Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000420.1 Hibiscus syriacus cultivar Beakdansim tig00000767_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: 127181
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3538 original size:104 final size:103
Alignment explanation
Indices: 3361--3548 Score: 295
Period size: 104 Copynumber: 1.8 Consensus size: 103
3351 TCCTAAGGTC
**
3361 TTATGCTGACACATTGATTCTCTATTTTCCATTTTTAGGATTAGCTTGGTTGAAGGTGATAATGA
1 TTATGCTGACACATTGATTCTCTATTTTCCATTTTTAGGATTAGCTTGGTCCAAGGTGATAATGA
3426 AAACATTTATATCATCTATATATATATTTCCCAAGGCT
66 AAACATTTATATCATCTATATATATATTTCCCAAGGCT
* * * * *
3464 TTATGCTGACACATTGGTTCTCTCTTTTCCCTTTCTTGGGATTAGCTTGGTCCAAGGTGATATTG
1 TTATGCTGACACATTGATTCTCTATTTTCCATTT-TTAGGATTAGCTTGGTCCAAGGTGATAATG
*
3529 AAAGCATTTATATCATCTAT
65 AAAACATTTATATCATCTAT
3549 TTAAATAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
103 31 0.41
104 45 0.59
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (103 bp):
TTATGCTGACACATTGATTCTCTATTTTCCATTTTTAGGATTAGCTTGGTCCAAGGTGATAATGA
AAACATTTATATCATCTATATATATATTTCCCAAGGCT
Found at i:9291 original size:182 final size:182
Alignment explanation
Indices: 8792--10831 Score: 2149
Period size: 182 Copynumber: 11.0 Consensus size: 182
8782 GATATAACAT
* * * * * * *
8792 GGTTCCTTCATGATGAGGAAGTCTGACTATCT-AAGGGTGACATTGCTCATTCGCGTTGAGGAGA
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAA-GATGACACTGCTCCTTCGTGTTGAGGAGA
** * * * * * *
8856 TCATGTCAATTTGATGTTAAAGACGACATTG-TCTGTCCGTGTTGAAGAGATCGGGTTGTTTTCG
65 TCGGGTCAATTTGATGTTGAAGACGACACTGCTC-ATCCGCGATGAAGAGATCGGGTCGTTTTCG
* * * *
8920 ATTATGACGTTCTTCCTTCATGATGAGGAAATCGGGTCAATCAAGAGATAATTTTGGGACAATAC
129 ATTATGACGTTGTTCCTTCGTGATGAGGAAATC--GT--GTC-------AATTTGGGGACAATAC
* * * *
8985 GATTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGATGACACTACTCCTTTGTGTTGAGGAGAT
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
* *
9050 CGGGTCAATTTGATGTTGAAGATGACACTGCTCATCCGCGATGAAGAGATCGAGTCGTTTTCGAT
66 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
* *
9115 TATGATGTTGTTCCTTCGTGATGA-GAAATCATGTCAATTTGGGGGACAATAC
131 TATGACGTTGTTCCTTCGTGATGAGGAAATCGTGTCAATTT-GGGGACAATAC
* * * *
9167 GGTTCATTCGTGATGAGGAAGTTTGATTGTCTGAGGATGACACTGCTCATTCGTGTTGAGGAGAT
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
*
9232 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATTGGGTCGTTTTCGAT
66 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
** * *
9297 TATGACAATGTTCCTTCGTGATGAGAAAATCGGGTCAATTTTGGGGACAATAC
131 TATGACGTTGTTCCTTCGTGATGAGGAAATCGTGTCAA-TTTGGGGACAATAC
* * *
9350 GGTTCCTTTGTGATGAGGAAGT-TGATTGTCTGAAGATGACACTGCTCATTCGTGTTGAAGAGAT
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
* * * * *
9414 CGAGTCAATTTGATGTTGAAGACGACACTGCTCATCCGTGTTGAAGAGATCAGGTCATTTTCGAT
66 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
* * * *
9479 TATGACGTTGTTTCTTCGTGATGAGGAAATTGGGTCAATTTAGGGACAATAC
131 TATGACGTTGTTCCTTCGTGATGAGGAAATCGTGTCAATTTGGGGACAATAC
* * * *
9531 GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATAACATTGCTCATTCGTGTTGAGGAGAT
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
* * * * * **
9596 CGAGTTAATTTGATGTTGAAGACGACATTGCTCATCCGTGTTG-AGAGATCGGGTCGTTTTTTAT
66 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
* * * * * * *
9660 TAAGACGTTCTT--TT-GTAATGAGGAAATTGGGTCAATTTGGGGACAACAT
131 TATGACGTTGTTCCTTCGTGATGAGGAAATCGTGTCAATTTGGGGACAATAC
* * * *
9709 GGTTCCTTCGTGATGAGGAAGTTTAATTGTCTGAAGATGACATTGCTCCTTCGTGTTGAAGAGAT
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
* * * * *
9774 CGGGTGAATTTGATGTTGAAGACGACACTGCTCATCCGTGTTGAAGAGATCGAGTCATTTTCGAT
66 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
* *
9839 TATGACGTTGTTCATTCGTGATGAGGAAATCGAGTCAATTTGGGGACAATAC
131 TATGACGTTGTTCCTTCGTGATGAGGAAATCGTGTCAATTTGGGGACAATAC
* * * * *
9891 GATTTCTTTGTGATGAGGAAGTCTGATTGTCTGAAGATGGCATTGCTCCTTCGTGTTGAGGAGAT
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
* * * * *
9956 GGGGTCAATTAGATGTTGAAGACGACATTGCTCATCCGCGATGAATAGATC-GGTCGTTTACGAT
66 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
* *
10020 TATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAATAGATAATTTGGGGACAATAT
131 TATGACGTTGTTCCTTCGTGATGAGGAAATC--GT--GTC-------AATTTGGGGACAATAC
* * * * * *
10083 GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTAACACTGCTCTTTCGTGATGAGGAGAT
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
** * ** * *
10148 TTGATCGGTTTGATGTTGAAGACGACACTTCTCATCCGCAATGAAGAGATCGGGTCGTTTTCGAT
66 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
* * *
10213 TATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGTACAACAC
131 TATGACGTTGTTCCTTCGTGATGAGGAAATC--GT--GTC-------AATTTGGGGACAATAC
* * * * * * *
10276 GGTTCCTTCGTGACGAGGAAGTCCTGATTGTCTGAGGGTGACATTGCTCTTTCGTGATGAAGAGA
1 GGTTCCTTCGTGATGAGGAAGT-CTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGA
* *** * * * *
10341 TCTGGTGGGTTTGATTTTGAAGATGACACTACTCATCCGCGATGAAGAGATCGGGTCATTTTCGA
65 TCGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGA
* * *
10406 TTATAACGATGTTCCTTCGTGATGAGGAAATCGAGTCAATCAATAGATAATTTGGGGACAATAC
130 TTATGACGTTGTTCCTTCGTGATGAGGAAATC--GT--GTC-------AATTTGGGGACAATAC
* * * * *
10470 GGTTCCTTCGTGATGAGTAAATATGATTGTCTGAAGATGACACTGCTCCTTTGCGTTGAGGAGAT
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
* * * *
10535 CGGGTCAATTTGATGTTGAAGATGACACTGCTCATCCGCGAAGAAGCGATCGAGTCGTTTTCGAT
66 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
* * * *
10600 TATGACGATGTTCCTTCGTGATGAGAAAATCGTGTCGATTTGGGGACAATGC
