Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001372.1 Hibiscus syriacus cultivar Beakdansim tig00002684_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: 540953
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:259061 original size:135 final size:131
Alignment explanation
Indices: 258771--259064 Score: 347
Period size: 131 Copynumber: 2.2 Consensus size: 131
258761 GATGGCTTAT
* *
258771 CATCCTCATCACGTAGGAGCCGTGTGACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACTG
1 CATCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCGTCCTCATCACGTAGGAACTG
* * * *
258836 TGTTATCATCCCTAAAGATGGACTATCATCCTCATAACGTATGAACCGTGTCATCCACCGACCAG
66 TGTTATCATCCCTAAAGATGGACAAACATCCTCATAACGTAGGAACAGTGTCATCCACCGACCAG
258901 A
131 A
* * * * **
258902 CCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAATCAATCGTTCTCATTGCGTAGGAA-TC
1 CATCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCGTCCTCATCACGTAGGAACT-
* * * * *
258966 GTGTTATCACCCTCTCTAAAGATGGCCAAGACGTCCTTATCACGTAGGAACAGTGTCATCCACCG
65 GTGTTATCA---TCCCTAAAGATGGACAA-ACATCCTCATAACGTAGGAACAGTGTCATCCACCG
*
259031 ACCATA
126 ACCAGA
* * *
259037 TATCCTCATCACGTAAGAGTCGTGTCAC
1 CATCCTCATCACGTAGGAGCCGTGTCAC
259065 TCTTAGACGA
Statistics
Matches: 136, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 1 0.01
131 63 0.46
134 14 0.10
135 58 0.43
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (131 bp):
CATCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCGTCCTCATCACGTAGGAACTG
TGTTATCATCCCTAAAGATGGACAAACATCCTCATAACGTAGGAACAGTGTCATCCACCGACCAG
A
Found at i:260143 original size:2 final size:2
Alignment explanation
Indices: 260136--260175 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
260126 GTTCACAGAA
260136 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
260176 TGTTTTGTTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:260708 original size:30 final size:30
Alignment explanation
Indices: 260664--260768 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
260654 ATATTTTTGG
* * *
260664 TTTAGCCCTCTAAATTTTTATTTTCT-CTAT
1 TTTAGTCCTTTAAATTTATATTTT-TACTAT
*
260694 TTTAGTCCTTTAAATTTATGTTTTTACTAT
1 TTTAGTCCTTTAAATTTATATTTTTACTAT
* * *
260724 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
1 TTTAGTCCTTTAAATTTATATTTTTACTAT
*
260754 TTTGGTCCTTTAAAT
1 TTTAGTCCTTTAAAT
260769 CGAATATGAT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 1 0.02
30 63 0.98
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.58
Consensus pattern (30 bp):
TTTAGTCCTTTAAATTTATATTTTTACTAT
Found at i:262234 original size:13 final size:13
Alignment explanation
Indices: 262216--262240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
262206 AGTGCTTATA
262216 GGCATGTTCGGGG
1 GGCATGTTCGGGG
262229 GGCATGTTCGGG
1 GGCATGTTCGGG
262241 AATTTAATCT
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:0.08, C:0.16, G:0.52, T:0.24
Consensus pattern (13 bp):
GGCATGTTCGGGG
Found at i:264104 original size:29 final size:29
Alignment explanation
Indices: 264072--264132 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
264062 AATAATATTT
* * * *
264072 AAAAATAAAACAGAGTTTGATTAAGTAAA
1 AAAAAGAAAACAAAGTTCGATTAACTAAA
* *
264101 AAAAAGGAAATAAAGTTCGATTAACTAAA
1 AAAAAGAAAACAAAGTTCGATTAACTAAA
264130 AAA
1 AAA
264133 TTTACAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (29 bp):
AAAAAGAAAACAAAGTTCGATTAACTAAA
Found at i:266109 original size:15 final size:16
Alignment explanation
Indices: 266091--266131 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
266081 TTTGAAACAA
266091 ACAAATAAATAATT-C
1 ACAAATAAATAATTAC
*
266106 AC-AATAAATTATTAC
1 ACAAATAAATAATTAC
*
266121 ATAAATAAATA
1 ACAAATAAATA
266132 TATTGTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 10 0.48
15 4 0.19
16 7 0.33
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (16 bp):
ACAAATAAATAATTAC
Found at i:266158 original size:53 final size:53
Alignment explanation
Indices: 266057--266167 Score: 120
Period size: 53 Copynumber: 2.1 Consensus size: 53
266047 TAAATTGCAC
* *
266057 TAAATTATTATAGAAATAAATAAATTTGAAACAAACAAATAAATAATTCACAA-
1 TAAATTATTACAGAAATAAATAAATTTGAAAAAAACAAATAAATAATTCA-AAG
* * * *
266110 TAAATTATTACATAAATAAATATATTGTTAAAAAAATTAAA-AAA-AATTCAAAG
1 TAAATTATTACAGAAATAAATAAATT-TGAAAAAAA-CAAATAAATAATTCAAAG
266163 TAAAT
1 TAAAT
266168 AAATAAGTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.04
53 34 0.69
54 10 0.20
55 3 0.06
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (53 bp):
TAAATTATTACAGAAATAAATAAATTTGAAAAAAACAAATAAATAATTCAAAG
Found at i:269222 original size:31 final size:32
Alignment explanation
Indices: 269161--269222 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
269151 TATTGTAGCT
269161 AGGGTTTTGCATGATATGGGTTAATATATAAC
1 AGGGTTTTGCATGATATGGGTTAATATATAAC
*
269193 AGGGTTTTGCATGATATGGG-TCATATATAA
1 AGGGTTTTGCATGATATGGGTTAATATATAA
269223 GAATGGCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (32 bp):
AGGGTTTTGCATGATATGGGTTAATATATAAC
Found at i:275744 original size:23 final size:23
Alignment explanation
Indices: 275718--275761 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
275708 TAATTTTTCT
275718 GAACATATTTGTTTAACGTTCGC
1 GAACATATTTGTTTAACGTTCGC
* *
275741 GAACATGTTTGTTTTACGTTC
1 GAACATATTTGTTTAACGTTC
275762 ATTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (23 bp):
GAACATATTTGTTTAACGTTCGC
Found at i:275959 original size:20 final size:19
Alignment explanation
Indices: 275917--275959 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
275907 ATCAATATTT
*
275917 AAAATGTAAAAATCTAATA
1 AAAATGTAAAAATCTAAAA
275936 AAAATGTCAAAAAT-TAAAA
1 AAAATGT-AAAAATCTAAAA
275955 GAAAA
1 -AAAA
275960 ACGAGAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (19 bp):
AAAATGTAAAAATCTAAAA
Found at i:291750 original size:107 final size:108
Alignment explanation
Indices: 291552--291816 Score: 263
Period size: 107 Copynumber: 2.5 Consensus size: 108
291542 GCTAAGTCCA
* * * *
291552 ATTTTTAAATGAGTTTTCAAAGATGCTAAGCTGATTTTTAGGGGTTTCTTGATGTTTTGAAAAGA
1 ATTTATAAATGAGTTTTCAAAGAAGCTAAGCTGATTTTTAGGGGTTTCTTAATGTTTTCAAAAGA
* *
291617 ATTTTCAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATG
66 ATGTTCAAAGAAACTAAGTCTAATTTTTAGAAGTTTCTTGATG
* * *
291660 ATTTATAAATGAGTTTTCAAATAAGCT-A-CTTGATTTTTATGGGTTTCTTAATGTTTTCAAATG
1 ATTTATAAATGAGTTTTCAAAGAAGCTAAGC-TGATTTTTAGGGGTTTCTTAATGTTTTCAAAAG
* * ** *
291723 AATGTTGAAAGAATA-TAAGTTTAATTTTCT-GGGGTTTCTTGACG
65 AATGTTCAAAGAA-ACTAAGTCTAATTTT-TAGAAGTTTCTTGATG
* ** * * *
291767 -TCTCCAAATGAATTTTTTAAAAAAGCTAAGCCT-ATTTTTAGGGGTTTCTT
1 ATTTATAAATG-AGTTTTCAAAGAAGCTAAG-CTGATTTTTAGGGGTTTCTT
291817 GATGATAACC
Statistics
Matches: 129, Mismatches: 21, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
106 8 0.06
107 76 0.59
108 43 0.33
109 1 0.01
110 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (108 bp):
ATTTATAAATGAGTTTTCAAAGAAGCTAAGCTGATTTTTAGGGGTTTCTTAATGTTTTCAAAAGA
ATGTTCAAAGAAACTAAGTCTAATTTTTAGAAGTTTCTTGATG
Found at i:293710 original size:202 final size:203
Alignment explanation
Indices: 293353--294200 Score: 1214
Period size: 203 Copynumber: 4.2 Consensus size: 203
293343 TTCAACCTTT
* ** * * *
293353 GCTCATCCATCGCATATGGAGTTGGATTAATATCATCACTTTGTTCGATTCAATCATAGAATGAG
1 GCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTTGTTTGATTCTATCACAGAATGAG
* *
293418 GTGGATCAACATTTCCAGTCGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAATAAGT
66 GTGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGT
* * *
293483 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCTTTTCCATCACATAAAGAGCTGGAACAACACC
131 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAGGAGTTGGAACAACACC
293548 AATACTTG
196 AATACTTG
* * * **
293556 GCTCATCCATCGCATACGAAGTTGGATCAGCATCATCACTTTGTTAGATTCTATCGTAGAATGAG
1 GCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTTGTTTGATTCTATCACAGAATGAG
* * * *
293621 GTGGATCAACATTTCCAATAGATA-TTCATAATGCGAAGAACTCATCCGATGAGGGAGAATAAGT
66 GTGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGT
* * * * *
293685 TCATAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCAGATAAGGAGTTGAAATAACACT
131 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAGGAGTTGGAACAACACC
293750 AATACTTG
196 AATACTTG
* * * *
293758 GCTCATCCATCGTATATGGAGTTGGATCCGCATCATCACTTTATTTGATTCTATCACAGAAGGAG
1 GCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTTGTTTGATTCTATCACAGAATGAG
* * * * *
293823 ATGGATCAACATTACCAGTGGAGAGTTCATAATGACAATAACTCATCCGATGAGGGAGAAAAAGT
66 GTGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGT
* ** *
293888 TCATAATGAGAAGAACTTGTTCAATCTTAGCTCGTTTCCATCACATAAGGAGTTGGTTCAATACC
131 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAGGAGTTGGAACAACACC
293953 AATACTTG
196 AATACTTG
* * * * *
293961 GCTTATCCATCGTATATGGAGTTGGAACAACATCATCACTTTGTTTGATTCCATCACAGAATGAG
1 GCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTTGTTTGATTCTATCACAGAATGAG
* * *
294026 GTGGATCAAAATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGATGAGGGAGAAGAAGT
66 GTGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGT
* *
294091 TCATAATGAGAAGAACTTGTTCAACCTTATCTCGTTTCCATCACATAAGGAGTTGGAACATCACC
131 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAGGAGTTGGAACAACACC
*
294156 AACA-TTG
196 AATACTTG
* * *
294163 GCTCATCCATCACATAAGGAGTTGGACCAGCATCATCA
1 GCTCATCCATCGCATATGGAGTTGGATCAGCATCATCA
