Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002235.1 Hibiscus syriacus cultivar Beakdansim tig00004545_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: 63377
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:210 original size:2 final size:2
Alignment explanation
Indices: 197--301 Score: 56
Period size: 2 Copynumber: 51.5 Consensus size: 2
187 TAAAACAACA
* * * *
197 AT AT AG AT AT AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* * *
241 -T AT GT AT -T AT AT AA AGT AT AT AT -T AT AT AT AT AA ACT AT AGT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT A-T
*
283 TT AT AT AT AT -T AGT AT AT A
1 AT AT AT AT AT AT A-T AT AT A
302 AAGTATAAAG
Statistics
Matches: 77, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
1 4 0.05
2 66 0.86
3 7 0.09
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:235 original size:20 final size:19
Alignment explanation
Indices: 210--291 Score: 84
Period size: 18 Copynumber: 4.4 Consensus size: 19
200 TAGATATATA
210 TATATATAAACTATATAGTT
1 TATATATAAACT-TATAGTT
*
230 TATATATAAA-TTAT-GTA
1 TATATATAAACTTATAGTT
*
247 T-TATATAAAGTATATA-TT
1 TATATATAAACT-TATAGTT
265 ATATATATAAAC-TATAGTT
1 -TATATATAAACTTATAGTT
284 TATATATA
1 TATATATA
292 TTAGTATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
16 8 0.15
17 4 0.08
18 19 0.36
19 4 0.08
20 18 0.34
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (19 bp):
TATATATAAACTTATAGTT
Found at i:237 original size:36 final size:36
Alignment explanation
Indices: 197--291 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 36
187 TAAAACAACA
*
197 ATATAGATATATATATATATAAACTATATAGTT-TAT
1 ATATAAATATATATATATATAAACTATATA-TTATAT
* *
233 ATATAAAT-TATGTATTATATAAAGTATATATTATAT
1 ATATAAATATATATA-TATATAAACTATATATTATAT
*
269 ATATAAACTATAGTTTATATATA
1 ATATAAA-TATA-TATATATATA
292 TTAGTATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
35 7 0.14
36 31 0.62
37 1 0.02
38 8 0.16
39 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (36 bp):
ATATAAATATATATATATATAAACTATATATTATAT
Found at i:292 original size:20 final size:20
Alignment explanation
Indices: 203--292 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
193 AACAATATAG
203 ATATA-TATATATATAAACT
1 ATATATTATATATATAAACT
222 ATATAGTT-TATATATAAA-T
1 ATATA-TTATATATATAAACT
* *
241 -TAT-GTAT-TATATAAAGT
1 ATATATTATATATATAAACT
258 ATATATTATATATATAAACT
1 ATATATTATATATATAAACT
278 ATAGT-TTATATATAT
1 ATA-TATTATATATAT
293 TAGTATATAA
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
16 9 0.15
17 2 0.03
18 6 0.10
19 9 0.15
20 32 0.53
21 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
ATATATTATATATATAAACT
Found at i:359 original size:10 final size:10
Alignment explanation
Indices: 336--390 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
326 TTTTATTTAT
336 GAACTAT-T-
1 GAACTATATA
344 GAACTATATA
1 GAACTATATA
354 GAACTATATA
1 GAACTATATA
**
364 G-TTTATATA
1 GAACTATATA
*
373 GAATTATATA
1 GAACTATATA
*
383 TAACTATA
1 GAACTATA
391 CAATTTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
8 7 0.18
9 8 0.21
10 24 0.62
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.38
Consensus pattern (10 bp):
GAACTATATA
Found at i:417 original size:32 final size:33
Alignment explanation
Indices: 375--479 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 33
365 TTTATATAGA
375 ATTATATATAACTATACAATT-TATATT-TATAT
1 ATTATATATAACTATA-AATTATATATTGTATAT
* *
407 ATTATGTATAATTATAAATTATATATTGTATA-
1 ATTATATATAACTATAAATTATATATTGTATAT
* *
439 A-TATATAGTTTATTAATAAATTATATAGTT-TATAT
1 ATTATATA--TAACT-ATAAATTATATA-TTGTATAT
474 A-TATAT
1 ATTATAT
480 GTATATATGG
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
31 9 0.15
32 21 0.34
33 8 0.13
34 16 0.26
35 8 0.13
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (33 bp):
ATTATATATAACTATAAATTATATATTGTATAT
Found at i:436 original size:22 final size:25
Alignment explanation
Indices: 401--445 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
391 CAATTTATAT
401 TTATATATTATGTATAAT-TATAAA
1 TTATATATTATGTATAATATATAAA
425 TTATATA-T-TGTATAATATATA
1 TTATATATTATGTATAATATATA
446 GTTTATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
24 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
TTATATATTATGTATAATATATAAA
Found at i:484 original size:6 final size:6
Alignment explanation
Indices: 396--1479 Score: 253
Period size: 6 Copynumber: 186.5 Consensus size: 6
386 CTATACAATT
* * * *
396 TATATT TATATA T-TATG TATA-A T-TATA AAT-TA TATAT- TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
439 -ATATA TAGTTTA T-TA-A TAAAT- TATATA GTTTATA TATATA TGTATA
1 TATATA TA-TATA TATATA TATATA TATATA -TATATA TATATA TATATA
* * * * * * * * *
485 TATGGTT TAT-TT TATATT TATATT TATAT- TTTAT- TTTATA TTTATT
1 TAT-ATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
531 TATATT TATATT TATATT TATATT TAT-TT TATTTA TATTTA TATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * *
578 TATTTA TATTTA TTTATA TATTTA TATTTA TATAT- TATATT TAT-TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * *
624 TTTATA TTTATA TTTATA TTTATA TTTATT TATATT TATATT TATATT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
672 TATATT TATTTA TATTTA TTTATA TTTAT- TTTATA TTTATA TATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
719 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA T-TTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * * *
766 TTTTTT TTTATC TTTATA T-TTTA TAT-TA TATTTA TAT-TT TATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
811 TATTTA TATTTA TATTTC TATTTA TATTTA TATTTA TAT-TA TATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * *
858 TATTTA TAT-TA TATTTA TATTTA TATTTA TAT-TA TAT-TA T-TTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * *
902 TATTTA TATATT TATATT TATTTA TATTTA TATTTA TTTATT TATATT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * *
950 TATTTA TATTTA TAT-TA TATTTA TATTTA TATTTA TAT-TA TATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
996 TATTTA TATTTA TATTTA TAT-TT TATAT- TATATT TATATT TATATT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * *
1042 TATATT TATATT TATATT TATATT TATATT TATAT- TATAT- TATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
1088 TATAT- TTTATT TAT-TT TCTAT- TTTATA T-TATA TTTATA TTTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
1132 TTTATA TTTATA TTTATA TTTATA T-TAT- TTTATA TTTATA TATATT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
1178 TATATT TATATT TAT-TT TATATT TATATT TATATT TATATT TATAT-
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * *
1224 TTTATT TATTTA TTTATA TTTACT- TTTATA TTTATA TTTATA TTTATA
1 TATATA TATATA TATATA TATA-TA TATATA TATATA TATATA TATATA
* * * * * * *
1272 TTTATA T-TATA TTTATA TTTATT TATATT TATATT TATTTA TAT-TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * *
1318 TATTTA TTTATA TTTATA TTTAT- TTTATT TATATT TATATT TATATT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * *
1365 TATATT TATTTA TATTTA TATTTA TATTTA TATA-A CTACATA CTATA-A
1 TATATA TATATA TATATA TATATA TATATA TATATA -TATATA -TATATA
* * * * * *
1413 TTTATA TGTATA TACTATA T-TTTA TACTATT TATATA AACTATA GTTTATA
1 TATATA TATATA TA-TATA TATATA TA-TATA TATATA TA-TATA -TATATA
*
1464 TTTATA CTATATA TAT
1 TATATA -TATATA TAT
1480 GAACTAGTTT
Statistics
Matches: 932, Mismatches: 93, Indels: 106
0.82 0.08 0.09
Matches are distributed among these distances:
4 6 0.01
5 179 0.19
6 706 0.76
7 41 0.04
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (6 bp):
TATATA
Found at i:512 original size:12 final size:12
Alignment explanation
Indices: 490--1397 Score: 1222
Period size: 12 Copynumber: 78.6 Consensus size: 12
480 GTATATATGG
490 TTTAT-TTTATA
1 TTTATATTTATA
501 TTTATATTTATA
1 TTTATATTTATA
513 TTT-TATTT-TA
1 TTTATATTTATA
523 TATT-TATTTATA
1 T-TTATATTTATA
535 TTTATATTTATA
1 TTTATATTTATA
547 TTTATA-TT-TA
1 TTTATATTTATA
557 TTT-TATTTATA
1 TTTATATTTATA
568 TTTATATTTATA
1 TTTATATTTATA
580 TTTATATTTAT-
1 TTTATATTTATA
591 TTATATATTTATA
1 TT-TATATTTATA
604 TTTATATATTATA
1 TTTATAT-TTATA
617 TTTATTATTTATA
1 TTTA-TATTTATA
630 TTTATATTTATA
1 TTTATATTTATA
642 TTTATA-TT-TA
1 TTTATATTTATA
652 TTTATATTTATA
1 TTTATATTTATA
664 TTTATATTTATA
1 TTTATATTTATA
676 -TT-TATTTATA
1 TTTATATTTATA
686 -TT-TATTTATA
1 TTTATATTTATA
696 TTTAT-TTTATA
1 TTTATATTTATA
707 TTTATATATTTATA
1 -TT-TATATTTATA
721 TTTATATTTATA
1 TTTATATTTATA
733 TTTATATTTATA
1 TTTATATTTATA
745 TTTATATTTATA
1 TTTATATTTATA
757 TTTAT-TTTAT-
1 TTTATATTTATA
* *
767 TTT-TTTTTATC
1 TTTATATTTATA
778 TTTATATTT-TA
1 TTTATATTTATA
789 TATTATATTTATA
1 T-TTATATTTATA
802 TTT-TATTTATA
1 TTTATATTTATA
813 TTTATATTTATA
1 TTTATATTTATA
*
825 TTTCTATTTATA
1 TTTATATTTATA
837 TTTATATTTATA
1 TTTATATTTATA
849 -TTATATTTATA
1 TTTATATTTATA
860 TTTATA-TTATA
1 TTTATATTTATA
871 TTTATATTTATA
1 TTTATATTTATA
883 TTTATA-TTATA
1 TTTATATTTATA
894 -TTAT-TTTATA
1 TTTATATTTATA
904 TTTATATATT-TA
1 TTTATAT-TTATA
916 TATT-TATTTATA
1 T-TTATATTTATA
928 TTTATATTTATTTA
1 TTTATATTTA--TA
942 TTTATA-TT-TA
1 TTTATATTTATA
952 TTTATATTTATA
1 TTTATATTTATA
964 -TTATATTTATA
1 TTTATATTTATA
975 TTTATATTTATA
1 TTTATATTTATA
987 -TTATATTTATA
1 TTTATATTTATA
998 TTTATATTTATA
1 TTTATATTTATA
1010 TTTATATTT-TA
1 TTTATATTTATA
1021 TATTATATTTATA
1 T-TTATATTTATA
1034 TTTATATTTATA
1 TTTATATTTATA
1046 TTTATATTTATA
1 TTTATATTTATA
1058 TTTATATTTATA
1 TTTATATTTATA
1070 TTTATATTATATTA
1 TTTATATT-TA-TA
*
1084 TTTATATATTTTA
1 TTTATAT-TTATA
*
1097 TTTAT-TTTCTA
1 TTTATATTTATA
1108 TTT-TATATTATA
1 TTTATAT-TTATA
1120 TTTATATTTATA
1 TTTATATTTATA
1132 TTTATATTTATA
1 TTTATATTTATA
1144 TTTATATTTATA
1 TTTATATTTATA
1156 -TTAT-TTTATA
1 TTTATATTTATA
1166 TTTATA--TATA
1 TTTATATTTATA
1176 TTTATATTTATA
1 TTTATATTTATA
1188 TTTAT-TTTATA
1 TTTATATTTATA
1199 TTTATATTTATA
1 TTTATATTTATA
1211 TTTATATTTATA
1 TTTATATTTATA
1223 TTT-TATTTATTTA
1 TTTATATTTA--TA
1236 TTTATATTTACT-
