Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006338.1 Hibiscus syriacus cultivar Beakdansim tig00015152_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: 149391
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:17 original size:7 final size:7
Alignment explanation
Indices: 1--996 Score: 1641
Period size: 7 Copynumber: 146.0 Consensus size: 7
1 ACCCT-A
1 ACCCTAA
7 ACCCTAA
1 ACCCTAA
14 ACCCTAA
1 ACCCTAA
21 ACCCTAA
1 ACCCTAA
28 ACCCTAA
1 ACCCTAA
35 ACCCTAA
1 ACCCTAA
42 ACCCTAA
1 ACCCTAA
49 ACCCT-A
1 ACCCTAA
55 ACCCTAA
1 ACCCTAA
62 ACCCT-A
1 ACCCTAA
68 ACCCTAA
1 ACCCTAA
75 ACCCTAA
1 ACCCTAA
82 ACCCTAA
1 ACCCTAA
*
89 CCCCTAA
1 ACCCTAA
96 ACCCTAA
1 ACCCTAA
103 ACCCTAA
1 ACCCTAA
110 ACCCTAA
1 ACCCTAA
117 ACCCT-A
1 ACCCTAA
123 ACCCTAA
1 ACCCTAA
130 ACCCTAA
1 ACCCTAA
137 ACCCT-A
1 ACCCTAA
143 ACCCTAA
1 ACCCTAA
150 ACCCTAA
1 ACCCTAA
157 ACCCTAA
1 ACCCTAA
164 ACCCTAA
1 ACCCTAA
171 ACCC-AA
1 ACCCTAA
177 ACCCTAA
1 ACCCTAA
184 ACCCT-A
1 ACCCTAA
190 ACCCTAA
1 ACCCTAA
197 ACCCT-A
1 ACCCTAA
203 ACCCTAA
1 ACCCTAA
210 ACCCTAA
1 ACCCTAA
217 ACCCTAA
1 ACCCTAA
224 ACCCT-A
1 ACCCTAA
230 ACCC-AA
1 ACCCTAA
236 ACCCT-A
1 ACCCTAA
242 ACCCTAA
1 ACCCTAA
249 ACCCTAA
1 ACCCTAA
256 ACCCT-A
1 ACCCTAA
262 ACCCTAA
1 ACCCTAA
269 ACCCT-A
1 ACCCTAA
275 ACCCTAA
1 ACCCTAA
282 ACCCTAA
1 ACCCTAA
289 ACCCTAA
1 ACCCTAA
296 ACCCTAA
1 ACCCTAA
303 ACCTACCTAA
1 A-C--CCTAA
313 ACCCTAA
1 ACCCTAA
320 ACCCTAA
1 ACCCTAA
327 ACCCTAA
1 ACCCTAA
334 ACCCT-A
1 ACCCTAA
340 ACCCTAA
1 ACCCTAA
347 ACCCTAAAA
1 ACCCT--AA
356 ACCCTAA
1 ACCCTAA
363 ACCCTAA
1 ACCCTAA
370 ACCCTAA
1 ACCCTAA
377 ACCCTAA
1 ACCCTAA
384 ACCCTAA
1 ACCCTAA
391 ACCCTAA
1 ACCCTAA
398 ACCCTAA
1 ACCCTAA
405 ACCC-AA
1 ACCCTAA
411 ACCCTAA
1 ACCCTAA
418 ACCCCTAAAAA
1 A-CCCT---AA
429 ACCCTAA
1 ACCCTAA
436 ACCCTAA
1 ACCCTAA
443 ACCCTAA
1 ACCCTAA
450 ACCCTAA
1 ACCCTAA
457 A-CCTAA
1 ACCCTAA
463 ACCCTAA
1 ACCCTAA
470 ACCCTAA
1 ACCCTAA
477 ACCCTAA
1 ACCCTAA
484 ACCCTAA
1 ACCCTAA
491 ACCCT-A
1 ACCCTAA
497 ACCCTAA
1 ACCCTAA
504 ACCCTAA
1 ACCCTAA
511 ACCCTAA
1 ACCCTAA
518 ACCCT-A
1 ACCCTAA
524 ACCCT-A
1 ACCCTAA
530 ACCCT-A
1 ACCCTAA
536 ACCCTAA
1 ACCCTAA
543 ACCCTAA
1 ACCCTAA
550 ACCCTAA
1 ACCCTAA
557 ACCCTAA
1 ACCCTAA
564 ACCCT-A
1 ACCCTAA
570 ACCCT--
1 ACCCTAA
575 ACCCTAA
1 ACCCTAA
582 ACCCTAA
1 ACCCTAA
589 ACCCTAA
1 ACCCTAA
596 ACCCTAA
1 ACCCTAA
603 A-CCT-A
1 ACCCTAA
608 ACCCTAA
1 ACCCTAA
615 ACCCT-A
1 ACCCTAA
621 ACCCTAA
1 ACCCTAA
628 ACCCTAA
1 ACCCTAA
635 ACCCT-A
1 ACCCTAA
641 ACCCTAA
1 ACCCTAA
648 ACCCTAA
1 ACCCTAA
655 ACCCTAA
1 ACCCTAA
662 ACCCTAA
1 ACCCTAA
669 ACCCTAA
1 ACCCTAA
676 ACCCT-A
1 ACCCTAA
682 ACCCT-A
1 ACCCTAA
688 ACCCTAA
1 ACCCTAA
695 A-CCTAA
1 ACCCTAA
701 ACCCTAA
1 ACCCTAA
708 ACCCTAA
1 ACCCTAA
715 ACCCT-A
1 ACCCTAA
721 ACCCTAA
1 ACCCTAA
728 ACCCT-A
1 ACCCTAA
734 ACCCT-A
1 ACCCTAA
740 ACCCTAA
1 ACCCTAA
747 ACCCTAA
1 ACCCTAA
754 ACCCTAA
1 ACCCTAA
761 ACCCTAA
1 ACCCTAA
768 ACCCTAA
1 ACCCTAA
775 ACCCTAA
1 ACCCTAA
782 ACCCTAA
1 ACCCTAA
789 ACCCTAA
1 ACCCTAA
796 ACCCTAA
1 ACCCTAA
803 ACCCTAA
1 ACCCTAA
810 ACCCTAA
1 ACCCTAA
817 ACCCTAA
1 ACCCTAA
824 ACCCTAA
1 ACCCTAA
831 ACCCTAA
1 ACCCTAA
838 ACCCT-A
1 ACCCTAA
844 ACCCTAA
1 ACCCTAA
851 ACCCTAA
1 ACCCTAA
858 ACCCTAA
1 ACCCTAA
865 ACCCTAA
1 ACCCTAA
872 ACCCTAA
1 ACCCTAA
879 ACCCT-A
1 ACCCTAA
885 ACCCTAA
1 ACCCTAA
892 ACCCTAA
1 ACCCTAA
899 ACCCTAA
1 ACCCTAA
906 ACCCTAA
1 ACCCTAA
913 ACCCTAA
1 ACCCTAA
920 ACCCTAA
1 ACCCTAA
927 ACCCTAA
1 ACCCTAA
934 ACCCTAA
1 ACCCTAA
941 ACCCTAAA
1 ACCCT-AA
949 ACCCTAA
1 ACCCTAA
956 ACCCTAA
1 ACCCTAA
963 ACCCTAA
1 ACCCTAA
970 ACCCTAA
1 ACCCTAA
977 ACCCT-A
1 ACCCTAA
983 ACCCTAA
1 ACCCTAA
990 ACCCTAA
1 ACCCTAA
997 CCCGACCCCG
Statistics
Matches: 947, Mismatches: 2, Indels: 81
0.92 0.00 0.08
Matches are distributed among these distances:
5 7 0.01
6 195 0.21
7 712 0.75
8 12 0.01
9 8 0.01
10 10 0.01
11 3 0.00
ACGTcount: A:0.42, C:0.44, G:0.00, T:0.14
Consensus pattern (7 bp):
ACCCTAA
Found at i:1021 original size:7 final size:7
Alignment explanation
Indices: 997--1367 Score: 638
Period size: 7 Copynumber: 54.6 Consensus size: 7
987 TAAACCCTAA
997 CCCGA-C
1 CCCGAGC
1003 CCCGAG-
1 CCCGAGC
1009 CCCGAGC
1 CCCGAGC
1016 CCCGAG-
1 CCCGAGC
1022 CCCGAGC
1 CCCGAGC
1029 CCCGAGC
1 CCCGAGC
1036 CCCGAG-
1 CCCGAGC
1042 CCCGAG-
1 CCCGAGC
1048 CCCGAGC
1 CCCGAGC
1055 CCCGAG-
1 CCCGAGC
1061 CCCGAGC
1 CCCGAGC
1068 CCCGAGC
1 CCCGAGC
1075 CCCGAGC
1 CCCGAGC
1082 CCCGAGC
1 CCCGAGC
1089 CCCGAGC
1 CCCGAGC
1096 CCCGAGC
1 CCCGAGC
1103 CCCGAGC
1 CCCGAGC
1110 CCCGAGC
1 CCCGAGC
1117 CCCGAGC
1 CCCGAGC
1124 CCCGAGC
1 CCCGAGC
1131 CCCGAGC
1 CCCGAGC
1138 CCCGAGC
1 CCCGAGC
1145 CCCGAGC
1 CCCGAGC
1152 CCCGAGC
1 CCCGAGC
1159 CCCGAGC
1 CCCGAGC
1166 CCCGAGC
1 CCCGAGC
1173 CCCGAGC
1 CCCGAGC
1180 CCCGAGC
1 CCCGAGC
1187 CCCGA-C
1 CCCGAGC
1193 CCCGAGC
1 CCCGAGC
1200 CCCGAGC
1 CCCGAGC
1207 CCCGAGC
1 CCCGAGC
1214 CCCGAGC
1 CCCGAGC
1221 CCCGAGC
1 CCCGAGC
1228 CCC--GC
1 CCCGAGC
1233 CCCGAGC
1 CCCGAGC
1240 CCCGAGC
1 CCCGAGC
1247 CCCGAGC
1 CCCGAGC
1254 CCCGAGC
1 CCCGAGC
1261 CCCGAGC
1 CCCGAGC
1268 CCCGAGC
1 CCCGAGC
1275 CCCGAGC
1 CCCGAGC
1282 CCCGAGC
1 CCCGAGC
1289 CCCGAGC
1 CCCGAGC
*
1296 CCCGATC
1 CCCGAGC
1303 CCCGAG-
1 CCCGAGC
1309 CCCGAGC
1 CCCGAGC
1316 CCCGAGC
1 CCCGAGC
1323 CCCGAGC
1 CCCGAGC
1330 CCCGAGC
1 CCCGAGC
1337 CCCGAGC
1 CCCGAGC
1344 CCCGAG-
1 CCCGAGC
*
1350 CCCGAAC
1 CCCGAGC
*
1357 CCCGAAC
1 CCCGAGC
1364 CCCG
1 CCCG
1368 GACCCTTTGT
Statistics
Matches: 352, Mismatches: 3, Indels: 19
0.94 0.01 0.05
Matches are distributed among these distances:
5 5 0.01
6 52 0.15
7 295 0.84
ACGTcount: A:0.15, C:0.57, G:0.28, T:0.00
Consensus pattern (7 bp):
CCCGAGC
Found at i:1959 original size:22 final size:23
Alignment explanation
Indices: 1931--2012 Score: 107
Period size: 22 Copynumber: 3.7 Consensus size: 23
1921 TCTACATCTA
1931 TATTCTTCAAAGATGATAGATT-
1 TATTCTTCAAAGATGATAGATTC
* *
1953 TATTCTTCAAATATGATAAATTC
1 TATTCTTCAAAGATGATAGATTC
* *
1976 T-CTCTTCAAAGATGGTAGATTC
1 TATTCTTCAAAGATGATAGATTC
1998 TATT-TTCAAAGATGA
1 TATTCTTCAAAGATGA
2013 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 48 0.96
23 2 0.04
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (23 bp):
TATTCTTCAAAGATGATAGATTC
Found at i:2789 original size:42 final size:43
Alignment explanation
Indices: 2697--2816 Score: 145
Period size: 42 Copynumber: 2.8 Consensus size: 43
2687 CCTGAATTTG
* * ** *
2697 TAAGTCCATCGGGCCATCTGTAAG-TCTTTAAAGCATGATGCT
1 TAAGTCCTTCGGGCCATCTGTAAGATCTTCAGTGCAAGATGCT
* * *
2739 TAAATCCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATG-T
1 TAAGTCCTTCGGGCCATCTGTAAGATCTTCAGTGCAAGATGCT
*
2781 TAAGTCCTTCGGGCCATCTATAAGATCTTCAGTGCA
1 TAAGTCCTTCGGGCCATCTGTAAGATCTTCAGTGCA
2817 GGATATTTTC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 54 0.83
43 11 0.17
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (43 bp):
TAAGTCCTTCGGGCCATCTGTAAGATCTTCAGTGCAAGATGCT
Found at i:3147 original size:42 final size:42
Alignment explanation
