Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005323.1 Hibiscus syriacus cultivar Beakdansim tig00012047_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: 48897
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:2880 original size:18 final size:17
Alignment explanation
Indices: 2843--2885 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2833 TGTTATGAAT
**
2843 TTAATATTTAATTTTTTA
1 TTAAT-TTTAATTTGATA
2861 TTATATTTTAATTTGATA
1 TTA-ATTTTAATTTGATA
2879 TTAATTT
1 TTAATTT
2886 AAAATTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTAATTTTAATTTGATA
Found at i:5586 original size:21 final size:22
Alignment explanation
Indices: 5550--5591 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5540 CTGGAAGATG
5550 CCAGCTCAGCACAGTT-GTTAT
1 CCAGCTCAGCACAGTTAGTTAT
**
5571 CCAGCTCAGCGTAGTTAGTTA
1 CCAGCTCAGCACAGTTAGTTA
5592 GGAGACTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (22 bp):
CCAGCTCAGCACAGTTAGTTAT
Found at i:10079 original size:19 final size:19
Alignment explanation
Indices: 10055--10091 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10045 ATGACCAACA
*
10055 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
10074 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
10092 CATTTATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:10189 original size:21 final size:20
Alignment explanation
Indices: 10121--10190 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
10111 TCCAGATTCA
*
10121 CAATGCGA-TTTTGACCATCG
1 CAATGCGATTTTTGA-AATCG
* *
10141 CATTGCGATTTTCGAAATCCG
1 CAATGCGATTTTTGAAAT-CG
**
10162 CGTTGCGATTTTTGATAATCG
1 CAATGCGATTTTTGA-AATCG
10183 CAATGCGA
1 CAATGCGA
10191 ATATGTAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
20 9 0.22
21 28 0.70
22 3 0.08
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
CAATGCGATTTTTGAAATCG
Found at i:10207 original size:20 final size:20
Alignment explanation
Indices: 10178--10222 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
10168 GATTTTTGAT
*
10178 AATCGCAATGCGAATATGTA
1 AATCGAAATGCGAATATGTA
*
10198 AATCGAAATGTGAATATGTA
1 AATCGAAATGCGAATATGTA
10218 AATCG
1 AATCG
10223 CAACGCGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
AATCGAAATGCGAATATGTA
Found at i:10270 original size:20 final size:20
Alignment explanation
Indices: 10244--10341 Score: 126
Period size: 20 Copynumber: 4.8 Consensus size: 20
10234 CACGTGATCA
*
10244 CAACGCGAATCTGACTATCG
1 CAACGCGATTCTGACTATCG
* *
10264 TAACGCGATTCAGACTATCG
1 CAACGCGATTCTGACTATCG
10284 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
**
10304 CAACGCGATAAT-ACGTGATCG
1 CAACGCGATTCTGAC-T-ATCG
10325 CAACGCGATTCTGACTA
1 CAACGCGATTCTGACTA
10342 ACACATCACT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 47 0.71
21 15 0.23
22 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (20 bp):
CAACGCGATTCTGACTATCG
Found at i:10337 original size:41 final size:41
Alignment explanation
Indices: 10219--10341 Score: 169
Period size: 41 Copynumber: 3.0 Consensus size: 41
10209 GAATATGTAA
* *
10219 ATCGCAACGCGATAACACGTGATCACAACGCGAATCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACT
* * *
10260 ATCGTAACGCGATTCAGAC-T-ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGA-TAACACGTGATCGCAACGCGATTCTGACT
*
10300 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACT
10341 A
1 A
10342 ACACATCACT
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
39 4 0.06
40 30 0.42
41 33 0.46
42 4 0.06
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACT
Found at i:11187 original size:24 final size:24
Alignment explanation
Indices: 11155--11232 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
11145 GTATTCGAAA
11155 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