1 TTTATATTTA-TA
1248 TTTATATTTATA
1 TTTATATTTATA
1260 TTTATATTTATA
1 TTTATATTTATA
1272 TTTATA-TTATA
1 TTTATATTTATA
1283 TTTATA-TT-TA
1 TTTATATTTATA
1293 TTTATATTTATA
1 TTTATATTTATA
1305 -TT-TATTTATA
1 TTTATATTTATA
1315 -TTATA-TT-TA
1 TTTATATTTATA
1324 TTTATATTTATA
1 TTTATATTTATA
1336 -TT-TATTT-TA
1 TTTATATTTATA
1345 TTTATATTTATA
1 TTTATATTTATA
1357 TTTATATTTATA
1 TTTATATTTATA
1369 -TT-TATTTATA
1 TTTATATTTATA
1379 TTTATATTTATA
1 TTTATATTTATA
1391 TTTATAT
1 TTTATAT
1398 AACTACATAC
Statistics
Matches: 822, Mismatches: 8, Indels: 133
0.85 0.01 0.14
Matches are distributed among these distances:
9 7 0.01
10 118 0.14
11 191 0.23
12 417 0.51
13 55 0.07
14 33 0.04
15 1 0.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATTTATA
Found at i:524 original size:18 final size:17
Alignment explanation
Indices: 490--1397 Score: 1056
Period size: 18 Copynumber: 53.7 Consensus size: 17
480 GTATATATGG
490 TTTATTTTATATTTATA
1 TTTATTTTATATTTATA
507 TTTATATTT-TATTTTATA
1 TTTAT-TTTATA-TTTATA
525 TTTA-TTTATATTTATA
1 TTTATTTTATATTTATA
541 TTTATATTTATATTTAT-
1 TTTAT-TTTATATTTATA
558 TTTA-TTTATATTTATA
1 TTTATTTTATATTTATA
574 TTTATATTTATATTTAT-
1 TTTAT-TTTATATTTATA
591 TTATATATTTATATTTATA
1 TT-TAT-TTTATATTTATA
610 TATTATATTTATTATTTATA
1 T-TTAT-TTTA-TATTTATA
630 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
648 TTTA-TTTATATTTATA
1 TTTATTTTATATTTATA
664 TTTATATTTATA-TT-TA
1 TTTAT-TTTATATTTATA
*
680 TTTATATT-TATTTATA
1 TTTATTTTATATTTATA
696 TTTATTTTATATTTATA
1 TTTATTTTATATTTATA
713 --TA-TTTATATTTATA
1 TTTATTTTATATTTATA
727 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
745 TTTATATTTATATTTAT-
1 TTTAT-TTTATATTTATA
* *
762 TTTATTTT-TTTTTATC
1 TTTATTTTATATTTATA
778 TTTATATTT-TATATTATA
1 TTTAT-TTTATAT-TTATA
796 TTTATATTT-TATTTATA
1 TTTAT-TTTATATTTATA
*
813 TTTATATTTATATTTCTA
1 TTTAT-TTTATATTTATA
831 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
849 -TTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
866 -TTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
* *
883 TTTATATTATA-TTATT
1 TTTATTTTATATTTATA
899 TTATATTTATATATTTATA
1 TT-TATTT-TATATTTATA
918 TTTA-TTTATATTTATA
1 TTTATTTTATATTTATA
934 TTTA--TT-TATTTATA
1 TTTATTTTATATTTATA
948 TTTA-TTTATATTTATA
1 TTTATTTTATATTTATA
964 -TTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
*
981 TTTATATTATATTTATA
1 TTTATTTTATATTTATA
998 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
*
1016 TTTTATATTATATTTATA
1 -TTTATTTTATATTTATA
1034 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
1052 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
*
1070 TTTATATTATA-TTAT-
1 TTTATTTTATATTTATA
*
1085 TTATATATTT-TATTTATT
1 TT-TAT-TTTATATTTATA
1103 TTCTATTTTATA-TTATA
1 TT-TATTTTATATTTATA
1120 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
1138 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
1156 -TTATTTTATATTTATA
1 TTTATTTTATATTTATA
*
1172 TATA-TTTATATTTATA
1 TTTATTTTATATTTATA
1188 TTTATTTTATATTTATA
1 TTTATTTTATATTTATA
1205 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
*
1223 TTT-TATT-TA-TT-TA
1 TTTATTTTATATTTATA
1236 TTTATATTTACT-TTTATA
1 TTTAT-TTTA-TATTTATA
1254 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
*
1272 TTTATATTATATTTATA
1 TTTATTTTATATTTATA
1289 TTTA-TTTATATTTATA
1 TTTATTTTATATTTATA
1305 TTTA-TTTATA-TTATA
1 TTTATTTTATATTTATA
1320 TTTA-TTTATATTTATA
1 TTTATTTTATATTTATA
1336 TTTA-TTT-TATTTATA
1 TTTATTTTATATTTATA
1351 TTTATATTTATATTTATA
1 TTTAT-TTTATATTTATA
1369 TTTA-TTTATATTTATA
1 TTTATTTTATATTTATA
1385 TTTATATTTATAT
1 TTTAT-TTTATAT
1398 AACTACATAC
Statistics
Matches: 806, Mismatches: 25, Indels: 119
0.85 0.03 0.13
Matches are distributed among these distances:
13 5 0.01
14 29 0.04
15 63 0.08
16 177 0.22
17 199 0.25
18 294 0.36
19 29 0.04
20 10 0.01
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTTATATTTATA
Found at i:1474 original size:25 final size:24
Alignment explanation
Indices: 1359--1474 Score: 59
Period size: 25 Copynumber: 4.9 Consensus size: 24
1349 TATTTATATT
* **
1359 TATA-TTTATATTTATTTAT-ATT
1 TATAGTTTATATTTATATATAAAC
1381 TATA-TTTATATTTATATAACTACATAC
1 TATAGTTTATATTTATAT-A-TA-A-AC
* *
1408 TATAATTTATA--TGTATAT--AC
1 TATAGTTTATATTTATATATAAAC
*
1428 TATATTTTATACTATT-TATATAAAC
1 TATAGTTTATA-T-TTATATATAAAC
1453 TATAGTTTATATTTATACTATA
1 TATAGTTTATATTTATA-TATA
1475 TATATGAACT
Statistics
Matches: 74, Mismatches: 6, Indels: 25
0.70 0.06 0.24
Matches are distributed among these distances:
20 12 0.16
22 16 0.22
23 8 0.11
24 6 0.08
25 17 0.23
26 5 0.07
27 4 0.05
28 6 0.08
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (24 bp):
TATAGTTTATATTTATATATAAAC
Found at i:1477 original size:45 final size:47
Alignment explanation
Indices: 1406--1529 Score: 121
Period size: 47 Copynumber: 2.7 Consensus size: 47
1396 ATAACTACAT
* *
1406 ACTATAATTTATATGTATA-TACTATATTTTATACTA-TTT-ATATAA
1 ACTATAGTTTATATATATACTA-TATATTTTATACTAGTTTAATATAA