131 TATGACGTTGTTCCTTCGTGATGAGGAAATCGTGTCAATTTGGGGACAATAC
* * **
10652 GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCCTTCGCATTGAGGAGAT
1 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
* * * * * * *
10717 C-GATCAATTTGATTTTGAAGATGACACTTCTCATCCGTGTTGAAGAGATCAGGTCGTTTTTTAT
66 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCG---TTT-T
** * * *
10781 AAATTATGACGTTGTTCCTTCGTG-TGGAGGAAACCGGGTCAATTTAGGGAC
127 CGATTATGACGTTGTTCCTTCGTGAT-GAGGAAATCGTGTCAATTTGGGGAC
10832 GCTTGGTTAT
Statistics
Matches: 1607, Mismatches: 212, Indels: 64
0.85 0.11 0.03
Matches are distributed among these distances:
178 130 0.08
179 29 0.02
181 153 0.10
182 569 0.35
183 42 0.03
184 7 0.00
185 44 0.03
188 2 0.00
189 2 0.00
190 1 0.00
191 2 0.00
192 116 0.07
193 334 0.21
194 176 0.11
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (182 bp):
GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
TATGACGTTGTTCCTTCGTGATGAGGAAATCGTGTCAATTTGGGGACAATAC
Found at i:9409 original size:25 final size:24
Alignment explanation
Indices: 9380--9462 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 24
9370 GTTGATTGTC
9380 TGAAGATGACACTGCTCATTCGTGT
1 TGAAGA-GACACTGCTCATTCGTGT
*
9405 TGAAGAGATCGA--G-TCAATTTGATGT
1 TGAAGAGA-C-ACTGCTC-ATTCG-TGT
*
9430 TGAAGACGACACTGCTCATCCGTGT
1 TGAAGA-GACACTGCTCATTCGTGT
9455 TGAAGAGA
1 TGAAGAGA
9463 TCAGGTCATT
Statistics
Matches: 47, Mismatches: 3, Indels: 17
0.70 0.04 0.25
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 26 0.55
26 7 0.15
27 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (24 bp):
TGAAGAGACACTGCTCATTCGTGT
Found at i:9847 original size:360 final size:362
Alignment explanation
Indices: 8792--10776 Score: 2160
Period size: 360 Copynumber: 5.3 Consensus size: 362
8782 GATATAACAT
* * * * * *
8792 GGTTCCTTCATGATGAGGAAGTCTGACTATCT-AAGGGTGACATTGCTCATTCGCGTTGAGGAGA
1 GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAA-GATGACATTGCTCATTCGTGTTGAGGAGA
* * * * *
8856 TC-ATGTCAATTTGATGTTAAAGACGACATTG-TCTGTCCGTGTTGAAGAGATCGGGTTGTTTTC
65 TCGA-GTCAATTTGATGTTGAAGACGACATTGCTC-ATCCGCGATGAAGAGATCGGGTCGTTTTC
* *
8919 GATTATGACGTTCTTCCTTCATGATGAGGAAATCGGGTCAATCAAGAGATAATTTTGGGACAATA
128 GATTATGACGTTCTT--TT-GTGATGAGGAAATCGGG----TC-----A-AATTTGGGGACAATA
* * * *
8984 CGATTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGATGACACTACTCCTTTGTGTTGAGGAGA
180 CGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGA
*
9049 TCGGGTCAATTTGATGTTGAAGATGACACTGCTCATCCGCGATGAAGAGATCGAGTCGTTTTCGA
245 TCGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGAGTCGTTTTCGA
* **
9114 TTATGATGTTGTTCCTTCGTGATGA-GAAATCATGTCAATTTGGGGGACAATAC
310 TTATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATTT-GGGGACAATAC
* * * *
9167 GGTTCATTCGTGATGAGGAAGTTTGATTGTCTGAGGATGACACTGCTCATTCGTGTTGAGGAGAT
1 GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCATTCGTGTTGAGGAGAT
* * *
9232 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATTGGGTCGTTTTCGAT
66 CGAGTCAATTTGATGTTGAAGACGACATTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
* * * * *
9297 TATGACAATGTTCCTTCGTGATGAGAAAATCGGGTCAATTTTGGGGACAATACGGTTCCTTTGTG
131 TATGAC---GTTCTTTTGTGATGAGGAAATCGGGTCAAATTTGGGGACAATACGGTTCCTTCGTG
* * *
9362 ATGAGGAAGT-TGATTGTCTGAAGATGACACTGCTCATTCGTGTTGAAGAGATCGAGTCAATTTG
193 ATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGATCGGGTCAATTTG
* * *
9426 ATGTTGAAGACGACACTGCTCATCCGTGTTGAAGAGATC-AGGTCATTTTCGATTATGACGTTGT
258 ATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGA-GTCGTTTTCGATTATGACGTTGT
* * *
9490 TTCTTCGTGATGAGGAAATTGGGTCAATTTAGGGACAATAC
322 TCCTTCGTGATGAGGAAATCGGGTCAATTTGGGGACAATAC
*
9531 GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATAACATTGCTCATTCGTGTTGAGGAGAT
1 GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCATTCGTGTTGAGGAGAT
* * * **
9596 CGAGTTAATTTGATGTTGAAGACGACATTGCTCATCCGTGTTG-AGAGATCGGGTCGTTTTTTAT
66 CGAGTCAATTTGATGTTGAAGACGACATTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
* * * * *
9660 TAAGACGTTCTTTTGTAATGAGGAAATTGGGTC-AATTTGGGGACAACATGGTTCCTTCGTGATG
131 TATGACGTTCTTTTGTGATGAGGAAATCGGGTCAAATTTGGGGACAATACGGTTCCTTCGTGATG
* * * * *
9724 AGGAAGTTTAATTGTCTGAAGATGACATTGCTCCTTCGTGTTGAAGAGATCGGGTGAATTTGATG
196 AGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGATCGGGTCAATTTGATG
* * * *
9789 TTGAAGACGACACTGCTCATCCGTGTTGAAGAGATCGAGTCATTTTCGATTATGACGTTGTTCAT
261 TTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGAGTCGTTTTCGATTATGACGTTGTTCCT
*
9854 TCGTGATGAGGAAATCGAGTCAATTTGGGGACAATAC
326 TCGTGATGAGGAAATCGGGTCAATTTGGGGACAATAC
* * *
9891 GATTTCTTT-GTGATGAGGAAGTCTGATTGTCTGAAGATGGCATTGCTCCTTCGTGTTGAGGAGA
1 G-GTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCATTCGTGTTGAGGAGA
* * * * *
9955 TGGGGTCAATTAGATGTTGAAGACGACATTGCTCATCCGCGATGAATAGATC-GGTCGTTTACGA
65 TCGAGTCAATTTGATGTTGAAGACGACATTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGA
* *
10019 TTATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAATAGATAATTTGGGGACAATATG
130 TTATGACGTTCTT--TT-GTGATGAGGAAATCGGG----TC-----A-AATTTGGGGACAATACG
* * * * * * *
10084 GTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTAACACTGCTCTTTCGTGATGAGGAGATT
182 GTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGATC
* * ** * * *
10149 TGATCGGTTTGATGTTGAAGACGACACTTCTCATCCGCAATGAAGAGATCGGGTCGTTTTCGATT
247 GGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGAGTCGTTTTCGATT
* *
10214 ATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGTACAACAC
312 ATGACGTTGTTCCTTCGTGATGAGGAAATCGGG----TC-------AATTTGGGGACAATAC
* * * * * * *
