Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006123.1 Hibiscus syriacus cultivar Beakdansim tig00014522_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: 40343
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1357 original size:2 final size:2
Alignment explanation
Indices: 1343--1437 Score: 149
Period size: 2 Copynumber: 48.5 Consensus size: 2
1333 AGGCTATAAT
* * *
1343 TA TA TA -A TG TA TA TA T- TA TG CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1425 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1438 TATCATTATA
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
1 2 0.02
2 83 0.98
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2798 original size:5 final size:5
Alignment explanation
Indices: 2788--2945 Score: 89
Period size: 5 Copynumber: 32.2 Consensus size: 5
2778 TTATCTTCTA
* ** * *
2788 TTTAT TTTAT TTTAT TTT-T TCTTGTT TTTAT TAGAT TTAAT CTTAT TTT-T
1 TTTAT TTTAT TTTAT TTTAT T-TT-AT TTTAT TTTAT TTTAT TTTAT TTTAT
* * * * * *
2838 TCTTGT TTAATT TTTAT TTTAT TTTAT TTTAT TTTAA TTTGT TTTGT TTT-G
1 T-TTAT TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
* * *
2889 TTTAT TTTA- TTTAT TATA- TTT-T TTTAT TTTAC TTTAT TTT-T GTTT-G
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT
2935 TTTAT TTTAT T
1 TTTAT TTTAT T
2946 GCTTTGCTTT
Statistics
Matches: 119, Mismatches: 22, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
4 20 0.17
5 89 0.75
6 8 0.07
7 2 0.02
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:2890 original size:46 final size:46
Alignment explanation
Indices: 2823--2942 Score: 140
Period size: 46 Copynumber: 2.6 Consensus size: 46
2813 TTTTATTAGA
2823 TTTAATCTTATTTTTTCTTGTTTAATTTTTA-TT-TTAT-TTTATTTTAT
1 TTTAAT-TTATTTTTT-TTGTTT-ATTTTTATTTATTATATTT-TTTTAT
*
2870 TTTAATTTGTTTTGTTTTGTTTA-TTTTATTTATTATATTTTTTTAT
1 TTTAATTTATTTT-TTTTGTTTATTTTTATTTATTATATTTTTTTAT
*
2916 TTTACTTTATTTTTGTTTGTTTATTTT
1 TTTAATTTATTTTT-TTTGTTTATTTT
2943 ATTGCTTTGC
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
44 5 0.08
45 4 0.06
46 41 0.64
47 14 0.22
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.76
Consensus pattern (46 bp):
TTTAATTTATTTTTTTTGTTTATTTTTATTTATTATATTTTTTTAT
Found at i:5542 original size:23 final size:23
Alignment explanation
Indices: 5507--5554 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5497 ATTAAGTACA
*
5507 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
5530 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
5553 AT
1 AT
5555 TGACTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:6504 original size:182 final size:182
Alignment explanation
Indices: 6194--6831 Score: 1021
Period size: 182 Copynumber: 3.5 Consensus size: 182
6184 ACTTTTTTAC
*
6194 TACCGGTTTTATCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTATCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
*
6259 TACATTTTTATAAAGTATCGACACTTTATTGACGAG--ATAACTTCTTTTCCTTTAAATTCCAAA
66 TACATTTTTATAAAGTATCGACACTTTATTG--GAGCTATAACTTCTTTTCTTTTAAATTCCAAA
* *
6322 AGTGTCGATACTTATAATAAAGTATCGACACTCTCAACATATTCGGTAGCTCTT
129 AGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
* * * *
6376 TATCGGTTTTGTCATTTCGAGACTGGTTTTGTCATATTTTTACCTGTTATATTGTTTTGGATCGA
1 TACCGGTTTTATCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
6441 TACATTTTTATAAAGTATCGACACTTTATTGGAGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTGGAGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
* *
6506 TGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGTTCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
