Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004766.1 Hibiscus syriacus cultivar Beakdansim tig00010749_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: 56272
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:8909 original size:27 final size:27
Alignment explanation
Indices: 8867--8929 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
8857 GTATTTCGCT
8867 TGAAAAAAAAATGAAAAAGACAA-AAAA
1 TGAAAAAAAAATGAAAAAGA-AAGAAAA
*
8894 TGAAAAATAAAA-GAAAGAGAAAGAAAA
1 TGAAAAA-AAAATGAAAAAGAAAGAAAA
8921 -GAAAAAAAA
1 TGAAAAAAAA
8930 TAAAAGGAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 3 0.09
26 8 0.24
27 18 0.55
28 4 0.12
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (27 bp):
TGAAAAAAAAATGAAAAAGAAAGAAAA
Found at i:10111 original size:48 final size:48
Alignment explanation
Indices: 10032--10832 Score: 945
Period size: 48 Copynumber: 17.4 Consensus size: 48
10022 CAAGTCTGCC
* * *
10032 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCACTCTTCTCAA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * * *
10080 AGATTTGATATTCCCTTTAGAGTAAGTGGAACAAG----TC-T-GCC-
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
10121 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* ** *
10169 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
10217 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
10265 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG--TC-C--C-CC-
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
10306 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * * *
10354 AGATTTGATATTCCCTTTAGAGTAAGTGGAACAAG----TC-T-GCC-
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
10395 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* ** *
10443 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
10491 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
10539 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG--TC-C--C-CC-
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
*
10580 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCAA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* ** *
10628 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
10676 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * *
10724 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-T-ACC-
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
10765 AGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-TTTTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
10812 TGATTTGATATTCCCTTCAGA
1 AGATCTGATATTCCCTTCAGA
10833 AGAAGCGGAA
Statistics
Matches: 636, Mismatches: 82, Indels: 71
0.81 0.10 0.09
Matches are distributed among these distances:
41 160 0.25
42 9 0.01
43 9 0.01
44 8 0.01
45 8 0.01
46 10 0.02
47 23 0.04
48 409 0.64
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (48 bp):
AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
Found at i:10125 original size:89 final size:89
Alignment explanation
Indices: 9974--10832 Score: 1270
Period size: 89 Copynumber: 9.4 Consensus size: 89
9964 CCAAGATTTT
*
9974 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTCTGCCAGATCTG
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTG
10039 ATATTCCCTTCAGAGTAAGCGGAA
66 ATATTCCCTTCAGAGTAAGCGGAA
* * *
10063 CAGGTCACTCTTCTCAAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTCTGCCAGATCTG
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTG
10128 ATATTCCCTTCAGAGTAAGCGGAA
66 ATATTCCCTTCAGAGTAAGCGGAA
* * *
10152 CAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAAC-AA---GTC-T-GCC-
*
10217 AGATCTGATATTTCCTTCAGAGTAAGCGGAA
59 AGATCTGATATTCCCTTCAGAGTAAGCGGAA
**
10248 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCCCCCAGATCTG
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTG
*
10313 ATATTCCCTTCAGAGTAAGTGGAA
66 ATATTCCCTTCAGAGTAAGCGGAA
*
10337 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTCTGCCAGATCTG
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTG
10402 ATATTCCCTTCAGAGTAAGCGGAA
66 ATATTCCCTTCAGAGTAAGCGGAA
* * *
10426 CAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAAC-AA---GTC-T-GCC-
*
10491 AGATCTGATATTTCCTTCAGAGTAAGCGGAA
59 AGATCTGATATTCCCTTCAGAGTAAGCGGAA
**
10522 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCCCCCAGATCTG
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTG
*
10587 ATATTCCCTTCAGAGTAAGTGGAA
66 ATATTCCCTTCAGAGTAAGCGGAA
* * *
10611 CAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAAC-AA---GTC-T-GCC-
*
10676 AGATCTGATATTTCCTTCAGAGTAAGCGGAA
59 AGATCTGATATTCCCTTCAGAGTAAGCGGAA
*
10707 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACCAGATCTG
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTG
* *
10772 ACATTCCCTTCAGAGTAAGTGGAA
66 ATATTCCCTTCAGAGTAAGCGGAA
* *
10796 CAGGTCTCT-TTTTCCATGATTTGATATTCCCTTCAGA
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGA
10833 AGAAGCGGAA
Statistics
Matches: 707, Mismatches: 42, Indels: 43
0.89 0.05 0.05
Matches are distributed among these distances:
88 26 0.04
89 409 0.58
90 12 0.02
91 1 0.00
92 6 0.01
93 6 0.01
94 2 0.00
95 12 0.02
96 233 0.33
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (89 bp):
CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTG
ATATTCCCTTCAGAGTAAGCGGAA
Found at i:10279 original size:185 final size:185
Alignment explanation
Indices: 9974--10832 Score: 1252
Period size: 185 Copynumber: 4.7 Consensus size: 185
9964 CCAAGATTTT
* * *
9974 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTC-T-GCCAGATC
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCATCTCCAGATC
* *
10037 TGATATTCCCTTCAGAGTAAGCGGAACAGGTCACTCTTCTCAAAGATTTGATATTCCCTTTAGAG
66 TGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAG
* *
10102 TAAGTGGAAC-AA-GTC-T-GCC-AGATCTGATATTCCCTTCAGAGTAAGCGGAA
131 TAAGTGGAACAAATATCTTCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAA
*
10152 CAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATC-A---TCTCC-
* *
10217 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
61 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTT
* * *
10282 CAGAGTAAGTGGAAC-AA-GTC--C-CCCAGATCTGATATTCCCTTCAGAGTAAGTGGAA
126 CAGAGTAAGTGGAACAAATATCTTCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAA
* * *
10337 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTC-T-GCCAGATC
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCATCTCCAGATC
10400 TGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAG
66 TGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAG
*
10465 TAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTTCAGAGTAAGCGGAA
131 TAAGTGGAACAAA--TATCTTCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAA
* *
10522 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTC--CCCCAGATC
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCATCTCCAGATC
*
10585 TGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAG
66 TGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAG
*
10650 TAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTTCAGAGTAAGCGGAA
131 TAAGTGGAACAAA--TATCTTCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAA
* *
10707 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTC-T-ACCAGATC
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCATCTCCAGATC
* * * * *
10770 TGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-TTTTCCATGATTTGATATTCCCTTCAGA
66 TGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGA
10833 AGAAGCGGAA
Statistics
Matches: 636, Mismatches: 27, Indels: 30
0.92 0.04 0.04
Matches are distributed among these distances:
178 129 0.20
179 4 0.01
180 1 0.00
182 2 0.00
183 1 0.00
184 30 0.05
185 469 0.74
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (185 bp):
CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCATCTCCAGATC
TGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAG
TAAGTGGAACAAATATCTTCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAA
Found at i:10463 original size:274 final size:274
Alignment explanation
Indices: 9974--10832 Score: 1446
Period size: 274 Copynumber: 3.1 Consensus size: 274
9964 CCAAGATTTT
* **
9974 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTCTGCCAGATCTG
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCCCCCAGATCTG
* *
10039 ATATTCCCTTCAGAGTAAGCGGAACAGGTCACTCTTCTCAAAGATTTGATATTCCCTTTAGAGTA
66 ATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTTAGAGTA
10104 AGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
131 AGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
10169 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
196 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
10234 CAGAGTAAGCGGAA
261 CAGAGTAAGCGGAA
10248 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCCCCCAGATCTG
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCCCCCAGATCTG
*
10313 ATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTTAGAGTA
66 ATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTTAGAGTA
10378 AGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
131 AGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
10443 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
196 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
10508 CAGAGTAAGCGGAA
261 CAGAGTAAGCGGAA
10522 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCCCCCAGATCTG
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCCCCCAGATCTG
*
10587 ATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTA
66 ATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTTAGAGTA
* * *
10652 AGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTC
131 AGTGGAAC-AA---GTC-T-GCC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTC
* * *
10717 TTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTA------CC-AGATCTGACA
189 TTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATA
* *
10775 TTCCCTTCAGAGTAAGTGGAA
254 TTTCCTTCAGAGTAAGCGGAA
* *
10796 CAGGTCTCT-TTTTCCATGATTTGATATTCCCTTCAGA
1 CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGA
10833 AGAAGCGGAA
Statistics
Matches: 560, Mismatches: 18, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
273 26 0.05
274 441 0.79
275 4 0.01
278 2 0.00
279 1 0.00
280 2 0.00
281 84 0.15
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (274 bp):
CAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCCCCCAGATCTG
ATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTTTAGAGTA
AGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
CAGAGTAAGCGGAA
Found at i:10875 original size:48 final size:47
Alignment explanation
Indices: 9978--10875 Score: 704
Period size: 48 Copynumber: 19.6 Consensus size: 47
9968 GATTTTCAGG
* * *
9978 TCTCTCTTCTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACA-A
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * *
10025 -GTC---TGCC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGG
1 TCTCTTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * * *
10067 TCACTCTTCTCAAAGATTTGATATTCCCTTTAGAGTAAGTGGAACA-A
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * *
10114 -GTC---TGCC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGG
1 TCTCTTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * *
10156 TCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAA
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * * *
10204 TCTATCTTCTCCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGG
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* *
10252 TCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACA-A
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * *
10299 GTC-C-----CCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGG
1 -TCTCTTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * *
10341 TCTCTCTTCTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACA-A
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * *
10388 -GTC---TGCC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGG
1 TCTCTTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * *
10430 TCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAA
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * * *
10478 TCTATCTTCTCCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGG
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* *
10526 TCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACA-A
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * *
10573 GTC-C-----CCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGG
1 -TCTCTTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * *
10615 TCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAA
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * * *
10663 TCTATCTTCTCCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGG
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* *
10711 TCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACA-A
1 TCTCT-TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* * * * * *
10758 -GTC---TACC-AGATCTGACATTCCCTTCAGAGTAAGTGGAACAGG
1 TCTCTTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
* *
10800 TCTCTTTTTCCATGATTTGATATTCCCTTCAGAAG-AAGCGGAACATA
1 TCTCTTTTTCCAAGATTTGATATTCCCTTCAG-AGTAAGCGGAACAGA
* * *
10847 TCTTTTTTTTCCAAGGTTTGGTATTCCCT
1 TC-TCTTTTTCCAAGATTTGATATTCCCT
10876 GTGACAGCGG
Statistics
Matches: 687, Mismatches: 117, Indels: 93
0.77 0.13 0.10
Matches are distributed among these distances:
41 193 0.28
42 9 0.01
43 7 0.01
46 10 0.01
47 33 0.05
48 435 0.63
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (47 bp):
TCTCTTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAGA
Found at i:11119 original size:3 final size:3
Alignment explanation
Indices: 11111--11151 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
11101 CATCTCGTTC
*
11111 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
11152 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:11159 original size:12 final size:12
Alignment explanation
Indices: 11111--11160 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
11101 CATCTCGTTC
*
11111 TTATTATTATTA
1 TTATTATTAATA
*
11123 -TATGTATTATTA
1 TTAT-TATTAATA
11135 TTATTATTAATA
1 TTATTATTAATA
11147 TTATT-TTACATA
1 TTATTATTA-ATA
11159 TT
1 TT
11161 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:11754 original size:105 final size:105
Alignment explanation
Indices: 11572--11891 Score: 622
Period size: 105 Copynumber: 3.0 Consensus size: 105
11562 AACACAGGAG
11572 AGGGGAGGCCATTCGAACCACCAGAGGCAAGCAAAACAGAGGGAAAACAGATTGTAAGGTTTAGT
1 AGGGGAGGCCATTCGAACCACCAGAGGCAAGCAAAACAGAGGGAAAACAGATTGTAAGGTTTAGT
11637 TCTTCAATAGAAAGAGGGGATCTTTCGAAAACAATTTGTA
66 TCTTCAATAGAAAGAGGGGATCTTTCGAAAACAATTTGTA
*
11677 AGGGGAGGCCATTCGAACGACCAGAGGCAAGCAAAACAGAGGGAAAACAGATTGTAAGGTTTAGT
1 AGGGGAGGCCATTCGAACCACCAGAGGCAAGCAAAACAGAGGGAAAACAGATTGTAAGGTTTAGT
11742 TCTTCAATAGAAAGAGGGGATCTTTCGAAAACAATTTGTA
66 TCTTCAATAGAAAGAGGGGATCTTTCGAAAACAATTTGTA
*
11782 AGGGGAGGCCATTCGAACCACCAGAGGCAAGCAAAACAGAGGGAAAACAGATTGTAAGGTTCAGT
1 AGGGGAGGCCATTCGAACCACCAGAGGCAAGCAAAACAGAGGGAAAACAGATTGTAAGGTTTAGT
11847 TCTTCAATAGAAAGAGGGGATCTTTCGAAAACAATTTGTA
66 TCTTCAATAGAAAGAGGGGATCTTTCGAAAACAATTTGTA
11887 AGGGG
1 AGGGG
11892 GGTCATTAGC
Statistics
Matches: 212, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 212 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (105 bp):
AGGGGAGGCCATTCGAACCACCAGAGGCAAGCAAAACAGAGGGAAAACAGATTGTAAGGTTTAGT
TCTTCAATAGAAAGAGGGGATCTTTCGAAAACAATTTGTA
Found at i:14856 original size:2 final size:2
Alignment explanation
Indices: 14849--14883 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14839 TACTGGCATA
