Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 35 of 35
Found at i:8238620 original size:17 final size:16
Alignment explanation
Indices: 8238580--8238635 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 16
8238570 TATTTCGCCT
8238580 GAAAAAAAATGAAAAA
1 GAAAAAAAATGAAAAA
*
8238596 GACTAAAAAATGAAAAA
1 GA-AAAAAAATGAAAAA
8238613 TGAAAAAAAA-G-AAAA
1 -GAAAAAAAATGAAAAA
8238628 GAAAAAAA
1 GAAAAAAA
8238636 TAAAAGGAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 8 0.22
15 4 0.11
16 3 0.08
17 19 0.53
18 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (16 bp):
GAAAAAAAATGAAAAA
Found at i:8239850 original size:48 final size:48
Alignment explanation
Indices: 8239774--8240158 Score: 433
Period size: 48 Copynumber: 8.3 Consensus size: 48
8239764 CAACTCCCCC
*
8239774 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * *
8239822 AGATTTGATATTCCCTTTAGAGTAAGTGGAACAAG----TC-T-GCC-
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * *
8239863 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
** *
8239911 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * *
8239959 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
8240007 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-T-ACC-
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * * *
8240048 AGATCTGACATTCCCTTCAGAGTAAGTGGAACATGTCTCT-TTTTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * *
8240095 TGATTTGATATTCCCTTCAGAAG-AAGCGGAACAGGTCTCTCTTTTCCA
1 AGATTTGATATTCCCTTCAG-AGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
8240143 AGGTTTGGTATTCCCT
1 AGATTTGATATTCCCT
8240159 GTGACAGCGG
Statistics
Matches: 282, Mismatches: 39, Indels: 32
0.80 0.11 0.09
Matches are distributed among these distances:
41 63 0.22
42 4 0.01
43 2 0.01
44 4 0.01
45 4 0.01
46 3 0.01
47 33 0.12
48 169 0.60
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
Found at i:8239923 original size:89 final size:89
Alignment explanation
Indices: 8239772--8240132 Score: 519
Period size: 89 Copynumber: 4.0 Consensus size: 89
8239762 ATCAACTCCC
*
8239772 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
8239837 TTTAGAGTAAGTGGAACAAGTCTG
66 TTCAGAGTAAGTGGAACAAGTCTA
*
8239861 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
*
8239926 TTCAGAGTAAGTGGAACAAATCTA
66 TTCAGAGTAAGTGGAACAAGTCTA
*
8239950 TCTTCTCCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGA
1 ------CC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGA
8240015 TATTCCCTTCAGAGTAAGTGGAACAAGTCTA
59 TATTCCCTTCAGAGTAAGTGGAACAAGTCTA
* * * * *
8240046 CCAGATCTGACATTCCCTTCAGAGTAAGTGGAACATGTCTCT-TTTTCCATGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
8240110 TTCAGAAG-AAGCGGAACAGGTCT
66 TTCAG-AGTAAGTGGAACAAGTCT
8240133 CTCTTTTCCA
Statistics
Matches: 248, Mismatches: 16, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
88 38 0.15
89 122 0.49
90 2 0.01
95 2 0.01
96 84 0.34
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (89 bp):
CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
TTCAGAGTAAGTGGAACAAGTCTA
Found at i:8240402 original size:3 final size:3
Alignment explanation
Indices: 8240394--8240434 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
8240384 CATCTCGTTC
*
8240394 TTA TTA TTA TTA -TA TGTA TTA TTA TTA TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
8240435 TTACATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:8240442 original size:12 final size:12
Alignment explanation
Indices: 8240394--8240443 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
8240384 CATCTCGTTC
*
8240394 TTATTATTATTA
1 TTATTATTAATA
*
8240406 -TATGTATTATTA
1 TTAT-TATTAATA
8240418 TTATTATTAATA
1 TTATTATTAATA
8240430 TTATT-TTACATA
1 TTATTATTA-ATA
8240442 TT
1 TT
8240444 TGGCAGGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 6 0.18
12 25 0.74
13 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:8245068 original size:12 final size:12
Alignment explanation
Indices: 8245051--8245093 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
8245041 ATATCTTTCC
8245051 TCTCATCCTTCT
1 TCTCATCCTTCT
*
8245063 TCTCATCTTTCT
1 TCTCATCCTTCT
*
8245075 TCTCGTCCTTCT
1 TCTCATCCTTCT
8245087 TCTCATC
1 TCTCATC
8245094 TTTCGCAGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.07, C:0.40, G:0.02, T:0.51
Consensus pattern (12 bp):
TCTCATCCTTCT
Found at i:8245078 original size:24 final size:24
Alignment explanation
Indices: 8245043--8245097 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
8245033 ATATTACAAT
8245043 ATCTTTCCTCTCATCCTTCTTCTC
1 ATCTTTCCTCTCATCCTTCTTCTC
* *
8245067 ATCTTTCTTCTCGTCCTTCTTCTC
1 ATCTTTCCTCTCATCCTTCTTCTC
8245091 ATCTTTC
1 ATCTTTC
8245098 GCAGCCCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.07, C:0.38, G:0.02, T:0.53
Consensus pattern (24 bp):
ATCTTTCCTCTCATCCTTCTTCTC
Found at i:8248007 original size:29 final size:29
Alignment explanation
Indices: 8247965--8248023 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
8247955 TATTTTATTT
