Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005021.1 Hibiscus syriacus cultivar Beakdansim tig00011271_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: 84293
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:9670 original size:5 final size:5
Alignment explanation
Indices: 9660--9700 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
9650 CTTCAACTTC
9660 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
9701 CTTTTTGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:12171 original size:15 final size:16
Alignment explanation
Indices: 12151--12193 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
12141 AGTTATCATC
12151 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
**
12166 ATAATATTTATAGATG
1 ATAATAACTATAGATG
*
12182 AAAATAACTATA
1 ATAATAACTATA
12194 TTAAAACTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:17302 original size:19 final size:19
Alignment explanation
Indices: 17278--17328 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
17268 ATTGGAGTGC
17278 AAAAAGAAAG-AAAAATACA
1 AAAAAGAAAGAAAAAAT-CA
*
17297 AAAAAGAAGGAAAAAATCA
1 AAAAAGAAAGAAAAAATCA
*
17316 GAAAAG-AAGAAAA
1 AAAAAGAAAGAAAA
17329 GAAAAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 16 0.57
20 6 0.21
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAATCA
Found at i:24940 original size:14 final size:16
Alignment explanation
Indices: 24923--24958 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
24913 TCCTTTTGAA
24923 TTTCTTA-TTTT-TCT
1 TTTCTTATTTTTGTCT
24937 TTTCTTATTTTTGTCT
1 TTTCTTATTTTTGTCT
24953 TTTCTT
1 TTTCTT
24959 TCTTTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 4 0.20
16 9 0.45
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTCTTATTTTTGTCT
Found at i:28011 original size:45 final size:45
Alignment explanation
Indices: 27956--28212 Score: 428
Period size: 45 Copynumber: 5.7 Consensus size: 45
27946 TATTCGTTAT
* *
27956 TTTCATTTATGGCATCCTTTCATGCCTTTATTGCACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
28001 TTTCATTTATGGCATCCTTTCATGTCTTTAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
28046 TTTCATTTATGGCATCCTTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCC-TTTCATGCCTTTAATGCACCGTTATGCA
28092 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
28137 TTTCATTTATGGCATCC-TTCATGCCTTTAATGCACC-TCTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGT-TATGCA
* *
28181 CTTCATTTATGACATCCTTTCATGCCTTTAAT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAAT
28213 AACCTTTTCA
Statistics
Matches: 201, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
43 1 0.00
44 40 0.20
45 117 0.58
46 43 0.21
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:28084 original size:91 final size:90
Alignment explanation
Indices: 27956--28212 Score: 428
Period size: 91 Copynumber: 2.9 Consensus size: 90
27946 TATTCGTTAT
* *
27956 TTTCATTTATGGCATCCTTTCATGCCTTTATTGCACCGTTATACATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTT
*
28021 CATGTCTTTAATGCACCATTATGCA
66 CATGCCTTTAATGCACCATTATGCA
28046 TTTCATTTATGGCATCCTTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTT
1 TTTCATTTATGGCATCC-TTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTT
*
28111 TCATGCCTTTAATGCACCGTTATGCA
65 TCATGCCTTTAATGCACCATTATGCA
* *
28137 TTTCATTTATGGCATCC-TTCATGCCTTTAATGCACC-TCTATGCACTTCATTTATGACATCCTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGT-TATGCATTTCATTTATGGCATCCTT
28200 TCATGCCTTTAAT
65 TCATGCCTTTAAT
28213 AACCTTTTCA
Statistics
Matches: 159, Mismatches: 6, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
88 1 0.01
89 55 0.35
90 17 0.11
91 86 0.54
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.44
Consensus pattern (90 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTT
CATGCCTTTAATGCACCATTATGCA
Found at i:28758 original size:95 final size:95
Alignment explanation
Indices: 28588--28787 Score: 262
Period size: 95 Copynumber: 2.1 Consensus size: 95
28578 TCCTACCATG
* *
28588 GTATCGATACTTCTACACTATGATACCGATATCCCCTTTCAGTATCGATACCATTTCTACATTTT
1 GTATCGATACTACTACACTATGATACCGATATCCCCTTTCAGTATCGATACCATTTCTACATTCT
** *
28653 TTAATTCATGGTATCGATACCTTT-CTCTCA
66 GGAATCCATGGTATCGATA-CTTTCCTCTCA
* * *
28683 GTATCGATACTACTATACTATGGTACCGATA-CTCCCTTTCAGTATCGATACCATTT-TGGCATT
1 GTATCGATACTACTACACTATGATACCGATATC-CCCTTTCAGTATCGATACCATTTCT-ACATT
* *