14849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14884 AAGAACATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17097 original size:2 final size:2
Alignment explanation
Indices: 17090--17124 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17080 AACTAAAAAT
17090 TA TA TA TA TA 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 TA TA TA TA TA T
17125 TGATACTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25057 original size:14 final size:14
Alignment explanation
Indices: 25038--25068 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25028 TGATTTTTGT
*
25038 ATAAACTTTTAAGC
1 ATAAACTTTTAACC
25052 ATAAACTTTTAACC
1 ATAAACTTTTAACC
25066 ATA
1 ATA
25069 CACTCATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.35
Consensus pattern (14 bp):
ATAAACTTTTAACC
Found at i:26358 original size:27 final size:28
Alignment explanation
Indices: 26328--26439 Score: 85
Period size: 25 Copynumber: 4.2 Consensus size: 28
26318 CAAAATGAAT
* *
26328 AAATGATTATTACATTT-TAAAATTATA
1 AAATAATTATTAAATTTATAAAATTATA
* *
26355 AAATAATTATTAAATTTATTAAATTATT
1 AAATAATTATTAAATTTATAAAATTATA
* * * *
26383 ATAGAATAATT--ATTT-TAATATTATA
1 AAATAATTATTAAATTTATAAAATTATA
* *
26408 AACTAATTATTAAAATTAT---ATTATA
1 AAATAATTATTAAATTTATAAAATTATA
26433 AAATAAT
1 AAATAAT
26440 CAATGAAAAT
Statistics
Matches: 65, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
25 26 0.40
26 4 0.06
27 18 0.28
28 17 0.26
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
AAATAATTATTAAATTTATAAAATTATA
Found at i:26364 original size:11 final size:11
Alignment explanation
Indices: 26348--26439 Score: 64
Period size: 11 Copynumber: 8.3 Consensus size: 11
26338 TACATTTTAA
26348 AATTATAAAAT
1 AATTATAAAAT
*
26359 AATTATTAAAT
1 AATTATAAAAT
*
26370 --TTATTAAAT
1 AATTATAAAAT
* *
26379 TATTATAGAAT
1 AATTATAAAAT
**
26390 AATTATTTTAAT
1 AATTA-TAAAAT
*
26402 -ATTATAAACT
1 AATTATAAAAT
26412 AATTATTAAAATT
1 AATTA-TAAAA-T
26425 ATATTATAAAAT
1 A-ATTATAAAAT
26437 AAT
1 AAT
26440 CAATGAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
9 9 0.14
10 3 0.05
11 31 0.48
12 10 0.16
13 7 0.11
14 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (11 bp):
AATTATAAAAT
Found at i:26373 original size:20 final size:20
Alignment explanation
Indices: 26344--26427 Score: 56
Period size: 20 Copynumber: 4.5 Consensus size: 20
26334 TTATTACATT
26344 TTAAAATTATAAAATAATTA
1 TTAAAATTATAAAATAATTA
* * *
26364 TTAAATTTATTAAATTATTA
1 TTAAAATTATAAAATAATTA
* *
26384 -T-AGA--AT--AATTATT-
1 TTAAAATTATAAAATAATTA
* *
26397 TTAATATTATAAACTAATTA
1 TTAAAATTATAAAATAATTA
26417 TTAAAATTATA
1 TTAAAATTATA
26428 TTATAAAATA
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
14 8 0.17
15 2 0.04
16 2 0.04
17 2 0.04
18 1 0.02
19 6 0.12
20 27 0.56
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (20 bp):
TTAAAATTATAAAATAATTA
Found at i:26823 original size:41 final size:41
Alignment explanation
Indices: 26762--26852 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
26752 TACTGACGTG
*
26762 GATGCCTAATCAAAATGACGTCGTTTTGAAACGACTGTTTT
1 GATGCCTAATCAAAACGACGTCGTTTTGAAACGACTGTTTT
* *
26803 GATGCCTAATTAAAACGACGTTGTTTTGAAACGACTGTTTT
1 GATGCCTAATCAAAACGACGTCGTTTTGAAACGACTGTTTT
26844 GATGCCTAA
1 GATGCCTAA
26853 AAATACAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (41 bp):
GATGCCTAATCAAAACGACGTCGTTTTGAAACGACTGTTTT
Found at i:27059 original size:12 final size:12
Alignment explanation
Indices: 27042--27105 Score: 62
Period size: 12 Copynumber: 5.3 Consensus size: 12
27032 TTAAAACTAA
*
27042 AATAATATGTAT
1 AATAATATATAT
27054 AATAATATATAT
1 AATAATATATAT
27066 -AT-ATATATAT
1 AATAATATATAT
27076 ATATAA-ATAATAT
1 A-ATAATAT-ATAT
*
27089 GATAATATTATAT
1 AATAATA-TATAT
27102 AATA
1 AATA
27106 TTTTTATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
10 8 0.19
11 2 0.05
12 19 0.44
13 13 0.30
