Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007851.1 Hibiscus syriacus cultivar Beakdansim tig00110210_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: 1608033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:741 original size:3 final size:3
Alignment explanation
Indices: 733--794 Score: 108
Period size: 3 Copynumber: 20.7 Consensus size: 3
723 TTCAGGTTTG
733 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
778 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
795 TAAATACGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:7623 original size:36 final size:36
Alignment explanation
Indices: 7573--7641 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
7563 CTATGCACAT
* *
7573 AAAGATCCTGTTAGATTAATACCAAAAGTATTCCAC
1 AAAGATCCTATTAGATTAATACCAAAAGCATTCCAC
*
7609 AAAGATCCTATTAGATTGATACCAAAAGCATTC
1 AAAGATCCTATTAGATTAATACCAAAAGCATTC
7642 TACGGTAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (36 bp):
AAAGATCCTATTAGATTAATACCAAAAGCATTCCAC
Found at i:8164 original size:43 final size:43
Alignment explanation
Indices: 8095--8184 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
8085 ATAAATTGTC
**
8095 TTTGGAGAAGTTGGGAATGAAAGTTATCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAAGAATGAAAGTTATCCCCTATATGTAAAGT
* *
8138 TTTGGAGAAGTTAAGAGTGAAGGTTATCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAAGAATGAAAGTTATCCCCTATATGTAAAGT
8181 TTTG
1 TTTG
8185 TTTGATGTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (43 bp):
TTTGGAGAAGTTAAGAATGAAAGTTATCCCCTATATGTAAAGT
Found at i:8959 original size:19 final size:19
Alignment explanation
Indices: 8935--8971 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8925 AGATCAAGTT
*
8935 GAAGCGAAGTATAGAAGAG
1 GAAGCGAAATATAGAAGAG
8954 GAAGCGAAATATAGAAGA
1 GAAGCGAAATATAGAAGA
8972 TGTTAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.32, T:0.11
Consensus pattern (19 bp):
GAAGCGAAATATAGAAGAG
Found at i:13091 original size:41 final size:41
Alignment explanation
Indices: 13027--13104 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
13017 CATCATCATG
* *
13027 TTGGGACATTTTGAAGGTCCATTT-TGACCAGAAATGAAAAT
1 TTGGGACATTTGGAAGGTCCATTTCAGA-CAGAAATGAAAAT
*
13068 TTGGTACATTTGGAAGG-CACATTTCAGACAGAAATGA
1 TTGGGACATTTGGAAGGTC-CATTTCAGACAGAAATGA
13105 TCCATGAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 1 0.03
41 29 0.91
42 2 0.06
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (41 bp):
TTGGGACATTTGGAAGGTCCATTTCAGACAGAAATGAAAAT
Found at i:15094 original size:97 final size:96
Alignment explanation
Indices: 14928--15152 Score: 272
Period size: 97 Copynumber: 2.3 Consensus size: 96
14918 TACCAATCAG
* *
14928 AACTCCTCATCACGAAGGAGTC-ACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAAC
1 AACTCCTCATCACGAAGGAG-CAACATCATCCTTAGACAACCAGACGTCATCATCACGAAAGAAC
* * * *
14992 TGTGTTATCTCCAATATCTTCAATGATGGTCA
65 AGTGTTATCTCAAATATCTTCAAAGATGGCCA
* * * * * *
15024 TAACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCATATGTCATCATCATGAAATAAC
1 -AACTCCTCATCACGAAGGAGCAACATCATCCTTAGACAACCAGACGTCATCATCACGAAAGAAC
*
15089 AGTGTTATCTCAAATATCTTTAAAGATGGCCA
65 AGTGTTATCTCAAATATCTTCAAAGATGGCCA
* * *
15121 GACGTCCTCATCACGAAGGAACAATATCATCC
1 AAC-TCCTCATCACGAAGGAGCAACATCATCC
15153 ACCGATAAGA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
96 3 0.03
97 106 0.97
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (96 bp):
AACTCCTCATCACGAAGGAGCAACATCATCCTTAGACAACCAGACGTCATCATCACGAAAGAACA
GTGTTATCTCAAATATCTTCAAAGATGGCCA
Found at i:15199 original size:137 final size:137
Alignment explanation
Indices: 15025--15564 Score: 739
Period size: 137 Copynumber: 4.0 Consensus size: 137
15015 TGATGGTCAT
* * *
15025 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCATATGTCATCATCATGAAATAACA
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
*
15090 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATATCATCCAC
66 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
*
15155 CGATAAG
131 CGATCAG
*
15162 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATATCCTCATCATGAAAGAACA
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
*
15227 TTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
66 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
15292 CGATCAG
131 CGATCAG
* * * * * * *
15299 AACTCCTCATCATG-ATGAGCAACATCATTCTTAGATAGCTAGATGTCCTCATCACGAATGAACC
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
* * *
15363 GTGTTATCTCAAATATATTT-AAGATGGCCAGACATCCTCATCACGAAGAAACAATGTCATCCAC
66 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
15427 CGATCAG
131 CGATCAG
* * * * * *
15434 AACTACTCATCACGTAGGAGC--CGAGTCATCCTCAGATAACCAGACGTCCTCATCA-CAAAGGA
1 AACTCCTCATCACGAAGGAGCAAC-A-TCATTCTTAGATAACCAGATGTCCTCATCATGAAA-GA
** * * * * * *
15496 ACCTTGTTATCTTAAATATCTTCAAAGGTGGTCAGACGTCCTCATCATGAAGGAACAATGTCATA
63 ACAGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATC
15561 CACC
128 CACC
15565 AGTTAGATCT
Statistics
Matches: 359, Mismatches: 39, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
134 1 0.00
135 64 0.18
136 112 0.31
137 182 0.51
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (137 bp):
AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
CGATCAG
Found at i:15311 original size:234 final size:233
Alignment explanation
Indices: 14875--15316 Score: 543
Period size: 234 Copynumber: 1.9 Consensus size: 233
14865 CCTAAATGTC
* * * *
14875 TTAAAGATGGCCAAATGTCCTCATCACGAGGAACAATGTCATCTACCAATCAGAACTCCTCATCA
1 TTAAAGATGGCCAAACGTCCTCATCACGAGGAACAATATCATCCACCAATAAGAACTCCTCATCA
* * *
14940 CGAAGGAGTCACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCCA
66 CGAAGGAGTCACATCATCCTTAGACAACCAGACATCCTCATCACGAAAGAACTGTGTTATCTCAA
* * * * ** * *
15005 ATATCTTCAATGATGGTCATAACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCATAT
131 ATATCTTCAAAGATGGCCATAACTCCTCATCACGAAGGAACAACATCATCCACAGATAAACATAC
*
15070 GTCATCATCATGAAATAACAGTGTTATCTCAAATATCT
196 CTCATCATCATGAAATAACAGTGTTATCTCAAATATCT
* *
15108 TTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATATCATCCACCGATAAGAACTCCTCATC
1 TTAAAGATGGCCAAACGTCCTCATCACG-AGGAACAATATCATCCACCAATAAGAACTCCTCATC
* * * *
15173 ACGAAGGAG-CAACATCATTCTTAGATAACCAGATATCCTCATCATGAAAGAACAT-TGTTATCT
65 ACGAAGGAGTC-ACATCATCCTTAGACAACCAGACATCCTCATCACGAAAGAAC-TGTGTTATCT
* * ** *
15236 CAAATATCTTTAAAGATGGCCA-GACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGA
128 CAAATATCTTCAAAGATGGCCATAAC-TCCTCATCACGAAGGAACAACATCATCCACAGAT-A-A
*
15300 AC-T-CCTCATCATGATGA
190 ACATACCTCATCATCATGA
15317 GCAACATCAT
Statistics
Matches: 175, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
233 29 0.17
234 141 0.81
235 3 0.02
236 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.25
Consensus pattern (233 bp):
TTAAAGATGGCCAAACGTCCTCATCACGAGGAACAATATCATCCACCAATAAGAACTCCTCATCA
CGAAGGAGTCACATCATCCTTAGACAACCAGACATCCTCATCACGAAAGAACTGTGTTATCTCAA
ATATCTTCAAAGATGGCCATAACTCCTCATCACGAAGGAACAACATCATCCACAGATAAACATAC
CTCATCATCATGAAATAACAGTGTTATCTCAAATATCT
Found at i:15534 original size:272 final size:273
Alignment explanation
Indices: 15025--15564 Score: 757
Period size: 272 Copynumber: 2.0 Consensus size: 273
15015 TGATGGTCAT
* *
15025 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCATATGTCATCATCATGAAATAACA
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCATCATCACGAAATAACA
* * *
15090 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATATCATCCAC
66 GTGTTATCTCAAATATATTTAAAGATGGCCAGACATCCTCATCACGAAGAAACAATATCATCCAC
* * * * *
15155 CGATAAGAACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATATCCTCATCATGA
131 CGATAAGAACTACTCATCACGAAGGAGC-ACATCATCCTCAGATAACCAGACATCCTCATCATCA
*
15220 AAGAACATTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGT
195 AAGAACATTGTTATCTCAAATATCTTCAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGT
*
15285 CATCCACCGATCAG
260 CATACACCGATCAG
* * * * *
15299 AACTCCTCATCATG-ATGAGCAACATCATTCTTAGATAGCTAGATGTCCTCATCACG-AATGAAC
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCATCATCACGAAAT-AAC
* *
15362 CGTGTTATCTCAAATATATTT-AAGATGGCCAGACATCCTCATCACGAAGAAACAATGTCATCCA
65 AGTGTTATCTCAAATATATTTAAAGATGGCCAGACATCCTCATCACGAAGAAACAATATCATCCA
* * *
15426 CCGATCAGAACTACTCATCACGTAGGAGC-CGAGTCATCCTCAGATAACCAGACGTCCTCATCA-
130 CCGATAAGAACTACTCATCACGAAGGAGCAC-A-TCATCCTCAGATAACCAGACATCCTCATCAT
* * * * *
15489 CAAAGGAACCTTGTTATCTTAAATATCTTCAAAGGTGGTCAGACGTCCTCATCATGAAGGAACAA
193 CAAA-GAACATTGTTATCTCAAATATCTTCAAAGATGGCCAGACGTCCTCATCACGAAGGAACAA
15554 TGTCATACACC
257 TGTCATACACC
15565 AGTTAGATCT
Statistics
Matches: 235, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
270 1 0.00
271 4 0.02
272 159 0.68
273 58 0.25
274 13 0.06
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (273 bp):
AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCATCATCACGAAATAACA
GTGTTATCTCAAATATATTTAAAGATGGCCAGACATCCTCATCACGAAGAAACAATATCATCCAC
