Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003453.1 Hibiscus syriacus cultivar Beakdansim tig00007300_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: 95717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:905 original size:14 final size:15
Alignment explanation
Indices: 881--909 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
871 TTTTGGTCAC
881 CGTCGGTCGTCGTCT
1 CGTCGGTCGTCGTCT
896 CGTC-GTCGTCGTCT
1 CGTCGGTCGTCGTCT
910 TCGGTGGCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (15 bp):
CGTCGGTCGTCGTCT
Found at i:3149 original size:42 final size:43
Alignment explanation
Indices: 3103--3237 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 43
3093 CCTGATCTTA
* * *
3103 TTTCTGTATGGGGTCCTCTACAGAGGGTAATAT-CTCATCATG
1 TTTCTATATGGGATCCTCTACAGAGGGTAATATCCCCATCATG
* * * *
3145 TTTCTACATGTGATCCTCTACGGAGGGTAATATCCCCGTCATG
1 TTTCTATATGGGATCCTCTACAGAGGGTAATATCCCCATCATG
* * * * * *
3188 TTTCTATTTGGGATCCTCTTCGGAGGCT-ATCTCCCCATCTTG
1 TTTCTATATGGGATCCTCTACAGAGGGTAATATCCCCATCATG
3230 ATTTCTAT
1 -TTTCTAT
3238 TTGACTAGGA
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
42 39 0.51
43 37 0.49
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.38
Consensus pattern (43 bp):
TTTCTATATGGGATCCTCTACAGAGGGTAATATCCCCATCATG
Found at i:3203 original size:43 final size:43
Alignment explanation
Indices: 3111--3240 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 43
3101 TATTTCTGTA
* * * **
3111 TGGGGTCCTCTACAGAGGGTAATAT-CTCATCATGTTTCTACA
1 TGGGATCCTCTACGGAGGGTAATATCCCCATCATGTTTCTATT
* *
3153 TGTGATCCTCTACGGAGGGTAATATCCCCGTCATGTTTCTATT
1 TGGGATCCTCTACGGAGGGTAATATCCCCATCATGTTTCTATT
* * * *
3196 TGGGATCCTCTTCGGAGGCT-ATCTCCCCATCTTGATTTCTATT
1 TGGGATCCTCTACGGAGGGTAATATCCCCATCATG-TTTCTATT
3239 TG
1 TG
3241 ACTAGGATCC
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
42 33 0.45
43 40 0.55
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (43 bp):
TGGGATCCTCTACGGAGGGTAATATCCCCATCATGTTTCTATT
Found at i:5191 original size:29 final size:31
Alignment explanation
Indices: 5157--5216 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
5147 AAATTTTGAA
*
5157 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5186 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5217 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:6443 original size:2 final size:2
Alignment explanation
Indices: 6431--6464 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6421 ATTAAAATCG
6431 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6465 ATGAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8548 original size:22 final size:22
Alignment explanation
Indices: 8523--8572 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
8513 CGTGTTGCTC
8523 TTGGTTCGGGTTAATTTCAATT
1 TTGGTTCGGGTTAATTTCAATT
*
8545 TTGGTTCGGGTTAATTTCGATT
1 TTGGTTCGGGTTAATTTCAATT
8567 TTGGTT
1 TTGGTT
8573 GATTTCGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.14, C:0.08, G:0.26, T:0.52
Consensus pattern (22 bp):
TTGGTTCGGGTTAATTTCAATT
Found at i:8572 original size:16 final size:16
Alignment explanation
Indices: 8553--8583 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8543 TTTTGGTTCG
8553 GGTTAATTTCGATTTT
1 GGTTAATTTCGATTTT
*
8569 GGTTGATTTCGATTT
1 GGTTAATTTCGATTT
8584 CGCTAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.23, T:0.55
Consensus pattern (16 bp):
GGTTAATTTCGATTTT