14 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
AATAATATATAT
Found at i:27065 original size:2 final size:2
Alignment explanation
Indices: 27046--27116 Score: 55
Period size: 2 Copynumber: 38.0 Consensus size: 2
27036 AACTAAAATA
* *
27046 AT AT GT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AA AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
27085 AT AT GAT A- AT AT -T AT AT A- AT AT TT TT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27117 GATTTATAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
1 6 0.11
2 48 0.86
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27146 original size:25 final size:24
Alignment explanation
Indices: 27055--27147 Score: 63
Period size: 25 Copynumber: 4.0 Consensus size: 24
27045 AATATGTATA
*
27055 ATAATA-TATATATATAT-ATATAT
1 ATAATATTAT-TATATATGATTTAT
* *
27078 ATAAATAATATGATA-AT-A-TTAT
1 AT-AATATTATTATATATGATTTAT
*
27100 ATAATATTTTTATATATGATTTAT
1 ATAATATTATTATATATGATTTAT
*
27124 AATAATAATTATTAT-TATTATTTA
1 -ATAAT-ATTATTATATATGATTTA
27148 AAAAACACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
21 9 0.16
22 7 0.12
23 6 0.11
24 11 0.20
25 16 0.29
26 7 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATAATATTATTATATATGATTTAT
Found at i:27836 original size:17 final size:18
Alignment explanation
Indices: 27814--27854 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
27804 TTTGGTTCAC
*
27814 GGAATATAAGAATACC-G
1 GGAATAAAAGAATACCAG
*
27831 GGAATAAAAGATTACCAG
1 GGAATAAAAGAATACCAG
27849 GGAATA
1 GGAATA
27855 GGATTACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.17
Consensus pattern (18 bp):
GGAATAAAAGAATACCAG
Found at i:29861 original size:24 final size:24
Alignment explanation
Indices: 29829--29877 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29819 TTTTAAAACT
29829 TAACGAAATTTGAGGGTGCGAGAG
1 TAACGAAATTTGAGGGTGCGAGAG
29853 TAACGAAATTTGAGGGTGCGAGAG
1 TAACGAAATTTGAGGGTGCGAGAG
29877 T
1 T
29878 TCTTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.37, T:0.22
Consensus pattern (24 bp):
TAACGAAATTTGAGGGTGCGAGAG
Found at i:33584 original size:92 final size:92
Alignment explanation
Indices: 33427--33622 Score: 293
Period size: 92 Copynumber: 2.1 Consensus size: 92
33417 CAATGAAACT
* *
33427 GGTTTTGTCATATTTTTACATGTTATATTGTTATGTATTGATACATTTTTATAAAGTATTAATAC
1 GGTTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCAATAC
*
33492 TTTTAACATATCCGATAGCTCTTTACC
66 TTTTAACATATCCGATAACTCTTTACC
* * *
33519 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATATATTTTTATAAAGTATCGATAC
1 GGTTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCAATAC
* * * *
33584 TTTTAACATATCTGGTAACTCTTTGCT
66 TTTTAACATATCCGATAACTCTTTACC
*
33611 AGTTTTGTCATA
1 GGTTTTGTCATA
33623 ATGAAACTGG
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (92 bp):
GGTTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCAATAC
TTTTAACATATCCGATAACTCTTTACC
Found at i:33635 original size:112 final size:112
Alignment explanation
Indices: 33519--33802 Score: 433
Period size: 112 Copynumber: 2.5 Consensus size: 112
33509 GCTCTTTACC
*
33519 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATATATTTTTATAAAGTATCGATAC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATAC
* * * *
33584 TTTTAACATATCTGGTAACTCTTTGCTAGTTTTGTCATAATGAAACT
66 TTTTAACATATCCGGTAACTCTTTACCAGTATTGTCATAATGAAACT
** * * *
33631 GGTTTTGTCAGGTTTTTATCTGTTATATTTTTATGTATCGATACATTTTTATAAAATATCGATAC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATAC
* *
33696 TTTTAACATATCCGGTAGCTCTTTACCGGTATTGTCATAATGAAACT
66 TTTTAACATATCCGGTAACTCTTTACCAGTATTGTCATAATGAAACT
* **
33743 GGTTTTGTCATATTTTTACTTGTTATATTGTTATGTATTAATACATTTTTATAAAGTATC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATC
33803 AATAGTTTAT
Statistics
Matches: 152, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
112 152 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (112 bp):
GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATAC
TTTTAACATATCCGGTAACTCTTTACCAGTATTGTCATAATGAAACT
Found at i:33699 original size:204 final size:204
Alignment explanation
Indices: 33367--33734 Score: 569
Period size: 204 Copynumber: 1.8 Consensus size: 204
33357 ACATATACAA
* *
33367 AAAGTATCAATACTTTTAACATATTCGGTAGCTCTTTACCGGTTTTGTCACAATGAAACTGGTTT
1 AAAGTATCAATACTTTTAACATATTCGGTAACTCTTTACCAGTTTTGTCACAATGAAACTGGTTT
* * * *
33432 TGTCATATTTTTACATGTTATATTGTTATGTATTGATACATTTTTATAAAGTATTAATACTTTTA
66 TGTCAGATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAATATCAATACTTTTA
*
33497 ACATATCCGATAGCTCTTTACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATA
131 ACATATCCGATAGCTCTTTACCGGTATTGTCATATTTTTACCTGTTATATTGTTATGTATCGATA
33562 TATTTTTAT
196 TATTTTTAT
* * * *
33571 AAAGTATCGATACTTTTAACATA-TCTGGTAACTCTTTGCTAGTTTTGTCATAATGAAACTGGTT
1 AAAGTATCAATACTTTTAACATATTC-GGTAACTCTTTACCAGTTTTGTCACAATGAAACTGGTT
* * *
33635 TTGTCAGGTTTTTATC-TGTTATATTTTTATGTATCGATACATTTTTATAAAATATCGATACTTT
65 TTGTCAGATTTTTA-CATGTTATATTGTTATGTATCGATACATTTTTATAAAATATCAATACTTT
*
33699 TAACATATCCGGTAGCTCTTTACCGGTATTGTCATA
129 TAACATATCCGATAGCTCTTTACCGGTATTGTCATA
33735 ATGAAACTGG
Statistics
Matches: 147, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
203 2 0.01
204 144 0.98
205 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (204 bp):
AAAGTATCAATACTTTTAACATATTCGGTAACTCTTTACCAGTTTTGTCACAATGAAACTGGTTT
TGTCAGATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAATATCAATACTTTTA
ACATATCCGATAGCTCTTTACCGGTATTGTCATATTTTTACCTGTTATATTGTTATGTATCGATA
TATTTTTAT
Found at i:34044 original size:75 final size:74
Alignment explanation
Indices: 33893--34149 Score: 367
Period size: 74 Copynumber: 3.5 Consensus size: 74
33883 AACATATCCG
* *
33893 GTAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTACCATTTACATTATTAGCAACCTTCA
1 GTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCATTTACATTATTAGCAACCTTAA
33957 AAAAAA-CTA
66 AAAAAATC-A
* *
33966 GTAGGTATTTTAATGTGATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGCAACCTTA
1 GTAGGTATTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCATTTACATTATTAGCAACCTTA
34031 AAAAAAATCA
65 AAAAAAATCA
* * * *
34041 GTAGGTATTTTAACGTAATAGGTAGCGTCTATTATTTTTACCATTTACATTTTTAGCAACCTTAA
1 GTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCATTTACATTATTAGCAACCTTAA
34106 AAAAAATC-
66 AAAAAATCA
* * *
34114 GATAGATATTTTAATGTAATAGGTAACACCTATTTT
1 G-TAGGTATTTTAATGTAATAGGTAGCGCCTATTTT
34150 ATATTTCCTG
Statistics
Matches: 164, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
73 30 0.18
74 67 0.41
75 66 0.40
76 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (74 bp):
GTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCATTTACATTATTAGCAACCTTAA
AAAAAATCA
Found at i:35751 original size:16 final size:16
Alignment explanation
Indices: 35730--35776 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
35720 AAATCTATGA
35730 AGGAATTGAAATCTGT
1 AGGAATTGAAATCTGT
*
35746 AGGAATTGAAATTTGT
1 AGGAATTGAAATCTGT
35762 AGGAATTGAAATCTG
1 AGGAATTGAAATCTG
35777 AAACCTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (16 bp):
AGGAATTGAAATCTGT
Found at i:36360 original size:6 final size:6
Alignment explanation
Indices: 36349--36379 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
36339 GACACGTATT
36349 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
36380 GACGAGACGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:36875 original size:5 final size:5
Alignment explanation
Indices: 36867--36923 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
36857 CCGTCTCGTC
* *
36867 TCGGT TCGGG TCGGG TCGGG TCGGG TCGTG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG
36915 TCGTGG TCG
1 TCG-GG TCG
36924 TGGTAATACG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
5 26 0.54
6 22 0.46
ACGTcount: A:0.00, C:0.19, G:0.51, T:0.30