28746 CTGGAATCCATGGTATCGATACTTTCCTTTTA
64 CTGGAATCCATGGTATCGATACTTTCCTCTCA
28778 GTATCGATAC
1 GTATCGATAC
28788 CCCATCAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
94 6 0.07
95 86 0.93
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (95 bp):
GTATCGATACTACTACACTATGATACCGATATCCCCTTTCAGTATCGATACCATTTCTACATTCT
GGAATCCATGGTATCGATACTTTCCTCTCA
Found at i:32103 original size:26 final size:26
Alignment explanation
Indices: 32069--32124 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
32059 CAATTACCCT
*
32069 TTCATCATTATTGAAGCATCCCTTCA
1 TTCATCATTATTCAAGCATCCCTTCA
32095 TTCATCATTATTCAAGCATCCCTTCA
1 TTCATCATTATTCAAGCATCCCTTCA
32121 TTCA
1 TTCA
32125 CCAATAAGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.29, G:0.05, T:0.39
Consensus pattern (26 bp):
TTCATCATTATTCAAGCATCCCTTCA
Found at i:35004 original size:19 final size:20
Alignment explanation
Indices: 34980--35019 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
34970 TATCCTTTCT
34980 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
34999 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
35019 T
1 T
35020 ATTATAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:40914 original size:17 final size:16
Alignment explanation
Indices: 40894--40963 Score: 71
Period size: 16 Copynumber: 4.6 Consensus size: 16
40884 ATTGGAGTAC
40894 AAAAAGAAAGAAAAGA
1 AAAAAGAAAGAAAAGA
40910 CAAAAAG-AAGAAGAA-A
1 -AAAAAGAAAGAA-AAGA
40926 AGAAAAG-AA-AAAAG-
1 A-AAAAGAAAGAAAAGA
40940 AAAAA-AAAGAAAAGA
1 AAAAAGAAAGAAAAGA
40955 AAAAAGAAA
1 AAAAAGAAA
40964 AATTCAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
13 6 0.13
14 8 0.17
15 8 0.17
16 16 0.35
17 8 0.17
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAGA
Found at i:40920 original size:16 final size:15
Alignment explanation
Indices: 40894--40962 Score: 81
Period size: 14 Copynumber: 4.5 Consensus size: 15
40884 ATTGGAGTAC
40894 AAAAAGAAAGAAAAGA
1 AAAAAG-AAGAAAAGA
40910 CAAAAAGAAGAAGAA-A
1 -AAAAAGAAGAA-AAGA
40926 AGAAAAGAA-AAAAGA
1 A-AAAAGAAGAAAAGA
40941 AAAAA-AAGAAAAGA
1 AAAAAGAAGAAAAGA
40955 AAAAAGAA
1 AAAAAGAA
40963 AAATTCAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.04
14 17 0.36
15 7 0.15
16 13 0.28
17 8 0.17
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAAAGA
Found at i:40926 original size:29 final size:28
Alignment explanation
Indices: 40894--40965 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
40884 ATTGGAGTAC
* *
40894 AAAAAGAAAGAAAAGACAAAAAGAAGAA
1 AAAAAGAAAGAAAAAACAAAAAAAAGAA
* *
40922 GAAAAGAAAAGAAAAAAGAAAAAAAAGAA
1 AAAAAG-AAAGAAAAAACAAAAAAAAGAA
40951 AAGAAA-AAAGAAAAA
1 AA-AAAGAAAGAAAAA
40966 TTCAAAAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 14 0.38
29 20 0.54
30 3 0.08
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (28 bp):
AAAAAGAAAGAAAAAACAAAAAAAAGAA
Found at i:40938 original size:12 final size:12
Alignment explanation
Indices: 40900--40964 Score: 77
Period size: 12 Copynumber: 5.7 Consensus size: 12
40890 GTACAAAAAG
40900 AAAGAAAAGACAA
1 AAAGAAAAGA-AA
40913 AAAG--AAGAAGA
1 AAAGAAAAGAA-A
40924 AAAGAAAAGAAA
1 AAAGAAAAGAAA
40936 AAAG--AA-AAA
1 AAAGAAAAGAAA
40945 AAAGAAAAGAAA
1 AAAGAAAAGAAA
40957 AAAGAAAA
1 AAAGAAAA
40965 ATTCAAAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
9 7 0.15
10 3 0.07
11 11 0.24
12 16 0.35
13 9 0.20
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:40964 original size:5 final size:5
Alignment explanation
Indices: 40895--40957 Score: 62
Period size: 5 Copynumber: 12.8 Consensus size: 5
40885 TTGGAGTACA
*
40895 AAAAG -AAAG AAAAG -ACA- AAAAG AAGAAG AAAAG AAAAG AAAAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG --AAAAG
40940 AAAA- AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAA
40958 AAGAAAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
4 12 0.24
5 27 0.55
6 5 0.10
7 5 0.10
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:40977 original size:26 final size:21
Alignment explanation
Indices: 40894--40965 Score: 108
Period size: 21 Copynumber: 3.2 Consensus size: 21
40884 ATTGGAGTAC
40894 AAAAAGAAAGAAAAGACAAAAAG
1 AAAAA-AAAGAAAAGA-AAAAAG
40917 AAGAAGAAAAGAAAAGAAAAAAG
1 AA-AA-AAAAGAAAAGAAAAAAG
40940 AAAAAAAAGAAAAGAAAAAAG
1 AAAAAAAAGAAAAGAAAAAAG
40961 AAAAA
1 AAAAA
40966 TTCAAAAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
21 22 0.47
22 2 0.04
23 10 0.21
24 12 0.26