* * * *
1451 ACTATAGTTTATATTTATACTATATATATGA-ACTAGTTTACATATGA
1 ACTATAGTTTATATATATACTATATATTTTATACTAGTTTA-ATATAA
* * *
1498 ACTATAGTTTACATATAAACTATATAGTTTAT
1 ACTATAGTTTATATATATACTATATATTTTAT
1530 GTACTAACTA
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
44 4 0.06
45 27 0.43
46 2 0.03
47 30 0.48
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (47 bp):
ACTATAGTTTATATATATACTATATATTTTATACTAGTTTAATATAA
Found at i:1505 original size:18 final size:18
Alignment explanation
Indices: 1476--1597 Score: 94
Period size: 18 Copynumber: 6.7 Consensus size: 18
1466 TATACTATAT
1476 ATATGAAC--TAGTTTAC
1 ATATGAACTATAGTTTAC
1492 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
1510 ATATAAACTATATAGTTTAT
1 ATATGAAC--TATAGTTTAC
*
1530 GTACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
*
1548 -TA--AATTATAGTTGATATTAC
1 ATATGAACTATA---G-T-TTAC
1568 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
1586 ATATGAACTATA
1 ATATGAACTATA
1598 TAATAAACTA
Statistics
Matches: 87, Mismatches: 6, Indels: 24
0.74 0.05 0.21
Matches are distributed among these distances:
15 6 0.07
16 8 0.09
17 2 0.02
18 41 0.47
19 2 0.02
20 19 0.22
21 3 0.03
23 6 0.07
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:1526 original size:38 final size:38
Alignment explanation
Indices: 1484--1599 Score: 123
Period size: 38 Copynumber: 3.1 Consensus size: 38
1474 ATATATGAAC
1484 TAGTTTACATATGAACTATAGTTTACATATAAACTATA
1 TAGTTTACATATGAACTATAGTTTACATATAAACTATA
** *
1522 TAGTTTATGTACT-AACTATAGTTTAC---TAAATTATA
1 TAGTTTACATA-TGAACTATAGTTTACATATAAACTATA
* *
1557 GTTGATATTACATATGAACTATAGTTTACATATGAACTATA
1 -TAG-T-TTACATATGAACTATAGTTTACATATAAACTATA
1598 TA
1 TA
1600 ATAAACTATA
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
35 8 0.13
36 2 0.03
37 2 0.03
38 40 0.66
39 1 0.02
40 1 0.02
41 7 0.11
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (38 bp):
TAGTTTACATATGAACTATAGTTTACATATAAACTATA
Found at i:1676 original size:13 final size:11
Alignment explanation
Indices: 1658--1735 Score: 50
Period size: 13 Copynumber: 6.5 Consensus size: 11
1648 ATACACTATT
*
1658 TATATAGTATA
1 TATATATTATA
1669 TACTTATATTTATA
1 TA--TATA-TTATA
*
1683 GTTTATATT-TA
1 -TATATATTATA
*
1694 TATATACTATA
1 TATATATTATA
*
1705 GTTTATATTTATA
1 -TATATA-TTATA
1718 CTATATATTATA
1 -TATATATTATA
1730 TATATA
1 TATATA
1736 AACCTAAATC
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
10 6 0.12
11 12 0.23
12 12 0.23
13 17 0.33
14 4 0.08
15 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (11 bp):
TATATATTATA
Found at i:1695 original size:34 final size:35
Alignment explanation
Indices: 1654--1735 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 35
1644 CTATATACAC
* *
1654 TATTTATATAGTA-TATA-CTTATATTTATAGTTTA
1 TATTTATATA-TACTATAGCTTATATTTATACTATA
*
1688 TATTTATATATACTATAGTTTATATTTATACTATA
1 TATTTATATATACTATAGCTTATATTTATACTATA
1723 TATTATATATATA
1 TATT-TATATATA
1736 AACCTAAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 2 0.05
34 14 0.33
35 18 0.43
36 8 0.19
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (35 bp):
TATTTATATATACTATAGCTTATATTTATACTATA
Found at i:1707 original size:22 final size:23
Alignment explanation
Indices: 1679--1722 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
1669 TACTTATATT
1679 TATAGTTTATATTTATA-TATAC
1 TATAGTTTATATTTATACTATAC
1701 TATAGTTTATATTTATACTATA
1 TATAGTTTATATTTATACTATA
1723 TATTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (23 bp):
TATAGTTTATATTTATACTATAC
Found at i:1709 original size:29 final size:27
Alignment explanation
Indices: 1668--1725 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1658 TATATAGTAT
*
1668 ATACTTATATTTATAGTTTATATTTATAT
1 ATACTTATATTTATA-TTTATA-CTATAT
1697 ATAC-TATAGTTTATATTTATACTATAT
1 ATACTTATA-TTTATATTTATACTATAT
1724 AT
1 AT
1726 TATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 7 0.26
28 10 0.37
29 10 0.37
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.55
Consensus pattern (27 bp):
ATACTTATATTTATATTTATACTATAT
Found at i:1719 original size:18 final size:18
Alignment explanation
Indices: 1658--1735 Score: 79
Period size: 18 Copynumber: 4.3 Consensus size: 18
1648 ATACACTATT
*
1658 TATATAGTATATACTTATA
1 TATATACTATATA-TTATA
* * *
1677 TTTATAGTTTATATT-TA
1 TATATACTATATATTATA
1694 TATATACTATAGT-TTATA
1 TATATACTATA-TATTATA
*
1712 TTTATACTATATATTATA
1 TATATACTATATATTATA
1730 TATATA
1 TATATA
1736 AACCTAAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.27
18 25 0.51
19 11 0.22
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (18 bp):
TATATACTATATATTATA
Found at i:1733 original size:22 final size:22
Alignment explanation
Indices: 1660--1734 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
1650 ACACTATTTA
*
1660 TATAGTATATACTTATAT-T--
1 TATAGTATATATTTATATATAC
*
1679 TATAGTTTATATTTATATATAC
1 TATAGTATATATTTATATATAC
*
1701 TATAGTTTATATTTATACTATA-
1 TATAGTATATATTTATA-TATAC
