Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003142.1 Hibiscus syriacus cultivar Beakdansim tig00006613_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: 553945
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 3
Found at i:1295 original size:7 final size:7
Alignment explanation
Indices: 1--1291 Score: 2140
Period size: 7 Copynumber: 189.3 Consensus size: 7
1 AAGCCCT
1 AAGCCCT
8 AAGCCCT
1 AAGCCCT
15 AAGCCCT
1 AAGCCCT
22 AAGCCCT
1 AAGCCCT
29 AAG-CCT
1 AAGCCCT
35 AAGCCCT
1 AAGCCCT
42 AAGCCCT
1 AAGCCCT
49 AAGCCCT
1 AAGCCCT
56 AAGCCCT
1 AAGCCCT
*
63 AAG--AT
1 AAGCCCT
68 AAGCCCT
1 AAGCCCT
75 AAGCCCT
1 AAGCCCT
82 AAGCCCT
1 AAGCCCT
89 AAGCCCT
1 AAGCCCT
96 AAGCCCT
1 AAGCCCT
103 AAGCCCT
1 AAGCCCT
110 AAGCCCT
1 AAGCCCT
117 AAGCCCT
1 AAGCCCT
124 AAGCCCT
1 AAGCCCT
131 AAGCCCT
1 AAGCCCT
138 AAG-CCT
1 AAGCCCT
144 AAGCCCT
1 AAGCCCT
151 AAGCCCCT
1 AAG-CCCT
159 AAGCCCT
1 AAGCCCT
166 AAGCCCT
1 AAGCCCT
173 AAG-CCT
1 AAGCCCT
179 AAGCCCT
1 AAGCCCT
186 AAGCCCT
1 AAGCCCT
193 AAGCCCT
1 AAGCCCT
200 AAGCCCT
1 AAGCCCT
207 AAGCCCT
1 AAGCCCT
214 AAGCCCT
1 AAGCCCT
221 AAGCCCT
1 AAGCCCT
228 AAGCCCT
1 AAGCCCT
235 AAGCCCT
1 AAGCCCT
242 AAGCCC-
1 AAGCCCT
248 AAGCCCT
1 AAGCCCT
255 AAGCCTCT
1 AAGCC-CT
263 AAG-CC-
1 AAGCCCT
268 AAGCCCT
1 AAGCCCT
275 AAG-CCT
1 AAGCCCT
281 AAGCCCT
1 AAGCCCT
288 AAG-CCT
1 AAGCCCT
294 AAGCCCT
1 AAGCCCT
301 AAGCCCT
1 AAGCCCT
308 AAGCCCT
1 AAGCCCT
315 AAGCCCT
1 AAGCCCT
322 AAGCCCT
1 AAGCCCT
329 AAG-CCT
1 AAGCCCT
335 AAGAAGCCCT
1 ---AAGCCCT
345 AAGCCCT
1 AAGCCCT
352 AAGCCCT
1 AAGCCCT
359 AAGCCCT
1 AAGCCCT
366 AAGCCCT
1 AAGCCCT
373 AAGCCCT
1 AAGCCCT
380 AAGCCCT
1 AAGCCCT
387 AAGCCCT
1 AAGCCCT
394 AAGCCCT
1 AAGCCCT
401 AAG-CCT
1 AAGCCCT
407 AAGCCCT
1 AAGCCCT
414 AAGCCCT
1 AAGCCCT
421 AAGCCCT
1 AAGCCCT
428 AAG-CCT
1 AAGCCCT
434 AAG-CCT
1 AAGCCCT
440 AAG-CCT
1 AAGCCCT
446 AAGCCCT
1 AAGCCCT
453 AAGCCCT
1 AAGCCCT
460 AAG-CCT
1 AAGCCCT
466 AAGCCCT
1 AAGCCCT
473 -AG--CT
1 AAGCCCT
477 AAGCCCT
1 AAGCCCT
484 AAGCCCT
1 AAGCCCT
491 AAGCCCT
1 AAGCCCT
498 AAGCCCT
1 AAGCCCT
*
505 AAGCCCG
1 AAGCCCT
512 AAG-CCT
1 AAGCCCT
518 AAGCCCT
1 AAGCCCT
525 AAGCCCT
1 AAGCCCT
532 AAGCCCT
1 AAGCCCT
539 AAGCCCT
1 AAGCCCT
*
546 AAGCCAT
1 AAGCCCT
553 AAGCCCT
1 AAGCCCT
560 AAGCCCT
1 AAGCCCT
567 AAGCCCT
1 AAGCCCT
574 AAG-CCT
1 AAGCCCT
580 AAGCCCT
1 AAGCCCT
587 AAG-CCT
1 AAGCCCT
593 AAGCCCT
1 AAGCCCT
600 AAGCCCT
1 AAGCCCT
607 AAGCCCT
1 AAGCCCT
614 -AGCCCT
1 AAGCCCT
620 AAGCCCT
1 AAGCCCT
627 AAGCCCT
1 AAGCCCT
634 AAG-CCT
1 AAGCCCT
640 AAGCCCT
1 AAGCCCT
647 AAGCCCT
1 AAGCCCT
654 AAG-CCT
1 AAGCCCT
660 AAGCCCT
1 AAGCCCT
667 AAG-CCT
1 AAGCCCT
673 AAGCCCT
1 AAGCCCT
680 AAGCCCT
1 AAGCCCT
687 AAGCCCT
1 AAGCCCT
694 AAGCCCT
1 AAGCCCT
701 AAGCCCT
1 AAGCCCT
708 AAG-CCT
1 AAGCCCT
714 AAGCCCT
1 AAGCCCT
721 AAGCCCT
1 AAGCCCT
728 AAGCCCT
1 AAGCCCT
735 AAGCCCT
1 AAGCCCT
742 AAGCCCT
1 AAGCCCT
749 AAGCCCT
1 AAGCCCT
756 AAGCCCT
1 AAGCCCT
763 AAGCCCT
1 AAGCCCT
770 AAGCCCT
1 AAGCCCT
777 AAGCCCT
1 AAGCCCT
784 AAGCCCT
1 AAGCCCT
791 AAGCCCT
1 AAGCCCT
798 AAGCCCT
1 AAGCCCT
805 AAGCCCT
1 AAGCCCT
812 AAGCCCT
1 AAGCCCT
819 AAGCCCT
1 AAGCCCT
826 AAG-CCT
1 AAGCCCT
832 AAG-CCT
1 AAGCCCT
838 AAGCCCT
1 AAGCCCT
845 AAGCCCT
1 AAGCCCT
852 AAG-CCT
1 AAGCCCT
858 AAGCCCT
1 AAGCCCT
865 AAG-CCT
1 AAGCCCT
871 AAGCCCT
1 AAGCCCT
878 AAGCCCT
1 AAGCCCT
885 AAGCCCT
1 AAGCCCT
892 AAGCCCT
1 AAGCCCT
899 AAG-CCT
1 AAGCCCT
905 AAGCCCT
1 AAGCCCT
912 AAGCCCT
1 AAGCCCT
919 AAG-CCT
1 AAGCCCT
925 AAGCCCT
1 AAGCCCT
932 AAGCCCT
1 AAGCCCT
939 AAGCCCT
1 AAGCCCT
946 AAG-CC-
1 AAGCCCT
951 AAGCCCT
1 AAGCCCT
958 AAGCCCT
1 AAGCCCT
965 AAGCCCT
1 AAGCCCT
972 AAGCCCT
1 AAGCCCT
979 AAGCCCT
1 AAGCCCT
986 AAGCCCT
1 AAGCCCT
993 AAG-CCT
1 AAGCCCT
999 AAGCCCT
1 AAGCCCT
1006 AAGCCCT
1 AAGCCCT
1013 AAGCCCT
1 AAGCCCT
1020 AAGCCCT
1 AAGCCCT
1027 AAG-CCT
1 AAGCCCT
1033 AAGCCCT
1 AAGCCCT
1040 AAGCCC-
1 AAGCCCT
1046 AAGCCCT
1 AAGCCCT
1053 AAGCCCT
1 AAGCCCT
*
1060 AAGAGCCT
1 AAG-CCCT
1068 AAGCCCT
1 AAGCCCT
1075 AAGCCCT
1 AAGCCCT
1082 AAG-CCT
1 AAGCCCT
1088 AAGCCCT
1 AAGCCCT
1095 AAGCCCT
1 AAGCCCT
1102 AAGCCCT
1 AAGCCCT
1109 AAGCCCT
1 AAGCCCT
1116 AAGCCCT
1 AAGCCCT
1123 AAGCCCT
1 AAGCCCT
1130 AAGCCCT
1 AAGCCCT
1137 AAGCCCT
1 AAGCCCT
1144 AAG-CCT
1 AAGCCCT
1150 AAGCCCT
1 AAGCCCT
1157 AAGCCCT
1 AAGCCCT
1164 AAGCCCT
1 AAGCCCT
1171 AAGCCCT
1 AAGCCCT
1178 AAGCCCT
1 AAGCCCT
1185 AAGCCCT
1 AAGCCCT
1192 AAGCCCT
1 AAGCCCT
1199 AAGCCCT
1 AAGCCCT
1206 AAGCCCT
1 AAGCCCT
1213 AAGCCCT
1 AAGCCCT
1220 AAGCCCT
1 AAGCCCT
1227 AAGCCCT
1 AAGCCCT
*
1234 AAACCCT
1 AAGCCCT
*
1241 AAACCCT
1 AAGCCCT
*
1248 AAACCCT
1 AAGCCCT
*
1255 AAACCCT
1 AAGCCCT
*
1262 AAACCCT
1 AAGCCCT
*
1269 AAACCCT
1 AAGCCCT
*
1276 AAACCCT
1 AAGCCCT
*
1283 AAACCCT
1 AAGCCCT
1290 AA
1 AA
1292 ACCCGAATCC
Statistics
Matches: 1232, Mismatches: 9, Indels: 86
0.93 0.01 0.06
Matches are distributed among these distances:
4 2 0.00
5 12 0.01
6 191 0.16
7 1003 0.81
8 18 0.01
9 3 0.00
10 3 0.00
ACGTcount: A:0.30, C:0.41, G:0.14, T:0.14
Consensus pattern (7 bp):
AAGCCCT
Found at i:1320 original size:14 final size:14
Alignment explanation
Indices: 1305--1373 Score: 93
Period size: 14 Copynumber: 4.9 Consensus size: 14
1295 CGAATCCCCG
* *
1305 AAACCCGAAACCCG
1 AAACCCTAAACCCT
*
1319 AAACCCGAAACCCT
1 AAACCCTAAACCCT
* *
1333 AAACCCGAAACCCG
1 AAACCCTAAACCCT
1347 AAACCCTAAACCCT
1 AAACCCTAAACCCT
1361 AAACCCTAAACCC
1 AAACCCTAAACCC
1374 AGGCCCCGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 51 1.00
ACGTcount: A:0.43, C:0.43, G:0.07, T:0.06
Consensus pattern (14 bp):
AAACCCTAAACCCT
Found at i:1327 original size:21 final size:21
Alignment explanation
Indices: 711--1373 Score: 236
Period size: 21 Copynumber: 32.1 Consensus size: 21
701 AAGCCCTAAG
* * * *
711 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
732 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
753 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
774 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
795 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
816 CCTAAGCCCT-AAGCC-TAAG
1 CCTAAACCCTAAACCCGAAAC
* * * *
835 CCTAAGCCCTAAGCCC-TAAG
1 CCTAAACCCTAAACCCGAAAC
* * * *
855 CCTAAGCCCT-AAGCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
875 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
896 CCT-AAGCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
916 CCT-AAGCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * *
936 CCTAAGCCCT-AAGCC-AAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
955 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
976 CCTAAGCCCTAAGCCC-TAAG
1 CCTAAACCCTAAACCCGAAAC
* * * *
996 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
1017 CCTAAGCCCT-AAGCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
1037 CCTAAGCCC-AAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
1057 CCTAAGAGCCTAAGCCCTAAGC
1 CCTAA-ACCCTAAACCCGAAAC
* * * *
1079 CCT-AAGCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
1099 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
1120 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
1141 CCT-AAGCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
1161 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
1182 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* * * *
1203 CCTAAGCCCTAAGCCCTAAGC
1 CCTAAACCCTAAACCCGAAAC
* *
1224 CCTAAGCCCTAAACCCTAAAC
1 CCTAAACCCTAAACCCGAAAC
*
1245 CCTAAACCCTAAACCCTAAAC
1 CCTAAACCCTAAACCCGAAAC
*
1266 CCTAAACCCTAAACCCTAAAC
1 CCTAAACCCTAAACCCGAAAC
* *
1287 CCTAAACCCGAATCCCCGAAAC
1 CCTAAACCCTAA-ACCCGAAAC
* *
1309 CCGAAACCCGAAACCCGAAAC
1 CCTAAACCCTAAACCCGAAAC
*
1330 CCTAAACCCGAAACCCGAAAC
1 CCTAAACCCTAAACCCGAAAC
*
1351 CCTAAACCCTAAACCCTAAAC
1 CCTAAACCCTAAACCCGAAAC
1372 CC
1 CC
1374 AGGCCCCGAG
Statistics
Matches: 578, Mismatches: 51, Indels: 26
0.88 0.08 0.04
Matches are distributed among these distances:
19 28 0.05
20 159 0.28
21 359 0.62
22 32 0.06
ACGTcount: A:0.32, C:0.42, G:0.13, T:0.13
Consensus pattern (21 bp):
CCTAAACCCTAAACCCGAAAC
Found at i:1386 original size:7 final size:7
Alignment explanation
Indices: 1376--1400 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1366 CTAAACCCAG
1376 GCCCCGA
1 GCCCCGA
1383 GCCCCGA
1 GCCCCGA
1390 GCCCCGA
1 GCCCCGA
1397 GCCC
1 GCCC
1401 GGACCCCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.60, G:0.28, T:0.00
Consensus pattern (7 bp):
GCCCCGA
Found at i:1408 original size:7 final size:7
Alignment explanation
Indices: 1398--1422 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1388 GAGCCCCGAG
1398 CCCGGAC
1 CCCGGAC
1405 CCCGGAC
1 CCCGGAC
1412 CCCGGAC
1 CCCGGAC
1419 CCCG
1 CCCG
1423 TACCATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.60, G:0.28, T:0.00
Consensus pattern (7 bp):
CCCGGAC
Found at i:2564 original size:21 final size:21
Alignment explanation
Indices: 2498--2564 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
2488 AGAGAAAAGT
*
2498 AAAAGTTAAGAATGAAATA-A
1 AAAATTTAAGAATGAAATAGA
*
2518 AAAAATTAAGAATGAAATAGA
1 AAAATTTAAGAATGAAATAGA
2539 AAAATTTAAGAATGAAATAGA
1 AAAATTTAAGAATGAAATAGA
2560 AAAAT
1 AAAAT
2565 AAAAAGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (21 bp):
AAAATTTAAGAATGAAATAGA
Found at i:4448 original size:7 final size:7
Alignment explanation
Indices: 4436--4819 Score: 453
Period size: 7 Copynumber: 54.9 Consensus size: 7
4426 AGTCTAGGCT
4436 TGGACCC
1 TGGACCC
4443 TGGACCC
1 TGGACCC
4450 TGGACCC
1 TGGACCC
4457 TGGACCC
1 TGGACCC
4464 TGGACCC
1 TGGACCC
*
4471 TAGACCC
1 TGGACCC
*
4478 TAGACCC
1 TGGACCC
4485 TGGACCC
1 TGGACCC
**
4492 TAAACCC
1 TGGACCC
*
4499 TAGACCC
1 TGGACCC
*
4506 TAGACCC
1 TGGACCC
*
4513 TAGACCC
1 TGGACCC
*
4520 TAGACCC
1 TGGACCC
*
4527 TCGACCC
1 TGGACCC
*
4534 TAGACCC
1 TGGACCC
*
4541 TAGACCC
1 TGGACCC
*
4548 TAGACCC
1 TGGACCC
*
4555 TAGACCC
1 TGGACCC
**
4562 TAAACCC
1 TGGACCC
*
4569 TAGACCC
1 TGGACCC
4576 TGGACCC
1 TGGACCC
*
4583 TAGACCC
1 TGGACCC
4590 TGGACCC
1 TGGACCC
4597 TGGACCC
1 TGGACCC
4604 TGGACCC
1 TGGACCC
4611 TGGACCC
1 TGGACCC
4618 TGGACCC
1 TGGACCC
4625 TGGACCC
1 TGGACCC
4632 TGGACCC
1 TGGACCC
4639 TGGACCC
1 TGGACCC
4646 TGGACCC
1 TGGACCC
4653 TGGACCC
1 TGGACCC
4660 TGGACCC
1 TGGACCC
4667 TGGACCC
1 TGGACCC
4674 TGGACCC
1 TGGACCC
4681 TGGACCC
1 TGGACCC
4688 TGGACCC
1 TGGACCC
4695 TGGACCC
1 TGGACCC
4702 TGGACCC
1 TGGACCC
4709 TGGACCC
1 TGGACCC
4716 TGGACCC
1 TGGACCC
4723 TGGACCC
1 TGGACCC
4730 TGGACCC
1 TGGACCC
**
4737 TAAACCC
1 TGGACCC
**
4744 TAAACCC
1 TGGACCC
**
4751 TAAACCC
1 TGGACCC
**
4758 TAAACCC
1 TGGACCC
*
4765 TAGACCC
1 TGGACCC
*
4772 TAGACCC
1 TGGACCC
**
4779 TAAACCC
1 TGGACCC
**
4786 TAAACCC
1 TGGACCC
**
4793 CAGACCC
1 TGGACCC
4800 TGGACCC
1 TGGACCC
*
4807 CGGACCC
1 TGGACCC
*
4814 CGGACC
1 TGGACC
4820 ATCTATATGC
Statistics
Matches: 356, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 356 1.00
ACGTcount: A:0.22, C:0.44, G:0.20, T:0.14
Consensus pattern (7 bp):
TGGACCC
Found at i:5919 original size:21 final size:19