294201 TTTCGCTTGT
Statistics
Matches: 569, Mismatches: 75, Indels: 3
0.88 0.12 0.00
Matches are distributed among these distances:
202 213 0.37
203 356 0.63
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (203 bp):
GCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTTGTTTGATTCTATCACAGAATGAG
GTGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGT
TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAGGAGTTGGAACAACACC
AATACTTG
Found at i:294112 original size:20 final size:19
Alignment explanation
Indices: 294050--294113 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
294040 CCAGTGGAGA
294050 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* **
294069 CATTCGATGAGGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
294089 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
294109 GTTCA
1 GTTCA
294114 ACCTTATCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 9 0.27
18 2 0.06
19 3 0.09
20 8 0.24
21 2 0.06
22 9 0.27
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:294166 original size:405 final size:405
Alignment explanation
Indices: 293345--294200 Score: 1205
Period size: 405 Copynumber: 2.1 Consensus size: 405
293335 AGAACTTGTT
* **** *
293345 CAAC-CTTTGCTCATCCATCGCATATGGAGTTGGATTAATATCATCACTTTGTTCGATTCAATCA
1 CAACACTTGGCTCATCCATCGCATATGGAGTTGGATCCGCATCATCACTTTATTCGATTCAATCA
* * * * * *
293409 TAGAATGAGGTGGATCAACATTTCCAGTCGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGG
66 CAGAAGGAGATGGATCAACATTACCAGTCGAGAGTTCATAATGACAAGAACTCATCCGATGAGGG
* *
293474 AGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCTTTTCCATCACATAAAGAGCTGG
131 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAAGAGCTGG
* *
293539 AACAACACCAATACTTGGCTCATCCATCGCATACGAAGTTGGATCAGCATCATCACTTTGTTAGA
196 AACAACACCAATACTTGGCTCATCCATCGCATACGAAGTTGGAACAACATCATCACTTTGTTAGA
* ** * * *
293604 TTCTATCGTAGAATGAGGTGGATCAACATTTCCAATAGATATTCATAATGCGAAGAACTCATCCG
261 TTCCATCACAGAATGAGGTGGATCAAAATTTCCAATAGAGATTCATAATGAGAAGAACTCATCCG
* * *
293669 ATGAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCAGATAAG
326 ATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAG
*
293734 GAGTTGAAATAACAC
391 GAGTTGAAACAACAC
* * * * *
293749 TAATACTTGGCTCATCCATCGTATATGGAGTTGGATCCGCATCATCACTTTATTTGATTCTATCA
1 CAACACTTGGCTCATCCATCGCATATGGAGTTGGATCCGCATCATCACTTTATTCGATTCAATCA
* *
293814 CAGAAGGAGATGGATCAACATTACCAGTGGAGAGTTCATAATGACAATAACTCATCCGATGAGGG
66 CAGAAGGAGATGGATCAACATTACCAGTCGAGAGTTCATAATGACAAGAACTCATCCGATGAGGG
* * *
293879 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAATCTTAGCTCGTTTCCATCACATAAGGAGTTGG
131 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAAGAGCTGG
** * * * * * *
293944 TTCAATACCAATACTTGGCTTATCCATCGTATATGGAGTTGGAACAACATCATCACTTTGTTTGA
196 AACAACACCAATACTTGGCTCATCCATCGCATACGAAGTTGGAACAACATCATCACTTTGTTAGA
* * *
294009 TTCCATCACAGAATGAGGTGGATCAAAATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTC
261 TTCCATCACAGAATGAGGTGGATCAAAATTTCCAATAGAGA-TTCATAATGAGAAGAACTCATCC
*
294074 GATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTATCTCGTTTCCATCACATAA
325 GATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAA
* *
294139 GGAGTTGGAACATCAC
390 GGAGTTGAAACAACAC
* *
294155 CAACA-TTGGCTCATCCATCACATAAGGAGTTGGA-CCAGCATCATCA
1 CAACACTTGGCTCATCCATCGCATATGGAGTTGGATCC-GCATCATCA
294201 TTTCGCTTGT
Statistics
Matches: 394, Mismatches: 55, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
404 4 0.01
405 292 0.74
406 98 0.25
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (405 bp):
CAACACTTGGCTCATCCATCGCATATGGAGTTGGATCCGCATCATCACTTTATTCGATTCAATCA
CAGAAGGAGATGGATCAACATTACCAGTCGAGAGTTCATAATGACAAGAACTCATCCGATGAGGG
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAAGAGCTGG
AACAACACCAATACTTGGCTCATCCATCGCATACGAAGTTGGAACAACATCATCACTTTGTTAGA
TTCCATCACAGAATGAGGTGGATCAAAATTTCCAATAGAGATTCATAATGAGAAGAACTCATCCG
ATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAG
GAGTTGAAACAACAC
Found at i:294172 original size:41 final size:41
Alignment explanation
Indices: 294127--294279 Score: 155
Period size: 42 Copynumber: 3.7 Consensus size: 41
294117 TTATCTCGTT
* *
294127 TCCATCACATAAGGAGTTGGAACATCACCAACATTGGCTCA
1 TCCATCACATAAGGAGTTGGAACAGCATCAACATTGGCTCA
* * * **
294168 TCCATCACATAAGGAGTTGGACCAGCATCATCATTTCGCTTG
1 TCCATCACATAAGGAGTTGGAACAGCATCAACA-TTGGCTCA
* * * *
294210 TCCATCACATTAGGAGTTGGATCAGCATC-ACCTTGGCTCT
1 TCCATCACATAAGGAGTTGGAACAGCATCAACATTGGCTCA
* * * *
294250 TCCATCATATAAGAAGTTAGATCAGCATCA
1 TCCATCACATAAGGAGTTGGAACAGCATCA
294280 CCTTGGGTTA
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
40 30 0.33
41 30 0.33
42 32 0.35
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (41 bp):
TCCATCACATAAGGAGTTGGAACAGCATCAACATTGGCTCA
Found at i:294273 original size:40 final size:40
Alignment explanation
Indices: 294126--294285 Score: 169
Period size: 40 Copynumber: 3.9 Consensus size: 40
294116 CTTATCTCGT
* * * *
294126 TTCCATCACATAAGGAGTTGGAACATCACCAACATTGGCTC
1 TTCCATCACATAAGGAGTTGGATCAGCATC-ACCTTGGCTC
* * * *
294167 ATCCATCACATAAGGAGTTGGACCAGCATCATCATTTCGCT-
1 TTCCATCACATAAGGAGTTGGATCAGCATCA-C-CTTGGCTC
*
294208 TGTCCATCACATTAGGAGTTGGATCAGCATCACCTTGGCTC
1 T-TCCATCACATAAGGAGTTGGATCAGCATCACCTTGGCTC
* * *
294249 TTCCATCATATAAGAAGTTAGATCAGCATCACCTTGG
1 TTCCATCACATAAGGAGTTGGATCAGCATCACCTTGG
294286 GTTAACCATC
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
40 38 0.38
41 29 0.29
42 33 0.33
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (40 bp):
TTCCATCACATAAGGAGTTGGATCAGCATCACCTTGGCTC
Found at i:294276 original size:82 final size:83
Alignment explanation
Indices: 294127--294279 Score: 209
Period size: 82 Copynumber: 1.9 Consensus size: 83
294117 TTATCTCGTT
* * *
294127 TCCATCACATAAGGAGTTGGAACATCACCAACATTGGCTCATCCATCACATAAGGAGTTGGACCA
1 TCCATCACATAAGGAGTTGGAACAGCACCAACATTGGCTCATCCATCACATAAGAAGTTAGACCA
294192 GCATCATCATTTCGCTTG
66 GCATCATCATTTCGCTTG
* * * * * * *
294210 TCCATCACATTAGGAGTTGGATCAGCATC-ACCTTGGCTCTTCCATCATATAAGAAGTTAGATCA
1 TCCATCACATAAGGAGTTGGAACAGCACCAACATTGGCTCATCCATCACATAAGAAGTTAGACCA
294274 GCATCA
66 GCATCA
294280 CCTTGGGTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
82 35 0.58
83 25 0.42
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (83 bp):
TCCATCACATAAGGAGTTGGAACAGCACCAACATTGGCTCATCCATCACATAAGAAGTTAGACCA
GCATCATCATTTCGCTTG
Found at i:297131 original size:18 final size:18
Alignment explanation
Indices: 297108--297170 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
297098 CATTCATTTA
297108 CATTGTGACACTTCGATG
1 CATTGTGACACTTCGATG
*
297126 CATTGTGTCACTTCGATG
1 CATTGTGACACTTCGATG
* *
297144 CCTTGTGTAGCATTTCGATG
1 CATTGTG-A-CACTTCGATG
*
297164 CCTTGTG
1 CATTGTG
297171 TAGCATTTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 23 0.59
20 16 0.41
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (18 bp):
CATTGTGACACTTCGATG
Found at i:297162 original size:20 final size:20
Alignment explanation
Indices: 297119--297183 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
297109 ATTGTGACAC
* *
297119 TTCGATGCATTGTGT--CAC
1 TTCGATGCCTTGTGTAGCAT
297137 TTCGATGCCTTGTGTAGCAT
1 TTCGATGCCTTGTGTAGCAT
297157 TTCGATGCCTTGTGTAGCAT
1 TTCGATGCCTTGTGTAGCAT
297177 TTCGATG
1 TTCGATG
297184 TTGGAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 14 0.33
20 29 0.67
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (20 bp):
TTCGATGCCTTGTGTAGCAT
Found at i:302053 original size:14 final size:14
Alignment explanation
Indices: 302034--302060 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
302024 AATATCTTTT
302034 AAAATAATTTTAAG
1 AAAATAATTTTAAG
302048 AAAATAATTTTAA
1 AAAATAATTTTAA
302061 AAGATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AAAATAATTTTAAG
Found at i:317180 original size:20 final size:21
Alignment explanation
Indices: 317147--317195 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
317137 TAAAATTTAA
*
317147 TGAT-AATTTTGTAAT-AGTC
1 TGATAAATTTAGTAATGAGTC
* *
317166 TGATAAATTTAGTAATGATTT
1 TGATAAATTTAGTAATGAGTC
317187 TGATAAATT
1 TGATAAATT
317196 ATTAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 10 0.40
21 11 0.44
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (21 bp):
TGATAAATTTAGTAATGAGTC
Found at i:318047 original size:3 final size:3
Alignment explanation
Indices: 318039--318122 Score: 138
Period size: 3 Copynumber: 29.0 Consensus size: 3
318029 GGTACCCAGT
318039 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
318087 TTA TTA TTA TTA TTA TTA -TA TTT TTA TT- TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
318123 AATTTTTATT
Statistics
Matches: 76, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
2 6 0.08
3 70 0.92
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:318127 original size:18 final size:19
Alignment explanation
Indices: 318038--318133 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 19
318028 TGGTACCCAG
*
318038 TTTATTATT--ATTATTAT
1 TTTATTATTAAATTTTTAT
*
318055 TATTATTATT--ATTATTAT
1 T-TTATTATTAAATTTTTAT
* *
318073 TATTATTATTATTATTATTAT
1 T-TTATTATTA-AATTTTTAT
*
318094 TATTATTATTATATTTTTAT
1 T-TTATTATTAAATTTTTAT
318114 TTTA-TATTAAATTTTTAT
1 TTTATTATTAAATTTTTAT
318132 TT
1 TT
318134 ATAATTCTCA
Statistics
Matches: 73, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
17 1 0.01
18 41 0.56
19 3 0.04
20 9 0.12