Indices: 3085--3212 Score: 175
Period size: 42 Copynumber: 3.0 Consensus size: 42
3075 GTTTCTTAAT
* * *
3085 TTAAATCCTTCGGGTTATCTGTAAGACCTTCAGTACAAGATG
1 TTAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATG
* * *
3127 TTAAAGCCTTTGGGTCATCTGTAAGACCTTCAATGCAAGATA
1 TTAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATG
** *
3169 TTAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATG
1 TTAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATG
3211 TT
1 TT
3213 TTCAAAGGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (42 bp):
TTAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATG
Found at i:3199 original size:129 final size:129
Alignment explanation
Indices: 2927--3167 Score: 324
Period size: 129 Copynumber: 1.9 Consensus size: 129
2917 TTGACAACTA
* *
2927 AGAAACTAAG-CCTTCGGGGGCTTCTTAATTTAAATCCTTCGTGTCATCTGTAAGACCTTCAGTG
1 AGAAACTAAGACCTTCGGGGGCTTCTTAATTTAAATCCTTCGGGTCATCTGTAAGACCTTCAGTA
* * * * * *
2991 CAAGATGTTAAAGCCTTCGAGCCATCCATAAGACTTTCAGTGCAGGATGTTTCCAAATGAGATTT
66 CAAGATGTTAAAGCCTTCGAGCCATCCATAAGACCTTCAATGCAAGATGATT-CAAATGACATTG
* *
3056 AGAAACTAA-ACCTTCGGGGGTTTCTTAATTTAAATCCTTCGGGTTATCTGTAAGACCTTCAGTA
1 AGAAACTAAGACCTTCGGGGGCTTCTTAATTTAAATCCTTCGGGTCATCTGTAAGACCTTCAGTA
* * * **
3120 CAAGATGTTAAAGCCTTTGGGTCATCTGTAAGACCTTCAATGCAAGAT
66 CAAGATGTTAAAGCCTTCGAGCCATCCATAAGACCTTCAATGCAAGAT
3168 ATTAAAGCCT
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
129 99 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (129 bp):
AGAAACTAAGACCTTCGGGGGCTTCTTAATTTAAATCCTTCGGGTCATCTGTAAGACCTTCAGTA
CAAGATGTTAAAGCCTTCGAGCCATCCATAAGACCTTCAATGCAAGATGATTCAAATGACATTG
Found at i:5248 original size:15 final size:16
Alignment explanation
Indices: 5220--5251 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5210 TTAGGACTAT
5220 TAATTTATATATTTTA
1 TAATTTATATATTTTA
5236 TAATTTA-ATATTTTA
1 TAATTTATATATTTTA
5251 T
1 T
5252 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTTATATATTTTA
Found at i:5296 original size:27 final size:25
Alignment explanation
Indices: 5222--5296 Score: 71
Period size: 27 Copynumber: 2.9 Consensus size: 25
5212 AGGACTATTA
* *
5222 ATTTATATATTTTATAATTTAATAT
1 ATTTATTTATTTTTTAATTTAATAT
* *
5247 -TTTATTTTTATTTTTATTCTTAATAAT
1 ATTTATTTAT-TTTTTAAT-TTAAT-AT
5274 ATTTATTTATTTTTTAATATTAA
1 ATTTATTTATTTTTTAAT-TTAA
5297 GAATGGGGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
24 7 0.18
25 6 0.15
26 5 0.13
27 13 0.33
28 8 0.21
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (25 bp):
ATTTATTTATTTTTTAATTTAATAT
Found at i:5374 original size:2 final size:2
Alignment explanation
Indices: 5367--5391 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5357 ATACTTTACT
5367 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5392 GACTTCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5999 original size:2 final size:2
Alignment explanation
Indices: 5975--6143 Score: 107
Period size: 2 Copynumber: 90.0 Consensus size: 2
5965 ACATATACAC
* * *
5975 TA TA TA -A TA TA AA TA TA CA -A TA TA TA AA 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 TA TA TA
* * *
6015 TA TA TA CA -A TA TA AA TA TA CTA TA -A T- TA TA -A TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
6054 TA TA -A TCA TA TA -A TA TG TA TA TA T- TA TA TA -A TA TA AA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
6093 TA CTA TA -A GA TA TA TA -A TA TA TA AA TA TA TA -A TA -A TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6132 -A TA TA CTA TA TA
1 TA TA TA -TA TA TA
6144 AAAAGGGTCG
Statistics
Matches: 131, Mismatches: 17, Indels: 38
0.70 0.09 0.20
Matches are distributed among these distances:
1 15 0.11
2 108 0.82
3 8 0.06
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (2 bp):
TA
Found at i:6120 original size:66 final size:62
Alignment explanation
Indices: 5977--6145 Score: 215
Period size: 64 Copynumber: 2.7 Consensus size: 62
5967 ATATACACTA
*
5977 TATAATATAAATATACAATATATAAATATATATATATATATATACAATATAAATATACTATAAT
1 TATAATATAAATATATAATATAT-AATATATATATATATATATA-AATATAAATATACTATAAT
*
6041 TATAATATAAATATATAATCATATAATATGTATATAT-TATAT-AATATAAATATACTATAA-
1 TATAATATAAATATATAAT-ATATAATATATATATATATATATAAATATAAATATACTATAAT
*
6101 GAT-ATAT-AATATATAAATATATAATA-ATATAATATACTATATAAA
1 TATAATATAAATATAT-AATATATAATATATAT-ATATA-TATATAAA
6146 AAGGGTCGGA
Statistics
Matches: 95, Mismatches: 4, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
57 3 0.03
58 19 0.20
59 7 0.07
60 7 0.07
61 20 0.21
63 5 0.05
64 30 0.32
65 4 0.04
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (62 bp):
TATAATATAAATATATAATATATAATATATATATATATATATAAATATAAATATACTATAAT
Found at i:20781 original size:31 final size:31
Alignment explanation
Indices: 20757--20929 Score: 319
Period size: 31 Copynumber: 5.6 Consensus size: 31
20747 CCATAGATTT
* *
20757 CGAAGAACCTAGGTAATCAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
20788 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
20819 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
20850 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
20881 CGAAGAACATAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
20912 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
20930 CCTCGACCCT
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 139 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:25139 original size:31 final size:31
Alignment explanation
Indices: 25101--25256 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
25091 CCCGAAGGAC
* * *
25101 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
25132 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
25163 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
25194 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25225 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25256 C
1 C
25257 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:27920 original size:25 final size:24
Alignment explanation
Indices: 27859--27922 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
27849 TGATTCATAC
* * *
27859 ATATATGTTCAGTTAATATGATAAA
1 ATATAAGTT-AGTGAATAAGATAAA
*
27884 ATAGAA-TTAGTGAATAAGATGAAA
1 ATATAAGTTAGTGAATAAGAT-AAA
27908 ATATAAGTTAGTGAA
1 ATATAAGTTAGTGAA
27923 ATATGCCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 10 0.31
24 10 0.31
25 12 0.38
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (24 bp):
ATATAAGTTAGTGAATAAGATAAA
Found at i:27925 original size:26 final size:23
Alignment explanation
Indices: 27873--27922 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
27863 ATGTTCAGTT
*
27873 AATATGATAAAATAGAATTAGTG
1 AATAAGATAAAATAGAATTAGTG
*
27896 AATAAGATGAAAATATAAGTTAGTG
1 AATAAGAT-AAAATAGAA-TTAGTG
27921 AA
1 AA
27923 ATATGCCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
24 8 0.35
25 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28
Consensus pattern (23 bp):
AATAAGATAAAATAGAATTAGTG
Found at i:28839 original size:19 final size:19
Alignment explanation