Alignment explanation
Indices: 5895--5979 Score: 66
Period size: 21 Copynumber: 4.3 Consensus size: 19
5885 AAATGAGAGA
5895 GAAAAAGTAAAAGTTAAGAAT
1 GAAAAAG-AAAA-TTAAGAAT
*
5916 GAAATAA-AAAAATAAGAAT
1 GAAA-AAGAAAATTAAGAAT
*
5935 GAAATAGAAAAATTTAAGAAT
1 GAAAAAG-AAAA-TTAAGAAT
* * *
5956 GAAATAGAAAAATAA-AAA
1 GAAAAAGAAAATTAAGAAT
5974 GAAAAA
1 GAAAAA
5980 AAATGAGAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
18 8 0.15
19 14 0.26
20 12 0.22
21 18 0.33
22 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.16
Consensus pattern (19 bp):
GAAAAAGAAAATTAAGAAT
Found at i:5931 original size:19 final size:19
Alignment explanation
Indices: 5909--5982 Score: 89
Period size: 19 Copynumber: 3.9 Consensus size: 19
5899 AAGTAAAAGT
5909 TAAGAATGAAATAAAAAAA
1 TAAGAATGAAATAAAAAAA
*
5928 TAAGAATGAAATAGAAAAATT
1 TAAGAATGAAATA-AAAAA-A
*
5949 TAAGAATGAAATAGAAAAA
1 TAAGAATGAAATAAAAAAA
*
5968 TAA-AAAGAAA-AAAAA
1 TAAGAATGAAATAAAAA
5983 TGAGAGGGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
17 4 0.08
18 6 0.12
19 16 0.33
20 9 0.19
21 13 0.27
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (19 bp):
TAAGAATGAAATAAAAAAA
Found at i:7860 original size:7 final size:7
Alignment explanation
Indices: 7848--8217 Score: 411
Period size: 7 Copynumber: 52.9 Consensus size: 7
7838 AGTCTAGGCT
7848 TGGACCC
1 TGGACCC
7855 TGGACCC
1 TGGACCC
7862 TGGACCC
1 TGGACCC
7869 TGGACCC
1 TGGACCC
*
7876 TAGACCC
1 TGGACCC
7883 TGGACCC
1 TGGACCC
*
7890 TAGACCC
1 TGGACCC
7897 TGGACCC
1 TGGACCC
**
7904 TAAACCC
1 TGGACCC
*
7911 TAGACCC
1 TGGACCC
*
7918 TAGACCC
1 TGGACCC
*
7925 TAGACCC
1 TGGACCC
*
7932 TAGACCC
1 TGGACCC
*
7939 TCGACCC
1 TGGACCC
*
7946 TAGACCC
1 TGGACCC
*
7953 TAGACCC
1 TGGACCC
*
7960 TAGACCC
1 TGGACCC
*
7967 TAGACCC
1 TGGACCC
**
7974 TAAACCC
1 TGGACCC
*
7981 TAGACCC
1 TGGACCC
7988 TGGACCC
1 TGGACCC
7995 TGGACCC
1 TGGACCC
8002 TGGACCC
1 TGGACCC
8009 TGGACCC
1 TGGACCC
8016 TGGACCC
1 TGGACCC
8023 TGGACCC
1 TGGACCC
8030 TGGACCC
1 TGGACCC
8037 TGGACCC
1 TGGACCC
8044 TGGACCC
1 TGGACCC
8051 TGGACCCCC
1 TGGA--CCC
8060 TGGA-CC
1 TGGACCC
8066 TGGACCC
1 TGGACCC
8073 TGGACCC
1 TGGACCC
8080 TGGACCC
1 TGGACCC
8087 TGGACCC
1 TGGACCC
8094 TGGACCC
1 TGGACCC
8101 TGGACCC
1 TGGACCC
8108 TGGACCC
1 TGGACCC
8115 TGGACCC
1 TGGACCC
8122 TGGACCC
1 TGGACCC
8129 TGGACCC
1 TGGACCC
**
8136 TAAACCC
1 TGGACCC
**
8143 TAAACCC
1 TGGACCC
**
8150 TAAACCC
1 TGGACCC
**
8157 TAAACCC
1 TGGACCC
8164 TGGA-CC
1 TGGACCC
*
8170 TAGACCC
1 TGGACCC
**
8177 TAAACCC
1 TGGACCC
**
8184 TAAACCC
1 TGGACCC
**
8191 CAGACCC
1 TGGACCC
8198 TGGACCC
1 TGGACCC
*
8205 CGGACCC
1 TGGACCC
*
8212 CGGACC
1 TGGACC
8218 ATCTATATGC
Statistics
Matches: 336, Mismatches: 23, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
6 11 0.03
7 318 0.95
9 7 0.02
ACGTcount: A:0.22, C:0.44, G:0.21, T:0.14
Consensus pattern (7 bp):
TGGACCC
Found at i:8196 original size:27 final size:27
Alignment explanation
Indices: 8141--8196 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
8131 GACCCTAAAC
**
8141 CCTAAACCCTAAACCCTAAACCCTGGA
1 CCTAAACCCTAAACCCTAAACCCCAGA
*
8168 CCTAGACCCTAAACCCTAAACCCCAGA
1 CCTAAACCCTAAACCCTAAACCCCAGA
8195 CC
1 CC
8197 CTGGACCCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.45, G:0.07, T:0.12
Consensus pattern (27 bp):
CCTAAACCCTAAACCCTAAACCCCAGA
Found at i:9321 original size:21 final size:20
Alignment explanation
Indices: 9297--9371 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 20
9287 AAATGAGAGA
*
9297 GAAAAAGTAAAAGTTAAGAAT
1 GAAAAAG-AAAAATTAAGAAT
9318 GAAATAA-AAAAATTAAGAAT
1 GAAA-AAGAAAAATTAAGAAT
*
9338 GAAATAGAAAAATTTAAGAAT
1 GAAAAAGAAAAA-TTAAGAAT
*
9359 GAAATAGAAAAAT
1 GAAAAAGAAAAAT
9372 AAAAAGAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
19 1 0.02
20 22 0.45
21 24 0.49
22 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
GAAAAAGAAAAATTAAGAAT
Found at i:9333 original size:20 final size:20
Alignment explanation
Indices: 9305--9371 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
9295 GAGAAAAAGT
*
9305 AAAAGTTAAGAATGAAATAA
1 AAAAATTAAGAATGAAATAA
9325 AAAAATTAAGAATGAAATAGA
1 AAAAATTAAGAATGAAATA-A
* *
9346 AAAATTTAAGAATGAAATAG
1 AAAAATTAAGAATGAAATAA
9366 AAAAAT
1 AAAAAT
9372 AAAAAGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 23 0.55
21 19 0.45
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (20 bp):
AAAAATTAAGAATGAAATAA
Found at i:11269 original size:7 final size:7
Alignment explanation
Indices: 11257--11640 Score: 471
Period size: 7 Copynumber: 54.9 Consensus size: 7
11247 AGTCTAGGCT
11257 TGGACCC
1 TGGACCC
11264 TGGACCC
1 TGGACCC
11271 TGGACCC
1 TGGACCC
11278 TGGACCC
1 TGGACCC
11285 TGGACCC
1 TGGACCC
*
11292 TAGACCC
1 TGGACCC
11299 TGGACCC
1 TGGACCC
**
11306 TAAACCC
1 TGGACCC
*
11313 TAGACCC
1 TGGACCC
*
11320 TAGACCC
1 TGGACCC
*
11327 TAGACCC
1 TGGACCC
*
11334 TCGACCC
1 TGGACCC
*
11341 TAGACCC
1 TGGACCC
*
11348 TAGACCC
1 TGGACCC
*
11355 TAGACCC
1 TGGACCC
*
11362 TAGACCC
1 TGGACCC
**
11369 TAAACCC
1 TGGACCC
*
11376 TAGACCC
1 TGGACCC
11383 TGGACCC
1 TGGACCC
*
11390 TAGACCC
1 TGGACCC
11397 TGGACCC
1 TGGACCC
11404 TGGACCC
1 TGGACCC
11411 TGGACCC
1 TGGACCC
11418 TGGACCC
1 TGGACCC
11425 TGGACCC
1 TGGACCC
11432 TGGACCC
1 TGGACCC
11439 TGGACCC
1 TGGACCC
11446 TGGACCC
1 TGGACCC
11453 TGGACCC
1 TGGACCC
*
11460 TAGACCC
1 TGGACCC
11467 TGGACCC
1 TGGACCC
11474 TGGACCC
1 TGGACCC
11481 TGGACCC
1 TGGACCC
11488 TGGACCC
1 TGGACCC
11495 TGGACCC
1 TGGACCC
11502 TGGACCC
1 TGGACCC
11509 TGGACCC
1 TGGACCC
11516 TGGACCC
1 TGGACCC
11523 TGGACCC
1 TGGACCC
11530 TGGACCC
1 TGGACCC
11537 TGGACCC
1 TGGACCC
11544 TGGACCC
1 TGGACCC
**
11551 TAAACCC
1 TGGACCC
**
11558 TAAACCC
1 TGGACCC
**
11565 TAAACCC
1 TGGACCC
**
11572 TAAACCC
1 TGGACCC
11579 TGGACCC
1 TGGACCC
11586 TGGACCC
1 TGGACCC
*
11593 TAGACCC
1 TGGACCC
**
11600 TAAACCC
1 TGGACCC
**
11607 TAAACCC
1 TGGACCC
**
11614 CAGACCC
1 TGGACCC
11621 TGGACCC
1 TGGACCC
*
11628 CGGACCC
1 TGGACCC
*
11635 CGGACC
1 TGGACC
11641 ATCTATATGC
Statistics
Matches: 352, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 352 1.00
ACGTcount: A:0.22, C:0.44, G:0.21, T:0.14
Consensus pattern (7 bp):
TGGACCC
Found at i:12745 original size:21 final size:20
Alignment explanation
Indices: 12721--12795 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 20
12711 AAATGAGAGA
*
12721 GAAAAAGTAAAAGTTAAGAAT
1 GAAAAAG-AAAAATTAAGAAT
*
12742 GAAAGAGAAAAATTAAGAAT
1 GAAAAAGAAAAATTAAGAAT
*
12762 GAAATAGAAAAATTTAAGAAT
1 GAAAAAGAAAAA-TTAAGAAT
*
12783 GAAATAGAAAAAT
1 GAAAAAGAAAAAT
12796 AAAAAGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
20 24 0.48
21 26 0.52
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAAAGAAAAATTAAGAAT
Found at i:12757 original size:20 final size:20
Alignment explanation
Indices: 12729--12795 Score: 107
Period size: 20 Copynumber: 3.3 Consensus size: 20
12719 GAGAAAAAGT
* *
12729 AAAAGTTAAGAATGAAAGAG
1 AAAAATTAAGAATGAAATAG
12749 AAAAATTAAGAATGAAATAG
1 AAAAATTAAGAATGAAATAG
12769 AAAAATTTAAGAATGAAATAG
1 AAAAA-TTAAGAATGAAATAG
12790 AAAAAT
1 AAAAAT
12796 AAAAAGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 24 0.55
21 20 0.45
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.19
Consensus pattern (20 bp):
AAAAATTAAGAATGAAATAG
Found at i:25784 original size:12 final size:13
Alignment explanation
Indices: 25767--25881 Score: 57
Period size: 12 Copynumber: 9.3 Consensus size: 13
25757 TTCAAAGAGG
25767 TTTTATATT-TAT
1 TTTTATATTATAT
25779 TTTTATATTATA-
1 TTTTATATTATAT
* *
25791 TTTGATTTTA-AT
1 TTTTATATTATAT
*
25803 TTTAATATTAT-T
1 TTTTATATTATAT
* *
25815 TTTTA-AATA-AA
1 TTTTATATTATAT
** *
25826 TTAAATATTAAAT
1 TTTTATATTATAT
25839 TTTTAATATTATAT
1 TTTT-ATATTATAT
**
25853 TATAGATATTA-AT
1 T-TTTATATTATAT
*
25866 TTTAATATTA-AT
1 TTTTATATTATAT
25878 TTTT
1 TTTT
25882 TAAATAAATT
Statistics
Matches: 76, Mismatches: 19, Indels: 16
0.68 0.17 0.14
Matches are distributed among these distances:
11 7 0.09
12 45 0.59
13 8 0.11
14 15 0.20
15 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTTATATTATAT
Found at i:25791 original size:17 final size:17
Alignment explanation
Indices: 25769--25817 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
25759 CAAAGAGGTT
25769 TTATATTTATTTTTATA
1 TTATATTTATTTTTATA
* *
25786 TTATATTTGATTTTAATT
1 TTATATTT-ATTTTTATA
25804 TTA-ATATTATTTTT
1 TTATAT-TTATTTTT
25818 TAAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTATATTTATTTTTATA
Found at i:25848 original size:14 final size:13
Alignment explanation
Indices: 25800--25934 Score: 77
Period size: 14 Copynumber: 10.5 Consensus size: 13
25790 ATTTGATTTT
25800 AATTTTAATATTA
1 AATTTTAATATTA
**
25813 TTTTTTAA-A-TA
1 AATTTTAATATTA
*
25824 AA-TTAAATATTA
1 AATTTTAATATTA
25836 AATTTTTAATATTA
1 AA-TTTTAATATTA
* *
25850 TATTATAGATATT-
1 AATTTTA-ATATTA
25863 AATTTTAATATTA
1 AATTTTAATATTA
*
25876 ATTTTTTAA-A-TA
1 A-ATTTTAATATTA
*
25888 AA-TTAAATATTA
1 AATTTTAATATTA
*
25900 AGTTTTTAATATTA
1 A-ATTTTAATATTA
* * *
25914 TATTATAGATATTT
1 AATTTTA-ATATTA
25928 AATTTTA
1 AATTTTA
25935 TATCATAAAA
Statistics
Matches: 89, Mismatches: 21, Indels: 23
0.67 0.16 0.17
Matches are distributed among these distances:
10 8 0.09
11 4 0.04
12 16 0.18
13 21 0.24
14 40 0.45
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
AATTTTAATATTA
Found at i:25895 original size:64 final size:63
Alignment explanation
Indices: 25777--25934 Score: 259
Period size: 64 Copynumber: 2.5 Consensus size: 63
25767 TTTTATATTT
*
25777 ATTTTT-ATATTATATT-T-GATTTTAATTTTAATATTATTTTTTAAATAAATTAAATATTAA
1 ATTTTTAATATTATATTATAGATATTAATTTTAATATTATTTTTTAAATAAATTAAATATTAA
25837 ATTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAA
1 ATTTTTAATATTATATTATAGATATTAATTTTAATATT-ATTTTTTAAATAAATTAAATATTAA
*
25901 GTTTTTAATATTATATTATAGATATTTAATTTTA
1 ATTTTTAATATTATATTATAGATA-TTAATTTTA
25935 TATCATAAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
60 6 0.07
61 10 0.11
62 1 0.01
63 17 0.19
64 48 0.53
65 9 0.10
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (63 bp):
ATTTTTAATATTATATTATAGATATTAATTTTAATATTATTTTTTAAATAAATTAAATATTAA
Found at i:25989 original size:20 final size:19
Alignment explanation
Indices: 25944--25990 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
25934 ATATCATAAA
25944 AATTATTTTATATATTATT
1 AATTATTTTATATATTATT
*
25963 AA-AATTTTATAT-TTATTTT
1 AATTATTTTATATATTA--TT
25982 AATTATTTT
1 AATTATTTT
25991 GATTTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 9 0.39
19 6 0.26
20 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATTTTATATATTATT
Found at i:26492 original size:31 final size:31
Alignment explanation
Indices: 26455--26514 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
26445 TAGTTGTATG
* *
26455 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
26486 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
26515 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:37611 original size:21 final size:20
