Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006047.1 Hibiscus syriacus cultivar Beakdansim tig00014304_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: 680228
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:268077 original size:120 final size:120
Alignment explanation
Indices: 267847--268064 Score: 258
Period size: 120 Copynumber: 1.8 Consensus size: 120
267837 TGGAGGAGCA
* * * * *
267847 GGTGGATATGGAGGTGGTGGCGGTAAAGGTGGTGGTGGTGGTAGTGGAGGTGGAGCTTCAGGGTA
1 GGTGGACATGGAGGTGGTGGCGGCAAAGGTGGTGGTAGTGGGAGTGGAGGTGGAGCTGCAGGGTA
** * *
267912 TGGAAGTGGAAGTGGGGAAGGCAGTGGGGCTGGCGGTGGAGCTGGTAATGGTGGT
66 TGGAAGTGGAAGTGGAAAAGGCAGTGGCGCTGGCGATGGAGCTGGTAATGGTGGT
*** * * *
267967 GGTGGACATGGAGGTGGTGGCGGCGGTGGTGGTGGTAGTGGGGGTGGGGGTGGAGCTGCTGGG-A
1 GGTGGACATGGAGGTGGTGGCGGCAAAGGTGGTGGTAGTGGGAGTGGAGGTGGAGCTGCAGGGTA
* * *
268031 GTGGAAGTGGAGGTGGAAAAGGCGGTGGCTCTGG
66 -TGGAAGTGGAAGTGGAAAAGGCAGTGGCGCTGG
268065 GTATGGCTCT
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
119 1 0.01
120 79 0.99
ACGTcount: A:0.16, C:0.07, G:0.56, T:0.21
Consensus pattern (120 bp):
GGTGGACATGGAGGTGGTGGCGGCAAAGGTGGTGGTAGTGGGAGTGGAGGTGGAGCTGCAGGGTA
TGGAAGTGGAAGTGGAAAAGGCAGTGGCGCTGGCGATGGAGCTGGTAATGGTGGT
Found at i:268120 original size:24 final size:24
Alignment explanation
Indices: 268093--268139 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
268083 TGGTTCCGGA
* *
268093 GGTGGAGGAGGCGGTGGTGGTGGT
1 GGTGGAGGAGGCGGAGGTAGTGGT
268117 GGTGGAGGAGGCGGAGGTAGTGG
1 GGTGGAGGAGGCGGAGGTAGTGG
268140 AGGGGCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.04, G:0.66, T:0.17
Consensus pattern (24 bp):
GGTGGAGGAGGCGGAGGTAGTGGT
Found at i:273981 original size:16 final size:16
Alignment explanation
Indices: 273960--273996 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
273950 AATCATGACG
273960 TGATATTATCTTACGA
1 TGATATTATCTTACGA
273976 TGATATTATCTTACGA
1 TGATATTATCTTACGA
273992 TGATA
1 TGATA
273997 CACCAACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (16 bp):
TGATATTATCTTACGA
Found at i:287397 original size:185 final size:184
Alignment explanation
Indices: 286981--287462 Score: 454
Period size: 185 Copynumber: 2.6 Consensus size: 184
286971 AAATGTATTT
* * * * * ** *
286981 TATTATTTTAAACAATTAATTTAATATTATATTAATATATCATAAAAAATGTTTAAACCATGAGC
1 TATTATTTTGAACAATTAATTTAATATTACATTAATAAATCATAGAAAATGATTAAATTATGGGC
* * * ** *
287046 CATCGATTATAAAAGTAGAAAGTATGAACTATTTTATAAAATTTAAAAATTAGGGGCCCCTAGTT
66 CATAGATTATAAAAGTAGAAAGTAGGAACTATTTTATAAAATTAAAAAATTAGGAACCCCTAATT
* * *
287111 ATAAACCTCGATAAAAAACTAAAAAAAAGTCCCTATAGAACGAAAAATATATTA
131 ATAAACCTCGAGAAAAAACTAAAAAAAAGTCCCTATAGAACGAAAAATAGACTA
* * * * *
287165 TATTATTTTGAAAAAAATAATTTAATATTACATTAATGAACCATAGAAGATGATTAAATTATGGG
1 TATTATTTTG-AACAATTAATTTAATATTACATTAATAAATCATAGAAAATGATTAAATTATGGG
* * * *
287230 CTCTTAG-TTATAAAAGTAGAAAGTAGGGACTATTTTATAAAATTGAAAAATAGTTAGGAATCCT
65 C-CATAGATTATAAAAGTAGAAAGTAGGAACTATTTTATAAAATT-AAAAA-A-TTAGGAACCCC
* ** ** * * * *
287294 TAATTATAAATCTTTAGCGAAAACTCAAAAATAG-CCTTATAGAATG-AAAATAGACTA
126 TAATTATAAACCTCGAGAAAAAACTAAAAAAAAGTCCCTATAGAACGAAAAATAGACTA
*
287351 TATTATTTTGAACAATTAATTTAATATTACATTAACAAATCATAGAAAAAAT-ATTAAATTATGG
1 TATTATTTTGAACAATTAATTTAATATTACATTAATAAATCATAG--AAAATGATTAAATTATGG
* * * * ** *
287415 TTCC-TCA-ATTATAAAAATAAAAAATAATAAATATTTTATAAAATTAAA
64 -GCCAT-AGATTATAAAAGTAGAAAGTAGGAACTATTTTATAAAATTAAA
287463 CTTTTTCCAT
Statistics
Matches: 239, Mismatches: 49, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
184 9 0.04
185 112 0.47
186 70 0.29
187 16 0.07
188 32 0.13
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.34
Consensus pattern (184 bp):
TATTATTTTGAACAATTAATTTAATATTACATTAATAAATCATAGAAAATGATTAAATTATGGGC