CGATAAGAACTACTCATCACGAAGGAGCACATCATCCTCAGATAACCAGACATCCTCATCATCAA
AGAACATTGTTATCTCAAATATCTTCAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTC
ATACACCGATCAG
Found at i:20166 original size:36 final size:36
Alignment explanation
Indices: 20125--20200 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
20115 ATTTTCGGGA
*
20125 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
20161 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
20197 TTTT
1 TTTT
20201 TAGCTATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:20639 original size:15 final size:15
Alignment explanation
Indices: 20619--20647 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20609 TATCACAATC
20619 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
20634 GCGCAGGATTCCGG
1 GCGCAGGATTCCGG
20648 AGCACCGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.45, T:0.14
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:25123 original size:36 final size:36
Alignment explanation
Indices: 25082--25157 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
25072 ATTTTCGGGA
*
25082 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
25118 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
25154 TTTT
1 TTTT
25158 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:39223 original size:17 final size:16
Alignment explanation
Indices: 39186--39235 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
39176 AACCGGTCTA
39186 ACCCGACCCGA-C-TG
1 ACCCGACCCGACCTTG
39200 A-CCGACCCGACCGTTG
1 ACCCGACCCGACC-TTG
39216 ACCCGACCCGACCATTG
1 ACCCGACCCGACC-TTG
39233 ACC
1 ACC
39236 ATTGACCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 9 0.29
14 2 0.06
16 3 0.10
17 17 0.55
ACGTcount: A:0.22, C:0.48, G:0.20, T:0.10
Consensus pattern (16 bp):
ACCCGACCCGACCTTG
Found at i:44866 original size:2 final size:2
Alignment explanation
Indices: 44859--44892 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
44849 TTTCTCAAAG
44859 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
44893 TTCATATGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49215 original size:16 final size:17
Alignment explanation
Indices: 49190--49231 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
49180 TTAATAATTG
49190 TATGATAACATAA-GTCT
1 TATGA-AACATAAGGTCT
49207 TATGAAACATAAGGTCT
1 TATGAAACATAAGGTCT
49224 TAGTGAAA
1 TA-TGAAA
49232 TAAGATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (17 bp):
TATGAAACATAAGGTCT
Found at i:54422 original size:18 final size:18
Alignment explanation
Indices: 54399--54440 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
54389 TCCTTCGCGT
54399 TGAGGAAGTCTGATTGTC
1 TGAGGAAGTCTGATTGTC
54417 TGAGGAAGTCTGATTGTC
1 TGAGGAAGTCTGATTGTC
54435 TGAGGA
1 TGAGGA
54441 TGACATTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.36, T:0.31
Consensus pattern (18 bp):
TGAGGAAGTCTGATTGTC
Found at i:55132 original size:66 final size:66
Alignment explanation
Indices: 55017--55141 Score: 155
Period size: 67 Copynumber: 1.9 Consensus size: 66
55007 AAAGAAATTT
* * * * *
55017 GTTTCAAGAGAAGCTATCTCAGGTGAGATAAAATTTTATTTCGAGGGAAACAATTTCAATATTTA
1 GTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTATTTCGAGGGAAACAATCTCAATATTTA
55082 C
66 C
* *
55083 GTTTCAAGGGAAAACTATCTCAAGCGAGACAAAATTTGT-TTT-TAGGGAAACAATCTCAA
1 GTTTCAAGAG-AAACTATCTCAAGCGAGACAAAATTT-TATTTCGAGGGAAACAATCTCAA
55142 GTGAGATCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
66 24 0.48
67 25 0.50
68 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (66 bp):
GTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTATTTCGAGGGAAACAATCTCAATATTTA
C
Found at i:55169 original size:36 final size:36
Alignment explanation
Indices: 55083--55171 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 36
55073 CAATATTTAC
*
55083 GTTTCAAGGGAAAACTATCTCAAGCGAGACAAAATTT
1 GTTTCAAGGG-AAACAATCTCAAGCGAGACAAAATTT
** * *
55120 GTTTTTAGGGAAACAATCTCAAGTGAGATC-AATTTT
1 GTTTCAAGGGAAACAATCTCAAGCGAGA-CAAAATTT
*
55156 GTTTCAAGTGAAACAA
1 GTTTCAAGGGAAACAA
55172 CTTCGAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
36 34 0.79
37 9 0.21
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
GTTTCAAGGGAAACAATCTCAAGCGAGACAAAATTT
Found at i:55235 original size:102 final size:104
Alignment explanation
Indices: 55011--55243 Score: 248
Period size: 102 Copynumber: 2.3 Consensus size: 104
55001 GAGTGGAAAG
* * * * *
55011 AAATTTG-TTTCAAGAGAAGCTATCTCAGGTGAGATAAAATTTTATTTCGAGGGAAACAATTTCA
1 AAATTTGTTTTCAAGAGAAACAATCTCAAGTGAGATAAAATTTTATTTCAAGGGAAACAACTTCA
55075 ATATTTACGTTTCAAGGGAAAACTATCTCAAGCGAGACA
66 ATATTTACGTTTCAAGGGAAAACTATCTCAAGCGAGACA
* * * * *
55114 AAATTTGTTTT-TAGGGAAACAATCTCAAGTGAGAT-CAATTTTGTTTCAAGTGAAACAACTTCG
1 AAATTTGTTTTCAAGAGAAACAATCTCAAGTGAGATAAAATTTTATTTCAAGGGAAACAACTTC-
* * *
55177 AA-ATTT-CGGCTTT-AAGGG-AAACTGTCTCAAGTGATACA
65 AATATTTAC-G-TTTCAAGGGAAAACTATCTCAAGCGAGACA
*
55215 AAACTTT-TTTTCGAGAGAAACAATCTCAA
1 AAA-TTTGTTTTCAAGAGAAACAATCTCAA
55244 AGGCTTATAT
Statistics
Matches: 109, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
101 25 0.23
102 50 0.46
103 31 0.28
104 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (104 bp):
AAATTTGTTTTCAAGAGAAACAATCTCAAGTGAGATAAAATTTTATTTCAAGGGAAACAACTTCA
ATATTTACGTTTCAAGGGAAAACTATCTCAAGCGAGACA
Found at i:55272 original size:67 final size:66
Alignment explanation
Indices: 55194--55372 Score: 211
Period size: 67 Copynumber: 2.7 Consensus size: 66
55184 GGCTTTAAGG
* * *
55194 GAAACTGTCTCAAGTGATACAAAACTTTTTTTCGAGAGAAACAATCTCAAAGGCTTATATTTCAA
1 GAAACTATCTCAAGTGAGACAAAACTTTTTTTAGAGA-AAACAATCTCAAAGGCTTATATTTCAA
55259 GA
65 GA
* * * * *
55261 GAAACTATCTCAAGTGAGACGAAACTTTGTTTGGAGAAAAACAATCTCAAAGGTTTATGTTTCAA
1 GAAACTATCTCAAGTGAGACAAAACTTTTTTTAGAG-AAAACAATCTCAAAGGCTTATATTTCAA
55326 GA
65 GA
* *
55328 GAAA-TGTTCTCAAGCGAGACAAAA-TTTGTTTTAG-GAAAACAATCT
1 GAAACT-ATCTCAAGTGAGACAAAACTTT-TTTTAGAGAAAACAATCT
55373 GAATTGAGAT
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
65 10 0.10
66 5 0.05
67 81 0.84
68 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (66 bp):
GAAACTATCTCAAGTGAGACAAAACTTTTTTTAGAGAAAACAATCTCAAAGGCTTATATTTCAAG
A
Found at i:55430 original size:234 final size:235
Alignment explanation
Indices: 55018--55480 Score: 635
Period size: 234 Copynumber: 2.0 Consensus size: 235
55008 AAGAAATTTG
* * * * ** *
55018 TTTCAAGAGAAGCTATCTCAGGTGAGATAAAATTTTATTTCGAGGGAAACAATTTCAATATTTAC
1 TTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTATTTCGAGAAAAACAATCTCAATATTTAC
* *
55083 GTTTCAAGGGAAAACTATCTCAAGCGAGACAAAATTTGTTTTTAGGGAAACAATCTCAAGTGAGA
66 GTTTCAAGAGAAAACTATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACAATCTCAAGTGAGA
* * * ** *
55148 TCAATTTTGTTTCAAGTGAAACAACTTCGAAATTTCGGCTTTAAGGGAAACTGTCTCAAGTGATA
131 TCAATTTTGTTTCAAGTGAAACAACTCCGAAATTTCGGCTTCAAGGGAAAATGTCTCAAGCAAGA
*
55213 CAAAACTTTTTTTCGAGAGAAACAATCTCAAAGGCTTATA
196 CAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGCTTATA
* * *
55253 TTTCAAGAGAAACTATCTCAAGTGAGACGAAACTTTGTTTGGAGAAAAACAATCTCAA-AGGTTT
1 TTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTATTTCGAGAAAAACAATCTCAATA--TTT
* ** * *
55317 ATGTTTCAAGAGAAATGT-TCTCAAGCGAGACAAAATTTG-TTTTAGGAAAACAATCTGAATTGA
64 ACGTTTCAAGAGAAAACTATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACAATCTCAAGTGA
*
55380 GATCAATTTTGTTTCAAGTGAAACAACTCCGAAATTTGGGCTTCAAGGGAAAATGTCTCAAGCAA
129 GATCAATTTTGTTTCAAGTGAAACAACTCCGAAATTTCGGCTTCAAGGGAAAATGTCTCAAGCAA
** *
55445 GATGAAACTTTGTTTCGAGAGAAACAATCTCCAAGG
194 GACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGG
55481 TGAAAGATAA
Statistics
Matches: 198, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
234 112 0.57
235 69 0.35
236 17 0.09
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (235 bp):
TTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTATTTCGAGAAAAACAATCTCAATATTTAC
GTTTCAAGAGAAAACTATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACAATCTCAAGTGAGA
TCAATTTTGTTTCAAGTGAAACAACTCCGAAATTTCGGCTTCAAGGGAAAATGTCTCAAGCAAGA
CAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGCTTATA
Found at i:56607 original size:18 final size:18
Alignment explanation
Indices: 56584--56618 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
56574 ACTGGATATT
*
56584 CGTCCCGGAGGACCACTA
1 CGTCCCGAAGGACCACTA
56602 CGTCCCGAAGGACCACT
1 CGTCCCGAAGGACCACT
56619 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.40, G:0.26, T:0.11
Consensus pattern (18 bp):
CGTCCCGAAGGACCACTA
Found at i:56884 original size:2 final size:2
Alignment explanation
Indices: 56877--56927 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
56867 TATAACAATA
56877 AT AT AT 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 AT AT AT
56919 AT AT AT AT A
1 AT AT AT AT A
56928 CATGTACATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58234 original size:16 final size:16
Alignment explanation
Indices: 58213--58253 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