21 19 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATTATTAAATTTTTAT
Found at i:318199 original size:38 final size:39
Alignment explanation
Indices: 318143--318247 Score: 128
Period size: 38 Copynumber: 2.7 Consensus size: 39
318133 TATAATTCTC
318143 AAATTATTTCAC-TCTAACATTCTAAATTCCTAATTTCGT
1 AAATTATTTCACAT-TAACATTCTAAATTCCTAATTTCGT
* *
318182 -AATT-TTTCCACCA-TAACATTCTAAATTCTTAATTTCTT
1 AAATTATTT-CA-CATTAACATTCTAAATTCCTAATTTCGT
*
318220 AAATTATTTCACATTAACCTTCTAAATT
1 AAATTATTTCACATTAACATTCTAAATT
318248 ATTTTTTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
37 3 0.05
38 31 0.54
39 20 0.35
40 3 0.05
ACGTcount: A:0.34, C:0.20, G:0.01, T:0.45
Consensus pattern (39 bp):
AAATTATTTCACATTAACATTCTAAATTCCTAATTTCGT
Found at i:318450 original size:18 final size:18
Alignment explanation
Indices: 318429--318465 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
318419 ATATTTTTTT
* *
318429 AAAATAATATAATTATAA
1 AAAATAAAAAAATTATAA
318447 AAAATAAAAAAATTATAA
1 AAAATAAAAAAATTATAA
318465 A
1 A
318466 TTGGGTATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATAAAAAAATTATAA
Found at i:325308 original size:19 final size:20
Alignment explanation
Indices: 325284--325321 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
325274 AATTTTTTAT
325284 AAATAAT-TTTTTTAATTAA
1 AAATAATATTTTTTAATTAA
*
325303 AAATAATATTTTTTTATTA
1 AAATAATATTTTTTAATTA
325322 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATAATATTTTTTAATTAA
Found at i:325315 original size:22 final size:23
Alignment explanation
Indices: 325285--325328 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
325275 ATTTTTTATA
325285 AATAATTTTTT-TAATTAAAAAT
1 AATAATTTTTTATAATTAAAAAT
* *
325307 AATATTTTTTTATTATTAAAAA
1 AATAATTTTTTATAATTAAAAA
325329 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATAATTTTTTATAATTAAAAAT
Found at i:328942 original size:29 final size:29
Alignment explanation
Indices: 328910--329029 Score: 120
Period size: 29 Copynumber: 4.2 Consensus size: 29
328900 TTTTTTTAAA
*
328910 TAATTACCAAAATAGCACCCTTTTCGAAT
1 TAATTACCAAAATAGCACCATTTTCGAAT
* *
328939 TAATTCCCAAAATAGCACCAATTTCGAAT
1 TAATTACCAAAATAGCACCATTTTCGAAT
* ** *
328968 TAATT-CCTAAAATATCACTTTTTTC-AAA
1 TAATTACC-AAAATAGCACCATTTTCGAAT
* *
328996 AAATTACCAAAATAGCA-CATATTTCAAAT
1 TAATTACCAAAATAGCACCAT-TTTCGAAT
329025 TAATT
1 TAATT
329030 CCCCGAATAG
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
27 1 0.01
28 20 0.27
29 52 0.71
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (29 bp):
TAATTACCAAAATAGCACCATTTTCGAAT
Found at i:329090 original size:13 final size:13
Alignment explanation
Indices: 329072--329101 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
329062 AAATAAAACC
329072 GGTCAACGGGTCG
1 GGTCAACGGGTCG
329085 GGTCAACGGGTCG
1 GGTCAACGGGTCG
329098 GGTC
1 GGTC
329102 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:329101 original size:18 final size:17
Alignment explanation
Indices: 329078--329117 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
329068 AACCGGTCAA
329078 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAAC-GGT
329096 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
329113 CGGGT
1 CGGGT
329118 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTCAACGGT
Found at i:329137 original size:30 final size:31
Alignment explanation
Indices: 329069--329138 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
329059 TCAAAATAAA
*
329069 ACCGGTCAACGGGTCGGGTCAACGGGTCGGG
1 ACCGGTCAACGGGTCGGGTAAACGGGTCGGG
* * *
329100 TCGGGTCAAC-GGTCGGGTAAACGGGTCGTG
1 ACCGGTCAACGGGTCGGGTAAACGGGTCGGG
329130 ACCGGTCAA
1 ACCGGTCAA
329139 ACCGGTCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 25 0.76
31 8 0.24
ACGTcount: A:0.19, C:0.24, G:0.41, T:0.16
Consensus pattern (31 bp):
ACCGGTCAACGGGTCGGGTAAACGGGTCGGG
Found at i:329154 original size:10 final size:10
Alignment explanation
Indices: 329130--329180 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
329120 ACGGGTCGTG
329130 ACCGGTC-AA
1 ACCGGTCAAA
329139 ACCGGTCAAA
1 ACCGGTCAAA
*
329149 ATCGGTTCAAA
1 ACCGG-TCAAA
*
329160 ACCGGGT-TAA
1 ACC-GGTCAAA
329170 ACCGGTCAAA
1 ACCGGTCAAA
329180 A
1 A
329181 TCAGTTTCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
9 10 0.29
10 14 0.41
11 8 0.24
12 2 0.06
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:336274 original size:29 final size:29
Alignment explanation
Indices: 336231--336354 Score: 115
Period size: 29 Copynumber: 4.3 Consensus size: 29
336221 CATTTTACAC
** *
336231 AAATAGCACTTTTTTTTAAATAATTCCCA
1 AAATAGCACCCTTTTTGAAATAATTCCCA
* *
336260 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAAATAATTCCCA
** *
336289 AAATAGCACCAATTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAAATAATTCCCA
* * * * *
336318 TAATATCA-CCTTTTCTAAAAAAATTACCA
1 AAATAGCACCCTTTT-TGAAATAATTCCCA
336347 AAATAGCA
1 AAATAGCA
336355 AACATTTCAA
Statistics
Matches: 76, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
28 4 0.05
29 72 0.95
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (29 bp):
AAATAGCACCCTTTTTGAAATAATTCCCA
Found at i:336439 original size:13 final size:13
Alignment explanation
Indices: 336421--336486 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 13
336411 ACCGGTCAAC
336421 GGTCAACGGGTCG
1 GGTCAACGGGTCG
336434 GGTCAACGAGTCAGGTCG
1 GGTCAAC--G---GGTCG
*
336452 GGTCAAC-GGTCA
1 GGTCAACGGGTCG
336464 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
336476 GGTAAACGGGT
1 GGTCAACGGGT
336487 AAACGGGTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 21 0.48
13 10 0.23
15 1 0.02
18 12 0.27
ACGTcount: A:0.21, C:0.21, G:0.41, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:336452 original size:18 final size:17
Alignment explanation
Indices: 336414--336467 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 17
336404 AAATAACACC
336414 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGTC-A--GGTCG
336434 GGTCAACGAGTCAGGTCG
1 GGTCAACG-GTCAGGTCG
336452 GGTCAACGGTCAGGTC
1 GGTCAACGGTCAGGTC
336468 AACGGTCGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.24
18 13 0.39
20 9 0.27
21 3 0.09
ACGTcount: A:0.20, C:0.24, G:0.39, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCAGGTCG
Found at i:336467 original size:12 final size:12
Alignment explanation
Indices: 336447--336484 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
336437 CAACGAGTCA
336447 GGTCGGGTCAAC
1 GGTCGGGTCAAC
*
336459 GGTCAGGTCAAC
1 GGTCGGGTCAAC
*
336471 GGTCGGGTAAAC
1 GGTCGGGTCAAC
336483 GG
1 GG
336485 GTAAACGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.16
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:336519 original size:10 final size:10
Alignment explanation
Indices: 336499--336553 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
336489 ACGGGTCGTG
336499 ACCGGTC-AA
1 ACCGGTCAAA
336508 ACCGGTCAAA
1 ACCGGTCAAA
*
336518 ACTGGTTCAAA
1 ACCGG-TCAAA
*
336529 ACCGGT-TAA
1 ACCGGTCAAA
336538 ACCGGTCAAA
1 ACCGGTCAAA
336548 ACCGGT
1 ACCGGT
336554 TTCCAGCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
9 15 0.38
10 15 0.38
11 9 0.23
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:336529 original size:11 final size:11
Alignment explanation
Indices: 336506--336554 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
336496 GTGACCGGTC
336506 AAACCGG-TCA
1 AAACCGGTTCA
*
336516 AAACTGGTTCA
1 AAACCGGTTCA
336527 AAACCGGTT--
1 AAACCGGTTCA
336536 AAACCGG-TCA
1 AAACCGGTTCA
336546 AAACCGGTT
1 AAACCGGTT
336555 TCCAGCGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 1 0.03
9 7 0.21
10 13 0.39
11 12 0.36
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:336548 original size:19 final size:19
Alignment explanation
Indices: 336499--336554 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
336489 ACGGGTCGTG
*
336499 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
*
336518 ACTGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
336538 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
336555 TCCAGCGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.50
20 8 0.25
21 8 0.25
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:338954 original size:2 final size:2
Alignment explanation
Indices: 338908--338945 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
338898 TATTTTTTAT
338908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
338946 GGGTATATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:343846 original size:31 final size:31
Alignment explanation
Indices: 343811--343884 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 31
343801 CAACCATTCC
*** *
343811 CAACTTTTTCCAAAATTTTGAATTGGTCCCT
1 CAACTTTTTCCAAAATTACAAAATGGTCCCT
*
343842 CAAC-TTTTCAAAAATTACAAAATGGTCCCT
1 CAACTTTTTCCAAAATTACAAAATGGTCCCT
*
343872 -AAATTTTTCCAAA
1 CAACTTTTTCCAAA
343885 GCCTGTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 2 0.06
30 29 0.83
31 4 0.11
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (31 bp):
CAACTTTTTCCAAAATTACAAAATGGTCCCT
Found at i:343925 original size:20 final size:20
Alignment explanation
Indices: 343896--343940 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
343886 CCTGTAAAAT
*
343896 ACTTTCTAC-ATTATTTCCAG
1 ACTTTATACAATT-TTTCCAG
*
343916 ACTTTATACAATTTTTCCAT
1 ACTTTATACAATTTTTCCAG
343936 ACTTT
1 ACTTT