1723 TATTA-TATATAT
1 TA-TAGTATATAT
1735 AAACCTAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 16 0.33
20 1 0.02
22 25 0.52
23 6 0.12
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (22 bp):
TATAGTATATATTTATATATAC
Found at i:1809 original size:33 final size:33
Alignment explanation
Indices: 1771--1952 Score: 237
Period size: 33 Copynumber: 5.5 Consensus size: 33
1761 CCCTAAACCC
* *
1771 TAAACTATACATTATATAGTTTATTAGTATATA
1 TAAACTATATATTATATAGTTCATTAGTATATA
*
1804 TAAACTATATGA-TATATAG-AC-TATAGATATATA
1 TAAACTATAT-ATTATATAGTTCAT-TAG-TATATA
*
1837 TAAACTATACATTATATA-TTCATTAGTATATA
1 TAAACTATATATTATATAGTTCATTAGTATATA
*
1869 TAAACTATATACTATATAGTTCATTAGTATATA
1 TAAACTATATATTATATAGTTCATTAGTATATA
* *
1902 TAAACTATATAATATATAGTTCATTAATATATA
1 TAAACTATATATTATATAGTTCATTAGTATATA
*
1935 TAAACTATATAGTATATA
1 TAAACTATATATTATATA
1953 TAAACTATAT
Statistics
Matches: 132, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.01
32 26 0.20
33 103 0.78
34 2 0.02
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (33 bp):
TAAACTATATATTATATAGTTCATTAGTATATA
Found at i:1879 original size:58 final size:58
Alignment explanation
Indices: 1816--2061 Score: 249
Period size: 58 Copynumber: 4.2 Consensus size: 58
1806 AACTATATGA
* *
1816 TATATAGACTATAGATATATATAAACTATACATTATATA-TTCATTAGTATATATAAAC
1 TATATAGA-TATAGATATATATAAACTATATAATATATAGTTCATTAGTATATATAAAC
* *
1874 TATATACTATATAGTTCATTAGTATATATAAACTATATAATATATAGTTCATTAATATATATAAA
1 TATATA-GATATAG------A-TATATATAAACTATATAATATATAGTTCATTAGTATATATAAA
1939 C
58 C
*
1940 ----T--ATATAG-TATATATAAACTATATAATATATAGTTCATTAGTATATATAACC
1 TATATAGATATAGATATATATAAACTATATAATATATAGTTCATTAGTATATATAAAC
* * * *
1991 TATATAG-TATATGGTATATACAAACTATATATTATATAGTTCATTAGCATATATAAAC
1 TATATAGATATA-GATATATATAAACTATATAATATATAGTTCATTAGTATATATAAAC
2049 TATATAGTATATA
1 TATATAG-ATATA
2062 TAAACTATAT
Statistics
Matches: 159, Mismatches: 10, Indels: 36
0.78 0.05 0.18
Matches are distributed among these distances:
51 42 0.26
55 1 0.01
56 4 0.03
57 1 0.01
58 58 0.36
59 7 0.04
60 4 0.03
62 1 0.01
64 1 0.01
65 22 0.14
66 18 0.11
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (58 bp):
TATATAGATATAGATATATATAAACTATATAATATATAGTTCATTAGTATATATAAAC
Found at i:1950 original size:51 final size:51
Alignment explanation
Indices: 1893--2072 Score: 261
Period size: 51 Copynumber: 3.4 Consensus size: 51
1883 TATAGTTCAT
*
1893 TAGTATATATAAACTATATAATATATAGTTCATTAATATATATAAACTATA
1 TAGTATATATAAACTATATAATATATAGTTCATTAGTATATATAAACTATA
*
1944 TAGTATATATAAACTATATAATATATAGTTCATTAGTATATATAACCTATA
1 TAGTATATATAAACTATATAATATATAGTTCATTAGTATATATAAACTATA
* *
1995 TAGTATATGGTATATACAAACTATATATTATATAGTTCATTAGCATATATAAACTATA
1 TAG--TA---TATAT--AAACTATATAATATATAGTTCATTAGTATATATAAACTATA
2053 TAGTATATATAAACTATATA
1 TAGTATATATAAACTATATA
2073 TTAATTTATT
Statistics
Matches: 117, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
51 62 0.53
53 7 0.06
56 7 0.06
58 41 0.35
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (51 bp):
TAGTATATATAAACTATATAATATATAGTTCATTAGTATATATAAACTATA
Found at i:1962 original size:109 final size:108
Alignment explanation
Indices: 1849--2098 Score: 296
Period size: 109 Copynumber: 2.3 Consensus size: 108
1839 AACTATACAT
*
1849 TATATATTCATTAGTATATATAAACTATATA-CTATATAGT-TCATTAGTATATATAAACTATAT
1 TATATATT-ATTAGTATATATAAACTATATACCTATATAGTAT-A-TAGTATATACAAACTATAT
*
1912 AATATATAGTTCATTAATATATATAAACTATATAGTATATATAAAC
63 AATATATAGTTCATTAACATATATAAACTATATAGTATATATAAAC
* * *
1958 TATATAATATATAGT-TCAT-TAGTA-TATATAACCTATATAGTATATGGTATATACAAACTATA
1 TATATATTAT-TAGTAT-ATATA-AACTATAT-ACCTATATAGTATATAGTATATACAAACTATA
* *
2020 TATTATATAGTTCATTAGCATATATAAACTATATAGTATATATAAAC
62 TAATATATAGTTCATTAACATATATAAACTATATAGTATATATAAAC
*
2067 TATATATTAATTTATTA-ATATAAACATATATA
1 TATATATT-A-TTAGTATATATAAAC-TATATA
2099 TTAATTGAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
108 10 0.08
109 85 0.71
110 17 0.14
111 7 0.06
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (108 bp):
TATATATTATTAGTATATATAAACTATATACCTATATAGTATATAGTATATACAAACTATATAAT
ATATAGTTCATTAACATATATAAACTATATAGTATATATAAAC
Found at i:1968 original size:98 final size:98
Alignment explanation
Indices: 1771--2073 Score: 292
Period size: 98 Copynumber: 3.0 Consensus size: 98
1761 CCCTAAACCC
* * * *
1771 TAAACTATACATTATATAGTTTATTAGTATATATAAACTATATGATATATAG-AC-TATAGATAT
1 TAAACTATATACTATATAG-TTATTAGTATATATAAACTATATAATATATAGTTCAT-TA-ATAT
* * **
1834 ATATAAACTATACATTATATATTCA-T-TAGTATATA
63 ATATAAACTATATAGTATATATAAACTATA-TATATA
1869 TAAACTATATACTATATAGTTCATTAGTATATATAAACTATATAATATATAGTTCATTAATATAT
1 TAAACTATATACTATATAGTT-ATTAGTATATATAAACTATATAATATATAGTTCATTAATATAT
1934 ATAAACTATATAGTATATATAAACTATATAATATA
65 ATAAACTATATAGTATATATAAACTATAT-ATATA
* * * *
1969 TAGTTCATTAGTATATATAACCTATATAG-TATATGGTATATACAAACTATATATTATATAGTTC
1 TA----A--A--CTATAT-A-CTATATAGTTAT-TAGTATATATAAACTATATAATATATAGTTC
