Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007948.1 Hibiscus syriacus cultivar Beakdansim tig00110370_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: 294181
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
File 2 of 2
Found at i:211455 original size:18 final size:18
Alignment explanation
Indices: 211419--211456 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
211409 TCATAACAAT
*
211419 TAAATAATTTTTATCATA
1 TAAATAATTTTTATAATA
211437 TAAATAATTCTTT-TAATA
1 TAAATAATT-TTTATAATA
211455 TA
1 TA
211457 TGTACTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATAATTTTTATAATA
Found at i:212804 original size:14 final size:13
Alignment explanation
Indices: 212772--212796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
212762 TTTGTTTAAT
212772 AATTTTAAAAATA
1 AATTTTAAAAATA
212785 AATTTTAAAAAT
1 AATTTTAAAAAT
212797 TCATTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTTTAAAAATA
Found at i:217677 original size:31 final size:31
Alignment explanation
Indices: 217639--217700 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
217629 GTTAACCAAC
217639 CCATCTCCTAAACATTCCTCTTTACTTTGGG
1 CCATCTCCTAAACATTCCTCTTTACTTTGGG
217670 CCATCTCCTAAACATTCCTCTTTACTTTGGG
1 CCATCTCCTAAACATTCCTCTTTACTTTGGG
217701 TTAATACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (31 bp):
CCATCTCCTAAACATTCCTCTTTACTTTGGG
Found at i:224267 original size:24 final size:24
Alignment explanation
Indices: 224237--224294 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
224227 ATTGCAAAAA
224237 TGTGTATAAATAGGCAATGTGGAG
1 TGTGTATAAATAGGCAATGTGGAG
224261 TGTGTATAAATAGGCAATGTGGAG
1 TGTGTATAAATAGGCAATGTGGAG
224285 TGTGTATAAA
1 TGTGTATAAA
224295 GAAGAGAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.31
Consensus pattern (24 bp):
TGTGTATAAATAGGCAATGTGGAG
Found at i:224449 original size:33 final size:34
Alignment explanation
Indices: 224367--224449 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 34
224357 ATTTGGCAAG
224367 TTGGAAAATTCATC-TTAGTTGATAACCAACTTA
1 TTGGAAAATTCATCTTTAGTTGATAACCAACTTA
* *
224400 TTGGAAAATTCATCTTTA-TTGGTAGCCAACTTA
1 TTGGAAAATTCATCTTTAGTTGATAACCAACTTA
224433 TTGGAAAATTCATCTTT
1 TTGGAAAATTCATCTTT
224450 GGTAGGTGAC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 44 0.94
34 3 0.06
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (34 bp):
TTGGAAAATTCATCTTTAGTTGATAACCAACTTA
Found at i:226015 original size:27 final size:28
Alignment explanation
Indices: 225965--226036 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
225955 AGTTGTGTAA
*
225965 ACACCATTTTTTAAACATCAATACCC-AC
1 ACACCA-TTTTTCAACATCAATACCCAAC
225993 -CATCTCATTTTTCAACATC-ATACCCAAC
1 ACA-C-CATTTTTCAACATCAATACCCAAC
226021 ACACCATTTTTCAACA
1 ACACCATTTTTCAACA
226037 CCAACCCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
27 20 0.51
28 15 0.38
29 4 0.10
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (28 bp):
ACACCATTTTTCAACATCAATACCCAAC
Found at i:232982 original size:37 final size:38
Alignment explanation
Indices: 232938--233120 Score: 183
Period size: 39 Copynumber: 4.8 Consensus size: 38
232928 GAAGGATTTA
* * **
232938 TCTCACTTGAGATTGTTTTTCTTAAA-ACAAGATTTTG
1 TCTCGCTTGAGATAGTTTCCCTTAAACACAAGATTTTG
* *
232975 TCTCACTTGAGATAGTTTCCCTTGAAACAGAAGATTTTG
1 TCTCGCTTGAGATAGTTTCCCTT-AAACACAAGATTTTG
* * * *
233014 TCTCGCTTGAGATAGTTTCTCTCGAAACAGAAGATTTTA
1 TCTCGCTTGAGATAGTTTCCCT-TAAACACAAGATTTTG
* * *
233053 TCTCGCTTTAGACAGTTTCCCTTGAA-ACAA-ATTTTG
1 TCTCGCTTGAGATAGTTTCCCTTAAACACAAGATTTTG
* *
233089 TCTCGCTTGAGACAGTTTCTCTTGAAACACAA
1 TCTCGCTTGAGATAGTTTCCCTT-AAACACAA
233121 AATCTTTGAA
Statistics
Matches: 123, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
36 26 0.21
37 25 0.20
38 9 0.07
39 63 0.51
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (38 bp):
TCTCGCTTGAGATAGTTTCCCTTAAACACAAGATTTTG
Found at i:233023 original size:39 final size:39
Alignment explanation
Indices: 232966--233117 Score: 211
Period size: 39 Copynumber: 4.0 Consensus size: 39
232956 TTCTTAAAAC
* *
232966 AAGATTTTGTCTCACTTGAGATAGTTTCCCTTGAAACAG