58203 GCTCCCACGT
58213 TGCTTCCTCTACTTTG
1 TGCTTCCTCTACTTTG
58229 TGCTTCCTCTACTTTG
1 TGCTTCCTCTACTTTG
*
58245 TGATTCCTC
1 TGCTTCCTC
58254 CACAAGACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.32, G:0.12, T:0.49
Consensus pattern (16 bp):
TGCTTCCTCTACTTTG
Found at i:63373 original size:49 final size:49
Alignment explanation
Indices: 63268--63366 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
63258 ATCCATCATA
63268 ACAATGCATTATACATGTATCTACTAAACTATGATATATATATAATTAT
1 ACAATGCATTATACATGTATCTACTAAACTATGATATATATATAATTAT
63317 ACAATGCATTATACATGTATCTACTAAACTATGATATATATATAATTAT
1 ACAATGCATTATACATGTATCTACTAAACTATGATATATATATAATTAT
63366 A
1 A
63367 ATATGCACAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.38
Consensus pattern (49 bp):
ACAATGCATTATACATGTATCTACTAAACTATGATATATATATAATTAT
Found at i:65519 original size:22 final size:22
Alignment explanation
Indices: 65491--65536 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
65481 AGGACCACCA
65491 TAGATCCATTTACTTATGGTAC
1 TAGATCCATTTACTTATGGTAC
65513 TAGATCCATTTACTTATGGTAC
1 TAGATCCATTTACTTATGGTAC
65535 TA
1 TA
65537 CCTGATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (22 bp):
TAGATCCATTTACTTATGGTAC
Found at i:69680 original size:53 final size:53
Alignment explanation
Indices: 69600--69706 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
69590 TCGTCAATCG
*
69600 TATTTTCGTAAGGATCTGTCCGAGCTGACGTCACGTAAGGTCAGCCACGCCTT
1 TATTTTCGTAAGGATCTGTCCGAGCTGACGTCACGTAAGGTCAACCACGCCTT
69653 TATTTTCGTAAGGATCTGTCCGAGCTGACGTCACGTAAGGTCAACCACGCCTT
1 TATTTTCGTAAGGATCTGTCCGAGCTGACGTCACGTAAGGTCAACCACGCCTT
69706 T
1 T
69707 GCTGAACGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.29
Consensus pattern (53 bp):
TATTTTCGTAAGGATCTGTCCGAGCTGACGTCACGTAAGGTCAACCACGCCTT
Found at i:69846 original size:84 final size:84
Alignment explanation
Indices: 69701--69857 Score: 242
Period size: 84 Copynumber: 1.9 Consensus size: 84
69691 GGTCAACCAC
* *
69701 GCCTTTGCTGAACGTGCACGTTGAATTATTGAATACTTAATTATTACTCGAACCTGAAAACTCGA
1 GCCTTCGCTGAACGTGCACGTTGAATTATTGAATACTTAATTATTACCCGAACCTGAAAACTCGA
69766 CTTTTTAACGATCATCCAT
66 CTTTTTAACGATCATCCAT
** * * * *
69785 GCCTTCGCTGAACGTGCACGTTGAATTATTGGGTATTTCATTATTACCCGATCCTGGAAACTCGA
1 GCCTTCGCTGAACGTGCACGTTGAATTATTGAATACTTAATTATTACCCGAACCTGAAAACTCGA
69850 CTTTTTAA
66 CTTTTTAA
69858 TAATCCCCTC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 65 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.35
Consensus pattern (84 bp):
GCCTTCGCTGAACGTGCACGTTGAATTATTGAATACTTAATTATTACCCGAACCTGAAAACTCGA
CTTTTTAACGATCATCCAT
Found at i:70902 original size:60 final size:60
Alignment explanation
Indices: 70795--70911 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
70785 CATTTGACAC
* * * * * *
70795 GATGTCTTCAAGTTTTAGGGGGAGACATTCAACTACAAGTTTTTTCGACCTCAATGTCAA
1 GATGCCTTCAAGTTTAAGGGGAAGACATTCAACTACAAGCTTATTCGACCTAAATGTCAA
*
70855 GATGCCTTCAAGTTTAAGGGGAAGACATTTAACTACCAA-CTTATTCGACCTAAATGT
1 GATGCCTTCAAGTTTAAGGGGAAGACATTCAACTA-CAAGCTTATTCGACCTAAATGT
70912 TAGCATCATG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 46 0.94
61 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (60 bp):
GATGCCTTCAAGTTTAAGGGGAAGACATTCAACTACAAGCTTATTCGACCTAAATGTCAA
Found at i:71324 original size:22 final size:22
Alignment explanation
Indices: 71296--71349 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
71286 GAATGAAAAT
71296 TATTACTGATTATCTCTCCTAA
1 TATTACTGATTATCTCTCCTAA
*
71318 TATTACTGATTATCTCTTCTAA
1 TATTACTGATTATCTCTCCTAA
*
71340 TATTATTGAT
1 TATTACTGAT
71350 CTAGTATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (22 bp):
TATTACTGATTATCTCTCCTAA
Found at i:74608 original size:20 final size:20
Alignment explanation
Indices: 74573--74624 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 20
74563 CCTTTCGATG
74573 AAAGGACTTAATATTTCAATT
1 AAAGGACTT-ATATTTCAATT
74594 AAAGGACTTATATTTCAATT
1 AAAGGACTTATATTTCAATT
74614 AAAGGACTTAT
1 AAAGGACTTAT
74625 CCTTTTGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (20 bp):
AAAGGACTTATATTTCAATT
Found at i:80472 original size:30 final size:30
Alignment explanation
Indices: 80396--80486 Score: 164
Period size: 31 Copynumber: 3.0 Consensus size: 30
80386 TGATTTAACA
80396 GGTTTATAATCTAAAATTTGTTGATAATAT
1 GGTTTATAATCTAAAATTTGTTGATAATAT
80426 GGTTCTATAATCTAAAATTTGTTGATAATAT
1 GGTT-TATAATCTAAAATTTGTTGATAATAT
*
80457 GGTTTATAATATAAAATTTGTTGATAATAT
1 GGTTTATAATCTAAAATTTGTTGATAATAT
80487 TTTGATCATT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
30 29 0.49
31 30 0.51
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.46
Consensus pattern (30 bp):
GGTTTATAATCTAAAATTTGTTGATAATAT
Found at i:81404 original size:2 final size:2
Alignment explanation
Indices: 81397--81428 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
81387 CATTTACTCC
81397 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
81429 TCTTTTTTTC
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:88107 original size:17 final size:18
Alignment explanation
Indices: 88085--88132 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
88075 ATGAACCAAT
*
88085 TTTAATGAATGAACTTG-
1 TTTAATGAATGAACTAGC
* *
88102 TTTAATTAGTGAACTAGC
1 TTTAATGAATGAACTAGC
*
88120 TTTATTGAATGAA
1 TTTAATGAATGAA
88133 ACAACATACT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (18 bp):
TTTAATGAATGAACTAGC
Found at i:95471 original size:14 final size:15
Alignment explanation
Indices: 95452--95493 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
95442 GGTAATTGTT
95452 TTATTTTCTTTT-TC
1 TTATTTTCTTTTATC
95466 TTATTTTTCTTTTGATC
1 TTA-TTTTCTTTT-ATC
95483 TTATTTT-TTTT
1 TTATTTTCTTTT
95494 CAATCGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 13 0.52
16 4 0.16
17 5 0.20
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (15 bp):
TTATTTTCTTTTATC
Found at i:95475 original size:15 final size:16
Alignment explanation
Indices: 95455--95490 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
95445 AATTGTTTTA
95455 TTTTCTTTT-TCTTAT
1 TTTTCTTTTATCTTAT
95470 TTTTCTTTTGATCTTAT
1 TTTTCTTTT-ATCTTAT
95487 TTTT
1 TTTT
95491 TTTCAATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
17 10 0.53
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTATCTTAT
Found at i:96242 original size:18 final size:19
Alignment explanation
Indices: 96219--96258 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
96209 AAATCTTTCC
*
96219 TTTTTATTTTAAAT-TATT
1 TTTTTACTTTAAATATATT
*
96237 TTTTTACTTTGAATATATT
1 TTTTTACTTTAAATATATT
96256 TTT
1 TTT
96259 AATTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTTACTTTAAATATATT
Found at i:99076 original size:21 final size:21
Alignment explanation
Indices: 99052--99120 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 21
99042 TAACCAAGGG
*
99052 GATCGATCATTTGAGAGAAAT
1 GATCGATCATTTGAAAGAAAT
* * ***
99073 GATCAATCTTTTTTCA-AAAT
1 GATCGATCATTTGAAAGAAAT
** *
99093 GATCGATCCCTCGAAAGAAAT
1 GATCGATCATTTGAAAGAAAT
99114 GATCGAT
1 GATCGAT
99121 AACTTCTCTG
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (21 bp):
GATCGATCATTTGAAAGAAAT
Found at i:104874 original size:20 final size:21
Alignment explanation
Indices: 104845--104885 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
104835 TATTAAGATT
104845 TTATTGCTTAATT-TTTTTCC
1 TTATTGCTTAATTATTTTTCC
* *
104865 TTATTTCTTATTTATTTTTCC
1 TTATTGCTTAATTATTTTTCC
104886 CTAATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (21 bp):
TTATTGCTTAATTATTTTTCC
Found at i:115793 original size:39 final size:39
Alignment explanation
Indices: 115739--115814 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
115729 GTGTAACTAA
* *
115739 GAGTTATATTATGATTAGGACTAATTATTATTATTTTAT
1 GAGTTATATTATGATTAAGACTAATTATTAGTATTTTAT
* *
115778 GAGTTGTATTATGATTAAGATTAATTATTAGTATTTT
1 GAGTTATATTATGATTAAGACTAATTATTAGTATTTT
115815 TTATTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.51
Consensus pattern (39 bp):
GAGTTATATTATGATTAAGACTAATTATTAGTATTTTAT
Found at i:117945 original size:74 final size:74
Alignment explanation
Indices: 117798--117938 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 74
117788 CAAAACACAA
* * * * * * *
117798 CCACCTAACACCACTATCTCACCTGACATTGAAAACATACATCAAACCATTAGCCCACTGAACTC
1 CCACCTAACACCACAAACACACCTGACATTGAAAAAAGACACCAAACCAGTAGCCCACTGAACTC
117863 TCCAAAAAT
66 TCCAAAAAT
* * *
117872 CCACCTAACACCACAAACACACCTGACATTGAAAAAAGACACCAAACTAGTAGCCCATTGGACTC
1 CCACCTAACACCACAAACACACCTGACATTGAAAAAAGACACCAAACCAGTAGCCCACTGAACTC
117937 TC
66 TC
117939 TTAAAATACC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 57 1.00
ACGTcount: A:0.40, C:0.35, G:0.08, T:0.18
Consensus pattern (74 bp):
CCACCTAACACCACAAACACACCTGACATTGAAAAAAGACACCAAACCAGTAGCCCACTGAACTC
TCCAAAAAT
Found at i:121284 original size:2 final size:2
Alignment explanation
Indices: 121279--121318 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
121269 TCACATACCC
