Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002655.1 Hibiscus syriacus cultivar Beakdansim tig00005429_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: 49645
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:10989 original size:37 final size:37
Alignment explanation
Indices: 10931--11035 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
10921 TCTTTTCGTC
*
10931 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
10968 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
11005 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
11036 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:11515 original size:18 final size:19
Alignment explanation
Indices: 11486--11521 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11476 TTGATTTTTT
11486 TATACTATATATTATTATA
1 TATACTATATATTATTATA
*
11505 TATAC-ATATATTTTTAT
1 TATACTATATATTATTAT
11522 TTTTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (19 bp):
TATACTATATATTATTATA
Found at i:11580 original size:23 final size:23
Alignment explanation
Indices: 11486--11581 Score: 62
Period size: 23 Copynumber: 4.3 Consensus size: 23
11476 TTGATTTTTT
*
11486 TATACTATATATTA-TTATATATA
1 TATA-TATTTATTATTTATATATA
*
11509 CATATATTT-TTATTT-T-T-TA
1 TATATATTTATTATTTATATATA
* * *
11528 TAT-TCATTTGGTTATTTTTTTA-A
1 TATAT-ATTT-ATTATTTATATATA
11551 TACTATATTTATTATTTATATATA
1 TA-TATATTTATTATTTATATATA
11575 TATATAT
1 TATATAT
11582 ATACTTTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
18 1 0.02
19 8 0.14
20 1 0.02
21 10 0.18
22 7 0.12
23 21 0.37
24 8 0.14
25 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATTTATTATTTATATATA
Found at i:11807 original size:18 final size:19
Alignment explanation
Indices: 11781--11816 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11771 TGTTTTTGGT
*
11781 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
11799 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
11817 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:16307 original size:9 final size:8
Alignment explanation
Indices: 16280--16348 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 8
16270 AGATCCAATC
*
16280 AAGAACAA
1 AAGAAGAA
16288 AA-AAGAA
1 AAGAAGAA
16295 AAGAAGCAA
1 AAGAAG-AA
16304 AAGAAG-A
1 AAGAAGAA
16311 AA-AA-AA
1 AAGAAGAA
16317 AAGAA-AA
1 AAGAAGAA
16324 AAG-AGAA
1 AAGAAGAA
*
16331 ACAAAAGAA
1 A-AGAAGAA
*
16340 AAAAAGAA
1 AAGAAGAA
16348 A
1 A
16349 GAACAAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
6 6 0.12
7 19 0.37
8 14 0.27
9 13 0.25
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:16324 original size:19 final size:17
Alignment explanation
Indices: 16280--16370 Score: 60
Period size: 19 Copynumber: 4.9 Consensus size: 17
16270 AGATCCAATC
*
16280 AAGAACAAAA-AAGAAAAG
1 AAGAA-AAAAGAA-AAAAA
16298 AAGCAAAAGAAGAAAAAAA
1 AAG-AAAA-AAGAAAAAAA
*
16317 AAGAAAAAAGAGAAACAA
1 AAGAAAAAAGA-AAAAAA
16335 AAGAAAAAAAGAAAGAACAA
1 AAG-AAAAAAGAAA-AA-AA
16355 AA-ATCAAAAAGAAAAA
1 AAGA--AAAAAGAAAAA
16371 GGGACAAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
17 4 0.07
18 20 0.33
19 22 0.36
20 15 0.25
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.01
Consensus pattern (17 bp):
AAGAAAAAAGAAAAAAA
Found at i:16339 original size:31 final size:31
Alignment explanation
Indices: 16296--16356 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
16286 AAAAAAGAAA
*
16296 AGAAGCAAAAGAAGAAAAAAAAAGAA-AAAAG
1 AGAAACAAAAGAA-AAAAAAAAAGAACAAAAG
*
16327 AGAAACAAAAGAAAAAAAGAAAGAACAAAA
1 AGAAACAAAAGAAAAAAAAAAAGAACAAAA
16357 ATCAAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (31 bp):
AGAAACAAAAGAAAAAAAAAAAGAACAAAAG
Found at i:16341 original size:27 final size:26
Alignment explanation
Indices: 16280--16357 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
16270 AGATCCAATC
*
16280 AAGAACAAAAAAGAAAAGAAGCAAAAG
1 AAGAA-AAAAAAGAAAAGAAGCAAAAA
*
16307 AAGAAAAAAAAAGAAAA-AAGAGAAACAA
1 AAG-AAAAAAAAGAAAAGAAG-CAAA-AA
16335 AAG-AAAAAAAG-AAAGAA-CAAAAA
1 AAGAAAAAAAAGAAAAGAAGCAAAAA
16358 TCAAAAAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
23 2 0.05
24 3 0.07
25 3 0.07
26 13 0.30
27 17 0.39
28 6 0.14
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (26 bp):
AAGAAAAAAAAGAAAAGAAGCAAAAA
Found at i:16348 original size:17 final size:16
Alignment explanation
Indices: 16286--16348 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 16
16276 AATCAAGAAC
*
16286 AAAAAAGAAAAGAAGCA
1 AAAAAAGAAAAAAAG-A
*
16303 AAAGAAGAAAAAAAAAGA
1 AAA-AA-AGAAAAAAAGA
16321 AAAAAGAGAAACAAAAGA
1 AAAAA-AGAAA-AAAAGA
16339 AAAAAAGAAA
1 AAAAAAGAAA
16349 GAACAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 15 0.38