10276 GGTTCCTTCGTGACGAGGAAGTCCTGATTGTCTGAGGGTGACATTGCTCTTTCGTGATGAAGAGA
1 GGTTCTTTCGTGATGAGGAAGT-CTGATTGTCTGAAGATGACATTGCTCATTCGTGTTGAGGAGA
*** * * * * *
10341 TCTG-GTGGGTTTGATTTTGAAGATGACACTACTCATCCGCGATGAAGAGATCGGGTCATTTTCG
65 TC-GAGTCAATTTGATGTTGAAGACGACATTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCG
* * * *
10405 ATTATAACGATGTTCCTTCGTGATGAGGAAATCGAGTCAATCAATAGATAATTTGGGGACAATAC
129 ATTAT---GACGTTCTTTTGTGATGAGGAAATCG-G---GTC-----A-AATTTGGGGACAATAC
* * * * *
10470 GGTTCCTTCGTGATGAGTAAATATGATTGTCTGAAGATGACACTGCTCCTTTGCGTTGAGGAGAT
181 GGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGAT
* * *
10535 CGGGTCAATTTGATGTTGAAGATGACACTGCTCATCCGCGAAGAAGCGATCGAGTCGTTTTCGAT
246 CGGGTCAATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGAGTCGTTTTCGAT
* * * * *
10600 TATGACGATGTTCCTTCGTGATGAGAAAATCGTGTCGATTTGGGGACAATGC
311 TATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATTTGGGGACAATAC
* **
10652 GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCCTTCGCATTGAGGAGAT
1 GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCATTCGTGTTGAGGAGAT
* * * * *
10717 CGA-TCAATTTGATTTTGAAGATGACACTT-CTCATCCGTGTTGAAGAGATCAGGTCGTTTT
66 CGAGTCAATTTGATGTTGAAGACGACA-TTGCTCATCCGCGATGAAGAGATCGGGTCGTTTT
10777 TTATAAATTA
Statistics
Matches: 1368, Mismatches: 192, Indels: 101
0.82 0.12 0.06
Matches are distributed among these distances:
359 34 0.02
360 280 0.20
361 13 0.01
362 2 0.00
363 39 0.03
364 225 0.16
365 47 0.03
366 1 0.00
367 2 0.00
371 2 0.00
374 203 0.15
375 166 0.12
376 36 0.03
378 7 0.01
383 2 0.00
384 5 0.00
385 27 0.02
386 76 0.06
387 193 0.14
388 2 0.00
390 6 0.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (362 bp):
GGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCATTCGTGTTGAGGAGAT
CGAGTCAATTTGATGTTGAAGACGACATTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAT
TATGACGTTCTTTTGTGATGAGGAAATCGGGTCAAATTTGGGGACAATACGGTTCCTTCGTGATG
AGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGTGTTGAGGAGATCGGGTCAATTTGATG
TTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGAGTCGTTTTCGATTATGACGTTGTTCCT
TCGTGATGAGGAAATCGGGTCAATTTGGGGACAATAC
Found at i:10354 original size:194 final size:193
Alignment explanation
Indices: 9875--10823 Score: 1106
Period size: 193 Copynumber: 5.0 Consensus size: 193
9865 AAATCGAGTC
* * * * *
9875 AATTTGGGGACAATACGATTTCTTTGTGATGAGGAAGTCTGATTGTCTGAAGATGGCATTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCT
* * * * *
9940 TTCGTGTTGAGGAGATGGGGTCAATTAGATGTTGAAGACGACA-TTGCTCATCCGCGATGAATAG
66 TTCGTGATGAGGAGATCGGGTCAATTTGATGTTGAAGATGACACTT-CTCATCCGCGATGAAGAG
*
10004 ATC-GGTCGTTTACGATTATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAATAGAT
130 ATCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAATAGAT
* * * * * *
10067 AATTTGGGGACAATATGGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTAACACTGCTCT
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCT
** * ** * *
10132 TTCGTGATGAGGAGATTTGATCGGTTTGATGTTGAAGACGACACTTCTCATCCGCAATGAAGAGA
66 TTCGTGATGAGGAGATCGGGTCAATTTGATGTTGAAGATGACACTTCTCATCCGCGATGAAGAGA
*
10197 TCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAAGAGAT
131 TCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAATAGAT
* * * * *
10260 AATTTGGGTACAACACGGTTCCTTCGTGACGAGGAAGTCCTGATTGTCTGAGGGTGACATTGCTC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGT-CTGATTGTCTGAAGATGACATTGCTC
* * *** * *
10325 TTTCGTGATGAAGAGATCTGGTGGGTTTGATTTTGAAGATGACACTACTCATCCGCGATGAAGAG
65 TTTCGTGATGAGGAGATCGGGTCAATTTGATGTTGAAGATGACACTTCTCATCCGCGATGAAGAG
* * * *
10390 ATCGGGTCATTTTCGATTATAACGATGTTCCTTCGTGATGAGGAAATCGAGTCAATCAATAGAT
130 ATCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAATAGAT
* * * *
10454 AATTTGGGGACAATACGGTTCCTTCGTGATGAGTAAATATGATTGTCTGAAGATGACACTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCT-C
* * *
10519 TTTGCGT--TGAGGAGATCGGGTCAATTTGATGTTGAAGATGACACTGCTCATCCGCGAAGAAGC
65 TTT-CGTGATGAGGAGATCGGGTCAATTTGATGTTGAAGATGACACTTCTCATCCGCGATGAAGA
* * * *
10582 GATCGAGTCGTTTTCGATTATGACGATGTTCCTTCGTGATGAGAAAATC--GT--GTC----G--
129 GATCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAATAGAT
* * *
10637 -ATTTGGGGACAATGCGGTTCTTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCT
* * * * *
10701 TTCG-CATTGAGGAGATC-GATCAATTTGATTTTGAAGATGACACTTCTCATCCGTGTTGAAGAG
66 TTCGTGA-TGAGGAGATCGGGTCAATTTGATGTTGAAGATGACACTTCTCATCCGCGATGAAGAG
* ** *
10764 ATCAGGTCGTTTTTTATAAATTATGACGTTGTTCCTTCGTG-TGGAGGAAACCGGGTCAAT
130 ATCGGGTCG---TTT-TCGATTATGACGTTGTTCCTTCGTGAT-GAGGAAATCGGGTCAAT
10824 TTAGGGACGC
Statistics
Matches: 653, Mismatches: 87, Indels: 37
0.84 0.11 0.05
Matches are distributed among these distances:
180 2 0.00
181 49 0.08
182 66 0.10
184 4 0.01
185 30 0.05
187 2 0.00
189 3 0.00
191 2 0.00
192 109 0.17
193 206 0.32
194 177 0.27
195 3 0.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (193 bp):
AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAAGATGACATTGCTCT
TTCGTGATGAGGAGATCGGGTCAATTTGATGTTGAAGATGACACTTCTCATCCGCGATGAAGAGA
TCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAATAGAT
Found at i:11558 original size:85 final size:83
Alignment explanation
Indices: 11252--11618 Score: 272
Period size: 85 Copynumber: 4.3 Consensus size: 83
11242 TCGACATATC
* * * * * * *
11252 CTTGAGCTGAATGTAATCGAACTCGAAGGTTTGTGTTGACAGATAGCTCTTCTAGCTTTGAGCTA
1 CTTGAGCTGAATGTAATCGAACTCGAAAGTTTGTATTAACAAATAACCCTTCTAGCTTTGAGTTA
* *
11317 TGCTGTGAATTTGGCTGT
66 TGCTGTGAATTTAGATGT
* * * * *
11335 ACTTGAGCTGAATGAAATCGAACTCGAAGGTCTTTTATTAACAAATAACCC-TCATCGCCTTGAG