121279 AT AT 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 AT AT
121319 TCTATCATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:126413 original size:16 final size:16
Alignment explanation
Indices: 126394--126482 Score: 72
Period size: 16 Copynumber: 5.6 Consensus size: 16
126384 AAAGCAATCT
126394 GAACTGAAATTAACCC
1 GAACTGAAATTAACCC
** *
126410 GAACCAAAAGTAACCC
1 GAACTGAAATTAACCC
*
126426 GAACTGAAATTAACTC
1 GAACTGAAATTAACCC
*
126442 GAA-TCAAAATTAACCC
1 GAACT-GAAATTAACCC
* * * **
126458 AAAATGATATTAACTT
1 GAACTGAAATTAACCC
126474 GAACTGAAA
1 GAACTGAAA
126483 GATACCCGAA
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
15 1 0.02
16 52 0.96
17 1 0.02
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.20
Consensus pattern (16 bp):
GAACTGAAATTAACCC
Found at i:126430 original size:32 final size:32
Alignment explanation
Indices: 126394--126471 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
126384 AAAGCAATCT
126394 GAACTGAAATTAACCCGAACCAAAAGTAACCC
1 GAACTGAAATTAACCCGAACCAAAAGTAACCC
* * *
126426 GAACTGAAATTAACTCGAATCAAAATTAACCC
1 GAACTGAAATTAACCCGAACCAAAAGTAACCC
* * *
126458 AAAATGATATTAAC
1 GAACTGAAATTAAC
126472 TTGAACTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.19
Consensus pattern (32 bp):
GAACTGAAATTAACCCGAACCAAAAGTAACCC
Found at i:126546 original size:32 final size:32
Alignment explanation
Indices: 126486--126567 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
126476 ACTGAAAGAT
* * * *
126486 ACCCGAACCAAATTTTAACCCTATCCGAAAGCA
1 ACCCGAA-CAAAATTTAACACGACCCGAAAGCA
*
126519 ACCCGAACTAAATTTAACACGACCCGAAAGCA
1 ACCCGAACAAAATTTAACACGACCCGAAAGCA
* *
126551 ACACGAACAAAAATTAA
1 ACCCGAACAAAATTTAA
126568 TCTAAACTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 34 0.83
33 7 0.17
ACGTcount: A:0.46, C:0.29, G:0.10, T:0.15
Consensus pattern (32 bp):
ACCCGAACAAAATTTAACACGACCCGAAAGCA
Found at i:127069 original size:27 final size:27
Alignment explanation
Indices: 127039--127094 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
127029 TTAAATATTG
127039 AAATCTATCTTGATATTATATATATAT
1 AAATCTATCTTGATATTATATATATAT
* * *
127066 AAATCTATCTTGATTTTTTTTATATAT
1 AAATCTATCTTGATATTATATATATAT
127093 AA
1 AA
127095 GGAAGTTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.52
Consensus pattern (27 bp):
AAATCTATCTTGATATTATATATATAT
Found at i:127183 original size:18 final size:19
Alignment explanation
Indices: 127162--127198 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
127152 TAAGATTAAT
127162 AATTTAT-TAAAAATATTA
1 AATTTATATAAAAATATTA
127180 AATTTATAATAAAAATATT
1 AATTTAT-ATAAAAATATT
127199 GAAAAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTATATAAAAATATTA
Found at i:127478 original size:12 final size:12
Alignment explanation
Indices: 127463--127487 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
127453 TATAATTAGA
127463 AATAAAAATTTT
1 AATAAAAATTTT
127475 AATAAAAATTTT
1 AATAAAAATTTT
127487 A
1 A
127488 TTTCTTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAAAAATTTT
Found at i:128717 original size:23 final size:22
Alignment explanation
Indices: 128677--128719 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
128667 TGTCCTTTTT
* *
128677 TTTTTTTTTTGGTTCTTTTCCC
1 TTTTTTTTCTGATTCTTTTCCC
128699 TTTTTTTTCTGATTACTTTTC
1 TTTTTTTTCTGATT-CTTTTC
128720 TAGTGGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTTTTTCTGATTCTTTTCCC
Found at i:129133 original size:60 final size:59
Alignment explanation
Indices: 129024--129180 Score: 147
Period size: 60 Copynumber: 2.6 Consensus size: 59
129014 AATAACTTAT
* * * * * *
129024 TAAAGTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCTTAAACTATG-GCTATTATTC
1 TAAATTAGTCCC-AAACTTTTGAACATTTCATTTTCATCCTCAAACTATGAGCT-TCATCC
* *
129084 TAAATTAGTCCTCAAACTTTTGAACATTTCATTTTCAT-CTCCAAGCTATGATCTTCATCC
1 TAAATTAGTCC-CAAACTTTTGAACATTTCATTTTCATCCT-CAAACTATGAGCTTCATCC
* *
129144 TAAATTGGTCCCCAAACTTTTTGAATATTTCAATTTT
1 TAAATTAGT-CCCAAAC-TTTTGAACATTTC-ATTTT
129181 GTCCTAAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
59 2 0.02
60 57 0.70
61 17 0.21
62 5 0.06
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (59 bp):
TAAATTAGTCCCAAACTTTTGAACATTTCATTTTCATCCTCAAACTATGAGCTTCATCC
Found at i:129464 original size:58 final size:59
Alignment explanation
Indices: 129315--129479 Score: 165
Period size: 58 Copynumber: 2.8 Consensus size: 59
129305 TGAAATTGGG
* * * * ***
129315 GATGAAATT-GAAAGATCTAAAAGTTTAGGGACCAATTTAGAATGAGATTCATAGTTTGGG
1 GATGAAATTAG-AATATTTAAAAGTTTAAGGACTAATTTAGAATGAGA-TCATAGTTTAAA
* * * *
129375 GAAGAAATTCA-AATGTTCAAAAGTTTGAGGACTAATTTAGAATGAG-TCATAGTTTAAA
1 GATGAAATT-AGAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGATCATAGTTTAAA
* *
129433 GATGAAATTAGAATATTTAAAAATTTAAGGACTAATTTAAAATGAGA
1 GATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGA
129480 GTCAATGTTT
Statistics
Matches: 84, Mismatches: 17, Indels: 9
0.76 0.15 0.08
Matches are distributed among these distances:
57 1 0.01
58 47 0.56
60 36 0.43
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (59 bp):
GATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGATCATAGTTTAAA
Found at i:130613 original size:105 final size:104
Alignment explanation
Indices: 130425--130630 Score: 267
Period size: 105 Copynumber: 2.0 Consensus size: 104
130415 TTGAATTTAA
*
130425 AAAAAATCAGAAAAATTAAAAAAAAAATTAGTATGTTTATTTATCTAATTTCAATATATTTTTAC
1 AAAAAATCAGAAAAATTAAAAAAAAAATTAGTATGTTTATATATCTAATTTCAATATATTTTTAC
* *
130490 CTATCTTGCAAATTAATCT-ATTTGAATTTAAAAAAATCAG
66 ATATATT-CAAATTAATCTAATTT-AATTTAAAAAAATCAG
* * *
130530 AAAAAATACA-AATAAATTACAAAAAAAA-TAGTATGTTTATATATTTAATTTCAATGTATTTTT
1 AAAAAAT-CAGAA-AAATTAAAAAAAAAATTAGTATGTTTATATATCTAATTTCAATATATTTTT
*
130593 ATATATATT-ATAATTGAATCTAATTTAATTTAAAAAAA
64 ACATATATTCA-AATT-AATCTAATTTAATTTAAAAAAA
130631 AGGAAAATGT
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
103 1 0.01
104 4 0.04
105 64 0.72
106 20 0.22
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (104 bp):
AAAAAATCAGAAAAATTAAAAAAAAAATTAGTATGTTTATATATCTAATTTCAATATATTTTTAC
ATATATTCAAATTAATCTAATTTAATTTAAAAAAATCAG
Found at i:132962 original size:450 final size:450
Alignment explanation
Indices: 132121--132962 Score: 1373
Period size: 450 Copynumber: 1.9 Consensus size: 450
132111 AGAGCCATTA
* * * *
132121 TGTAGGATCGAGTCATTCATTTCTAAACAACTTCCCAGTGGGTCACCCATCCCTGGATTTCCTTG
1 TGTAGGATCAAGTCATTCATTTCTAAACAACTTCCCAGTGGGTCACCCACCCCTGGATTTCCCTA
*
132186 GTCCAAGCACGCTTAAGTACAGAGTTCTGAAATGAATGGTCACCATTCCTTCTTAAAACTAATCG
66 GTCCAAGCACGCTTAACTACAGAGTTCTGAAATGAATGGTCACCATTCCTTCTTAAAACTAATCG
* * *
132251 GTGATAAATAGGTGGGTCATTTTAACCTCATATCTTTGTAGTGGGTGATCATTGGGTTTCCCCAA
131 GTGATAAATAGGTGGGTCATTTTAACCTCATATCTTTGTAGTGGGTAATCACTGGGTTCCCCCAA
* * *
132316 GCCAAGGTGGATTCTTGTGGGGCACCCCATACAGTTCACCACGGCATTGCAGAGCATCACATCTA
196 GCCAAGGTAGATTCTTGTGGGGCACCCCATACAGTTCACCACGGCATTGCAAAGCACCACATCTA
* * * * * *
132381 TAGTGTGCTGCGGGCATGCTTAGGGGTTTCGCAAGGCACACGTGGGCCTCGGCAGGTTGGACAGT
261 TAGCGTGCTGCAGGCAGGCCTAGGGGCTTCGCAAGGCACACGTGGGCCTCGGCAGGTTAGACAGT
*
132446 CACGTACCGATATCACGCCCATACATGATAGAATCCCTAAGGGTGATCGCTGGACCCCATAACCC
326 CACGTACCGATATCACGCCCATACACGATAGAATCCCTAAGGGTGATCGCTGGACCCCATAACCC
132511 AATAATCACCCCCTAACGACACCTGGGGGATTCGAACCTATAACATGCTCTGATACTAAT
391 AATAATCACCCCCTAACGACACCTGGGGGATTCGAACCTATAACATGCTCTGATACTAAT
* * *
132571 TGTAGGATTAAGTCATTCATTTCTGAACAACTTCCTAGTGGGTCACCCACCCCTGGATTTCCCTA
1 TGTAGGATCAAGTCATTCATTTCTAAACAACTTCCCAGTGGGTCACCCACCCCTGGATTTCCCTA
* *
132636 GTCCAAGCACGCTTAACTACAGAGTTCTGAAATGAATGGTCACCATTTCTTCTTAAAA-TCAATT
66 GTCCAAGCACGCTTAACTACAGAGTTCTGAAATGAATGGTCACCATTCCTTCTTAAAACT-AATC
*
132700 GGTGATAAGTAGGTGGGTCATTTTAACCTCATATCTTTGTAGTGGGTAATCACTGGGTTCCCCCA
130 GGTGATAAATAGGTGGGTCATTTTAACCTCATATCTTTGTAGTGGGTAATCACTGGGTTCCCCCA
* * * *
132765 AGCCAAGGTAGATTCTTGTGGGGCACTCC-TCACAGTTCACCACGGTATTGCAAAGCCCCGCATC
195 AGCCAAGGTAGATTCTTGTGGGGCACCCCAT-ACAGTTCACCACGGCATTGCAAAGCACCACATC
* *
132829 TATAGCGTGCTGCAGGCGGGCCTAGGGGCTTCGCAAGGCACACGTGGGCCTCGGTAGGTTAGACA
259 TATAGCGTGCTGCAGGCAGGCCTAGGGGCTTCGCAAGGCACACGTGGGCCTCGGCAGGTTAGACA
*
132894 GTCACGTACCGATATCGCGCCCATACACGATAGAATCCCTAAGGGTGATCGCTGGACCCCATAAC
324 GTCACGTACCGATATCACGCCCATACACGATAGAATCCCTAAGGGTGATCGCTGGACCCCATAAC
132959 CCAA
389 CCAA
132963 CACATTGAGA
Statistics
Matches: 359, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
449 2 0.01
450 357 0.99
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (450 bp):
TGTAGGATCAAGTCATTCATTTCTAAACAACTTCCCAGTGGGTCACCCACCCCTGGATTTCCCTA
GTCCAAGCACGCTTAACTACAGAGTTCTGAAATGAATGGTCACCATTCCTTCTTAAAACTAATCG
GTGATAAATAGGTGGGTCATTTTAACCTCATATCTTTGTAGTGGGTAATCACTGGGTTCCCCCAA
GCCAAGGTAGATTCTTGTGGGGCACCCCATACAGTTCACCACGGCATTGCAAAGCACCACATCTA
TAGCGTGCTGCAGGCAGGCCTAGGGGCTTCGCAAGGCACACGTGGGCCTCGGCAGGTTAGACAGT
CACGTACCGATATCACGCCCATACACGATAGAATCCCTAAGGGTGATCGCTGGACCCCATAACCC
AATAATCACCCCCTAACGACACCTGGGGGATTCGAACCTATAACATGCTCTGATACTAAT