18 17 0.43
19 8 0.20
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAGA
Found at i:16369 original size:26 final size:24
Alignment explanation
Indices: 16286--16371 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 24
16276 AATCAAGAAC
16286 AAAAAAGAAAAGAAGCAAAAGA-AGAAA
1 AAAAAAGAAAA-AA-CAAAA-ACA-AAA
* *
16313 AAAAAAGAAAAAAGAGAAACAAAAGA
1 AAAAAAGAAAAAACAAAAAC-AAA-A
*
16339 AAAAAAGAAAGAACAAAAATCAAAA
1 AAAAAAGAAAAAACAAAAA-CAAAA
16364 AGAAAAAG
1 A-AAAAAG
16372 GGACAAAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
24 1 0.02
25 7 0.14
26 29 0.59
27 12 0.24
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.01
Consensus pattern (24 bp):
AAAAAAGAAAAAACAAAAACAAAA
Found at i:28198 original size:17 final size:16
Alignment explanation
Indices: 28167--28200 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28157 CACGTGAGGA
28167 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
28183 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
28200 T
1 T
28201 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:29213 original size:18 final size:18
Alignment explanation
Indices: 29190--29225 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29180 TCAACATCAA
*
29190 ATATTGGGGCATTTTTTG
1 ATATTGGGGCATTATTTG
29208 ATATTGGGGCATTATTTG
1 ATATTGGGGCATTATTTG
29226 GGGATTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47
Consensus pattern (18 bp):
ATATTGGGGCATTATTTG
Found at i:29868 original size:106 final size:106
Alignment explanation
Indices: 29738--31003 Score: 1926
Period size: 106 Copynumber: 12.0 Consensus size: 106
29728 ATATCGTGCC
* * * * * *
29738 ACTCGAGACAACACAAGTTCAACTTCACGATGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
29803 AATTTCAGAGCCAATTTTAACTTCACAGCGAGGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
29844 ACTCCAGACAAAGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** *
29909 AATTTCAGAGTTAATTTTAACTTCACAGCGAAGGATATT-G
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
29949 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
30014 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
30055 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
30120 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
30161 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
30226 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
30267 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAT-AACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
30331 AATTTCAGAGCCAGTTTCAA-TTCGCAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
30371 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
30436 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
30477 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
30542 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
30583 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAT-AACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
30647 AATTTCAGAGCCAGTTTCAACTTCGCAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
30688 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
30753 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
30794 ACTCCAGACAACGCAAGTTCAACTTCAGGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
30859 AATTTTAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** *** * *
30900 AC-CCAAGACAACACAAGCCCAACTTCACGACGAAGGGGTGGCTGATTGTCAA-CAA-AATTT--
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
* * *
30960 C-A-TTCATAGTCAATTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
31000 ACTC
1 ACTC
31004 GGAACAATGC
Statistics
Matches: 1066, Mismatches: 87, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
99 1 0.00
100 32 0.03
101 2 0.00
102 1 0.00
104 72 0.07
105 254 0.24
106 704 0.66
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:30329 original size:317 final size:317
Alignment explanation
Indices: 29738--31003 Score: 2008
Period size: 317 Copynumber: 4.0 Consensus size: 317
29728 ATATCGTGCC
* * * * *
29738 ACTCGAGACAACACAAGTTCAACTTCACGATGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
29803 AATTTCAGAGCCAATTTTAACTTCACAGCGAGGGATATTGGACTCCAGACAAAGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * * ** *
29868 TCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCCAATTTCAGAGTTAATTTTAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* * * *
29933 ACAGCGAAGGATATT-GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
* *
29997 TCAATAAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
261 TCAAT-AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