1 AAGATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAG
* * *
233005 AAGATTTTGTCTCGCTTGAGATAGTTTCTCTCGAAACAG
1 AAGATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAG
* *
233044 AAGATTTTATCTCGCTTTAGACAGTTTCCCTTGAAAC--
1 AAGATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAG
*
233081 AA-ATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
1 AAGATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACA
233118 CAAAATCTTT
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
36 31 0.31
37 2 0.02
39 68 0.67
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (39 bp):
AAGATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAG
Found at i:233094 original size:36 final size:36
Alignment explanation
Indices: 232962--233320 Score: 258
Period size: 36 Copynumber: 10.1 Consensus size: 36
232952 GTTTTTCTTA
* *
232962 AAACAAGATTTTGTCTCACTTGAGATAGTTTCCCTTG
1 AAACAA-ATTTTGTCTCGCTTGAGACAGTTTCCCTTG
* * *
232999 AAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCTCTCG
1 AAAC--AA-ATTTTGTCTCGCTTGAGACAGTTTCCCTTG
* *
233038 AAACAGAAGATTTTATCTCGCTTTAGACAGTTTCCCTTG
1 AAAC--AA-ATTTTGTCTCGCTTGAGACAGTTTCCCTTG
*
233077 AAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTG
** * **
233113 AAACACAA---AATCT---TTGA-ATATGTTTCTATTG
1 AAACA-AATTTTGTCTCGCTTGAGACA-GTTTCCCTTG
* * * *
233144 AAATAAATTTTGTCTCCCTTAAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTG
** * *
233180 AAACAAA---AATCT---TTGAGACCGTTTCCATTG
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTG
* * *
233210 AAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTT
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTG
* * * * *
233246 AAACGAGTTTTGTCTCTCTTGAGACAATCTCCCTTG
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTG
** *
233282 AAACAAATTTTGTCTCTATTAAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTG
233318 AAA
1 AAA
233321 GAAGTAATGT
Statistics
Matches: 260, Mismatches: 45, Indels: 35
0.76 0.13 0.10
Matches are distributed among these distances:
30 25 0.10
31 17 0.07
33 9 0.03
34 3 0.01
36 128 0.49
37 10 0.04
39 68 0.26
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTG
Found at i:233235 original size:66 final size:67
Alignment explanation
Indices: 233058--233249 Score: 255
Period size: 66 Copynumber: 2.9 Consensus size: 67
233048 TTTTATCTCG
* *
233058 CTTT-AGACAGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACACAAA
1 CTTTGAGACAGTTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
233122 AT
66 AT
* * * *
233124 CTTTGA-ATATGTTTCTATTGAAATAAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACA-AA
1 CTTTGAGACA-GTTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
233187 AAT
65 AAT
* * * * *
233190 CTTTGAGACCGTTTCCATTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTTAAAC
1 CTTTGAGACAGTTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
233250 GAGTTTTGTC
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
66 60 0.56
67 48 0.44
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (67 bp):
CTTTGAGACAGTTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
AT
Found at i:234164 original size:133 final size:133
Alignment explanation
Indices: 233731--235471 Score: 2469
Period size: 133 Copynumber: 13.2 Consensus size: 133
233721 AAGAGATACA
* * * * *
233731 TCAACTTTTTACTCGATTCTATCACAGAAAGAGATAGATCAACACCGACGTCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * * *
233796 TCACAGAAGGAGGTGGATCGACATTTTTAT-TTCTCTTAAATCTATCGCAGAAAGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
233860 ACG
131 GCG
* *
233863 TCAATTTTTTGCTCGATTCTATCACA-AAAGGAGGTAGATCAGCATCAACATCTCGTTCGATTCC
1 TCAACTTTTTGCTCGATTCTATCACAGAAA-GAGGTAGATCAGCATCGACATCTCGTTCGATTCC
* *
233927 ATCACAGAAGGAGGTGGATCGACA---TT-TGTTCGCTCAAATCCATCGTAGAAGGAGTTGGATC
65 ATCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
233988 AGCG
130 AGCG
* ** *
233992 TCAACTTTTTGCTCGTTTCTATCATGGAATGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * *
234057 TCACAAAAGGAGGTGGATTGACATTTTTATCTTCGCTCAAATCTATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
234122 GCA
131 GCG