343941 TTCTCATCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.27, C:0.22, G:0.02, T:0.49
Consensus pattern (20 bp):
ACTTTATACAATTTTTCCAG
Found at i:344858 original size:30 final size:30
Alignment explanation
Indices: 344822--344894 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
344812 AAAATTACAT
* *
344822 TTTGGTCCCTAAACTTT-TCAAATTTTATAC
1 TTTGGTCCCTAAACTTTACCAAA-TTTATAA
344852 TTTGGTCACC-AAACTTTACCAAATTTATAA
1 TTTGGTC-CCTAAACTTTACCAAATTTATAA
*
344882 TTTGGTCACTAAA
1 TTTGGTCCCTAAA
344895 TAAATCTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.03
30 30 0.81
31 6 0.16
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (30 bp):
TTTGGTCCCTAAACTTTACCAAATTTATAA
Found at i:345923 original size:6 final size:6
Alignment explanation
Indices: 345893--345948 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
345883 ATCTATCATA
* * * *
345893 TTTT-T TTTTCA TTTT-T TTCTGT TTTTCT TTTTCT TTTTCT TCTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
*
345939 TCTTCT TTTT
1 TTTTCT TTTT
345949 AGTTTTTTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
5 7 0.17
6 35 0.83
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:348731 original size:131 final size:131
Alignment explanation
Indices: 348497--348758 Score: 497
Period size: 131 Copynumber: 2.0 Consensus size: 131
348487 ACAAAGTTCT
*
348497 CCAACTTATAATTTGACCGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
1 CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
*
348562 AAATCATGCTTGGAAATGAATCTATAACCTTTGATTAATCAAGATTTATCATCAATTTCATGAAT
66 AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
348627 C
131 C
*
348628 CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGATCATGTTTTAACCAT
1 CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
348693 AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
66 AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
348758 C
131 C
348759 TCATCATGAA
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 128 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (131 bp):
CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
C
Found at i:355107 original size:23 final size:22
Alignment explanation
Indices: 355081--355153 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
355071 GCATGTTATT
355081 TACCTTTATGACAAGTTTATCTA
1 TACCTTTATGACAA-TTTATCTA
* * * *
355104 TACCTTTGTGGC-ATGT-TCTC
1 TACCTTTATGACAATTTATCTA
*
355124 TGCCTTTATGACACATTTATCTA
1 TACCTTTATGACA-ATTTATCTA
355147 TACCTTT
1 TACCTTT
355154 GTGGCACGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 12 0.32
21 2 0.05
22 4 0.11
23 19 0.51
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (22 bp):
TACCTTTATGACAATTTATCTA
Found at i:355130 original size:43 final size:43
Alignment explanation
Indices: 355064--355159 Score: 140
Period size: 43 Copynumber: 2.2 Consensus size: 43
355054 ATAATTATGT
* *
355064 CTTTGTAGCATGTTATTTACCTTTATGACA-AGTTTATCTATAC
1 CTTTGTGGCATGTTATCTACCTTTATGACACA-TTTATCTATAC
* *
355107 CTTTGTGGCATGTTCTCTGCCTTTATGACACATTTATCTATAC
1 CTTTGTGGCATGTTATCTACCTTTATGACACATTTATCTATAC
355150 CTTTGTGGCA
1 CTTTGTGGCA
355160 CGTTTTTCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 47 0.98
44 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.45
Consensus pattern (43 bp):
CTTTGTGGCATGTTATCTACCTTTATGACACATTTATCTATAC
Found at i:355175 original size:23 final size:23
Alignment explanation
Indices: 355119--355176 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
355109 TTGTGGCATG
355119 TTCTCTGCCTTTATGACACATTT
1 TTCTCTGCCTTTATGACACATTT
* * * * * *
355142 ATCTATACCTTTGTGGCACGTTT
1 TTCTCTGCCTTTATGACACATTT
355165 TTCTCTGCCTTT
1 TTCTCTGCCTTT
355177 TGGTAGTTTA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.26, G:0.12, T:0.48
Consensus pattern (23 bp):
TTCTCTGCCTTTATGACACATTT
Found at i:356130 original size:20 final size:21
Alignment explanation
Indices: 356085--356130 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
356075 TTTGACCAGA
356085 AGTTTCGAAACTTCTACAAGAT
1 AGTTTCGAAACTTC-ACAAGAT
356107 --TTTCGAAACTTC-CAAGAT
1 AGTTTCGAAACTTCACAAGAT
356125 AGTTTC
1 AGTTTC
356131 CAAAAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (21 bp):
AGTTTCGAAACTTCACAAGAT
Found at i:358797 original size:19 final size:20
Alignment explanation
Indices: 358773--358824 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
358763 TTCCCAAAAT
358773 GTTTCGATACTTTA-C-AAGA
1 GTTTCGATACTTTACCTAA-A
*
358792 GTTTCGAAACTTTACCTAAA
1 GTTTCGATACTTTACCTAAA
358812 GTTTCGATACTTT
1 GTTTCGATACTTT
358825 GTGTCCAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 14 0.48
21 2 0.07
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
GTTTCGATACTTTACCTAAA
Found at i:362599 original size:18 final size:18
Alignment explanation
Indices: 362572--362606 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
362562 ACAGAGAAGT
* *
362572 AAATACTGAAATTTAAAA
1 AAATAATGAAATATAAAA
362590 AAATAATGAAATATAAA
1 AAATAATGAAATATAAA
362607 TATTAGAAAT
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:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATAATGAAATATAAAA
Found at i:363484 original size:57 final size:57
Alignment explanation
Indices: 363204--363485 Score: 331
Period size: 57 Copynumber: 4.9 Consensus size: 57
363194 CGAATTACTT
* * * * * * * *
363204 ATCATCGAGAAACCTTTGAAAATCA-AATATGGCTTCCTAAAAAATTCACTTAAAGTA
1 ATCATCAAGAAACCCTTGAAAATCAGACT-TAGCTTCTTTAAAAATTCATTTGAAGTA
* *
363261 ATCATCAATAAACTCC-TGAAAATCAGGA-TTAGCTTCTTTAAAAATTCACTTGAAGTA
1 ATCATCAAGAAAC-CCTTGAAAATCA-GACTTAGCTTCTTTAAAAATTCATTTGAAGTA
* * * *
363318 CTCAT-AAAAAAACCTCTAAAAATCAGACTTAGCTTCTTTAAAAATTCATTTGAAGTA
1 ATCATCAAGAAACCCT-TGAAAATCAGACTTAGCTTCTTTAAAAATTCATTTGAAGTA
* *
363375 ATCATCAAGAAA-CCTCTAAAAATCATACTTAGCTTCTTTAAAAATTCATTTGAAGTA
1 ATCATCAAGAAACCCT-TGAAAATCAGACTTAGCTTCTTTAAAAATTCATTTGAAGTA
*
363432 ATCATCAAGAAACCCTTGAAAATCAGACTTAGCTTCTTTAAAAATTCTTTTGAA
1 ATCATCAAGAAACCCTTGAAAATCAGACTTAGCTTCTTTAAAAATTCATTTGAA
363486 AACATCATAT
Statistics
Matches: 199, Mismatches: 18, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
55 2 0.01
56 7 0.04
57 179 0.90
58 10 0.05
59 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (57 bp):
ATCATCAAGAAACCCTTGAAAATCAGACTTAGCTTCTTTAAAAATTCATTTGAAGTA
Found at i:363493 original size:57 final size:58
Alignment explanation
Indices: 363243--363485 Score: 334
Period size: 57 Copynumber: 4.3 Consensus size: 58
363233 TGGCTTCCTA
* * * * *
363243 AAAAATTCACTTAAAGTAATCATCAATAAACTC-CTGAAAATCAGGA-TTAGCTTCTTT
1 AAAAATTCATTTGAAGTAATCATCAAGAAACCCTCTAAAAATCA-GACTTAGCTTCTTT
* * * *
363300 AAAAATTCACTTGAAGTACTCAT-AAAAAAACCTCTAAAAATCAGACTTAGCTTCTTT
1 AAAAATTCATTTGAAGTAATCATCAAGAAACCCTCTAAAAATCAGACTTAGCTTCTTT
*
363357 AAAAATTCATTTGAAGTAATCATCAAGAAA-CCTCTAAAAATCATACTTAGCTTCTTT
1 AAAAATTCATTTGAAGTAATCATCAAGAAACCCTCTAAAAATCAGACTTAGCTTCTTT
*
363414 AAAAATTCATTTGAAGTAATCATCAAGAAACCCT-TGAAAATCAGACTTAGCTTCTTT
1 AAAAATTCATTTGAAGTAATCATCAAGAAACCCTCTAAAAATCAGACTTAGCTTCTTT
*
363471 AAAAATTCTTTTGAA
1 AAAAATTCATTTGAA
363486 AACATCATAT
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
56 8 0.05
57 153 0.91
58 8 0.05
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (58 bp):
AAAAATTCATTTGAAGTAATCATCAAGAAACCCTCTAAAAATCAGACTTAGCTTCTTT
Found at i:364864 original size:28 final size:28
Alignment explanation
Indices: 364833--364898 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
364823 ATGTGGACTA
* *
364833 TTTCAGGTTGATTTGGGGAGGTAGA-GTG
1 TTTCAGGTTGATTCGAGGAGGTA-ATGTG
*
364861 TTTCGGGTTGATTCGAGGAGGTAATGTG
1 TTTCAGGTTGATTCGAGGAGGTAATGTG
*
364889 TTTCAAGTTG
1 TTTCAGGTTG
364899 GCTTCTATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.18, C:0.06, G:0.38, T:0.38
Consensus pattern (28 bp):
TTTCAGGTTGATTCGAGGAGGTAATGTG
Found at i:368620 original size:20 final size:21
Alignment explanation
Indices: 368566--368628 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
368556 GATTCCCCTG
368566 TGGGGGGAATCGGTTCCCATTCAA
1 TGGGGGG-ATCGGTTCCC--TCAA
* *
368590 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
368610 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
368629 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
23 10 0.29
24 5 0.15
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:384076 original size:21 final size:21
Alignment explanation
Indices: 384007--384159 Score: 105
Period size: 21 Copynumber: 7.4 Consensus size: 21
383997 GCGCTGCATT
*
384007 TCGCGTTGCGATAGGTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
384028 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
384048 TTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * * ** **
384069 CCGCGTTGCGGT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
384089 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
384110 TCGCGTTGCGGT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
384130 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
384151 TCGCGTTGC
1 TCGCGTTGC
384160 AGTTTTCCAT
Statistics
Matches: 90, Mismatches: 39, Indels: 6
0.67 0.29 0.04
Matches are distributed among these distances:
20 40 0.44
21 50 0.56
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:384200 original size:21 final size:21
Alignment explanation
Indices: 384174--384242 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
384164 TTCCATTTCA
384174 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