11179 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
11203 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
11227 TTTGAT
1 TTTGAT
11233 GATGTTTCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:11964 original size:17 final size:17
Alignment explanation
Indices: 11942--11977 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
11932 ATTCTCAAGC
11942 TTGTTTATGCACATCAA
1 TTGTTTATGCACATCAA
11959 TTGTTTATGCACATCAA
1 TTGTTTATGCACATCAA
11976 TT
1 TT
11978 TCACGCAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (17 bp):
TTGTTTATGCACATCAA
Found at i:13294 original size:21 final size:21
Alignment explanation
Indices: 13245--13351 Score: 97
Period size: 21 Copynumber: 5.1 Consensus size: 21
13235 TCTAAAATGT
* *
13245 TGGGAGGGACCTCTTCAACGA
1 TGGGAGGGGCCTCTTGAACGA
** *
13266 TGACAGGGGCCTCTTGAACGG
1 TGGGAGGGGCCTCTTGAACGA
* **
13287 TGGGAGGGGACTCTTGAGGGA
1 TGGGAGGGGCCTCTTGAACGA
**
13308 TGATAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
* * *
13329 TAGGAGAGGCCTCTTGAATGA
1 TGGGAGGGGCCTCTTGAACGA
13350 TG
1 TG
13352 ACAGGTGAGT
Statistics
Matches: 64, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.21
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTGAACGA
Found at i:13310 original size:42 final size:42
Alignment explanation
Indices: 13247--13356 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
13237 TAAAATGTTG
* * * *
13247 GGAG-GGACCTCTTCAACGATGACAGGGGCCTCTTGAACGGTG
1 GGAGAGGA-CTCTTGAAGGATGACAGGGGCCTCTTGAACGATA
* * *
13289 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAAGGATGACAGGGGCCTCTTGAACGATA
* *
13331 GGAGAGGCCTCTTGAATGATGACAGG
1 GGAGAGGACTCTTGAAGGATGACAGG
13357 TGAGTCGGGC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 53 0.95
43 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.20
Consensus pattern (42 bp):
GGAGAGGACTCTTGAAGGATGACAGGGGCCTCTTGAACGATA
Found at i:13858 original size:20 final size:20
Alignment explanation
Indices: 13833--13895 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
13823 AATAGTTTCT
13833 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
13853 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
* * **
13873 GAAAATGATTATCGCAACAC
1 GAAACTTAAAATCGCAACAC
13893 GAA
1 GAA
13896 TTTGACTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.49, C:0.22, G:0.13, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:13905 original size:20 final size:20
Alignment explanation
Indices: 13863--13930 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
13853 GAAACTTAAA
** *
13863 ATCGCAACACGAAAATGATT
1 ATCGCAACACGAATTTGACT
13883 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAATTTGACT
13903 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAATTTGACT
13923 ATCGCAAC
1 ATCGCAAC
13931 GAGATAATCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (20 bp):
ATCGCAACACGAATTTGACT
Found at i:13942 original size:14 final size:14
Alignment explanation
Indices: 13923--13978 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
13913 GAATTTGACT
13923 ATCGCAACGAGATA
1 ATCGCAACGAGATA
*
13937 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGAT-A
13954 CTATCGCAACGAGATA
1 --ATCGCAACGAGATA
13970 ATCGCAACG
1 ATCGCAACG
13979 CGAAACTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.14
Consensus pattern (14 bp):
ATCGCAACGAGATA
Found at i:13958 original size:33 final size:33
Alignment explanation
Indices: 13903--13983 Score: 135
Period size: 33 Copynumber: 2.4 Consensus size: 33
13893 GAATTTGACT
* *
13903 ATCGCAACACGAATTTGACTATCGCAACGAGATA
1 ATCGCAACGCGAA-ATGACTATCGCAACGAGATA
13937 ATCGCAACGCGAAATGACTATCGCAACGAGATA
1 ATCGCAACGCGAAATGACTATCGCAACGAGATA
13970 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