** *
234125 TCATTTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAACATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * *
234190 TCACAGAAGGAGGTGGATCGACA--TTTGT-TT-GCTCAAATCTATCGTAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
234251 GCG
131 GCG
* * * *
234254 TCAACTTTTTGCTCGTTTCTATCACGGAATGAGATAGATCAGCATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* *
234319 TCACAAAAGGAGGTGGATTGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
234384 GCA
131 GCG
** *
234387 TCATTTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAACATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * *
234452 TCACAGAAGGAGGTGGATCGACA--TTTGT-TT-GCTCAAATCTATCGTAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
234513 GCG
131 GCG
* * * *
234516 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCGATTTCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * *
234581 TCACAGAAGGAGCTGGATCGACATTTTTATCTTTGCTCAAATCCATCGCAGAATGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
* *
234646 ACA
131 GCG
* * * *
234649 TCAACTTTTTGCGCGATTCTATCACAGAAAGAGGTAGATCAGCACCAACATTTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * * *
234714 TCATAGAAGGAGATGGATCGACA--TTTGT-TT-GCTCAAATCCATCGTAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
234775 GCG
131 GCG
*
234778 TCAACTTTTTGCTC-ATTTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTTC
1 TCAACTTTTTGCTCGA-TTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCC
*
234842 ATCACAGAATGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
65 ATCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
234907 AGCG
130 AGCG
*
234911 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* *
234976 TCACAAAAGGAGGTGGATCAACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
235041 ACG
131 GCG
* * * *
235044 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATATCGTTCGATTTCC
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGA-TTCC
* * * *
235109 ATCACAGAAGAAGGTGGATCCACATTTTTTATTTTCGCTCAAATCCATCGCAGAATGAGTTGGAT
65 ATCACAGAAGGAGGTGGATCGACA-TTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
235174 CAGCG
129 CAGCG
* * * *
235179 TCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCATCGACATATCATTCGATTTCC
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGA-TTCC
* **
235244 ATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCAAAGAAGGAGTTGGATC
65 ATCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
235309 AGCG
130 AGCG
* * * * *
235313 TCAACTTTTAGCTCGATTTTATCACAGAAGGAGGTAGATCAGCATCGATATATCGTTCGATTTCC
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGA-TTCC
* * * * *
235378 ATCACAGAAAGAGGTGGATCGATATTTTTATTTTTGCTCAAATCCATCGTAGAAGGAGTTGGATC
65 ATCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
*
235443 AGCA
130 AGCG
*
235447 TCAACTTCTTGCTCGATTC-ATCACA
1 TCAACTTTTTGCTCGATTCTATCACA
235472 TATGGAGTTA
Statistics
Matches: 1450, Mismatches: 136, Indels: 45
0.89 0.08 0.03
Matches are distributed among these distances:
128 2 0.00
129 442 0.30
130 8 0.01
131 27 0.02
132 85 0.06
133 552 0.38
134 208 0.14
135 126 0.09
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (133 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
GCG
Found at i:234195 original size:262 final size:262
Alignment explanation
Indices: 233731--235471 Score: 2563
Period size: 262 Copynumber: 6.6 Consensus size: 262
233721 AAGAGATACA
* * * * * * *
233731 TCAACTTTTTACTCGATTCTATCACAGAAAGAGATAGATCAACACCGACGTCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * * *
233796 TCACAGAAGGAGGTGGATCGACATTTTTAT-TTCTCTTAAATCTATCGCAGAAAGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
* * * *
233860 ACGTCAATTTTTTGCTCGATTCTATCACA-AAAGGAGGTAGATCAGCATCAACATCTCGTTCGAT
131 GCATCAACTTTTTGCTCGATTCTATCACAGAAA-GAGGTAGATCAGCATCGACATCTCGTTCGAT
233924 TCCATCACAGAAGGAGGTGGATCGACATTTGTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCA
195 TCCATCACAGAAGGAGGTGGATCGACATTTGTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCA
233989 GCG
260 GCG
** *
233992 TCAACTTTTTGCTCGTTTCTATCATGGAATGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * *
234057 TCACAAAAGGAGGTGGATTGACATTTTTATCTTCGCTCAAATCTATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
** *
234122 GCATCATTTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAACATCGACATCTCGTTCGATT
131 GCATCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATT
* *
234187 CCATCACAGAAGGAGGTGGATCGACATTTGTTTGCTCAAATCTATCGTAGAAGGAGTTGGATCAG
196 CCATCACAGAAGGAGGTGGATCGACATTTGTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAG
234252 CG
261 CG
* * *
234254 TCAACTTTTTGCTCGTTTCTATCACGGAATGAGATAGATCAGCATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* *
234319 TCACAAAAGGAGGTGGATTGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
** *
234384 GCATCATTTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAACATCGACATCTCGTTCGATT
131 GCATCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATT
* *
234449 CCATCACAGAAGGAGGTGGATCGACATTTGTTTGCTCAAATCTATCGTAGAAGGAGTTGGATCAG
196 CCATCACAGAAGGAGGTGGATCGACATTTGTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAG
234514 CG
261 CG
* *
234516 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCGATTTCA
1 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * *
234581 TCACAGAAGGAGCTGGATCGACATTTTTATCTTTGCTCAAATCCATCGCAGAATGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
* * * * *
234646 ACATCAACTTTTTGCGCGATTCTATCACAGAAAGAGGTAGATCAGCACCAACATTTCGTTCGATT
131 GCATCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATT
* * *
234711 CCATCATAGAAGGAGATGGATCGACATTTGTTTGCTCAAATCCATCGTAGAAGGAGTTGGATCAG
196 CCATCACAGAAGGAGGTGGATCGACATTTGTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAG
234776 CG
261 CG
* * *
234778 TCAACTTTTTGCTCATTTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTTCA
1 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
*
234843 TCACAGAATGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
* *
234908 GCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATT
131 GCATCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATT
* * * *
234973 CCATCACAAAAGGAGGTGGATCAACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGA
196 CCATCACAGAAGGAGGTGGATCGACA---TT-TGTTCGCTCAAATCCATCGTAGAAGGAGTTGGA
*
235038 TCAACG
257 TCAGCG
* * * *
235044 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATATCGTTCGATTTCC
1 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGA-TTCC
* * * *
235109 ATCACAGAAGAAGGTGGATCCACATTTTTTATTTTCGCTCAAATCCATCGCAGAATGAGTTGGAT
65 ATCACAGAAGGAGGTGGATCGACA-TTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
* * * * *
235174 CAGCGTCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCATCGACATATCATTCGA
129 CAGCATCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGA
* **
235239 TTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCAAAGAAGGAGTT
194 -TTCCATCACAGAAGGAGGTGGATCGACA---TT-TGTTCGCTCAAATCCATCGTAGAAGGAGTT
235304 GGATCAGCG
254 GGATCAGCG
* * *
235313 TCAACTTTTAGCTCGATTT-TATCACAGAAGGAGGTAGATCAGCATCGATATATCGTTCGATTTC
1 TCAACTTTTTGCTCG-TTTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGA-TTC
* * * * *
235377 CATCACAGAAAGAGGTGGATCGATATTTTTATTTTTGCTCAAATCCATCGTAGAAGGAGTTGGAT
64 CATCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
*
235442 CAGCATCAACTTCTTGCTCGATTC-ATCACA
129 CAGCATCAACTTTTTGCTCGATTCTATCACA
235472 TATGGAGTTA
Statistics
Matches: 1368, Mismatches: 102, Indels: 14
0.92 0.07 0.01
Matches are distributed among these distances:
261 84 0.06
262 855 0.62
263 3 0.00
265 2 0.00
266 89 0.07
267 30 0.02
268 157 0.11
269 146 0.11
270 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (262 bp):
TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
GCATCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATT
CCATCACAGAAGGAGGTGGATCGACATTTGTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAG
CG
Found at i:235209 original size:44 final size:44
Alignment explanation
Indices: 233729--235471 Score: 691
Period size: 44 Copynumber: 39.6 Consensus size: 44
233719 AGAAGAGATA
** * * * * *
233729 CATCAACTTTTTACTCGATTCTATCACAGAAAGAGATAGATCAA
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * *
233773 CACCGACGTCTCGTTCGATTCCATCACAGAAGGAGGTGGATC-G
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
*** * ** * * * * * *
233816 ACAT-TTTTATTTCTCTTAAATCTATCGCAGAAAGAGTTGGATCAA
1 -CATCAACT-TTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * * *
233861 CGTCAATTTTTTGCTCGATTCTATCACAAAAGGAGGTAGATCAG
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * *
233905 CATCAACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATC-G
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * ** *
233948 -A-C-ATTTGTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAG
1 CATCAACTT-TTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * ** * *
233990 CGTCAACTTTTTGCTCGTTTCTATCATGGAATGAGGTAGATCAG
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * * *
234034 CATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGAT-TG
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
** * * * * * *
234077 ACATTTTTA-TCTTCGCTCAAATCTATCGCAGAAGGAGTTGGATCAG
1 -CA--TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
** * * * * *
234123 CATCATTTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAA
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * *
234167 CATCGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATC-G
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * * ** *
234210 -A-C-ATTTGTTTGCTCAAATCTATCGTAGAAGGAGTTGGATCAG
1 CATCAACTT-TTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * * * * *
234252 CGTCAACTTTTTGCTCGTTTCTATCACGGAATGAGATAGATCAG
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * * *
234296 CATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGAT-TG
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
** * * * * *
234339 ACATTTTTA-TCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
1 -CA--TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
** * * * * *
234385 CATCATTTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAA
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * *
234429 CATCGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATC-G
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * * ** *
234472 -A-C-ATTTGTTTGCTCAAATCTATCGTAGAAGGAGTTGGATCAG
1 CATCAACTT-TTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * * *
234514 CGTCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAA
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * * *
234558 CATCGACATCTCGTTCGATTTCATCACAGAAGGAGCTGGATC-G
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
** * * * * * *
234601 -A-CATTTTTATCTTTGCTCAAATCCATCGCAGAATGAGTTGGATCAA
1 CATCAACTTT-TC---GCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * *
234647 CATCAACTTTTTGCGCGATTCTATCACAGAAAGAGGTAGATCAG
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * *
234691 CACCAACATTTCGTTCGATTCCATCATAGAAGGAGATGGATC-G
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * ** *
234734 -A-C-ATTTGTTTGCTCAAATCCATCGTAGAAGGAGTTGGATCAG
1 CATCAACTT-TTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * *
234776 CGTCAACTTTTTGCTC-ATTTCTATCACAGAAAGAGGTAGATCAG
1 CATCAACTTTTCGCTCGA-TTCCATCACAGAAGGAGGTGGATCAG
* * * * * *
234820 CATCGACATCTCGTTCGATTTCATCACAGAATGAGGTGGATC-G
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
** * * * * *
234863 ACATTTTTA-TCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
1 -CA--TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * *
234909 CGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAG
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * * *
234953 CATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCAA
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
** * * * * * *
234997 CATTTTTA-TCTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAA
1 CA--TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * *
235042 CGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAA
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * *
235086 CATCGACATATCGTTCGATTTCCATCACAGAAGAAGGTGGATCCA-
1 CATCAACTTTTCGCTCGA-TTCCATCACAGAAGGAGGTGGAT-CAG
** * * * * *
235131 CATTTTTTA-TTTTCGCTCAAATCCATCGCAGAATGAGTTGGATCAG