384195 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
384213 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
384236 CGTTGCG
1 CGTTGCG
384243 GTTTTCCATT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.05
19 4 0.11
20 9 0.24
21 16 0.43
22 4 0.11
23 2 0.05
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:384267 original size:41 final size:40
Alignment explanation
Indices: 384003--384268 Score: 347
Period size: 41 Copynumber: 6.5 Consensus size: 40
383993 ATTCGCGCTG
* *
384003 CATTTCGCGTTGCGATAGGTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAAT-GCGTTGCGGTTTTC
* *
384044 CATTTTGCGTTGCGATAGTTGAAAACCGCGTTGCGGTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAA-TGCGTTGCGGTTTTC
384085 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAAT-GCGTTGCGGTTTTC
*
384126 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAGTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAAT-GCGTTGCGGTTTTC
* * * *
384167 CATTTCACGTTGCGATAGTCT-ACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATG-CGTTGCGGTTTTC
* *
384208 CATTTCGCGTTGCGATAGTCT-ACAGTGTCGTTGCGGTTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATG-CGTTGCGGTTTTC
384249 CATTTCGCGTTGCGATAGTT
1 CATTTCGCGTTGCGATAGTT
384269 TTAAAAATGG
Statistics
Matches: 207, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
40 2 0.01
41 204 0.99
42 1 0.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAAATGCGTTGCGGTTTTC
Found at i:385230 original size:41 final size:41
Alignment explanation
Indices: 385173--385377 Score: 315
Period size: 41 Copynumber: 5.0 Consensus size: 41
385163 TAAGTGAATT
385173 GAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
1 GAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
* *
385214 GAAAATTGTAACGACACTGTAGACTATCGCAACGCGAAATG
1 GAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
* *
385255 GAAAACCGCAACGTCACTGTAGACTATCGCAACGCGAAATG
1 GAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
385296 GAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
1 GAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
* * *
385337 GAAAACCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAATG
1 GAAAATCGCAACGAC-ACTGT-AGACTATCGCAACGCGAAATG
385378 CAGCGCGAAT
Statistics
Matches: 151, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 1 0.01
41 149 0.99
42 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.16
Consensus pattern (41 bp):
GAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
Found at i:385266 original size:20 final size:20
Alignment explanation
Indices: 385239--385352 Score: 74
Period size: 20 Copynumber: 5.6 Consensus size: 20
385229 ACTGTAGACT
385239 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
385259 ACCGCAACGTC--ACTGTAGACT
1 ATCGCAACG-CGAAATG--GAAA
385280 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
385300 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
385321 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
385341 ACCGCAACGCGA
1 ATCGCAACGCGA
385353 TTTTCAACTA
Statistics
Matches: 69, Mismatches: 15, Indels: 20
0.66 0.14 0.19
Matches are distributed among these distances:
18 3 0.04
19 6 0.09
20 31 0.45
21 20 0.29
22 6 0.09
23 3 0.04
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:389207 original size:24 final size:25
Alignment explanation
Indices: 389175--389221 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
389165 CTATTCTTTC
389175 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
389199 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
389222 TTTTTGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:391783 original size:20 final size:20
Alignment explanation
Indices: 391758--391798 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
391748 AAACTAGATC
*
391758 CACTCATTTTTACATCTGCT
1 CACTCATTCTTACATCTGCT
391778 CACTCATTCTTACATCTGCT
1 CACTCATTCTTACATCTGCT
391798 C
1 C
391799 TGACCTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.34, G:0.05, T:0.41
Consensus pattern (20 bp):
CACTCATTCTTACATCTGCT
Found at i:406904 original size:60 final size:60
Alignment explanation
Indices: 406811--406935 Score: 241
Period size: 60 Copynumber: 2.1 Consensus size: 60
406801 CTCCTCGAAT
*
406811 TTTAATGTTTGAATTCTAAAATTTACCTTGTATTTAATTTAGTTCATACTTTCATTAATA
1 TTTAATGTTTGAATTCAAAAATTTACCTTGTATTTAATTTAGTTCATACTTTCATTAATA
406871 TTTAATGTTTGAATTCAAAAATTTACCTTGTATTTAATTTAGTTCATACTTTCATTAATA
1 TTTAATGTTTGAATTCAAAAATTTACCTTGTATTTAATTTAGTTCATACTTTCATTAATA
406931 TTTAA
1 TTTAA
406936 AATGTAAAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (60 bp):
TTTAATGTTTGAATTCAAAAATTTACCTTGTATTTAATTTAGTTCATACTTTCATTAATA
Found at i:406933 original size:28 final size:28
Alignment explanation
Indices: 406841--406935 Score: 93
Period size: 28 Copynumber: 3.2 Consensus size: 28
406831 ATTTACCTTG
406841 TATTTAATTTAGTTCATACTTTCATTAA
1 TATTTAATTTAGTTCATACTTTCATTAA
* * * * *
406869 TATTTAATGTTTGAATTCAAAAATTTACCTT-G
1 TATTTAA--TTT-AGTTC-ATACTTT-CATTAA
406901 TATTTAATTTAGTTCATACTTTCATTAA
1 TATTTAATTTAGTTCATACTTTCATTAA
406929 TATTTAA
1 TATTTAA
406936 AATGTAAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
27 3 0.06
28 19 0.37
29 4 0.08
30 6 0.12
31 4 0.08
32 12 0.24
33 3 0.06
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (28 bp):
TATTTAATTTAGTTCATACTTTCATTAA
Found at i:419323 original size:28 final size:28
Alignment explanation
Indices: 419283--419367 Score: 161
Period size: 28 Copynumber: 3.0 Consensus size: 28
419273 CTCTCCATGT
*
419283 ACATTATGTTGTCGAGCCAGTGCTTGAA
1 ACATTGTGTTGTCGAGCCAGTGCTTGAA
419311 ACATTGTGTTGTCGAGCCAGTGCTTGAA
1 ACATTGTGTTGTCGAGCCAGTGCTTGAA
419339 ACATTGTGTTGTCGAGCCAGTGCTTGAA
1 ACATTGTGTTGTCGAGCCAGTGCTTGAA
419367 A
1 A
419368 GCAATAGCGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.32
Consensus pattern (28 bp):
ACATTGTGTTGTCGAGCCAGTGCTTGAA
Found at i:421797 original size:16 final size:16
Alignment explanation
Indices: 421752--421800 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
421742 TGAGTAATTG
*
421752 GAATTTTAGGAGTTGA
1 GAATTTTAGGATTTGA
421768 -AA-TTTAGGGATTTGA
1 GAATTTTA-GGATTTGA
*
421783 GAATTTTAGGTTTTGA
1 GAATTTTAGGATTTGA
421799 GA
1 GA
421801 TCATAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 4 0.14
15 9 0.32
16 11 0.39
17 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.41
Consensus pattern (16 bp):
GAATTTTAGGATTTGA
Found at i:422485 original size:13 final size:13
Alignment explanation
Indices: 422456--422496 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
422446 ACCATTTGAG
*
422456 AGAAAGAGAGAAGA
1 AGAAAGA-AGAAAA
422470 AGAAAGAAGAAAA
1 AGAAAGAAGAAAA
*
422483 AGAAAAAAGAAAA
1 AGAAAGAAGAAAA
422496 A
1 A
422497 ATAAGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAAGAAGAAAA
Found at i:434490 original size:2 final size:2
Alignment explanation
Indices: 434483--434523 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
434473 CCAGGTTTGA
434483 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
434524 TAACAGTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:435927 original size:14 final size:15
Alignment explanation
Indices: 435908--435943 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
435898 ATTATAAAAC
435908 AATAAAATAT-TTAA
1 AATAAAATATATTAA
435922 AATAAAATATATTAA
1 AATAAAATATATTAA
435937 AA-AAAAT
1 AATAAAAT
435944 CAATCGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAAATATATTAA
Found at i:436293 original size:24 final size:24
Alignment explanation
Indices: 436239--436287 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
436229 ATTTATTGTA
436239 TAAATTTCTCTTCATTTCATCACT
1 TAAATTTCTCTTCATTTCATCACT
436263 TAAATTTCTCTTCATTTCATCACT
1 TAAATTTCTCTTCATTTCATCACT
436287 T
1 T
436288 GTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (24 bp):
TAAATTTCTCTTCATTTCATCACT
Found at i:439846 original size:20 final size:21
Alignment explanation
Indices: 439784--439846 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
439774 CCCTCGAGGA
* *
439784 AAAGGATCGATCCCTTTACCA
1 AAAGGATCAATCCCTTTACCT
**
439805 AAAGGATCAATCCCTTCCCCT
1 AAAGGATCAATCCCTTTACCT
* *
439826 AAATGATCAA-CCCTTTTCCT
1 AAAGGATCAATCCCTTTACCT
439846 A
1 A
439847 TAACGCTTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
20 9 0.26
21 26 0.74
ACGTcount: A:0.32, C:0.32, G:0.10, T:0.27
Consensus pattern (21 bp):
AAAGGATCAATCCCTTTACCT
Found at i:443206 original size:18 final size:19
Alignment explanation
Indices: 443183--443223 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
443173 TTTTTAGACT
*
443183 AAGTCAAT-GGCTAGGTTA
1 AAGTCAATAGGCTAGGTCA
*
443201 AAGTCAATAGTCTAGGTCA
1 AAGTCAATAGGCTAGGTCA
443220 AAGT
1 AAGT
443224 TAACGATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (19 bp):
AAGTCAATAGGCTAGGTCA
Found at i:451286 original size:13 final size:14
Alignment explanation
Indices: 451268--451303 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
451258 TATTACCAAA
451268 ATCACATAATTAT-
1 ATCACATAATTATC
451281 ATCACATAATTATC
1 ATCACATAATTATC
*
451295 ATCAAATAA
1 ATCACATAA
451304 CATCAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCACATAATTATC
Found at i:451417 original size:5 final size:5
Alignment explanation
Indices: 451407--451436 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
451397 TTCACATTAC