Indices: 28815--28891 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
28805 TTTATTGGGA
*
28815 TATGAATTTGAAAGTAAGT
1 TATGAATCTGAAAGTAAGT
* *
28834 TATGAATCTGACAGTAAGC
1 TATGAATCTGAAAGTAAGT
* *
28853 TATGAGTCTGAAAATAAGT
1 TATGAATCTGAAAGTAAGT
*
28872 TATGAATATGGAAA-TAAGT
1 TATGAATCT-GAAAGTAAGT
28891 T
1 T
28892 CTAATTCAGA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
19 44 0.92
20 4 0.08
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (19 bp):
TATGAATCTGAAAGTAAGT
Found at i:28961 original size:19 final size:19
Alignment explanation
Indices: 28933--28974 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
28923 AGTATTTATT
28933 ATGAACATGAAA-TATGAAA
1 ATGAACATGAAAGTA-GAAA
*
28952 ATGAATATGAAAGTAGAAA
1 ATGAACATGAAAGTAGAAA
28971 ATGA
1 ATGA
28975 GAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.57, C:0.02, G:0.19, T:0.21
Consensus pattern (19 bp):
ATGAACATGAAAGTAGAAA
Found at i:37589 original size:23 final size:23
Alignment explanation
Indices: 37550--37593 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
37540 GACGACCGGA
37550 TTTTTTACCGGATAAAAAATTGG
1 TTTTTTACCGGATAAAAAATTGG
37573 TTTTTTATCCGGA-AAAAAATT
1 TTTTTTA-CCGGATAAAAAATT
37594 CGGTCTGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (23 bp):
TTTTTTACCGGATAAAAAATTGG
Found at i:37612 original size:20 final size:20
Alignment explanation
Indices: 37587--37631 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
37577 TTATCCGGAA
*
37587 AAAAATTCGGTCTGGGGTTT
1 AAAAATCCGGTCTGGGGTTT
37607 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGGGGTTT
37627 AAAAA
1 AAAAA
37632 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (20 bp):
AAAAATCCGGTCTGGGGTTT
Found at i:43959 original size:139 final size:136
Alignment explanation
Indices: 43770--44111 Score: 370
Period size: 139 Copynumber: 2.5 Consensus size: 136
43760 AGTTCTCCTT
* * * *
43770 AATTAAAGGACTAAAGTGCAATTAAACCTAAGATAGAAGTTTTAATATTAAAACCTAATCAATTT
1 AATTAAAGGACTAAAGTGAAATTAAACCTAA-AT-GGAGGTCTAATATTAAAACCTAATCAATTT
* * * *
43835 TAACC-AATTATTGAATCGAATAACTAAAAAAGAACCTCGGGTC-AAAGCGAATGACCAAATCAG
64 T-ACCTAATTATTGAATCAAATAACCAAAAAAGAACCTCGGG-CAAAAGCGAA-AACCAAAGCAG
43898 AAACTCTC-T-TA
126 -AACT-TCATATA
43909 AATTAAAGGACTAAAGTGTAAATTAAACCTAAATGGAGGATCTCAA-ATTAAAACCTAATCAATT
1 AATTAAAGGACTAAAGTG-AAATTAAACCTAAATGGAGG-TCT-AATATTAAAACCTAATCAATT
* ** * * *
43973 TTACCTAATTATTGAATCAAATAACCGAAATGGAATCTCGGGCAAAAGTGAAAATCAAAGCAGAA
63 TTACCTAATTATTGAATCAAATAACCAAAAAAGAACCTCGGGCAAAAGCGAAAACCAAAGCAGAA
*
44038 GTTCATATA
128 CTTCATATA
* * * *
44047 AATTAAAGAATTAAAGTGAAATTAATCATAAAATGGAGGCTCTAATATTAAAACCTAATCAATTT
1 AATTAAAGGACTAAAGTGAAATTAAACCT-AAATGGAGG-TCTAATATTAAAACCTAATCAATTT
44112 CATCAAATTA
Statistics
Matches: 174, Mismatches: 20, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
136 2 0.01
137 15 0.09
138 64 0.37
139 79 0.45
140 14 0.08
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (136 bp):
AATTAAAGGACTAAAGTGAAATTAAACCTAAATGGAGGTCTAATATTAAAACCTAATCAATTTTA
CCTAATTATTGAATCAAATAACCAAAAAAGAACCTCGGGCAAAAGCGAAAACCAAAGCAGAACTT
CATATA
Found at i:44825 original size:45 final size:45
Alignment explanation
Indices: 44701--44936 Score: 319
Period size: 45 Copynumber: 5.2 Consensus size: 45
44691 TATTCTTTAT
*
44701 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * * * *
44746 TTTTCATTTACGACATCGTTTCATGTCGTTAATGCATCGTTATGCA
1 -TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * *
44792 TTTCATATATGGCATTCTTTTATGCCGATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
44837 TTTTATTTATGGCATCCTTTCATACCGATAATGCACCGTTGTGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
**
44882 TTTCATTTATGGCATCCTTTCATGGTGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
44927 TTTCATTTAT
1 TTTCATTTAT
44937 TCATTTATTT
Statistics
Matches: 161, Mismatches: 29, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
45 123 0.76
46 38 0.24
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
Found at i:46418 original size:18 final size:20
Alignment explanation
Indices: 46379--46433 Score: 87
Period size: 18 Copynumber: 2.9 Consensus size: 20
46369 AATATTTTTC
46379 CCGAAGGACCACTGATTGTT
1 CCGAAGGACCACTGATTGTT
*
46399 CCGAAGAACCACT-A-TGTT
1 CCGAAGGACCACTGATTGTT
46417 CCGAAGGACCACTGATT
1 CCGAAGGACCACTGATT
46434 ATCCCTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.52
19 2 0.06
20 13 0.42
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (20 bp):
CCGAAGGACCACTGATTGTT
Found at i:47612 original size:8 final size:8
Alignment explanation
Indices: 47599--47624 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
47589 GTTGGGAGGA
47599 AAGAAGAG
1 AAGAAGAG
47607 AAGAAGAG
1 AAGAAGAG
47615 AAGAAGAG
1 AAGAAGAG
47623 AA
1 AA
47625 TTCTGGAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (8 bp):
AAGAAGAG
Found at i:53225 original size:20 final size:19
Alignment explanation
Indices: 53197--53252 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
53187 CACTGAATAT
53197 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACT-A
* *
53217 TTGTTCCGAAGAACCACTA
1 TTGTCCCGAAGGACCACTA
*
53236 -TGTCCCGAAAGACCACT
1 TTGTCCCGAAGGACCACT
53253 TATTATCCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 1 0.03
20 16 0.52
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (19 bp):
TTGTCCCGAAGGACCACTA
Found at i:56834 original size:6 final size:6
Alignment explanation
Indices: 56823--56852 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
56813 CTTTAATTGC
56823 TAAAAT TAAAAT TAAAAT TAAAAT TGAAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT T-AAAA
56853 CCCGATTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (6 bp):
TAAAAT
Found at i:56973 original size:40 final size:40
Alignment explanation
Indices: 56906--56988 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
56896 AAAAAATCGA
* * *
56906 AAATGTTAGATAAATAATAATAGTAATAATAATAATAAA-C
1 AAATATTAAATAAATAATAATAATAATAA-AATAATAAATC
56946 AAATATTAAATAAATCAA-AATAATAATAAAATAATAAATC
1 AAATATTAAATAAAT-AATAATAATAATAAAATAATAAATC
56986 AAA
1 AAA
56989 AAGGAAGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 9 0.24
40 27 0.71
41 2 0.05
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (40 bp):
AAATATTAAATAAATAATAATAATAATAAAATAATAAATC
Found at i:57104 original size:3 final size:3
Alignment explanation
Indices: 57073--57127 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
57063 GTTTAAAAGC
* *
57073 AAT AA- AAT AAA AAT AAT -AT GAAG AA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
57116 AAT AAT AAT AAT
1 AAT AAT AAT AAT
57128 GACAAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
2 6 0.13
3 38 0.84
4 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:58267 original size:3 final size:3
Alignment explanation
Indices: 58247--58298 Score: 77
Period size: 3 Copynumber: 16.7 Consensus size: 3
58237 ACCCTAGAAA
*
58247 AAT AAT AAA AAGT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
58294 AAT AA
