACACGAGCTATCGAGGACTCACAACATATGCGATACCCTAGCCATCGGTATGATAAC
Found at i:44614 original size:13 final size:13
Alignment explanation
Indices: 44596--44620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44586 TATACATATA
44596 TCTTTTTTTTTTC
1 TCTTTTTTTTTTC
44609 TCTTTTTTTTTT
1 TCTTTTTTTTTT
44621 TTATAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TCTTTTTTTTTTC
Found at i:45209 original size:17 final size:17
Alignment explanation
Indices: 45177--45219 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
45167 ACTAAATTCT
*
45177 AATGACAAATGGAAATGC
1 AATGAC-AATGCAAATGC
45195 AATGACAATGCAAATGC
1 AATGACAATGCAAATGC
45212 AATGACAA
1 AATGACAA
45220 CGAGAATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (17 bp):
AATGACAATGCAAATGC
Found at i:56280 original size:192 final size:192
Alignment explanation
Indices: 55953--56391 Score: 556
Period size: 192 Copynumber: 2.3 Consensus size: 192
55943 CCAAGTACTG
* * * *
55953 GATGCTGCTCACACGAGCTGTTGAGGACTCACAACATATGCGGTACCCCAACCATCGGTACGGTG
1 GATGCTGCTCACACGAGCTATCGAGGACTCACAACATATACGGTACCCCAACCATCAGTACGGTG
* * * * *
56018 TTTATCTGTAAATTGTCCCCTAATGATGCTGCTCACACGAGTTGTCGAGAATATGCATTTAAGCA
66 TTTATCTGTAAACTGTCCCCTAACGATGATGCTCACACGAGCTATCGAGAATATGCATTTAAGCA
** * *
56083 TAAAT-CTCAGCCATCGTAGGGTATATAATCCATTTAGGATTCACATCTCTTTTTCGACTCAT
131 TAAATCCT-AGCCATCAAAGGGCATATAATCCATTTAGGATTCACATCTCTTTTTCGACTCAC
* * * * * *
56145 GATGCTGCTCACATGAGCTATCGTGGACTCGCAACATATATGTTACCCCAACCATCAGTATGGTG
1 GATGCTGCTCACACGAGCTATCGAGGACTCACAACATATACGGTACCCCAACCATCAGTACGGTG
* *
56210 TTTGTTTGTAAACTGTCCCCTAACGATGATGCTCACACGAGCTATCGAGAATATGCATTTAAGCA
66 TTTATCTGTAAACTGTCCCCTAACGATGATGCTCACACGAGCTATCGAGAATATGCATTTAAGCA
* * * * *
56275 TAAATCCTAGTCATTAAAGGGCCTATAATCCATTTAGTATTCATATCTCTTTTTCGACTCAC
131 TAAATCCTAGCCATCAAAGGGCATATAATCCATTTAGGATTCACATCTCTTTTTCGACTCAC
* * ** * * * *
56337 GATGATGCTCACACGAGCTGTCGACTAATCCCAACATATGCGGTACCCCAGCCAT
1 GATGCTGCTCACACGAGCTATCGAGGACTCACAACATATACGGTACCCCAACCAT
56392 TGCATCGATT
Statistics
Matches: 208, Mismatches: 38, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
192 206 0.99
193 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (192 bp):
GATGCTGCTCACACGAGCTATCGAGGACTCACAACATATACGGTACCCCAACCATCAGTACGGTG
TTTATCTGTAAACTGTCCCCTAACGATGATGCTCACACGAGCTATCGAGAATATGCATTTAAGCA
TAAATCCTAGCCATCAAAGGGCATATAATCCATTTAGGATTCACATCTCTTTTTCGACTCAC
Found at i:62817 original size:37 final size:37
Alignment explanation
Indices: 62766--62887 Score: 147
Period size: 37 Copynumber: 3.3 Consensus size: 37
62756 CGATGTAATC
**
62766 GGCTTTGTATCTAGTAGGCTTTGTCTCGGTGTATTCG
1 GGCTTTGTGCCTAGTAGGCTTTGTCTCGGTGTATTCG