25 1 0.02
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAAAAGAAAAAAG
Found at i:43814 original size:35 final size:37
Alignment explanation
Indices: 43745--43822 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 37
43735 ATACTATTTC
*
43745 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
43782 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
43817 CATCAC
1 CATCAC
43823 AAAATTCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 20 0.51
36 3 0.08
37 16 0.41
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:47162 original size:35 final size:37
Alignment explanation
Indices: 47094--47172 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 37
47084 TACTATTTCA
*
47094 ATCACCATAATCCATCTTCCATTATCACACCTATATC
1 ATCACCATAATCCATCTACCATTATCACACCTATATC
* *
47131 ATCACCATAGTCCATC-ACCA-TATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACACCTATATC
47166 ATCACCA
1 ATCACCA
47173 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.33, C:0.37, G:0.03, T:0.28
Consensus pattern (37 bp):
ATCACCATAATCCATCTACCATTATCACACCTATATC
Found at i:47957 original size:37 final size:36
Alignment explanation
Indices: 47872--48007 Score: 168
Period size: 37 Copynumber: 3.8 Consensus size: 36
47862 TTTCGTCCTA
47872 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
47907 -TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
47942 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-TT
** * *
47980 CTATTATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
48008 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 29 0.33
35 3 0.03
37 54 0.62
38 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:51050 original size:16 final size:16
Alignment explanation
Indices: 51024--51065 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
51014 AGATCCAATC
51024 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGTAA
51039 AAGAAGCAAAAAAGTAA
1 AAGAA-CAAAAAAGTAA
51056 AA-AA-AAAAAA
1 AAGAACAAAAAA
51066 CAAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 10 0.40
17 4 0.16
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (16 bp):
AAGAACAAAAAAGTAA
Found at i:51059 original size:8 final size:7
Alignment explanation
Indices: 51030--51121 Score: 64
Period size: 7 Copynumber: 12.7 Consensus size: 7
51020 AATCAAGAAC
51030 AAAAAAG
1 AAAAAAG
51037 AAAAGAAG
1 AAAA-AAG
51045 CAAAAAAG
1 -AAAAAAG
*
51053 -TAAAA-
1 AAAAAAG
51058 AAAAAA-
1 AAAAAAG
*
51064 AACAAAG
1 AAAAAAG
51071 AAAAAGAG
1 AAAAA-AG
*
51079 AAACAAG
1 AAAAAAG
51086 AACAAAAG
1 AA-AAAAG
51094 AAAAAAG
1 AAAAAAG
*
51101 AGCAAAAAT
1 A--AAAAAG
*
51110 CAAAAAG
1 AAAAAAG
51117 AAAAA
1 AAAAA
51122 GGGACAAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
6 13 0.19
7 27 0.40
8 18 0.27
9 9 0.13
ACGTcount: A:0.78, C:0.07, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:51092 original size:17 final size:15
Alignment explanation
Indices: 51024--51107 Score: 54
Period size: 15 Copynumber: 5.7 Consensus size: 15
51014 AGATCCAATC
51024 AAGAACAAAA-AAGAA
1 AAGAACAAAAGAA-AA
51039 AAGAAGCAAAA-AAGTAA
1 AAGAA-CAAAAGAA--AA
*
51056 AA-AA-AAAA-AACA
1 AAGAACAAAAGAAAA
*
51068 AAGAA-AAAGAGAAAC
1 AAGAACAAA-AGAAAA
51083 AAGAACAAAAGAAAA
1 AAGAACAAAAGAAAA
*
51098 AAGAGCAAAA
1 AAGAACAAAA
51108 ATCAAAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
12 3 0.05
13 5 0.09
14 7 0.12
15 26 0.46
16 12 0.21
17 4 0.07
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.01
Consensus pattern (15 bp):
AAGAACAAAAGAAAA
Found at i:51122 original size:22 final size:23
Alignment explanation
Indices: 51058--51131 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
51048 AAAAGTAAAA
*
51058 AAAAAAAAC-AAAGAAAAAGAG-
1 AAAAAGAACAAAAGAAAAAGAGC
51079 AAACAAGAACAAAAGAAAAAAGAGC
1 AAA-AAGAACAAAAG-AAAAAGAGC
** *
51104 AAAAATCA-AAAAGAAAAAGGGAC
1 AAAAAGAACAAAAGAAAAAGAG-C
51127 AAAAA
1 AAAAA
51132 ACACATGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.07
22 12 0.27
23 15 0.34
24 11 0.25
25 3 0.07
ACGTcount: A:0.76, C:0.08, G:0.15, T:0.01
Consensus pattern (23 bp):
AAAAAGAACAAAAGAAAAAGAGC
Found at i:51771 original size:22 final size:22
Alignment explanation
Indices: 51746--51794 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
51736 CCATCAATCT
*
51746 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
51768 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
51790 TTTGA