1 AAT AA
58299 ATAAAGTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 42 0.93
4 1 0.02
5 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:58339 original size:38 final size:38
Alignment explanation
Indices: 58297--58561 Score: 174
Period size: 39 Copynumber: 6.8 Consensus size: 38
58287 TAATAATAAT
*
58297 AAATAAAGTTTCAAAAACTATATAATATATATTTTCAA
1 AAATAATGTTTCAAAAACTATATAATATATATTTTCAA
* ** * *
58335 AAAT-ATTTTTTTAAAACTATATAATATTTTTTTTTTCAAA
1 AAATAATGTTTCAAAAACTATATAATA--TATATTTTC-AA
*
58375 AAACAAT-TTT--AAAACTATATAATATATATTTTCAA
1 AAATAATGTTTCAAAAACTATATAATATATATTTTCAA
* * *
58410 AAA-ATATTTTTGAAAAACTATAATATATATATATATATAT-AT
1 AAATA-ATGTTTCAAAAACTAT-ATA-ATATATAT-T-T-TCAA
* *
58452 ATATAATGTTTGAAAAACTATATATTATATATAAGTTTTCAA
1 AAATAATGTTTCAAAAACTATATA--ATATAT-A-TTTTCAA
* **
58494 AAAT-GT-TTTC-AAAACTATATATTATATATATTTT-TT
1 AAATAATGTTTCAAAAACTATATA--ATATATATTTTCAA
58530 AAA-AATGTTTTCAAAAACTATATAATATATAT
1 AAATAATG-TTTCAAAAACTATATAATATATAT
58562 ATATATATTC
Statistics
Matches: 186, Mismatches: 19, Indels: 45
0.74 0.08 0.18
Matches are distributed among these distances:
34 1 0.01
35 7 0.04
36 14 0.08
37 30 0.16
38 31 0.17
39 40 0.22
40 19 0.10
41 8 0.04
42 31 0.17
43 4 0.02
44 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (38 bp):
AAATAATGTTTCAAAAACTATATAATATATATTTTCAA
Found at i:58432 original size:36 final size:35
Alignment explanation
Indices: 58310--58439 Score: 136
Period size: 36 Copynumber: 3.5 Consensus size: 35
58300 TAAAGTTTCA
*
58310 AAAACTATATAATATATATTTTCAAAAATATTTTTTT
1 AAAAC-ATATAATATATATTTTCAAAAA-ATATTTTT
* * * *
58347 AAAACTATATAATATTTTTTTTTTCAAAAAACAATTTT
1 AAAAC-ATATAATA--TATATTTTCAAAAAATATTTTT
58385 AAAACTATATAATATATATTTTCAAAAAATATTTTT
1 AAAAC-ATATAATATATATTTTCAAAAAATATTTTT
58421 GAAAA-ACTATAATATATAT
1 -AAAACA-TATAATATATAT
58440 ATATATATAT
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
35 1 0.01
36 30 0.38
37 18 0.22
38 19 0.24
39 12 0.15
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (35 bp):
AAAACATATAATATATATTTTCAAAAAATATTTTT
Found at i:58475 original size:2 final size:2
Alignment explanation
Indices: 58428--58456 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
58418 TTTGAAAAAC
58428 TA TA -A 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
58457 ATGTTTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:58495 original size:28 final size:29
Alignment explanation
Indices: 58441--58496 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
58431 AATATATATA
*
58441 TATATATATATATATAATGTTTGAAAAAC
1 TATATATATATATATAATGTTTCAAAAAC
58470 TATATAT-TATATATAA-GTTTTCAAAAA
1 TATATATATATATATAATG-TTTCAAAAA
58497 TGTTTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 17 0.68
29 7 0.28
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (29 bp):
TATATATATATATATAATGTTTCAAAAAC
Found at i:58499 original size:39 final size:38
Alignment explanation
Indices: 58385--58582 Score: 161
Period size: 39 Copynumber: 4.9 Consensus size: 38
58375 AAACAATTTT
*
58385 AAAACTATATA--ATATAT-ATTTTCAAAAAATATTTTTGA
1 AAAACTATATATTATATATAATTTTC--AAAA-ATGTTTGA
* *
58423 AAAACTATAATATATATATATATATATAT-ATATAATGTTTGA
1 AAAACTAT-ATAT-TATATATA-AT-TTTCA-AAAATGTTTGA
**
58465 AAAACTATATATTATATATAAGTTTTCAAAAATGTTTTC
1 AAAACTATATATTATATATAA-TTTTCAAAAATGTTTGA
* * *
58504 AAAACTATATATTATATATATTTTTTAAAAATGTTTTCA
1 AAAACTATATATTATATATAATTTTCAAAAATG-TTTGA
*
58543 AAAACTATATAATATATATATATATATTCAAAAATCGTTT
1 AAAACTATAT-AT-TATATATA-ATTTTCAAAAAT-GTTT
58583 TCTGAAAATT
Statistics
Matches: 131, Mismatches: 14, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
38 19 0.15
39 47 0.36
40 12 0.09
41 12 0.09
42 34 0.26
43 3 0.02
44 2 0.02
45 2 0.02
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (38 bp):
AAAACTATATATTATATATAATTTTCAAAAATGTTTGA
Found at i:58597 original size:39 final size:38
Alignment explanation
Indices: 58456--58603 Score: 163
Period size: 39 Copynumber: 3.7 Consensus size: 38
58446 ATATATATAT
**
58456 AATGTTTGAAAAACTATATATTATATATAAGTTTTCAAA
1 AATGTTTTCAAAACTATATATTATATAT-AGTTTTCAAA
* *
58495 AATGTTTTCAAAACTATATATTATATATATTTTTTAAA
1 AATGTTTTCAAAACTATATATTATATATAGTTTTCAAA
58533 AATGTTTTCAAAAACTATATAATATATATATA-TATATTCAAA
1 AATGTTTTC-AAAACTATAT-AT-TATATATAGT-T-TTCAAA
*
58575 AATCGTTTTCTGAAAATTATATATTATAT
1 AAT-GTTTTC--AAAACTATATATTATAT
58604 TTTTTCAAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
38 17 0.18
39 36 0.38
40 3 0.03
41 9 0.09
42 13 0.14
43 8 0.08
44 9 0.09
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (38 bp):
AATGTTTTCAAAACTATATATTATATATAGTTTTCAAA
Found at i:58623 original size:80 final size:79
Alignment explanation
Indices: 58390--58649 Score: 214
Period size: 80 Copynumber: 3.2 Consensus size: 79
58380 ATTTTAAAAC
* * * * *
58390 TATATA-ATATATATTTTCAAAAAATATTTTTGAAAAACTATAATATATATATATATATATATAT
1 TATATATATATATATATTC-AAAAAT-GTTTT-CAAAACTAT-ATAT-TATATATAT-TTTTTA-
* *
58454 ATAATG-TTTGAAAAACTATA
59 AAAATGTTTTCAAAAACTATA
*
58474 TAT-TATATATA-AGTTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTTTAAAAATG
1 TATATATATATATA-TATTCAAAAATGTTTTCAAAACTATATATTATATATATTTTTTAAAAATG
58537 TTTTCAAAAACTATA
65 TTTTCAAAAACTATA
*
58552 TAATATATATATATATATTCAAAAATCGTTTTCTGAAAA-T-TATA-TAT-TATATTTTTT-CAA
1 T-ATATATATATATATATTCAAAAAT-GTTTTC--AAAACTATATATTATATATATTTTTTAAAA
*
58612 ATGCATTTTCAAAAATTATA
62 ATG--TTTTCAAAAACTATA
* *
58632 TTATATTTCTATATATAT
1 -TATATATATATATATAT
58650 ATAATAAAAT
Statistics
Matches: 153, Mismatches: 11, Indels: 28
0.80 0.06 0.15
Matches are distributed among these distances:
77 5 0.03
78 23 0.15
79 21 0.14
80 53 0.35
81 20 0.13
82 5 0.03
83 13 0.08
84 13 0.08
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (79 bp):
TATATATATATATATATTCAAAAATGTTTTCAAAACTATATATTATATATATTTTTTAAAAATGT
TTTCAAAAACTATA
Found at i:58668 original size:19 final size:19
Alignment explanation
Indices: 58646--58682 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58636 ATTTCTATAT
* *
58646 ATATATAATAAAATAAATA
1 ATATATAAAAAAACAAATA
58665 ATATATAAAAAAACAAAT
1 ATATATAAAAAAACAAAT
58683 TCAGACGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
ATATATAAAAAAACAAATA
Found at i:62096 original size:43 final size:43
Alignment explanation
Indices: 62037--62304 Score: 204
Period size: 43 Copynumber: 6.2 Consensus size: 43
62027 TGAGAACAAA
* *
62037 AAACGCCGCAATAGGTCAATATCTATTA-CGGCATTTTTTGAAC
1 AAACGCCGCAAAAGGTCAATATCTA-TAGCGGCATTTTTGGAAC
* * *
62080 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGAAC
* * * * * * *
62123 AAACGCCGCAAAAAGT-TATGATATATAGCGGCGTTTCTAGAAAA
1 AAACGCCGCAAAAGGTCAAT-ATCTATAGCGGCATTT-TTGGAAC
* * * *
62167 AAATGCCGCAAAAAGTC-AGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGA-AC
* * * ** * *
62210 AAACGCCGCAAAAGGT-TAGACCTATAATGGCGTTTTTGAACAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGA-AC
* * * *
62253 AAACGCCGCAAAAAGTC-AGACCTATAGCGGCTTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGA-AC
62296 AAACGCCGC
1 AAACGCCGC