* **
6558 TACCGGTTTTATCATTTCGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATTAA
1 TACCGGTTTTATCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
6623 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTGGAGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
*
6688 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
** * * **
6740 TACCTATTTTGTAATTTATAGACCGGTTTTGTCAT-TTGTTTACCTGTTATATTGTTATGGATCG
1 TACCGGTTTTATCATTTCGAGACCGGTTTTGTCATATT-TTTACCTGTTATATTGTTATGGATCG
6804 ATACATTTTTATAAAGTATCGACACTTT
65 ATACATTTTTATAAAGTATCGACACTTT
6832 CAATATATCT
Statistics
Matches: 422, Mismatches: 31, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
180 3 0.01
181 2 0.00
182 417 0.99
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
TACCGGTTTTATCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTGGAGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
Found at i:6933 original size:21 final size:21
Alignment explanation
Indices: 6909--6957 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
6899 ATATTGTTAT
6909 GGATCGATACATTTTTATAAA
1 GGATCGATACATTTTTATAAA
6930 GGATCGATACATTTTTATAAA
1 GGATCGATACATTTTTATAAA
*
6951 GTATCGA
1 GGATCGA
6958 CACTTTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (21 bp):
GGATCGATACATTTTTATAAA
Found at i:6984 original size:132 final size:133
Alignment explanation
Indices: 6798--7069 Score: 474
Period size: 132 Copynumber: 2.1 Consensus size: 133
6788 ATATTGTTAT
*
6798 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTG
1 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTG
*
6863 TCATTTATAGACTGATTTTATCA-TTTTTTACCTATTATATTGTTATGGATCGATACATTTTTAT
66 TCATTTATAGACCGATTTTATCATTTTTTTACCTATTATATTGTTATGGATCGATACATTTTTAT
6927 AAA
131 AAA
*
6930 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGTGCTTTACCTGTTTTG
1 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTG
* * *
6995 TCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
66 TCATTTATAGACCGATTTTATCATTTTTTTACCTATTATATTGTTATGGATCGATACATTTTTAT
7060 AAA
131 AAA
*
7063 GTATCGA
1 GGATCGA
7070 CACTTTCAAT
Statistics
Matches: 132, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
132 83 0.63
133 49 0.37
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (133 bp):
GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTG
TCATTTATAGACCGATTTTATCATTTTTTTACCTATTATATTGTTATGGATCGATACATTTTTAT
AAA
Found at i:7080 original size:112 final size:113
Alignment explanation
Indices: 6930--7185 Score: 424
Period size: 112 Copynumber: 2.3 Consensus size: 113
6920 TTTTTATAAA
*
6930 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGTGCTTTACCTGTTTTG
1 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTG
* * *
6995 TCATTTATAGACCGGTTTTGTCA-TTTTTTTACCTGTTATATTGTTAT
66 TAATTTATAAACCGATTTTGTCATTTTTTTTACCTGTTATATTGTTAT
7042 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTG
1 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTG
*
7107 TAATTTATAAATCGATTTTGTCATTTTTTTTACCTGTTATATTGTTAT
66 TAATTTATAAACCGATTTTGTCATTTTTTTTACCTGTTATATTGTTAT
** * *
7155 GGATTTATATATTTTTATAAAGCATCGACAC
1 GGATCGATACATTTTTATAAAGTATCGACAC
7186 AAACCAAAAA
Statistics
Matches: 134, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
112 83 0.62
113 51 0.38
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (113 bp):
GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTG
TAATTTATAAACCGATTTTGTCATTTTTTTTACCTGTTATATTGTTAT
Found at i:7133 original size:244 final size:245
Alignment explanation
Indices: 6702--7182 Score: 795