1 TTTGA
51795 CCAAACACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:52245 original size:18 final size:18
Alignment explanation
Indices: 52210--52245 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52200 TCAACATCAA
**
52210 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCGTTGG
52228 ATATTGGGGCATCGTTGG
1 ATATTGGGGCATCGTTGG
52246 GGATTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.08, G:0.36, T:0.39
Consensus pattern (18 bp):
ATATTGGGGCATCGTTGG
Found at i:52424 original size:29 final size:29
Alignment explanation
Indices: 52382--52440 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
52372 TACAGCTTTT
52382 AGAGTCAAGTTTCGACTTTAAGACGAAGG
1 AGAGTCAAGTTTCGACTTTAAGACGAAGG
52411 AGAGTCAAGTTTCGACTTTAAGACGAAGG
1 AGAGTCAAGTTTCGACTTTAAGACGAAGG
52440 A
1 A
52441 TACTCGATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.24
Consensus pattern (29 bp):
AGAGTCAAGTTTCGACTTTAAGACGAAGG
Found at i:52661 original size:36 final size:37
Alignment explanation
Indices: 52614--52748 Score: 100
Period size: 36 Copynumber: 3.8 Consensus size: 37
52604 CAGATGATTA
* *
52614 TCTCACTTGAGATTGTTTTTCTTAAAACAAGA-TTTG
1 TCTCGCTTGAGATAGTTTTTCTTAAAACAAGACTTTG
** ** * * *
52650 TCTCGCTTGAGACCG-TTTTC--ACTAGAAGATTTTA
1 TCTCGCTTGAGATAGTTTTTCTTAAAACAAGACTTTG
* *
52684 TCTCGCTTGAGATAGTTTCTCTTGAAACAA-ACTTTG
1 TCTCGCTTGAGATAGTTTTTCTTAAAACAAGACTTTG
* * * *
52720 TCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TCTCGCTTGAGATAGTTTTTCTTAAAACA
52749 TCTACTTTGA
Statistics
Matches: 77, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
33 6 0.08
34 16 0.21
35 9 0.12
36 43 0.56
37 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (37 bp):
TCTCGCTTGAGATAGTTTTTCTTAAAACAAGACTTTG
Found at i:52849 original size:36 final size:35
Alignment explanation
Indices: 52794--52868 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 35
52784 TTGAATATGT
*
52794 TTTCCTTAAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCTTAAAACAAATTTTGTCTCCCATGAGACAG
* *
52829 TTTCTTTAGAAACAAATTTTGTCTCCCATGAGGCAG
1 TTTCCTTA-AAACAAATTTTGTCTCCCATGAGACAG
52865 TTTC
1 TTTC
52869 GCTCGAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 7 0.19
36 29 0.81
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (35 bp):
TTTCCTTAAAACAAATTTTGTCTCCCATGAGACAG
Found at i:52877 original size:36 final size:36
Alignment explanation
Indices: 52802--52879 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
52792 GTTTTCCTTA
* **
52802 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTAG
1 AAACAAATTTTGTCTCCCATGAGACAGTTTCGCTAG
* *
52838 AAACAAATTTTGTCTCCCATGAGGCAGTTTCGCTCG
1 AAACAAATTTTGTCTCCCATGAGACAGTTTCGCTAG
52874 AAACAA
1 AAACAA
52880 CACAATGTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (36 bp):
AAACAAATTTTGTCTCCCATGAGACAGTTTCGCTAG
Found at i:53371 original size:64 final size:65
Alignment explanation
Indices: 53218--53400 Score: 307
Period size: 64 Copynumber: 2.8 Consensus size: 65
53208 ATATTGGAAC
*
53218 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTTAACAAAAATTTCCCAGT
1 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGT
53283 A
65 A
53284 TC-AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGT-
1 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTA
* **
53347 TCAAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAA
1 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA
53401 CAACTTCCCA
Statistics
Matches: 112, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
63 2 0.02
64 61 0.54
65 47 0.42
66 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (65 bp):
TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTA
Found at i:53400 original size:229 final size:230
Alignment explanation
Indices: 53121--53571 Score: 762
Period size: 235 Copynumber: 1.9 Consensus size: 230
53111 GTGCCACTCG
* *
53121 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTTCCCAA-T-
1 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTA
53184 CCAATTTCAACTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAACGA
66 CCAATTTCAACTTCACAGCGAAGGATATTGG-ACTCAAGACAACACAAGTTCAACTTCACAACGA
* * *
53249 AGGGGCCGCTGGTTGTTAACAAAAATTTCCCAGTATCAGACAACACAAGTTCAACTTCACAACGA
130 AGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGA
*
53314 AGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTCA
195 AGGGGCCGCTGGCTGTCAACAAAATTTCCCAGTTCA