CATAGATTATAAAAGTAGAAAGTAGGAACTATTTTATAAAATTAAAAAATTAGGAACCCCTAATT
ATAAACCTCGAGAAAAAACTAAAAAAAAGTCCCTATAGAACGAAAAATAGACTA
Found at i:289182 original size:60 final size:60
Alignment explanation
Indices: 289115--289227 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
289105 AACATAATGA
* *
289115 ATAGTTGG-GTGACCATTTTGCAACTTTTAATAGTCGA-GAGACTTAATAAAACAACATTCT
1 ATAGTTGGAG-GAACATTTTACAACTTTTAATAGTCGATG-GACTTAATAAAACAACATTCT
* *
289175 ATAGTTGGAGGAATATTTTATAACTTTTAATAGTCGATGGACTTAATAAAACA
1 ATAGTTGGAGGAACATTTTACAACTTTTAATAGTCGATGGACTTAATAAAACA
289228 GTACCCTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
60 45 0.96
61 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (60 bp):
ATAGTTGGAGGAACATTTTACAACTTTTAATAGTCGATGGACTTAATAAAACAACATTCT
Found at i:289336 original size:12 final size:12
Alignment explanation
Indices: 289319--289345 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
289309 GATGAAATAA
289319 TTATTTTATTTT
1 TTATTTTATTTT
289331 TTATTTTATTTT
1 TTATTTTATTTT
289343 TTA
1 TTA
289346 AATATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:289575 original size:32 final size:32
Alignment explanation
Indices: 289505--289584 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
289495 TATGCATTGT
* * *
289505 ATCATCACCGAT-TACACGTGATATGTACCAC
1 ATCATCACTGATGTACACATGATATGTAACAC
*
289536 ATCATCACTGATGTACACATGATATGTAATAC
1 ATCATCACTGATGTACACATGATATGTAACAC
* * *
289568 GTTATCACTAATGTACA
1 ATCATCACTGATGTACA
289585 TATAACATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 11 0.27
32 30 0.73
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (32 bp):
ATCATCACTGATGTACACATGATATGTAACAC
Found at i:306586 original size:37 final size:38
Alignment explanation
Indices: 306555--306629 Score: 105
Period size: 40 Copynumber: 1.9 Consensus size: 38
306545 AAATTTTGAA
306555 CGATGTACTAAAATAAAACAAAAACTAAAATTTTTAACAG
1 CGATGTACTAAAATAAAACAAAAACT-AAA-TTTTAACAG
* * *
306595 CGATGTACTAAAATGATACAAATACTAAATTTTAA
1 CGATGTACTAAAATAAAACAAAAACTAAATTTTAA
306630 GTATGATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 6 0.19
39 3 0.09
40 23 0.72
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (38 bp):
CGATGTACTAAAATAAAACAAAAACTAAATTTTAACAG
Found at i:308132 original size:30 final size:34
Alignment explanation
Indices: 308083--308144 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
308073 TCAACACATA
308083 AAAAATTAATAATATTAATA-ATT-TATTTTTTT
1 AAAAATTAATAATATTAATATATTATATTTTTTT
*
308115 AAAAA-TAA-AATCTTAATATATTATATTTTT
1 AAAAATTAATAATATTAATATATTATATTTTT
308145 CGATTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 9 0.33
31 6 0.22
32 12 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (34 bp):
AAAAATTAATAATATTAATATATTATATTTTTTT
Found at i:314104 original size:31 final size:31
Alignment explanation
Indices: 314066--314215 Score: 229
Period size: 31 Copynumber: 5.0 Consensus size: 31
314056 GGGTCGAGGG
314066 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
314097 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
314128 TTACCTATG-TCTTC-GGA-ATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
314156 TTACCTATGTTCTTCGGGAC-TATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
314186 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
314216 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 3, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
28 20 0.18
29 8 0.07
30 34 0.30
31 50 0.45
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:314161 original size:59 final size:59
Alignment explanation
Indices: 314066--314215 Score: 230
Period size: 59 Copynumber: 2.5 Consensus size: 59
314056 GGGTCGAGGG
*