Alignment explanation
Indices: 37586--37662 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 20
37576 TAGTGTACTA
37586 TATAGTTTATACTTTATAACC
1 TATAGTTTATA-TTTATAACC
* *
37607 TATAGTATATAATTTATAAAC
1 TATAGTTTAT-ATTTATAACC
* *
37628 TATAGTTTATATTAATATACTA
1 TATAGTTTATATTTATA-AC-C
37650 TATAGTTTATATT
1 TATAGTTTATATT
37663 AATGTTAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
20 6 0.13
21 27 0.57
22 14 0.30
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.49
Consensus pattern (20 bp):
TATAGTTTATATTTATAACC
Found at i:37741 original size:21 final size:20
Alignment explanation
Indices: 37681--37741 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
37671 TTATCTTAAC
*
37681 TATAATTTATATTAATATAGTA
1 TATAATTTATA--AATATACTA
*
37703 TATAGTTTATAAACTATACTA
1 TATAATTTATAAA-TATACTA
37724 TATAATTTATAACATATA
1 TATAATTTATAA-ATATA
37742 GTTTATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 2 0.06
21 21 0.62
22 11 0.32
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
TATAATTTATAAATATACTA
Found at i:37759 original size:88 final size:89
Alignment explanation
Indices: 37607--37786 Score: 251
Period size: 88 Copynumber: 2.0 Consensus size: 89
37597 CTTTATAACC
* * *
37607 TATAGTATATAATTTATAAACTATAGTTTATATTAATATACTATATAGTTTATATTAATGTTAAT
1 TATAGTATATAATTTATAAACTATACTATATATTAATATACTATATAGTTTATATTAATATTAAT
37672 TATCT-TA-ACTATAATTTATATTAA
66 T-T-TATAGACTATAATTTATATTAA
* *
37696 TATAGTATATAGTTTATAAACTATACTATATAATTTATA-AC-ATATAGTTTATATTAATATTAA
1 TATAGTATATAATTTATAAACTATACTATAT-ATTAATATACTATATAGTTTATATTAATATTAA
*
37759 TTTTATAGACTATATTTTATATTAA
65 TTTTATAGACTATAATTTATATTAA
37784 TAT
1 TAT
37787 TAATTACAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
86 1 0.01
87 3 0.04
88 42 0.51
89 30 0.37
90 6 0.07
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (89 bp):
TATAGTATATAATTTATAAACTATACTATATATTAATATACTATATAGTTTATATTAATATTAAT
TTTATAGACTATAATTTATATTAA
Found at i:37778 original size:31 final size:31
Alignment explanation
Indices: 37729--37791 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
37719 TACTATATAA
37729 TTTATAACATATAGTTTATATTAATATTAAT
1 TTTATAACATATAGTTTATATTAATATTAAT
*
37760 TTTATAGAC-TATATTTTATATTAATATTAAT
1 TTTATA-ACATATAGTTTATATTAATATTAAT
37791 T
1 T
37792 ACAAATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTATAACATATAGTTTATATTAATATTAAT
Found at i:37801 original size:88 final size:89
Alignment explanation
Indices: 37620--37865 Score: 225
Period size: 88 Copynumber: 2.9 Consensus size: 89
37610 AGTATATAAT
* * *
37620 TTATAAACTATAGTTTATATTAATATACTATATAGTTTATATTAATGTTAATTATCTTAACTATA
1 TTATAAACTATACTATATATTAATATACTATATAGTTTATATTAATATTAATTATCTTAACTATA
* * **
37685 ATTTATATTAATATAGTATATAGT
66 ATTTATATTAATATAATATACAAA
*
37709 TTATAAACTATACTATATAATTTATA-AC-ATATAGTTTATATTAATATTAATT-T-TATAGACT
1 TTATAAACTATACTATAT-ATTAATATACTATATAGTTTATATTAATATTAATTATCT-TA-ACT
*
37770 ATATTTTATATTAATATTAAT-TACAAA
63 ATAATTTATATTAATA-TAATATACAAA
* * * *
37797 TTATAAACTA-A-TGT-TA-T-AT-TAATATA-AGTTAATATTAATATTAATTATATT-A-TATA
1 TTATAAACTATACTATATATTAATATACTATATAGTTTATATTAATATTAATTATCTTAACTATA
*
37853 A-TTATTTTAATAT
66 ATTTATATTAATAT
37866 TAATTATATT
Statistics
Matches: 135, Mismatches: 14, Indels: 27
0.77 0.08 0.15
Matches are distributed among these distances:
78 1 0.01
79 10 0.07
80 4 0.03
81 1 0.01
82 22 0.16
83 6 0.04
84 2 0.01
85 1 0.01
86 3 0.02
87 4 0.03
88 54 0.40
89 21 0.16
90 6 0.04
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (89 bp):
TTATAAACTATACTATATATTAATATACTATATAGTTTATATTAATATTAATTATCTTAACTATA
ATTTATATTAATATAATATACAAA
Found at i:37801 original size:110 final size:109
Alignment explanation
Indices: 37585--37801 Score: 251
Period size: 110 Copynumber: 2.0 Consensus size: 109
37575 TTAGTGTACT
* * *
37585 ATATAGTTTATACTTTATAACCTATAGTATATAATTTATAAACTATAGTTTATATTAATATACTA
1 ATATAGTATATACTTTATAAACTATACTATATAATTTATAAACTATAGTTTATATTAATATACTA
** * * *
37650 TATAGTTTATATTAATGTTAATTATCTTAACTATAATTTATATTA
66 TATAGACTATATTAATATTAATTA-CTTAACTACAAATTATATTA
*
37695 ATATAGTATATAGTTTATAAACTATACTATATAATTTAT-AACATATAGTTTATATTAATATTAA
1 ATATAGTATATACTTTATAAACTATACTATATAATTTATAAAC-TATAGTTTATATTAATA-T-A
* * * *
37759 TTTTATAGACTATATTTTATATTAA-TA-TTAATTACAAATTATA
63 CTATATAGACTATA-TTAATATTAATTACTTAACTACAAATTATA
37802 AACTAATGTT
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
109 3 0.03
110 65 0.72
111 1 0.01
112 13 0.14
113 8 0.09
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (109 bp):
ATATAGTATATACTTTATAAACTATACTATATAATTTATAAACTATAGTTTATATTAATATACTA
TATAGACTATATTAATATTAATTACTTAACTACAAATTATATTA
Found at i:37833 original size:16 final size:14
Alignment explanation
Indices: 37810--37919 Score: 108
Period size: 13 Copynumber: 8.0 Consensus size: 14
37800 TAAACTAATG
37810 TTATATTAATATAA
1 TTATATTAATATAA
37824 GTTAATATTAATATTAA
1 -TT-ATATTAATA-TAA
37841 TTATATT-ATATAA
1 TTATATTAATATAA
*
37854 TTATTTTAATATTAA
1 TTATATTAATA-TAA
37869 TTATATT-ATATAA
1 TTATATTAATATAA
*
37882 TTATTTTAATATTAA
1 TTATATTAATA-TAA
37897 -T-TA-TAA-ATAA
1 TTATATTAATATAA
37907 TT-TATTAATATAA
1 TTATATTAATATAA
37920 ATTTGATAAG
Statistics
Matches: 82, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.04
11 4 0.05
12 6 0.07
13 23 0.28
14 13 0.16
15 19 0.23
16 11 0.13
17 3 0.04
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (14 bp):
TTATATTAATATAA
Found at i:37862 original size:28 final size:28
Alignment explanation
Indices: 37810--37901 Score: 148
Period size: 28 Copynumber: 3.2 Consensus size: 28
37800 TAAACTAATG
*
37810 TTATATTAATATAAGTTAATATTAATATTAA
1 TTATATT-ATATAA-TT-ATTTTAATATTAA
37841 TTATATTATATAATTATTTTAATATTAA
1 TTATATTATATAATTATTTTAATATTAA
37869 TTATATTATATAATTATTTTAATATTAA
1 TTATATTATATAATTATTTTAATATTAA
37897 TTATA
1 TTATA
37902 AATAATTTAT
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
28 45 0.75
29 2 0.03
30 6 0.10
31 7 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
TTATATTATATAATTATTTTAATATTAA
Found at i:37866 original size:8 final size:9
Alignment explanation
Indices: 37829--37895 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 9
37819 TATAAGTTAA
37829 TATTAATAT
1 TATTAATAT
37838 TAATT-ATAT
1 T-ATTAATAT
37847 TATATAATTAT
1 TAT-TAA-TAT
37858 T-TTAATAT
1 TATTAATAT
37866 TAATT-ATAT
1 T-ATTAATAT
37875 TATATAATTAT
1 TAT-TAA-TAT
37886 T-TTAATAT
1 TATTAATAT
37894 TA
1 TA
37896 ATTATAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
8 12 0.25
9 19 0.40
10 9 0.19
11 8 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATTAATAT
Found at i:37866 original size:34 final size:32
Alignment explanation
Indices: 37825--37917 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 32
37815 TTAATATAAG
37825 TTAATATTAATATTAATTATATTATATAATTA
1 TTAATATTAATATTAATTATATTATATAATTA
37857 -T--T-TTAATATTAATTATATTATATAATTA
1 TTAATATTAATATTAATTATATTATATAATTA
37885 -T--T-TTAATATTAATTATA--A-ATAATTTA
1 TTAATATTAATATTAATTATATTATATAA-TTA
37911 TTAATAT
1 TTAATAT
37918 AAATTTGATA
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
25 4 0.07
26 4 0.07
27 1 0.02
28 43 0.77
29 2 0.04
30 1 0.02
31 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTAATATTAATATTAATTATATTATATAATTA
Found at i:41063 original size:13 final size:13
Alignment explanation
Indices: 41044--41081 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
41034 TAATTTAGTG
41044 ATTATAAATAA-A
1 ATTATAAATAAGA
41056 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
41071 ATTATAAATAA
1 ATTATAAATAA
41082 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:41091 original size:19 final size:19
Alignment explanation
Indices: 41060--41106 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
41050 AATAAAATTT
*
41060 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTAGAA
41078 ATAATATAAAGAATTAGAA
1 ATAATATAAAGAATTAGAA
*
41097 TTAATATAAA
1 ATAATATAAA
41107 AATCAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (19 bp):
ATAATATAAAGAATTAGAA
Found at i:41145 original size:18 final size:17
Alignment explanation
Indices: 41061--41151 Score: 92
Period size: 18 Copynumber: 5.1 Consensus size: 17
41051 ATAAAATTTA
* *
41061 TAATATAAGAATTATAAA
1 TAATATAAAAATTA-AAT
41079 TAATATAAAGAATTAGAAT
1 TAATATAAA-AATTA-AAT
*
41098 TAATATAAAAATCAAAT
1 TAATATAAAAATTAAAT
* *
41115 TTATAATATAAATTATAAT
1 TAAT-ATAAAAATTA-AAT
41134 TAATATAAAAATTAAAT
1 TAATATAAAAATTAAAT
41151 T
1 T
41152 TCAAAAAGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
17 10 0.16
18 29 0.48
19 22 0.36
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (17 bp):
TAATATAAAAATTAAAT
Found at i:41317 original size:16 final size:16
Alignment explanation
Indices: 41298--41336 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
41288 TGAGTCAATT
*
41298 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
41314 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
41330 ACAGGTC
1 ACAGGTC
41337 GGACAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:41408 original size:32 final size:31
Alignment explanation
Indices: 41367--41469 Score: 93
Period size: 32 Copynumber: 3.3 Consensus size: 31
41357 CAGGTCAATC
41367 TCGGGTTCGGGTTCATATCAGTCGGATGCAGT
1 TCGGGTTCGGGTTCATATCAGTCGG-TGCAGT
* * *
41399 TCGGGTTCGGGTATCATATTA-TCGGTTCAAT
1 TCGGGTTCGGGT-TCATATCAGTCGGTGCAGT
* * * *
41430 TCGGGTTCAGG-TCGTTCTCAGTCGGGTGCAGG
1 TCGGGTTCGGGTTC-ATATCAGTC-GGTGCAGT
41462 TCGGGTTC
1 TCGGGTTC
41470 AGATCCACAA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 2 0.04
30 3 0.05
31 16 0.28
32 29 0.51
33 7 0.12
ACGTcount: A:0.14, C:0.19, G:0.34, T:0.33
Consensus pattern (31 bp):
TCGGGTTCGGGTTCATATCAGTCGGTGCAGT
Found at i:51180 original size:9 final size:9
Alignment explanation
Indices: 51166--51190 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
51156 TTCTGTAGAC
51166 AGAGAAACA
1 AGAGAAACA
51175 AGAGAAACA
1 AGAGAAACA
51184 AGAGAAA
1 AGAGAAA
51191 TAGTGCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (9 bp):
AGAGAAACA
Found at i:61849 original size:2 final size:2
Alignment explanation
Indices: 61842--61877 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
61832 AAGGAAACTT
61842 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
61878 CCAAACAACT
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:67377 original size:20 final size:20
Alignment explanation
Indices: 67352--67393 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
67342 TTGAGCACTA
67352 AAAAGAATTATCCTTTAGGG
1 AAAAGAATTATCCTTTAGGG
*
67372 AAAAGAATTATCTTTTAGGG
1 AAAAGAATTATCCTTTAGGG
67392 AA
1 AA
67394 TGATGTCGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (20 bp):
AAAAGAATTATCCTTTAGGG
Found at i:74121 original size:38 final size:38
Alignment explanation
Indices: 74041--74121 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
74031 AACCAATCGG
* * *
74041 CGGTGGTGTGATACGTTAGAGGTACAACAGTGATACGG
1 CGGTGGTGTGATACGATAGAGGTACAACAGGGATACGA
* * * *
74079 CGGTGGTGTGATACGATAGAGGTGCAGCGGGGATGCGA