8247965 TTTATTAATATGCAGGGAATATAAAATAA
1 TTTATTAATATGCAGGGAATATAAAATAA
8247994 TTTATTAATATGCAGGGAATATAAAATAA
1 TTTATTAATATGCAGGGAATATAAAATAA
8248023 T
1 T
8248024 ATCTATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (29 bp):
TTTATTAATATGCAGGGAATATAAAATAA
Found at i:8249298 original size:10 final size:10
Alignment explanation
Indices: 8249283--8249340 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
8249273 CGACCTCCAT
8249283 GCCCATGCAC
1 GCCCATGCAC
8249293 GCCCATGCAC
1 GCCCATGCAC
*
8249303 GCCCAT-CTC
1 GCCCATGCAC
* *
8249312 GCCAAAGGAGCAC
1 GCC-CA--TGCAC
8249325 GCCCATGCAC
1 GCCCATGCAC
8249335 GCCCAT
1 GCCCAT
8249341 CCATGCCCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 5 0.13
10 27 0.71
12 1 0.03
13 5 0.13
ACGTcount: A:0.22, C:0.47, G:0.21, T:0.10
Consensus pattern (10 bp):
GCCCATGCAC
Found at i:8249623 original size:29 final size:29
Alignment explanation
Indices: 8249562--8249645 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
8249552 ATGAATCCTT
** * **
8249562 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
8249591 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
8249620 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
8249646 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:8264154 original size:20 final size:20
Alignment explanation
Indices: 8264131--8264195 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
8264121 GTTTCCAGAT
*
8264131 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
*
8264151 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
8264172 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
8264192 TCGC
1 TCGC
8264196 GTTGCGATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 2 0.05
20 19 0.50
21 15 0.39
22 2 0.05
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:8264182 original size:41 final size:41
Alignment explanation
Indices: 8264131--8264227 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 41
8264121 GTTTCCAGAT
*
8264131 TCGCAACGCGATTTTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
* *** *
8264172 TCGCAACGCGATTCTGACTATCGCGTTGCGATAATATAAAA
1 TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
*
8264213 TCGCAATGCGATTTT
1 TCGCAACGCGATTTT
8264228 CAAAGCGCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (41 bp):
TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
Found at i:8264395 original size:22 final size:22
Alignment explanation
Indices: 8264370--8264420 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
8264360 CTACGGCGAC
8264370 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
8264392 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
8264414 ATCCGTC
1 ATCCGTC
8264421 TATCTTCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:8264528 original size:22 final size:22
Alignment explanation
Indices: 8264503--8264556 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
8264493 TTTTTTTAAT
*
8264503 TATTTTTATTTTGAAAATTTTG
1 TATTATTATTTTGAAAATTTTG
8264525 TATTATTATTTTGAAAATTTTG
1 TATTATTATTTTGAAAATTTTG
*
8264547 CATTATTATT
1 TATTATTATT
8264557 AGGTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (22 bp):
TATTATTATTTTGAAAATTTTG
Found at i:8264554 original size:25 final size:24
Alignment explanation
Indices: 8264496--8264557 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 24
8264486 GGGTTAGTTT
* *
8264496 TTTTAATTATTTTTATTTTGAAAA
1 TTTTGATTATTATTATTTTGAAAA
8264520 TTTTG--TATTATTATTTTGAAAA
1 TTTTGATTATTATTATTTTGAAAA
8264542 TTTTGCATTATTATTA
1 TTTTG-ATTATTATTA
8264558 GGTTTTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 21 0.64
24 4 0.12
25 8 0.24
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTTGATTATTATTATTTTGAAAA
Found at i:8264896 original size:20 final size:20
Alignment explanation
Indices: 8264853--8264920 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
8264843 CGATTATCTC
** *
8264853 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGT
*
8264873 GTTGCGATAGTCATTTTTGT
1 GTTGCGATAGTCATTTTCGT
* **
8264893 GTTGTGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
*
8264913 GTTACGAT
1 GTTGCGAT
8264921 TTTAAGTTTC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.18, C:0.13, G:0.24, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:8266794 original size:20 final size:20
Alignment explanation
Indices: 8266740--8266828 Score: 88
Period size: 20 Copynumber: 4.5 Consensus size: 20
8266730 AAAATAACCC
**
8266740 TGTTGCGATAGTCAAATTCG
1 TGTTGCGATAGTCATTTTCG
*
8266760 AGTTGCGATAGTCATTTTCG
1 TGTTGCGATAGTCATTTTCG
* *
8266780 CGTTGCGATATTCATTTTCG
1 TGTTGCGATAGTCATTTTCG
* ** * *
8266800 TGTTGCAATTTTAAGTTTCG
1 TGTTGCGATAGTCATTTTCG
8266820 TGTTGCGAT
1 TGTTGCGAT
8266829 TTTAAGTTTC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.43
Consensus pattern (20 bp):
TGTTGCGATAGTCATTTTCG
Found at i:8266830 original size:20 final size:20
Alignment explanation
Indices: 8266775--8266838 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
8266765 CGATAGTCAT
* * * *