Found at i:10888 original size:31 final size:30
Alignment explanation
Indices: 10814--10889 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
10804 AATATTAGAT
* *
10814 AAAAAACAAATAAATATTAAATAAATCAAA
1 AAAAAACAAAAAAATAATAAATAAATCAAA
* *
10844 GAAAAACATAAAAATAATAAATCAAAAT-AAA
1 AAAAAACAAAAAAATAATAAAT--AAATCAAA
*
10875 AAAAAATAAAAAAAT
1 AAAAAACAAAAAAAT
10890 CAAAGGAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 18 0.49
31 15 0.41
32 4 0.11
ACGTcount: A:0.76, C:0.05, G:0.01, T:0.17
Consensus pattern (30 bp):
AAAAAACAAAAAAATAATAAATAAATCAAA
Found at i:10904 original size:29 final size:29
Alignment explanation
Indices: 10845--10923 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
10835 TAAATCAAAG
* * *
10845 AAAAACATAAAAATAAT-AAATCAAAATAA
1 AAAAAAATAAAAA-AATCAAAGCAAAAGAA
*
10874 AAAAAAATAAAAAAATCAAAGGAAAAGAA
1 AAAAAAATAAAAAAATCAAAGCAAAAGAA
* *
10903 AAGAAAATACAAAATATCAAA
1 AAAAAAATA-AAAAAATCAAA
10924 TAAATTAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 3 0.07
29 29 0.69
30 10 0.24
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.13
Consensus pattern (29 bp):
AAAAAAATAAAAAAATCAAAGCAAAAGAA
Found at i:10997 original size:5 final size:5
Alignment explanation
Indices: 10974--11034 Score: 72
Period size: 5 Copynumber: 12.0 Consensus size: 5
10964 GGGAAAAAGG
*
10974 TAAAA TAATAGA T-AAA TAAAA TAAAA TAAAA TAAAA -AACAA AAAAA
1 TAAAA TAA-A-A TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA
11020 TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA
11035 AATAATTAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
4 4 0.08
5 40 0.80
6 4 0.08
7 2 0.04
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:21817 original size:27 final size:27
Alignment explanation
Indices: 21776--21827 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
21766 ACCAACGGAC
* *
21776 TAAATTTGATCTATAAATTTTAAATCT
1 TAAATTTAATATATAAATTTTAAATCT
*
21803 TAAATTTAATATATAATTTTTAAAT
1 TAAATTTAATATATAAATTTTAAAT
21828 GTATAACCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (27 bp):
TAAATTTAATATATAAATTTTAAATCT
Found at i:22421 original size:2 final size:2
Alignment explanation
Indices: 22414--22459 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
22404 TAAATTATTA
22414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22456 AT AT
1 AT AT
22460 TCAAACTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29617 original size:37 final size:37
Alignment explanation
Indices: 29576--29680 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 37
29566 TGGATCCTAC
* *
29576 TTTTAGGAGTTTGAATCATAGTAGAACTCTATTATAT
1 TTTTAGGAGTTTGAATCATAGTAAAACTCTATCATAT
* *
29613 TTTTAGGAGTTTGAATCCTAGTAAAACTCTATCCTAT
1 TTTTAGGAGTTTGAATCATAGTAAAACTCTATCATAT
*
29650 TTTTAGGAGTTTGAATCATAGTAAAAGTCTA
1 TTTTAGGAGTTTGAATCATAGTAAAACTCTA
29681 ACGTTATGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (37 bp):
TTTTAGGAGTTTGAATCATAGTAAAACTCTATCATAT
Found at i:31004 original size:110 final size:110
Alignment explanation
Indices: 30818--31331 Score: 776
Period size: 110 Copynumber: 4.7 Consensus size: 110
30808 TTGTGTCGCT
* * * *
30818 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTAACTGTGAATGAAACTAAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
30883 TGACAGCCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTC
* *
30928 TCGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