Period size: 244 Copynumber: 2.0 Consensus size: 245
6692 GATACTTATA
6702 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTATTTTGTAATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTATTTTGTAATTTATAGACCGGT
6767 TTTGTCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* * *
6832 CAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGATTTTATCA-TTTTTTACCT
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTAATTTATAAACTGATTTTATCATTTTTTTACCT
*
6896 ATTATATTGTTATGGATCGATACATTTTTATAAAGGATCGATACATTTTT
196 ATTATATTGTTATGGATCGATACATTTTTATAAAGCATCGATACATTTTT
* * * * *
6946 ATAAAGTATCGACACTTTCAATATATCCGGTAGTGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTATTTTGTAATTTATAGACCGGT
*
7011 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
*
7076 CAATATATCCGGTAGCGCTTTACCTGTTTTGTAATTTATAAA-TCGATTTTGTCATTTTTTTTAC
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTAATTTATAAACT-GATTTTATCA-TTTTTTTAC
* ** *
7140 CTGTTATATTGTTATGGATTTATATATTTTTATAAAGCATCGA
194 CTATTATATTGTTATGGATCGATACATTTTTATAAAGCATCGA
7183 CACAAACCAA
Statistics
Matches: 219, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
243 1 0.00
244 172 0.79
246 46 0.21
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (245 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTATTTTGTAATTTATAGACCGGT
TTTGTCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACCTGTTTTGTAATTTATAAACTGATTTTATCATTTTTTTACCT
ATTATATTGTTATGGATCGATACATTTTTATAAAGCATCGATACATTTTT
Found at i:9228 original size:129 final size:129
Alignment explanation
Indices: 8994--9242 Score: 311
Period size: 129 Copynumber: 1.9 Consensus size: 129
8984 ATCAGATTTG
* * * * * *
8994 GAAATTTTAATTCATTTCACTGCTTTTCAGAAAAAATTGAATCATGGTTAATTTGCGTCGGTGCT
1 GAAATTTTAATTAATTTCACTACTATTAAGAAAAAACTGAATCATGGTTAATTTGCGTCGCTGCT
* * ** * *
9059 CTTCAGGAAGATCAAATCTTAAAAATGGGGATCTATTCTGCTAATCTTTAAGGGATATTATTCA
66 CTTCAGGAAGATCAAATATGAAAAATAAGGATATACTCTGCTAATCTTTAAGGGATATTATTCA
* * * *
9123 GAAATTTTGATTAATTTCACTACTCATTAAG-AAAAACTGAATCATGGTTGATTTGCTTTGCTGC
1 GAAATTTTAATTAATTTCACTACT-ATTAAGAAAAAACTGAATCATGGTTAATTTGCGTCGCTGC
* * *
9187 TCTTCAGGAAGATCAAATATGAAATATAAGGATATACTCTGCTACTCTTTAGGGGA
65 TCTTCAGGAAGATCAAATATGAAAAATAAGGATATACTCTGCTAATCTTTAAGGGA
9243 GACTATATCT
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
129 96 0.96
130 4 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (129 bp):
GAAATTTTAATTAATTTCACTACTATTAAGAAAAAACTGAATCATGGTTAATTTGCGTCGCTGCT
CTTCAGGAAGATCAAATATGAAAAATAAGGATATACTCTGCTAATCTTTAAGGGATATTATTCA
Found at i:13337 original size:18 final size:19
Alignment explanation
Indices: 13311--13346 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
13301 CCACTAAATT
*
13311 AATATTTTTTATTTTATTA
1 AATATTTTTTATATTATTA
13330 AATA-TTTTTATATTATT
1 AATATTTTTTATATTATT
13347 TTTTGTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
AATATTTTTTATATTATTA
Found at i:19486 original size:16 final size:16
Alignment explanation
Indices: 19465--19497 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19455 TCAAATAATC
19465 ATATA-TAAAAAATATT
1 ATATATTAAAAAA-ATT
19481 ATATATTAAAAAAATT
1 ATATATTAAAAAAATT
19497 A
1 A
19498 CCTTACAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATATTAAAAAAATT
Found at i:20230 original size:16 final size:16
Alignment explanation
Indices: 20206--20244 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
20196 TATAATATAT
*
20206 ATATACACATACATAC
1 ATATTCACATACATAC
*
20222 ATATTCACATACATAT
1 ATATTCACATACATAC
20238 ATATTCA
1 ATATTCA
20245 TAATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATTCACATACATAC
Found at i:20252 original size:13 final size:14
Alignment explanation
Indices: 20213--20265 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 14
20203 TATATATACA
*
20213 CATACATACATATT
1 CATACATATATATT
20227 CACATACATATATATT
1 --CATACATATATATT
20243 CATA-ATATATATAT
1 CATACATATATAT-T
20257 -ATACATATA
1 CATACATATA
20266 CACGCATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 11 0.32
14 10 0.29
16 13 0.38
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
CATACATATATATT
Found at i:20290 original size:5 final size:5
Alignment explanation
Indices: 20280--20425 Score: 207
Period size: 5 Copynumber: 30.2 Consensus size: 5
20270 CATATGTATT
20280 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
20330 TATAA TATAATA TATAA TATAA TAT-A -ATAA TATAA TATAA TATAA -AT-A
1 TATAA TAT-A-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* *
20378 TATAA TATAA TATAA -ATAA TATAA CATAA T-TTA TATAA TATAA T-TAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
20425 T
1 T
20426 TAACCCCTTA
Statistics
Matches: 129, Mismatches: 4, Indels: 17
0.86 0.03 0.11
Matches are distributed among these distances:
3 3 0.02
4 17 0.13
5 103 0.80
6 2 0.02
7 4 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:22298 original size:59 final size:60
Alignment explanation
Indices: 22209--22344 Score: 163
Period size: 59 Copynumber: 2.3 Consensus size: 60
22199 AAGCTTTAAT
* **
22209 TATTAAAAGTTACAAAATAGTCTCTTAATTATAGGA-CAT-TGTTTGTTGAG-TCTTTTGAC
1 TATTAAAAGTTACAAAATAGTCTCTCAATTATAGGATCATGT-TTTGTTGAGTTC-TCCGAC
* *
22268 TATTAAAAGTTACAAAATAGTC-CTCCAATTATAGTATGATGTTTTGTTGAGTTCTCCGAC
1 TATTAAAAGTTACAAAATAGTCTCT-CAATTATAGGATCATGTTTTGTTGAGTTCTCCGAC
*
22328 TATTAAAAGTAACAAAA
1 TATTAAAAGTTACAAAA
22345 CTCGTCTTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
58 2 0.03
59 31 0.46
60 31 0.46
61 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (60 bp):
TATTAAAAGTTACAAAATAGTCTCTCAATTATAGGATCATGTTTTGTTGAGTTCTCCGAC
Found at i:30535 original size:10 final size:10
Alignment explanation
Indices: 30503--30536 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
30493 TTACTATGTT
30503 TAAATATATA
1 TAAATATATA
*
30513 TATATATATA
1 TAAATATATA
30523 TAAATATATA
1 TAAATATATA
30533 TAAA
1 TAAA
30537 AGTAGAGAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAATATATA
Found at i:31911 original size:68 final size:67
Alignment explanation
Indices: 31823--31952 Score: 172
Period size: 68 Copynumber: 1.9 Consensus size: 67
31813 TATTATTTTA
* * *
31823 TATTTTATATTTGTTTTAGGTATTTTAGTTTAAAAAGATTTT-AGTACTTTAGTTAGGATTTAGA
1 TATTTTAAATTTATTTTAGGTATTTTAGTTTAAAAAG-TTTTAAGTACTTTAATTAGGATTTAGA
31887 ATT
65 ATT
* * **
31890 TATTTTAAATATTATTTTAGGTATTTTTGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TATTTTAAAT-TTATTTTAGGTATTTTAGTTTAAAAAGTTTTAAGTACTTTAATTAGGATTTA
31953 AGATGTTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 13 0.24
68 41 0.76
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (67 bp):
TATTTTAAATTTATTTTAGGTATTTTAGTTTAAAAAGTTTTAAGTACTTTAATTAGGATTTAGAA
TT
Found at i:32563 original size:18 final size:19
Alignment explanation
Indices: 32524--32567 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
32514 CTTTAATTTG
* *
32524 TTTATTTAATTATTTTTCT
1 TTTATTTAATTACTTATCT
32543 TTTATTTAATT-CTTATCT
1 TTTATTTAATTACTTATCT
32561 TTTATTT
1 TTTATTT
32568 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTAATTACTTATCT
Found at i:32610 original size:15 final size:15
Alignment explanation