Found at i:133576 original size:26 final size:26
Alignment explanation
Indices: 133540--133602 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
133530 TTTTAAATAT
*
133540 TATTATTATTATTATTATAAATAAAA
1 TATTATTATTATTATTAGAAATAAAA
133566 TATTATTATTATTATTAGAAATAAAA
1 TATTATTATTATTATTAGAAATAAAA
133592 TATTATTATTA
1 TATTATTATTA
133603 AATATTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TATTATTATTATTATTAGAAATAAAA
Found at i:136162 original size:31 final size:30
Alignment explanation
Indices: 136127--136195 Score: 85
Period size: 25 Copynumber: 2.4 Consensus size: 30
136117 TTAAGTTCAA
136127 CCTTTAGATTTAGGTTTATCACACTTTTAGC
1 CCTTTA-ATTTAGGTTTATCACACTTTTAGC
*
136158 CC-----TTTAGGTTTATCACACTTTTAGT
1 CCTTTAATTTAGGTTTATCACACTTTTAGC
136183 CCTTTAATTTAGG
1 CCTTTAATTTAGG
136196 GAGTAATCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
25 24 0.75
30 6 0.19
31 2 0.06
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (30 bp):
CCTTTAATTTAGGTTTATCACACTTTTAGC
Found at i:136163 original size:25 final size:25
Alignment explanation
Indices: 136135--136188 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
136125 AACCTTTAGA
136135 TTTAGGTTTATCACACTTTTAGCCC
1 TTTAGGTTTATCACACTTTTAGCCC
*
136160 TTTAGGTTTATCACACTTTTAGTCC
1 TTTAGGTTTATCACACTTTTAGCCC
136185 TTTA
1 TTTA
136189 ATTTAGGGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.48
Consensus pattern (25 bp):
TTTAGGTTTATCACACTTTTAGCCC
Found at i:136415 original size:142 final size:142
Alignment explanation
Indices: 136159--136423 Score: 356
Period size: 142 Copynumber: 1.9 Consensus size: 142
136149 ACTTTTAGCC
* * *
136159 CTTTAGGTTTATCACACTTTTAGTCCTTTAATTTAGGGAGTAATCTGAATTGGCTTCCGTATTTA
1 CTTTAGGTTTATCACACTTTTAGTCCTTTAATTTAGGGAATAATCTAAATTGGCTTCCGCATTTA
* ** * *
136224 ACATGCTCGGAAGATCATTTTGATTATTCAACTAAATAATAGGTTAAAATTAATTAGGTCATTAA
66 ACATGCTCGGAAGACCATTTCAATTATTCAACTAAATAATAGATTAAAATAAATTAGGTCATTAA
136289 TTAGATCCTCCA
131 TTAGATCCTCCA
* *
136301 CTTTAGGTTTAAT-ATCAC-TTTAGTTCTTTAATTTAGGGAATAATCTAAATTGGCTTCTGCATT
1 CTTTAGGTTT-ATCA-CACTTTTAGTCCTTTAATTTAGGGAATAATCTAAATTGGCTTCCGCATT
* * * *
136364 TAACATG-TCTGGAGGACCATTTCAATTATTCGATTAAATAATTGATTAAAATAAATTAGG
64 TAACATGCTC-GGAAGACCATTTCAATTATTCAACTAAATAATAGATTAAAATAAATTAGG
136424 GTTAATAGTA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
141 2 0.02
142 99 0.93
143 5 0.05
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (142 bp):
CTTTAGGTTTATCACACTTTTAGTCCTTTAATTTAGGGAATAATCTAAATTGGCTTCCGCATTTA
ACATGCTCGGAAGACCATTTCAATTATTCAACTAAATAATAGATTAAAATAAATTAGGTCATTAA
TTAGATCCTCCA
Found at i:138344 original size:134 final size:135
Alignment explanation
Indices: 138104--138374 Score: 535
Period size: 134 Copynumber: 2.0 Consensus size: 135
138094 TACCAAACAT
138104 TATAAGATGTTCGATTTATACCAAGTCAACTCGACCCAAGGGTTTTGTCACAAGCGCAGCTCACT
1 TATAAGATGTTCGATTTATACCAAGTCAACTCGACCCAAGGGTTTTGTCACAAGCGCAGCTCACT
138169 ATAAAACCAAAGGAATTGATAGAAAAGCATACTCAAAATGATGGAATCTCTTGGGCAAGCTT-AA
66 ATAAAACCAAAGGAATTGATAGAAAAGCATACTCAAAATGATGGAATCTCTTGGGCAAGCTTAAA
138233 AAGGG
131 AAGGG
138238 TATAAGATGTTCGATTTATACCAAGTCAACTCGACCCAAGGGTTTTGTCACAAGCGCAGCTCACT
1 TATAAGATGTTCGATTTATACCAAGTCAACTCGACCCAAGGGTTTTGTCACAAGCGCAGCTCACT
138303 ATAAAACCAAAGGAATTGATAGAAAAGCATACTCAAAATGATGGAATCTCTTGGGCAAGCTTAAA
66 ATAAAACCAAAGGAATTGATAGAAAAGCATACTCAAAATGATGGAATCTCTTGGGCAAGCTTAAA
138368 AAGGG
131 AAGGG
138373 TA
1 TA
138375 ATTCATGAAC
Statistics
Matches: 136, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
134 127 0.93
135 9 0.07
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (135 bp):
TATAAGATGTTCGATTTATACCAAGTCAACTCGACCCAAGGGTTTTGTCACAAGCGCAGCTCACT
ATAAAACCAAAGGAATTGATAGAAAAGCATACTCAAAATGATGGAATCTCTTGGGCAAGCTTAAA
AAGGG
Found at i:140917 original size:24 final size:24
Alignment explanation
Indices: 140885--140953 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
140875 TTGATAACAG
*
140885 CCCCACAAGGTCATGTGTTTCCAA
1 CCCCACAAGGTCATGTATTTCCAA
* *
140909 CCCCACAAGGTCCTGTATTTCCAG
1 CCCCACAAGGTCATGTATTTCCAA
*
140933 CCCCACAAGGTCATGTTTTTC
1 CCCCACAAGGTCATGTATTTC
140954 GCCCAAAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.28
Consensus pattern (24 bp):
CCCCACAAGGTCATGTATTTCCAA
Found at i:142838 original size:33 final size:33
Alignment explanation
Indices: 142801--142871 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
142791 CACAACTGCT
142801 ACATCACTACAACAATCTT-CATCTTCATCATCA
1 ACATCACTACAACAAT-TTCCATCTTCATCATCA
** * *
142834 ACATCACTATTACCATTTCCATCTTCATCATCT
1 ACATCACTACAACAATTTCCATCTTCATCATCA
142867 ACATC
1 ACATC
142872 TCCACCACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (33 bp):
ACATCACTACAACAATTTCCATCTTCATCATCA
Found at i:142890 original size:30 final size:30
Alignment explanation
Indices: 142856--142916 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
142846 CCATTTCCAT
142856 CTTCATCATCTACATCTCCACCACCACCAC
1 CTTCATCATCTACATCTCCACCACCACCAC
*
142886 CTTCATCATCTACATCTTCACCACCACCAC
1 CTTCATCATCTACATCTCCACCACCACCAC
142916 C
1 C
142917 ACCACCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.49, G:0.00, T:0.25
Consensus pattern (30 bp):
CTTCATCATCTACATCTCCACCACCACCAC
Found at i:149593 original size:184 final size:180
Alignment explanation
Indices: 149168--149550 Score: 488
Period size: 184 Copynumber: 2.1 Consensus size: 180
149158 ATTAAATTTT
* * *** * * *
149168 AAATATTAAATATATTATATATAAC-ATTGGACTCAA-CCCAAATCATTAAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACAAATGGGCT-AAGAAAAAACCATTTAAAACCAAATTAATA
*
149231 ATTTAAGATCCAATAACTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATAAATTTTTTA
65 ATTTAAGATCCAATAACTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATAAAATTTTTA
*
149296 TTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
130 TTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
* *** *
149347 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACAAATGGGCTAAGAAAAAACCATTTAAAACCAAATTAATAA
** *
149412 TTTAAGATTTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTTATCTAAAATTT
66 TTTAAGATCCAATAAC-TTTAAACTTAAATCAATATTAATTAATTAAAAA-ATTA--TAAAATTT
*
149477 TTATTTTATAATTATTTATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
127 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAA
*
149531 AAACTATTTAAT-T-TTATATA
1 AAA-TATTAAATATATTATATA
149551 AATTAGAAAA
Statistics
Matches: 184, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
179 27 0.15
180 45 0.24
181 33 0.18
182 3 0.02
183 13 0.07
184 56 0.30
185 7 0.04
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (180 bp):
AAATATTAAATATATTATATATAACAAATGGGCTAAGAAAAAACCATTTAAAACCAAATTAATAA
TTTAAGATCCAATAACTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATAAAATTTTTAT
TTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:156935 original size:16 final size:17
Alignment explanation
Indices: 156907--156939 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
156897 ATCGCCGACA
156907 AAATTTCACTATTCACG
1 AAATTTCACTATTCACG
156924 AAATTT-ACTATTCACG
1 AAATTTCACTATTCACG
156940 TGAACAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (17 bp):
AAATTTCACTATTCACG
Found at i:158874 original size:25 final size:25
Alignment explanation
Indices: 158846--158899 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
158836 TTTATATTCT
* *
158846 AAAATTAAATAATTTCTTAATTTAAA
1 AAAATTAAATAA-GTCTTAATTAAAA
158872 AAAATTAAATAAGTCTTAATTAAAA
1 AAAATTAAATAAGTCTTAATTAAAA
158897 AAA
1 AAA
158900 TAATTATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAATTAAATAAGTCTTAATTAAAA
Found at i:158899 original size:24 final size:26
Alignment explanation
Indices: 158846--158900 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
158836 TTTATATTCT
*
158846 AAAATTAAATAATTTCTTAATTTAAA
1 AAAATTAAATAATGTCTTAATTTAAA
158872 AAAATTAAATAA-GTCTTAA-TTAAA
1 AAAATTAAATAATGTCTTAATTTAAA
158896 AAAAT
1 AAAAT
158901 AATTATACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 10 0.36
25 6 0.21
26 12 0.43
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAATTAAATAATGTCTTAATTTAAA
Found at i:159534 original size:26 final size:26
Alignment explanation
Indices: 159504--159565 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
159494 ATATATTTTA
*
159504 ATTTTCAGAAAAATAAAAT-TGAAAAC
1 ATTTTCAGAAAAA-AAAATCAGAAAAC
* *
159530 ATTTTC-TAAAAAAAAATCAGAAAAT
1 ATTTTCAGAAAAAAAAATCAGAAAAC
159555 ATTTTCTAGAA
1 ATTTTC-AGAA
159566 TTAAACATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
24 5 0.17
25 16 0.55
26 6 0.21
27 2 0.07
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (26 bp):
ATTTTCAGAAAAAAAAATCAGAAAAC
Found at i:160142 original size:16 final size:16
Alignment explanation
Indices: 160121--160153 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
160111 TAATAAATAA
160121 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
160137 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
160153 A
1 A