30993 TGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGTTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTC
* * * * * *
31038 TCAAGTCTAATATCCTTTGATGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGC
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * * * * *
31103 TGAAATTCAGTCGCCCATTCGCTATGAAGTTGAGCTTGTTTTGTC
66 TGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTC
*
31148 TCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * * *
31213 TGATAGTTAGTCACCCCTTCACTGTGAAGTTGAGGTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTC
* *
31258 TCAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
31323 TGACAGTCA
66 TGACAGTCA
31332 ACTTGTCTTG
Statistics
Matches: 360, Mismatches: 44, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 360 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTC
Found at i:32995 original size:14 final size:13
Alignment explanation
Indices: 32986--33048 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 13
32976 TTTTTCTTTG
32986 TTTTTGTTTCTCT
1 TTTTTGTTTCTCT
32999 TTTTTGTTTTCTCTT
1 TTTTTG-TTTCTC-T
*
33014 TGCTTTTTTTTCTTCTT
1 T--TTTTGTTTC-TC-T
*
33031 TTTTTTTTTCTCT
1 TTTTTGTTTCTCT
33044 TTTTT
1 TTTTT
33049 CTTTTTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
13 12 0.27
14 8 0.18
15 11 0.25
16 4 0.09
17 9 0.20
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (13 bp):
TTTTTGTTTCTCT
Found at i:33026 original size:30 final size:31
Alignment explanation
Indices: 32975--33045 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
32965 TTTTCTTCAA
*
32975 TTTTTTCTTTGTTTTTGTTTC-TCTTTTTTG
1 TTTTCTCTTTGTTTTTGTTTCTTCTTTTTTG
*
33005 TTTTCTCTTTGCTTTTT-TTTCTTCTTTTTTT
1 TTTTCTCTTTG-TTTTTGTTTCTTCTTTTTTG
33036 TTTTCTCTTT
1 TTTTCTCTTT
33046 TTTCTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 14 0.38
31 23 0.62
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (31 bp):
TTTTCTCTTTGTTTTTGTTTCTTCTTTTTTG
Found at i:33035 original size:33 final size:33
Alignment explanation
Indices: 32993--33060 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
32983 TTGTTTTTGT
*
32993 TTCTCTTTTTTGTTT-TCTCTTTGCTTTTTTTTC
1 TTCTCTTTTTT-TTTCTCTCTTTGCTTTTTATTC
* * *
33026 TTCTTTTTTTTTTTCTCTTTTTTCTTTTTATTC
1 TTCTCTTTTTTTTTCTCTCTTTGCTTTTTATTC
33059 TT
1 TT
33061 ATTGGATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.79
Consensus pattern (33 bp):
TTCTCTTTTTTTTTCTCTCTTTGCTTTTTATTC
Found at i:33053 original size:14 final size:14
Alignment explanation
Indices: 32975--33054 Score: 90
Period size: 14 Copynumber: 5.4 Consensus size: 14
32965 TTTTCTTCAA
32975 TTTTTTCT-TTGTTT
1 TTTTTTCTCTT-TTT
*
32989 TTGTTTCTCTTTTT
1 TTTTTTCTCTTTTT
*
33003 TGTTTTCTCTTTGCTT
1 TTTTTTCTCTTT--TT
33019 TTTTTTCTTCTTTTT
1 TTTTTTC-TCTTTTT
33034 TTTTTTCTCTTTTT
1 TTTTTTCTCTTTTT
33048 TCTTTTT
1 T-TTTTT
33055 ATTCTTATTG
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
14 28 0.49
15 16 0.28
16 8 0.14
17 5 0.09
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (14 bp):
TTTTTTCTCTTTTT
Found at i:33054 original size:30 final size:29
Alignment explanation
Indices: 32975--33060 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
32965 TTTTCTTCAA
*
32975 TTTTTTCT-TTGTTTTTGTTTC-TCTTTTT
1 TTTTTTCTCTT-TTTTTTTTTCTTCTTTTT
*
33003 TGTTTTCTCTTTGCTTTTTTTTCTTCTTTTT
1 TTTTTTCTCTTT--TTTTTTTTCTTCTTTTT
*
33034 TTTTTTCTCTTTTTTCTTTTTATTCTT
1 TTTTTTCTCTTTTTT-TTTTTCTTCTT