Indices: 32590--32619 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
32580 TTAAAATCCC
32590 CTATTATATTTATTA
1 CTATTATATTTATTA
32605 CTATTATATTTATTA
1 CTATTATATTTATTA
32620 TTTTTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
CTATTATATTTATTA
Found at i:37774 original size:5 final size:5
Alignment explanation
Indices: 37772--37848 Score: 52
Period size: 5 Copynumber: 15.8 Consensus size: 5
37762 TTTTTTTTGT
* **** *
37772 TTTTA TTTTA TTTTA TTTT- GTTTA TTTT- TTTTA TTTTTA ACGAA CTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
* *
37821 TTTCA TTCTA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
37849 TTCTCTGAAC
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
4 10 0.19
5 38 0.72
6 5 0.09
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:37797 original size:9 final size:9
Alignment explanation
Indices: 37758--37809 Score: 70
Period size: 9 Copynumber: 5.8 Consensus size: 9
37748 TTTCGTTATA
37758 TATTTTTTT
1 TATTTTTTT
*
37767 T-TTGTTTT
1 TATTTTTTT
37775 TATTTTATTT
1 TATTTT-TTT
*
37785 TATTTTGTT
1 TATTTTTTT
37794 TATTTTTTT
1 TATTTTTTT
37803 TATTTTT
1 TATTTTT
37810 AACGAACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
8 7 0.19
9 21 0.57
10 9 0.24
ACGTcount: A:0.12, C:0.00, G:0.04, T:0.85
Consensus pattern (9 bp):
TATTTTTTT
Found at i:38622 original size:70 final size:69
Alignment explanation
Indices: 38471--38632 Score: 213
Period size: 69 Copynumber: 2.3 Consensus size: 69
38461 TTTTATCTTT
* * * * * *
38471 GTATTTTAGTTTAAATAGGTCTTGGTATTTTTAAGTTTTAGGATATTATTTTATATTTATATTTT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTTAAGGTTTAGAATATTATTTTAAATATATATTTT
38536 TTAG
66 TTAG
*
38540 GTATTTTAGTTTAAATAGGTTTTAGTAGTTTAGTTAGGGTTTAGAATATTATTTTAAATAT-TA-
1 GTATTTTAGTTTAAATAGGTTTTAGTA-TTT--TTAAGGTTTAGAATATTATTTTAAATATATAT
38603 TTTTTAG
63 TTTTTAG
38610 GTATTTTAGTTTAAATA-GTTTTA
1 GTATTTTAGTTTAAATAGGTTTTA
38633 AGTGTTTTAA
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
69 31 0.37
70 27 0.33
71 2 0.02
72 23 0.28
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.56
Consensus pattern (69 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTTAAGGTTTAGAATATTATTTTAAATATATATTTT
TTAG
Found at i:38647 original size:70 final size:72
Alignment explanation
Indices: 38471--38652 Score: 216
Period size: 70 Copynumber: 2.6 Consensus size: 72
38461 TTTTATCTTT
* * * * * * *
38471 GTATTTTAGTTTAAATAGGTCTTGGTA-TTT--TTAAGTTTTAGGATATTATTTTATATTTATAT
1 GTATTTTAGTTTAAATAGGTTTTAGTAGTTTAATTAGGATTTAGAATATTATTTTAAATATATAT
38533 TTTTTAG
66 TTTTTAG
* *
38540 GTATTTTAGTTTAAATAGGTTTTAGTAGTTTAGTTAGGGTTTAGAATATTATTTTAAATAT-TA-
1 GTATTTTAGTTTAAATAGGTTTTAGTAGTTTAATTAGGATTTAGAATATTATTTTAAATATATAT
38603 TTTTTAG
66 TTTTTAG
38610 GTATTTTAGTTTAAATA-GTTTTAAGT-GTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTAG-TTTAATTAGGATTTA
38653 AGATGTTTTA
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
69 31 0.31
70 43 0.43
71 2 0.02
72 23 0.23
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.55
Consensus pattern (72 bp):
GTATTTTAGTTTAAATAGGTTTTAGTAGTTTAATTAGGATTTAGAATATTATTTTAAATATATAT
TTTTTAG
Found at i:39272 original size:17 final size:19
Alignment explanation
Indices: 39234--39276 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
39224 CTTTAATTTG
*
39234 TTTATTTAATTATTTTTCT
1 TTTATTTAATTATTTATCT
39253 TTTATTTAA-T-TTTATCT
1 TTTATTTAATTATTTATCT
39270 TTTATTT
1 TTTATTT
39277 TAAAACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.57
18 1 0.04
19 9 0.39
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTTAATTATTTATCT
Done.