Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006165.1 Hibiscus syriacus cultivar Beakdansim tig00014644_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: 39949
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:950 original size:44 final size:45
Alignment explanation
Indices: 856--971 Score: 198
Period size: 44 Copynumber: 2.6 Consensus size: 45
846 AGGTCTTATG
* *
856 GATGACCCGGAGGTTTTGAAAACATCATGCACTGAAGGTCTTACA
1 GATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACA
901 GATGACCCGAAGGTTTTGAAAACATCATGC-CTGAAGGGCTTACA
1 GATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACA
*
945 GATGACCCGAAGGCTTTGAAAACATCA
1 GATGACCCGAAGGTTTTGAAAACATCA
972 AAAAGCTCCC
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
44 39 0.57
45 29 0.43
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (45 bp):
GATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACA
Found at i:1026 original size:121 final size:121
Alignment explanation
Indices: 869--1093 Score: 389
Period size: 121 Copynumber: 1.9 Consensus size: 121
859 GACCCGGAGG
*
869 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGC-CT
1 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACT
*
933 GAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
66 GAAAGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
* *
989 TTTTGAAAAACATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCAC
1 TTTTG-AAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCAC
*
1054 TGAAAGGCTTATAGATGACCCGAAGGCTTTGAAAACATCA
65 TGAAAGGCTTACAGATGACCCGAAGGCTTTGAAAACATCA
1094 TGCTCTGAAG
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
120 5 0.05
121 54 0.55
122 39 0.40
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (121 bp):
TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACT
GAAAGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
Found at i:1029 original size:77 final size:73
Alignment explanation
Indices: 906--1048 Score: 223
Period size: 77 Copynumber: 1.9 Consensus size: 73
896 TTACAGATGA
906 CCCGAAGGTTTTGAAAACATCATGCCTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC
1 CCCGAAGGTTTTGAAAACATCATGCCTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC
971 AAAAAGCT
66 AAAAAGCT
* * *
979 CCCGAAGGCTTTTTGAAAAACATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
1 CCCGAAGG--TTTTG-AAAACATCATGC-CTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
1044 CATCA
62 CATCA
1049 TGCACTGAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
73 8 0.13
75 5 0.08
76 11 0.17
77 39 0.62
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (73 bp):
CCCGAAGGTTTTGAAAACATCATGCCTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC
AAAAAGCT
Found at i:1053 original size:45 final size:44
Alignment explanation
Indices: 979--1137 Score: 203
Period size: 45 Copynumber: 3.5 Consensus size: 44
969 TCAAAAAGCT
* *
979 CCCGAAGGCTTTTTGAAAAACATCTTGCACTGTAGGTCTTACAGATGA
1 CCCGAAGGC--TTTG-AAAACATCATGCACTGAAGG-CTTACAGATGA
*
1027 CCCGAAGGCTTTGAAAACATCATGCACTGAAAGGCTTATAGATGA
1 CCCGAAGGCTTTGAAAACATCATGCACTG-AAGGCTTACAGATGA
*
1072 CCCGAAGGCTTTGAAAACATCATGCTCTGAAGGGCTTACAGA-GA
1 CCCGAAGGCTTTGAAAACATCATGCACTGAA-GGCTTACAGATGA
* *
1116 CCCGAAGGTTTTGAAAATATCA
1 CCCGAAGGCTTTGAAAACATCA
1138 AAAAGCTCCC
Statistics
Matches: 102, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
44 24 0.24
45 62 0.61
46 7 0.07
48 9 0.09
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (44 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGCTTACAGATGA
Found at i:1197 original size:120 final size:121
Alignment explanation
Indices: 1027--1307 Score: 462
Period size: 121 Copynumber: 2.3 Consensus size: 121
1017 TTACAGATGA
* * *
1027 CCCGAAGGC--TTTGAAAACATCATGCACTGAAAGG-CTTATAGATGACCCGAAGGCTTTGAAAA
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTG-TAGGTCTTATGGATGACCCGAAGGCTTTGAAAA
* *
1089 CATCATGCTCTGAAGGGCTTACAGA-GACCCGAAGGTTTTGAAAATATCAAAAAGCT