314066 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTC-GGA-ATATGGACTGTTTACCTATGTTCTTCGGGAC-TATGGACTGA
314128 TTACCTATG-TCTTCGGAATATGGACTGTTTACCTATGTTCTTCGGGACTATGGACTGA
1 TTACCTATGTTCTTCGGAATATGGACTGTTTACCTATGTTCTTCGGGACTATGGACTGA
*
314186 TTACCTAGGTTCTTCGGAATCTATGGACTG
1 TTACCTATGTTCTTCGGAA--TATGGACTG
314216 GTCCTTCGGG
Statistics
Matches: 83, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
58 17 0.20
59 40 0.48
60 3 0.04
61 14 0.17
62 9 0.11
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (59 bp):
TTACCTATGTTCTTCGGAATATGGACTGTTTACCTATGTTCTTCGGGACTATGGACTGA
Found at i:318451 original size:31 final size:31
Alignment explanation
Indices: 318374--318525 Score: 231
Period size: 31 Copynumber: 5.0 Consensus size: 31
318364 GGGTCGAGGG
318374 TTACCTATGTTCTTCGGG--ATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
318403 TTACCTATGTTTCTTCGGGACATATGGACTGT
1 TTACCTATG-TTCTTCGGGACATATGGACTGT
318435 TTACCTATGTTCTTC-GGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
318465 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
318496 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
318526 GACCTTCGGG
Statistics
Matches: 115, Mismatches: 3, Indels: 8
0.91 0.02 0.06
Matches are distributed among these distances:
29 9 0.08
30 39 0.34
31 46 0.40
32 21 0.18
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:318478 original size:61 final size:62
Alignment explanation
Indices: 318374--318513 Score: 239
Period size: 61 Copynumber: 2.3 Consensus size: 62
318364 GGGTCGAGGG
* *
318374 TTACCTATGTTCTTCGG-GATATGGACTGTTTACCTATGTTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGACATATGGACTGTTTACCTATGTTTCTTCGGGACATATGGACTGA
318435 TTACCTATGTTCTTCGGACATATGGACTGTTTACCTATG-TTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGACATATGGACTGTTTACCTATGTTTCTTCGGGACATATGGACTGA
*
318496 TTACCTAGGTTCTTCGGA
1 TTACCTATGTTCTTCGGA
318514 ATCTATGGAC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
61 55 0.73
62 20 0.27
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGACATATGGACTGTTTACCTATGTTTCTTCGGGACATATGGACTGA
Found at i:320377 original size:14 final size:15
Alignment explanation
Indices: 320358--320387 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
320348 TAGCTGGACA
320358 GGCGGATGCGG-GCG
1 GGCGGATGCGGTGCG
320372 GGCGGATGCGGTGCG
1 GGCGGATGCGGTGCG
320387 G
1 G
320388 AATCCACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.07, C:0.20, G:0.63, T:0.10
Consensus pattern (15 bp):
GGCGGATGCGGTGCG
Found at i:321782 original size:37 final size:37
Alignment explanation
Indices: 321669--321782 Score: 96
Period size: 37 Copynumber: 3.1 Consensus size: 37
321659 CTCGTGCTCC
*
321669 TAACATTCTTGGTGTTCAAA-CTCAAGACCTCAAGGAA
1 TAACATTCTTGATGTTCAAACCTC-AGACCTCAAGGAA
* * **
321706 TAACA-ACAATTTAT-TT---ACCATCAGACCTCAAGGGT
1 TAACATTC--TTGATGTTCAAACC-TCAGACCTCAAGGAA
*
321741 TAACATTCTTGATGTTCAAACCTCAGACCTCAAAGAA
1 TAACATTCTTGATGTTCAAACCTCAGACCTCAAGGAA
321778 TAACA
1 TAACA
321783 CTCCATTACC
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
34 5 0.09
35 19 0.33
36 4 0.07
37 24 0.41
38 6 0.10
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (37 bp):
TAACATTCTTGATGTTCAAACCTCAGACCTCAAGGAA
Found at i:335147 original size:26 final size:26
Alignment explanation
Indices: 335107--335158 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
335097 TAATTATGAA
335107 AAAATTAAAAGTTTAAATACTAAACC
1 AAAATTAAAAGTTTAAATACTAAACC
*
335133 AAAATTAATAA-TTTAGATACTAAACC
1 AAAATTAA-AAGTTTAAATACTAAACC
335159 TCTAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.29
Consensus pattern (26 bp):
AAAATTAAAAGTTTAAATACTAAACC
Found at i:335166 original size:20 final size:20
Alignment explanation