160154 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:160246 original size:14 final size:14
Alignment explanation
Indices: 160227--160265 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
160217 ATCGAATATA
*
160227 AACGAACACGAACG
1 AACGAACACAAACG
*
160241 AACGAACATAAACG
1 AACGAACACAAACG
160255 AAC-AACACAAA
1 AACGAACACAAA
160266 GACAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.59, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:161271 original size:16 final size:16
Alignment explanation
Indices: 161250--161284 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
161240 TGTAAGTGAA
161250 AAGAGCTTCATGCAAG
1 AAGAGCTTCATGCAAG
*
161266 AAGAGCTTCCTGCAAG
1 AAGAGCTTCATGCAAG
161282 AAG
1 AAG
161285 TTTCTTCCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (16 bp):
AAGAGCTTCATGCAAG
Found at i:162282 original size:25 final size:25
Alignment explanation
Indices: 162245--162303 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
162235 CCTAAAATTT
* *
162245 TATAATTTGATAATTAAAATTTTAA
1 TATAATTTCATAAGTAAAATTTTAA
162270 TATAATTTCATAAGTAAAATTTTAA
1 TATAATTTCATAAGTAAAATTTTAA
162295 TATAATTTC
1 TATAATTTC
162304 TTAAACTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (25 bp):
TATAATTTCATAAGTAAAATTTTAA
Found at i:163974 original size:16 final size:16
Alignment explanation
Indices: 163953--164011 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
163943 CATTTAATAA
*
163953 ATAAACGAACACGAAC
1 ATAAACAAACACGAAC
163969 ATAAACAAACACGAAC
1 ATAAACAAACACGAAC
** *
163985 ATAAATGAACACGAAT
1 ATAAACAAACACGAAC
164001 ATAAACAAACA
1 ATAAACAAACA
164012 TAAACGTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.61, C:0.20, G:0.08, T:0.10
Consensus pattern (16 bp):
ATAAACAAACACGAAC
Found at i:164926 original size:14 final size:14
Alignment explanation
Indices: 164909--164951 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
164899 GAACATAAAT
164909 GAACATAACCGAAC
1 GAACATAACCGAAC
*
164923 GAACATAAACGAAC
1 GAACATAACCGAAC
164937 GAACATAACCGAAC
1 GAACATAACCGAAC
164951 G
1 G
164952 TTCATGAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.51, C:0.26, G:0.16, T:0.07
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:169142 original size:15 final size:15
Alignment explanation
Indices: 169122--169164 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
169112 TATAATTCAT
*
169122 TATTATATTTATTAA
1 TATTATATATATTAA
*
169137 TATTATATATATTAT
1 TATTATATATATTAA
169152 TATGTATATATAT
1 TAT-TATATATAT
169165 ACATGTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TATTATATATATTAA
Found at i:180327 original size:45 final size:45
Alignment explanation
Indices: 180263--180368 Score: 194
Period size: 45 Copynumber: 2.4 Consensus size: 45
180253 AGTGCACTAA
*
180263 GAGTGCATTGATGCATAAAATGCATTTGATATTTCAAAATAGCCT
1 GAGTGCATCGATGCATAAAATGCATTTGATATTTCAAAATAGCCT
*
180308 GAGTGCATCGATGCATAAAATGTATTTGATATTTCAAAATAGCCT
1 GAGTGCATCGATGCATAAAATGCATTTGATATTTCAAAATAGCCT
180353 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
180369 GGCTGGTGCA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTTGATATTTCAAAATAGCCT
Found at i:180378 original size:64 final size:65
Alignment explanation
Indices: 180310--180434 Score: 175
Period size: 65 Copynumber: 1.9 Consensus size: 65
180300 AATAGCCTGA
* *
180310 GTGCATCGATGCATAAAATGTATTTGAT-ATTTCA-AAATAGC-CTGAGTGCATCGATGCATGGC
1 GTGCATCGATGCATAAAATGCATTCGATGATTTCATAAA-A-CTCTGAGTGCATCGATGCATGGC
180372 TG
64 TG
* *
180374 GTGCATCGATGTATCAAATGCATTCGATGATTTCATAAAACTCTGAGTGCATCGATGCATG
1 GTGCATCGATGCATAAAATGCATTCGATGATTTCATAAAACTCTGAGTGCATCGATGCATG
180435 AAATGCATTC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
64 25 0.46
65 26 0.48
66 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGATTTCATAAAACTCTGAGTGCATCGATGCATGGCTG
Found at i:187098 original size:22 final size:21
Alignment explanation
Indices: 187056--187095 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
187046 GAGCTTATTT
*
187056 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
187077 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
187096 ACAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:188595 original size:151 final size:151
Alignment explanation
Indices: 188321--188620 Score: 478
Period size: 151 Copynumber: 2.0 Consensus size: 151
188311 ATACCAATTA
* *
188321 TTGAGTTAATCGATCGATGGAATTGGCCAAGAGGGGGTGAATTGACAATTAAAATTTTGGTGAAA
1 TTGAGTTAATCGATCGACGGAATCGGCCAAGAGGGGGTGAATTGACAATTAAAATTTTGGTGAAA
* *
188386 GCTTTTGTAGAAAATTGAAAAGATTTACACAACGATTTAGAGTGGTTCGACTTTCTCAACCAAAG
66 GCTTTTGCAGAAAATTGAAAAGAATTACACAACGATTTAGAGTGGTTCGACTTTCTCAACCAAAG
188451 TCTACGTCCACTACCTTAGTG
131 TCTACGTCCACTACCTTAGTG
* * *
188472 TTGAGTTAATCGATTGACGGAATCGGCCAAGAGTGGGGTGAATTGGCAATTAAAATTTT-GTGGA
1 TTGAGTTAATCGATCGACGGAATCGGCCAAGAG-GGGGTGAATTGACAATTAAAATTTTGGTGAA
* * *
188536 AGCTTTTGCAGAAAATTG-AAAGTAATTGCACAACGATTTAGAGTGGTTTGACTTTCTCAATCAA
65 AGCTTTTGCAGAAAATTGAAAAG-AATTACACAACGATTTAGAGTGGTTCGACTTTCTCAACCAA
188600 AGTCTACGTCCACTACCTTAG
129 AGTCTACGTCCACTACCTTAG
188621 CTATCCACAC
Statistics
Matches: 137, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
150 4 0.03
151 109 0.80
152 24 0.18
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (151 bp):
TTGAGTTAATCGATCGACGGAATCGGCCAAGAGGGGGTGAATTGACAATTAAAATTTTGGTGAAA
GCTTTTGCAGAAAATTGAAAAGAATTACACAACGATTTAGAGTGGTTCGACTTTCTCAACCAAAG
TCTACGTCCACTACCTTAGTG
Found at i:195016 original size:5 final size:5
Alignment explanation
Indices: 195008--195057 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
194998 AAAAGAGAAG
*
195008 AAAAT AAAAT -TAAT AAAAT AAAAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
195058 AATCAAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 3 0.08
5 32 0.80
7 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:195031 original size:15 final size:13
Alignment explanation
Indices: 195008--195057 Score: 66
Period size: 12 Copynumber: 3.7 Consensus size: 13
194998 AAAAGAGAAG
195008 AAAATAAAATTAAT
1 AAAATAAAA-TAAT
195022 AAAATAAAA-AAT
1 AAAATAAAATAAT
195034 AAAATAAAATAAAAT
1 AAAATAAAAT--AAT
195049 AAAATAAAA
1 AAAATAAAA
195058 AATCAAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.36
14 9 0.27
15 12 0.36
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:195047 original size:22 final size:21
Alignment explanation
Indices: 195008--195060 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
194998 AAAAGAGAAG
*
195008 AAAATAAAATTAATAAAATAA
1 AAAATAAAATAAATAAAATAA
195029 AAAATAAAATAAAATAAAATAA
1 AAAATAAAAT-AAATAAAATAA
195051 AATAA-AAAAT
1 AA-AATAAAAT
195061 CAAACTAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 10 0.34
22 17 0.59
23 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAATAAAATAAATAAAATAA
Found at i:195055 original size:27 final size:26
Alignment explanation
Indices: 195008--195060 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
194998 AAAAGAGAAG
*
195008 AAAATAAAATTAATAAAATAAAAAAT
1 AAAATAAAATAAATAAAATAAAAAAT
195034 AAAATAAAATAAAATAAAATAAAAAAT
1 AAAATAAAAT-AAATAAAATAAAAAAT
195061 CAAACTAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (26 bp):
AAAATAAAATAAATAAAATAAAAAAT
Found at i:205570 original size:21 final size:21
Alignment explanation
Indices: 205533--205614 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
205523 TTTTGGTGCA
*
205533 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
205553 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
*
205574 GAAGGGGAACCGATTCCCCCCAC
1 G-A-GGGAACCGATTCCCCCCAT
* * *
205597 AAGGGAATCGATACCCCC
1 GAGGGAACCGATTCCCCC
205615 TGGGGTTCTA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 10 0.20
21 22 0.44
22 2 0.04
23 16 0.32
ACGTcount: A:0.26, C:0.35, G:0.24, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:210057 original size:84 final size:84
Alignment explanation
Indices: 209903--210067 Score: 244
Period size: 84 Copynumber: 2.0 Consensus size: 84
209893 ATATACTCTC
209903 TGACACACAATGTGTGTCATCTTCATTTATGACTGGGGCTTCAATGACACGCAATGTAAGTCATA
1 TGACACACAATGTGTGTCATCTTCATTTATGACTGGGGCTTCAATGACACGCAATGTAAGTCATA
* *
209968 CATGCATGTCATAAATTTA
66 AATGCACGTCATAAATTTA
* * * *
209987 TGACACACAAATGTGTGTCATCTTCATTTATGA-TGGGGCTTCAATGACGCTCAATGTGTA-TTA
1 TGACACAC-AATGTGTGTCATCTTCATTTATGACTGGGGCTTCAATGACACGCAATGT-AAGTCA
210050 TAAATGCACGTCATAAAT
64 TAAATGCACGTCATAAAT
210068 GTGTGTCATA
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
84 48 0.66
85 25 0.34
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (84 bp):
TGACACACAATGTGTGTCATCTTCATTTATGACTGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCACGTCATAAATTTA
Found at i:210065 original size:13 final size:13
Alignment explanation
Indices: 210049--210090 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
210039 AATGTGTATT
*
210049 ATAAATGCACGTC
1 ATAAATGCGCGTC
* *
210062 ATAAATGTGTGTC
1 ATAAATGCGCGTC
210075 ATAAATGCGCGTC
1 ATAAATGCGCGTC
210088 ATA
1 ATA