33061 ATTGGATCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
28 8 0.16
29 5 0.10
30 18 0.37
31 18 0.37
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.80
Consensus pattern (29 bp):
TTTTTTCTCTTTTTTTTTTTCTTCTTTTT
Found at i:33054 original size:31 final size:29
Alignment explanation
Indices: 32975--33054 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
32965 TTTTCTTCAA
* *
32975 TTTTTTCT-TTGTTTTTGTTTCTCTTTTT
1 TTTTTTCTCTTTTTTTTTTTTCTCTTTTT
* *
33003 TGTTTTCTCTTTGCTTTTTTTTCTTCTTTTT
1 TTTTTTCTCTTT-TTTTTTTTTC-TCTTTTT
*
33034 TTTTTTCTCTTTTTTCTTTTT
1 TTTTTTCTCTTTTTTTTTTTT
33055 ATTCTTATTG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.17
29 2 0.05
30 15 0.36
31 18 0.43
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (29 bp):
TTTTTTCTCTTTTTTTTTTTTCTCTTTTT
Found at i:33060 original size:9 final size:8
Alignment explanation
Indices: 33018--33060 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 8
33008 TCTCTTTGCT
33018 TTTTTTTC
1 TTTTTTTC
*
33026 TTCTTTT-
1 TTTTTTTC
33033 TTTTTTTC
1 TTTTTTTC
33041 TCTTTTTTC
1 T-TTTTTTC
33050 TTTTTATTC
1 TTTTT-TTC
33059 TT
1 TT
33061 ATTGGATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 6 0.20
8 11 0.37
9 13 0.43
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTC
Found at i:36122 original size:26 final size:26
Alignment explanation
Indices: 36080--36129 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
36070 AAAGGTAAGA
*
36080 AAGAAAGAAATAAATTAAATTAAAATG
1 AAGAAAGAAACAAATTAAA-TAAAATG
36107 AAGAAA-AAACAAATTAAATAAAA
1 AAGAAAGAAACAAATTAAATAAAA
36130 GATAAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 11 0.50
27 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.18
Consensus pattern (26 bp):
AAGAAAGAAACAAATTAAATAAAATG
Found at i:36136 original size:26 final size:27
Alignment explanation
Indices: 36076--36136 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
36066 ATAAAAAGGT
* *
36076 AAGA-AAGAAAGAAATAAATTAAATTA
1 AAGATAAGAAAGAAACAAATTAAATAA
36102 AA-ATGAAGAAA-AAACAAATTAAATAA
1 AAGAT-AAGAAAGAAACAAATTAAATAA
36128 AAGATAAGA
1 AAGATAAGA
36137 TAAAGAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.03
26 21 0.70
27 8 0.27
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.16
Consensus pattern (27 bp):
AAGATAAGAAAGAAACAAATTAAATAA
Found at i:36175 original size:21 final size:21
Alignment explanation
Indices: 36151--36242 Score: 66
Period size: 21 Copynumber: 4.4 Consensus size: 21
36141 GAAATCAAAG
36151 ATAAAATAGTAAGTAAAATAA
1 ATAAAATAGTAAGTAAAATAA
* *
36172 ATAAAA-AATATA-TAAAAAAA
1 ATAAAATAGTA-AGTAAAATAA
* * *
36192 TATAAAAAAG-AAGAAAAAATAT
1 -ATAAAATAGTAAG-TAAAATAA
*
36214 ATAAATATA-TAAATAAAATAA
1 ATAAA-ATAGTAAGTAAAATAA
36235 ATAAAATA
1 ATAAAATA
36243 ATAATAAGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
20 14 0.26
21 30 0.56
22 10 0.19
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (21 bp):
ATAAAATAGTAAGTAAAATAA
Found at i:36226 original size:50 final size:50
Alignment explanation
Indices: 36166--36285 Score: 131
Period size: 50 Copynumber: 2.4 Consensus size: 50
36156 ATAGTAAGTA
*
36166 AAATAAATAAAAAATATATAAAAAAAT-ATAAAAAAGAAGAAAAAAT-ATAT
1 AAATATATAAAAAATATA-AAAAAAATAAT-AAAAAGAAGAAAAAATAATAT
* * *
36216 AAATATATAAATAAA-ATAAATAAAATAATAATAAGAAGTAAAAATAATAT
1 AAATATATAAA-AAATATAAAAAAAATAATAAAAAGAAGAAAAAATAATAT
* *
36266 ATATATATAATAAATA-AAAA
1 AAATATATAAAAAATATAAAA