13984 CTAAATTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 33 0.73
34 12 0.27
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.16
Consensus pattern (33 bp):
ATCGCAACGCGAAATGACTATCGCAACGAGATA
Found at i:14141 original size:20 final size:20
Alignment explanation
Indices: 13995--14149 Score: 98
Period size: 20 Copynumber: 8.3 Consensus size: 20
13985 TAAATTTTCA
*
13995 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCG
*
14015 TTGCGAT--T-A---TCCCG
1 TTGCGATAGTCATTTTCGCG
**
14029 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCG
* * *
14049 TTACGATAGTTATTTCCGCG
1 TTGCGATAGTCATTTTCGCG
* *
14069 TTGCGATAGTCGTTTTCGCA
1 TTGCGATAGTCATTTTCGCG
* *
14089 TTGCGAT--T-A--TCCCCG
1 TTGCGATAGTCATTTTCGCG
**
14104 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCG
* *
14124 TTGCGATAATCATTTTCGTG
1 TTGCGATAGTCATTTTCGCG
14144 TTGCGA
1 TTGCGA
14150 CTATTATTCT
Statistics
Matches: 101, Mismatches: 23, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
14 10 0.10
15 10 0.10
16 1 0.01
17 3 0.03
18 3 0.03
20 74 0.73
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:14147 original size:75 final size:74
Alignment explanation
Indices: 13995--14149 Score: 247
Period size: 75 Copynumber: 2.1 Consensus size: 74
13985 TAAATTTTCA
* *
13995 TTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTACGATAGTT
1 TTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTACGATAATC
14060 ATTTCCGCG
66 ATTTCCGCG
* *
14069 TTGCGATAGTCGTTTTCGCATTGCGATTATCCCCGTTGCGATAGTCAAATTCGCGTTGCGATAAT
1 TTGCGATAGTCATTTTCGCATTGCGATTAT-CCCGTTGCGATAGTCAAATTCGCGTTACGATAAT
* *
14134 CATTTTCGTG
65 CATTTCCGCG
14144 TTGCGA
1 TTGCGA
14150 CTATTATTCT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 29 0.39
75 45 0.61
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (74 bp):
TTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTACGATAATC
ATTTCCGCG
Found at i:16200 original size:20 final size:20
Alignment explanation
Indices: 16150--16190 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
16140 TCTGAAACTT
16150 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
16170 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
16190 A
1 A
16191 TTATTGCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:16562 original size:22 final size:22
Alignment explanation
Indices: 16534--16606 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
16524 GATGGAGATA
16534 GACGGATTTTTCTGGAGATGGG
1 GACGGATTTTTCTGGAGATGGG
** * *
16556 GACGGATTTCGCCGGAAATGGG
1 GACGGATTTTTCTGGAGATGGG
16578 GACGGA--TTTCGTAGGAGATGGG
1 GACGGATTTTTC-T-GGAGATGGG
16600 GACGGAT
1 GACGGAT
16607 GTCGCCGTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
20 2 0.05
22 38 0.95
ACGTcount: A:0.22, C:0.12, G:0.42, T:0.23
Consensus pattern (22 bp):
GACGGATTTTTCTGGAGATGGG
Found at i:16801 original size:20 final size:20
Alignment explanation
Indices: 16776--16820 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
16766 TTATCGCAAC
* *
16776 GCGATAGTCAGAATCTCGTT
1 GCGATAGTAAGAATCGCGTT
16796 GCGATAGTAAGAATCGCGTT
1 GCGATAGTAAGAATCGCGTT
16816 GCGAT
1 GCGAT
16821 CACGTGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (20 bp):
GCGATAGTAAGAATCGCGTT
Found at i:16858 original size:20 final size:20
Alignment explanation
Indices: 16830--16882 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
16820 TCACGTGTTA
*
16830 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
16850 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
16870 TCACATTGCGATT
1 TCGCATTGCGATT
16883 ATCTAAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:16980 original size:20 final size:19
Alignment explanation
Indices: 16956--17002 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