62305 TAATTATCTT
Statistics
Matches: 188, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
42 7 0.04
43 161 0.86
44 20 0.11
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGAAC
Found at i:62175 original size:130 final size:131
Alignment explanation
Indices: 62017--62268 Score: 307
Period size: 130 Copynumber: 1.9 Consensus size: 131
62007 CCGCTAAAGT
* * * *
62017 TAGCGGCGTTTGAGAACAAAAAACGCCGCAATAGGTCAATATCTATTA-CGGCATTTTTTGA-AC
1 TAGCGGCGTTTGAGAACAAAAAACGCCGCAAAAAGTC-AGATCTA-TAGCGGCATTTTTGGATAC
* * * * *
62080 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-ATAAACGCCGCAAAAAGTTATGA
64 AAACGCCGCAAAAGGT-GAGACCTATAACGGCGTTTTTGAACACAAACGCCGCAAAAAGTTATGA
62144 TATA
128 TATA
* * *
62148 TAGCGGCGTTTCTAG-A-AAAAAATGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGATACA
1 TAGCGGCGTTT-GAGAACAAAAAACGCCGCAAAAAGTCAGATCTATAGCGGCATTTTTGGATACA
* *
62211 AACGCCGCAAAAGGTTAGACCTATAATGGCGTTTTTGAACACAAACGCCGCAAAAAGT
65 AACGCCGCAAAAGGTGAGACCTATAACGGCGTTTTTGAACACAAACGCCGCAAAAAGT
62269 CAGACCTATA
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
128 2 0.02
129 35 0.34
130 52 0.50
131 12 0.12
132 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (131 bp):
TAGCGGCGTTTGAGAACAAAAAACGCCGCAAAAAGTCAGATCTATAGCGGCATTTTTGGATACAA
ACGCCGCAAAAGGTGAGACCTATAACGGCGTTTTTGAACACAAACGCCGCAAAAAGTTATGATAT
A
Found at i:62190 original size:86 final size:86
Alignment explanation
Indices: 62080--62304 Score: 292
Period size: 86 Copynumber: 2.6 Consensus size: 86
62070 TTTTTTGAAC
* * *
62080 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-ATAAACGCCGCAAAAAGTTATGA
1 AAACGCCGCAAAAAGTC-AGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAAGTTA-GA
* *
62144 TATATAGCGGCGTTTCTAGAA-AA
64 CATATAACGGCGTTT-TAGAACAA
* * *
62167 AAATGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTTAGACC
1 AAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAAGTTAGACA
* * *
62232 TATAATGGCGTTTTTGAACAC
66 TATAACGGCGTTTTAGAACAA
* *
62253 AAACGCCGCAAAAAGTCAGACCTATAGCGGCTTTTTTGGATACAAACGCCGC
1 AAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGC
62305 TAATTATCTT
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
85 4 0.03
86 85 0.70
87 33 0.27
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.23
Consensus pattern (86 bp):
AAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAAGTTAGACA
TATAACGGCGTTTTAGAACAA
Found at i:64788 original size:80 final size:79
Alignment explanation
Indices: 64676--64840 Score: 251
Period size: 80 Copynumber: 2.1 Consensus size: 79
64666 TACGGAATCC
* * *
64676 TTGCAAGTAATATGAAGGACTAAACTTCTCAATTTACATTCAGGTCAAATTGATAACAGATATTT
1 TTGCAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGATAACAAATATTT
64741 ATAGACCA-CTGCTAA
66 A-AGA-CAGCTGCTAA
* *
64756 TTGCAAGTAAAATGAAGGACTAAACTTCTCAATTTTCATTCAGATCAAATTTATAACAAATATTT
1 TTGCAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGATAACAAATATTT
*
64821 AAGACAGCTGCTCA
66 AAGACAGCTGCTAA
64835 TTGCAA
1 TTGCAA
64841 CATAATCTAA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
78 2 0.03
79 15 0.19
80 61 0.78
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (79 bp):
TTGCAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGATAACAAATATTT
AAGACAGCTGCTAA
Found at i:67034 original size:38 final size:39
Alignment explanation
Indices: 66983--67071 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 39
66973 GAGAATTGGC
*
66983 AACGCCACTATAGTACATGTGTAT-AACGTTTATATAAA
1 AACGCCACTATAGTACATGTGTATAAACATTTATATAAA
*
67021 AACGCCACTATAGTACATGTGTATAACAACATTTGTATAAA
1 AACGCCACTATAGTACATGTGTAT-A-AACATTTATATAAA
67062 AACGCCACTA
1 AACGCCACTA
67072 AATTACAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 24 0.52
41 22 0.48
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (39 bp):
AACGCCACTATAGTACATGTGTATAAACATTTATATAAA
Found at i:67097 original size:41 final size:41
Alignment explanation
Indices: 67052--67195 Score: 191
Period size: 41 Copynumber: 3.5 Consensus size: 41
67042 TATAACAACA
* *
67052 TTTGTATAAAAACGCCACTAAATTACAATTCTATAGCGGCG
1 TTTGTATAAAAACGCCACTAAATTACAACTCTTTAGCGGCG
* * *
67093 TTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCG
1 TTTGTATAAAAACGCCACTAAATTACAACTCTTTAGCGGCG
* * *
67134 TTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCGGCG
1 TTTGTATAAAAACGCCACTAAATTACAACTCTTTAGCGGCG
67175 TTTGT-TGAAAAAACGCCACTA
1 TTTGTAT--AAAAACGCCACTA
67196 TCGATGAACC
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.01
41 78 0.85
42 13 0.14
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (41 bp):
TTTGTATAAAAACGCCACTAAATTACAACTCTTTAGCGGCG
Found at i:74668 original size:17 final size:17
Alignment explanation
Indices: 74648--74694 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
74638 TAAATTTACT
74648 TTTATTTTAGTTTACCA
1 TTTATTTTAGTTTACCA
74665 TTTATTTTAGTTTACCA
1 TTTATTTTAGTTTACCA
74682 TTTATTTTAGTTT
1 TTTATTTTAGTTT
74695 TTTCTCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (17 bp):
TTTATTTTAGTTTACCA
Found at i:82329 original size:23 final size:23
Alignment explanation
Indices: 82287--82334 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
82277 TATTTTGAGT
82287 AACAAAATAAAACATGAAAC-AA
1 AACAAAATAAAACATGAAACTAA
*
82309 AACAAACATAAGACACT-AAACTAA
1 AACAAA-ATAAAACA-TGAAACTAA
82333 AA
1 AA
82335 AAATGGACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.69, C:0.17, G:0.04, T:0.10
Consensus pattern (23 bp):
AACAAAATAAAACATGAAACTAA
Found at i:84051 original size:8 final size:8
Alignment explanation
Indices: 84029--84095 Score: 53
Period size: 8 Copynumber: 7.9 Consensus size: 8
84019 AATTAATTAT
84029 AATATATAA
1 AATA-ATAA
*
84038 ATTAATAA
1 AATAATAA
84046 AATAATAA
1 AATAATAA
*
84054 CAATAAAAA
1 -AATAATAA
*
84063 TAAAAATAA
1 -AATAATAA
*
84072 TAATAATAT
1 -AATAATAA
84081 AATAATAA
1 AATAATAA
*
84089 TATAATA
1 AATAATA
84096 TTTTTGTAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
8 24 0.51
9 23 0.49
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (8 bp):
AATAATAA
Found at i:84075 original size:3 final size:3
Alignment explanation
Indices: 84022--84095 Score: 66
Period size: 3 Copynumber: 25.7 Consensus size: 3
84012 TGCAAAAAAT
* * * *
84022 TAA TTA TAA TATA TAA -AT TAA TAA -AA TAA TAA CAA TAA AAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
84066 AAA TAA TAA TAA T-A TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
84096 TTTTTGTAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
2 7 0.12
3 46 0.82
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:84442 original size:124 final size:124
Alignment explanation
Indices: 84212--84508 Score: 477
Period size: 124 Copynumber: 2.4 Consensus size: 124
84202 CATTGGGCAT
* * * * *
84212 GATATCCTTCTTCGTAAAGTTGAAATTCAATCTGAAGATAAATGTTGTTGGTGGGCACGATTCCC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGCTGGTGGGCACGATTCCC
* * *
84277 TTCATCATGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGTCTTGAATTG
66 TTCATCATGAAGTTGAAACCGTGGATGGCACATTCGCTGTGAAGTTGAGTCTTGAATTG