451407 TAAAA TAAAA TAAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA TAAA
451437 GAGTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:451424 original size:11 final size:10
Alignment explanation
Indices: 451407--451436 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
451397 TTCACATTAC
451407 TAAAATAAAA
1 TAAAATAAAA
451417 TAAAAATAAAA
1 T-AAAATAAAA
451428 TAAAATAAA
1 TAAAATAAA
451437 GAGTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:452645 original size:3 final size:3
Alignment explanation
Indices: 452639--452679 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
452629 TATTATTATT
* *
452639 TAA TAA TAA TAA T-A TAA TGA TAA TAA T-A TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
452680 GGGGTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:452656 original size:14 final size:14
Alignment explanation
Indices: 452639--452679 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
452629 TATTATTATT
452639 TAATAATAATAATA
1 TAATAATAATAATA
*
452653 TAATGATAATAATA
1 TAATAATAATAATA
*
452667 TAATAATGATAAT
1 TAATAATAATAAT
452680 GGGGTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:452661 original size:17 final size:17
Alignment explanation
Indices: 452641--452679 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
452631 TTATTATTTA
452641 ATAATAATA-ATATAATG
1 ATAATAATATA-ATAATG
452658 ATAATAATATAATAATG
1 ATAATAATATAATAATG
452675 ATAAT
1 ATAAT
452680 GGGGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
ATAATAATATAATAATG
Found at i:453287 original size:177 final size:175
Alignment explanation
Indices: 452981--453909 Score: 1396
Period size: 177 Copynumber: 5.3 Consensus size: 175
452971 TCAAGTGAGA
* * *
452981 TAAAAT-TTATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGTCCATAGGATTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGG-CCGTAGGATTTACAAATC
* * *
453045 AAAAAACCCCCAAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCATTTGTTAGGCTTAACTTCCTT
65 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCC-TTTGTTAGGCTTAGCTTCCTT
*
453110 TAACAACTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
129 TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
*
453157 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCTGTAGGACTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCC-GTAGGATTTACAAATC
* * *
453222 AAGAAACCCCCGAAGGCTTGGTTTTTTAGTTGTCAAGGAACCTCTTTGTTAGGCTTAGTTTCCTT
65 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACC-CTTTGTTAGGCTTAGCTTCCTT
* *
453287 TAACAGCTCTTTTGAGATAATTAGTAAACCCACAAAGGCTTGGTTTC
129 TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
* * * *
453334 TAAAATATCATTTGAAAACATCCTGCATTTAAGGTCTTATGGATGGCTCATAGGATTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGC-CGTAGGATTTACAAATC
* * *
453399 AAGAAA-CCCTGAAGGCTT-GTTTCTTAATTGTCAATGAACCTCTTTGTTAGGCTTAGCTTCCTT
65 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACC-CTTTGTTAGGCTTAGCTTCCTT
* *
453462 TAACAGCTTTTTTGAGATAATTAGTAAACCCCCGAAGTCTTGGTTTC
129 TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
* *
453509 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCGTAGGACTTATAAATCA
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCGTAGGATTTACAAATCA
* *
453574 AGAAACCCCTGAAGGCTTGGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTT
66 AGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAA-CCCTTTGTTAGGCTTAGCTTCCTTT
* ** * *
453639 TACAATTCTTTTGAGATAATTAGTAAACCCCTGAAGACTTGGTTTC
130 AACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
*
453685 TAAAATCTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGATTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGG-CCGTAGGATTTACAAATC
* *
453750 AAGAAACCCCCGAAGGCTTAGTTTATTAGTTGTCAAGTAACCCTTTTGTTAGGCTTAGCTTCCTT
65 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCC-TTTGTTAGGCTTAGCTTCCTT
** * *
453815 TAATGGCTCTTTTGAGATAATTAGTAAACCCCCAAAAGCTTGGTTTC
129 TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
* *
453862 TAAAATCTCATTTGGAAACATCCTGCACTAAAGGTCTTATGGATGGCC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCC
453910 CGAAGGTCTT
Statistics
Matches: 686, Mismatches: 58, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
174 20 0.03
175 140 0.20
176 150 0.22
177 374 0.55
178 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (175 bp):
TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCGTAGGATTTACAAATCA
AGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCTTTGTTAGGCTTAGCTTCCTTTA
ACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
Found at i:455752 original size:51 final size:52
Alignment explanation
Indices: 455572--455766 Score: 277
Period size: 52 Copynumber: 3.8 Consensus size: 52
455562 TATCCCAACC
* * * * *
455572 TTTTCATGCTGGTGTGAGCTTTCAAGATGCCCCACATGGATTACTTTTGTCT
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCT
* *
455624 TTTTCATGCTGATGTGAGCCTTCAAAATGCCCCACATGGATTACTTCTATCT
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCT
* **
455676 TTTTCATGCTGATGTGAGCATTCAAGATACCCTTCATGGATTACTTCTATC-
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCT
*
455727 TTTTCATGTTGATGTGAGCCTTCAAGATA-CCCACATGGAT
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGAT
455767 AATATGGACC
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
50 9 0.07
51 27 0.21
52 93 0.72
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (52 bp):
TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCT
Found at i:457276 original size:1 final size:1
Alignment explanation
Indices: 457265--457334 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
457255 CTATTTTCTC
* * * * * * * * * *
457265 TTTTCTTTTTTTCTTTTTTTTTTCTTTTTTTTCTATTTTTTCTTCTTTTTTCTTCTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
457330 TTTTT
1 TTTTT
457335 CTGATGGATG
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:457284 original size:9 final size:9
Alignment explanation
Indices: 457265--457336 Score: 99
Period size: 9 Copynumber: 7.7 Consensus size: 9
457255 CTATTTTCTC
457265 TTTTCTTTT
1 TTTTCTTTT
*
457274 TTTCTTTTTT
1 TTT-TCTTTT
457284 TTTTCTTTT
1 TTTTCTTTT
*
457293 TTTTCTATT
1 TTTTCTTTT
457302 TTTTCTTCTT
1 TTTTCTT-TT
457312 TTTTCTTCTT
1 TTTTCTT-TT
457322 TTTTCTTTT
1 TTTTCTTTT
457331 TTTTCT
1 TTTTCT
457337 GATGGATGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
9 30 0.53
10 27 0.47
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:457285 original size:10 final size:10
Alignment explanation
Indices: 457265--457334 Score: 83
Period size: 10 Copynumber: 7.3 Consensus size: 10
457255 CTATTTTCTC
457265 TTTTCTTTTT
1 TTTTCTTTTT
*
457275 TTCT-TTTTT
1 TTTTCTTTTT
457284 TTTTC-TTTT
1 TTTTCTTTTT
*
457293 TTTTC-TATT
1 TTTTCTTTTT
*
457302 TTTTCTTCTT
1 TTTTCTTTTT
*
457312 TTTTCTTCTT
1 TTTTCTTTTT
457322 TTTTCTTTTT
1 TTTTCTTTTT
457332 TTT
1 TTT
457335 CTGATGGATG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
9 25 0.47
10 28 0.53
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:457297 original size:42 final size:38
Alignment explanation
Indices: 457246--457336 Score: 119
Period size: 38 Copynumber: 2.3 Consensus size: 38
457236 TTTGTTCTTA
* *
457246 TTTTCTTTTCTATTTTCTCTTTTCTTTTTTTCTTTTTTTTTTC
1 TTTT-TTTTCTATTTT-T-TCTTC-TTTTTTC-TTCTTTTTTC
457289 TTTTTTTTCTATTTTTTCTTCTTTTTTCTTCTTTTTTC
1 TTTTTTTTCTATTTTTTCTTCTTTTTTCTTCTTTTTTC
457327 TTTTTTTTCT
1 TTTTTTTTCT
457337 GATGGATGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
38 19 0.41
39 7 0.15
40 4 0.09
41 1 0.02
42 11 0.24
43 4 0.09
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.82
Consensus pattern (38 bp):
TTTTTTTTCTATTTTTTCTTCTTTTTTCTTCTTTTTTC
Found at i:457332 original size:7 final size:7
Alignment explanation
Indices: 457232--457332 Score: 77
Period size: 7 Copynumber: 14.4 Consensus size: 7
457222 CTTGATTCAA
457232 TTTCTTT
1 TTTCTTT
*
457239 GTTCTTAT
1 TTTCTT-T
457247 TTTC--T
1 TTTCTTT
*
457252 TTTCTAT
1 TTTCTTT
*
457259 TTTCTCT
1 TTTCTTT
457266 TTTCTTTT
1 TTTC-TTT
457274 TTTCTTT
1 TTTCTTT
457281 TTT-TTT
1 TTTCTTT
457287 TCTT-TTT
1 T-TTCTTT
457294 TTTCTATTT
1 TTTC--TTT
*
457303 TTTCTTC
1 TTTCTTT
457310 TTT-TTT
1 TTTCTTT
*
457316 CTTCTTT
1 TTTCTTT
457323 TTTCTTT
1 TTTCTTT
457330 TTT
1 TTT
457333 TTCTGATGGA
Statistics
Matches: 77, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
5 5 0.06
6 10 0.13
7 45 0.58
8 10 0.13
9 7 0.09
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.81
Consensus pattern (7 bp):
TTTCTTT
Found at i:457334 original size:19 final size:19
Alignment explanation
Indices: 457240--457336 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
457230 AATTTCTTTG
*
457240 TTCTTATTTTCTTTTCTATT-
1 TTCTT-TTTTCTTTT-TTTTC
*
457260 TTCTCTTTTC-TTTTTTTC
1 TTCTTTTTTCTTTTTTTTC
*
457278 TTTTTTTTTTCTTTTTTTTC
1 -TTCTTTTTTCTTTTTTTTC
*
457298 -TATTTTTTCTTCTTTTTTC
1 TTCTTTTTTCTT-TTTTTTC
457317 TTCTTTTTTCTTTTTTTTC
1 TTCTTTTTTCTTTTTTTTC
457336 T
1 T
457337 GATGGATGAG
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.05
18 13 0.20
19 28 0.42
20 22 0.33
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.81
Consensus pattern (19 bp):
TTCTTTTTTCTTTTTTTTC
Found at i:457334 original size:29 final size:29
Alignment explanation
Indices: 457260--457336 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
457250 CTTTTCTATT
* *
457260 TTCTCTTTTC-TTTTTTTCTTTTTTTTTTC
1 TTCTTTTTTCTTTTTTTTC-TTCTTTTTTC
*