65 CATCATGCACTGAAGGGCTTACAGATGACCCGAAAGTTTTGAAAATATCAAAAAGCT
* *
1145 CCCGAAGGCTTTTTGAAAACATCCTGTACTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAAC
1210 ATCATGCACTGAAGGGCTTACAGATGACCCGAAAGTTTTGAAAATATCAAAAAGCT
66 ATCATGCACTGAAGGGCTTACAGATGACCCGAAAGTTTTGAAAATATCAAAAAGCT
1266 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATG
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATG
1308 ACCCAGAGGC
Statistics
Matches: 151, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
118 9 0.06
119 3 0.02
120 68 0.45
121 71 0.47
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (121 bp):
CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAAC
ATCATGCACTGAAGGGCTTACAGATGACCCGAAAGTTTTGAAAATATCAAAAAGCT
Found at i:1205 original size:76 final size:73
Alignment explanation
Indices: 1072--1213 Score: 187
Period size: 75 Copynumber: 1.9 Consensus size: 73
1062 TTATAGATGA
*
1072 CCCGAAGGCTTTGAAAACATCATGCTCTGAAGGGCTTACAGAGACCCGAAGGTTTTGAAAATATC
1 CCCGAAGGCTTTGAAAACATCATGCTCTGAAGGGCTTACAGAGACCCGAAGGCTTTGAAAATATC
1137 AAAAAGCT
66 AAAAAGCT
* * * **
1145 CCCGAAGGCTTTTTGAAAACATCCTG-TACTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAA
1 CCCGAAGGC--TTTGAAAACATCATGCT-CTGAAGGGCTTACAGA-GACCCGAAGGCTTTGAAAA
1209 TATCA
62 TATCA
1214 TGCACTGAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
73 9 0.15
74 1 0.02
75 26 0.44
76 23 0.39
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (73 bp):
CCCGAAGGCTTTGAAAACATCATGCTCTGAAGGGCTTACAGAGACCCGAAGGCTTTGAAAATATC
AAAAAGCT
Found at i:1236 original size:45 final size:45
Alignment explanation
Indices: 1145--1258 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 45
1135 TCAAAAAGCT
* * * * * **
1145 CCCGAAGGCTTTTTGAAAACATCCTGTACTGTAGGTCTTATGGATGA
1 CCCGAAGGC--TTTGAAAATATCATGCACTGAAGGGCTTACAGATGA
1192 CCCGAAGGCTTTGAAAATATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGCTTTGAAAATATCATGCACTGAAGGGCTTACAGATGA
* *
1237 CCCGAAAGTTTTGAAAATATCA
1 CCCGAAGGCTTTGAAAATATCA
1259 AAAAGCTCCC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 49 0.84
47 9 0.16
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (45 bp):
CCCGAAGGCTTTGAAAATATCATGCACTGAAGGGCTTACAGATGA
Found at i:1252 original size:165 final size:166
Alignment explanation
Indices: 833--1258 Score: 676
Period size: 166 Copynumber: 2.6 Consensus size: 166
823 TGAGGTCTAT
* * * * *
833 CATCTTGCAATGTAGGTCTTATGGATGACCCGGAGGTTTTGAAAACATCATGCACTGAAGGTCTT
1 CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTT
898 ACAGATGACCCGAAGGTTTTGAAAACATCATGCCTGAAGGGCTTACAGATGACCCGAAGGCTTTG
66 ACAGATGACCCGAAGGTTTTGAAAACATCATGCCTGAAGGGCTTACAGATGACCCGAAGGCTTTG
963 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAAA
131 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAAA
* ** *
999 CATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAAGGCTT
1 CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTT
* * *
1064 ATAGATGACCCGAAGGCTTTGAAAACATCATGCTCTGAAGGGCTTACAGA-GACCCGAAGGTTTT
66 ACAGATGACCCGAAGGTTTTGAAAACATCATGC-CTGAAGGGCTTACAGATGACCCGAAGGCTTT
*
1128 GAAAATATCAAAAAGCTCCCGAAGGCTTTTTG-AAAA
130 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAAA
* *
1164 CATCCTGTACTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAATATCATGCACTGAAGGGCTT
1 CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTT
* *
1229 ACAGATGACCCGAAAGTTTTGAAAATATCA
66 ACAGATGACCCGAAGGTTTTGAAAACATCA
1259 AAAAGCTCCC
Statistics
Matches: 238, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
165 89 0.37
166 133 0.56
167 16 0.07
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (166 bp):
CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTT
ACAGATGACCCGAAGGTTTTGAAAACATCATGCCTGAAGGGCTTACAGATGACCCGAAGGCTTTG
AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAAA
Found at i:2087 original size:22 final size:22
Alignment explanation
Indices: 2026--2088 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
2016 AAATCCAATA
* * *