1 CGGTGGTGTGATACGATAGAGGTACAACAGGGATACGA
74117 CGGTG
1 CGGTG
74122 ACTCACCAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.21
Consensus pattern (38 bp):
CGGTGGTGTGATACGATAGAGGTACAACAGGGATACGA
Found at i:78018 original size:23 final size:23
Alignment explanation
Indices: 77992--78060 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
77982 CACCACAGCT
* *
77992 CGTATAATTGCACTGAAGTTCCA
1 CGTAGAATTGCACTGAAGTGCCA
* * *
78015 CGTAGAATTACACTGTAGTGCCG
1 CGTAGAATTGCACTGAAGTGCCA
* *
78038 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAATTGCACTGAAGTGCCA
78061 TATAAGATGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACTGAAGTGCCA
Found at i:79678 original size:21 final size:21
Alignment explanation
Indices: 79653--79695 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
79643 TCTGGTTCGT
*
79653 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
79674 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
79695 T
1 T
79696 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:83342 original size:18 final size:19
Alignment explanation
Indices: 83301--83342 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 19
83291 TAAATATTAT
83301 TTTAATATAAAAGACTAAAA
1 TTTAA-ATAAAAGACTAAAA
83321 --TAAATAAAA-ACTAAAA
1 TTTAAATAAAAGACTAAAA
83337 TTTAAA
1 TTTAAA
83343 GATCAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.35
17 6 0.30
18 7 0.35
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (19 bp):
TTTAAATAAAAGACTAAAA
Found at i:83744 original size:191 final size:190
Alignment explanation
Indices: 83420--83773 Score: 699
Period size: 191 Copynumber: 1.9 Consensus size: 190
83410 CGGACGGGAT
83420 TTAACAATTAAAATTTGCACAAATAGTCCTTCCCGAAACGACGTCGTTCGGGAAGGCCTATTTAA
1 TTAACAATTAAAATTTGCACAAATAGTCCTTCCCGAAACGACGTCGTTCGGGAAGGCCTATTTAA
83485 GGTCTGAAATGGGCCAGCCTTCATTTCTCAGTTTCTCCTCTCTCTCTCTTCTCTGAGAGAGAATT
66 GGTCTGAAATGGGCCAGCCTTCATTTCTCAGTTTCTCCTCTCTCTCTCTTCTCTGAGAGAGAATT
83550 TTCTCTCTCGCTTCTCTCTAAAACAGAGAGAAGCCAGCCGCCCGGCAGCCGTCTGCCGGTG
131 TTCTCTCTC-CTTCTCTCTAAAACAGAGAGAAGCCAGCCGCCCGGCAGCCGTCTGCCGGTG
83611 TTAACAATTAAAATTTGCACAAATAGTCCTTCCCGAAACGACGTCGTTCGGGAAGGCCTATTTAA
1 TTAACAATTAAAATTTGCACAAATAGTCCTTCCCGAAACGACGTCGTTCGGGAAGGCCTATTTAA
83676 GGTCTGAAATGGGCCAGCCTTCATTTCTCAGTTTCTCCTCTCTCTCTCTTCTCTGAGAGAGAATT
66 GGTCTGAAATGGGCCAGCCTTCATTTCTCAGTTTCTCCTCTCTCTCTCTTCTCTGAGAGAGAATT
83741 TTCTCTCTCCTTCTCTCTAAAACAGAGAGAAGC
131 TTCTCTCTCCTTCTCTCTAAAACAGAGAGAAGC
83774 TGCCGGTGTT
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
190 24 0.15
191 139 0.85
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (190 bp):
TTAACAATTAAAATTTGCACAAATAGTCCTTCCCGAAACGACGTCGTTCGGGAAGGCCTATTTAA
GGTCTGAAATGGGCCAGCCTTCATTTCTCAGTTTCTCCTCTCTCTCTCTTCTCTGAGAGAGAATT
TTCTCTCTCCTTCTCTCTAAAACAGAGAGAAGCCAGCCGCCCGGCAGCCGTCTGCCGGTG
Found at i:84473 original size:3 final size:3
Alignment explanation
Indices: 84457--84552 Score: 99
Period size: 3 Copynumber: 31.7 Consensus size: 3
84447 TTTGGGCTTG
* * *
84457 TAA TAA TATT TAA TAA T-A TTA TAA TAAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
*
84503 TAA TTA TAA TAA TAA TAA -ATA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA T-AA
84548 TAA TA
1 TAA TA
84553 TTTAAATGAA
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
2 5 0.06
3 66 0.84
4 8 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:94177 original size:20 final size:21
Alignment explanation
Indices: 94140--94178 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
94130 AAGCTTTAAC
* *
94140 ATCATCAATTTTCTTTTGATG
1 ATCATCAATTTACCTTTGATG
94161 ATCATC-ATTTACCTTTGA
1 ATCATCAATTTACCTTTGA
94179 AAGTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Consensus pattern (21 bp):
ATCATCAATTTACCTTTGATG
Found at i:94333 original size:20 final size:21
Alignment explanation
Indices: 94287--94333 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
94277 GAGATTATTT
94287 TCAATTTTCAATTTTAAAATA
1 TCAATTTTCAATTTTAAAATA
*
94308 TC-ATTTTTATATTTTAAAA-A
1 TCAATTTTCA-ATTTTAAAATA
94328 -CAATTT
1 TCAATTT
94334 CTCATAATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 11 0.48
21 11 0.48
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (21 bp):
TCAATTTTCAATTTTAAAATA
Found at i:101508 original size:2 final size:2
Alignment explanation
Indices: 101503--101537 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
101493 ATTAGAAGAA
101503 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
101538 AAAGAGCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:104169 original size:42 final size:42
Alignment explanation
Indices: 104122--104210 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
104112 CAAATGACAC
* *
104122 AATAGAGTGGTAATTTAGCGGCGTTTATACCACAAACGCCGT
1 AATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCAT
*
104164 AATAGAGTGGTAAATTAGCGGCGTTTATACCTCAAACGCCAT
1 AATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCAT
104206 AATAG
1 AATAG
104211 GGTTTTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (42 bp):
AATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCAT
Found at i:105938 original size:42 final size:42
Alignment explanation
Indices: 105889--105980 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
105879 ATTTTTGAGT
*
105889 AAACGCCGCAATAAAGTTGGAATATAGTGGCGTTTGGTTTAC
1 AAACGCCGCAATAAAGTTGGAATATAGTGGCGTTTGATTTAC
* * *
105931 AAACGCCGCAATAGAGTTGGCATGTAGTGGCGTTTGATTTAC
1 AAACGCCGCAATAAAGTTGGAATATAGTGGCGTTTGATTTAC
105973 AAACGCCG
1 AAACGCCG
105981 TAAACTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAATAAAGTTGGAATATAGTGGCGTTTGATTTAC
Found at i:107278 original size:23 final size:23
Alignment explanation
Indices: 107248--107296 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
107238 TGGTGGTTAG
*
107248 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
107271 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
107294 TTT
1 TTT
107297 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:114202 original size:26 final size:23
Alignment explanation
Indices: 114173--114238 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
114163 TCTCAAATTT
*
114173 TTAACTTTTTCTTTTCTCTTTCATCC
1 TTAACTTTTTCTTTTCTCTTT--T-A
114199 TTAAC-TTTTCTATTTCT-TTTTA
1 TTAACTTTTTCT-TTTCTCTTTTA
*
114221 TTAACTTTTACTTTTCTC
1 TTAACTTTTTCTTTTCTC
114239 GCTCATTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 10 0.29
23 6 0.17
25 9 0.26
26 10 0.29
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (23 bp):
TTAACTTTTTCTTTTCTCTTTTA
Found at i:118586 original size:23 final size:23
Alignment explanation
Indices: 118559--118607 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
118549 GTTTATGCCC
118559 TGAAACATACAAATGTTGTGTGT
1 TGAAACATACAAATGTTGTGTGT
*
118582 TGAAACATACAAATGTTTTGTGT
1 TGAAACATACAAATGTTGTGTGT
118605 TGA
1 TGA
118608 CACGTTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (23 bp):
TGAAACATACAAATGTTGTGTGT
Found at i:123451 original size:16 final size:16
Alignment explanation
Indices: 123427--123463 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
123417 GGGAAAGTTA
*
123427 TGATGGTTGAAGAACT
1 TGATAGTTGAAGAACT
123443 TGATAGTTGAAGAACT
1 TGATAGTTGAAGAACT
123459 TGATA
1 TGATA
123464 AACTACAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (16 bp):
TGATAGTTGAAGAACT
Found at i:127119 original size:43 final size:42
Alignment explanation
Indices: 127047--127269 Score: 243
Period size: 43 Copynumber: 5.2 Consensus size: 42
127037 AGCATTTTAT
* * *
127047 GGCGTTTGTG-GGAAAACGCCGTTAAATATCAACACCTATTGC
1 GGCGTTTGTGAGAAAAATGCCGCTAAATATC-ACACCTATTGC
* * *
127089 GGCATTTGTGAGAAAAATGTCGTTAAATATCACAACCTATTGC
1 GGCGTTTGTGAGAAAAATGCCGCTAAATATCAC-ACCTATTGC
* * *
127132 GGCATTTGTGAGAAAAACGCCGCTAAATCTCACAACCTATTGC
1 GGCGTTTGTGAGAAAAATGCCGCTAAATATCAC-ACCTATTGC
* * *
127175 GTCGTTTTTGAGAAAAATGCCGCTAAATATAAACACCTATTGC
1 GGCGTTTGTGAGAAAAATGCCGCTAAATAT-CACACCTATTGC
* **
127218 AGCGTTTGTG-GAAAAAATGCCGCTAAACCTCCACACCTATTGC
1 GGCGTTTGTGAG-AAAAATGCCGCTAAATAT-CACACCTATTGC
127261 GGCGTTTGT
1 GGCGTTTGT
127270 AAATATAAAC
Statistics
Matches: 155, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
42 12 0.08
43 141 0.91
44 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
GGCGTTTGTGAGAAAAATGCCGCTAAATATCACACCTATTGC
Found at i:132254 original size:2 final size:2
Alignment explanation
Indices: 132247--132282 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
132237 ATATCATGGG
132247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132283 GAAATTTCAA
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):
AT
Found at i:134839 original size:12 final size:12
Alignment explanation
Indices: 134805--134839 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
134795 GTATCGCAAA
*
134805 TTCGCGTTGCAT
1 TTCGCGTTGCGT
134817 TTCGCGTTGCGT
1 TTCGCGTTGCGT
134829 TTCGCGTTGCG
1 TTCGCGTTGCG
134840 ATAGTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.26, G:0.31, T:0.40
Consensus pattern (12 bp):
TTCGCGTTGCGT
Found at i:134880 original size:21 final size:21
Alignment explanation
Indices: 134854--134965 Score: 90
Period size: 21 Copynumber: 5.4 Consensus size: 21
134844 TTGAAAATCG
134854 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * * *
134875 CATTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
134893 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
** * *
134916 CGTTGCGATTTTCCATA-TCG-
1 CGTTGCGATAGTCTACAGT-GT
134936 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
134957 CGTTGCGAT
1 CGTTGCGAT
134966 TTTCCATCTC
Statistics
Matches: 67, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 23 0.34
21 32 0.48
22 4 0.06
23 2 0.03
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:134900 original size:41 final size:41
Alignment explanation
Indices: 134850--134995 Score: 247
Period size: 41 Copynumber: 3.6 Consensus size: 41
134840 ATAGTTGAAA
*
134850 ATCGCGTTGCGATAGTCTACAGTGTCATTGCGATTTTCCAT
1 ATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAT
*
134891 TTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAT
1 ATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAT
134932 ATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAT
1 ATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAT
* * *
134973 CTCGCGTTGCGAGAGTGTACAGT
1 ATCGCGTTGCGATAGTCTACAGT
134996 ACACTCTCGC
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAT
Found at i:134902 original size:20 final size:20
Alignment explanation
Indices: 134877--134984 Score: 71
Period size: 20 Copynumber: 5.3 Consensus size: 20
134867 TACAGTGTCA
*
134877 TTGCGATTTTCCATTTCGCG
1 TTGCGATTTTCCATGTCGCG
* *
134897 TTGCGATAGTCTACA-GT-GTCG
1 TTGCGAT--TTTCCATGTCG-CG
*
134918 TTGCGATTTTCCATATCGCG
1 TTGCGATTTTCCATGTCGCG
* *
134938 TTGCGATAGTCTACA-GT-GTCG
1 TTGCGAT--TTTCCATGTCG-CG
*
134959 TTGCGATTTTCCATCTCGCG
1 TTGCGATTTTCCATGTCGCG
134979 TTGCGA
1 TTGCGA
134985 GAGTGTACAG
Statistics
Matches: 66, Mismatches: 12, Indels: 20