53350 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTT
1 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAA-TT
53415 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
65 ---A-CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
* *
53480 ACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTAAGACAGCACAAGTTCAACTTCACA
126 ACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACA
53545 ACGAAGGGGCCGCTGGCTGTCAACAAA
191 ACGAAGGGGCCGCTGGCTGTCAACAAA
53572 CAACTTCCCA
Statistics
Matches: 207, Mismatches: 8, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
229 60 0.29
231 1 0.00
235 115 0.56
236 31 0.15
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.20
Consensus pattern (230 bp):
AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTA
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAA
GGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGAA
GGGGCCGCTGGCTGTCAACAAAATTTCCCAGTTCA
Found at i:53489 original size:170 final size:171
Alignment explanation
Indices: 53286--53621 Score: 620
Period size: 171 Copynumber: 2.0 Consensus size: 171
53276 TCCCAGTATC
*
53286 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTTCA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTCA
53350 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTT
66 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTT
53415 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
131 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
*
53456 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTCA
* *
53521 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTTT
66 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTT
*
53586 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
131 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
53622 CCTCGAAACA
Statistics
Matches: 160, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
170 48 0.30
171 112 0.70
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (171 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTCA
AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
Found at i:53535 original size:65 final size:66
Alignment explanation
Indices: 53455--53614 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 66
53445 TATTGGACTC
* *
53455 AAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AA-TTCCCCAGT
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTT-CCCAGT
53518 TT
65 TT
53520 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
53585 T
66 T
* * * *
53586 CAG--AG-TCAATTTCAACTTCACAGCGAAGG
1 AAGACAGCACAAGTTCAACTTCACAACGAAGG
53615 ATATTGGCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
63 21 0.24
64 2 0.02
65 50 0.57
66 12 0.14
67 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (66 bp):
AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
T
Found at i:53569 original size:106 final size:104
Alignment explanation
Indices: 53350--53551 Score: 255
Period size: 106 Copynumber: 1.9 Consensus size: 104
53340 TCCCAGTTCA
*
53350 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTT
* * * * *
53415 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
66 AAGAGCCAAGTTCAACTTCACAACGAAGGACACTGGACT
** *
53454 CAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AA-TTCCCCAG
1 --AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTT-CCCAA
53517 TTTAAGACAGCACAAGTTCAACTTCACAACGAAGG
63 TTTAAG--AGC-CAAGTTCAACTTCACAACGAAGG
53552 GGCCGCTGGC
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
104 2 0.02
105 11 0.13
106 48 0.56
107 3 0.04
108 21 0.25
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (104 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTT
AAGAGCCAAGTTCAACTTCACAACGAAGGACACTGGACT
Found at i:54217 original size:37 final size:36
Alignment explanation
Indices: 54132--54267 Score: 168
Period size: 37 Copynumber: 3.8 Consensus size: 36
54122 TTTCGTCCTA
54132 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
54167 -TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
54202 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-TT
** * *
54240 CTATTATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
54268 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 29 0.33
35 3 0.03
37 54 0.62
38 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:57872 original size:35 final size:37
Alignment explanation