1 CA---TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * * *
235177 CGTCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAG
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * **
235221 CATCGACATATCATTCGATTTCCATCACAGAAGGAGGTGGATC-G
1 CATCAACTTTTCGCTCGA-TTCCATCACAGAAGGAGGTGGATCAG
** * * * *
235265 ACATTTTTA-TTTTCGCTCAAATCCATCAAAGAAGGAGTTGGATCAG
1 -CA--TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * ** *
235311 CGTCAACTTTTAGCTCGATTTTATCACAGAAGGAGGTAGATCAG
1 CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
* * * *
235355 CATCGA-TATATCGTTCGATTTCCATCACAGAAAGAGGTGGATC-G
1 CATCAACT-TTTCGCTCGA-TTCCATCACAGAAGGAGGTGGATCAG
* ** * * * ** *
235399 ATATTTTTA-TTTTTGCTCAAATCCATCGTAGAAGGAGTTGGATCAG
1 -CA--TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
235445 CATCAACTTCTT-GCTCGATT-CATCACA
1 CATCAACTT-TTCGCTCGATTCCATCACA
235472 TATGGAGTTA
Statistics
Matches: 1194, Mismatches: 433, Indels: 145
0.67 0.24 0.08
Matches are distributed among these distances:
40 8 0.01
41 107 0.09
42 11 0.01
43 24 0.02
44 719 0.60
45 258 0.22
46 46 0.04
47 14 0.01
48 7 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (44 bp):
CATCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG
Found at i:235834 original size:29 final size:26
Alignment explanation
Indices: 235767--235846 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 26
235757 GCAGCTGTAA
235767 ACACCATTTTTCAAACATCAACACCCAC
1 ACACCATTTTTC-AACATCAA-ACCCAC
235795 -CATCTCATTTTTCAACATCAATACCCAC
1 ACA-C-CATTTTTCAACATCAA-ACCCAC
235823 TACACCATTTTTCAACA-CAAACCC
1 -ACACCATTTTTCAACATCAAACCC
235847 TATCATCCCT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
26 4 0.09
27 5 0.11
28 27 0.57
29 9 0.19
30 2 0.04
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (26 bp):
ACACCATTTTTCAACATCAAACCCAC
Found at i:238420 original size:14 final size:14
Alignment explanation
Indices: 238401--238429 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
238391 GGGCATCAAA
238401 AAAAAATAATTTGT
1 AAAAAATAATTTGT
238415 AAAAAATAATTTGT
1 AAAAAATAATTTGT
238429 A
1 A
238430 TTACTACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (14 bp):
AAAAAATAATTTGT
Found at i:241457 original size:34 final size:33
Alignment explanation
Indices: 241330--241450 Score: 199
Period size: 33 Copynumber: 3.6 Consensus size: 33
241320 GGCAAGTTGG
*
241330 AAAATTCATCTTGGTTGGTGGACAACTTATTGA
1 AAAATTCATCTTGGTTGGTGGTCAACTTATTGA
241363 AAAATTCATCTTGGTTGGTGGTCAACTTATTGA
1 AAAATTCATCTTGGTTGGTGGTCAACTTATTGA
241396 AAAATTCATCTTGGTTGGTGGTCAACTTATT-A
1 AAAATTCATCTTGGTTGGTGGTCAACTTATTGA
*
241428 GAAAATTCATCTTTGGTAGGTGG
1 -AAAATTCATC-TTGGTTGGTGG
241451 CTAACTTTGC
Statistics
Matches: 84, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
32 1 0.01
33 73 0.87
34 10 0.12
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (33 bp):
AAAATTCATCTTGGTTGGTGGTCAACTTATTGA
Found at i:246486 original size:20 final size:20
Alignment explanation
Indices: 246461--246506 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
246451 CACACGTTGC
246461 ATATTCTGGAATGCACAAGT
1 ATATTCTGGAATGCACAAGT
246481 ATATTCTGGAATGCACAAGT
1 ATATTCTGGAATGCACAAGT
246501 ATATTC
1 ATATTC
246507 CAGACTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (20 bp):
ATATTCTGGAATGCACAAGT
Found at i:251273 original size:179 final size:179
Alignment explanation
Indices: 250973--251327 Score: 665
Period size: 179 Copynumber: 2.0 Consensus size: 179
250963 TACACCTAGT
*
250973 TTATATAGAAGTTTATACCTTCAAGCTTACTCTACATTTCTAACAGATTCTTAACAAACTTTATA
1 TTATATAGAAGCTTATACCTTCAAGCTTACTCTACATTTCTAACAGATTCTTAACAAACTTTATA
*
251038 ACAAATTCTAATATTCATAACTGACTCACGCACACAATGCCCTTAATAGGAGCTCATGCACACGT
66 ACAAATTCTAATATTCATAACTGACTCACGCACACAATGCCCTTAATAGGAGCTCATGCACACAT
251103 TGCATATTCTGGAATGCACAAGTATATTCCAGACTTCATATTCCAAAGC
131 TGCATATTCTGGAATGCACAAGTATATTCCAGACTTCATATTCCAAAGC
*
251152 TTATATAGAAGCTTATACCTTCAAGCTTACTCTACCTTTCTAACAGATTCTTAACAAACTTTATA
1 TTATATAGAAGCTTATACCTTCAAGCTTACTCTACATTTCTAACAGATTCTTAACAAACTTTATA
*
251217 ACAAATTCTAATATTTATAACTGACTCACGCACACAATGCCCTTAATAGGAGCTCATGCACACAT