Indices: 335141--335178 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
335131 CCAAAATTAA
*
335141 TAATTTAGATACTAAACCTC
1 TAATTTAAATACTAAACCTC
335161 TAATTTAAATACTAAACC
1 TAATTTAAATACTAAACC
335179 AACATTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (20 bp):
TAATTTAAATACTAAACCTC
Found at i:335389 original size:267 final size:267
Alignment explanation
Indices: 334914--335701 Score: 1560
Period size: 267 Copynumber: 3.0 Consensus size: 267
334904 GTTTTTATTT
334914 CATTAGTATCTCGTTGTTGAAAATTTAATGCATTTAGTACCTAAACTATCAGTTTTGGTCTAGTA
1 CATTAGTATCTCGTTGTTGAAAATTTAATGCATTTAGTACCTAAACTATCAGTTTTGGTCTAGTA
334979 TCTAAACTTTTAATTTTTTTCAAAAACGTTAAATTTTGAATGGGAGTACAAAAATGAAACAAAAA
66 TCTAAACTTTTAATTTTTTTCAAAAACGTTAAATTTTGAATGGGAGTACAAAAATGAAACAAAAA
335044 CTAAAGTTTTAATTGCATGATACTAAAATAAAACAAAAATTAAACTTTAGATATAATTATGAAAA
131 CTAAAGTTTTAATTGCATGATACTAAAATAAAACAAAAATTAAACTTTAGATATAATTATGAAAA
335109 AATTAAAAGTTTAAATACTAAACCAAAATTAATAATTTAGATACTAAACCTCTAATTTAAATACT
196 AATTAAAAGTTTAAATACTAAACCAAAATTAATAATTTAGATACTAAACCTCTAATTTAAATACT
335174 AAACCAA
261 AAACCAA
335181 CATTAGTATCTCGTTGTTGAAAATTTAATGCATTTAGTACCTAAACTATCAGTTTTGGTCTAGTA
1 CATTAGTATCTCGTTGTTGAAAATTTAATGCATTTAGTACCTAAACTATCAGTTTTGGTCTAGTA
335246 TCTAAACTTTTAATTTTTTTCAAAAACGTTAAA-TTTGAATGGGAGTACAAAAATGAAACAAAAA
66 TCTAAACTTTTAATTTTTTTCAAAAACGTTAAATTTTGAATGGGAGTACAAAAATGAAACAAAAA
335310 CTAAAGTTTTAATTGCATGATACTAAAATAAAACAAAAATTAAACTTTAGATATAATTATGAAAA
131 CTAAAGTTTTAATTGCATGATACTAAAATAAAACAAAAATTAAACTTTAGATATAATTATG-AAA
335375 AAATTAAAAGTTTAAATACTAAACCAAAATTAATAATTTAGATACTAAACCTCTAATTTAAATAC
195 AAATTAAAAGTTTAAATACTAAACCAAAATTAATAATTTAGATACTAAACCTCTAATTTAAATAC
335440 TAAACCAA
260 TAAACCAA
335448 CATTAGTATCTCGTTGTTGAAAATTTAATGCATTTAGTACCTAAACTATCAGTTTTGGTCTAGTA
1 CATTAGTATCTCGTTGTTGAAAATTTAATGCATTTAGTACCTAAACTATCAGTTTTGGTCTAGTA
335513 TCTAAACTTTTAATTTTTTTCAAAAACGTTAAATTTTGAATGGGAGTACAAAAATGAAACAAAAA
66 TCTAAACTTTTAATTTTTTTCAAAAACGTTAAATTTTGAATGGGAGTACAAAAATGAAACAAAAA
335578 CTAAAGTTTTAATTGCATGATACTAAAATAAAACAAAAATTAAACTTTAGATATAATTATGAAAA
131 CTAAAGTTTTAATTGCATGATACTAAAATAAAACAAAAATTAAACTTTAGATATAATTATGAAAA
335643 AATTAAAAGTTTAAATACTAAACCAAAATTAATAATTTAGATACTAAACCTCTAATTTA
196 AATTAAAAGTTTAAATACTAAACCAAAATTAATAATTTAGATACTAAACCTCTAATTTA
335702 CTTTAAAAAA
Statistics
Matches: 519, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
266 92 0.18
267 335 0.65
268 92 0.18
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (267 bp):
CATTAGTATCTCGTTGTTGAAAATTTAATGCATTTAGTACCTAAACTATCAGTTTTGGTCTAGTA
TCTAAACTTTTAATTTTTTTCAAAAACGTTAAATTTTGAATGGGAGTACAAAAATGAAACAAAAA
CTAAAGTTTTAATTGCATGATACTAAAATAAAACAAAAATTAAACTTTAGATATAATTATGAAAA
AATTAAAAGTTTAAATACTAAACCAAAATTAATAATTTAGATACTAAACCTCTAATTTAAATACT
AAACCAA
Found at i:335414 original size:26 final size:26
Alignment explanation
Indices: 335374--335425 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
335364 AATTATGAAA
335374 AAAATTAAAAGTTTAAATACTAAACC
1 AAAATTAAAAGTTTAAATACTAAACC
*
335400 AAAATTAATAA-TTTAGATACTAAACC
1 AAAATTAA-AAGTTTAAATACTAAACC
335426 TCTAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.29
Consensus pattern (26 bp):
AAAATTAAAAGTTTAAATACTAAACC
Found at i:335433 original size:20 final size:20
Alignment explanation
Indices: 335408--335445 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
335398 CCAAAATTAA
*
335408 TAATTTAGATACTAAACCTC
1 TAATTTAAATACTAAACCTC
335428 TAATTTAAATACTAAACC
1 TAATTTAAATACTAAACC
335446 AACATTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (20 bp):
TAATTTAAATACTAAACCTC
Found at i:335681 original size:26 final size:26
Alignment explanation
Indices: 335641--335692 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
335631 TAATTATGAA
335641 AAAATTAAAAGTTTAAATACTAAACC