* * * * *
62803 GGCTTTATGCCTAGTAGGATTTGTGTCGATGTAATCG
1 GGCTTTGTGCCTAGTAGGCTTTGTCTCGGTGTATTCG
* *
62840 GGCTTTGTGCCTAGTAGGCTTTGAGC-CGGTGTATTTG
1 GGCTTTGTGCCTAGTAGGCTTTG-TCTCGGTGTATTCG
62877 GGCTTTGTGCC
1 GGCTTTGTGCC
62888 GGTGTATTCA
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.12, C:0.16, G:0.32, T:0.39
Consensus pattern (37 bp):
GGCTTTGTGCCTAGTAGGCTTTGTCTCGGTGTATTCG
Found at i:62870 original size:74 final size:73
Alignment explanation
Indices: 62749--62887 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 73
62739 ATATTCGGGC
* *
62749 TTTGTGCCGATGTAATCGGCTTTGTATCTAGTAGGCTTTGTCTCGGTGTATTCGGGCTTTATGCC
1 TTTGTGCCGATGTAATCGGCTTTGTACCTAGTAGGCTTTGGCTCGGTGTATTCGGGCTTTATGCC
62814 TAGTAGGA
66 TAGTAGGA
* * * *
62822 TTTGTGTCGATGTAATCGGGCTTTGTGCCTAGTAGGCTTTGAGC-CGGTGTATTTGGGCTTTGTG
1 TTTGTGCCGATGTAATC-GGCTTTGTACCTAGTAGGCTTTG-GCTCGGTGTATTCGGGCTTTATG
62886 CC
64 CC
62888 GGTGTATTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 16 0.28
74 41 0.71
75 1 0.02
ACGTcount: A:0.13, C:0.17, G:0.31, T:0.40
Consensus pattern (73 bp):
TTTGTGCCGATGTAATCGGCTTTGTACCTAGTAGGCTTTGGCTCGGTGTATTCGGGCTTTATGCC
TAGTAGGA
Found at i:62882 original size:21 final size:21
Alignment explanation
Indices: 62856--62895 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
62846 GTGCCTAGTA
62856 GGCTTTGAGCCGGTGTATTTG
1 GGCTTTGAGCCGGTGTATTTG
*
62877 GGCTTTGTGCCGGTGTATT
1 GGCTTTGAGCCGGTGTATT
62896 CAGGCTATGT
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:0.07, C:0.15, G:0.38, T:0.40
Consensus pattern (21 bp):
GGCTTTGAGCCGGTGTATTTG
Found at i:62901 original size:21 final size:21
Alignment explanation
Indices: 62855--62901 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
62845 TGTGCCTAGT
*
62855 AGGCTTTGAGCCGGTGTATTT
1 AGGCTTTGAGCCGGTGTATTC
* *
62876 GGGCTTTGTGCCGGTGTATTC
1 AGGCTTTGAGCCGGTGTATTC
62897 AGGCT
1 AGGCT
62902 ATGTACCTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.17, G:0.36, T:0.36
Consensus pattern (21 bp):
AGGCTTTGAGCCGGTGTATTC
Found at i:65814 original size:13 final size:13
Alignment explanation
Indices: 65796--65840 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
65786 ACATTTATCA
65796 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
*
65809 TTTTTTTTCTTCC
1 TTTTTTTTCTTCT
*
65822 TTTTTCTTCTT-T
1 TTTTTTTTCTTCT
65834 TTTTTTT
1 TTTTTTT
65841 CAAGTGACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 6 0.21
13 22 0.79
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:90764 original size:21 final size:20
Alignment explanation
Indices: 90736--90776 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
90726 TCAGTCACTT