2026 AATCTTTCATCTTTGAAAAGAT
1 AATCTATCATCTTTGAAGAGAG
*
2048 AATATATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
2070 AATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
2089 ATGTAGATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:2579 original size:54 final size:54
Alignment explanation
Indices: 2450--2601 Score: 182
Period size: 54 Copynumber: 2.9 Consensus size: 54
2440 AATAACTGGT
* * * * * * *
2450 TCGT-AAACATTTGACAACACATTCATCATCTCAT-AGGTTTTTGCTCAGATGC
1 TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGATGC
* *
2502 TCGTAAAACATTTGACAACACATTCATTCTTTCCTGTGGCTTCTGCCCAGATGT
1 TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGATGC
* * *
2556 TTGTAAAGCATTTGACAATACATTCATCCTTTCCTGTGGCTTCTGC
1 TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
2602 TTAGATTTCT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 4 0.05
53 26 0.31
54 55 0.65
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (54 bp):
TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGATGC
Found at i:7935 original size:20 final size:20
Alignment explanation
Indices: 7859--7922 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
7849 TGCAAATATA
* *
7859 AAATGAAA-ATGAAAAA-GT
1 AAATGAAACATAAAAAATGC
*
7877 AAATGAAAATATAAAAAATGC
1 AAATG-AAACATAAAAAATGC
7898 AAATGAAACATAAAAAATGC
1 AAATGAAACATAAAAAATGC
7918 AAATG
1 AAATG
7923 TAATGAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.12
19 3 0.08
20 26 0.65
21 6 0.15
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.17
Consensus pattern (20 bp):
AAATGAAACATAAAAAATGC
Found at i:10287 original size:17 final size:18
Alignment explanation
Indices: 10249--10297 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
10239 AAAAATAAAA
10249 ATATAAACATTAATATAAGG
1 ATATAAA-A-TAATATAAGG
10269 ATATAAAATAATA-AAGG
1 ATATAAAATAATATAAGG
*
10286 ATAAAAAATAAT
1 ATATAAAATAAT
10298 TGAATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 15 0.54
18 5 0.18
19 1 0.04
20 7 0.25
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (18 bp):
ATATAAAATAATATAAGG
Found at i:10316 original size:14 final size:15
Alignment explanation
Indices: 10271--10316 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
10261 ATATAAGGAT
*
10271 ATAAAATAATAAAGG
1 ATAAAATAATAAAGA
*
10286 ATAAAA-AATAATTGA
1 ATAAAATAATAA-AGA
10301 ATAAAATAA-AAAGA
1 ATAAAATAATAAAGA
10315 AT
1 AT
10317 CATAAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.35
15 15 0.58
16 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.22
Consensus pattern (15 bp):
ATAAAATAATAAAGA
Found at i:10836 original size:17 final size:18
Alignment explanation
Indices: 10806--10841 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
10796 AATTCCAAGA
10806 AAATATATTATTTTTTAT
1 AAATATATTATTTTTTAT
10824 AAATATA-TATTTTTTAT
1 AAATATATTATTTTTTAT
10841 A
1 A
10842 TTTTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AAATATATTATTTTTTAT
Found at i:12583 original size:22 final size:22
Alignment explanation
Indices: 12526--12584 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
12516 ACGCGATTCT
*
12526 GACTATCGCATTGCAATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
12548 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
12569 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
12585 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:12598 original size:20 final size:20
Alignment explanation
Indices: 12573--12642 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
12563 TTTTCCGACT
12573 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
12593 ATCGCAACGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
12613 ATCGCAATGCGATTAT-TACT
1 ATCGCAATGCGAATATGTA-A
12633 ATCGCAATGC
1 ATCGCAATGC
12643 TATTCTAACT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 2 0.04
20 43 0.96
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:12653 original size:20 final size:20
Alignment explanation