1 -CTTGAGCTGAATGTAATCGAACTCGAAAGT-TTGTATTAACAAATAACCCTTC-TAGCTTTGAG
* * * *
11399 TTATGTTGTAAATTTGACATAT
63 TTATGCTGTGAATTT-AGATGT
* * * * * ** *
11421 CCTTAAGCTGAATGTAATCGAACTC-AAAGGTTTGTGTTGATAGATAGTCCTTCTAGCTTTAAGT
1 -CTTGAGCTGAATGTAATCGAACTCGAAA-GTTTGTATTAACAAATAACCCTTCTAGCTTTGAGT
11485 TATGCTGTGAATTTAGATGT
64 TATGCTGTGAATTTAGATGT
* * * * * *
11505 CTTTGAGCTGAATGGAATCAAACTCGAAAGTCTTTTATTAACAAATAACCCTTCTCGCCTTGAGC
1 C-TTGAGCTGAATGTAATCGAACTCGAAAGT-TTGTATTAACAAATAACCCTTCTAGCTTTGAGT
* * * *
11570 TATACTATAAATTT-GATAT
64 TATGCTGTGAATTTAGATGT
* *
11589 GCATTTGAGCTGAGTGTAATCGATCTCGAA
1 -C--TTGAGCTGAATGTAATCGAACTCGAA
11619 GGTCTTTAGT
Statistics
Matches: 217, Mismatches: 56, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
83 1 0.00
84 61 0.28
85 104 0.48
86 51 0.24
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (83 bp):
CTTGAGCTGAATGTAATCGAACTCGAAAGTTTGTATTAACAAATAACCCTTCTAGCTTTGAGTTA
TGCTGTGAATTTAGATGT
Found at i:11681 original size:170 final size:165
Alignment explanation
Indices: 11253--11988 Score: 614
Period size: 170 Copynumber: 4.4 Consensus size: 165
11243 CGACATATCC
* * * * * * *
11253 TTGAGCTGAATGTAATCGAACTCGAAGGT-TTGTGTTGACAGATAGCTCTTCTAGCTTTGAGCTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTAGCCTTAAGTTA
** * * * *
11317 TGCTGTGAAT-TTGGCTGTACTTGAGCTGAATGAAATCGAACTCGAAGGTCTTTTATTAACAAAT
65 TGCTGCAAATGATGGC-CT--TTGAGCTGAATGTAATCGAACTCGAAAGTC-TTTATTAACAAAT
*
11381 AACCC-TCATCGCCTTGAGTTATGTTGTAAATTTGACATAT-CC-
126 AACCCTTC-TCGCCTTGAGCTATGTTGTAAA--TG--ATATGCCT
* * * * * ** *
11423 TTAAGCTGAATGTAATCGAACTCAAAGGT-TTGTGTTGATAGATAGTCCTTCTAGCTTTAAGTTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTAGCCTTAAGTTA
* * * * *
11487 TGCTGTGAATTTAGAT-GTCTTTGAGCTGAATGGAATCAAACTCGAAAGTCTTTTATTAACAAAT
65 TGCTG-CAA-AT-GATGGCCTTTGAGCTGAATGTAATCGAACTCGAAAGTC-TTTATTAACAAAT
** * *
11551 AACCCTTCTCGCCTTGAGCTATACTATAAATTTGATATGCAT
126 AACCCTTCTCGCCTTGAGCTATGTTGTAAA--TGATATGCCT
* * * * * *
11593 TTGAGCTGAGTGTAATCGATCTCGAAGGTCTTTAGTTGGCAGATAGCCCTTCTCGCCTTAAGCTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTAAGTTA
* * * * * * *
11658 TACTGCAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACCCGAAGGTCTTTGTTGACAGATAAC
65 TGCTGCAAATGATG-GCCTTTGAGCTGAATGTAATCGAACTCGAAAGTCTTTATTAACAAATAA-
* * *
11723 CCCTT-TAGCCTTGAGCTATGTTGTAAACGATGTGCCT
128 CCCTTCTCGCCTTGAGCTATGTTGTAAATGATATGCCT
* *
11760 TTGAGCTTAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTAT
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTAT
** * * ** *
11825 GCTATAAATGATGTGCCTTTGAGCT-AAGTGTAATCGAACTCG-AAGGC-CT-TTGGCAGATAAC
66 GCTGCAAATGATG-GCCTTTGAGCTGAA-TGTAATCGAACTCGAAAGTCTTTATTAACAAATAAC
* * *
11886 CCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
129 CCTTCTCGCCTTGAGCTATGTTGTAAATGATATGCCT
* * * *
11923 TTGAACTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGTTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTAAGTTA
11988 T
65 T
11989 CATCCGTCGT
Statistics
Matches: 476, Mismatches: 75, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
162 5 0.01
163 67 0.14
164 34 0.07
165 4 0.01
166 61 0.13
167 37 0.08
168 7 0.01
169 32 0.07
170 191 0.40
171 34 0.07
172 2 0.00
173 1 0.00
174 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (165 bp):
TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTAT
GCTGCAAATGATGGCCTTTGAGCTGAATGTAATCGAACTCGAAAGTCTTTATTAACAAATAACCC
TTCTCGCCTTGAGCTATGTTGTAAATGATATGCCT
Found at i:11772 original size:83 final size:83
Alignment explanation
Indices: 11253--11984 Score: 599
Period size: 83 Copynumber: 8.7 Consensus size: 83
11243 CGACATATCC
* * * *
11253 TTGAGCTGAATGTAATCGAACTCGAAGGT-TTGTGTTGACAGATAGCTCTTCTAGCTTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTAGCCTTGAGCTA
** * *
11317 TGCTGTGAAT-TTG-GCTGT
65 TGCTGCAAATGATGTGC-CT
* * * * * *
11335 ACTTGAGCTGAATGAAATCGAACTCGAAGGTCTTTTATTAACAAATAACCC-TCATCGCCTTGAG
1 --TTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTC-TAGCCTTGAG
* * * *
11399 TTATGTTGTAAATTTGACATAT-CC-
62 CTATGCTGCAAA--TG--ATGTGCCT
* * * * ** * * *
11423 TTAAGCTGAATGTAATCGAACTCAAAGGT-TTGTGTTGATAGATAGTCCTTCTAGCTTTAAGTTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTAGCCTTGAGCTA
* *
11487 TGCTGTGAATTTAGATGT--CT
65 TGCTG-CAA-AT-GATGTGCCT
* * * * * * * *
11507 TTGAGCTGAATGGAATCAAACTCGAAAGTCTTTTATTAACAAATAACCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGCTA
* ** * *
11572 TACTATAAATTTGATATGCAT
65 TGCTGCAAA--TGATGTGCCT
* * * * *
11593 TTGAGCTGAGTGTAATCGATCTCGAAGGTCTTTAGTTGGCAGATAGCCCTTCTCGCCTTAAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTGAGCTA
* *
11658 TACTGCAAATGATGCGCCT
65 TGCTGCAAATGATGTGCCT
*
11677 TTGAGCTGAGTGTAATCGAACCCGAAGGTCTTTGTTGACAGATAACCCCTT-TAGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAA-CCCTTCTAGCCTTGAGCTA
* * *
11741 TGTTGTAAACGATGTGCCT
65 TGCTGCAAATGATGTGCCT
* * *
11760 TTGAGCTTAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTAT
**
11825 GCTATAAATGATGTGCCT
66 GCTGCAAATGATGTGCCT
* * *
11843 TTGAGCTAAGTGTAATCGAACTCGAAGGCCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTAT
*
11905 GTTGCAAATGATGTGCCT
66 GCTGCAAATGATGTGCCT
* * * *
11923 TTGAACTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAG
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAG
11985 TTATCATCCG
Statistics
Matches: 522, Mismatches: 98, Indels: 56
0.77 0.14 0.08
Matches are distributed among these distances:
80 66 0.13
81 5 0.01
82 5 0.01
83 138 0.26
84 130 0.25
85 82 0.16
86 93 0.18
87 1 0.00
90 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (83 bp):
TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTAT
GCTGCAAATGATGTGCCT
Found at i:11916 original size:246 final size:252
Alignment explanation
Indices: 11505--11984 Score: 650
Period size: 246 Copynumber: 1.9 Consensus size: 252
11495 ATTTAGATGT
*
11505 CTTTGAGCTGAATGGAATCAAACTCGAAAGTCTTTTATTAACAAATAACCCTTCTCGCCTTGAGC
1 CTTTGAGCTGAATGGAATCAAACTCGAAAGTCTTTTATTAACAAATAACCCTTCTAGCCTTGAGC
* * *
11570 TATACTATAAATTTGATATGCATTTGAGCTGAGTGTAATCGATCTCGAAGGTCTTTAGTTGGCAG
66 TATACTATAAA-TTGATATGCATTTGAGCTAAGTGTAATCGAACTCGAAGGTCTCTA-TTGGCAG
* * *
11635 ATAGCCCTTCTCGCCTTAAGCTATACTGCAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACCC
129 ATAACCCTTCTCGCCTTAAGCTATACTGCAAATGATGCGCCTTTGAACTGAGTGTAATCAAACCC
11700 GAAGGTC-TTTGTTGACAGATAACCCCTT-TAGCCTTGAGCTATGTTGTAAACGATGTGC
194 GAAGGTCTTTTGTTGACAGATAA-CCCTTCTAGCCTTGAGCTATGTTGTAAACGATGTGC
* * * * * * * *
11758 CTTTGAGCTTAGTGTAATCAAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGT
1 CTTTGAGCTGAATGGAATCAAACTCGAAAGTCTTTTATTAACAAATAACCCTTCTAGCCTTGAGC
* * *
11822 TATGCTATAAA-TGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAGG-C-CT-TTGGCAGAT
66 TATACTATAAATTGATATGCATTTGAGCTAAGTGTAATCGAACTCGAAGGTCTCTATTGGCAGAT
* * ** * *
11883 AACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAACTGAGTGTAATCAAACTCGA
131 AACCCTTCTCGCCTTAAGCTATACTGCAAATGATGCGCCTTTGAACTGAGTGTAATCAAACCCGA
* *
11948 AGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAG
196 AGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAG
11985 TTATCATCCG
Statistics
Matches: 199, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
246 75 0.38
247 23 0.12
248 1 0.01
249 1 0.01
250 34 0.17
252 37 0.19
253 28 0.14
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (252 bp):
CTTTGAGCTGAATGGAATCAAACTCGAAAGTCTTTTATTAACAAATAACCCTTCTAGCCTTGAGC
TATACTATAAATTGATATGCATTTGAGCTAAGTGTAATCGAACTCGAAGGTCTCTATTGGCAGAT
AACCCTTCTCGCCTTAAGCTATACTGCAAATGATGCGCCTTTGAACTGAGTGTAATCAAACCCGA
AGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGTTGTAAACGATGTGC
Found at i:12389 original size:32 final size:32
Alignment explanation
Indices: 12282--12397 Score: 153
Period size: 32 Copynumber: 3.6 Consensus size: 32
12272 CACGCATCAA
* *
12282 GATGTTGAATC-CCTAAAGATGTCCCAATATTC
1 GATGTTGAATCTCC-AAAGATGCCCCAATATTT
* *
12314 GATGTTGAATCTCCAAATATGCCCTAATATTT
1 GATGTTGAATCTCCAAAGATGCCCCAATATTT
* *
12346 GATGTTGAATCTTCAAAGATGCCCCAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAATATTT
*
12378 GATGTTGAATCTTCAAAGAT
1 GATGTTGAATCTCCAAAGAT
12398 ACCCTCTATT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
32 73 0.97
33 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAATATTT
Found at i:13454 original size:20 final size:20
Alignment explanation
Indices: 13429--13466 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13419 TCTTGTTTTC
13429 TTTTTCTTTGTTTCTTTTGA
1 TTTTTCTTTGTTTCTTTTGA
13449 TTTTTCTTTGTTTCTTTT
1 TTTTTCTTTGTTTCTTTT
13467 TTCTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTGTTTCTTTTGA
Found at i:13468 original size:35 final size:34
Alignment explanation
Indices: 13418--13503 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
13408 TCATTCATGG
*
13418 TTCTTGTTTTC-TTTTTCTTTGTTTCT-TTTGA-TTT
1 TTCTT-TTTTCTTTTTTCTTT-TTTCTATAT-ATTTT
13452 TTCTTTGTTTCTTTTTTCTTTTTTCTGATATATTTT
1 TTCTTT-TTTCTTTTTTCTTTTTTCT-ATATATTTT
13488 TTCTTTTTTCTTTTTT
1 TTCTTTTTTCTTTTTT
13504 GTTATTCTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
33 1 0.02
34 14 0.30
35 20 0.43
36 11 0.24
ACGTcount: A:0.05, C:0.12, G:0.06, T:0.78
Consensus pattern (34 bp):
TTCTTTTTTCTTTTTTCTTTTTTCTATATATTTT
Found at i:13473 original size:20 final size:20
Alignment explanation
Indices: 13418--13473 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
13408 TCATTCATGG
13418 TTCTTGTTTTCTTTTTCTTTGT
1 TTCTT-TTTTC-TTTTCTTTGT
*
13440 TTCTTTTGAT-TTTTCTTTGT
1 TTCTTTT-TTCTTTTCTTTGT
13460 TTCTTTTTTCTTTT
1 TTCTTTTTTCTTTT
13474 TTCTGATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 21 0.70
21 2 0.07
22 6 0.20
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (20 bp):
TTCTTTTTTCTTTTCTTTGT
Found at i:13501 original size:6 final size:7
Alignment explanation
Indices: 13418--13503 Score: 70
Period size: 7 Copynumber: 12.3 Consensus size: 7
13408 TCATTCATGG
13418 TTCTTGTT
1 TTCTT-TT
13426 TTC-TTT
1 TTCTTTT
13432 TTCTTTGT
1 TTCTTT-T
13440 TTC--TT
1 TTCTTTT
**
13445 TTGATTT
1 TTCTTTT
13452 TTCTTTGT
1 TTCTTT-T
13460 TTCTTTT
1 TTCTTTT
13467 TTCTTTT
1 TTCTTTT
**
13474 TTCTGAT
1 TTCTTTT
* *
13481 ATATTTT
1 TTCTTTT
13488 TTCTTTT
1 TTCTTTT
13495 TTCTTTT
1 TTCTTTT
13502 TT
1 TT
13504 GTTATTCTCT
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
5 3 0.05
6 6 0.10
7 39 0.63
8 14 0.23
ACGTcount: A:0.05, C:0.12, G:0.06, T:0.78
Consensus pattern (7 bp):
TTCTTTT
Found at i:24235 original size:32 final size:32
Alignment explanation
Indices: 24199--24268 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
24189 CTCCGGCAAA
*
24199 CGACGACCTCCTTCCCGGCGACCTTGTTATTC
1 CGACGACCTCCTTCCCGGCAACCTTGTTATTC
24231 CGACGACCTCCTTCCCGGCAACCTTGTTATTC
1 CGACGACCTCCTTCCCGGCAACCTTGTTATTC
24263 CGACGA
1 CGACGA
24269 GCTCACCGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.16, C:0.40, G:0.19, T:0.26
Consensus pattern (32 bp):
CGACGACCTCCTTCCCGGCAACCTTGTTATTC
Found at i:24282 original size:29 final size:31
Alignment explanation
Indices: 24199--24282 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
24189 CTCCGGCAAA
* * *
24199 CGACGACCTCCTTCCCGGCGACCTTGTTATTC
1 CGACGACCTCC-TACCGACAACCTTGTTATTC