1 AAAATTAAAAGTTTAAATACTAAACC
*
335667 AAAATTAATAA-TTTAGATACTAAACC
1 AAAATTAA-AAGTTTAAATACTAAACC
335693 TCTAATTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.29
Consensus pattern (26 bp):
AAAATTAAAAGTTTAAATACTAAACC
Found at i:341520 original size:60 final size:60
Alignment explanation
Indices: 341443--341565 Score: 210
Period size: 60 Copynumber: 2.0 Consensus size: 60
341433 AACTTTTAAA
* * *
341443 AGTCGAGGGAGTTAAAAAAGTAACAATCTATAGTTGGAGGACCACTTTATAATTTATAAT
1 AGTCAAGGGAGTTAAAAAAGTAACAATCTATAGTCGGAGGAACACTTTATAATTTATAAT
*
341503 AGTCAAGGGAGTTAAAAAAGTAATAATCTATAGTCGGAGGAACACTTTATAATTTATAAT
1 AGTCAAGGGAGTTAAAAAAGTAACAATCTATAGTCGGAGGAACACTTTATAATTTATAAT
341563 AGT
1 AGT
341566 AAAAAAAAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (60 bp):
AGTCAAGGGAGTTAAAAAAGTAACAATCTATAGTCGGAGGAACACTTTATAATTTATAAT
Found at i:346987 original size:11 final size:11
Alignment explanation
Indices: 346973--347015 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
346963 AGAAACAAAT
346973 ATTATCTTATA
1 ATTATCTTATA
*
346984 ATTATC-TATT
1 ATTATCTTATA
346994 ATTATCTTATA
1 ATTATCTTATA
*
347005 ATAATCTTATA
1 ATTATCTTATA
347016 CTTGTAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTATCTTATA
Found at i:346998 original size:21 final size:21
Alignment explanation
Indices: 346972--347011 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
346962 TAGAAACAAA
*
346972 TATTATCTTATAATTATCTAT
1 TATTATCTTATAATAATCTAT
346993 TATTATCTTATAATAATCT
1 TATTATCTTATAATAATCT
347012 TATACTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATCTTATAATAATCTAT
Found at i:351489 original size:28 final size:28
Alignment explanation
Indices: 351449--351504 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
351439 GAGATATATT
351449 ATTCGCCTTCTCAAAGAATATTTTCCAC
1 ATTCGCCTTCTCAAAGAATATTTTCCAC
351477 ATTCGCCTTCTCAAAGAATATTTTCCAC
1 ATTCGCCTTCTCAAAGAATATTTTCCAC
351505 CATTTGAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (28 bp):
ATTCGCCTTCTCAAAGAATATTTTCCAC
Found at i:360337 original size:23 final size:23
Alignment explanation
Indices: 360301--360344 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
360291 CATAATTATT
360301 AAAAAAATTAAATAAAAAATACC
1 AAAAAAATTAAATAAAAAATACC
* *
360324 AAAAATATTTAATAAAAAATA
1 AAAAAAATTAAATAAAAAATA
360345 ATTTTGTATA
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:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAAAAATTAAATAAAAAATACC
Found at i:371062 original size:279 final size:278
Alignment explanation
Indices: 370519--371351 Score: 1424
Period size: 279 Copynumber: 3.0 Consensus size: 278
370509 AATAAAAAAA
* *
370519 TAAAAGCTTCAGTTGTTGTTTCATTTTAGTACTTCTGTTCAAAATTTAACGTTATGTTTTGAAAA
1 TAAAAGCTTCAGTTGTTGTTTCATTTTAGTACTTCTGTTTAAAATTTAACATTATGTTTTGAAAA
* * * * * * **
370584 TATTGAAAGTTTAGGTACTAAAAACATACCAAAATTGATAGTTCAGATACTAAACATGTTAAATT
66 TGTTGAAAGTTTTGGTA-TTAAAACAGACCAAAACTGATAGTTTAGATACTAAATGTGTTAAATT
* * * * *
370649 TTTAACATCGAATACTAAAATAAAATGAAAACTAAACGTTAAGCATGATTTTG--AAAA-AAAAA
130 TTTAACAGCGGATACTAAAATGAAATAAAAACTAAACGTTAGGCATGATTTTGAAAAAATAAAAA
370711 -TTAGATACTAAAACGGATCAAAATTGATAGTTTAAGTACTAAAAACATAACTTACCCATATTAT
195 TTTAGATACTAAAACGGATCAAAATTGATAGTTTAAGTACTAAAAACATAACTTACCCATATTAT
370775 ACTTATAAAAATAAATAGT
260 ACTTATAAAAATAAATAGT
370794 TAAAAGCTTCAGTTGTTGTTTCATTTTAGTACTTCTGTTTAAAATTTAACATTATGTTTTGAAAA
1 TAAAAGCTTCAGTTGTTGTTTCATTTTAGTACTTCTGTTTAAAATTTAACATTATGTTTTGAAAA
370859 TGTTGAAAGTTTTGGTATTAAAACAGACCAAAACTGATAGTTTAGATACTAAATGTGTTAAATTT
66 TGTTGAAAGTTTTGGTATTAAAACAGACCAAAACTGATAGTTTAGATACTAAATGTGTTAAATTT
*
370924 TTAACAGCGGATACTAAAGTGAAATAAAAACTAAACGTTAGGCATGATTTTGAAAAAAATAAAAA
131 TTAACAGCGGATACTAAAATGAAATAAAAACTAAACGTTAGGCATGATTTTG-AAAAAATAAAAA