36286 CATAAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
49 27 0.46
50 29 0.49
51 3 0.05
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (50 bp):
AAATATATAAAAAATATAAAAAAAATAATAAAAAGAAGAAAAAATAATAT
Found at i:36236 original size:9 final size:9
Alignment explanation
Indices: 36164--36243 Score: 51
Period size: 9 Copynumber: 8.9 Consensus size: 9
36154 AAATAGTAAG
36164 TAAAATAAA
1 TAAAATAAA
36173 TAAAA-AATA
1 TAAAATAA-A
*
36182 TATAAAAAAA
1 TA-AAATAAA
36192 TATAAA-AAA
1 TA-AAATAAA
* *
36201 GAAGAAAAAA
1 TAA-AATAAA
*
36211 T-ATATAAA
1 TAAAATAAA
*
36219 T-ATATAAA
1 TAAAATAAA
36227 TAAAATAAA
1 TAAAATAAA
36236 TAAAATAA
1 TAAAATAA
36244 TAATAAGAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
8 16 0.27
9 29 0.48
10 13 0.22
11 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (9 bp):
TAAAATAAA
Found at i:36403 original size:24 final size:22
Alignment explanation
Indices: 36376--36442 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 22
36366 ATATATATAT
36376 ATATATATATGTAAAAAAGTAAAA
1 ATATATATATGTAAAAAAG--AAA
*
36400 ATATATACTAAAGTAAAAAAGAAA
1 ATATATA-T-ATGTAAAAAAGAAA
* *
36424 ATACATAAAATGTAAAAAA
1 ATATAT-ATATGTAAAAAA
36443 ATATTACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
23 9 0.25
24 15 0.42
25 2 0.06
26 10 0.28
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (22 bp):
ATATATATATGTAAAAAAGAAA
Found at i:36403 original size:26 final size:23
Alignment explanation
Indices: 36374--36442 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 23
36364 ATATATATAT
36374 ATATATATATATGTAAAAAAGTAAAA
1 ATATATATA-ATGTAAAAAAG--AAA
*
36400 ATATATACTAAAGTAAAAAAGAAA
1 ATATATA-TAATGTAAAAAAGAAA
* *
36424 ATACATAAAATGTAAAAAA
1 ATATATATAATGTAAAAAA
36443 ATATTACATG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 10 0.26
24 9 0.24
26 17 0.45
27 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (23 bp):
ATATATATAATGTAAAAAAGAAA
Found at i:36405 original size:2 final size:2
Alignment explanation
Indices: 36350--36385 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
36340 AAAAAATAGC
36350 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
36386 GTAAAAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36450 original size:22 final size:21
Alignment explanation
Indices: 36390--36456 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 21
36380 ATATATGTAA
*
36390 AAAAGTAAAAATATA-TAC-T
1 AAAAGTAAAAAAATATTACAT
* *
36409 -AAAGTAAAAAAGAAAATACAT
1 AAAAGTAAAAAA-ATATTACAT
36430 AAAATGTAAAAAAATATTACAT
1 AAAA-GTAAAAAAATATTACAT
36452 GAAAA
1 -AAAA
36457 AAAGAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 10 0.26
19 2 0.05
20 3 0.08
21 1 0.03
22 10 0.26
23 12 0.32
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAAGTAAAAAAATATTACAT
Found at i:37000 original size:37 final size:37
Alignment explanation
Indices: 36950--37057 Score: 180
Period size: 37 Copynumber: 2.9 Consensus size: 37
36940 TTGTGGATCC
*
36950 TATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
* *
36987 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
*
37024 TATTTTTAGGAGTTTGAATCATAGTAAAAGTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
37058 ACGTTATGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
Found at i:37081 original size:74 final size:73
Alignment explanation
Indices: 36946--37088 Score: 171
Period size: 74 Copynumber: 1.9 Consensus size: 73
36936 ATGCTTGTGG
* * * * *