* *
90736 GAAAAAAATGAGAAAAATAA
1 GAAAAAAAAGAAAAAAATAA
90756 GAAAGAAAAAGAAAAAAATAA
1 GAAA-AAAAAGAAAAAAATAA
90777 ATTGCTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (20 bp):
GAAAAAAAAGAAAAAAATAA
Found at i:93208 original size:7 final size:7
Alignment explanation
Indices: 93196--93274 Score: 86
Period size: 7 Copynumber: 11.3 Consensus size: 7
93186 CCGGCTCGAC
93196 CCGTTGA
1 CCGTTGA
93203 CCGTTGA
1 CCGTTGA
*
93210 CAGTTGA
1 CCGTTGA
*
93217 TCGTTGA
1 CCGTTGA
93224 CCGTTGA
1 CCGTTGA
**
93231 CAATTGA
1 CCGTTGA
*
93238 TCGTTGA
1 CCGTTGA
*
93245 TCGTTGA
1 CCGTTGA
93252 CCGTTGA
1 CCGTTGA
*
93259 TCGTTGA
1 CCGTTGA
*
93266 CCTTTGA
1 CCGTTGA
93273 CC
1 CC
93275 ATTAAATTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (7 bp):
CCGTTGA
Found at i:93274 original size:21 final size:21
Alignment explanation
Indices: 93197--93273 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
93187 CGGCTCGACC
93197 CGTTGACCGTTGACAGTTGAT
1 CGTTGACCGTTGACAGTTGAT
*
93218 CGTTGACCGTTGACAATTGAT
1 CGTTGACCGTTGACAGTTGAT
* *
93239 CGTTGATCGTTGACCGTTGAT
1 CGTTGACCGTTGACAGTTGAT
*
93260 CGTTGACCTTTGAC
1 CGTTGACCGTTGAC
93274 CATTAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (21 bp):
CGTTGACCGTTGACAGTTGAT
Found at i:98950 original size:21 final size:21
Alignment explanation
Indices: 98919--98987 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
98909 AACCCACCCA
* *
98919 TTGACCATTGATCGTTGACTG
1 TTGACTATTGATCGTTGACAG
*
98940 TTGA-TAGTTGACCGTTGACAG
1 TTGACTA-TTGATCGTTGACAG
98961 TTGACTATTGATCGTTGATC-G
1 TTGACTATTGATCGTTGA-CAG
98982 TTGACT
1 TTGACT
98988 TTTTTTTAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.02
21 37 0.90
22 3 0.07
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (21 bp):
TTGACTATTGATCGTTGACAG
Found at i:98985 original size:14 final size:14
Alignment explanation
Indices: 98926--98978 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
98916 CCATTGACCA
98926 TTGATCGTTGACTG
1 TTGATCGTTGACTG
* *
98940 TTGATAGTTGACCG
1 TTGATCGTTGACTG
*
98954 TTGA-CAGTTGACTA
1 TTGATC-GTTGACTG
98968 TTGATCGTTGA
1 TTGATCGTTGA
98979 TCGTTGACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 31 0.97
15 1 0.03
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (14 bp):
TTGATCGTTGACTG
Found at i:101376 original size:29 final size:29
Alignment explanation
Indices: 101331--101406 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
101321 ATTTTTTACA
*
101331 AAATTTG-GGATTAAAAT-TGAACTTTTGG
1 AAATTTGAGGATTAAAATGTG-ACTTTTAG
*
101359 AAATTTGAGG-TTGAAAATGTGATTTTTAG
1 AAATTTGAGGATT-AAAATGTGACTTTTAG
* *
101388 AAATTTGAGGGTAAAAATG
1 AAATTTGAGGATTAAAATG