457289 TT-TTTTTTCTATTTTTTCTTCTTTTTTC
1 TTCTTTTTTCTTTTTTTTCTTCTTTTTTC
457317 TTCTTTTTTCTTTTTTTTCT
1 TTCTTTTTTCTTTTTTTTCT
457337 GATGGATGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 17 0.40
29 25 0.60
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (29 bp):
TTCTTTTTTCTTTTTTTTCTTCTTTTTTC
Found at i:459788 original size:42 final size:42
Alignment explanation
Indices: 459729--459817 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
459719 TCTGATTTTC
459729 TTTTTGCCATTATCTTGAAAACCTTGTGAATGTTCGTATAGA
1 TTTTTGCCATTATCTTGAAAACCTTGTGAATGTTCGTATAGA
*
459771 TTTTTGTCATTATCTTGAAAACCTTGTGAATGTTCGTATAGA
1 TTTTTGCCATTATCTTGAAAACCTTGTGAATGTTCGTATAGA
459813 TTTTT
1 TTTTT
459818 TCTTTGTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (42 bp):
TTTTTGCCATTATCTTGAAAACCTTGTGAATGTTCGTATAGA
Found at i:465322 original size:3 final size:3
Alignment explanation
Indices: 465316--465368 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
465306 TATTATTATT
465316 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
465362 TGA TAA T
1 TAA TAA T
465369 GGGGCAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:465343 original size:14 final size:14
Alignment explanation
Indices: 465316--465362 Score: 85
Period size: 14 Copynumber: 3.3 Consensus size: 14
465306 TATTATTATT
465316 TAATAATAATAATAA
1 TAATAAT-ATAATAA
465331 TAATAATATAATAA
1 TAATAATATAATAA
465345 TAATAATATAATAA
1 TAATAATATAATAA
465359 TAAT
1 TAAT
465363 GATAATGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 25 0.78
15 7 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:481362 original size:18 final size:18
Alignment explanation
Indices: 481321--481363 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
481311 AAATTCAAGT
* *
481321 CAATTTTCTTTCAATATT
1 CAATTTTCTTTCAAGATA
481339 CAATTTTCTTTCAAGA-A
1 CAATTTTCTTTCAAGATA
481356 CACATTTT
1 CA-ATTTT
481364 GTGCTCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.30, C:0.19, G:0.02, T:0.49
Consensus pattern (18 bp):
CAATTTTCTTTCAAGATA
Found at i:490423 original size:17 final size:17
Alignment explanation
Indices: 490401--490439 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
490391 TATAACTCCT
490401 TTCTTCCTTTTACTTTC
1 TTCTTCCTTTTACTTTC
490418 TTCTTCCTTTTACTTTC
1 TTCTTCCTTTTACTTTC
490435 TTCTT
1 TTCTT
490440 TCTCTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCTTCCTTTTACTTTC
Found at i:491078 original size:17 final size:17
Alignment explanation
Indices: 491056--491094 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
491046 TTAAAAGAGA
491056 AAGAAGAAAGTAAAAGG
1 AAGAAGAAAGTAAAAGG
491073 AAGAAGAAAGTAAAAGG
1 AAGAAGAAAGTAAAAGG
491090 AAGAA
1 AAGAA
491095 AGGAGTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (17 bp):
AAGAAGAAAGTAAAAGG
Found at i:492708 original size:21 final size:21
Alignment explanation
Indices: 492684--492727 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
492674 ATATGTAGGA
* *
492684 TATGGTGTGGGATTTAGGGTT
1 TATGGTGTGGAATTTAGGATT
*
492705 TATGGTTTGGAATTTAGGATT
1 TATGGTGTGGAATTTAGGATT
492726 TA
1 TA
492728 GTATTTAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.45
Consensus pattern (21 bp):
TATGGTGTGGAATTTAGGATT
Found at i:497483 original size:28 final size:29
Alignment explanation
Indices: 497426--497488 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
497416 TAATAGTTAT
* *
497426 AATTTAGAGATAAAATTAAAATGTTTAAA
1 AATTTAGAAATAAAATTAAAATGTTAAAA
*
497455 AATTTA-AAATAAAAGTTATAAT-TTAAAA
1 AATTTAGAAATAAAA-TTAAAATGTTAAAA
497483 ACATTT
1 A-ATTT
497489 GATGTAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (29 bp):
AATTTAGAAATAAAATTAAAATGTTAAAA
Found at i:497564 original size:15 final size:16
Alignment explanation
Indices: 497546--497580 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
497536 GGGTAAATTA
497546 TACTATTTA-CCATTT
1 TACTATTTAGCCATTT
*
497561 TACTATTTAGCCCTTT
1 TACTATTTAGCCATTT
497577 TACT
1 TACT
497581 TTTGTCATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (16 bp):
TACTATTTAGCCATTT
Found at i:498201 original size:20 final size:22
Alignment explanation
Indices: 498176--498215 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
498166 TAACATAAGC
498176 AATAATTTTA-A-ATTTTTATT
1 AATAATTTTATATATTTTTATT
498196 AATAATTTTATATATTTTTA
1 AATAATTTTATATATTTTTA
498216 ACATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AATAATTTTATATATTTTTATT
Found at i:498221 original size:21 final size:19
Alignment explanation
Indices: 498176--498224 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 19
498166 TAACATAAGC
498176 AATAATTTTAAATTTTTATT
1 AATAATTTTAAATTTTTA-T
498196 AATAATTTTATATATTTTTA-
1 AATAATTTTA-A-ATTTTTAT
498216 ACATAATTT
1 A-ATAATTT
498225 ATTTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.42
21 8 0.31
22 7 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AATAATTTTAAATTTTTAT
Found at i:499084 original size:26 final size:24
Alignment explanation
Indices: 499048--499111 Score: 96
Period size: 26 Copynumber: 2.7 Consensus size: 24
499038 GAATAGAGAT
499048 AAAAAAAAGTGATCCATGTACCCA
1 AAAAAAAAGTGATCCATGTACCCA
499072 AAAAAATATAGTGATCCATGTACCC-
1 AAAAAA-A-AGTGATCCATGTACCCA
499097 -AAAAAAAGTGATCCA
1 AAAAAAAAGTGATCCA
499112 AGTTGGATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.24
23 1 0.03
24 11 0.29
25 1 0.03
26 16 0.42
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (24 bp):
AAAAAAAAGTGATCCATGTACCCA
Found at i:500126 original size:34 final size:34
Alignment explanation
Indices: 500083--500161 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
500073 TTCATTACTC
500083 TAGAGAAGTAGGGTAATCGAGTGTATATTCCTGA
1 TAGAGAAGTAGGGTAATCGAGTGTATATTCCTGA
500117 TAGAGAAGTAGGGTAATCGAGTGTATATTCCTGA
1 TAGAGAAGTAGGGTAATCGAGTGTATATTCCTGA
* *
500151 TATAGATGTAG
1 TAGAGAAGTAG
500162 CCAATTCTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (34 bp):
TAGAGAAGTAGGGTAATCGAGTGTATATTCCTGA
Found at i:505160 original size:43 final size:44
Alignment explanation
Indices: 505021--505164 Score: 166
Period size: 44 Copynumber: 3.3 Consensus size: 44
505011 TAACCTTAAA
* * * *
505021 CTCGTAAGCTTATTTTATCAAAATACTTACCATTTGCACCATAAG
1 CTCGTAAGCTTACTTTA-CCATATACTTACCATTTGTACCATAAG
* * * *
505066 CTCGCAAGTTTATTTTACCATATACTTACCATTTGTACCATAAA
1 CTCGTAAGCTTACTTTACCATATACTTACCATTTGTACCATAAG
**
505110 CTCGTAAGCTTACTTTACCATATACTTGTCATTAT-T-CCATAAG
1 CTCGTAAGCTTACTTTACCATATACTTACCATT-TGTACCATAAG
505153 CTCGTAAGCTTA
1 CTCGTAAGCTTA
505165 TTTGCATACT
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
43 18 0.21
44 52 0.60
45 16 0.19
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.38
Consensus pattern (44 bp):
CTCGTAAGCTTACTTTACCATATACTTACCATTTGTACCATAAG
Found at i:505315 original size:40 final size:40
Alignment explanation
Indices: 505271--505349 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
505261 ACCGTAGTGC
* *
505271 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCAAAGTGTAT
505311 TACACATAAGGTCATGCCCACCATATACACCAAAGTGTA
1 TACACATAAGGTCATGCCCACCATATACACCAAAGTGTA
505350 CTATAAACCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (40 bp):
TACACATAAGGTCATGCCCACCATATACACCAAAGTGTAT
Found at i:506257 original size:28 final size:28
Alignment explanation
Indices: 506193--506257 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
506183 AACAACACAT
* *
506193 CAATTTTCTAAAATTTACAAAATGATCCT
1 CAATTTT-TAAAACTTACAAAATGATCCC
* *
506222 CAACTTTTAAAACTTACAAAATGGTCCC
1 CAATTTTTAAAACTTACAAAATGATCCC
506250 CAATTTTT
1 CAATTTTT
506258 CTAAGGCTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 25 0.81
29 6 0.19
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (28 bp):
CAATTTTTAAAACTTACAAAATGATCCC
Found at i:512391 original size:44 final size:44
Alignment explanation
Indices: 512294--512448 Score: 206
Period size: 44 Copynumber: 3.5 Consensus size: 44
512284 CCATTTATTA
* *
512294 ACCATAAACTCGTAAGCTTATTTTATCAAAATACTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCATTTGT
*
512339 ACCATAAGCTCGTAAGCTTATTTTACTATATACTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTGT
* * * **
512383 ACCGTAAGCTCGTAAGCTTACTTTACCATATACTTGTCATTAT-T
1 ACCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATT-TGT
512427 -CCATAAGCTCGTAAGCTTATTT
1 ACCATAAGCTCGTAAGCTTATTT
512449 GCATGCTTAC
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
43 20 0.20
44 54 0.55
45 25 0.25
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (44 bp):
ACCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTGT
Found at i:512601 original size:40 final size:40
Alignment explanation
Indices: 512546--512624 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
512536 ACCGTAGTGC
* *
512546 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAA
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAA
512586 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTA
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTA
512625 CTATAAACCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAA
Found at i:513658 original size:83 final size:82
Alignment explanation
Indices: 513505--513669 Score: 303
Period size: 83 Copynumber: 2.0 Consensus size: 82
513495 ATTTTTCCAT
* *
513505 AATTTTTATCACTTAACCATTCATGGCCGAAATTTAAAGAACAAGTTGTAGAAAGATTAAACATG
1 AATTTTTACCACTAAACCATTCATGGCCGAAATTTAAAGAACAAGTTGTAGAAAGATTAAACATG