16946 TGGAAACTGA
*
16956 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
16976 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
16995 ATTGCGAT
1 ATTGCGAT
17003 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:16992 original size:19 final size:19
Alignment explanation
Indices: 16968--17004 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16958 TGCGATAATG
*
16968 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
16987 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
17005 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:17926 original size:13 final size:13
Alignment explanation
Indices: 17889--17935 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
17879 AAATTTTGAT
17889 TTTTTTTAAAAT-
1 TTTTTTTAAAATC
*
17901 TTTAATATTAAAATC
1 TTT--TTTTAAAATC
17916 TTTTTTTAAAATC
1 TTTTTTTAAAATC
17929 TTTTTTT
1 TTTTTTT
17936 TTTTTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 3 0.10
13 16 0.53
14 8 0.27
15 3 0.10
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTTAAAATC
Found at i:21657 original size:63 final size:63
Alignment explanation
Indices: 21540--21662 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
21530 TAATAATATC
* * * * **
21540 TTTTAATTTGCAATATTCAAAAGATTTAAACTCTTTTTACTATTTAAATTTAAATAGATATTA
1 TTTTAATTTGAAATATTCAAAAGATATAAACTCTTTTAACTATTCAAAGCTAAATAGATATTA
*
21603 TTTTAATTTGAAATATTC-AAAGTATATAATCATCTTTTAAC-ATTCAAAGCTAAATAGATA
1 TTTTAATTTGAAATATTCAAAAG-ATATAAAC-TCTTTTAACTATTCAAAGCTAAATAGATA
21663 ATAAATACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 4 0.08
63 39 0.76
64 8 0.16
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (63 bp):
TTTTAATTTGAAATATTCAAAAGATATAAACTCTTTTAACTATTCAAAGCTAAATAGATATTA
Found at i:24279 original size:29 final size:29
Alignment explanation
Indices: 24199--24280 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 29
24189 GCTAGTGACT
** *
24199 AAAATGTAAGTTTTGAAATTTTAAGGGCTA
1 AAAATGTAA-TTTTGAAAAGTTAAGGGATA
* * *
24229 AAGTAT-AAACTTTGTAAAAGTTAAGGGATA
1 AA-AATGTAATTTTG-AAAAGTTAAGGGATA
24259 AAAATGTAATTTTGAAAAGTTA
1 AAAATGTAATTTTGAAAAGTTA
24281 TAGATTTTAG
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
29 14 0.35
30 24 0.60
31 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTGAAAAGTTAAGGGATA
Found at i:27064 original size:18 final size:18
Alignment explanation
Indices: 27009--27101 Score: 91
Period size: 18 Copynumber: 5.2 Consensus size: 18
26999 ATTCTAAATG
*
27009 TTTACAGTTATCAGA-CA
1 TTTACAGTTATCAGATGA
* *
27026 TTTCACAATTATCATAT-A
1 TTT-ACAGTTATCAGATGA
*
27044 TTTACAGTTATCCGATGA
1 TTTACAGTTATCAGATGA
*
27062 TTTTCAGTTATCAGATGA
1 TTTACAGTTATCAGATGA
** *
27080 TTTTTAGTTATCAGATGT
1 TTTACAGTTATCAGATGA
27098 TTTA
1 TTTA
27102 TAATTATCAA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
17 13 0.21
18 50 0.79
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTACAGTTATCAGATGA
Found at i:27073 original size:35 final size:35
Alignment explanation
Indices: 27009--27100 Score: 87
Period size: 35 Copynumber: 2.6 Consensus size: 35
26999 ATTCTAAATG
** * * *
27009 TTTACAGTTATCAGACATTTCACAATTATCATAT-A
1 TTTACAGTTATCAGATGTTT-TCAGTTATCAGATGA
*
27044 TTTACAGTTATCCGATGATTTTCAGTTATCAGATGA
1 TTTACAGTTATCAGATG-TTTTCAGTTATCAGATGA
**
27080 TTTTTAGTTATCAGATGTTTT
1 TTTACAGTTATCAGATGTTTT
27101 ATAATTATCA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
35 28 0.61
36 18 0.39
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTACAGTTATCAGATGTTTTCAGTTATCAGATGA
Found at i:27108 original size:18 final size:18
Alignment explanation
Indices: 27051--27110 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
27041 ATATTTACAG
* * *
27051 TTATCCGATGATTTTCAG
1 TTATCAGATGATTTTTAA
*
27069 TTATCAGATGATTTTTAG