66 ACAAATTCTAATATTCATAACTGACTCACGCACACAATGCCCTTAATAGGAGCTCATGCACACAT
*
251282 TGCATATTCTGGAATGCACAAGTATATTCCATACTTCATATTCCAA
131 TGCATATTCTGGAATGCACAAGTATATTCCAGACTTCATATTCCAA
251328 TAGAGGTAAA
Statistics
Matches: 171, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
179 171 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (179 bp):
TTATATAGAAGCTTATACCTTCAAGCTTACTCTACATTTCTAACAGATTCTTAACAAACTTTATA
ACAAATTCTAATATTCATAACTGACTCACGCACACAATGCCCTTAATAGGAGCTCATGCACACAT
TGCATATTCTGGAATGCACAAGTATATTCCAGACTTCATATTCCAAAGC
Found at i:255367 original size:2 final size:2
Alignment explanation
Indices: 255360--255395 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
255350 CACATATTTA
255360 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
255396 CATTCTATTA
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:256641 original size:41 final size:41
Alignment explanation
Indices: 256596--256685 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
256586 GCTAGGCGGG
* *
256596 AGGGGGAGACGCGCCACATTAGACATGCCTTTGTAGGGTGA
1 AGGGGGAGACGCGCCACATGAGACACGCCTTTGTAGGGTGA
** * *
256637 AGGGGGAGGTGCGCCACGTGGGACACGCCTTTGTAGGGTGA
1 AGGGGGAGACGCGCCACATGAGACACGCCTTTGTAGGGTGA
256678 AGGGGGAG
1 AGGGGGAG
256686 GTACTTCACG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.21, C:0.18, G:0.44, T:0.17
Consensus pattern (41 bp):
AGGGGGAGACGCGCCACATGAGACACGCCTTTGTAGGGTGA
Found at i:256686 original size:41 final size:41
Alignment explanation
Indices: 256617--256709 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
256607 CGCCACATTA
* *
256617 GACATGCCTTTGTAGGGTGAAGGGGGAGGTGCGCCACGTGG
1 GACACGCCTTTGTAGGGTGAAGGGGGAGGTACGCCACGTGG
**
256658 GACACGCCTTTGTAGGGTGAAGGGGGAGGTACTTCACGTGG
1 GACACGCCTTTGTAGGGTGAAGGGGGAGGTACGCCACGTGG
*
256699 GACACGTCTTT
1 GACACGCCTTT
256710 TACGGTGGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.18, C:0.18, G:0.41, T:0.23
Consensus pattern (41 bp):
GACACGCCTTTGTAGGGTGAAGGGGGAGGTACGCCACGTGG
Found at i:267432 original size:20 final size:20
Alignment explanation
Indices: 267407--267449 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
267397 GCCTACCTCA
* * *
267407 TTCTTCTTCTTGTTTTTCTT
1 TTCTTCATCTTCTTTGTCTT
267427 TTCTTCATCTTCTTTGTCTT
1 TTCTTCATCTTCTTTGTCTT
267447 TTC
1 TTC
267450 CCTCCTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.23, G:0.05, T:0.70
Consensus pattern (20 bp):
TTCTTCATCTTCTTTGTCTT
Found at i:276313 original size:31 final size:31
Alignment explanation
Indices: 276227--276313 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
276217 GTTTTAAAAG
* * *
276227 TAACAAATTGGTCACCAACGTTATCGATTTA
1 TAACAAAATGGTCACTAATGTTATCGATTTA
*
276258 TAACAAAATGGTCACTAGTGTTATCGATTTA
1 TAACAAAATGGTCACTAATGTTATCGATTTA
*
276289 TAACAAAATGGTCACTAATATTATC
1 TAACAAAATGGTCACTAATGTTATC
276314 TCTATTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (31 bp):
TAACAAAATGGTCACTAATGTTATCGATTTA
Found at i:276929 original size:31 final size:31
Alignment explanation
Indices: 276894--276955 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
276884 GGTGGAGTAT
*
276894 TCATTTTGTTATAAATCGATAACATTAGTGA
1 TCATTTTGTTATAAATAGATAACATTAGTGA
* *
276925 TCATTTTGTTATAACTAGATAACGTTAGTGA
1 TCATTTTGTTATAAATAGATAACATTAGTGA
276956 CTAATTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (31 bp):
TCATTTTGTTATAAATAGATAACATTAGTGA
Found at i:276964 original size:31 final size:31
Alignment explanation
Indices: 276898--276966 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
276888 GAGTATTCAT
* *
276898 TTTGTTATAAATCGATAACATTAGTGATCAT
1 TTTGTTATAAATAGATAACATTAGTGATCAA
* *
276929 TTTGTTATAACTAGATAACGTTAGTGA-CTAA
1 TTTGTTATAAATAGATAACATTAGTGATC-AA
276960 TTTGTTA
1 TTTGTTA
276967 CTGTGGTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.43
Consensus pattern (31 bp):
TTTGTTATAAATAGATAACATTAGTGATCAA
Found at i:277174 original size:23 final size:23
Alignment explanation
Indices: 277131--277178 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
277121 TGTTAATTTT
277131 AATATATAATTAATATAAATTAA
1 AATATATAATTAATATAAATTAA
* *
277154 AATATTTAATT-ATCATTAATTAA