101407 GTAATTTTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 9 0.22
29 29 0.71
30 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (29 bp):
AAATTTGAGGATTAAAATGTGACTTTTAG
Found at i:101551 original size:59 final size:60
Alignment explanation
Indices: 101396--101768 Score: 319
Period size: 59 Copynumber: 6.4 Consensus size: 60
101386 AGAAATTTGA
* * ** * *
101396 GGGTAAAAATG-GTAATTTTGGATGTTCGGGGGTAA-AATGGTAATTTTTGG--ATG-TTCG
1 GGGTAAAAATGTG-ATTTTTGGAAGTTCAAGGGTAATAAT-GTAATTTTTGGAAAAGTTTAG
* ** * *
101453 AGGTAAAAATAAGATTTTTGGAAGTTCGAGGG-AAAAATGTAATTTTTGGAAAAGTTTAG
1 GGGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAATAATGTAATTTTTGGAAAAGTTTAG
*
101512 GGGTAAAAA-GTGATTTTCGGAAGTTCAAGGGTAATAATGTAATTTTTGG--AAGTTTAG
1 GGGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAATAATGTAATTTTTGGAAAAGTTTAG
* * *
101569 GGGTAAAAATGTAATTTTTAAGAAGTT-AGAGGGTAATAATGTGATTTTT-G-AAAGTTTAG
1 GGGTAAAAATGTGATTTTT-GGAAGTTCA-AGGGTAATAATGTAATTTTTGGAAAAGTTTAG
* * * * *
101628 GGGTAAAAATGTGATTTTTGAAAGTTCAAGGGTAAAAATGTAAATTTT-GAGAAGTTTAA
1 GGGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAATAATGTAATTTTTGGAAAAGTTTAG
* * * * * * *
101687 CGGTAAAACTATAAGTTTTGTGAAGTTCGAGGGTCATAATGTAA-TTTTGGAAAAGTTT-G
1 GGGTAAAAATGTGATTTTTG-GAAGTTCAAGGGTAATAATGTAATTTTTGGAAAAGTTTAG
* *
101746 TGGGTCAAAATGT-AATTTTGGAA
1 -GGGTAAAAATGTGATTTTTGGAA
101769 AAGTTTGGTG
Statistics
Matches: 260, Mismatches: 41, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
56 13 0.05
57 45 0.17
58 56 0.22
59 111 0.43
60 35 0.13
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (60 bp):
GGGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAATAATGTAATTTTTGGAAAAGTTTAG
Found at i:101683 original size:30 final size:29
Alignment explanation
Indices: 101372--101738 Score: 273
Period size: 29 Copynumber: 12.6 Consensus size: 29
101362 TTTGAGGTTG
* * * **
101372 AAAATGTGATTTTTAGAAATTTGAGGGTA
1 AAAATGTAATTTTTGGAAGTTCAAGGGTA
* **
101401 AAAATGGTAA-TTTTGGATGTTCGGGGGT-
1 AAAAT-GTAATTTTTGGAAGTTCAAGGGTA
* *
101429 AAAATGGTAATTTTTGGATGTTCGA-GGTA
1 AAAAT-GTAATTTTTGGAAGTTCAAGGGTA
* *
101458 AAAAT-AAGATTTTTGGAAGTTCGAGGG-A
1 AAAATGTA-ATTTTTGGAAGTTCAAGGGTA
* *
101486 AAAATGTAATTTTTGGAAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGG--AAGTTCAAGGGTA
* *
101517 AAAA-GTGATTTTCGGAAGTTCAAGGGTA
1 AAAATGTAATTTTTGGAAGTTCAAGGGTA
* * *
101545 ATAATGTAATTTTTGGAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAGTTCAAGGGTA
*
101574 AAAATGTAATTTTTAAGAAGTT-AGAGGGTA
1 AAAATGTAATTTTT-GGAAGTTCA-AGGGTA
* * * * *
101604 ATAATGTGATTTTTGAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAGTTCAAGGGTA
* *