0.67 0.12 0.20
Matches are distributed among these distances:
19 8 0.12
20 28 0.42
21 22 0.33
22 8 0.12
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCCATGTCGCG
Found at i:135051 original size:41 final size:41
Alignment explanation
Indices: 134994--135138 Score: 177
Period size: 41 Copynumber: 3.5 Consensus size: 41
134984 AGAGTGTACA
* * *
134994 GTACACTCTCGCAACGCGAGATGGAAAATCGCAACGATACT
1 GTACACTATCGCAACGCGAAATGGAAAATCGCAACGACACT
*
135035 GTACACTATCGCAACGCGAAATGGAAAATCACAACGACACT
1 GTACACTATCGCAACGCGAAATGGAAAATCGCAACGACACT
* * *
135076 GTAGACTATCGCAACGCAAAAAGGAAAATCGCAACG-CGA-T
1 GTACACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ACT
* *
135116 TTTCAACTATCGCAACGCGAAAT
1 GTAC-ACTATCGCAACGCGAAAT
135139 ACAACGCGAA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 3 0.03
41 86 0.97
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
GTACACTATCGCAACGCGAAATGGAAAATCGCAACGACACT
Found at i:135143 original size:21 final size:21
Alignment explanation
Indices: 135103--135143 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
135093 AAAAAGGAAA
** *
135103 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATACAACT
135124 ATCGCAACGCGAAATACAAC
1 ATCGCAACGCGAAATACAAC
135144 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATACAACT
Found at i:145168 original size:30 final size:30
Alignment explanation
Indices: 145121--145180 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
145111 AAACTTTGAA
145121 TAAATTCAAATAAGTCCAAAAA-CATTTTG
1 TAAATTCAAATAAGTCCAAAAACCATTTTG
*
145150 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAAAT-AAGTCCAAAAACCATTTTG
145181 CCTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.32
Consensus pattern (30 bp):
TAAATTCAAATAAGTCCAAAAACCATTTTG
Found at i:146471 original size:19 final size:20
Alignment explanation
Indices: 146428--146475 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
146418 CTCTAAATCC
*
146428 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
146448 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
146467 TTTTCAAAA
1 TTTTCAAAA
146476 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:147379 original size:32 final size:33
Alignment explanation
Indices: 147335--147404 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
147325 ACCTTCCAAC
* *
147335 TCCCTAG-TTTTTACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
*
147367 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTA-ACGGGATAAACTAGAACCTT
147401 TCCC
1 TCCC
147405 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (33 bp):
TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
Found at i:147644 original size:20 final size:22
Alignment explanation
Indices: 147619--147658 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
147609 TGTTGTATAT
147619 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
147639 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
147659 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:147804 original size:20 final size:20
Alignment explanation
Indices: 147771--147844 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
147761 GCAGCCTTTG
*
147771 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* **
147791 TGCATCGATACACAGCCTTGA
1 TGCATCGATGCACAG-CAGGA
* *
147812 TTCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
*
147832 AGCATCGATGCAC
1 TGCATCGATGCAC
147845 TAATTGCATT
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:147912 original size:42 final size:42
Alignment explanation
Indices: 147865--147963 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
147855 CGGTGTTTGA
* *
147865 GTGCATGGATGCACTGCA-TGATGCATCGATGCACTAGTACAG
1 GTGCATGGATGCACTGCAGGGATGCATCGATGCACTA-CACAG
* **
147907 GTGCATGGATGCACTGCAGGGATGCATGGATGCACTACAGGG
1 GTGCATGGATGCACTGCAGGGATGCATCGATGCACTACACAG
147949 GTGCATGGATGCACT
1 GTGCATGGATGCACT
147964 TTGACACCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 35 0.69
43 16 0.31
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAGGGATGCATCGATGCACTACACAG
Found at i:147934 original size:21 final size:20
Alignment explanation
Indices: 147866--147963 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 20
147856 GGTGTTTGAG
*
147866 TGCATGGATGCACTGCATGA
1 TGCATGGATGCACTGCAGGA
*
147886 TGCATCGATGCACTAGTACAGG-
1 TGCATGGATGCACT-G--CAGGA
147908 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
* *
147929 TGCATGGATGCACTACAGGGG
1 TGCATGGATGCACTGCA-GGA
147950 TGCATGGATGCACT
1 TGCATGGATGCACT
147964 TTGACACCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.03
20 15 0.22
21 35 0.51
22 13 0.19
23 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:148078 original size:30 final size:32
Alignment explanation
Indices: 148044--148102 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
148034 AACTTTGAAT
148044 AAATTCAATT-AAGTCCAAAAA-CATTTTTGG
1 AAATTCAATTCAAGTCCAAAAACCATTTTTGG
148074 AAATTCAATTCAAGTCCAAAAACCATTTT
1 AAATTCAATTCAAGTCCAAAAACCATTTT
148103 GTCTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 10 0.37
31 11 0.41
32 6 0.22
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (32 bp):
AAATTCAATTCAAGTCCAAAAACCATTTTTGG
Found at i:149394 original size:19 final size:20
Alignment explanation
Indices: 149351--149398 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
149341 TCTAAATCAT
*
149351 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
149371 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
149390 TTTTCAAAA
1 TTTTCAAAA
149399 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:149403 original size:24 final size:24
Alignment explanation
Indices: 149376--149421 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
149366 TTTGGCTTTC
*
149376 AAAATCTATTTTTG-TTTTCAAAAG
1 AAAATC-ATTTTCGATTTTCAAAAG
149400 AAAATCATTTTCGATTTTCAAA
1 AAAATCATTTTCGATTTTCAAA
149422 TTTGAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (24 bp):
AAAATCATTTTCGATTTTCAAAAG
Found at i:150293 original size:32 final size:34
Alignment explanation
Indices: 150257--150326 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
150247 AACCTTAAAC
*
150257 TCCCTAG-TTTTTC-CGGGATAAACTAGAACATT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
* *
150289 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
150323 TCCC
1 TCCC
150327 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACATT
Found at i:150710 original size:20 final size:20
Alignment explanation
Indices: 150681--150754 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
150671 GCAGCCTTCG
*
150681 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* **
150701 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCAC-AGCAGGA
* *
150722 TGCATCGATGCATAGAAGGA
1 TGCATCGATGCACAGCAGGA
150742 TGCATCGATGCAC
1 TGCATCGATGCAC
150755 TAATTGCATT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:150835 original size:13 final size:13
Alignment explanation
Indices: 150798--150827 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
150788 CTAGTGCATG
*
150798 TGCATGGATGCAC
1 TGCAAGGATGCAC
150811 TGCAAGGATGCAC
1 TGCAAGGATGCAC
150824 TGCA
1 TGCA
150828 GGGGTGCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (13 bp):
TGCAAGGATGCAC
Found at i:150946 original size:29 final size:29
Alignment explanation
Indices: 150925--150982 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
150915 AAACTTTGAA
150925 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
150954 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
150983 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:150972 original size:30 final size:30
Alignment explanation
Indices: 150925--150984 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
150915 AAACTTTGAA
150925 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
150954 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
150985 CCTTAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:172662 original size:23 final size:23
Alignment explanation
Indices: 172636--172680 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
172626 CACCACAGCT
*
172636 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
172659 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
172681 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:172898 original size:149 final size:148
Alignment explanation
Indices: 172648--172961 Score: 443
Period size: 149 Copynumber: 2.1 Consensus size: 148
172638 TATAATTGCA
172648 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
* * * * * *
172712 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTC-AAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTG-C-CTCAAAGACCTCACAAATGT
* *
172776 TCCACAGAATATATATATATC
128 TCCAAAGAATATACATATATC
* * * **
172797 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTTCATAAGGATCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
* *
172862 TCCTTAATAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCATAAATGTTCC
66 TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTCC
*
172927 AAAGAATATACATATGTC
131 AAAGAATATACATATATC
172945 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
172962 CCCTCGACTC
Statistics
Matches: 147, Mismatches: 16, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
147 2 0.01
148 50 0.34
149 95 0.65
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTCC
AAAGAATATACATATATC
Found at i:174535 original size:64 final size:63
Alignment explanation
Indices: 174379--174539 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 63
174369 TAATGAAGGT
* * *
174379 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
* * * * *
174444 ATGCATCGATGCACTCCTTAAGAATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGC
* *
174508 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
174540 CCTTAAACAA
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 54 0.67
65 24 0.30
66 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:179080 original size:20 final size:20
Alignment explanation
Indices: 179055--179102 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
179045 GCTTCTCAAC
179055 TCACTCTCAACATTCAGAAT
1 TCACTCTCAACATTCAGAAT
179075 TCACTCTCAACATTCAGAAT
1 TCACTCTCAACATTCAGAAT
179095 TCACTCTC
1 TCACTCTC
179103 CAAGTATTTT
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:0.31, C:0.33, G:0.04, T:0.31
Consensus pattern (20 bp):
TCACTCTCAACATTCAGAAT
Found at i:183189 original size:182 final size:181
Alignment explanation
Indices: 182880--183312 Score: 665
Period size: 182 Copynumber: 2.4 Consensus size: 181
182870 TTTCGGTTTA
* * *
182880 TGTCGATACTTTATAAAAATGTATCGATCCACATCAATATAACAGGAAAAAATATGACAAAACCG
1 TGTCGATACTTTAT-AAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* *
182945 GTCA-CGAAAGGACAAAATCGATAAAGCGCTACCGGATATATTAAAAGTGTCGATAATTTAATAA
65 GT-ATCGAAAAGACAAAATCGATAAAGAGCTACCGGATATATTAAAAGTGTCGATAATTTAATAA
183009 AAGTATCGACACATTG-TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