8266775 TTTCGCGTTGCGATATTCAT
1 TTTCGTGTTGCGATTTTAAG
*
8266795 TTTCGTGTTGCAATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
8266815 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
8266835 TTTC
1 TTTC
8266839 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:8267402 original size:21 final size:21
Alignment explanation
Indices: 8267309--8267410 Score: 80
Period size: 21 Copynumber: 4.9 Consensus size: 21
8267299 CCCGACTCAT
* **
8267309 CTGTCATCGTTCAAAAGGCTT
1 CTGTCATCGTTCAAGAGGCCC
*
8267330 CT-CCTATCGTTCAAGAGGCCC
1 CTGTC-ATCGTTCAAGAGGCCC
* ** *
8267351 CTATCATCCCTCAAGAGTCCC
1 CTGTCATCGTTCAAGAGGCCC
** *
8267372 CTCCCTTCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCC
*
8267393 CTGTCATCGTTGAAGAGG
1 CTGTCATCGTTCAAGAGG
8267411 TCTCTCCAAC
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 59 0.97
22 1 0.02
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (21 bp):
CTGTCATCGTTCAAGAGGCCC
Found at i:8268921 original size:20 final size:20
Alignment explanation
Indices: 8268898--8268961 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
8268888 AACGCTAAAC
* *
8268898 TCAAAATTGTAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
*
8268918 TCAAAATCGCAATACGAAAG
1 TCAAAATCGCAATGCGAAAG
* *
8268938 CCAAAATCGCAACGCGAAAG
1 TCAAAATCGCAATGCGAAAG
8268958 TCAA
1 TCAA
8268962 TTTACGTTGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.16
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:8269200 original size:20 final size:20
Alignment explanation
Indices: 8269000--8269210 Score: 245
Period size: 20 Copynumber: 10.8 Consensus size: 20
8268990 GTGATTTTCT
* *
8269000 CGTTGCGATAGTTAAATTCT
1 CGTTGCGATAGTCAAATTCG
* *
8269020 CGTTGTGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
*
8269040 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
8269060 CATTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
8269080 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
8269100 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
8269120 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
8269140 CGTTGCAATAGCCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
8269160 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
8269174 AGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
8269194 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
8269211 GAATATGTAA
Statistics
Matches: 165, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
14 11 0.07
16 1 0.01
20 153 0.93
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:8269433 original size:140 final size:140
Alignment explanation
Indices: 8269181--8269463 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
8269171 TTGAGTTGCG
*
8269181 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
8269246 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
8269311 AATACACATA
131 AATACACATA
*
8269321 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
*
8269386 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
8269451 AATACACATA
131 AATACACATA
8269461 ATA
1 ATA
8269464 CAACGTTTGC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:8271836 original size:24 final size:24
Alignment explanation
Indices: 8271769--8271828 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
8271759 CTGAAACATC
8271769 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
8271793 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
8271817 ATCAAATTTCGA
1 ATCAAAATTCGA
8271829 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:8272730 original size:20 final size:20
Alignment explanation
Indices: 8272644--8272770 Score: 114
Period size: 20 Copynumber: 6.3 Consensus size: 20
8272634 AAATTCAGCA
*
8272644 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* * *
8272664 TTGCGTTAGTTAGAATCGTG
1 TTGCGATAGTCAGAATCGCG
**
8272684 TTGCGATTATGT-ATTATCGCG
1 TTGCGA-TA-GTCAGAATCGCG
8272705 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* * * *
8272725 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCG
*
8272745 TTGCGATAGTCAAAATCGCG
1 TTGCGATAGTCAGAATCGCG
8272765 TTGCGA
1 TTGCGA
8272771 ATCTGGAAAC
Statistics
Matches: 84, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.04
20 64 0.76
21 15 0.18
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:8280889 original size:13 final size:13
Alignment explanation
Indices: 8280871--8280910 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
8280861 TGACCATGGA
*
8280871 AAGGGGAAAAGGG
1 AAGGGGAAGAGGG
8280884 AAGGGGAAGAGGG
1 AAGGGGAAGAGGG
8280897 AAGAGGGAAGAGGG
1 AAG-GGGAAGAGGG
8280911 GAAAAGGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.57, T:0.00
Consensus pattern (13 bp):
AAGGGGAAGAGGG
Found at i:8281192 original size:2 final size:2
Alignment explanation
Indices: 8281185--8281220 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8281175 TAGGTCTTCA
8281185 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
8281221 TCTTTAAATT
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
Done.