*
84336 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGTATGTTGCTGGTGGGCACGATTCCC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGCTGGTGGGCACGATTCCC
* *
84401 TTCGTCGTGAAGTTGAAACCGTGGATGGCACATTCGCTGTGAAGTTGAGTCTTGAATTG
66 TTCATCATGAAGTTGAAACCGTGGATGGCACATTCGCTGTGAAGTTGAGTCTTGAATTG
* *
84460 GATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGCT
84509 TCGAGTCCAA
Statistics
Matches: 159, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 159 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (124 bp):
GATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGCTGGTGGGCACGATTCCC
TTCATCATGAAGTTGAAACCGTGGATGGCACATTCGCTGTGAAGTTGAGTCTTGAATTG
Found at i:84695 original size:32 final size:32
Alignment explanation
Indices: 84659--84761 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 32
84649 TCGTCATGAA
84659 GTTGAACTCGTGGATGGCCCCTTCTTTGTGAT
1 GTTGAACTCGTGGATGGCCCCTTCTTTGTGAT
* * * ** * * *
84691 GTTGAGGCTTGACTTGAAT--ATCCTTCGTCGTGAA
1 GTTGA-AC-T--CGTGGATGGCCCCTTCTTTGTGAT
84725 GTTGAACTCGTGGATGGCCCCTTCTTTGTGAT
1 GTTGAACTCGTGGATGGCCCCTTCTTTGTGAT
84757 GTTGA
1 GTTGA
84762 GGCTTGACTT
Statistics
Matches: 49, Mismatches: 16, Indels: 12
0.64 0.21 0.16
Matches are distributed among these distances:
30 5 0.10
32 21 0.43
33 2 0.04
34 16 0.33
36 5 0.10
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (32 bp):
GTTGAACTCGTGGATGGCCCCTTCTTTGTGAT
Found at i:84716 original size:34 final size:34
Alignment explanation
Indices: 84678--84782 Score: 92
Period size: 34 Copynumber: 3.1 Consensus size: 34
84668 GTGGATGGCC
84678 CCTTCTTTGTGATGTTGAGGCTTGACTTGAATAT
1 CCTTCTTTGTGATGTTGAGGCTTGACTTGAATAT
* * * * * * **
84712 CCTTCGTCGTGAAGTTGA-AC-T--CGTGGATGGCC
1 CCTTCTTTGTGATGTTGAGGCTTGACTTGAAT--AT
84744 CCTTCTTTGTGATGTTGAGGCTTGACTTGAATAT
1 CCTTCTTTGTGATGTTGAGGCTTGACTTGAATAT
84778 CCTTC
1 CCTTC
84783 GTCGTGAAGT
Statistics
Matches: 49, Mismatches: 16, Indels: 12
0.64 0.21 0.16
Matches are distributed among these distances:
30 5 0.10
32 16 0.33
33 2 0.04
34 21 0.43
36 5 0.10
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (34 bp):
CCTTCTTTGTGATGTTGAGGCTTGACTTGAATAT
Found at i:84725 original size:66 final size:66
Alignment explanation
Indices: 84642--84796 Score: 301
Period size: 66 Copynumber: 2.3 Consensus size: 66
84632 AGTTAACACG
*
84642 ATATCCTTCGTCATGAAGTTGAACTCGTGGATGGCCCCTTCTTTGTGATGTTGAGGCTTGACTTG
1 ATATCCTTCGTCGTGAAGTTGAACTCGTGGATGGCCCCTTCTTTGTGATGTTGAGGCTTGACTTG
84707 A
66 A
84708 ATATCCTTCGTCGTGAAGTTGAACTCGTGGATGGCCCCTTCTTTGTGATGTTGAGGCTTGACTTG
1 ATATCCTTCGTCGTGAAGTTGAACTCGTGGATGGCCCCTTCTTTGTGATGTTGAGGCTTGACTTG
84773 A
66 A
84774 ATATCCTTCGTCGTGAAGTTGAA
1 ATATCCTTCGTCGTGAAGTTGAA
84797 ATCCAAGCTT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 88 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (66 bp):
ATATCCTTCGTCGTGAAGTTGAACTCGTGGATGGCCCCTTCTTTGTGATGTTGAGGCTTGACTTG
A
Found at i:85323 original size:253 final size:248
Alignment explanation
Indices: 84992--85445 Score: 656
Period size: 253 Copynumber: 1.8 Consensus size: 248
84982 TTTGTGGCAC
* * * *
84992 GATATCCTCCGTCGTGGAGTTGAAATCCAAGCTTGTATTGTTGCTGGTGAGCATGATTCCCTTCG
1 GATATCCTCCGTCGTGAAGTTGAAATCCAAGCTAGGATTGTTGCTGGTGAGCACGATTCCCTTCG
* * * * * *
85057 TCTTGAAGTTGAAACCGTGGATGGCCCCTTCGTCATGAAGTTGAGCCTTGAATTGGATATCCTTC
66 TCGTGAAGTTGAAACCGCGGATGGCACATTCGTCATGAAGTTGAGCATGGAATTGGATATCCTTC
* * *
85122 GTCGTGAAGTTGAAATCCAATGTAAGCTGCATTGTTCCGAGGCCAATATCCTTCGCTGTGAAGTT
131 GTCGTGAAGTTGAAATCCAA-GTAAGCTGCATTGTTCCGAGGCCAATATCCTCCACCGTGAAGTT
85187 GAAATTGACTCTAAAACTGGAAAGTTTATTGACATGCACTCTTTCTTTGAGTTA
195 GAAATTGACTCTAAAACTGGAAAGTTTATTGACATGCACTCTTTCTTTGAGTTA
* * * *
85241 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGATGTTGCTTGTGTGCACGATTCCC
1 GATATCCTCCGTCGTGAAGTTGAAATCCAAGCTAG-GAT---TGTTGCTGGTGAGCACGATTCCC
* *
85306 TTCTTCGTGAAGTTGAAACCGCGGGTGGCACATTCGTCATGAAGTTGAGCATGGAATTGGATATC
62 TTCGTCGTGAAGTTGAAACCGCGGATGGCACATTCGTCATGAAGTTGAGCATGGAATTGGATATC
* * * *
85371 CTTCGTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCACCGTGAA
127 CTTCGTCGTGAAGTTGAAATCCAAGTAAGCTGCATTGTTCCGAGGCCAATATCCTCCACCGTGAA
85436 GTTGAAATTG
192 GTTGAAATTG
85446 GTTCTGAAAC
Statistics
Matches: 178, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
249 31 0.17
250 2 0.01
252 44 0.25
253 101 0.57
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (248 bp):
GATATCCTCCGTCGTGAAGTTGAAATCCAAGCTAGGATTGTTGCTGGTGAGCACGATTCCCTTCG
TCGTGAAGTTGAAACCGCGGATGGCACATTCGTCATGAAGTTGAGCATGGAATTGGATATCCTTC
GTCGTGAAGTTGAAATCCAAGTAAGCTGCATTGTTCCGAGGCCAATATCCTCCACCGTGAAGTTG
AAATTGACTCTAAAACTGGAAAGTTTATTGACATGCACTCTTTCTTTGAGTTA
Found at i:91097 original size:3 final size:3
Alignment explanation
Indices: 91064--91136 Score: 64
Period size: 3 Copynumber: 25.3 Consensus size: 3
91054 CCTGTAAAAA
* * * *
91064 AAT AAT TAT AAT ATAT AA- AAT AAT AAC AAT AAT AAT AAA AAT AAA
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
91109 AAT AGT -AT AAT AAT AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
91137 TTTTTATAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
2 7 0.13
3 45 0.82
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:91123 original size:11 final size:11
Alignment explanation
Indices: 91064--91137 Score: 64
Period size: 11 Copynumber: 6.7 Consensus size: 11
91054 CCTGTAAAAA
91064 AATAATTATAAT
1 AATAA-TATAAT
*
91076 ATATAAAATAAT
1 A-ATAATATAAT
*
91088 AACAATAATAAT
1 AATAAT-ATAAT
*
91100 AA-AA-ATAAA
1 AATAATATAAT
*
91109 AATAGTATAAT
1 AATAATATAAT
91120 AATAATATAAT
1 AATAATATAAT
91131 -ATAATAT
1 AATAATAT
91138 TTTTATAGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
9 6 0.12
10 8 0.16
11 19 0.37
12 14 0.27
13 4 0.08
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (11 bp):
AATAATATAAT
Found at i:96416 original size:48 final size:48
Alignment explanation
Indices: 96345--96448 Score: 138
Period size: 48 Copynumber: 2.2 Consensus size: 48
96335 GGTCCCTCTA
* *
96345 ATCAACGTGATCCTCAAACTCATAAAATAA-GTATAATATGGCATTTTG
1 ATCAACGTGATCCTCAAACTCATAAAATAACCT-TAATATGACATTTTG
* * * *
96393 ATCAACGTGGTCCTCCAACTCATAAAATAACCTTAATGTGACCTTTTG
1 ATCAACGTGATCCTCAAACTCATAAAATAACCTTAATATGACATTTTG
96441 ATCAACGT
1 ATCAACGT
96449 TTTTTCGTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
48 48 0.98
49 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (48 bp):
ATCAACGTGATCCTCAAACTCATAAAATAACCTTAATATGACATTTTG
Found at i:99369 original size:17 final size:17
Alignment explanation
Indices: 99347--99385 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
99337 TGAATCAAAT
*
99347 TAATTAGATATTATTTA
1 TAATTAGATACTATTTA
99364 TAATTAGATACTATTTA
1 TAATTAGATACTATTTA
99381 -AATTA
1 TAATTA
99386 ATTGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (17 bp):
TAATTAGATACTATTTA
Found at i:107659 original size:20 final size:20
Alignment explanation
Indices: 107636--107676 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
107626 GTTCATATGC