Indices: 12613--12686 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
12603 GAATATGTAA
* *
12613 ATCGCAATGCGATTATTACT
1 ATCGCAATGCGATTCTAACT
*
12633 ATCGCAATGCTATTCTAACT
1 ATCGCAATGCGATTCTAACT
* *
12653 ATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATTCTAACT
* *
12673 GTCGCAATACGATT
1 ATCGCAATGCGATT
12687 TTCAAAGCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (20 bp):
ATCGCAATGCGATTCTAACT
Found at i:12876 original size:22 final size:22
Alignment explanation
Indices: 12862--12903 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
12852 ACGACATCCG
12862 TCCCCATCTCCGACGAAATCAA
1 TCCCCATCTCCGACGAAATCAA
12884 TCCCCATCTCCGACGAAATC
1 TCCCCATCTCCGACGAAATC
12904 TGTCTATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.43, G:0.10, T:0.19
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAA
Found at i:13341 original size:20 final size:20
Alignment explanation
Indices: 13316--13387 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
13306 GTTGCGATTC
*
13316 TCGCGTTGCAATAGTCAAAT
1 TCGCGTTGCGATAGTCAAAT
13336 TCGCGTTGCGATAGTCAAAT
1 TCGCGTTGCGATAGTCAAAT
**
13356 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCAAAT
*
13376 TCGTGTTGCGAT
1 TCGCGTTGCGAT
13388 TTTGATTTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
TCGCGTTGCGATAGTCAAAT
Found at i:13395 original size:20 final size:20
Alignment explanation
Indices: 13372--13410 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
13362 TGCGATAGTC
13372 ATTTTCGTGTTGCGATTTTG
1 ATTTTCGTGTTGCGATTTTG
13392 ATTTTCGTGTTGCGATTTT
1 ATTTTCGTGTTGCGATTTT
13411 AAGTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.56
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTG
Found at i:13417 original size:20 final size:20
Alignment explanation
Indices: 13374--13417 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
13364 CGATAGTCAT
* *
13374 TTTCGTGTTGCGATTTTGAT
1 TTTCGTGTTGCGATTTTAAG
13394 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
13414 TTTC
1 TTTC
13418 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:15165 original size:18 final size:18
Alignment explanation
Indices: 15142--15191 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
15132 TTTACTCGTA
15142 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
15160 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
15178 ATTTCACTTAGATT
1 ATTTCACTTAGATT
15192 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:15374 original size:20 final size:20
Alignment explanation
Indices: 15345--15407 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
15335 TACTTTCACC
*
15345 ACGCGGAAATGACTATCGCA
1 ACGCGAAAATGACTATCGCA
*
15365 ACGCGAAAATGACCATCGCA
1 ACGCGAAAATGACTATCGCA
**
15385 ACGCGAATTTGACTATCGCA
1 ACGCGAAAATGACTATCGCA
15405 ACG
1 ACG
15408 AAAGAATCGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (20 bp):
ACGCGAAAATGACTATCGCA
Found at i:15475 original size:20 final size:20
Alignment explanation
Indices: 15450--15545 Score: 138
Period size: 20 Copynumber: 4.8 Consensus size: 20
15440 GCGATTCTCT
**
15450 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
15470 CGTTGCGATGGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
15490 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
15510 CATTTCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
15530 CATTGCGATAGTCATT
1 CGTTGCGATAGTCATT
15546 CGTGTTGCGA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:16137 original size:21 final size:21
Alignment explanation
Indices: 16046--16150 Score: 104
Period size: 21 Copynumber: 5.0 Consensus size: 21
16036 GACTCACATG
*
16046 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
16068 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
16088 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
16109 TCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
16130 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
16151 CCAACATTCT