* *
24231 CGACGACCTCCTTCCCGGCAACCTTGTTATTC
1 CGACGACCTCC-TACCGACAACCTTGTTATTC
*
24263 CGACGAGCT-C-ACCGACAACC
1 CGACGACCTCCTACCGACAACC
24283 AGGTAAACCG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
29 8 0.17
31 1 0.02
32 39 0.81
ACGTcount: A:0.18, C:0.42, G:0.18, T:0.23
Consensus pattern (31 bp):
CGACGACCTCCTACCGACAACCTTGTTATTC
Found at i:32572 original size:22 final size:22
Alignment explanation
Indices: 32541--32586 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
32531 TAATTAATTT
* *
32541 TATTTTTATATTATAAAATAAA
1 TATTTATATAGTATAAAATAAA
*
32563 TATTTATATAGTATTAAATAAA
1 TATTTATATAGTATAAAATAAA
32585 TA
1 TA
32587 CAATGACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTTATATAGTATAAAATAAA
Found at i:36828 original size:21 final size:21
Alignment explanation
Indices: 36815--36863 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
36805 AAGGTTTTCC
36815 CTTGATGCAGCAAGGATGTCA
1 CTTGATGCAGCAAGGATGTCA
*
36836 TTTGATGCAGCAAGGATGTCA
1 CTTGATGCAGCAAGGATGTCA
*
36857 TTTGATG
1 CTTGATG
36864 ATCCGAGGTA
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:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (21 bp):
CTTGATGCAGCAAGGATGTCA
Found at i:45676 original size:15 final size:15
Alignment explanation
Indices: 45656--45686 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45646 CAACAGATAA
45656 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
45671 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
45686 A
1 A
45687 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:53935 original size:2 final size:2
Alignment explanation
Indices: 53930--53965 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
53920 GTAATAGGAT
53930 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
53966 GTACGACGTG
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):
TA
Found at i:54489 original size:33 final size:33
Alignment explanation
Indices: 54426--54489 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
54416 AAATTTTATT
* *
54426 AATAAAAATATTAATATTGATATATTTTATTGA
1 AATAAAAATATTAAAATTGATATATATTATTGA
54459 AATAAAAATATTATAAATT-ATAT-TAATTATT
1 AATAAAAATATTA-AAATTGATATAT-ATTATT
54490 TATTAATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 22 0.81
34 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (33 bp):
AATAAAAATATTAAAATTGATATATATTATTGA
Found at i:54562 original size:23 final size:23
Alignment explanation
Indices: 54513--54563 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
54503 GTGTTATATT
**
54513 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
54536 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
54559 ATATT
1 ATATT
54564 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:54668 original size:8 final size:8
Alignment explanation
Indices: 54657--54731 Score: 59
Period size: 8 Copynumber: 9.6 Consensus size: 8
54647 TAATATCTTA
54657 TATTATAT
1 TATTATAT
*
54665 TATTATAA
1 TATTATAT
54673 TA-TA-AT
1 TATTATAT
*
54679 TGATTATTT
1 T-ATTATAT
*
54688 TATTATAA
1 TATTATAT
54696 TATTA-A-
1 TATTATAT
* *
54702 AATTATAA
1 TATTATAT
54710 TATTATAT
1 TATTATAT
54718 TATTATAAT
1 TATTAT-AT
54727 TATTA
1 TATTA
54732 ATAAATATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
6 6 0.11
7 5 0.09
8 33 0.62
9 9 0.17
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (8 bp):
TATTATAT
Found at i:54670 original size:23 final size:22
Alignment explanation
Indices: 54643--54729 Score: 70
Period size: 23 Copynumber: 3.9 Consensus size: 22
54633 TTAAAATAAA
*
54643 ATTATAATATCTTATATTATATT
1 ATTATAATAT-TTAAATTATATT
* *
54666 ATTATAATATAATT-GATTATTTT
1 ATTATAATAT--TTAAATTATATT
* *
54689 ATTATAATATTAAAATTATAAT
1 ATTATAATATTTAAATTATATT
*
54711 ATTATATTA-TTATAATTAT
1 ATTATAATATTTA-AATTAT
54730 TAATAAATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
21 3 0.06
22 20 0.38
23 27 0.52
24 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (22 bp):
ATTATAATATTTAAATTATATT
Found at i:54713 original size:22 final size:23
Alignment explanation
Indices: 54688--54734 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
54678 TTGATTATTT
54688 TATTATAATATTAAAATTA-TAA
1 TATTATAATATTAAAATTATTAA
* *
54710 TATTATATTATTATAATTATTAA
1 TATTATAATATTAAAATTATTAA
54733 TA
1 TA
54735 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTATAATATTAAAATTATTAA
Found at i:54739 original size:22 final size:22
Alignment explanation
Indices: 54696--54766 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 22
54686 TTTATTATAA
*
54696 TATTAAAATTATAATATTATAT
1 TATTAAAATTATAATATAATAT
*
54718 TATTATAATTATTAATA-AATAT
1 TATTAAAATTA-TAATATAATAT
* *
54740 ATTTTAAATATTGTAATAATTAATAT
1 -TATTAAA-ATTATAAT-A-TAATAT
54766 T
1 T
54767 TTGATTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
22 14 0.37
23 14 0.37
24 4 0.11
25 1 0.03
26 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
TATTAAAATTATAATATAATAT
Found at i:54757 original size:60 final size:60
Alignment explanation
Indices: 54615--54762 Score: 141
Period size: 60 Copynumber: 2.5 Consensus size: 60
54605 TAAATATTAA
54615 ATAATTTATTAT-ATATTATTAA-AA-TAAAATTATAATATCTTATATTATATTATTATAAT
1 ATAA-TTATTATAATATTA-TAATAATTAAAATTATAATATCTTATATTATATTATTATAAT
**
54674 ATAATTGATTATTTTATTATAAT-ATTAAAATTATAATAT-TATATTATTATAATTATTAATAA-
1 ATAATT-ATTATAATATTATAATAATTAAAATTATAATATCT-TA-TATTAT-ATTATT-ATAAT
*
54736 ATATATT-TTA-AATATTGTAATAATTAA
1 ATA-ATTATTATAATATTATAATAATTAA
54763 TATTTTGATT
Statistics
Matches: 75, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
58 2 0.03
59 14 0.19