513570 TTCTAATCATAAATCAA
66 TTCTAATCATAAATCAA
513587 AATTTTTACCACTCAAACCATTCATGGCCGAAATTTAAAGAACAAGTTGTAGAAAGATTAAACAT
1 AATTTTTACCACT-AAACCATTCATGGCCGAAATTTAAAGAACAAGTTGTAGAAAGATTAAACAT
513652 GTTCTAATCATAAATCAA
65 GTTCTAATCATAAATCAA
513670 GCTTGAAAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
82 12 0.15
83 68 0.85
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (82 bp):
AATTTTTACCACTAAACCATTCATGGCCGAAATTTAAAGAACAAGTTGTAGAAAGATTAAACATG
TTCTAATCATAAATCAA
Found at i:515511 original size:20 final size:20
Alignment explanation
Indices: 515486--515534 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
515476 CCCATAGGAA
*
515486 TATCGATACTCGA-GGTTCAG
1 TATCGATACTC-ACGATTCAG
515506 TATCGATACTCACGATTCAG
1 TATCGATACTCACGATTCAG
515526 TATCGATAC
1 TATCGATAC
515535 AAAAGTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (20 bp):
TATCGATACTCACGATTCAG
Found at i:520826 original size:22 final size:22
Alignment explanation
Indices: 520798--521097 Score: 66
Period size: 22 Copynumber: 13.0 Consensus size: 22
520788 TTACTTTATA
520798 TTTTTCTTATTTTATTTGT-TTT
1 TTTTTCTTATTTTATTT-TATTT
520820 TTTTTCTT-TTCTTATTTTATTT
1 TTTTTCTTATT-TTATTTTATTT
* *
520842 TTTATATTAGTTTTATTTATATATT
1 TTTTTCTTA-TTTTATTT-TAT-TT
*
520867 TATTTTC--ATTTGTATTTT-TCT
1 T-TTTTCTTATTT-TATTTTATTT
* *
520888 CTTGT-TTA-TTTA-TTTATTT
1 TTTTTCTTATTTTATTTTATTT
* * * *** * *
520907 ATTATGTATATACAATTATTAGTA
1 TTTTTCT-TATTTTATT-TTATTT
520931 TTTTTCTTTATTTTATTCTTATTT
1 TTTTTC-TTATTTTATT-TTATTT
* * *
520955 TTATT-TTATTTTGCTCGTTATCTT
1 TTTTTCTTATTTT-AT-TTTAT-TT
*
520979 TATTTTGATTATTTTA-TTTATTT
1 T-TTTT-CTTATTTTATTTTATTT
* *
521002 TTCTTCATTATTTTATTTCTTTTGT
1 TTTTTC-TTATTTTATTT-TATT-T
*
521027 TTTTTATGT-TCTTTATTTTATTT
1 TTTTTCT-TAT-TTTATTTTATTT
** *
521050 AATTT-TTATCTTTGTTTTATTT
1 TTTTTCTTAT-TTTATTTTATTT
* *
521072 TTTATGTCTTTTCTTTATCTTATTT
1 TTT-T-TCTTAT-TTTATTTTATTT
521097 T
1 T
521098 CCTTTTTTTC
Statistics
Matches: 201, Mismatches: 44, Indels: 63
0.65 0.14 0.20
Matches are distributed among these distances:
18 3 0.01
19 7 0.03
20 6 0.03
21 8 0.04
22 58 0.29
23 26 0.13
24 48 0.24
25 35 0.17
26 3 0.01
27 7 0.03
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTTTCTTATTTTATTTTATTT
Found at i:520877 original size:18 final size:17
Alignment explanation
Indices: 520831--520877 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
520821 TTTTCTTTTC
*
520831 TTATTTTATTTTTTATA
1 TTATTTTATTTTATATA
520848 TTAGTTTTA-TTTATATA
1 TTA-TTTTATTTTATATA
520865 TTTATTTTCATTT
1 -TTATTTT-ATTT
520878 GTATTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 14 0.56
18 9 0.36
19 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TTATTTTATTTTATATA
Found at i:520946 original size:21 final size:22
Alignment explanation
Indices: 520922--520966 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
520912 GTATATACAA
520922 TTATTAGTATTTTT-CTTTATT
1 TTATTAGTATTTTTACTTTATT
** *
520943 TTATTCTTATTTTTATTTTATT
1 TTATTAGTATTTTTACTTTATT
520965 TT
1 TT
520967 GCTCGTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (22 bp):
TTATTAGTATTTTTACTTTATT
Found at i:521016 original size:18 final size:19
Alignment explanation
Indices: 520955--521019 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 19
520945 ATTCTTATTT
*
520955 TTAT-TTTATTTTGC-TCG
1 TTATATTTATTTTGCTTCA
* *
520972 TTATCTTTATTTTGATT-A
1 TTATATTTATTTTGCTTCA
* *
520990 TTTTATTTATTTTTCTTCA
1 TTATATTTATTTTGCTTCA
521009 TTAT-TTTATTT
1 TTATATTTATTT
521020 CTTTTGTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.11
18 29 0.76
19 5 0.13
ACGTcount: A:0.17, C:0.08, G:0.05, T:0.71
Consensus pattern (19 bp):
TTATATTTATTTTGCTTCA
Found at i:521045 original size:16 final size:15
Alignment explanation
Indices: 520991--521151 Score: 53
Period size: 16 Copynumber: 9.8 Consensus size: 15
520981 TTTTGATTAT
*
520991 TTTATTTATT-TTTC
1 TTTATTTTTTATTTC
*
521005 TTCATTATTTTATTTC
1 TTTATT-TTTTATTTC
*
521021 TTTTGTTTTTTATGTTC
1 -TTTATTTTTTAT-TTC
521038 TTTATTTTATTTAATTT-
1 TTTA-TTT-TTT-ATTTC
*
521055 TTATCTTTGTTTTATTT-
1 TT-T-ATT-TTTTATTTC
* *
521072 TTTATGTCTTTTCTTTA
1 TTTAT-T-TTTTATTTC
*
521089 TCTTATTTTCCTTTTTTTC
1 T-TTA-TTT--TTTATTTC
521108 ATTTA-TTTTTATTTCC
1 -TTTATTTTTTATTT-C
521124 TTTATTTTTT-TTTC
1 TTTATTTTTTATTTC
521138 TTTAGTTTATTTAT
1 TTTA-TTT-TTTAT
521152 CTTCATTAGC
Statistics
Matches: 113, Mismatches: 12, Indels: 41
0.68 0.07 0.25
Matches are distributed among these distances:
14 10 0.09
15 20 0.18
16 31 0.27
17 23 0.20
18 15 0.13
19 13 0.12
20 1 0.01
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTATTTTTTATTTC
Found at i:521095 original size:52 final size:52
Alignment explanation
Indices: 520987--521151 Score: 130
Period size: 52 Copynumber: 3.2 Consensus size: 52
520977 TTTATTTTGA
* *
520987 TTATTTTATTTATTTTTCTTCATTATTTTATTTCTTTTGTTTTTTATGTTCT
1 TTATTTTATTTATTTTTCATCATTATTTTATTTCTTTTGTCTTTTATGTTCT
* * * *
521039 TTATTTTATTTAATTTTT-ATCTTTGTTTTATTT-TTTATGTCTTTTCT-TTAT
1 TTATTTTATTT-ATTTTTCATCATTATTTTATTTCTTT-TGTCTTTTATGTTCT
** * * *
521090 CTTATTTTCCTT-TTTTTCAT--TTATTTTTATTTCCTTTAT-TTTT-TTTTCT
1 -TTATTTTATTTATTTTTCATCATTA-TTTTATTTCTTTTGTCTTTTATGTTCT
*
521139 TTAGTTTATTTAT
1 TTATTTTATTTAT
521152 CTTCATTAGC
Statistics
Matches: 90, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
48 9 0.10
49 10 0.11
50 15 0.17
51 10 0.11
52 40 0.44
53 6 0.07
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (52 bp):
TTATTTTATTTATTTTTCATCATTATTTTATTTCTTTTGTCTTTTATGTTCT
Found at i:521112 original size:24 final size:24
Alignment explanation
Indices: 521080--521131 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
521070 TTTTTATGTC
521080 TTTTCTTTATCTTAT-TTTCCTTT-
1 TTTTCTTTAT-TTATATTTCCTTTA
*
521103 TTTTCATTTATTTTTATTTCCTTTA
1 TTTTC-TTTATTTATATTTCCTTTA
521128 TTTT
1 TTTT
521132 TTTTTCTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 8 0.32
24 13 0.52
25 4 0.16
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTCTTTATTTATATTTCCTTTA
Found at i:521130 original size:19 final size:19
Alignment explanation
Indices: 521108--521151 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
521098 CCTTTTTTTC
*
521108 ATTTATTTTTATTTCCTTT
1 ATTTATTTTTATTTACTTT
* * *
521127 ATTTTTTTTTCTTTAGTTT
1 ATTTATTTTTATTTACTTT
521146 ATTTAT
1 ATTTAT
521152 CTTCATTAGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (19 bp):
ATTTATTTTTATTTACTTT
Found at i:521746 original size:17 final size:18
Alignment explanation
Indices: 521724--521772 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
521714 GGTTCATATT
*
521724 CAGATTCCAATTCC-TGA
1 CAGATTCCAATTCCTTCA
521741 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
521759 CAGATTCCAATTCC
1 CAGATTCCAATTCC
521773 CTCATAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.29, C:0.33, G:0.08, T:0.31
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:524821 original size:26 final size:26
Alignment explanation
Indices: 524792--524875 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
524782 CTATAATGTT
524792 AAAATATAGTGATATATATAGTTTTG
1 AAAATATAGTGATATATATAGTTTTG
* *
524818 -AAA-ATAGTGTATTATATATAATTTTAA
1 AAAATATAGTG-A-TATATATAGTTTT-G
524845 AAAATATTA-T-ATATATATAGTTTTG
1 AAAATA-TAGTGATATATATAGTTTTG
*
524870 GAAATA
1 AAAATA
524876 AGTACATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
24 6 0.13
25 9 0.19
26 24 0.51
27 1 0.02
28 3 0.06
29 2 0.04
30 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (26 bp):
AAAATATAGTGATATATATAGTTTTG
Found at i:524824 original size:52 final size:52
Alignment explanation
Indices: 524767--524875 Score: 130
Period size: 52 Copynumber: 2.1 Consensus size: 52
524757 ATATATATAT
* *
524767 AAATAGTATAGTATTCTATAATGTTAAAATATAGT-GATATATATAGTTTTGA
1 AAATAGTATAGTA-TATATAATGTTAAAAAATAGTAGATATATATAGTTTTGA
* * * * * *
524819 AAATAGTGTATTATATATAATTTTAAAAAATATTATATATATATAGTTTTGG
1 AAATAGTATAGTATATATAATGTTAAAAAATAGTAGATATATATAGTTTTGA
524871 AAATA
1 AAATA
524876 AGTACATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 17 0.35
52 31 0.65
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.43
Consensus pattern (52 bp):
AAATAGTATAGTATATATAATGTTAAAAAATAGTAGATATATATAGTTTTGA
Found at i:524920 original size:31 final size:29
Alignment explanation
Indices: 524803--524921 Score: 99
Period size: 26 Copynumber: 4.2 Consensus size: 29
524793 AAATATAGTG
* *
524803 ATATATATAGTTTTGAAAAT-AGT-GTAT
1 ATATATATAGTTTTGGAAATAAGTATTAT
* *
524830 -TATATATAATTTT--AAA-AAATATTAT
1 ATATATATAGTTTTGGAAATAAGTATTAT
*
524855 ATATATATAGTTTTGGAAATAAGTACATTTT
1 ATATATATAGTTTTGGAAATAAGT--ATTAT
524886 ATATATTATAGTTTT-GAAATTAAGTATTAGT
1 ATATA-TATAGTTTTGGAAA-TAAGTATTA-T
524917 ATATA
1 ATATA
524922 AAATACAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
24 5 0.07
25 3 0.04
26 24 0.32
28 3 0.04
29 3 0.04
30 3 0.04
31 19 0.26
32 14 0.19
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (29 bp):
ATATATATAGTTTTGGAAATAAGTATTAT
Found at i:531473 original size:27 final size:26
Alignment explanation
Indices: 531425--531480 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
531415 TAGTATTTTT
* *
531425 AATATATAGTTATATATGTGTATATTA
1 AATATATAGTAATATATATGTATA-TA
531452 AATATAT-GTAATATTATATGTATATA
1 AATATATAGTAATA-TATATGTATATA
531478 AAT
1 AAT
531481 TTTATCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (26 bp):
AATATATAGTAATATATATGTATATA
Done.