1 TTATCAGATGATTTTTAA
27087 TTATCAGATG-TTTTATAA
1 TTATCAGATGATTTT-TAA
27105 TTATCA
1 TTATCA
27111 AACGTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 4 0.11
18 34 0.89
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.48
Consensus pattern (18 bp):
TTATCAGATGATTTTTAA
Found at i:29478 original size:34 final size:34
Alignment explanation
Indices: 29434--29538 Score: 83
Period size: 34 Copynumber: 3.1 Consensus size: 34
29424 ACTCCAACTA
*
29434 AATATTTTTTACTATTTAAATTTAAACATATAAT
1 AATATCTTTTACTATTTAAATTTAAACATATAAT
* *
29468 AATATCTTTTA--ATTTGAAATGTTGAAAAGATTTAA-
1 AATATCTTTTACTATTT-AAAT-TT--AAACATATAAT
* * * *
29503 ACT-TCTTTTACTATTCAAATTTAAATATATATT
1 AATATCTTTTACTATTTAAATTTAAACATATAAT
29536 AAT
1 AAT
29539 TTAATTTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
32 11 0.20
33 6 0.11
34 21 0.38
35 6 0.11
36 11 0.20
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.48
Consensus pattern (34 bp):
AATATCTTTTACTATTTAAATTTAAACATATAAT
Found at i:33295 original size:45 final size:45
Alignment explanation
Indices: 33246--33457 Score: 343
Period size: 45 Copynumber: 4.7 Consensus size: 45
33236 AATTCTTGCG
*
33246 AACTAGATATCATGCGGTTATGTTTATTTTTCGAACAAGCATGCA
1 AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCA
* *
33291 AACTAGATATCATGCAGTTAGGTTTATTTTTCGAACAAGCATGCG
1 AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCA
*
33336 AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCG
1 AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCA
* *
33381 AATTAGATATCATGAGGTTAGGTTTATTTTTCGAACAAGCATGCA
1 AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCA
* *
33426 AATTAGATATCATGCGGTTAGGATTTCTTTTT
1 AACTAGATATCATGCGGTTAGG-TTTATTTTT
33458 GTGAATAACA
Statistics
Matches: 157, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 149 0.95
46 8 0.05
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (45 bp):
AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCA
Found at i:37460 original size:30 final size:31
Alignment explanation
Indices: 37408--37467 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
37398 CTTAGCTTTA
**
37408 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
37438 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
37468 GGAAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:38401 original size:19 final size:20
Alignment explanation
Indices: 38377--38427 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
38367 CGGCCAAGAG
* *
38377 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
38396 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
38416 CATGTATTTTCA
1 CATGTATTTTCA
38428 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:38823 original size:19 final size:20
Alignment explanation
Indices: 38799--38849 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
38789 CGGCCAAGAG
* *
38799 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
38818 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
38838 CATGTATTTTCA
1 CATGTATTTTCA
38850 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:38887 original size:422 final size:422
Alignment explanation
Indices: 38103--38954 Score: 1650
Period size: 422 Copynumber: 2.0 Consensus size: 422
38093 TGAAGCTAGT
38103 TCATCTCTAGGCTATCCATGGACTTCAAGACATCATCCTATGGTTACAACCTCACCAAAGCCTTG
1 TCATCTCTAGGCTATCCATGGACTTCAAGACATCATCCTATGGTTACAACCTCACCAAAGCCTTG
*
38168 CAAGAAGACCCATGTGCATTCAAGTAGGTTTCCATGTGCATCATTCAACCATATGCACTCCATGT
66 CAAGAAGACCCATGTGCATTCAAGTAGGTTGCCATGTGCATCATTCAACCATATGCACTCCATGT
38233 GATATCAAATTGGCGCCAAAACACCAAGGGATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCC
131 GATATCAAATTGGCGCCAAAACACCAAGGGATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCC
38298 ATTTTGGTGCCCAAATAACTTCCAAATGCATTCAAATCATCCTTAAGGCCGAACCAACACATAAC
196 ATTTTGGTGCCCAAATAACTTCCAAATGCATTCAAATCATCCTTAAGGCCGAACCAACACATAAC
38363 AATTCGGCCAAGAGCATGTATCTTCATTAAAATCATGTATTTTCATCAAAAATCATGTATTTTCA
261 AATTCGGCCAAGAGCATGTATCTTCATTAAAATCATGTATTTTCATCAAAAATCATGTATTTTCA
38428 AAGGGGTTTCAACCTTGGCCGAACCATCATGTGTCTATTCGGCCTAAACCCTTTGAAAAAACTAT
326 AAGGGGTTTCAACCTTGGCCGAACCATCATGTGTCTATTCGGCCTAAACCCTTTGAAAAAACTAT
38493 AAATAGGCTAGTGCATTTCATTTGTAATGATC
391 AAATAGGCTAGTGCATTTCATTTGTAATGATC
*
38525 TCATCTCTAGGCTATCCATGGACTTCAAGACATCATCCTATGGTTGCAACCTCACCAAAGCCTTG
1 TCATCTCTAGGCTATCCATGGACTTCAAGACATCATCCTATGGTTACAACCTCACCAAAGCCTTG
*
38590 CAAGAAGACCCATGTGCATTCAAGTAGGTTGCCATGTGCATCATTCAAGCATATGCACTCCATGT
66 CAAGAAGACCCATGTGCATTCAAGTAGGTTGCCATGTGCATCATTCAACCATATGCACTCCATGT
*
38655 GATATCAAATTGGCGCCAAAACACCAATGGATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCC
131 GATATCAAATTGGCGCCAAAACACCAAGGGATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCC
*
38720 ATTTTGGTGCCCAAATAACTTCCAAATGCATTCAAATCATCCTTAGGGCCGAACCAACACATAAC
196 ATTTTGGTGCCCAAATAACTTCCAAATGCATTCAAATCATCCTTAAGGCCGAACCAACACATAAC
*
38785 CATTCGGCCAAGAGCATGTATCTTCATTAAAATCATGTATTTTCATCAAAAATCATGTATTTTCA
261 AATTCGGCCAAGAGCATGTATCTTCATTAAAATCATGTATTTTCATCAAAAATCATGTATTTTCA
38850 AAGGGGTTTCAACCTTGGCCGAACCATCATGTGTCTATTCGGCCTAAACCCTTTGAAAAAACTAT
326 AAGGGGTTTCAACCTTGGCCGAACCATCATGTGTCTATTCGGCCTAAACCCTTTGAAAAAACTAT
38915 AAATAGGCTAGTGCATTTCATTTGTAATGATC
391 AAATAGGCTAGTGCATTTCATTTGTAATGATC
38947 TCATCTCT
1 TCATCTCT
38955 TATATAAAAC
Statistics
Matches: 424, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
422 424 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (422 bp):
TCATCTCTAGGCTATCCATGGACTTCAAGACATCATCCTATGGTTACAACCTCACCAAAGCCTTG
CAAGAAGACCCATGTGCATTCAAGTAGGTTGCCATGTGCATCATTCAACCATATGCACTCCATGT
GATATCAAATTGGCGCCAAAACACCAAGGGATGCTTCCTATTCGGCCAAAGACTCCTTCCTCTCC
ATTTTGGTGCCCAAATAACTTCCAAATGCATTCAAATCATCCTTAAGGCCGAACCAACACATAAC
AATTCGGCCAAGAGCATGTATCTTCATTAAAATCATGTATTTTCATCAAAAATCATGTATTTTCA
AAGGGGTTTCAACCTTGGCCGAACCATCATGTGTCTATTCGGCCTAAACCCTTTGAAAAAACTAT
AAATAGGCTAGTGCATTTCATTTGTAATGATC
Found at i:39289 original size:19 final size:20
Alignment explanation
Indices: 39273--39322 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
39263 CTTTATTTCA
39273 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
39292 TTTCATTACTTA-TA-TTAT
1 TTTCATTACTTATTATTTAT
*
39310 TATTCATTTCTTA
1 T-TTCATTACTTA
39323 AACCCATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.18
19 19 0.68
20 4 0.14
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Found at i:43014 original size:19 final size:20
Alignment explanation
Indices: 42990--43040 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
42980 CGACCAAGAG
* *
42990 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
43009 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
43029 CATGTATTTTCA
1 CATGTATTTTCA
43041 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:43479 original size:19 final size:20
Alignment explanation
Indices: 43463--43512 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
43453 CTTTATTTCA
43463 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
43482 TTTCATTACTTA-TA-TTAT
1 TTTCATTACTTATTATTTAT
*
43500 TATTCATTTCTTA
1 T-TTCATTACTTA
43513 AACCCATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.18
19 19 0.68
20 4 0.14
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Found at i:46412 original size:12 final size:12
Alignment explanation
Indices: 46395--46558 Score: 69
Period size: 12 Copynumber: 13.2 Consensus size: 12
46385 AAAAATGAAG
46395 AAATGAAGAAAA
1 AAATGAAGAAAA
46407 AAATG-AG-AAA
1 AAATGAAGAAAA
46417 AAA-GAA-AAGAA
1 AAATGAAGAA-AA