60 29 0.39
61 14 0.19
62 9 0.12
63 7 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (60 bp):
ATAATTATTATAATATTATAATAATTAAAATTATAATATCTTATATTATATTATTATAAT
Found at i:54764 original size:53 final size:53
Alignment explanation
Indices: 54656--54805 Score: 127
Period size: 53 Copynumber: 2.9 Consensus size: 53
54646 ATAATATCTT
* * * *
54656 ATATTATATTATTATAATATAATTGATTATTTTATTATAATATTAAAATTATA
1 ATATTATATTATTATAATATAATTAAATATATTATTATAATATTAAAATAATA
**
54709 ATATTATATTATTATAATTATTAA-TAAATATATT-TTA-AATATTGTAATAATTA
1 ATATTATATTATTATAA-TA-TAATTAAATATATTATTATAATATTAAAATAA-TA
* *
54762 ATATT-T-TGATTAAAATGAT-ATTAAA-ATATT-TTATTAATATTAAA
1 ATATTATATTATTATAAT-ATAATTAAATATATTATTA-TAATATTAAA
54806 TTCATAAAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 16
0.75 0.09 0.15
Matches are distributed among these distances:
49 9 0.11
50 6 0.08
51 15 0.19
52 11 0.14
53 27 0.34
54 9 0.11
55 3 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (53 bp):
ATATTATATTATTATAATATAATTAAATATATTATTATAATATTAAAATAATA
Found at i:54987 original size:42 final size:42
Alignment explanation
Indices: 54927--55019 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
54917 TTCATTCAAC
*
54927 CAAACACTGGAAACCA-TTTTCTGAAAAACGAATTACGTGAAA
1 CAAACACTGGAAAACATTTTTC-GAAAAACGAATTACGTGAAA
* *
54969 TAAACAC-GAGAAAACATTTTTCGAAAAACGAATTACTTGAAA
1 CAAACACTG-GAAAACATTTTTCGAAAAACGAATTACGTGAAA
55011 CAAACACTG
1 CAAACACTG
55020 AATTTCAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 1 0.02
42 37 0.84
43 6 0.14
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (42 bp):
CAAACACTGGAAAACATTTTTCGAAAAACGAATTACGTGAAA
Found at i:58668 original size:24 final size:24
Alignment explanation
Indices: 58641--58717 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
58631 TAACTTTCAC
58641 AACTTAGTTTACCTGTAAATGGTA
1 AACTTAGTTTACCTGTAAATGGTA
* ****
58665 AACTTAGTTTACCTTTCTATAAAAAAA
1 AACTTAGTTTACC--TGTA-AATGGTA
58692 AACTTAGTTTACCTGTAAATGGTA
1 AACTTAGTTTACCTGTAAATGGTA
58716 AA
1 AA
58718 GTATTTCATG
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
24 18 0.45
25 3 0.08
26 3 0.08
27 16 0.40
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (24 bp):
AACTTAGTTTACCTGTAAATGGTA
Found at i:60992 original size:2 final size:2
Alignment explanation
Indices: 60985--61018 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
60975 CCGATACGTG
60985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
61019 TTACGCATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67659 original size:22 final size:22
Alignment explanation
Indices: 67624--67665 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
67614 AAAGCAGCAG
* *
67624 CTGGGAATGCCATTTACCGCAA
1 CTGGGAACGCCATTAACCGCAA
*
67646 CTGGGAACGTCATTAACCGC
1 CTGGGAACGCCATTAACCGC
67666 CACCATGGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (22 bp):
CTGGGAACGCCATTAACCGCAA
Found at i:72953 original size:43 final size:43
Alignment explanation
Indices: 72889--72977 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
72879 GGTGTTGATG
* * *
72889 TTTAGCGGCGTTTTCCCTACAAACGCCGTAGTAGTTTTTGAGA
1 TTTAGCGGCGTTTTACCTACAAACGCCGTAGAAGGTTTTGAGA
* *
72932 TTTAGCGGCGTTTTACTTACAAACGCCGTAGAAGGTTTTGATA
1 TTTAGCGGCGTTTTACCTACAAACGCCGTAGAAGGTTTTGAGA
72975 TTT
1 TTT
72978 TGTAGCATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TTTAGCGGCGTTTTACCTACAAACGCCGTAGAAGGTTTTGAGA
Found at i:72997 original size:43 final size:43
Alignment explanation
Indices: 72899--72999 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 43
72889 TTTAGCGGCG
* * * *
72899 TTTTCCCTACAAACGCCGTAGTAGTTTTTGAGATTTAGCGGCGT
1 TTTTCCC-ACAAACGCCGTAGAAGGTTTTGAGATTTAGCAGCAT
* ** * * *
72943 TTTACTTACAAACGCCGTAGAAGGTTTTGATATTTTGTAGCAT
1 TTTTCCCACAAACGCCGTAGAAGGTTTTGAGATTTAGCAGCAT
72986 TTTTCCCACAAACG
1 TTTTCCCACAAACG
73000 TCGCAGTAGG
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
43 40 0.91
44 4 0.09
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (43 bp):
TTTTCCCACAAACGCCGTAGAAGGTTTTGAGATTTAGCAGCAT
Found at i:73557 original size:21 final size:21
Alignment explanation
Indices: 73532--73686 Score: 79
Period size: 21 Copynumber: 7.4 Consensus size: 21
73522 CTGTTGATAT
73532 GCTGCTTCTCTTTGTGCTTCC
1 GCTGCTTCTCTTTGTGCTTCC
*
73553 GCTGCTTCTCTTTGAGCTAT-C
1 GCTGCTTCTCTTTGTGCT-TCC
* *
73574 GATGCTTCTCTCTGTG-TTGCC
1 GCTGCTTCTCTTTGTGCTT-CC
** *
73595 ATTGCTTCT-TTCTCTGCTTCC
1 GCTGCTTCTCTT-TGTGCTTCC
* * *
73616 GCTACTGCTC-TGGCTGCTTCC
1 GCTGCTTCTCTTTG-TGCTTCC
* *
73637 GCTGCTGCTC-TGGCTGCTTCC
1 GCTGCTTCTCTTTG-TGCTTCC
* * * *
73658 GCTACTGCTCTCTCTGCTTCC
1 GCTGCTTCTCTTTGTGCTTCC
73679 -CTTGCTTC
1 GC-TGCTTC
73687 ATTTTCTGCT
Statistics
Matches: 104, Mismatches: 21, Indels: 18
0.73 0.15 0.13
Matches are distributed among these distances:
19 1 0.01
20 3 0.03
21 97 0.93
22 3 0.03
ACGTcount: A:0.04, C:0.35, G:0.19, T:0.42
Consensus pattern (21 bp):
GCTGCTTCTCTTTGTGCTTCC
Found at i:73696 original size:42 final size:42
Alignment explanation
Indices: 73596--73697 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
73586 TGTGTTGCCA
*
73596 TTGCTTCTTTCTCTGCTTCCGCTACTGCTCTGGCTGCTTCCGC
1 TTGCTTCTTT-TCTGCTTCCGCTACTGCTCTCGCTGCTTCCGC
* ** *
73639 -TGCTGCTCTGGCTGCTTCCGCTACTGCTCTCTCTGCTTCC-C
1 TTGCTTCT-TTTCTGCTTCCGCTACTGCTCTCGCTGCTTCCGC
73680 TTGCTTCATTTTCTGCTT
1 TTGCTTC-TTTTCTGCTT
73698 TCAAGTTAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.02
42 45 0.94
43 2 0.04
ACGTcount: A:0.03, C:0.36, G:0.18, T:0.43
Consensus pattern (42 bp):
TTGCTTCTTTTCTGCTTCCGCTACTGCTCTCGCTGCTTCCGC