101633 AAAATGTGATTTTTGAAAGTTCAAGGGTA
1 AAAATGTAATTTTTGGAAGTTCAAGGGTA
* * *
101662 AAAATGTAAATTTTGAGAAGTTTAACGGTA
1 AAAATGTAATTTTTG-GAAGTTCAAGGGTA
* * * * *
101692 AAACTATAAGTTTTGTGAAGTTCGAGGGTC
1 AAAATGTAATTTTTG-GAAGTTCAAGGGTA
*
101722 ATAATGTAA-TTTTGGAA
1 AAAATGTAATTTTTGGAA
101739 AAGTTTGTGG
Statistics
Matches: 275, Mismatches: 49, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
27 1 0.00
28 59 0.21
29 127 0.46
30 83 0.30
31 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTCAAGGGTA
Found at i:101692 original size:88 final size:87
Alignment explanation
Indices: 101454--101694 Score: 279
Period size: 88 Copynumber: 2.8 Consensus size: 87
101444 GGATGTTCGA
** * * *
101454 GGTAAAAATAAGATTTTTGGAAGTTCGAGGG-AAAAATGTAATTTTTGGAAAAGTTTAGGGGTAA
1 GGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTT-GAGAAGTTTAAGGGTAA
*
101518 AAAGTGATTTTCGGAAGTTCAAG
65 AAAGTGATTTTCGAAAGTTCAAG
* * * * *
101541 GGTAATAATGTAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTAAGAAG-TTAGAGGGTAA
1 GGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTTA-AGGGTAA
* * * *
101605 TAATGTGATTTTTGAAAGTTTAGG
65 -AAAGTGATTTTCGAAAGTTCAAG
* * *
101629 GGTAAAAATGTGATTTTTGAAAGTTCAAGGGTAAAAATGTAAATTTTGAGAAGTTTAACGGTAAA
1 GGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTTAAGGGTAAA
101694 A
66 A
101695 CTATAAGTTT
Statistics
Matches: 127, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
86 3 0.02
87 36 0.28
88 85 0.67
89 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (87 bp):
GGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTTAAGGGTAAA
AAGTGATTTTCGAAAGTTCAAG
Found at i:101706 original size:88 final size:86
Alignment explanation
Indices: 101454--101774 Score: 254
Period size: 88 Copynumber: 3.7 Consensus size: 86
101444 GGATGTTCGA
** * * *
101454 GGTAAAAATAAGATTTTTGGAAGTTCGAGGG-AAAAATGTAATTTTTGGAAAAGTTTAGGGGTAA
1 GGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTT-GAGAAGTTTAAGGGTAA
*
101518 AA-AGTGATTTTCGGAAGTTCAAG
65 AATA-TGATTTT-GAAAGTTCAAG
* * * * *
101541 GGTAATAATGTAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTAAGAAG-TTAGAGGGTAA
1 GGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTTA-AGGGTAA
* * *
101605 TAATGTGATTTTTGAAAGTTTAGG
65 -AATATGA-TTTTGAAAGTTCAAG
* * *
101629 GGTAAAAATGTGATTTTTGAAAGTTCAAGGGTAAAAATGTAAATTTTGAGAAGTTTAACGGTAAA
1 GGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTTAAGGGTAAA
* * *
101694 ACTATAAGTTTTGTGAAGTTCGAG
66 A-TATGA-TTTTG-AAAGTTCAAG
* * * *** * * *
101718 GGTCATAATGT-AATTTTGGAAAAGTTTGTGGGTCAAAATGTAATTTTGGAAAAGTTT
1 GGTAAAAATGTGATTTTTGG--AAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTT
101775 GGTGGTCCAA
Statistics
Matches: 184, Mismatches: 40, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
86 3 0.02
87 36 0.20
88 94 0.51
89 22 0.12
90 29 0.16
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (86 bp):
GGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTTAAGGGTAAA
ATATGATTTTGAAAGTTCAAG
Found at i:101743 original size:30 final size:30
Alignment explanation
Indices: 101474--101773 Score: 132
Period size: 30 Copynumber: 10.2 Consensus size: 30
101464 AGATTTTTGG
*
101474 AAGTTCGAGGG-AAAAATGTAATTTTTGGAA
1 AAGTTCGAGGGTCAAAATGTAA-TTTTGGAA
* * *
101504 AAGTT-TAGGGGT-AAAAAGTGATTTTCGG--
1 AAGTTCGA-GGGTCAAAATGTAATTTT-GGAA
*
101532 AAGTTCAAGGGT-AATAATGTAATTTTTGG--
1 AAGTTCGAGGGTCAA-AATGTAA-TTTTGGAA
* * *
101561 AAGTT-TAGGGGTAAAAATGTAATTTT-TAA
1 AAGTTCGA-GGGTCAAAATGTAATTTTGGAA
* * *
101590 GAAGTTAGAGGGT-AATAATGTGATTTTTG-A
1 -AAGTTCGAGGGTCAA-AATGTAATTTTGGAA
* * * *
101620 AAGTT-TAGGGGTAAAAATGTGATTTTTG-A
1 AAGTTCGA-GGGTCAAAATGTAATTTTGGAA
* * *
101649 AAGTTCAAGGGTAAAAATGTAAATTTT-GAG
1 AAGTTCGAGGGTCAAAATGT-AATTTTGGAA
** * *
101679 AAGTTTAACGGT-AAAACTATAAGTTTTGTG--
1 AAGTTCGAGGGTCAAAA-TGTAA-TTTTG-GAA
*
101709 AAGTTCGAGGGTCATAATGTAATTTTGGAA
1 AAGTTCGAGGGTCAAAATGTAATTTTGGAA
* *
101739 AAGTTTGTGGGTCAAAATGTAATTTTGGAA
1 AAGTTCGAGGGTCAAAATGTAATTTTGGAA
101769 AAGTT
1 AAGTT
101774 TGGTGGTCCA
Statistics
Matches: 218, Mismatches: 26, Indels: 52
0.74 0.09 0.18
Matches are distributed among these distances:
28 18 0.08
29 83 0.38
30 112 0.51
31 4 0.02
32 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
AAGTTCGAGGGTCAAAATGTAATTTTGGAA
Found at i:101774 original size:30 final size:28
Alignment explanation
Indices: 101353--101775 Score: 199
Period size: 29 Copynumber: 14.5 Consensus size: 28
101343 AAAATTGAAC
* *
101353 TTTTGGAAA-TTTGAGGTTGAAAATGTGAT
1 TTTTGGAAAGTTTGAGGGT-AAAATGT-AA
*
101382 TTTTAGAAA-TTTGAGGGTAAAAATGGTAA
1 TTTTGGAAAGTTTGAGGGT-AAAAT-GTAA
* * *
101411 TTTTGG-ATGTTCGGGGGTAAAATGGTAA
1 TTTTGGAAAGTTTGAGGGTAAAAT-GTAA
* * *
101439 TTTTTGG-ATGTTCGA-GGTAAAAATAAG-AT
1 -TTTTGGAAAGTTTGAGGGT-AAAAT--GTAA
* *
101468 TTTTGG-AAGTTCGAGGGAAAAATGTAA
1 TTTTGGAAAGTTTGAGGGTAAAATGTAA
* *
101495 TTTTTGGAAAAGTTT-AGGGGTAAAAAGTGA
1 -TTTTGG-AAAGTTTGA-GGGTAAAATGTAA
**
101525 TTTTCGG-AAGTTCAAGGGTAATAATGTAA
1 TTTT-GGAAAGTTTGAGGGTAA-AATGTAA
101554 TTTTTGG-AAGTTT-AGGGGTAAAAATGTAA
1 -TTTTGGAAAGTTTGA-GGGT-AAAATGTAA
** * *
101583 TTTTTAAGAAGTTAGAGGGTAATAATGTGA
1 TTTTGGA-AAGTTTGAGGGTAA-AATGTAA
* *
101613 TTTTTGAAAGTTT-AGGGGTAAAAATGTGA
1 TTTTGGAAAGTTTGA-GGGT-AAAATGTAA
* **
101642 TTTTTGAAAGTTCAAGGGTAAAAATGTAAA
1 TTTTGGAAAGTTTGAGGGT-AAAATGT-AA
* * *