Consensus pattern (5 bp):
TCGGG
Found at i:36907 original size:6 final size:6
Alignment explanation
Indices: 36875--36927 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
36865 TCTCGGTTCG
36875 GGTCG- GGTCG- GGTCG- GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
36919 GGTCGT GGT
1 GGTCGT GGT
36928 AATACGTGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 20 0.43
6 26 0.57
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:37065 original size:20 final size:20
Alignment explanation
Indices: 37040--37132 Score: 123
Period size: 20 Copynumber: 4.6 Consensus size: 20
37030 ACTGTAGACT
37040 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
37060 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
37080 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
37101 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
37121 ATCGCAATGCGA
1 ATCGCAACGCGA
37133 TTTTCAACTA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 46 0.75
21 15 0.25
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:37106 original size:21 final size:21
Alignment explanation
Indices: 37080--37153 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
37070 GAAATGGAAA
37080 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
37101 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
37121 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
37142 ATCGCAACGCGA
1 ATCGCAACGCGA
37154 ATTTGCGATG
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:37112 original size:41 final size:41
Alignment explanation
Indices: 37060--37222 Score: 202
Period size: 41 Copynumber: 3.8 Consensus size: 41
37050 GAAATGGAAA
37060 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
*
37101 ATCGCAACGCGAAATGGAAAATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
* ***
37142 ATCGCAACGCGAATTTGCGATGATAGAGATCGCGTTGCGA-TTTCAACT
1 ATCGCAACGCGAA-AT--G--GA-A-A-ATCGCAACGCGATTTTCAACT
37190 ATCGCAACGCGAAATGGAAAATCGCAACGCGAT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGAT
37223 CTCTAACTAT
Statistics
Matches: 105, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
40 9 0.09
41 54 0.51
42 2 0.02
43 2 0.02
44 1 0.01
45 1 0.01
46 2 0.02
47 2 0.02
48 22 0.21
49 10 0.10
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:37484 original size:28 final size:28
Alignment explanation
Indices: 37450--37517 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
37440 CCTAAACCCG
*
37450 AACCCGACCCGAATATCACACATAAAAA
1 AACCCGACCCGAATATCAAACATAAAAA
* *
37478 AGCCCGACCCGAATATCAAACTTAAAAA
1 AACCCGACCCGAATATCAAACATAAAAA
*
37506 AACCTGACCCGA
1 AACCCGACCCGA
37518 TCCTGATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.46, C:0.32, G:0.10, T:0.12
Consensus pattern (28 bp):
AACCCGACCCGAATATCAAACATAAAAA
Found at i:41886 original size:5 final size:5
Alignment explanation
Indices: 41844--41888 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
41834 AAATGTGTAC
* * *
41844 AAAAT TAAAT AACAT -AAAT AAAAT ACAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
41889 TTAATATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 3 0.09
5 30 0.91
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:42556 original size:3 final size:3
Alignment explanation
Indices: 42548--42582 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
42538 ATAAATGTTG
42548 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT T
42583 TTAGATCCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:50723 original size:14 final size:15
Alignment explanation
Indices: 50698--50736 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
50688 TAGACGGGCA
*
50698 GATGTGGGGCAGGTG
1 GATGTGGGGCAGGCG
50713 GATGT-GGGCAGGCG
1 GATGTGGGGCAGGCG
*
50727 GATGCGGGGC
1 GATGTGGGGC
50737 GGGTAAGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.13, C:0.13, G:0.59, T:0.15
Consensus pattern (15 bp):
GATGTGGGGCAGGCG
Done.