30055 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
30120 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
30185 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCATAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
30250 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
196 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
* *
30315 TCAATAACAATTTCCCAATTTCAGAGCCAGTTTCAA-TTCGCAGCGAAGGATATTGG
261 TCAATAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
30371 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
30436 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
30501 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCATAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
30566 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
196 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
* *
30631 TCAATAACAATTTCCCAATTTCAGAGCCAGTTTCAACTTCGCAGCGAAGGATATTGG
261 TCAATAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
30688 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
30753 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * *
30818 TCAGGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* * * ** * ** *
30883 TCAGCGAAGGATCTTGGACCCAAGACAACACAAGCCCAACTTCACGACGAAGGGGTGGCTGATTG
196 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
* * * *
30948 TCAACAA-AATTT--C-A-TTCATAGTCAATTTCAACTTCAC-GACGGAGGATATTGG
261 TCAATAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
31000 ACTC
1 ACTC
31004 GGAACAATGC
Statistics
Matches: 896, Mismatches: 50, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
311 1 0.00
312 35 0.04
313 1 0.00
314 1 0.00
316 315 0.35
317 493 0.55
318 50 0.06
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (317 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
TCAATAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:30951 original size:633 final size:632
Alignment explanation
Indices: 29738--30960 Score: 2016
Period size: 633 Copynumber: 1.9 Consensus size: 632
29728 ATATCGTGCC
* * *
29738 ACTCGAGACAACACAAGTTCAACTTCACGATGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
29803 AATTTCAGAGCCAATTTTAACTTCACAGCGAGGGATATTGGACTCCAGACAAAGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAAGCAAGTTCAACT
* * * ** *
29868 TCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCCAATTTCAGAGTTAATTTTAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
29933 ACAGCGAAGGATATTGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
196 ACAGCGAAGGATATTGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGT
* *
29998 CAATAAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGA
261 CAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* *
30063 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAATTTCAG
326 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
30128 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
391 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
30193 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCATAGCCAATTTCAACTTCACAGCGAA
456 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
* ** * *
30258 GGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAAC
521 GGATATTGGACCCAAGACAACACAAGCCCAACTTCACAACGAAGGGACGGCTGATTGTCAACAA-
30323 AATTTCCCAATTTCAGAGCCAGTTTCAATTCGCAGCGAAGGATATTGG
585 AATTTCCCAATTTCAGAGCCAGTTTCAATTCGCAGCGAAGGATATTGG
* * * *
30371 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
30436 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAAGCAAGTTCAACT
* *
30501 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCATAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
*
30566 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
196 ACAGCGAAGGATATT-GACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTG
* *
30631 TCAAT-AACAATTTCCCAATTTCAGAGCCAGTTTCAACTTCGCAGCGAAGGATATTGGACTCCAG
260 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* *
30695 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCAATTTCA
325 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
*
30760 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAGGAC
390 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* * *
30825 GAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCTCAGCGA
455 GAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
* * **
30890 AGGATCTTGGACCCAAGACAACACAAGCCCAACTTCACGACGAAGGGGTGGCTGATTGTCAACAA
520 AGGATATTGGACCCAAGACAACACAAGCCCAACTTCACAACGAAGGGACGGCTGATTGTCAACAA
30955 AATTTC
585 AATTTC
30961 ATTCATAGTC
Statistics
Matches: 544, Mismatches: 45, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