**
2033 ATTAGCATATATAAACTATATAGTATATATAAACTATATAT
55 ATTAATATATATAAACTATATAGTATATATAAACTATATAT
2074 TAATTTATTA
Statistics
Matches: 174, Mismatches: 14, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
97 2 0.01
98 71 0.41
99 5 0.03
100 10 0.06
104 1 0.01
106 1 0.01
108 9 0.05
109 67 0.39
110 8 0.05
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (98 bp):
TAAACTATATACTATATAGTTATTAGTATATATAAACTATATAATATATAGTTCATTAATATATA
TAAACTATATAGTATATATAAACTATATATATA
Found at i:1981 original size:33 final size:33
Alignment explanation
Indices: 1944--2061 Score: 135
Period size: 33 Copynumber: 3.8 Consensus size: 33
1934 ATAAACTATA
*
1944 TAGTATATATAAACTATATAATATATAGTTCAT
1 TAGTATATATAAACTATATAGTATATAGTTCAT
*
1977 TAGTATATATAACCTATATAGTATAT-G-----
1 TAGTATATATAAACTATATAGTATATAGTTCAT
* *
2004 --GTATATACAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATAGTATATAGTTCAT
*
2035 TAGCATATATAAACTATATAGTATATA
1 TAGTATATATAAACTATATAGTATATA
2062 TAAACTATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
25 21 0.30
26 1 0.01
32 1 0.01
33 46 0.67
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (33 bp):
TAGTATATATAAACTATATAGTATATAGTTCAT
Found at i:2096 original size:51 final size:51
Alignment explanation
Indices: 1998--2096 Score: 112
Period size: 51 Copynumber: 1.9 Consensus size: 51
1988 ACCTATATAG
* * * *
1998 TATATGGTATATACAAACTATATATTATATAGTTCATTAGCATATATAAAC
1 TATATAGTATATACAAACTATATATTATATAGTTAATTAGAACATATAAAC
* *
2049 TATATAGTATATATAAACTATATATTAATTTA-TTAATATA-AACATATA
1 TATATAGTATATACAAACTATATATT-ATATAGTTAAT-TAGAACATATA
2097 TATTAATTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
51 34 0.85
52 6 0.15
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (51 bp):
TATATAGTATATACAAACTATATATTATATAGTTAATTAGAACATATAAAC
Found at i:4414 original size:20 final size:20
Alignment explanation
Indices: 4389--4429 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4379 TCTTTTGTAG
*
4389 GGTGCCTTATTGCCTTACAA
1 GGTGCCTTACTGCCTTACAA
4409 GGTGCCTTACTGCCTTACAA
1 GGTGCCTTACTGCCTTACAA
4429 G
1 G
4430 ATGCAATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (20 bp):
GGTGCCTTACTGCCTTACAA
Found at i:4439 original size:20 final size:20
Alignment explanation
Indices: 4399--4439 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4389 GGTGCCTTAT
* **
4399 TGCCTTACAAGGTGCCTTAC
1 TGCCTTACAAGATGCAATAC
4419 TGCCTTACAAGATGCAATAC
1 TGCCTTACAAGATGCAATAC
4439 T
1 T
4440 TGGTGTTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (20 bp):
TGCCTTACAAGATGCAATAC
Found at i:4483 original size:20 final size:20
Alignment explanation
Indices: 4460--4503 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4450 CTCTGCTTTA
*
4460 TTCTGTTTTATATTGTTTGC
1 TTCTGTTTTATATTGCTTGC
4480 TTCTGTTTTATATTGCTTGC
1 TTCTGTTTTATATTGCTTGC
4500 TTCT
1 TTCT
4504 ACTTGATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.64
Consensus pattern (20 bp):
TTCTGTTTTATATTGCTTGC
Found at i:4512 original size:20 final size:20
Alignment explanation
Indices: 4469--4513 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4459 ATTCTGTTTT
* ** *
4469 ATATTGTTTGCTTCTGTTTT
1 ATATTGCTTGCTTCTACTTG
4489 ATATTGCTTGCTTCTACTTG
1 ATATTGCTTGCTTCTACTTG
4509 ATATT
1 ATATT
4514 TGTAAGGGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (20 bp):
ATATTGCTTGCTTCTACTTG
Found at i:5813 original size:16 final size:16
Alignment explanation
Indices: 5794--5827 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5784 CAATATACGA
5794 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
5810 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
5826 AT
1 AT
5828 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:5902 original size:14 final size:16
Alignment explanation
Indices: 5866--5902 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5856 ATATAATGTA
5866 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
5883 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
5898 T-AATA
1 TGAATA
5903 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:6568 original size:130 final size:130
Alignment explanation
Indices: 6364--6611 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
6354 AATTTTCTTC
* * *
6364 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAAGACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
6429 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
6494 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
6559 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
6612 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:7058 original size:35 final size:35
Alignment explanation
Indices: 7008--7083 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
6998 AATTGAATTT
* *
7008 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
7043 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
7078 AATTGA
1 AATTGA
7084 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:7593 original size:35 final size:35