101672 TTTT-GAGAAGTTTAACGGTAAAACTATAA
1 TTTTGGA-AAGTTTGAGGGTAAAA-TGTAA
* *
101701 GTTTTGTG-AAGTTCGAGGGTCATAATGTAA
1 -TTTTG-GAAAGTTTGAGGGT-AAAATGTAA
*
101731 TTTTGGAAAAGTTTGTGGGTCAAAATGTAA
1 TTTTGG-AAAGTTTGAGGGT-AAAATGTAA
101761 TTTTGGAAAAGTTTG
1 TTTTGG-AAAGTTTG
101776 GTGGTCCAAA
Statistics
Matches: 320, Mismatches: 41, Indels: 65
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.00
27 1 0.00
28 56 0.17
29 139 0.43
30 118 0.37
31 4 0.01
32 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
TTTTGGAAAGTTTGAGGGTAAAATGTAA
Found at i:101794 original size:30 final size:30
Alignment explanation
Indices: 101717--101794 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
101707 TGAAGTTCGA
* *
101717 GGGTCATAATGTAATTTTGGAAAAGTTTGT
1 GGGTCAAAATATAATTTTGGAAAAGTTTGT
*
101747 GGGTCAAAATGTAATTTTGGAAAAGTTTG-
1 GGGTCAAAATATAATTTTGGAAAAGTTTGT
* *
101776 GTGGTCCAAATATGATTTT
1 G-GGTCAAAATATAATTTT
101795 TAGAAAGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTGGAAAAGTTTGT
Found at i:102854 original size:18 final size:16
Alignment explanation
Indices: 102822--102872 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
102812 GTACATTCAA
102822 AAATAATA-AAT-AAT
1 AAATAATATAATAAAT
102836 AAGGATAATATAATAAAT
1 AA--ATAATATAATAAAT
102854 AAATATATATTAATAAAT
1 AAATA-ATA-TAATAAAT
102872 A
1 A
102873 TATGTATAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.06
16 9 0.29
17 6 0.19
18 14 0.45
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (16 bp):
AAATAATATAATAAAT
Found at i:102868 original size:14 final size:14
Alignment explanation
Indices: 102842--102875 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
102832 TAATAAGGAT
102842 AATATA-ATAAATA
1 AATATATATAAATA
*
102855 AATATATATTAATA
1 AATATATATAAATA
102869 AATATAT
1 AATATAT
102876 GTATAGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATATATAAATA
Found at i:104049 original size:39 final size:39
Alignment explanation
Indices: 104006--104427 Score: 255
Period size: 39 Copynumber: 10.8 Consensus size: 39
103996 CCAAGGTCAG
* * *
104006 GGTAAAAGATCGAATGGTTGCAATCTGCCCTAGGCTCGA
1 GGTAAGAGATCGAATGATTGTAATCTGCCCTAGGCTCGA
* * ** * *
104045 GGTAAGAAATTGGCTGATGGTGATCTGTCCTAGCCTAGGCTCGA
1 GGTAAGAGATCGAATGATTGTAATCTG--C---CCTAGGCTCGA
* * *
104089 GGTAAGAGATCGAATGACTGCAATCTGCTCC-AGGCTTGA
1 GGTAAGAGATCGAATGATTGTAATCTGC-CCTAGGCTCGA
* * * * * * *
104128 GGTAAGAGATTGACTGGTGGTGATCTACCCTAGGCTCGG
1 GGTAAGAGATCGAATGATTGTAATCTGCCCTAGGCTCGA
* * * *
104167 GGTAAGAGATCGAATGACTGTAATTTGCCCCAGGCTCGT
1 GGTAAGAGATCGAATGATTGTAATCTGCCCTAGGCTCGA
* ** * * * * *
104206 GGTAAGAGATTGGTTGATGGTGATCTATCCC-ATGCTCGG