1 AATATATAATTAAT-ATAAATTAA
277177 AA
1 AA
277179 AATGTAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AATATATAATTAATATAAATTAA
Found at i:279913 original size:21 final size:22
Alignment explanation
Indices: 279867--279913 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
279857 AATGTTAAGA
* *
279867 CCTTTCGATGAAAGGACTTAAT
1 CCTTTCAATGAAAGGACATAAT
*
279889 -CTTTCAATTAAAGGACAT-AT
1 CCTTTCAATGAAAGGACATAAT
279909 CCTTT
1 CCTTT
279914 TGATAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (22 bp):
CCTTTCAATGAAAGGACATAAT
Found at i:282870 original size:13 final size:13
Alignment explanation
Indices: 282852--282876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
282842 GATTTATCAT
282852 TTTGATGAAAAGG
1 TTTGATGAAAAGG
282865 TTTGATGAAAAG
1 TTTGATGAAAAG
282877 TGCTTAACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (13 bp):
TTTGATGAAAAGG
Found at i:286682 original size:2 final size:2
Alignment explanation
Indices: 286642--286673 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
286632 AGACAACATG
286642 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
286674 TTGTATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:290672 original size:44 final size:42
Alignment explanation
Indices: 290555--290719 Score: 122
Period size: 43 Copynumber: 3.8 Consensus size: 42
290545 TGAGGGAGTC
*
290555 AATTATAAATGTAAAAAATGAGATTAAAAGAAA-TAGAGACCTA
1 AATTATAAA-GTAAAAAGTGAGATTAAAA-AAATTAGAGACCTA
* *
290598 AATTATAAAATCAAAAAGT-ATGATTGAAAAAAATTAG-GAACCTT
1 AATTATAAAGT-AAAAAGTGA-GATT-AAAAAAATTAGAG-ACCTA
* *** *
290642 AATTATAAAGGTAAAAATGTGAGATTAAAAAAA-TAAAGGTTTC
1 AATTATAAA-GTAAAAA-GTGAGATTAAAAAAATTAGAGACCTA
* * *
290685 AATTATAAAAGTAAAAAATGAGGTTGAAAAAATTA
1 AATTAT-AAAGTAAAAAGTGAGATTAAAAAAATTA
290720 AGGGTAGTGA
Statistics
Matches: 99, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
42 14 0.14
43 41 0.41
44 36 0.36
45 7 0.07
46 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.26
Consensus pattern (42 bp):
AATTATAAAGTAAAAAGTGAGATTAAAAAAATTAGAGACCTA
Found at i:290937 original size:41 final size:41
Alignment explanation
Indices: 290887--290967 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
290877 TTGTTTATAA
* * * *
290887 AAATTAAAAAATTATAAATTTTAATTATAAATGTATAATTG
1 AAATTAAAAAATTAAAAATCTTAATTATAAAAGTAAAATTG
*
290928 AAATTAAAAAATTAAAAATCTTAATTGTAAAAGTAAAATT
1 AAATTAAAAAATTAAAAATCTTAATTATAAAAGTAAAATT
290968 TAAAAATCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (41 bp):
AAATTAAAAAATTAAAAATCTTAATTATAAAAGTAAAATTG
Found at i:290939 original size:21 final size:21
Alignment explanation
Indices: 290887--290946 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
290877 TTGTTTATAA
*
290887 AAATTAAAAAATTATAAATTT
1 AAATTAAAAAATTATAAATTG
* *
290908 TAATT-ATAAATGTAT-AATTG
1 AAATTAAAAAAT-TATAAATTG
*
290928 AAATTAAAAAATTAAAAAT
1 AAATTAAAAAATTATAAAT
290947 CTTAATTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (21 bp):
AAATTAAAAAATTATAAATTG
Found at i:291276 original size:25 final size:25
Alignment explanation
Indices: 291242--291290 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
291232 AGTTATTGAC
291242 GTGACATTTCATAATAATTAATGAT
1 GTGACATTTCATAATAATTAATGAT
291267 GTGACATTTCATAATAATTAATGA
1 GTGACATTTCATAATAATTAATGA
291291 CGTAACAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (25 bp):
GTGACATTTCATAATAATTAATGAT
Found at i:291786 original size:7 final size:7
Alignment explanation
Indices: 291774--291798 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
291764 TCTTTCGTAA
291774 ATTTAAG
1 ATTTAAG
291781 ATTTAAG
1 ATTTAAG
291788 ATTTAAG
1 ATTTAAG
291795 ATTT
1 ATTT
291799 GATCTTATTA
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (7 bp):
ATTTAAG
Found at i:292493 original size:17 final size:17
Alignment explanation
Indices: 292473--292506 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
292463 AATATAGAAG
292473 ATATATATATATAATTA
1 ATATATATATATAATTA
*
292490 ATATATTTATATAATTA
1 ATATATATATATAATTA
292507 TGACTAAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATATATAATTA
Done.