Alignment explanation
Indices: 7547--7622 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
7537 AAAACAGTCC
* *
7547 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
7582 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
7617 TCAATT
1 TCAATT
7623 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:8164 original size:130 final size:130
Alignment explanation
Indices: 8018--8265 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
8008 TATTTATATA
* **
8018 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
8083 TTAGCACATGATCATGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
8148 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
8213 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTA
8266 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:8296 original size:130 final size:129
Alignment explanation
Indices: 8032--8296 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
8022 ATTTGGTCCT
* ** *
8032 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * * **** *
8097 TGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTAACAAAGAAGT-CA
8162 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *
8227 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAG-TAACAAAGAAGT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTAACAAAGAAGT
8291 -A
128 CA
8292 AAATT
1 AAATT
8297 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 10 0.09
133 3 0.03
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTAACAAAGAAGTCA
Found at i:8618 original size:28 final size:27
Alignment explanation
Indices: 8587--8649 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
8577 AGTTGATACA
*
8587 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
8615 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
8643 ATATTTT
1 ATATTTT
8650 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:8750 original size:16 final size:18
Alignment explanation
Indices: 8729--8762 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
8719 ATTTCTTATT
8729 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
8745 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
8763 TAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:10322 original size:4 final size:4
Alignment explanation
Indices: 10313--10367 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
10303 AATATGATCA
*
10313 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
10361 TTTC TTT
1 TTTC TTT
10368 TTTTATGATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:22618 original size:7 final size:7
Alignment explanation
Indices: 22606--22632 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
22596 TAATAATAAT
22606 CTGAAAA
1 CTGAAAA
22613 CTGAAAA
1 CTGAAAA
22620 CTGAAAA
1 CTGAAAA
22627 CTGAAA
1 CTGAAA
22633 TTTAAGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CTGAAAA
Found at i:23123 original size:3 final size:3
Alignment explanation
Indices: 23115--23153 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
23105 GGTTTTACTT
23115 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23154 CATTCTTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:25757 original size:4 final size:4
Alignment explanation
Indices: 25748--25774 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
25738 ACTTTAACCT
25748 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
25775 TCGAATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:29252 original size:18 final size:18
Alignment explanation
Indices: 29229--29265 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29219 GTGCCAGAAC
29229 ATCTAAAAGACTGGTGCA
1 ATCTAAAAGACTGGTGCA
29247 ATCTAAAAGACTGGTGCA
1 ATCTAAAAGACTGGTGCA
29265 A
1 A
29266 GGTCTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (18 bp):
ATCTAAAAGACTGGTGCA
Found at i:30486 original size:12 final size:12
Alignment explanation
Indices: 30459--30502 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
30449 ACACCAAAAC
*
30459 AAAAACTTAAAG
1 AAAAACTTAATG
30471 -AAAACTTAATG
1 AAAAACTTAATG
*
30482 AAAAACTTGATG
1 AAAAACTTAATG
*
30494 TAAAACTTA
1 AAAAACTTA
30503 TGCCTCTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (12 bp):
AAAAACTTAATG
Found at i:30800 original size:13 final size:13
Alignment explanation
Indices: 30782--30811 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
30772 CCGTGCCCAC
30782 ACCTTATGCAAAA
1 ACCTTATGCAAAA
30795 ACCTTATGCAAAA
1 ACCTTATGCAAAA
30808 ACCT
1 ACCT
30812 CTTCTGGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.27, G:0.07, T:0.23
Consensus pattern (13 bp):
ACCTTATGCAAAA
Found at i:31641 original size:7 final size:8
Alignment explanation
Indices: 31622--31649 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
31612 TGCTTCTTTT
31622 TTTTTTCC
1 TTTTTTCC
31630 TTTTTTCC
1 TTTTTTCC
31638 TTTTTTCC
1 TTTTTTCC
31646 TTTT
1 TTTT
31650 GTTTGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCC
Found at i:37495 original size:12 final size:12
Alignment explanation
Indices: 37468--37511 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
37458 ACACCAAAAC
*
37468 AAAAACTTAAAG
1 AAAAACTTAATG
37480 -AAAACTTAATG
1 AAAAACTTAATG
*
37491 AAAAACTTGATG
1 AAAAACTTAATG
*
37503 TAAAACTTA
1 AAAAACTTA
37512 TGCCTCCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (12 bp):
AAAAACTTAATG
Found at i:46882 original size:43 final size:43
Alignment explanation
Indices: 46685--46871 Score: 311
Period size: 43 Copynumber: 4.3 Consensus size: 43
46675 TTAATTATCG
* ** *
46685 TTACAGTTCTCCCATATCCCTTTGCTATGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
46728 TTACATTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
46771 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
46814 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
46857 TTACAGTTTCCCCAG
1 TTACAGTTCCCCCAG
46872 ACTCTTTTGC
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 136 1.00
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.30
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:48202 original size:51 final size:51
Alignment explanation
Indices: 48147--48305 Score: 132
Period size: 51 Copynumber: 3.1 Consensus size: 51
48137 TTCAAATTGG
48147 ATGAACGCTATCAATATTGGAAAGTTGATAAATTCCATGCAGAACATAACA
1 ATGAACGCTATCAATATTGGAAAGTTGATAAATTCCATGCAGAACATAACA
* * * * * * * **
48198 ATGAAAC-CTGTCATCAGAGTTGG-ATG-TGATACATT-TAT-TAGATTCA-AATTGG
1 ATG-AACGCTATCA--ATA-TTGGAAAGTTGATAAATTCCATGCAGA-ACATAA--CA
48250 ATGAACGCTATCAATATTGGAAAGTTGATAAATTCCATGCAGAACATAACA
1 ATGAACGCTATCAATATTGGAAAGTTGATAAATTCCATGCAGAACATAACA
48301 ATGAA
1 ATGAA
48306 ATGGTTCAGC
Statistics
Matches: 77, Mismatches: 18, Indels: 26
0.64 0.15 0.21
Matches are distributed among these distances:
49 4 0.05
50 9 0.12
51 28 0.36
52 23 0.30
53 9 0.12
54 4 0.05
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (51 bp):
ATGAACGCTATCAATATTGGAAAGTTGATAAATTCCATGCAGAACATAACA
Found at i:48279 original size:103 final size:103
Alignment explanation
Indices: 48100--48306 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
48090 GTCAACAACG
48100 ACCTGTCATCAGAGTTGGATGTGATACATTTATTAGATTCAAATTGGATGAACGCTATCAATATT
1 ACCTGTCATCAGAGTTGGATGTGATACATTTATTAGATTCAAATTGGATGAACGCTATCAATATT
48165 GGAAAGTTGATAAATTCCATGCAGAACATAACAATGAA
66 GGAAAGTTGATAAATTCCATGCAGAACATAACAATGAA
48203 ACCTGTCATCAGAGTTGGATGTGATACATTTATTAGATTCAAATTGGATGAACGCTATCAATATT
1 ACCTGTCATCAGAGTTGGATGTGATACATTTATTAGATTCAAATTGGATGAACGCTATCAATATT
48268 GGAAAGTTGATAAATTCCATGCAGAACATAACAATGAA
66 GGAAAGTTGATAAATTCCATGCAGAACATAACAATGAA
48306 A
1 A
48307 TGGTTCAGCC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (103 bp):
ACCTGTCATCAGAGTTGGATGTGATACATTTATTAGATTCAAATTGGATGAACGCTATCAATATT
GGAAAGTTGATAAATTCCATGCAGAACATAACAATGAA
Found at i:53920 original size:36 final size:36
Alignment explanation
Indices: 53879--53958 Score: 160
Period size: 36 Copynumber: 2.2 Consensus size: 36
53869 GTTTCAAGAT
53879 GATGACGAGGATGATGTTGATGGCGATGGTGATGAC
1 GATGACGAGGATGATGTTGATGGCGATGGTGATGAC
53915 GATGACGAGGATGATGTTGATGGCGATGGTGATGAC
1 GATGACGAGGATGATGTTGATGGCGATGGTGATGAC
53951 GATGACGA
1 GATGACGA
53959 TGCAGCGGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.09, G:0.41, T:0.24
Consensus pattern (36 bp):
GATGACGAGGATGATGTTGATGGCGATGGTGATGAC
Found at i:55111 original size:21 final size:20
Alignment explanation
Indices: 55065--55117 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
55055 ATATGCTCAC
*
55065 TAATTTTTCAAATTAGCCAT
1 TAATTTTTAAAATTAGCCAT
55085 TCAATTTTTAAAATT-GACCTAT
1 T-AATTTTTAAAATTAG-CC-AT
55107 TAATTCTTTAA
1 TAATT-TTTAA
55118 TTTGACCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.07
21 18 0.64
22 8 0.29
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (20 bp):
TAATTTTTAAAATTAGCCAT
Found at i:57037 original size:15 final size:13
Alignment explanation
Indices: 57002--57035 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
56992 AACATTCTTT
57002 TATTTTTATTATA
1 TATTTTTATTATA
57015 TATTTTTATTATA
1 TATTTTTATTATA
57028 TATATTTT
1 TAT-TTTT
57036 TAGATTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTTTATTATA
Found at i:57962 original size:15 final size:16
Alignment explanation
Indices: 57944--57979 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
57934 AAAATAGTAA
*
57944 TTAAAATTTTATT-AT
1 TTAAAAGTTTATTAAT
57959 TTAAAAGTTTATTAAT
1 TTAAAAGTTTATTAAT
57975 TTAAA
1 TTAAA
57980 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTAAAAGTTTATTAAT
Found at i:59696 original size:20 final size:20
Alignment explanation
Indices: 59671--59718 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
59661 AGGAAGTATT
59671 GATACTCTACTTGTAATATC
1 GATACTCTACTTGTAATATC
59691 GATACTCTACTTGTAATATC
1 GATACTCTACTTGTAATATC
59711 GATACTCT
1 GATACTCT
59719 GAGATCAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (20 bp):
GATACTCTACTTGTAATATC
Done.