Indices: 57804--57882 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
57794 TACTATTTCA
*
57804 ATCACCATAATCCATCTTCCATTATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
*
57841 ATCACCATAGTCCATC-ACCA-TATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
57876 ATCACCA
1 ATCACCA
57883 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (37 bp):
ATCACCATAATCCATCTACCATTATCACGCCTATATC
Found at i:61808 original size:35 final size:37
Alignment explanation
Indices: 61740--61818 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
61730 TACTATTTTT
*
61740 ATCACCATAATCCATCTTCCATTATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
*
61777 ATCACCATAGTCCATC-ACCA-TATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
61812 ATCACCA
1 ATCACCA
61819 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (37 bp):
ATCACCATAATCCATCTACCATTATCACGCCTATATC
Found at i:64733 original size:36 final size:36
Alignment explanation
Indices: 64681--64793 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
64671 GATACTATTT
*
64681 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
64717 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
64753 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
64788 ACATCA
1 TCATCA
64794 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:64736 original size:13 final size:11
Alignment explanation
Indices: 64681--64779 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
64671 GATACTATTT
64681 TCATCACCATAA
1 TCATCACCAT-A
*
64693 TCCATCTCCATTA
1 T-CATCACCA-TA
*
64706 TCA-CGCCTATA
1 TCATCACC-ATA
64717 TCATCACCATA
1 TCATCACCATA
64728 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
64742 TCA-CGCCTATA
1 TCATCACC-ATA
64753 TCATCACCATA
1 TCATCACCATA
64764 TTCCATCACCATA
1 -T-CATCACCATA
64777 TCA
1 TCA
64780 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:64808 original size:33 final size:33
Alignment explanation
Indices: 64693--64832 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
64683 ATCACCATAA
* * *
64693 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
64727 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
64765 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
64798 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
64831 TC
1 TC
64833 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:66375 original size:19 final size:21
Alignment explanation
Indices: 66351--66402 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
66341 CGGCCAAGAG
*
66351 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
66370 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
66391 CATGTATTTTCA
1 CATGTATTTTCA
66403 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:67164 original size:13 final size:13
Alignment explanation
Indices: 67146--67179 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
67136 GAGAAAAATC
67146 AGAAAAGAAGAAA
1 AGAAAAGAAGAAA
67159 AGAAAAGAA-AAA
1 AGAAAAGAAGAAA
67171 A-AAAAGAAG
1 AGAAAAGAAG
67180 TTCAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.35
12 4 0.20
13 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAGAAA
Found at i:70471 original size:19 final size:21
Alignment explanation
Indices: 70447--70498 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
70437 CGGCCAAGAG
*
70447 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
70466 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
70487 CATGTATTTTCA
1 CATGTATTTTCA
70499 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:71197 original size:14 final size:15
Alignment explanation
Indices: 71163--71209 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
71153 AAATTTGAGT
71163 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
71178 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
71192 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
71209 G
1 G
71210 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:74708 original size:36 final size:36
Alignment explanation
Indices: 74656--74768 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
74646 GATACTATTT
*
74656 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
74692 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
74728 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
74763 ACATCA
1 TCATCA
74769 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:74711 original size:13 final size:11