370989 TTTAGATACTAAAACGGATCAAAATTGATAGTTTAAGTACTAAAAACATAACTTACCCATATTAT
195 TTTAGATACTAAAACGGATCAAAATTGATAGTTTAAGTACTAAAAACATAACTTACCCATATTAT
371054 ACTTATAAAAATAAATAGT
260 ACTTATAAAAATAAATAGT
371073 TAAAAGCTTTC-GTTGTTGTTTCATTTTAGTACTTCTGTTTAAAATTTAACATTATGTTTTGAAA
1 TAAAAGC-TTCAGTTGTTGTTTCATTTTAGTACTTCTGTTTAAAATTTAACATTATGTTTTGAAA
*
371137 ATGTTGAAAGTTTTGGTACTAAAACAGACCAAAACTGATAGTTTAGATACTAAATGTGTTAAATT
65 ATGTTGAAAGTTTTGGTATTAAAACAGACCAAAACTGATAGTTTAGATACTAAATGTGTTAAATT
* *
371202 TTTAACAGCGGATACTAAATTGAAATAAAAACTAAACGTTAGACATGATTTTGAAAAAATAAAAA
130 TTTAACAGCGGATACTAAAATGAAATAAAAACTAAACGTTAGGCATGATTTTGAAAAAATAAAAA
*
371267 TTTAGATACTAAAACGGATCAAAATTGATAGTTTAGGTACTAAAAACATAACTTACCCATATTAT
195 TTTAGATACTAAAACGGATCAAAATTGATAGTTTAAGTACTAAAAACATAACTTACCCATATTAT
371332 ACTTATAAAAATAAATAGT
260 ACTTATAAAAATAAATAGT
371351 T
1 T
371352 CTTTTAGATT
Statistics
Matches: 532, Mismatches: 20, Indels: 9
0.95 0.04 0.02
Matches are distributed among these distances:
274 88 0.17
275 78 0.15
277 4 0.01
278 101 0.19
279 258 0.48
280 3 0.01
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (278 bp):
TAAAAGCTTCAGTTGTTGTTTCATTTTAGTACTTCTGTTTAAAATTTAACATTATGTTTTGAAAA
TGTTGAAAGTTTTGGTATTAAAACAGACCAAAACTGATAGTTTAGATACTAAATGTGTTAAATTT
TTAACAGCGGATACTAAAATGAAATAAAAACTAAACGTTAGGCATGATTTTGAAAAAATAAAAAT
TTAGATACTAAAACGGATCAAAATTGATAGTTTAAGTACTAAAAACATAACTTACCCATATTATA
CTTATAAAAATAAATAGT
Found at i:373332 original size:60 final size:60
Alignment explanation
Indices: 373261--373376 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
373251 ATAATCAGGT
* ** *
373261 GATCATTTTGTAACTTTTAATAATTGAGGGACTTAACAAAGCAACATTCTATAGTCAAAG
1 GATCATATTGTAACTTTTAATAATCCAGGGACTTAACAAAGCAACATCCTATAGTCAAAG
* * *
373321 GATCATATTGTAACTTTTAATAATCCAGGGACTTAATAAAGTAACATCCTTTAGTC
1 GATCATATTGTAACTTTTAATAATCCAGGGACTTAACAAAGCAACATCCTATAGTC
373377 GGGGACCATT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (60 bp):
GATCATATTGTAACTTTTAATAATCCAGGGACTTAACAAAGCAACATCCTATAGTCAAAG
Found at i:373828 original size:20 final size:20
Alignment explanation
Indices: 373781--374214 Score: 413
Period size: 20 Copynumber: 21.2 Consensus size: 20
373771 AATGACCAAC
373781 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
373800 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
373820 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
373840 AAGATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
373862 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
373882 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
373904 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
373924 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
373944 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
373964 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
373986 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
374006 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
374026 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
374046 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
374066 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
374086 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
374106 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
374128 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
374148 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
* *
374168 TAATTCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
374190 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
374210 AAAAT
1 AAAAT
374215 GAGTAAATTC
Statistics
Matches: 349, Mismatches: 38, Indels: 55
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.00
19 29 0.08
20 228 0.65