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 3 0.05
21 61 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:17615 original size:36 final size:30
Alignment explanation
Indices: 17535--17600 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
17525 ATAAGAGTTG
*
17535 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGCAAATAATTCTT
17565 ATTTGTTTAATTGATGTGCAAATAATTCTT
1 ATTTGTTTAATTGATGTGCAAATAATTCTT
17595 ATTTGT
1 ATTTGT
17601 GCTTGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGCAAATAATTCTT
Found at i:17741 original size:54 final size:54
Alignment explanation
Indices: 17574--17724 Score: 293
Period size: 54 Copynumber: 2.8 Consensus size: 54
17564 TATTTGTTTA
*
17574 ATTGATGTGCAAATAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTTGATT
1 ATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTTGATT
17628 ATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTTGATT
1 ATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTTGATT
17682 ATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATT
1 ATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATT
17725 GAAATGTAAA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.50
Consensus pattern (54 bp):
ATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTTGATT
Found at i:17828 original size:20 final size:20
Alignment explanation
Indices: 17803--18061 Score: 162
Period size: 20 Copynumber: 13.8 Consensus size: 20
17793 GCGATTTTCT
*
17803 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
17823 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
17843 TGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
17862 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
17876 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** *
17896 CGATTATG-TAGGTTAAATTCG
1 CG-TTGCGATA-GTCAAATTCG
* * **
17917 CGTTGTGATAGTTATTTTCG
1 CGTTGCGATAGTCAAATTCG
**
17937 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
17957 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
*
17971 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** *
17991 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCG
* *
18011 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
18025 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
18045 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
18062 GAATGTGTAA
Statistics
Matches: 187, Mismatches: 31, Indels: 42
0.72 0.12 0.16
Matches are distributed among these distances:
14 31 0.17
16 3 0.02
17 1 0.01
18 2 0.01
19 16 0.09
20 118 0.63
21 16 0.09
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:17886 original size:33 final size:33
Alignment explanation
Indices: 17770--17890 Score: 116
Period size: 33 Copynumber: 3.5 Consensus size: 33
17760 ATCATATTCG
* * *
17770 CGTTGCGATAGTCAATACACTTTGCGATTTTCT
1 CGTTGCGATAGTCAATTCACGTTGCGATTATCT
* *
17803 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATT
1 CGTTGCGATAGTC-AATTCACGTTGCGATTATC----T
* *
17841 CGTGTTGCGATAGTCATTTCGCGTTGCGATTATCT
1 C--GTTGCGATAGTCAATTCACGTTGCGATTATCT
17876 CGTTGCGATAGTCAA
1 CGTTGCGATAGTCAA
17891 ATTCGCGATT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
33 26 0.36
34 14 0.19
35 2 0.03
38 2 0.03
39 16 0.22
40 12 0.17
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (33 bp):
CGTTGCGATAGTCAATTCACGTTGCGATTATCT
Found at i:18005 original size:54 final size:54
Alignment explanation
Indices: 17933--18058 Score: 234
Period size: 54 Copynumber: 2.3 Consensus size: 54
17923 GATAGTTATT
17933 TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCATTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCATTGCGATAGTCAAA
* *
17987 TTCGCGTTGCGATAGTCATTTTTGCATTGCGATTATCCCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCATTGCGATAGTCAAA
18041 TTCGCGTTGCGATAGTCA
1 TTCGCGTTGCGATAGTCA
18059 AATGAATGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (54 bp):
TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCATTGCGATAGTCAAA
Found at i:18051 original size:74 final size:73
Alignment explanation
Indices: 17765--18061 Score: 278
Period size: 74 Copynumber: 4.0 Consensus size: 73
17755 TCTGCATCAT
* * * * * *
17765 ATTCGCGTTGCGATAGTCAATACACTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGCG
1 ATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCCCGTTGCGATAGTCAAATTCCCGTTGCG
*
17830 ATAATCAA
66 ATAGTCAA
* * * **
17838 ATTCGTGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCGATTAT
1 ATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCCCGTTGCGATAGTCAAATTCCCG-TTGC
*
17903 G-TAGGTTAA
65 GATA-GTCAA
* * ** * * * * *
17912 ATTCGCGTTGTGATAGTTATTTTCGCGTTGCGA-TAGT-CATTTTCGCATTG-CGATTATCCCAT
1 ATTCGCGTTGCGATAGTCA-TTTCGCGTTGCGATTA-TCCCGTTGCG-ATAGTCAAAT-TCCCGT
17974 TGCGATAGTCAA
62 TGCGATAGTCAA
* * *
17986 ATTCGCGTTGCGATAGTCATTTTTGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGC
1 ATTCGCGTTGCGATAGTCA-TTTCGCGTTGCGATTATCCCGTTGCGATAGTCAAATTCCCGTTGC
18051 GATAGTCAA
65 GATAGTCAA
18060 AT
1 AT
18062 GAATGTGTAA
Statistics
Matches: 176, Mismatches: 38, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
73 55 0.31
74 89 0.51
75 32 0.18
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (73 bp):
ATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCCCGTTGCGATAGTCAAATTCCCGTTGCG
ATAGTCAA
Found at i:20571 original size:24 final size:24
Alignment explanation
Indices: 20539--20585 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
20529 TCATCAAAAA
20539 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
20563 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
20586 TTTCGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:21429 original size:20 final size:20
Alignment explanation
Indices: 21420--21536 Score: 121
Period size: 20 Copynumber: 5.8 Consensus size: 20
21410 TGACAGTCAG
21420 AATCGCATTGCGATAGTAAT
1 AATCGCATTGCGATAGTAAT
21440 AATCGCATTGCGATAGTAAT
1 AATCGCATTGCGATAGTAAT
*
21460 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGTA-AT
* * * **
21480 ATTCACGTTGCGATAGCCAT
1 AATCGCATTGCGATAGTAAT
* *
21500 ACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGTA-AT
*
21520 ATTCGCATTGCGATAGT
1 AATCGCATTGCGATAGT
21537 CGAAAAATCG
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.03
20 75 0.96
21 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (20 bp):
AATCGCATTGCGATAGTAAT
Found at i:21491 original size:40 final size:40
Alignment explanation
Indices: 21420--21536 Score: 155
Period size: 40 Copynumber: 2.9 Consensus size: 40
21410 TGACAGTCAG
* *
21420 AATCGCATTGCGATAGTA-ATAATCGCATTGCGATAGTAAT
1 AATCGCATTGCGAT-TTACATATTCGCATTGCGATAGTAAT
* * **
21460 AATCGCATTGCGATTTACATATTCACGTTGCGATAGCCAT
1 AATCGCATTGCGATTTACATATTCGCATTGCGATAGTAAT
*
21500 ACTCGCATTGCGATTTACATATTCGCATTGCGATAGT
1 AATCGCATTGCGATTTACATATTCGCATTGCGATAGT
21537 CGAAAAATCG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
39 2 0.03
40 64 0.97
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (40 bp):
AATCGCATTGCGATTTACATATTCGCATTGCGATAGTAAT
Found at i:21554 original size:22 final size:22
Alignment explanation
Indices: 21529--21580 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
21519 TATTCGCATT
21529 GCGATAGTCGAAAAATCGCAAC
1 GCGATAGTCGAAAAATCGCAAC
* * * *
21551 GCGA-ATTTGGAAAATCGCAAT
1 GCGATAGTCGAAAAATCGCAAC
21572 GCGATAGTC
1 GCGATAGTC
21581 AGAATCGCGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (22 bp):
GCGATAGTCGAAAAATCGCAAC
Found at i:21753 original size:3 final size:3
Alignment explanation
Indices: 21745--21799 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
21735 TTTTCTTTAT
* * **
21745 TAA TAA TAA TAA TATA TAA TAT TAT TAA TAA TAA TAA TTT TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21791 TAA TAA TAA
1 TAA TAA TAA
21800 AAAATAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:23006 original size:21 final size:21
Alignment explanation
Indices: 22977--23132 Score: 129