107636 ATCATAAGATATTCAAATGA
1 ATCATAAGATATTCAAATGA
107656 ATCATAAGATATTCAAATGA
1 ATCATAAGATATTCAAATGA
107676 A
1 A
107677 ATACTTACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (20 bp):
ATCATAAGATATTCAAATGA
Found at i:119802 original size:24 final size:20
Alignment explanation
Indices: 119775--119832 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
119765 GCATGGGTAG
119775 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
119799 TGCATCGATGTACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
119819 TGTATCGATGCACT
1 TGCATCGATGCACT
119833 TCAAGAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:120553 original size:26 final size:28
Alignment explanation
Indices: 120511--120562 Score: 65
Period size: 26 Copynumber: 1.9 Consensus size: 28
120501 GCTATGAGCT
*
120511 TATATGAACATGTGAT-A-TGAAAATTG
1 TATATGAACATGAGATAAGTGAAAATTG
120537 TATAGTGAA-ATGAGATAAGTGAAAAT
1 TATA-TGAACATGAGATAAGTGAAAAT
120563 GCCCATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 10 0.45
27 5 0.23
28 7 0.32
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (28 bp):
TATATGAACATGAGATAAGTGAAAATTG
Found at i:123749 original size:22 final size:22
Alignment explanation
Indices: 123721--123764 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
123711 AATAATTATT
123721 ATGTCGTCCGGTTCTTCCGACC
1 ATGTCGTCCGGTTCTTCCGACC
123743 ATGTCGTCCGGTTCTTCCGACC
1 ATGTCGTCCGGTTCTTCCGACC
123765 GGTCGGGCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.36, G:0.23, T:0.32
Consensus pattern (22 bp):
ATGTCGTCCGGTTCTTCCGACC
Found at i:123775 original size:22 final size:22
Alignment explanation
Indices: 123723--123777 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
123713 TAATTATTAT
* *
123723 GTCGTCCGGTTCTTCCGACCAT
1 GTCGGCCGGTTCTTCCGACCAG
*
123745 GTCGTCCGGTTCTTCCGACC-G
1 GTCGGCCGGTTCTTCCGACCAG
123766 GTCGGGCCGGTT
1 GTC-GGCCGGTT
123778 TGACTGGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.05, C:0.35, G:0.31, T:0.29
Consensus pattern (22 bp):
GTCGGCCGGTTCTTCCGACCAG
Found at i:124851 original size:64 final size:65
Alignment explanation
Indices: 124715--124856 Score: 150
Period size: 64 Copynumber: 2.2 Consensus size: 65
124705 AATTGCTAGT
* * * *
124715 GTGTATCGATGCA-CAGGAAATGCATCGATGCACCCATTAAAAATGGAAACATTGAATGCAGTTA
1 GTGTATCGATGCATAAGGAAATACATCGATGCACCCATTAAAAATGAAAACATCGAATGCAGTTA
* * *
124779 GTGCATCGATGCATAAGG-AGTACATCGATGCACCTCCTT-AAAATGAAAACATCGAAGGTG-A-
1 GTGTATCGATGCATAAGGAAATACATCGATGCACC-CATTAAAAATGAAAACATCGAA--TGCAG
*
124840 TTG
63 TTA
124843 GTGTATCGATGCAT
1 GTGTATCGATGCAT
124857 GGTTAGTGCA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
64 56 0.86
65 7 0.11
66 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (65 bp):
GTGTATCGATGCATAAGGAAATACATCGATGCACCCATTAAAAATGAAAACATCGAATGCAGTTA
Found at i:124908 original size:20 final size:21
Alignment explanation
Indices: 124863--124926 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
124853 GCATGGTTAG
124863 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-T-TT-AAGAA
124887 TGCATCGATGCACTTT-AGAA
1 TGCATCGATGCACTTTAAGAA
* * *
124907 TGTACCGATGCACTTCAAGA
1 TGCATCGATGCACTTTAAGA
124927 GGAAATTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 17 0.47
21 3 0.08
22 2 0.06
23 1 0.03
24 13 0.36
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCACTTTAAGAA
Found at i:128395 original size:7 final size:7
Alignment explanation
Indices: 128383--128473 Score: 67
Period size: 7 Copynumber: 13.1 Consensus size: 7
128373 AATTAGATTA
128383 AGGGTTT
1 AGGGTTT
128390 AGGGTTT
1 AGGGTTT
*
128397 AGGGCTT
1 AGGGTTT
*
128404 A-GATTT
1 AGGGTTT
*
128410 AGGGCTT
1 AGGGTTT
128417 AGGGTTT
1 AGGGTTT
*
128424 AGGATTT
1 AGGGTTT
**
128431 ATAGTTT
1 AGGGTTT
*
128438 AAGGTTT
1 AGGGTTT
**
128445 ATAGTTT
1 AGGGTTT
**
128452 ATAGTTT
1 AGGGTTT
*
128459 AGAGTTT
1 AGGGTTT
128466 AGGGTTT
1 AGGGTTT
128473 A
1 A
128474 AGGTGTAATC
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
6 4 0.06
7 63 0.94
ACGTcount: A:0.23, C:0.02, G:0.31, T:0.44
Consensus pattern (7 bp):
AGGGTTT
Found at i:128410 original size:13 final size:13
Alignment explanation
Indices: 128375--128418 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
128365 TATCACATAA
* *
128375 TTAGATTAAGGGT
1 TTAGATTTAGGGC
*
128388 TTAGGGTTTAGGGC
1 TTA-GATTTAGGGC
128402 TTAGATTTAGGGC
1 TTAGATTTAGGGC
128415 TTAG
1 TTAG
128419 GGTTTAGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.23, C:0.05, G:0.34, T:0.39
Consensus pattern (13 bp):
TTAGATTTAGGGC
Found at i:128410 original size:20 final size:21
Alignment explanation
Indices: 128387--128431 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
128377 AGATTAAGGG
*
128387 TTTAGGGTTTAGGGCTTA-GA
1 TTTAGGGCTTAGGGCTTAGGA
*
128407 TTTAGGGCTTAGGGTTTAGGA
1 TTTAGGGCTTAGGGCTTAGGA
128428 TTTA
1 TTTA
128432 TAGTTTAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.20, C:0.04, G:0.33, T:0.42
Consensus pattern (21 bp):
TTTAGGGCTTAGGGCTTAGGA
Found at i:128413 original size:27 final size:27
Alignment explanation
Indices: 128375--128426 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
128365 TATCACATAA
*
128375 TTAGATTAAGGGTTTAGGGTTTAGGGC
1 TTAGATTAAGGGCTTAGGGTTTAGGGC
*
128402 TTAGATTTAGGGCTTAGGGTTTAGG
1 TTAGATTAAGGGCTTAGGGTTTAGG
128427 ATTTATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.04, G:0.37, T:0.38
Consensus pattern (27 bp):
TTAGATTAAGGGCTTAGGGTTTAGGGC
Found at i:128616 original size:11 final size:11
Alignment explanation
Indices: 128600--128659 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
128590 GTATTATAGA
128600 ATTTTTAATAT
1 ATTTTTAATAT
128611 ATTTTTAA-A-
1 ATTTTTAATAT
128620 ATTTTATAAT-T
1 ATTTT-TAATAT
***
128631 ATCAATAATAT
1 ATTTTTAATAT
*
128642 ATTTTTAATAA
1 ATTTTTAATAT
128653 ATTTTTA
1 ATTTTTA
128660 TAATGTAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 25 0.66
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:129495 original size:39 final size:37
Alignment explanation
Indices: 129452--129537 Score: 95
Period size: 39 Copynumber: 2.3 Consensus size: 37
129442 GATAATATTT
* *
129452 TATTATTTA-AGGATTTATATTCGATTGAAA-ACATGGATA
1 TATTATTTATA-GATCTATATTCGATT-AAATACA--AATA
*
129491 TATTATTTATATATCTATATTCGATTAAATACAAATA
1 TATTATTTATAGATCTATATTCGATTAAATACAAATA
129528 TATTATTTAT
1 TATTATTTAT
129538 GAATTCAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 13 0.31
38 3 0.07
39 25 0.60
40 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (37 bp):
TATTATTTATAGATCTATATTCGATTAAATACAAATA
Found at i:132180 original size:13 final size:13
Alignment explanation
Indices: 132164--132192 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
132154 ATTATATATT
132164 ATAAAAATATTTA
1 ATAAAAATATTTA
132177 AT-AAAATATTTA
1 ATAAAAATATTTA
132189 ATAA
1 ATAA
132193 TATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAAAATATTTA
Found at i:132184 original size:12 final size:12
Alignment explanation
Indices: 132167--132192 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