21 7 0.02
22 78 0.22
23 6 0.02
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:373959 original size:82 final size:81
Alignment explanation
Indices: 373783--374214 Score: 529
Period size: 82 Copynumber: 5.3 Consensus size: 81
373773 TGACCAACAA
* ** * * ** *
373783 AATCGCAACGCGATATC--AAAACCGCAACGCGATTTAGAA-AAGCGCAACGTTGA-AAAGAAGA
1 AATCGCAACGCGAT-TCAGAAAATCGCAACGCGATTTCCAAGAATCGCAACG-CGATTCAGAAAA
373844 TCGCAACGCGATCTTCCAAG
64 TCGCAACGCGA--TTCCAAG
* *
373864 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAGAAAAT
*
373929 CGCAACGCGATT-CAGAA
65 CGCAACGCGATTCCA-AG
* *
373946 AATCGCAACGCGATTTAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAGAAAAT
374011 CGCAACGCGATTCCAAG
65 CGCAACGCGATTCCAAG
374028 AATCGCAACGCGATTCAGAAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATTCAGAAAATC
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAGAAAATC
374092 GCAACGCGATTCCAAG
66 GCAACGCGATTCCAAG
* *** *
374108 AATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTAAGAA-AATCGCAACGCGATTCAGTAA
1 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAGAAA
*
374171 TTCGCAACGCGATCTTCCAAG
63 ATCGCAACGCGA--TTCCAAG
374192 AATCGCAACGCGATTCAGAAAAT
1 AATCGCAACGCGATTCAGAAAAT
374215 GAGTAAATTC
Statistics
Matches: 313, Mismatches: 24, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
80 61 0.19
81 17 0.05
82 177 0.57
83 13 0.04
84 45 0.14
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (81 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAGAAAATC
GCAACGCGATTCCAAG
Found at i:374184 original size:62 final size:59
Alignment explanation
Indices: 373781--374214 Score: 384
Period size: 62 Copynumber: 7.1 Consensus size: 59
373771 AATGACCAAC
* * ** * * *
373781 AAAATCGCAACGCGATATCAAAACCGCAACGCGATTTAGAA-AAGCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGAT-TCAGAATCGCAACGCGATTTCCAAGAATCGCAACG-CGATTAAG
* * * ***
373840 AAGATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-TT-CATAAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGA--TT-C-AGAATCGCAACGCGATTTCCA-AGAATCGCAACGCGAT-TAAG
* *
373903 AAGAATCGCAACGCGATTCAGAAAATCGCAACGCGA-TT-CAGAAAATCGCAACGCGATTTAG
1 AA-AATCGCAACGCGATTCAG--AATCGCAACGCGATTTCCA-AGAATCGCAACGCGATTAAG
***
373964 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA-AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGA--TT-C-AGAATCGCAACGCGATTTCCAAGAATCGCAACGCGATT--AAG
*
374028 --AATCGCAACGCGATTCAGAAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG--AATCGCAACGCGATTTCCAAGAATCGCAACGCGATTAAG
374086 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATT-C-AGAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTAAG
*
374148 AAAATCGCAACGCGATTCAGTAATTCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG-AA-TCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTAAG
374210 AAAAT
1 AAAAT
374215 GAGTAAATTC
Statistics
Matches: 320, Mismatches: 25, Indels: 57
0.80 0.06 0.14
Matches are distributed among these distances:
58 4 0.01
59 18 0.06
60 77 0.24
61 16 0.05
62 183 0.57
63 5 0.02
64 17 0.05
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (59 bp):
AAAATCGCAACGCGATTCAGAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTAAG
Found at i:374321 original size:6 final size:6
Alignment explanation
Indices: 374310--374353 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
374300 GACACGTATT
*
374310 ACCACG ACCACG ACCACG ACCACG ACCACG ACCCCG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
374354 CGAGACGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.30, C:0.55, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:374866 original size:6 final size:6
Alignment explanation
Indices: 374850--374905 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