Period size: 21 Copynumber: 7.6 Consensus size: 21
22967 ATTTTCCATT
22977 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
22998 TCACGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
23018 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
23039 TCGCGTTGTGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
23059 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
23080 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
23100 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
23121 TCGCGTTGCGAT
1 TCGCGTTGCGAT
23133 TTTCCATTTC
Statistics
Matches: 96, Mismatches: 36, Indels: 6
0.70 0.26 0.04
Matches are distributed among these distances:
20 42 0.44
21 54 0.56
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:23017 original size:41 final size:41
Alignment explanation
Indices: 22957--23155 Score: 371
Period size: 41 Copynumber: 4.9 Consensus size: 41
22947 TATCGCAAAT
22957 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
22998 TCACGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
23039 TCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
23080 TCGCGTTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
23121 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
23156 CTACAATGTC
Statistics
Matches: 152, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 152 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:23211 original size:22 final size:22
Alignment explanation
Indices: 23144--23257 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 22
23134 TTCCATTTCG
23144 CGTTGCGATAGTCTACAA-TGT
1 CGTTGCGATAGTCTACAATTGT
* * *
23165 CG-TGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAATTGT
*
23183 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATTGT
* *
23205 TGTTGCGAAAGTCTACAATTGT
1 CGTTGCGATAGTCTACAATTGT
**
23227 CGTTGCGATTTTCTA-AA-T-T
1 CGTTGCGATAGTCTACAATTGT
23246 CGTTGCGATAGT
1 CGTTGCGATAGT
23258 TAAAAAAAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
18 8 0.11
19 18 0.25
20 7 0.10
21 9 0.12
22 31 0.42
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAATTGT
Found at i:24026 original size:20 final size:20
Alignment explanation
Indices: 24001--24052 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
23991 ATTTTCAACT
*
24001 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
24021 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
24041 ATCGCAACGCGA
1 ATCGCAACGCGA
24053 TTTTCGCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:24814 original size:20 final size:20
Alignment explanation
Indices: 24789--24832 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
24779 TTGTAAATCG
* *
24789 CAACACAGAAGTTAAATTCA
1 CAACACAAAAGTCAAATTCA
24809 CAACACAAAAGTCAAATTCA
1 CAACACAAAAGTCAAATTCA
24829 CAAC
1 CAAC
24833 GCGTTAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.25, G:0.07, T:0.16
Consensus pattern (20 bp):
CAACACAAAAGTCAAATTCA
Found at i:24891 original size:20 final size:20
Alignment explanation
Indices: 24850--24928 Score: 113
Period size: 20 Copynumber: 3.9 Consensus size: 20
24840 TCAAATTCGC
*
24850 AACGTGAATAGTAAAAACCGT
1 AACGTGAATAGT-AAAATCGT
*
24871 AACATGAATAGTAAAATCGT
1 AACGTGAATAGTAAAATCGT
*
24891 AACGTGAATAGTAAAATCGC
1 AACGTGAATAGTAAAATCGT
*
24911 AACGTAAATAGTAAAATC
1 AACGTGAATAGTAAAATC
24929 ACAATGAATC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 42 0.79
21 11 0.21
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (20 bp):
AACGTGAATAGTAAAATCGT
Found at i:25132 original size:39 final size:39
Alignment explanation
Indices: 25078--25158 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
25068 GTCAATCTTT
25078 ATTACAAATTATTCTAAATTCAATTAGTTAAAGTTTGAA
1 ATTACAAATTATTCTAAATTCAATTAGTTAAAGTTTGAA
25117 ATTACAAATTATTCTAAATTCAATTAGTTAAAGTTTGAA
1 ATTACAAATTATTCTAAATTCAATTAGTTAAAGTTTGAA
25156 ATT
1 ATT
25159 TGAAAAAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (39 bp):
ATTACAAATTATTCTAAATTCAATTAGTTAAAGTTTGAA