Alignment explanation
Indices: 74656--74754 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
74646 GATACTATTT
74656 TCATCACCATAA
1 TCATCACCAT-A
*
74668 TCCATCTCCATTA
1 T-CATCACCA-TA
*
74681 TCA-CGCCTATA
1 TCATCACC-ATA
74692 TCATCACCATA
1 TCATCACCATA
74703 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
74717 TCA-CGCCTATA
1 TCATCACC-ATA
74728 TCATCACCATA
1 TCATCACCATA
74739 TTCCATCACCATA
1 -T-CATCACCATA
74752 TCA
1 TCA
74755 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:74783 original size:33 final size:33
Alignment explanation
Indices: 74668--74807 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
74658 ATCACCATAA
* * *
74668 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
74702 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
74740 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
74773 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
74806 TC
1 TC
74808 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:75350 original size:8 final size:8
Alignment explanation
Indices: 75337--75373 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
75327 TCTTTTTCCT
75337 TTCTTTTC
1 TTCTTTTC
75345 TTCTTTTC
1 TTCTTTTC
75353 TTCTTTTC
1 TTCTTTTC
75361 TTCTTTTC
1 TTCTTTTC
75369 TTCTT
1 TTCTT
75374 CTTTTTGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:75354 original size:24 final size:24
Alignment explanation
Indices: 75327--75373 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
75317 TTTGAACTTC
75327 TCTT-TTTCCTTTCTTTTCTTCTTT
1 TCTTCTTTCC-TTCTTTTCTTCTTT
*
75351 TCTTCTTTTCTTCTTTTCTTCTT
1 TCTTCTTTCCTTCTTTTCTTCTT
75374 CTTTTTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (24 bp):
TCTTCTTTCCTTCTTTTCTTCTTT
Found at i:75356 original size:3 final size:3
Alignment explanation
Indices: 75337--75376 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
75327 TCTTTTTCCT
75337 TTC TT- TTC TTC TT- TTC TTC TT- TTC TTC TT- TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
75377 TTTGCTCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.24
3 25 0.76
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:75356 original size:11 final size:11
Alignment explanation
Indices: 75337--75378 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
75327 TCTTTTTCCT
75337 TTCTTTTCTTC
1 TTCTTTTCTTC
75348 TT-TTCTTCTTTTC
1 TTCTT-TTC--TTC
75361 TTCTTTTCTTC
1 TTCTTTTCTTC
75372 TTCTTTT
1 TTCTTTT
75379 TGCTCTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
13 8 0.30
14 2 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTCTTTTCTTC
Found at i:77615 original size:19 final size:20
Alignment explanation
Indices: 77593--77633 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
77583 TTATTAAGTT
77593 TTCATTTTA-ATAACTTTGA
1 TTCATTTTACATAACTTTGA
*
77612 TTCATTTTACATCACTTTGA
1 TTCATTTTACATAACTTTGA
77632 TT
1 TT
77634 ATTATAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.27, C:0.15, G:0.05, T:0.54
Consensus pattern (20 bp):
TTCATTTTACATAACTTTGA
Found at i:83549 original size:17 final size:16
Alignment explanation
Indices: 83516--83581 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 16
83506 TTTGATAACA
83516 TTTC-TATCTATTTCTT
1 TTTCTTATC-ATTTCTT
83532 TTTCTTATCATTTCCTT
1 TTTCTTATCATTT-CTT
*
83549 TCTTCTT-TCATATTCTA
1 T-TTCTTATCAT-TTCTT
*
83566 TTT-TAATCATTT-TT
1 TTTCTTATCATTTCTT
83580 TT
1 TT
83582 CTTTAATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 14 0.33
17 15 0.36
18 7 0.17
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTCTTATCATTTCTT
Found at i:83771 original size:22 final size:22
Alignment explanation
Indices: 83746--83792 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
83736 TGCTGCAACA
83746 AAAGCAACAAAAAGAGA-AAAAG
1 AAAG-AACAAAAAGAGAGAAAAG
* *
83768 AAAGAAGAAAAATAGAGAAAAG
1 AAAGAACAAAAAGAGAGAAAAG
83790 AAA
1 AAA
83793 AAGACTCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.02
Consensus pattern (22 bp):
AAAGAACAAAAAGAGAGAAAAG
Found at i:83779 original size:21 final size:21
Alignment explanation
Indices: 83754--83796 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
83744 CAAAAGCAAC
83754 AAAAAGAGA-AAAAGAAAGAAG
1 AAAAAGAGAGAAAAGAAA-AAG
*
83775 AAAAATAGAGAAAAGAAAAAG
1 AAAAAGAGAGAAAAGAAAAAG
83796 A
1 A
83797 CTCCTACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (21 bp):
AAAAAGAGAGAAAAGAAAAAG
Done.