210091 GATTTATGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (13 bp):
ATAAATGCGCGTC
Found at i:210068 original size:26 final size:26
Alignment explanation
Indices: 210039--210090 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
210029 AATGACGCTC
*
210039 AATGTGTATTATAAATGCACGTCATA
1 AATGTGTATCATAAATGCACGTCATA
* *
210065 AATGTGTGTCATAAATGCGCGTCATA
1 AATGTGTATCATAAATGCACGTCATA
210091 GATTTATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (26 bp):
AATGTGTATCATAAATGCACGTCATA
Found at i:222837 original size:22 final size:22
Alignment explanation
Indices: 222812--222866 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 22
222802 TTATAATGTT
222812 AAAATATATTATTTAATTATTA
1 AAAATATATTATTTAATTATTA
*
222834 AAAATATA--A-TAAATTATTA
1 AAAATATATTATTTAATTATTA
*
222853 TAAATATATTATTT
1 AAAATATATTATTT
222867 TAAAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 16 0.59
20 1 0.04
21 1 0.04
22 9 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATATATTATTTAATTATTA
Found at i:236599 original size:30 final size:30
Alignment explanation
Indices: 236531--236619 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 30
236521 AGAGTTGAGG
* *
236531 GTTACCTATGTCTTTCGAGACATATGGACT
1 GTTACCTATGTCCTTCGGGACATATGGACT
236561 GTTTACCTATGTCCTTCGGGACATATGGACT
1 G-TTACCTATGTCCTTCGGGACATATGGACT
* * *
236592 GTTACCTATGTTCTACGGAACATATGGA
1 GTTACCTATGTCCTTCGGGACATATGGA
236620 TAGGTCCTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
30 25 0.47
31 28 0.53
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGGGACATATGGACT
Found at i:243745 original size:18 final size:18
Alignment explanation
Indices: 243722--243766 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
243712 ACCGGTCACA
243722 ACCCGACCCAACCCGTTT
1 ACCCGACCCAACCCGTTT
* *
243740 ACCCGACTCGACCCGTTT
1 ACCCGACCCAACCCGTTT
243758 ACCCGACCC
1 ACCCGACCC
243767 GTTGACCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.51, G:0.13, T:0.16
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTT
Found at i:243766 original size:13 final size:13
Alignment explanation
Indices: 243748--243806 Score: 64
Period size: 13 Copynumber: 4.2 Consensus size: 13
243738 TTACCCGACT
*
243748 CGACCCGTTTACC
1 CGACCCGTTGACC
243761 CGACCCGTTGACC
1 CGACCCGTTGACC
243774 CGACTCGACTCGTTGACC
1 CGA--C--C-CGTTGACC
243792 CGACCCGTTGACC
1 CGACCCGTTGACC
243805 CG
1 CG
243807 TTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 25 0.62
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.28
ACGTcount: A:0.15, C:0.44, G:0.22, T:0.19
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:243767 original size:31 final size:31
Alignment explanation
Indices: 243726--243821 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
243716 GTCACAACCC
* *
243726 GACCCAACCCGTTTACCCGACTCGACCCGTT
1 GACCCGACCCGTTGACCCGACTCGACCCGTT
* *
243757 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACTCGACCCGTT
*
243788 GACCCGACCCGTTGACCCG--TTGA-CCGTT
1 GACCCGACCCGTTGACCCGACTCGACCCGTT
243816 GACCCG
1 GACCCG
243822 TTGACCGTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
28 10 0.17
29 3 0.05
31 45 0.78
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.20
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACTCGACCCGTT
Found at i:243773 original size:8 final size:8
Alignment explanation
Indices: 243762--243833 Score: 73
Period size: 8 Copynumber: 9.4 Consensus size: 8
243752 CCGTTTACCC
243762 GACCCGTT
1 GACCCGTT
*
243770 GACCCGACTC
1 GACCCG--TT
*
243780 GACTCGTT
1 GACCCGTT
243788 GACCC---
1 GACCCGTT
243793 GACCCGTT
1 GACCCGTT
243801 GACCCGTT
1 GACCCGTT
243809 GA-CCGTT
1 GACCCGTT
243816 GACCCGTT
1 GACCCGTT
243824 GA-CCGTT
1 GACCCGTT
243831 GAC
1 GAC
243834 TACTGTTGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
5 5 0.09
7 14 0.26
8 28 0.53
10 6 0.11
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:243782 original size:18 final size:18
Alignment explanation
Indices: 243722--243795 Score: 68
Period size: 18 Copynumber: 4.4 Consensus size: 18
243712 ACCGGTCACA
* * *
243722 ACCCGACCCAACCCGTTT
1 ACCCGACTCGACCCGTTG
*
243740 ACCCGACTCGACCCGTTT
1 ACCCGACTCGACCCGTTG
243758 A--C--C-CGACCCGTTG
1 ACCCGACTCGACCCGTTG
*
243771 ACCCGACTCGACTCGTTG
1 ACCCGACTCGACCCGTTG
243789 ACCCGAC
1 ACCCGAC
243796 CCGTTGACCC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 33 0.70
ACGTcount: A:0.19, C:0.46, G:0.18, T:0.18
Consensus pattern (18 bp):
ACCCGACTCGACCCGTTG
Found at i:243816 original size:7 final size:7
Alignment explanation
Indices: 243796--243833 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
243786 TTGACCCGAC
243796 CCGTTGA
1 CCGTTGA
243803 CCCGTTGA
1 -CCGTTGA
243811 CCGTTGA
1 CCGTTGA
243818 CCCGTTGA
1 -CCGTTGA
243826 CCGTTGA
1 CCGTTGA
243833 C
1 C
243834 TACTGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:243816 original size:15 final size:15
Alignment explanation
Indices: 243796--243833 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
243786 TTGACCCGAC
243796 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
243811 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
243826 CCGTTGAC
1 CCGTTGAC
243834 TACTGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:245139 original size:18 final size:18
Alignment explanation
Indices: 245113--245147 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
245103 TTGAAAGGAC
*
245113 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
245131 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
245148 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:248811 original size:18 final size:18
Alignment explanation
Indices: 248788--248832 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
248778 ACCGGTCACA
248788 ACCCGACCCAACCCGTTT
1 ACCCGACCCAACCCGTTT
* *
248806 ACCCGACTCGACCCGTTT
1 ACCCGACCCAACCCGTTT
248824 ACCCGACCC
1 ACCCGACCC
248833 GTTGACCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.51, G:0.13, T:0.16
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTT
Found at i:248832 original size:13 final size:13
Alignment explanation
Indices: 248814--248872 Score: 64
Period size: 13 Copynumber: 4.2 Consensus size: 13
248804 TTACCCGACT
*
248814 CGACCCGTTTACC
1 CGACCCGTTGACC
248827 CGACCCGTTGACC
1 CGACCCGTTGACC
248840 CGACTCGACTCGTTGACC
1 CGA--C--C-CGTTGACC
248858 CGACCCGTTGACC
1 CGACCCGTTGACC
248871 CG
1 CG
248873 TTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 25 0.62
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.28
ACGTcount: A:0.15, C:0.44, G:0.22, T:0.19
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:248833 original size:31 final size:31
Alignment explanation
Indices: 248792--248887 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
248782 GTCACAACCC
* *
248792 GACCCAACCCGTTTACCCGACTCGACCCGTT
1 GACCCGACCCGTTGACCCGACTCGACCCGTT
* *
248823 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACTCGACCCGTT
*
248854 GACCCGACCCGTTGACCCG--TTGA-CCGTT
1 GACCCGACCCGTTGACCCGACTCGACCCGTT
248882 GACCCG
1 GACCCG
248888 TTGACCGTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
28 10 0.17
29 3 0.05
31 45 0.78
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.20
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACTCGACCCGTT
Found at i:248839 original size:8 final size:8
Alignment explanation
Indices: 248828--248899 Score: 73
Period size: 8 Copynumber: 9.4 Consensus size: 8
248818 CCGTTTACCC
248828 GACCCGTT
1 GACCCGTT
*
248836 GACCCGACTC
1 GACCCG--TT
*
248846 GACTCGTT
1 GACCCGTT
248854 GACCC---
1 GACCCGTT
248859 GACCCGTT
1 GACCCGTT
248867 GACCCGTT
1 GACCCGTT
248875 GA-CCGTT
1 GACCCGTT
248882 GACCCGTT
1 GACCCGTT
248890 GA-CCGTT
1 GACCCGTT
248897 GAC
1 GAC
248900 TACTGTTGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
5 5 0.09
7 14 0.26
8 28 0.53
10 6 0.11
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:248848 original size:18 final size:18
Alignment explanation
Indices: 248788--248861 Score: 68
Period size: 18 Copynumber: 4.4 Consensus size: 18
248778 ACCGGTCACA
* * *
248788 ACCCGACCCAACCCGTTT
1 ACCCGACTCGACCCGTTG
*
248806 ACCCGACTCGACCCGTTT
1 ACCCGACTCGACCCGTTG
248824 A--C--C-CGACCCGTTG
1 ACCCGACTCGACCCGTTG
*
248837 ACCCGACTCGACTCGTTG
1 ACCCGACTCGACCCGTTG
248855 ACCCGAC
1 ACCCGAC
248862 CCGTTGACCC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 33 0.70
ACGTcount: A:0.19, C:0.46, G:0.18, T:0.18
Consensus pattern (18 bp):
ACCCGACTCGACCCGTTG
Found at i:248882 original size:7 final size:7
Alignment explanation
Indices: 248862--248899 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
248852 TTGACCCGAC
248862 CCGTTGA
1 CCGTTGA
248869 CCCGTTGA
1 -CCGTTGA
248877 CCGTTGA
1 CCGTTGA
248884 CCCGTTGA
1 -CCGTTGA
248892 CCGTTGA
1 CCGTTGA
248899 C
1 C
248900 TACTGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:248882 original size:15 final size:15
Alignment explanation
Indices: 248862--248899 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