Found at i:25366 original size:20 final size:20
Alignment explanation
Indices: 25343--25433 Score: 128
Period size: 20 Copynumber: 4.5 Consensus size: 20
25333 TAAATTCGCG
25343 TTGCGATTTTACTATTCACA
1 TTGCGATTTTACTATTCACA
*
25363 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACA
* *
25383 TTGCAATTTTACTATTCACG
1 TTGCGATTTTACTATTCACA
25403 TTGCGATTTTTACTATTCACA
1 TTGCGA-TTTTACTATTCACA
* *
25424 CTACGATTTT
1 TTGCGATTTT
25434 GGAAACTGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 47 0.73
21 17 0.27
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTACTATTCACA
Found at i:25415 original size:21 final size:20
Alignment explanation
Indices: 25322--25422 Score: 141
Period size: 20 Copynumber: 5.0 Consensus size: 20
25312 CAACGCGATT
*
25322 TTGCGATTTT-CTAAATTCGCG
1 TTGCGATTTTACT--ATTCACG
*
25343 TTGCGATTTTACTATTCACA
1 TTGCGATTTTACTATTCACG
25363 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
*
25383 TTGCAATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
25403 TTGCGATTTTTACTATTCAC
1 TTGCGA-TTTTACTATTCAC
25423 ACTACGATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
20 48 0.66
21 23 0.32
22 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTACTATTCACG
Found at i:29962 original size:18 final size:18
Alignment explanation
Indices: 29939--29974 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29929 CAGAGAAGAA
29939 GCATAAAGTTACAAATTT
1 GCATAAAGTTACAAATTT
29957 GCATAAAGTTACAAATTT
1 GCATAAAGTTACAAATTT
29975 TAATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
GCATAAAGTTACAAATTT
Found at i:36556 original size:20 final size:20
Alignment explanation
Indices: 36528--36568 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
36518 TTGCTAACAG
36528 GGAACCGATACCCTACTACA
1 GGAACCGATACCCTACTACA
* *
36548 GGAATCGATACCCTGCTACA
1 GGAACCGATACCCTACTACA
36568 G
1 G
36569 TACTGCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.17
Consensus pattern (20 bp):
GGAACCGATACCCTACTACA
Found at i:37513 original size:32 final size:31
Alignment explanation
Indices: 37429--37515 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 31
37419 ATTCCTTAGA
37429 ACATAGGT-ATGTTGTCCATATGTCTCAAAAG
1 ACATAGGTAAT-TTGTCCATATGTCTCAAAAG
*
37460 ACATAGGTAATTCTCTCCATATGTC-CATAAAG
1 ACATAGGTAATT-TGTCCATATGTCTCA-AAAG
*
37492 ACATAGGTAATTATGTTCATATGT
1 ACATAGGTAATT-TGTCCATATGT
37516 TCTGTAGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 11 0.22
32 38 0.78
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (31 bp):
ACATAGGTAATTTGTCCATATGTCTCAAAAG
Found at i:38330 original size:21 final size:21
Alignment explanation
Indices: 38288--38330 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
38278 TTCCTGGTCT
* *
38288 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
38309 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
38330 A
1 A
38331 ACGACTATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:39028 original size:102 final size:101
Alignment explanation
Indices: 38851--39059 Score: 325
Period size: 102 Copynumber: 2.1 Consensus size: 101
38841 GGTAGAGGTC
*
38851 TATGTGGTCCCTTCGGGACATATATATATTCTTTGGAACATGTTGAGGTCTGGTGAGAACACATA
1 TATGTGGTCCCTTCGGGACATATATATATTCTTTGGAACATGTTGAAGTCTGGTGAGAACACATA
*
38916 CTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 CTGATCCTTGGCATATGTATAT-ATTCTT-AGGAATGA
* *
38954 TATGTGGT-CTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAG-AC-CAT
1 TATGTGGTCCCTTCGGGACATATATATATTCTTTGGAACATGT-TGAAGTCTGGTGAGAACACAT
39016 ACTTGATCCTTGGCATATGTATATATTCTTAGGAATGA
65 AC-TGATCCTTGGCATATGTATATATTCTTAGGAATGA
39054 TATGTG
1 TATGTG
39060 ATCCTTATGG
Statistics
Matches: 100, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
100 14 0.14
101 11 0.11
102 54 0.54
103 21 0.21
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (101 bp):
TATGTGGTCCCTTCGGGACATATATATATTCTTTGGAACATGTTGAAGTCTGGTGAGAACACATA
CTGATCCTTGGCATATGTATATATTCTTAGGAATGA
Done.