36946 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCATATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCTAACATATGTTTA-GAGTTTAAATCCTAC
37011 TAAAACTCT
65 TAAAACTCT
* * **
37020 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAAGTCTAACGTTATGTTT-GTTTTCTAAATCCTA
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCTAAC-ATATGTTTAGAGTT-TAAATCCTA
37084 CTAAA
64 CTAAA
37089 TCGAGGTTGT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
73 3 0.05
74 49 0.84
75 6 0.10
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (73 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCTAACATATGTTTAGAGTTTAAATCCTACT
AAAACTCT
Found at i:42022 original size:21 final size:21
Alignment explanation
Indices: 41998--42039 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41988 CAAAATTCCA
41998 GGTTAATTT-AGGTTCAGATCG
1 GGTTAATTTCA-GTTCAGATCG
42019 GGTTAATTTCAGTTCAGATCG
1 GGTTAATTTCAGTTCAGATCG
42040 ATGTTAGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (21 bp):
GGTTAATTTCAGTTCAGATCG
Found at i:43016 original size:23 final size:23
Alignment explanation
Indices: 42982--43073 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
42972 CACCACAGCT
*
42982 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
43005 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* * *
43028 TGTAGAAATGCAACGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
43051 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
43074 TATAAGGTTG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:45681 original size:16 final size:16
Alignment explanation
Indices: 45660--45691 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45650 ATTAAAATAA
45660 TTATTATTATTTGATT
1 TTATTATTATTTGATT
45676 TTATTATTATTTGATT
1 TTATTATTATTTGATT
45692 AAGCTAACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TTATTATTATTTGATT
Found at i:46358 original size:23 final size:24
Alignment explanation
Indices: 46302--46348 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
46292 CAAACAATGA
46302 AGGGAATTATCTTTTGTAATTTTT
1 AGGGAATTATCTTTTGTAATTTTT
*
46326 AGGGAATTATCTTTT-TCATTTTT
1 AGGGAATTATCTTTTGTAATTTTT
46349 TAGTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.55
Consensus pattern (24 bp):
AGGGAATTATCTTTTGTAATTTTT
Found at i:59037 original size:7 final size:7
Alignment explanation
Indices: 59027--59051 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59017 AAAAGTGTGA
59027 AGTGAGT
1 AGTGAGT
59034 AGTGAGT
1 AGTGAGT
59041 AGTGAGT
1 AGTGAGT
59048 AGTG
1 AGTG
59052 GAGTTTTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28
Consensus pattern (7 bp):
AGTGAGT
Found at i:63501 original size:64 final size:65
Alignment explanation
Indices: 63448--63610 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 65
63438 TGGTGCACTA
* * *
63448 AGTGTGCATCGATGCATAAAATGCATTGGATGTTTTGAAT-AAGCCTAAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTTGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
* * * *
63512 TGTGTGCATCGATGCATAAAATGCATTTGATGATTTCATTAAAACCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTTGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
* * *
63577 AGAGTGCATCGATGTATAAACTGCATTTGATGTT
1 AGTGTGCATCGATGCATAAAATGCATTTGATGTT
63611 CAATTTATTC
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 35 0.41
65 51 0.59
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (65 bp):