132157 ATATATTATA
132167 AAAATATTTAAT
1 AAAATATTTAAT
132179 AAAATATTTAAT
1 AAAATATTTAAT
132191 AA
1 AA
132193 TATAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATATTTAAT
Found at i:132260 original size:19 final size:18
Alignment explanation
Indices: 132232--132283 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 18
132222 AATATATTTA
*
132232 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAACG
132250 AAAACATATAAAATAAACG
1 AAAACA-ATAAAATAAACG
*
132269 AAAA-AATAAATTAAA
1 AAAACAATAAAATAAA
132284 AATCTAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
19 15 0.48
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (18 bp):
AAAACAATAAAATAAACG
Found at i:133114 original size:24 final size:25
Alignment explanation
Indices: 133068--133119 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
133058 GTTTGTATTT
*
133068 TCTCTGTTTTTTTTTTCTATGTCTC
1 TCTCTATTTTTTTTTTCTATGTCTC
133093 TCTCTATTCTTTTTTTT-T-TGTCTC
1 TCTCTATT-TTTTTTTTCTATGTCTC
133117 TCT
1 TCT
133120 GTCTCGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 8 0.32
26 8 0.32
ACGTcount: A:0.04, C:0.21, G:0.06, T:0.69
Consensus pattern (25 bp):
TCTCTATTTTTTTTTTCTATGTCTC
Found at i:133589 original size:11 final size:11
Alignment explanation
Indices: 133566--133597 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
133556 ATGTAATTAT
133566 TATTTATATATA
1 TATTTA-ATATA
133578 TATTTAATATA
1 TATTTAATATA
133589 TATTTAATA
1 TATTTAATA
133598 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:133601 original size:3 final size:3
Alignment explanation
Indices: 133593--133672 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
133583 AATATATATT
*
133593 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
133641 TAA TAT TAT TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
133673 TGGATAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:134278 original size:114 final size:114
Alignment explanation
Indices: 133991--134770 Score: 1233
Period size: 114 Copynumber: 6.9 Consensus size: 114
133981 AGAATTATGC
* *
133991 AAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
134056 TATGAACTTTCTCTGGAAAAGCTGATCCATCAA-ATGATGGATTCAAGT
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAAGT
134104 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
134169 TATGAACTTTCTCTGGAAAAGTTAATCCATCAATTTGATGAATTCAGGT
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAAGT
*
134218 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
134283 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAAGT
134332 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
134397 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAAGT
*
134446 AAAAGGTTGAACTAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**
134511 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAAAC
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAAGT
* *
134560 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * * **
134625 TATGAACCTTCTCTCGCAATGTTGATCCATCAA-ATGATGAATTTAAAC
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAAGT
* *
134673 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
134738 TATGAA-CTTATCTGGCAATGAATGATCCATCAA
66 TATGAACCTTCTCTGGAAAAG-ATAATCCATCAA
134771 GTGGATTTGA
Statistics
Matches: 637, Mismatches: 28, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
112 12 0.02
113 189 0.30
114 436 0.68
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (114 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAAGT
Found at i:135856 original size:83 final size:83
Alignment explanation
Indices: 135513--136082 Score: 894
Period size: 83 Copynumber: 6.9 Consensus size: 83
135503 CCTACTGAAT
* * *
135513 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
135578 TGATT-GTTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
*
135595 CAGATCGGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-AGCAAATTCATCTTCCAAATTCA
* *
135660 ATGATTGATTATGTCCAAC
65 ATGATTGGTTCTGTCCAAC
135679 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-AGCAAATTCATCTTCCAAATTCA
*
135744 ATGATTGGTTCTGTCCGAC
65 ATGATTGGTTCTGTCCAAC
* * * *
135763 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGTTATTAGCACATTTATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
135828 TGATTGGTTCTG-CTAAAC
66 TGATTGGTTCTGTC-CAAC
* * *
135846 CAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
135911 TGATTGGTTCTGTCCGAC
66 TGATTGGTTCTGTCCAAC
* *
135929 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
135994 TGATTGGTTCTGTCCGAC
66 TGATTGGTTCTGTCCAAC
* *
136012 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATT-AA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
136076 TGTTTGG
66 TGATTGG
136083 AATAGGATAT
Statistics
Matches: 457, Mismatches: 27, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
82 49 0.11
83 278 0.61
84 130 0.28
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
TGATTGGTTCTGTCCAAC
Found at i:137115 original size:8 final size:8
Alignment explanation
Indices: 137097--137173 Score: 83
Period size: 8 Copynumber: 10.1 Consensus size: 8
137087 ACCTTGACCC
137097 TTTTTTC-
1 TTTTTTCT
137104 TTTTTTCT
1 TTTTTTCT
137112 TTTTTTCT
1 TTTTTTCT
137120 TTTTTTCT
1 TTTTTTCT
137128 TTTTTTC-
1 TTTTTTCT
137135 --TTTTCT
1 TTTTTTCT
**
137141 TTTCTCCCT
1 TTT-TTTCT
137150 TTTTTTCT
1 TTTTTTCT
*
137158 TTTCTT-T
1 TTTTTTCT
137165 TTTTTTCT
1 TTTTTTCT
137173 T
1 T
137174 CAAGCATAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
5 5 0.09
7 13 0.22
8 34 0.59
9 6 0.10
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:137121 original size:22 final size:22
Alignment explanation
Indices: 137096--137173 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
137086 CACCTTGACC
137096 CTTTTTTCTTTTTTCTTTTTTT
1 CTTTTTTCTTTTTTCTTTTTTT
*
137118 CTTTTTT-TCTTTTT-TTCTTTT
1 CTTTTTTCT-TTTTTCTTTTTTT
*
137139 CTTTTCTCCCTTTTTTTCTTTTCTTT
1 CTTTT-T-TC-TTTTTTCTTTT-TTT
137165 -TTTTTTCTT
1 CTTTTTTCTT
137174 CAAGCATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
21 12 0.27
22 15 0.33
23 1 0.02
24 6 0.13
25 8 0.18
26 3 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
CTTTTTTCTTTTTTCTTTTTTT
Found at i:148406 original size:14 final size:14
Alignment explanation
Indices: 148387--148418 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
148377 CTTTTCTTCG
*
148387 ATATTTAAAAATAA
1 ATATTTAAAAAAAA
148401 ATATTTAAAAAAAA
1 ATATTTAAAAAAAA
148415 ATAT
1 ATAT
148419 ATTTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATATTTAAAAAAAA
Found at i:148519 original size:19 final size:18
Alignment explanation
Indices: 148491--148539 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
148481 CAATATATTT
*
148491 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAACG
148509 AAAACATATAAAATAAACG
1 AAAACA-ATAAAATAAACG
148528 AAAA-AATAAAAT
1 AAAACAATAAAAT
148540 TAAAAATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (18 bp):
AAAACAATAAAATAAACG
Done.