Found at i:79478 original size:27 final size:25
Alignment explanation
Indices: 79436--79512 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 25
79426 TCATAATAAG
*
79436 TTTGTCTCT-TAAAACAATACTTCA
1 TTTGTCTCTAAAAAACAATACTTCA
* *
79460 TTTGTCTCTCAAAATAACACTTCATT-A
1 TTTGTCTCT-AAAA-AACAATAC-TTCA
* *
79487 TTTGTCTCTTAAAAACAACACTTCA
1 TTTGTCTCTAAAAAACAATACTTCA
79512 T
1 T
79513 GCATCCTAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
24 11 0.27
25 7 0.17
26 5 0.12
27 16 0.39
28 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (25 bp):
TTTGTCTCTAAAAAACAATACTTCA
Found at i:79510 original size:28 final size:26
Alignment explanation
Indices: 79436--79512 Score: 95
Period size: 24 Copynumber: 3.0 Consensus size: 26
79426 TCATAATAAG
*
79436 TTTGTCTCTTAAAACAATACTTC--A
1 TTTGTCTCTTAAAACAACACTTCATA
* *
79460 TTTGTCTCTCAAAATAACACTTCATTA
1 TTTGTCTCTTAAAACAACACTTCA-TA
79487 TTTGTCTCTTAAAAACAACACTTCAT
1 TTTGTCTCTT-AAAACAACACTTCAT
79513 GCATCCTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
24 20 0.45
27 11 0.25
28 13 0.30
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (26 bp):
TTTGTCTCTTAAAACAACACTTCATA
Found at i:81620 original size:12 final size:12
Alignment explanation
Indices: 81603--81644 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
81593 TAGGGCCATT
81603 AGTTTTACATCA
1 AGTTTTACATCA
81615 AGTTTTACATCA
1 AGTTTTACATCA
*
81627 AGTTTTACATTA
1 AGTTTTACATCA
81639 AGTTTT
1 AGTTTT
81645 CTTTATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:85347 original size:21 final size:21
Alignment explanation
Indices: 85289--85348 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
85279 GGAGGCAACC
**
85289 CAATTTTTCTTTTTTCAATTT
1 CAATTTTTCTTTTTTTTATTT
* * *
85310 CTATTTTTGTTGTTTTTATTT
1 CAATTTTTCTTTTTTTTATTT
*
85331 CAATTTTTTTTTATTTTT
1 CAATTTTTCTTT-TTTTT
85349 TCCTTGACTT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.73
Consensus pattern (21 bp):
CAATTTTTCTTTTTTTTATTT
Found at i:85575 original size:42 final size:42
Alignment explanation
Indices: 85516--85600 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
85506 TCAACACCAC
85516 TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
1 TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
85558 TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
1 TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
85600 T
1 T
85601 AAATATGCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.36
Consensus pattern (42 bp):
TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
Found at i:87667 original size:12 final size:12
Alignment explanation
Indices: 87650--87691 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
87640 TAGGGCCATT
87650 AGTTTTACATCA
1 AGTTTTACATCA
87662 AGTTTTACATCA
1 AGTTTTACATCA
*
87674 AGTTTTACATTA
1 AGTTTTACATCA
87686 AGTTTT
1 AGTTTT
87692 CTTTATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:91540 original size:25 final size:25
Alignment explanation
Indices: 91512--91562 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
91502 CATTATAAAC
*
91512 AACATATGGTAGCGTTTGTATAACA
1 AACATATGGCAGCGTTTGTATAACA
91537 AACATATGGCAGCGTTTGTATAACA
1 AACATATGGCAGCGTTTGTATAACA
91562 A
1 A
91563 CGCCACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (25 bp):
AACATATGGCAGCGTTTGTATAACA
Found at i:95502 original size:21 final size:21
Alignment explanation
Indices: 95469--95511 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
95459 GAATGTCATA
* *
95469 TCAGTACTATTGATTGACATG
1 TCAGTACCATTGACTGACATG
* *
95490 TCAGTACCGTTGACTGTCATG
1 TCAGTACCATTGACTGACATG
95511 T
1 T
95512 TAATACTGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (21 bp):
TCAGTACCATTGACTGACATG
Found at i:97172 original size:3 final size:3
Alignment explanation
Indices: 97157--97223 Score: 84
Period size: 3 Copynumber: 22.0 Consensus size: 3
97147 CTATTTTAAT
*
97157 TTA TTA CTA TTA TTA TT- TGT- TTA TTA TTA TTAA TTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A TTA TTA TT-A TTA
97203 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
97224 CAAATGGACA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:97181 original size:20 final size:20
Alignment explanation
Indices: 97155--97223 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
97145 TTCTATTTTA
*
97155 ATTTATTACTATTATTATTT
1 ATTTATTATTATTATTATTT
*
97175 GTTTATTATTATTAATTA-TT
1 ATTTATTATTATT-ATTATTT
*
97195 ATTAATTATTATTATTA-TT
1 ATTTATTATTATTATTATTT
97214 A-TTATTATTA
1 ATTTATTATTA
97224 CAAATGGACA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
18 8 0.19
19 7 0.16
20 24 0.56
21 4 0.09
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (20 bp):
ATTTATTATTATTATTATTT
Found at i:120923 original size:88 final size:85
Alignment explanation
Indices: 120822--120987 Score: 219
Period size: 86 Copynumber: 1.9 Consensus size: 85
120812 ATTTCTTTGT
*
120822 TAAAATCATGTGTCTGTCATGTAACATATGTTTTGGC-TTAAGAATTTTGGATGAGAATGAAGAA
1 TAAAATCATGTGTCTGTCATGTAACATA--TTTTGGCATTAA-AATTTTAGATGAGAATGAAGAA
120886 TTCGAGTTGACATGTTTTCCCTGC
63 TTC-AGTTGACATGTTTTCCCTGC
* * * *
120910 TAAAATTCA-GTGTCTGTCATGTAACATATTTTGGCATTTATATTTTAGTTGGGAATGAAGAATT
1 TAAAA-TCATGTGTCTGTCATGTAACATATTTTGGCATTAAAATTTTAGATGAGAATGAAGAATT
*
120974 CCGTTGACATGTTT
65 CAGTTGACATGTTT
120988 GGGTGTTTGA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
85 12 0.17
86 28 0.40
87 3 0.04
88 24 0.34
89 3 0.04
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.40
Consensus pattern (85 bp):
TAAAATCATGTGTCTGTCATGTAACATATTTTGGCATTAAAATTTTAGATGAGAATGAAGAATTC
AGTTGACATGTTTTCCCTGC
Done.