46428 AAATGAA-AAGAA
1 AAATGAAGAA-AA
46440 AAATGAA-AAGAA
1 AAATGAAGAA-AA
*
46452 AAATGAAAAAATGAA
1 AAATG-AAGAA--AA
46467 AAATGAA-AAAA
1 AAATGAAGAAAA
* *
46478 AAAAGAAAAAATGAA
1 AAATG-AAGAA--AA
46493 AAATGAAAAGAAAA
1 AAATG--AAGAAAA
*
46507 AAA-GAAAAAATA
1 AAATGAAGAAA-A
46519 GAAATGGAAG-AAA
1 -AAAT-GAAGAAAA
*
46532 AAA-GAAAAGAAA
1 AAATGAAGA-AAA
*
46544 AAATGATGAAAA
1 AAATGAAGAAAA
46556 AAA
1 AAA
46559 ATAGAGAAAA
Statistics
Matches: 125, Mismatches: 8, Indels: 38
0.73 0.05 0.22
Matches are distributed among these distances:
9 1 0.01
10 11 0.09
11 18 0.14
12 48 0.38
13 14 0.11
14 11 0.09
15 17 0.14
16 5 0.04
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAATGAAGAAAA
Found at i:46421 original size:18 final size:20
Alignment explanation
Indices: 46385--46424 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
46375 GAAGAAATGG
*
46385 AAAAATGAAGAAATGAAGAA
1 AAAAATGAAGAAATAAAGAA
46405 AAAAATG-AGAAA-AAAGAA
1 AAAAATGAAGAAATAAAGAA
46423 AA
1 AA
46425 GAAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AAAAATGAAGAAATAAAGAA
Found at i:46461 original size:53 final size:54
Alignment explanation
Indices: 46372--46545 Score: 171
Period size: 53 Copynumber: 3.2 Consensus size: 54
46362 TATTTCGCTT
**
46372 AAAGAAGAAATGGAAAAATG--AAGAAATGAAGAAAAAAATGAGAAAAAAGAAAAGAAA
1 AAAGAA-AAAT-GAAAAATGAAAAGAAAAAAAG-AAAAAAT-AGAAAAAAGAAAA-AAA
* * *
46429 AATG-AAAA-GAAAAATGAAAAG-AAAAATGAAAAAAT-GAAAAATGAAAAAAA
1 AAAGAAAAATGAAAAATGAAAAGAAAAAAAGAAAAAATAGAAAAAAGAAAAAAA
*
46479 AAAGAAAAAATGAAAAATGAAAAGAAAAAAAGAAAAAATAGAAATGGAAGAAAAAAGA
1 AAAG-AAAAATGAAAAATGAAAAGAAAAAAAGAAAAAATAGAAA--AAAGAAAAAA-A
46537 AAAGAAAAA
1 AAAGAAAAA
46546 ATGATGAAAA
Statistics
Matches: 98, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
50 6 0.06
51 11 0.11
52 4 0.04
53 28 0.29
54 17 0.17
55 10 0.10
56 1 0.01
57 16 0.16
58 5 0.05
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.07
Consensus pattern (54 bp):
AAAGAAAAATGAAAAATGAAAAGAAAAAAAGAAAAAATAGAAAAAAGAAAAAAA
Found at i:46506 original size:58 final size:57
Alignment explanation
Indices: 46418--46575 Score: 143
Period size: 58 Copynumber: 2.7 Consensus size: 57
46408 AATGAGAAAA
46418 AAGAAAAG-AAAAATG-AAAAGAAAAATGAAAAGAAAAATGAAAAAAT-GAAA-AATGAAAA
1 AAGAAAAGAAAAAATGAAAAAGAAAAATG--AA-AAAAA-GAAAAAATAGAAAGAA-GAAAA
46476 AA-AAAAGAAAAAATGAAAAATG-AAAA-GAAAAAAAGAAAAAATAGAAATGGAAGAAAA
1 AAGAAAAGAAAAAATGAAAAA-GAAAAATGAAAAAAAGAAAAAATAGAAA--GAAGAAAA
* * *
46533 AAGAAAAGAAAAAATGATGAAA-AAAAATAGAGAAAAATAAAAA
1 AAGAAAAGAAAAAATGA-AAAAGAAAAAT-GAAAAAAAGAAAAA
46576 GGGGGTTCAA
Statistics
Matches: 85, Mismatches: 3, Indels: 22
0.77 0.03 0.20
Matches are distributed among these distances:
54 8 0.09
55 9 0.11
56 2 0.02
57 12 0.14
58 30 0.35
59 11 0.13
60 13 0.15
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (57 bp):
AAGAAAAGAAAAAATGAAAAAGAAAAATGAAAAAAAGAAAAAATAGAAAGAAGAAAA
Found at i:46546 original size:7 final size:7
Alignment explanation
Indices: 46412--46539 Score: 70
Period size: 7 Copynumber: 17.9 Consensus size: 7
46402 GAAAAAAATG
46412 AGAAAAA
1 AGAAAAA
46419 AG--AAA
1 AGAAAAA
46424 AGAAAAA
1 AGAAAAA
*
46431 TGAAAAGA
1 AGAAAA-A
*
46439 AAAATGAAA
1 AGAA--AAA
46448 AGAAAAA
1 AGAAAAA
*
46455 TGAAAAA
1 AGAAAAA
46462 ATGAAAAA
1 A-GAAAAA
*
46470 TG--AAA
1 AGAAAAA
46475 A-AAAAA
1 AGAAAAA
46481 AGAAAAA
1 AGAAAAA
46488 ATGAAAAA
1 A-GAAAAA
* *
46496 TGAAAAG
1 AGAAAAA
46503 A-AAAAA
1 AGAAAAA
46509 AGAAAAAA
1 AG-AAAAA
*
46517 TAGAAATGGA
1 -AGAAA--AA
46527 AGAAAAA
1 AGAAAAA
46534 AGAAAA
1 AGAAAA
46540 GAAAAAATGA
Statistics
Matches: 92, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
5 8 0.09
6 9 0.10
7 38 0.41
8 23 0.25
9 11 0.12
10 3 0.03
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (7 bp):