632 6 0.01
633 488 0.90
634 50 0.09
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (632 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAAGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGT
CAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
GGATATTGGACCCAAGACAACACAAGCCCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA
ATTTCCCAATTTCAGAGCCAGTTTCAATTCGCAGCGAAGGATATTGG
Found at i:31760 original size:37 final size:37
Alignment explanation
Indices: 31702--31798 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
31692 CCTTTTCGTC
*
31702 CTACTAGAATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* * *
31739 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* *
31776 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
31799 GATAGGATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:32358 original size:23 final size:22
Alignment explanation
Indices: 32331--32391 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
32321 ATTCATTTGG
*
32331 TTATTTTTTTAATACTATATTTA
1 TTATTTTTTTAATA-TATATATA
*
32354 TTATTTTTATATATATATATATA
1 TTATTTTTTTA-ATATATATATA
*
32377 CT-TTTTTTTAA-ATAT
1 TTATTTTTTTAATATAT
32392 TTTACTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 4 0.12
21 1 0.03
22 7 0.21
23 18 0.55
24 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTTTTTTAATATATATATA
Found at i:32360 original size:20 final size:19
Alignment explanation
Indices: 32331--32369 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
32321 ATTCATTTGG
*
32331 TTATTTTTTTAATACTATAT
1 TTATTATTTTAATA-TATAT
*
32351 TTATTATTTTTATATATAT
1 TTATTATTTTAATATATAT
32370 ATATATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTATTTTAATATATAT
Found at i:32362 original size:21 final size:20
Alignment explanation
Indices: 32331--32371 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
32321 ATTCATTTGG
32331 TTATTTTTTTA-ATACTATAT
1 TTATTTTTTTATATA-TATAT
32351 TTATTATTTTTATATATATAT
1 TTATT-TTTTTATATATATAT
32372 ATATACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 11 0.58
22 3 0.16
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTTTTTATATATATAT
Found at i:32655 original size:2 final size:2
Alignment explanation
Indices: 32648--32672 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32638 TTTACTCATT
32648 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
32673 TAATATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33142 original size:13 final size:13
Alignment explanation
Indices: 33126--33150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33116 GGGTCAATGG
33126 GTCGGGTCGGGCT
1 GTCGGGTCGGGCT
33139 GTCGGGTCGGGC
1 GTCGGGTCGGGC
33151 CGGTCAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.56, T:0.20
Consensus pattern (13 bp):
GTCGGGTCGGGCT
Found at i:37328 original size:25 final size:25
Alignment explanation
Indices: 37300--37348 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
37290 CCATACTTGG
37300 TTACAAGTCCAAGTATAGAAGTCAC
1 TTACAAGTCCAAGTATAGAAGTCAC
37325 TTACAAGTCCAAGTATAGAAGTCA
1 TTACAAGTCCAAGTATAGAAGTCA
37349 TTTGAGCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (25 bp):
TTACAAGTCCAAGTATAGAAGTCAC
Found at i:42221 original size:32 final size:29
Alignment explanation
Indices: 42155--42252 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 29
42145 AATTGTAAAA
*
42155 GTTTGATAAATTTAATGACTAATTTT-TAATT
1 GTTTGA-AAATTTAATGAC-CATTTTGTAA-T
*
42186 GTTTGACAAAATTTAATGACCGTTTTGTAACT
1 GTTTG--AAAATTTAATGACCATTTTGTAA-T
*
42218 GTTT--AAATTTAATGATCATTTTGTAAT
1 GTTTGAAAATTTAATGACCATTTTGTAAT
42245 GTTTGAAA
1 GTTTGAAA
42253 GTTCATGGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
27 5 0.09
28 20 0.35
29 2 0.04
31 9 0.16
32 20 0.35
33 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (29 bp):
GTTTGAAAATTTAATGACCATTTTGTAAT
Found at i:42558 original size:19 final size:19
Alignment explanation
Indices: 42528--42568 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
42518 AAATATATGA
42528 AAATTCATAATTTACTTTTT
1 AAATTCATAATTT-CTTTTT
*
42548 AAATT-ATAATTTTTTTTT
1 AAATTCATAATTTCTTTTT
42566 AAA
1 AAA
42569 AAAATCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 7 0.35
20 5 0.25
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTCATAATTTCTTTTT
Found at i:47464 original size:15 final size:15
Alignment explanation
Indices: 47444--47476 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
47434 ACAACTCTAT
47444 AATTATATCATGCAA
1 AATTATATCATGCAA
47459 AATTATATCATGCAA
1 AATTATATCATGCAA
47474 AAT
1 AAT
47477 GAAATTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (15 bp):
AATTATATCATGCAA
Done.