1 GGTAAGAGATCGAATGATTGTAATCT-GCCCTAGGCTCGA
** *
104245 GGTAAGAGATCGAATGGCTGCAATCTGCCCTAGGCTCGA
1 GGTAAGAGATCGAATGATTGTAATCTGCCCTAGGCTCGA
* * * * * *
104284 GGTAAGAGATTGACTAATGGTGATCTGCCCTAGGCTCGG
1 GGTAAGAGATCGAATGATTGTAATCTGCCCTAGGCTCGA
* * * * *
104323 GGTAAGAGATCGAATGACTGTAATCAGCTCAAGGCTCGG
1 GGTAAGAGATCGAATGATTGTAATCTGCCCTAGGCTCGA
* * * * *
104362 GGTAAGAGAT-G--GGCTTGTTGATCTACCCCAGGCTCGA
1 GGTAAGAGATCGAATGATTG-TAATCTGCCCTAGGCTCGA
* *
104399 GGTAAAAGATCGAAT-CTT-TAATCTGCCCT
1 GGTAAGAGATCGAATGATTGTAATCTGCCCT
104428 TCTTGATTAA
Statistics
Matches: 279, Mismatches: 92, Indels: 26
0.70 0.23 0.07
Matches are distributed among these distances:
36 3 0.01
37 30 0.11
38 7 0.03
39 202 0.72
40 5 0.02
41 1 0.00
42 1 0.00
44 30 0.11
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (39 bp):
GGTAAGAGATCGAATGATTGTAATCTGCCCTAGGCTCGA
Found at i:104069 original size:78 final size:79
Alignment explanation
Indices: 103939--104413 Score: 516
Period size: 78 Copynumber: 6.1 Consensus size: 79
103929 TTATTGCTTT
* * * * * *
103939 GAATGACTGCAATCTACCCTATGATCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGG-T
1 GAATGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCTAGGCT
* *
104003 CAGGGTAAAAGATC
66 CGGGGTAAGAGATC
** *
104017 GAATGGTTGCAATCTGCCCTAGGCTCGAGGTAAGAAATTGGCTGATGGTGATCTGTCCTAGCCTA
1 GAATGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTG-CC---CCTA
*
104082 GGCTCGAGGTAAGAGATC
62 GGCTCGGGGTAAGAGATC
* * * *
104100 GAATGACTGCAATCTGCTCC-AGGCTTGAGGTAAGAGATTGACTGGTGGTGATCT-ACCCTAGGC
1 GAATGACTGCAATCTGC-CCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCTAGGC
104163 TCGGGGTAAGAGATC
65 TCGGGGTAAGAGATC
* * * * * ** *
104178 GAATGACTGTAATTTGCCCCAGGCTCGTGGTAAGAGATTGGTTGATGGTGATCTATCCC-ATGCT
1 GAATGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCTAGGCT
104242 CGGGGTAAGAGATC
66 CGGGGTAAGAGATC
* * *
104256 GAATGGCTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGACTAATGGTGATCTG-CCCTAGGCT
1 GAATGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCTAGGCT
104320 CGGGGTAAGAGATC
66 CGGGGTAAGAGATC
* * * * * * * *
104334 GAATGACTGTAATCAGCTCAAGGCTCGGGGTAAGAGATGGGCT--TGTTGATCTACCCC-AGGCT
1 GAATGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCTAGGCT
* *
104396 CGAGGTAAAAGATC
66 CGGGGTAAGAGATC
104410 GAAT
1 GAAT
104414 CTTTAATCTG
Statistics
Matches: 336, Mismatches: 51, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
76 29 0.09
77 8 0.02
78 229 0.68
79 5 0.01
81 1 0.00
82 5 0.01
83 57 0.17
84 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (79 bp):
GAATGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCTAGGCT
CGGGGTAAGAGATC
Done.