AGAAAAA
Found at i:46657 original size:45 final size:44
Alignment explanation
Indices: 46573--46657 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
46563 AGAAAAATAA
* * *
46573 AAAGGGGGTTCAAGATGAAAATCCGCAAAGGGCGTCTTGAAACC
1 AAAGGAGGTTCAAGATGAAAACCCGCAAAGGGCGACTTGAAACC
* *
46617 AAAGGAGGTCTCAAGTTGAAAACCCGCAAAGGGTGACTTGA
1 AAAGGAGGT-TCAAGATGAAAACCCGCAAAGGGCGACTTGA
46658 GTTTTGTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 8 0.23
45 27 0.77
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.16
Consensus pattern (44 bp):
AAAGGAGGTTCAAGATGAAAACCCGCAAAGGGCGACTTGAAACC
Found at i:47906 original size:37 final size:37
Alignment explanation
Indices: 47839--47911 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
47829 TCGAAACAGG
*
47839 TCAATCTTAAGCCATCACGAAAGAGCAGTGAAGCAAT
1 TCAAACTTAAGCCATCACGAAAGAGCAGTGAAGCAAT
* * * *
47876 TCAAACTTATGCCTTCACGGAAGAGTAGTGAAGCAA
1 TCAAACTTAAGCCATCACGAAAGAGCAGTGAAGCAA
47912 ACTCGTTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (37 bp):
TCAAACTTAAGCCATCACGAAAGAGCAGTGAAGCAAT
Found at i:48010 original size:55 final size:55
Alignment explanation
Indices: 47907--48234 Score: 237
Period size: 55 Copynumber: 6.0 Consensus size: 55
47897 AGAGTAGTGA
** *
47907 AGCAAACTCGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGG
1 AGCAAACAAGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGG
* * *
47958 AGCAAACAAGTTTGTTGAAGATTGTTCAAGTCCCATACTGTCTGAAGAAATAGGG
1 AGCAAACAAGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGG
** * * *
48013 AGCGGACATA-TTTGTTGAGGATTGTTCGAGTTCTATACTCTCTGAATG-AATAGAG
1 AGCAAACA-AGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAA-GAAATAGGG
* ** * * *
48068 AGCAGACCCGTTT-TATGAAGATTGTTTGAGTTCTATACTCTCTGAAGAAATAGAG
1 AGCAAACAAGTTTGT-TGAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGG
** * * * * *
48123 AGGGGACCCA-TTT-TATGAAGATTGTTTGAGTTCTATACTCCCTGAATG-AATAGGG
1 A-GCAAACAAGTTTGT-TGAAGATTGTTCGAGTCCTATACTCTCTGAA-GAAATAGGG
** ** * * *
48178 AGCGGACCCGTTTATTGAAGATTGTTCGAGTCTTATACTCCCTGAACG-AATAGGG
1 AGCAAACAAGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAA-GAAATAGGG
48233 AG
1 AG
48235 TGGACTCGTC
Statistics
Matches: 230, Mismatches: 34, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
51 19 0.08
54 8 0.03
55 196 0.85
56 7 0.03
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (55 bp):
AGCAAACAAGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGG
Found at i:48230 original size:110 final size:109
Alignment explanation
Indices: 47928--48239 Score: 360
Period size: 110 Copynumber: 2.8 Consensus size: 109
47918 TTGTTGAAGA
* * * ** * **
47928 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCAAACAAGTTTGTTGAAGATTGTTCAAGTCCCA
1 TTGAGTTCTATACTCTCTGAATGAATAGGGAGCAGACCCGTTT-TTGAAGATTGTTCGAGTCTTA
* * *
47993 TACTGTCTGAAGAAATAGGGAGCGGACATATTTGTTGAGGATTGT
65 TACTCTCTGAAGAAATAGGGAGCGGACACATTTGTTGAAGATTGT
* * *
48038 TCGAGTTCTATACTCTCTGAATGAATAGAGAGCAGACCCGTTTTATGAAGATTGTTTGAGT-TCT
1 TTGAGTTCTATACTCTCTGAATGAATAGGGAGCAGACCCGTTTT-TGAAGATTGTTCGAGTCT-T
* * *
48102 ATACTCTCTGAAGAAATAGAGAGGGGACCCATTT-TATGAAGATTGT
64 ATACTCTCTGAAGAAATAGGGAGCGGACACATTTGT-TGAAGATTGT
* *
48148 TTGAGTTCTATACTCCCTGAATGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTCTTA
1 TTGAGTTCTATACTCTCTGAATGAATAGGGAGCAGACCCGTTT-TTGAAGATTGTTCGAGTCTTA
* *
48213 TACTCCCTGAACG-AATAGGGAGTGGAC
65 TACTCTCTGAA-GAAATAGGGAGCGGAC
48240 TCGTCATTCG
Statistics
Matches: 171, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
109 2 0.01
110 166 0.97
111 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (109 bp):
TTGAGTTCTATACTCTCTGAATGAATAGGGAGCAGACCCGTTTTTGAAGATTGTTCGAGTCTTAT
ACTCTCTGAAGAAATAGGGAGCGGACACATTTGTTGAAGATTGT
Done.