129 AAGTATCGACACATTGTTG-ATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
*
183062 TGTCGATACTTTATAAATATGTATGGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAA-ATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * *
183127 GTATCGAAAAGACAAAA-CTGGTAACGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATAT
65 GTATCGAAAAGACAAAATC-GATAAAGAGCTACCGGATATATTAAAAGTGTCGATAATTTAATAA
*
183191 AAGTATCGACACTTTGTTGATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
129 AAGTATCGACACATTGTTGATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* *
183244 TGTCGATATTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAACCCG
1 TGTCGATACTTTATAA-AATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
183309 GTAT
65 GTAT
183313 AGAGCGACCG
Statistics
Matches: 231, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
181 5 0.02
182 223 0.97
183 3 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (181 bp):
TGTCGATACTTTATAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGG
TATCGAAAAGACAAAATCGATAAAGAGCTACCGGATATATTAAAAGTGTCGATAATTTAATAAAA
GTATCGACACATTGTTGATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
Found at i:185874 original size:21 final size:21
Alignment explanation
Indices: 185850--185890 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
185840 AAGATAATCA
*
185850 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCCAAGAGAAACTTGAG
*
185871 AGAGTCCAAGAGACACTTGA
1 AGAGTCCAAGAGAAACTTGA
185891 TAGGCATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCCAAGAGAAACTTGAG
Found at i:185964 original size:33 final size:33
Alignment explanation
Indices: 185927--186026 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
185917 AAATAGATGG
185927 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
*
185960 AGTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
* *
185993 AGTGGTGAAAGAAGTTGAGGAGTTGAGAGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
186026 A
1 A
186027 CTTAAGATGG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
Found at i:189601 original size:27 final size:26
Alignment explanation
Indices: 189570--189620 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
189560 AGCATTTTTA
189570 TTTTACTTGTTCATTATTT-TTGTATAG
1 TTTTACTTGTT-ATT-TTTCTTGTATAG
189597 TTTTACTTGTTATTTTTCTTGTAT
1 TTTTACTTGTTATTTTTCTTGTAT
189621 TTTCAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.13
26 9 0.39
27 11 0.48
ACGTcount: A:0.16, C:0.08, G:0.10, T:0.67
Consensus pattern (26 bp):
TTTTACTTGTTATTTTTCTTGTATAG
Found at i:195750 original size:200 final size:200
Alignment explanation
Indices: 195407--196569 Score: 1456
Period size: 200 Copynumber: 5.8 Consensus size: 200
195397 GTAAGCATAT
* *
195407 GTGTCGATACATTTATAAAATGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
195472 GGTAATTTTGT-AATATAATCGGTATAGATATACCAGTTTTATGAGAGAATAGGTCTACAACATG
66 GGTAATTTT-TCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATG
* ** *
195536 TATCGACACTTGTTGAATTTGTGTTGATACTATTTGTATAGAATGAATGCCCCAAAGGGTGCACC
130 TATCGACACTTGTTGAATTTGTGTCGATACTATTTGTCCAGAATGAATGCCCAAAAGGGTGCACC
195601 CATAAA
195 CATAAA
*
195607 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
195672 GGTAATTTTTCAATATAACCGGTGA-AAATATACTGGTTTTATGAGAGAATAGGTCTATAACATG
66 GGTAATTTTTCAATATAACCGGT-ATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATG
* * *
195736 TATCGACACTTGTTGAATTTGTGTCGATACTATTTGTCAAGAA-GAATGCCCCAAAGGATGCACC
130 TATCGACACTTGTTGAATTTGTGTCGATACTATTTGTCCAGAATGAATGCCCAAAAGGGTGCACC
195800 CATAAA
195 CATAAA
* * *
195806 GTATCGATACATTTAT-AAAAGTATCGATCCCAGAAACATCAAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
195870 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTATAACATGT
66 GGTAATTTTTCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
* * * * * * * * * *
195935 ATCAACACTT-TTTAATTTTGTGTCGATACTTTTTGTCCATAATGGATGGCAAAAAGGTTGAACG
131 ATCGACACTTGTTGAA-TTTGTGTCGATACTATTTGTCCAGAATGAATGCCCAAAAGGGTGCACC
*
195999 CATACA
195 CATAAA
* * *
196005 GTGTCAATACATTT-TCAAAAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTAT-AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* *
196069 AGGTAATTTTGT-AATATAACAGGTATAAATATACCGGATTTATGTA-AG-ATAGGTCTACATA-
65 AGGTAATTTT-TCAATATAACCGGTATAAATATACCGGTTTTATG-AGAGAATAGGTCTACA-AC
* * * * * * *
196130 ATATATTGACACTT-TTTAATGTTGTGTCGATATTTTTTGTCCAGAATAAATGTCCAAAAAGGGT
127 ATGTATCGACACTTGTTGAAT-TTGTGTCGATACTATTTGTCCAGAATGAATG-CCCAAAAGGGT
196194 GCACCCATAAA
190 GCACCCATAAA
* *
196205 GTGTCGATAAATTTATAAAAAGTATCGATCCCATAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* ** * *
196270 GGTAATTTTTCAATGTAACCAATATAAATATATCGGTTTTATGAGATAATAGGTCTACAACATGT
66 GGTAATTTTTCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
* * * *
196335 ATCGACACTTGTGGAGA-TCGTGTCGATACT-TTTGGTCCAGAATCAAAGCCCAAAAAGGGTGCA
131 ATCGACACTTGTTGA-ATTTGTGTCGATACTATTT-GTCCAGAATGAATGCCC-AAAAGGGTGCA
196398 CCCATAAA
193 CCCATAAA
* * * * * *
196406 GTGTCGATAAATTTTTAGAAAGTGTTGATCCCAAAAACATCGAAATCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * ** * *
196471 GGTAATTTTTTAATATAACCGGTATAACTATACCAATTTTATGAGAAAATAGGTC-ATCATA-AA
66 GGTAATTTTTCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CA-ACAT
* * * * *
196534 GTATCGATAATTTTTAAATTTGTGTCGATACCATTT
129 GTATCGACACTTGTTGAATTTGTGTCGATACTATTT
196570 TAAATATCGC
Statistics
Matches: 845, Mismatches: 93, Indels: 48
0.86 0.09 0.05
Matches are distributed among these distances:
197 5 0.01
198 142 0.17
199 128 0.15
200 363 0.43
201 200 0.24
202 6 0.01
203 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
ATCGACACTTGTTGAATTTGTGTCGATACTATTTGTCCAGAATGAATGCCCAAAAGGGTGCACCC
ATAAA
Found at i:197144 original size:201 final size:200
Alignment explanation
Indices: 196798--197245 Score: 575
Period size: 201 Copynumber: 2.2 Consensus size: 200
196788 ATATTTATCG
* * * * *
196798 ATAAATATACC-AGTTTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTTTAATGTTGTG
1 ATAAATATACCGA-TTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTGTGAATGTCGTG
* * *
196862 TCGATACTTTTTGTCCATAATAAATGCCCAAAAAGGGTACACTCATAAAGTGTCGATAAATTTAT
65 TCGATACTTTTGGTCCAGAATAAATGCCCAAAAAGGGTACACCCATAAAGTGTCGATAAATTTAT
* * *
196927 AAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGT
130 AAAAACTATCGATCCCAAAAACATCGAAA-CCATAATTATAATGTAATAGGTAATTTTTCAATAT
196992 AATC-GGT
194 AA-CAGGT
* *
196999 ATAAATATACCGATTTTATGAGATAATAGGTCTACA-ACATGTATCGACACTTGTGGA-GATCGT
1 ATAAATATACCGATTTTATGAGAAAATAGGTCTACATA-ATGTATCGACACTTGTGAATG-TCGT
*
197062 GTCGATACTTTTGGTCCAGAATCAAA-GCCCAAAAAGGGTGCACCCATAAAGTGTCGATAAATTT
64 GTCGATACTTTTGGTCCAGAAT-AAATGCCCAAAAAGGGTACACCCATAAAGTGTCGATAAATTT
* * * * *
197126 TTAAAAACTGTTGATCCCAAAAACATCGAAATCATAATTATAATGTAATAGGTAATTTTTTAATA
128 ATAAAAACTATCGATCCCAAAAACATCGAAACCATAATTATAATGTAATAGGTAATTTTTCAATA
197191 TAACAGGT
193 TAACAGGT
* * * * *
197199 ATAACTATATCGGTTTTATGAGAAAATATGTC-ATCATAAAGTATCGA
1 ATAAATATACCGATTTTATGAGAAAATAGGTCTA-CATAATGTATCGA
197246 TAATTTTTAA
Statistics
Matches: 216, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
199 2 0.01
200 76 0.35
201 134 0.62
202 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (200 bp):
ATAAATATACCGATTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTGTGAATGTCGTGT
CGATACTTTTGGTCCAGAATAAATGCCCAAAAAGGGTACACCCATAAAGTGTCGATAAATTTATA
AAAACTATCGATCCCAAAAACATCGAAACCATAATTATAATGTAATAGGTAATTTTTCAATATAA
CAGGT
Found at i:198707 original size:12 final size:12
Alignment explanation
Indices: 198687--198726 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
198677 CAAGCGGTCA
*
198687 ATGAAGATGAAG
1 ATGACGATGAAG
198699 ATGACGATGAAG
1 ATGACGATGAAG
*
198711 ATGACGATGATG
1 ATGACGATGAAG
198723 ATGA
1 ATGA
198727 TGATCCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:198710 original size:18 final size:18
Alignment explanation
Indices: 198687--198726 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
198677 CAAGCGGTCA
198687 ATGAAGATGAAGATGACG
1 ATGAAGATGAAGATGACG
* *
198705 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
198723 ATGA
1 ATGA
198727 TGATCCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:198730 original size:6 final size:6
Alignment explanation
Indices: 198687--198726 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
198677 CAAGCGGTCA
* * *
198687 ATGAAG ATGAAG ATGACG ATGAAG ATGACG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
198727 TGATCCAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:200743 original size:200 final size:199
Alignment explanation
Indices: 200083--200894 Score: 1356
Period size: 200 Copynumber: 4.1 Consensus size: 199
200073 TTCCCATAAA
* * *
200083 GTGTTGATACATTTTGTACAGAATGGATGGCAAAAAGGTTGAACGCATAAAGTGTCGATACATTT
1 GTGTCGATACTTTTTGTCCAGAATGGATGGCAAAAAGGTTGAACGCATAAAGTGTCGATACATTT
* * *
200148 TCAAAAAGTATCAATCCCAAAAATATCGAAACCCATAATTATAATGTAATATGTAATTTTGTAAT
66 TCAAAAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
* *
200213 ATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTA
131 ATAACCGGTATAAATATACC-GTTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTTTTTA
200278 ATTTT
195 ATTTT
*
200283 GTGTCGATACTTTCTGTCCAGAATGGATGGCAAAAAGGTTGAACGCATAAAGTGTCGATACATTT
1 GTGTCGATACTTTTTGTCCAGAATGGATGGCAAAAAGGTTGAACGCATAAAGTGTCGATACATTT
* *
200348 TCAAAATGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
66 TCAAAAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
* *
200413 ATAACCGGTATAAATATATCGGTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTTTTTAA
131 ATAACCGGTATAAATATACCGTTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTTTTTAA
200478 TTTT
196 TTTT
* * *
200482 ATGTCGATACTTTTTGTCCATAATGGATGGCAAAAAGGTTAAACGCATAAAGTGTCGATACATTT
1 GTGTCGATACTTTTTGTCCAGAATGGATGGCAAAAAGGTTGAACGCATAAAGTGTCGATACATTT
* *
200547 TCAAAAAGTCTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
66 TCAAAAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
* *
200612 ATAACCGGTATAAATATACCAGTTTTATGAGAGAATATGTCTACAAAAAGTATCGACGCTTTTTA
131 ATAACCGGTATAAATATACC-GTTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTTTTTA
200677 ATTTT
195 ATTTT
*
200682 GTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGTTGAACGCATAAAGTGTCGATACATTT
1 GTGTCGATACTTTTTGTCCAGAATGGATGGCAAAAAGGTTGAACGCATAAAGTGTCGATACATTT
* *
200747 TAAAAAAGTGTCAATCCCAAAAATATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
66 TCAAAAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
* * *
200812 ATAACCGGTATAAATATACCGATTTTATGAGGGAATAAGTCTACAAAATGTATCGACACTTTTTA
131 ATAACCGGTATAAATATACCG-TTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTTTTTA
200877 A-TTT
195 ATTTT
200881 GTGTCGATACTTTT
1 GTGTCGATACTTTT
200895 AAATAACGCG
Statistics
Matches: 575, Mismatches: 35, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
199 207 0.36
200 368 0.64
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (199 bp):
GTGTCGATACTTTTTGTCCAGAATGGATGGCAAAAAGGTTGAACGCATAAAGTGTCGATACATTT
TCAAAAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
ATAACCGGTATAAATATACCGTTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTTTTTAA
TTTT
Found at i:200888 original size:399 final size:399
Alignment explanation
Indices: 200083--200894 Score: 1374
Period size: 399 Copynumber: 2.0 Consensus size: 399
200073 TTCCCATAAA
* * *
200083 GTGTTGATACATTTTGTACAGAATGGATGGCAAAAAGGTTGAACGCATAAAGTGTCGATACATTT
1 GTGTCGATACTTTTTGTACAGAATGGATGGCAAAAAGGTTAAACGCATAAAGTGTCGATACATTT
* *
200148 TCAAAAAGTATCAATCCCAAAAATATCGAAACCCATAATTATAATGTAATATGTAATTTTGTAAT
66 TCAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
* * *
200213 ATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTA
131 ATAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTTTTTA
*
200278 ATTTTGTGTCGATACTTTCTGTCCAGAATGGATGGCAAAAAGGTTGAACGCATAAAGTGTCGATA
196 ATTTTGTGTCGATACTTTCTGTCCAGAATGGATGCCAAAAAGGTTGAACGCATAAAGTGTCGATA
* * *
200343 CATTTTCAAAATGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT
261 CATTTTAAAAAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT
* *
200408 GTAATATAACCGGTATAAATATATCGGTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTT
326 GTAATATAACCGGTATAAATATACCGGTTTATGAGAGAATAAGTCTACAAAAAGTATCGACACTT
200473 TTTAATTTT
391 TTTAATTTT
* * *
200482 ATGTCGATACTTTTTGTCCATAATGGATGGCAAAAAGGTTAAACGCATAAAGTGTCGATACATTT
1 GTGTCGATACTTTTTGTACAGAATGGATGGCAAAAAGGTTAAACGCATAAAGTGTCGATACATTT
* *
200547 TCAAAAAGTCTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
66 TCAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
* *
200612 ATAACCGGTATAAATATACCAGTTTTATGAGAGAATATGTCTACAAAAAGTATCGACGCTTTTTA
131 ATAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTTTTTA
*
200677 ATTTTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGTTGAACGCATAAAGTGTCGATA
196 ATTTTGTGTCGATACTTTCTGTCCAGAATGGATGCCAAAAAGGTTGAACGCATAAAGTGTCGATA
*
200742 CATTTTAAAAAAGTGTCAATCCCAAAAATATCGAAACCCATAATTATAATGTAATAGGTAATTTT
261 CATTTTAAAAAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT
* * *
200807 GTAATATAACCGGTATAAATATACCGATTTTATGAGGGAATAAGTCTACAAAATGTATCGACACT
326 GTAATATAACCGGTATAAATATACCG-GTTTATGAGAGAATAAGTCTACAAAAAGTATCGACACT
200872 TTTTAA-TTT
390 TTTTAATTTT
200881 GTGTCGATACTTTT
1 GTGTCGATACTTTT
200895 AAATAACGCG
Statistics
Matches: 385, Mismatches: 27, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
399 345 0.90
400 40 0.10
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (399 bp):
GTGTCGATACTTTTTGTACAGAATGGATGGCAAAAAGGTTAAACGCATAAAGTGTCGATACATTT
TCAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAAT
ATAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAAAAAGTATCGACACTTTTTA
ATTTTGTGTCGATACTTTCTGTCCAGAATGGATGCCAAAAAGGTTGAACGCATAAAGTGTCGATA
CATTTTAAAAAAGTGTCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT
GTAATATAACCGGTATAAATATACCGGTTTATGAGAGAATAAGTCTACAAAAAGTATCGACACTT
TTTAATTTT
Found at i:209621 original size:3 final size:3
Alignment explanation
Indices: 209613--209661 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
209603 ACTTGTAATT
* * *
209613 TAA TAA TAA GAA TAA TAA -AA TAA TAG TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
209660 TA
1 TA
209662 GAAAAAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:210036 original size:43 final size:42
Alignment explanation
Indices: 209912--210166 Score: 138
Period size: 43 Copynumber: 5.8 Consensus size: 42
209902 CTGGTCAAGG
* * ** *
209912 GTTGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAG
1 GTTGACACGGCTCCTACGTGATGAAGAG-TC-TGGTTATC-TAAA
* * * * *
209957 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTACA
1 GT--TGACACGGCTCCTACGTGATGAAGA-GTCTGGTTATCTAAA
* ***
210002 GTTGACACAGCTCCTACGTGATGAAGAGATCTGG---TCTGGG
1 GTTGACACGGCTCCTACGTGATGAAGAG-TCTGGTTATCTAAA
* * **
210042 GAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAA
1 G-TTGACACGGCTCCTACGTGATGAAGAG-TCTGGTTATCTAAA
* * * * **
210086 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATG
1 -GT--TGACACGGCTCCTACGTGATGAAGA-GTCTGGTTATCTAAA
*
210132 GTTGACACGGCTCATACGTGATGAAGAGATCTGGT
1 GTTGACACGGCTCCTACGTGATGAAGAG-TCTGGT
210167 CTGGGGATGA
Statistics
Matches: 157, Mismatches: 40, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
40 4 0.03
41 29 0.18
42 2 0.01
43 51 0.32
44 3 0.02
45 9 0.06
46 36 0.23
47 22 0.14
48 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (42 bp):
GTTGACACGGCTCCTACGTGATGAAGAGTCTGGTTATCTAAA
Found at i:210078 original size:130 final size:129
Alignment explanation
Indices: 209883--210212 Score: 482
Period size: 130 Copynumber: 2.5 Consensus size: 129
209873 GTGACATGGT
* * ** * *
209883 TCCTACGTGATGAGGAAATCTGGTCAAGGGTTGACACTGCTCATACGTGATGAAGAGTTCTTGGC
1 TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGC
209948 CATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTACAGTTGACACAGC
65 CATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTACAGTTGACACAGC
210013 TCCTACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGC
1 TCCTACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTGGC
* ** *
210078 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
65 CATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTACAGTTGACACAGC
* * * * * *
210143 TCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGACG-ACTGGC
1 TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA-GTTCTGGC
210207 CATCTT
65 CATCTT
210213 TAGGAGTTAT
Statistics
Matches: 181, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
129 32 0.18
130 121 0.67
131 28 0.15
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (129 bp):
TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
ATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTACAGTTGACACAGC
Found at i:210165 original size:89 final size:83
Alignment explanation
Indices: 210045--210205 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
210035 GTCTGGGGAA
* * *
210045 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGATAACACGGTTCCTACATGA
*
210110 TGAGGACGGCTGGTTATCTATGGT
60 TGAGGACGACTGGTTATCTATGGT
*
210134 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
210199 CGACTGG
66 CGACTGG
210206 CCATCTTTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 33 0.49
86 3 0.04
89 31 0.46
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (83 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
CGACTGGTTATCTATGGT
Found at i:210297 original size:28 final size:28
Alignment explanation
Indices: 210244--210305 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
210234 AAACCAAATT
210244 AAAGATTTGTTTAAAAAGAAACAAACCC
1 AAAGATTTGTTTAAAAAGAAACAAACCC
* * *
210272 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTT-AAAAAGAAACAAACCC
210300 AAAGAT
1 AAAGAT
210306 GATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTAAAAAGAAACAAACCC
Found at i:210664 original size:15 final size:15
Alignment explanation
Indices: 210640--210683 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
210630 AAGATGATCT
*
210640 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
210655 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
210670 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
210684 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:210912 original size:63 final size:66
Alignment explanation
Indices: 210826--210964 Score: 194
Period size: 64 Copynumber: 2.1 Consensus size: 66
210816 TCTAAACGAT
* * *
210826 CTCAAAGATTGGTATTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACA
1 CTCAAAGATT-GTATTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACA
210890 AA
65 AA
* * *
210892 CTCAAAGATT-T-TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAT
1 CTCAAAGATTGTATTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAA
210955 A
66 A
210956 CTCAAAGAT
1 CTCAAAGAT
210965 GAATCACATC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
63 17 0.26
64 39 0.59
66 10 0.15
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (66 bp):
CTCAAAGATTGTATTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAA
A
Found at i:211079 original size:120 final size:119
Alignment explanation
Indices: 210862--211086 Score: 269
Period size: 120 Copynumber: 1.9 Consensus size: 119
210852 GTTGTCTCGA
* *
210862 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
* *
210927 AGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATGAATCACATCTTAAGT
66 AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGAATCACATCTTAAGT
* * * **
210981 GAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAA-AGTTAGTTTTTCATTAGAAACTGTC-TC
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT--TTTTTCAAAAGAAACTGTCTTC
** *
211043 AAGAGAGACAACA-TTTGTTTTTAAAGAAATAGACTCAAAGATGA
63 AAGAGAGA-AA-ATTTTGTTTCAAAAGAAACAGACTCAAAGATGA
211087 TTTTGTTAAG
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
117 1 0.01
118 26 0.29
119 16 0.18
120 45 0.51
121 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (119 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGAATCACATCTTAAGT
Found at i:211253 original size:37 final size:37
Alignment explanation
Indices: 211197--211322 Score: 115
Period size: 37 Copynumber: 3.6 Consensus size: 37
211187 GAAATAGATT
211197 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
* ** * *
211234 CAAAATTTTGTTTCCAAAGAAACAAAC-TCA-A-AG-
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
* *
211267 ---ATTTTTGTTTTAAAAGAAATTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
*
211301 CAAAATTTTGTTTCCAAAGAAA
1 CAAAATTTTGTTTCAAAAGAAA
211323 CAAACTCAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
30 18 0.27
31 2 0.03
32 1 0.02
33 2 0.03
34 2 0.03
35 1 0.02
36 7 0.11
37 33 0.50
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
Found at i:211295 original size:67 final size:66
Alignment explanation
Indices: 211196--211350 Score: 278
Period size: 67 Copynumber: 2.4 Consensus size: 66
211186 AGAAATAGAT
211196 TCAAAGA-TTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAA
1 TCAAAGATTTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAA
211260 C
66 C
*
211261 TCAAAGATTTTTGTTTTAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGATTTTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
211326 AC
65 AC
211328 TCAAAGA-TTTTTTTCAAAAGAAA
1 TCAAAGATTTTTTTTCAAAAGAAA
211351 CAATCTCAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
65 18 0.21
66 8 0.09
67 60 0.70
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (66 bp):
TCAAAGATTTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAA
C
Found at i:211366 original size:27 final size:28
Alignment explanation
Indices: 211301--211370 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
211291 TTAAGAGAGA
*
211301 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
211329 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
211357 CAAAGATTTTTTTC
1 CAAAGATTTTTTTC
211371 TTTTCAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 34 0.87
29 5 0.13