248852 TTGACCCGAC
248862 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
248877 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
248892 CCGTTGAC
1 CCGTTGAC
248900 TACTGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:250200 original size:18 final size:18
Alignment explanation
Indices: 250174--250208 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
250164 TTGAAAGGAC
*
250174 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
250192 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
250209 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:253849 original size:18 final size:18
Alignment explanation
Indices: 253826--253870 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
253816 ACCGGTCACA
253826 ACCCGACCCAACCCGTTT
1 ACCCGACCCAACCCGTTT
* *
253844 ACCCGACTCGACCCGTTT
1 ACCCGACCCAACCCGTTT
253862 ACCCGACCC
1 ACCCGACCC
253871 GTTGACCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.51, G:0.13, T:0.16
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTT
Found at i:253870 original size:13 final size:13
Alignment explanation
Indices: 253852--253881 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
253842 TTACCCGACT
*
253852 CGACCCGTTTACC
1 CGACCCGTTGACC
253865 CGACCCGTTGACC
1 CGACCCGTTGACC
253878 CGAC
1 CGAC
253882 TCGACTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.17
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:253871 original size:31 final size:30
Alignment explanation
Indices: 253830--253908 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 30
253820 GTCACAACCC
*
253830 GACCCAACCCGTTTACCCGACTCGACCCGTT
1 GACCC-ACCCGTTGACCCGACTCGACCCGTT
* *
253861 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCC-ACCCGTTGACCCGACTCGACCCGTT
253892 GACCC-CCCGTTGACCCG
1 GACCCACCCGTTGACCCG
253909 TGACCGTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 12 0.28
31 31 0.72
ACGTcount: A:0.16, C:0.46, G:0.19, T:0.19
Consensus pattern (30 bp):
GACCCACCCGTTGACCCGACTCGACCCGTT
Found at i:253877 original size:8 final size:8
Alignment explanation
Indices: 253866--253934 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
253856 CCGTTTACCC
253866 GACCCGTT
1 GACCCGTT
*
253874 GACCCGACTC
1 GACCCG--TT
*
253884 GACTCGTT
1 GACCCGTT
253892 GACCCCCCGTT
1 GA--C-CCGTT
253903 GACCCG-T
1 GACCCGTT
253910 GA-CCGTT
1 GACCCGTT
253917 GACCCGTT
1 GACCCGTT
253925 GA-CCGTT
1 GACCCGTT
253932 GAC
1 GAC
253935 TACTGTTGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
6 3 0.06
7 13 0.27
8 19 0.39
9 1 0.02
10 7 0.14
11 6 0.12
ACGTcount: A:0.14, C:0.39, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:253886 original size:18 final size:18
Alignment explanation
Indices: 253826--253896 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 18
253816 ACCGGTCACA
* * *
253826 ACCCGACCCAACCCGTTT
1 ACCCGACTCGACCCGTTG
*
253844 ACCCGACTCGACCCGTTT
1 ACCCGACTCGACCCGTTG
253862 A--C--C-CGACCCGTTG
1 ACCCGACTCGACCCGTTG
*
253875 ACCCGACTCGACTCGTTG
1 ACCCGACTCGACCCGTTG
253893 ACCC
1 ACCC
253897 CCCGTTGACC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 10 0.23
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 30 0.68
ACGTcount: A:0.18, C:0.46, G:0.17, T:0.18
Consensus pattern (18 bp):
ACCCGACTCGACCCGTTG
Found at i:253929 original size:15 final size:14
Alignment explanation
Indices: 253898--253934 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
253888 CGTTGACCCC
253898 CCGTTGACCCGTGA
1 CCGTTGACCCGTGA
253912 CCGTTGACCCGTTGA
1 CCGTTGACCCG-TGA
253927 CCGTTGAC
1 CCGTTGAC
253935 TACTGTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (14 bp):
CCGTTGACCCGTGA
Found at i:255213 original size:18 final size:18
Alignment explanation
Indices: 255187--255221 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
255177 TCGAAAGGAC
*
255187 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
255205 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
255222 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:265472 original size:20 final size:20
Alignment explanation
Indices: 265447--265487 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
265437 ACCGATATAG
265447 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
265467 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
265487 G
1 G
265488 CGATTTTTAA
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:265539 original size:77 final size:77
Alignment explanation
Indices: 265436--265619 Score: 287
Period size: 77 Copynumber: 2.4 Consensus size: 77
265426 GCGATAGTAC
* *
265436 TACCGATATAGGTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTTAAATT
1 TACCGATATAGGTAAACACTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATT
** *
265501 CGCAACGTTAAT
66 AACAACGCTAAT
* *
265513 TACCGATATAGGTAAACACTATTATCGCAATGTAAATAGTACTATCGCAATGCGATTTTCAAATT
1 TACCGATATAGGTAAACACTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATT
*
265578 AATAACGCTAAT
66 AACAACGCTAAT
*
265590 TACCGATATAGGTAAACACAACTATCGCAA
1 TACCGATATAGGTAAACACTACTATCGCAA
265620 CGCGAATTTC
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 97 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (77 bp):
TACCGATATAGGTAAACACTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATT
AACAACGCTAAT
Found at i:265656 original size:20 final size:20
Alignment explanation
Indices: 265621--265672 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
265611 CTATCGCAAC
*
265621 GCGAATTTCCGAAACTG-AGTT
1 GCGAATTT-GGAAACTGTA-TT
265642 GCGAATTTGGAAACTGTATT
1 GCGAATTTGGAAACTGTATT
*
265662 GCGAAATTGGA
1 GCGAATTTGGA
265673 GTTCGTGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (20 bp):
GCGAATTTGGAAACTGTATT
Found at i:267273 original size:2 final size:2
Alignment explanation
Indices: 267266--267318 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
267256 GCTACTTTTG
267266 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
267308 CT CT CT CT CT C
1 CT CT CT CT CT C
267319 ACACACACAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:268721 original size:23 final size:23
Alignment explanation
Indices: 268695--268742 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
268685 CGTTCGTTTT
268695 TGCTCTTTAACGTTCTTTTATTG
1 TGCTCTTTAACGTTCTTTTATTG
268718 TGCTCTTTAACGTTCTTTTATTG
1 TGCTCTTTAACGTTCTTTTATTG
268741 TG
1 TG
268743 TTCATTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.56
Consensus pattern (23 bp):
TGCTCTTTAACGTTCTTTTATTG
Found at i:274833 original size:28 final size:28
Alignment explanation
Indices: 274801--274856 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
274791 TATGAGTAAG
* *
274801 AATATTGTATATTGATTTATAAAATTTT
1 AATATTATATATTAATTTATAAAATTTT
* *
274829 AATATTATGTATTAATTTATATAATTTT
1 AATATTATATATTAATTTATAAAATTTT
274857 TTATACATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
AATATTATATATTAATTTATAAAATTTT
Found at i:283559 original size:17 final size:17
Alignment explanation
Indices: 283487--283559 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
283477 TACGAGACAT
283487 ATGATAGGTCCTTCGGG
1 ATGATAGGTCCTTCGGG
* *
283504 ATCATAGGTCCTTTGGG
1 ATGATAGGTCCTTCGGG
* **
283521 ACACAGATGACATCCTTCGGG
1 --A-TGAT-AGGTCCTTCGGG
*
283542 ATGATAGGTCCTTTGGG
1 ATGATAGGTCCTTCGGG
283559 A
1 A
283560 CATAGTTTAT
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
17 25 0.61
18 3 0.07
19 2 0.05
20 2 0.05
21 9 0.22
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (17 bp):
ATGATAGGTCCTTCGGG
Found at i:289144 original size:30 final size:30
Alignment explanation
Indices: 289110--289168 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
289100 ACAAGCTTTA
* * *
289110 AAAAAAATCAGGGACCATTTTGTAATTTTC
1 AAAAAAATAAGGGACCAATTCGTAATTTTC
**
289140 AAAAAGTTAAGGGACCAATTCGTAATTTT
1 AAAAAAATAAGGGACCAATTCGTAATTTT
289169 GGAAAAAGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (30 bp):
AAAAAAATAAGGGACCAATTCGTAATTTTC
Found at i:289178 original size:31 final size:30
Alignment explanation
Indices: 289119--289178 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
289109 AAAAAAAATC
* *
289119 AGGGACCATTTTGTAATTTTCAAAAAGTTA
1 AGGGACCAATTCGTAATTTTCAAAAAGTTA
*
289149 AGGGACCAATTCGTAATTTTGGAAAAAGTT
1 AGGGACCAATTCGTAATTTT-CAAAAAGTT
289179 GGGAATGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (30 bp):
AGGGACCAATTCGTAATTTTCAAAAAGTTA
Found at i:290120 original size:21 final size:21
Alignment explanation
Indices: 290096--290164 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
290086 ATATGATAGG
290096 TCCTTCGGGACACAGATTACA
1 TCCTTCGGGACACAGATTACA
* **
290117 TCCTTCGGG--A-TGA-TAGG
1 TCCTTCGGGACACAGATTACA
* *
290134 TCCTTCGGGACACATATAACA
1 TCCTTCGGGACACAGATTACA
290155 TCCTTCGGGA
1 TCCTTCGGGA
290165 TGATAGGTCC
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
17 11 0.31
18 2 0.06
19 2 0.06
20 1 0.03
21 20 0.56
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (21 bp):
TCCTTCGGGACACAGATTACA
Done.