AGTGTGCATCGATGCATAAAATGCATTTGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
Found at i:63649 original size:65 final size:65
Alignment explanation
Indices: 63451--63651 Score: 202
Period size: 65 Copynumber: 3.1 Consensus size: 65
63441 TGCACTAAGT
* *
63451 GTGCATCGATGCATAAAATGCATTGGATG-TT--TTGAATAAGCCTAAGTGCATCGATGCATGG-
1 GTGCATCGATGCATAAAATGCATTTGATGATTCATT-AA-AA-CCTGAGTGCATCGATGCATGGA
*
63512 TGT
63 TGA
63515 GTGCATCGATGCATAAAATGCATTTGATGATTTCATTAAAACCTGAGTGCATCGATGCATGGA-G
1 GTGCATCGATGCATAAAATGCATTTGATGA-TTCATTAAAACCTGAGTGCATCGATGCATGGATG
63579 A
65 A
* * * ** *
63580 GTGCATCGATGTATAAACTGCATTTGATG-TTCAATTTATTCATTG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTTGATGATTC-ATTAAAAC-CTGAGTGCATCGATGCATGGA-
63643 TG-
63 TGA
63645 GTGCATC
1 GTGCATC
63652 CCTTTGAAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
63 3 0.03
64 50 0.42
65 57 0.48
66 5 0.04
67 2 0.02
68 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTTGATGATTCATTAAAACCTGAGTGCATCGATGCATGGATGA
Found at i:72824 original size:22 final size:20
Alignment explanation
Indices: 72774--72824 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 20
72764 CAATCTTTAA
72774 AAATCTCTTACAAAGACTAGG
1 AAATCT-TTACAAAGACTAGG
72795 -AATGCTTTACAAAGGCACTAGG
1 AAAT-CTTTACAAA-G-ACTAGG
72817 AAATCTTT
1 AAATCTTT
72825 CAGAAGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 10 0.38
21 3 0.12
22 10 0.38
23 3 0.12
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
AAATCTTTACAAAGACTAGG
Found at i:77959 original size:19 final size:19
Alignment explanation
Indices: 77910--77960 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
77900 ATTATTCCAG
*
77910 TAGTATCGATACTAACCCT
1 TAGTATCAATACTAACCCT
* * *
77929 TGGGTATTAATACTCACCCT
1 T-AGTATCAATACTAACCCT
77949 TAGTATCAATAC
1 TAGTATCAATAC
77961 AAAAATAGCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (19 bp):
TAGTATCAATACTAACCCT
Found at i:81679 original size:16 final size:16
Alignment explanation
Indices: 81654--81684 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
81644 GTATGCCAAG
*
81654 AAGTTGAGTAAAGTTC
1 AAGTTAAGTAAAGTTC
81670 AAGTTAAGTAAAGTT
1 AAGTTAAGTAAAGTT
81685 ATGATACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (16 bp):
AAGTTAAGTAAAGTTC
Found at i:81899 original size:19 final size:19
Alignment explanation
Indices: 81844--81902 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
81834 GCATTGGGTG
* * *
81844 ATGAATTTGAAAGTAAGCT
1 ATGAATATGAAAATAAGTT
*
81863 ATGAATCT-AAAATTAAGTT
1 ATGAATATGAAAA-TAAGTT
81882 ATGAATATGAAAATAAGTT
1 ATGAATATGAAAATAAGTT
81901 AT
1 AT
81903 AATTCAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.09
19 27 0.79
20 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.34
Consensus pattern (19 bp):
ATGAATATGAAAATAAGTT
Found at i:81972 original size:13 final size:13
Alignment explanation
Indices: 81954--81992 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
81944 GTAAATGAAT
*
81954 ATGAAAGTGAAAG
1 ATGAAAATGAAAG
*
81967 ATGAAAATGAAAT
1 ATGAAAATGAAAG
81980 ATGAAATATGAAA
1 ATGAAA-ATGAAA
81993 TTTCTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (13 bp):
ATGAAAATGAAAG
Found at i:81983 original size:7 final size:7
Alignment explanation
Indices: 81951--81993 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
81941 TATGTAAATG
81951 AATATGA
1 AATATGA
*
81958 AA-GTGA
1 AATATGA
*
81964 AAGATGA
1 AATATGA
81971 AA-ATGA
1 AATATGA