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:211405 original size:94 final size:95
Alignment explanation
Indices: 211234--211408 Score: 239
Period size: 95 Copynumber: 1.9 Consensus size: 95
211224 TTAAGAGAGA
* *
211234 CAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTTAAAAGAAATTATCTTAAGAGA
1 CAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTGTTTTAAAAGAAATTATCTCAAGAGA
*
211299 GACAAAATTTTGTTTCCAAAGAAACAAACT
66 GACAAAACTTTGTTTCCAAAGAAACAAACT
* *** *
211329 CAAAGATTTT-TTTCAAAAGAAACAATCTCAAAGATTTTT-TTCTTTTCA-AAATTGTCTCAAGA
1 CAAA-ATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTGTT-TTAAAAGAAATTATCTCAAGA
211391 GAGACAAAACTTTGTTTC
64 GAGACAAAACTTTGTTTC
211409 AGACTCAAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
94 31 0.44
95 34 0.49
96 5 0.07
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (95 bp):
CAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTGTTTTAAAAGAAATTATCTCAAGAGA
GACAAAACTTTGTTTCCAAAGAAACAAACT
Found at i:211485 original size:25 final size:24
Alignment explanation
Indices: 211457--211565 Score: 74
Period size: 28 Copynumber: 4.1 Consensus size: 24
211447 CAAAACTTTG
* *
211457 TTTCAAAATAAATAGACTCAAAGAT
1 TTTCAAAAGAAACA-ACTCAAAGAT
211482 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--A-T
* *
211509 TATTCAAAAGGAACAGACTCCAAGAT
1 T-TTCAAAAGAAACA-ACTCAAAGAT
* *
211535 TTTTATTCAAAGGAACAAACTCAAAGAT
1 TTTCA---AAAGAAAC-AACTCAAAGAT
211563 TTT
1 TTT
211566 TTCAAGAGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
24 8 0.12
25 15 0.22
26 3 0.04
27 3 0.04
28 32 0.46
29 8 0.12
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.28
Consensus pattern (24 bp):
TTTCAAAAGAAACAACTCAAAGAT
Found at i:211518 original size:28 final size:29
Alignment explanation
Indices: 211483--211725 Score: 162
Period size: 28 Copynumber: 8.4 Consensus size: 29
211473 CTCAAAGATT
211483 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATATTTA
* * * *
211511 TTCAAAAGGAACAGACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATATTTA
*
211540 TTC-AAAGGAACAAACTCAAAGAT-TTT-
1 TTCAAAAGAAACAAACTCAAAGATATTTA
* *** * *
211566 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT
1 TTCAAAAGAAACAAACTC-A-A-AG---ATA-TTT-A
* * *
211603 TTCAAAATAAATAGACTCAAAG--ATTT-
1 TTCAAAAGAAACAAACTCAAAGATATTTA
211629 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATATTTA
* * *
211657 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATATTTA
* * *
211686 TTCTAAAGGAACAAACTCAAAGAT-TTTT
1 TTCAAAAGAAACAAACTCAAAGATATTTA
*
211714 TTCAAGAGAAAC
1 TTCAAAAGAAAC
211726 TGTCTCAAGA
Statistics
Matches: 170, Mismatches: 29, Indels: 32
0.74 0.13 0.14
Matches are distributed among these distances:
25 8 0.05
26 13 0.08
27 16 0.09
28 56 0.33
29 54 0.32
30 2 0.01
33 1 0.01
34 2 0.01
35 4 0.02
36 1 0.01
37 13 0.08
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATATTTA
Found at i:211539 original size:29 final size:29
Alignment explanation
Indices: 211483--211725 Score: 164
Period size: 29 Copynumber: 8.4 Consensus size: 29
211473 CTCAAAGATT
*
211483 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* * *
211511 TTCAAAAGGAACAGACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
211540 TTC-AAAGGAACAAACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *** *
211566 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT-
1 TTCAAAAGAAACAAACTC-A-A-AG-----A-TTTTTA
* * *
211603 TTCAAAATAAATAGACTCAAAGA--TTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
211629 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
211657 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
211686 TTCTAAAGGAACAAACTCAAAGATTTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
211714 TTCAAGAGAAAC
1 TTCAAAAGAAAC
211726 TGTCTCAAGA
Statistics
Matches: 170, Mismatches: 29, Indels: 32
0.74 0.13 0.14
Matches are distributed among these distances:
25 9 0.05
26 15 0.09
27 16 0.09
28 49 0.29
29 58 0.34
30 2 0.01
34 2 0.01
35 2 0.01
36 1 0.01
37 16 0.09
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTA
Found at i:211610 original size:145 final size:147
Alignment explanation
Indices: 211411--211744 Score: 597
Period size: 146 Copynumber: 2.3 Consensus size: 147
211401 TTTGTTTCAG
* *
211411 ACTCAAAGA-TTTTTC-A-CGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
*
211473 CTCAAAGA-TTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAGACTCCAAGATTT
66 CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
211537 TTATTC-AAAGGAACAA
131 TTATTCTAAAGGAACAA
211553 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
211618 CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
66 CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
211683 TTATTCTAAAGGAACAA
131 TTATTCTAAAGGAACAA
211700 ACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 ACTCAAAGA-TTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
211745 AAAAAATCGT
Statistics
Matches: 183, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
142 9 0.05
143 6 0.03
144 1 0.01
145 52 0.28
146 61 0.33
147 19 0.10
148 35 0.19
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (147 bp):
ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
TTATTCTAAAGGAACAA
Found at i:212053 original size:36 final size:35
Alignment explanation
Indices: 211969--212066 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 35
211959 GAGAAAATGA
* *
211969 TGTCTCAAGCGAGACAAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
* ** *
212003 AGTCTCAAATGAGACAAAATTTGTTTTTAGTGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
*
212039 TGTCTCAAGCGAGACAAAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
212067 GAGGAAACGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 20 0.38
35 4 0.08
36 28 0.54
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:212081 original size:36 final size:36
Alignment explanation
Indices: 211970--212088 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
211960 AGAAAATGAT
* * * *
211970 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGTGAAATC
** *
212004 GTCTCAAATGAGACAAAATTTGTTTTTAGTGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGTGAAATC
*
212040 GTCTCAAGCGAGACAAAGTTTGTTTTTGAG-GAAA-C
1 GTCTCAAGCGAGACAAAATTTGTTTTT-AGTGAAATC
*
212075 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
212089 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 20 0.29
35 5 0.07
36 43 0.61
37 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGTGAAATC
Found at i:212227 original size:105 final size:100
Alignment explanation
Indices: 212040--212272 Score: 272
Period size: 105 Copynumber: 2.2 Consensus size: 100
212030 TAGTGAAATT
*
212040 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGGAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACAAA-TTTG-TTTTGAAGAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
* *
212105 TGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 TGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
212142 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAAGAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGAC-AAATTTGTTTTG-AAGAAAC--G-ATCTCAA-GTGAGATCAACTTTGTTT
* * * *
212206 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 AAT-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
212247 GTCTCAAGCGAAACACAATTTGTTTT
1 GTCTCAAGCGAGACA-AATTTGTTTT
212273 AAAATTCTCA
Statistics
Matches: 113, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
101 5 0.04
102 24 0.21
103 3 0.03
104 5 0.04
105 76 0.67
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAATTTGTTTTGAAGAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:219470 original size:3 final size:3
Alignment explanation
Indices: 219462--219513 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
219452 ACTTGTAATT
* * *
219462 TAA TAA TAA GAA TAA TAA -AA TAA TAG TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
219509 TAA TA
1 TAA TA
219514 GAAAAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:249564 original size:18 final size:19
Alignment explanation
Indices: 249528--249564 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
249518 ATCTATTAAA
249528 TTCTTTTACTTTATTTATT
1 TTCTTTTACTTTATTTATT
249547 TTCTTATTA-TTT-TTTATT
1 TTCTT-TTACTTTATTTATT
249565 CAATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 8 0.47
20 3 0.18
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (19 bp):
TTCTTTTACTTTATTTATT
Found at i:260724 original size:21 final size:21
Alignment explanation
Indices: 260700--260739 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
260690 TTTATTTTAT
260700 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
260721 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
260740 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:260787 original size:33 final size:33
Alignment explanation
Indices: 260734--260832 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
260724 TTTGTTTCAA
260734 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
260766 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
260799 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
260832 T
1 T
260833 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:260861 original size:13 final size:13
Alignment explanation
Indices: 260818--260872 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
260808 TTGGAAGTAT
260818 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
260831 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
260845 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
260858 TTAAGTATTTAAA
1 TTAAGTATTTCAA
260871 TT
1 TT
260873 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:261440 original size:15 final size:17
Alignment explanation
Indices: 261414--261445 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
261404 TTCTATGAGA
261414 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
261430 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
261446 CGGTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:273405 original size:26 final size:26
Alignment explanation
Indices: 273369--273422 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
273359 ATGTTGGGCA
273369 AAATGCTTCTTAAAAGCTAAGGTGCT
1 AAATGCTTCTTAAAAGCTAAGGTGCT
273395 AAATGCTTCTTAAAAGCTAAGGTGCT
1 AAATGCTTCTTAAAAGCTAAGGTGCT
273421 AA
1 AA
273423 GCATTTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (26 bp):
AAATGCTTCTTAAAAGCTAAGGTGCT
Found at i:292471 original size:17 final size:17
Alignment explanation
Indices: 292446--292505 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
292436 TTTTATATCC
*
292446 AAATAATAATTTTAACT
1 AAATTATAATTTTAACT
* *
292463 AAATTATAAATTTATC-
1 AAATTATAATTTTAACT
*
292479 AAATTATTAATTATAA-T
1 AAATTA-TAATTTTAACT
292496 AAATATATAA
1 AAAT-TATAA
292506 ATATTCTACA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 6 0.18
17 26 0.76
18 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTATAATTTTAACT
Done.