81977 AATATGA
1 AATATGA
81984 AATATGA
1 AATATGA
81991 AAT
1 AAT
81994 TTCTGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (7 bp):
AATATGA
Found at i:84113 original size:21 final size:22
Alignment explanation
Indices: 84081--84163 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 22
84071 ATAATTTACA
84081 CCGAACTG-CCACATA-TTTTTC
1 CCGAA-TGACCACATAGTTTTTC
**
84102 CTAAATGACCACATAGTTTTGTC
1 CCGAATGACCACATAGTTTT-TC
* *
84125 CCGAAGGACCACATAGGATTTTC
1 CCGAATGACCACATA-GTTTTTC
84148 CCGAATGACCACATAG
1 CCGAATGACCACATAG
84164 AACCCTCAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.04
21 10 0.20
22 5 0.10
23 30 0.59
24 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (22 bp):
CCGAATGACCACATAGTTTTTC
Found at i:84718 original size:19 final size:20
Alignment explanation
Indices: 84694--84744 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
84684 TCCAACGCAG
84694 TAGTATCG-TACCTCTCCTA
1 TAGTATCGATACCTCTCCTA
*
84713 TAGTATCGATA-CTCTCCTC
1 TAGTATCGATACCTCTCCTA
*
84732 TGGTATCGATACC
1 TAGTATCGATACC
84745 CCCATTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 25 0.89
20 3 0.11
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.35
Consensus pattern (20 bp):
TAGTATCGATACCTCTCCTA
Found at i:86971 original size:3 final size:3
Alignment explanation
Indices: 86963--86992 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
86953 GCAAGTCTGC
86963 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
86993 CAATGAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:87177 original size:3 final size:3
Alignment explanation
Indices: 87169--87205 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
87159 CAATAAATGC
87169 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
87206 ACCCTTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:87501 original size:24 final size:25
Alignment explanation
Indices: 87451--87501 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
87441 TAAAGAACCA
87451 AAATGATTATTTTAACCCATAATTTTT
1 AAATGATTATTTTAA--CATAATTTTT
87478 AAATGATTATTTTAA-ATAATTTTT
1 AAATGATTATTTTAACATAATTTTT
87502 TAACCCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
27 15 0.62
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (25 bp):
AAATGATTATTTTAACATAATTTTT
Found at i:91356 original size:2 final size:2
Alignment explanation
Indices: 91349--91404 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
91339 TTGAAGTTTG
91349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
91391 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
91405 TAGTATAGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93055 original size:20 final size:20
Alignment explanation
Indices: 93032--93075 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
93022 GTCACAACCC
*
93032 GACCCGACCCGTTGACCGTT
1 GACCCGACACGTTGACCGTT
93052 GACCCGACACGTTGACCGTT
1 GACCCGACACGTTGACCGTT
93072 GACC
1 GACC
93076 GGCGTTGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.39, G:0.25, T:0.18
Consensus pattern (20 bp):
GACCCGACACGTTGACCGTT
Found at i:94398 original size:18 final size:18
Alignment explanation
Indices: 94372--94407 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
94362 TCGAAAGGAC
*
94372 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
94390 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
94408 CGGATGAAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Done.