374840 TCTCGTCTCG
374850 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
374897 GGTCGT GGT
1 GGTCGT GGT
374906 AATACGTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:375057 original size:20 final size:19
Alignment explanation
Indices: 375004--375333 Score: 235
Period size: 20 Copynumber: 16.2 Consensus size: 19
374994 TTTACTCATT
375004 TTCTGAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
375022 TTCTTGGAAGATCGCGTTGCGAA
1 TTC-T-G-A-ATCGCGTTGCGAA
*
375045 TTACTGAATCGCGTTGCGATT
1 TT-CTGAATCGCGTTGCGA-A
*
375066 TTCTTAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
375084 TTCTTGGAAGATCGCGTTGCG-A
1 TTC-T-G-A-ATCGCGTTGCGAA
*
375106 TTCTTGGAATCGCGTTGCGATT
1 TTC-T-GAATCGCGTTGCGA-A
375128 TTCTGAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
*
375146 TTCTTGGAATCGCGTTGCGATT
1 TTC-T-GAATCGCGTTGCGA-A
375168 TTCTGAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
*
375186 TTCTTGGAATCGCGTTGCGATT
1 TTC-T-GAATCGCGTTGCGA-A
*
375208 TTCTTAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
375226 TTCTTGGAAGATCGCGTTGCGAA
1 TTC-T-G-A-ATCGCGTTGCGAA
*
375249 TTACTGAATCGCGTTGCGATT
1 TT-CTGAATCGCGTTGCGA-A
*
375270 TTCTTAATCGCGTTGCG-A
1 TTCTGAATCGCGTTGCGAA
*
375288 TTCTTGGAAGATCGCGTTGCGATT
1 TTC-T-G-A-ATCGCGTTGCGA-A
* *
375312 TTATGAATCGCATTGCG-A
1 TTCTGAATCGCGTTGCGAA
375330 TTCT
1 TTCT
375334 TGGAAGATCG
Statistics
Matches: 257, Mismatches: 21, Indels: 68
0.74 0.06 0.20
Matches are distributed among these distances:
18 21 0.08
19 6 0.02
20 138 0.54
21 15 0.06
22 64 0.25
23 9 0.04
24 4 0.02
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (19 bp):
TTCTGAATCGCGTTGCGAA
Found at i:375077 original size:62 final size:61
Alignment explanation
Indices: 375001--375412 Score: 439
Period size: 62 Copynumber: 6.7 Consensus size: 61
374991 GAATTTACTC
375001 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAATTAC-T-GAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCG-ATT-CTTGGAATCGCGTTGCG
*
375063 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
375125 ATTTTCTGAATCGCGTTGCGATTCTTGG-AATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* ***
375185 ATTCTT-GGAATCGCGTTGCGATT-TTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * ***
375247 AATTACTGAATCGCGTTGCGATT-TTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * * **** *
375309 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGTGTTGCGA-TCTTCTTTTCAACGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGATTCTTGGAATC-GCGTTGCG
* * * *
375371 CTTTTCTAAATCGCGTTGCGGTT-TT-GATATCGCGTTGCGATT
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATT
375413 TTGTTGGTCA
Statistics
Matches: 307, Mismatches: 30, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
59 15 0.05
60 66 0.21
61 15 0.05
62 193 0.63
63 7 0.02
64 11 0.04
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (61 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:375110 original size:40 final size:39
Alignment explanation
Indices: 375008--375352 Score: 323
Period size: 40 Copynumber: 8.4 Consensus size: 39
374998 CTCATTTTCT
375008 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAATTAC-T-
1 GAATCGCGTTGCGATTCTT-G-A-ATCGCGTTGCG-ATT-CTTG
375050 GAATCGCGTTGCGATTTTCTT-AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGA--TTCTTGAATCGCGTTGCGATTCTTG
*
375090 GAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTT-GAATCGCGTTGCGATTCTT-G
*
375132 GAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-GAATCGCGTTGCGATTCTT-G
375172 GAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGATTCTT-GAATCGCGTTGCGA--TTCTTG
375213 -AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAATTAC-T-
1 GAATCGCGTTGCGATTCTT-G-A-ATCGCGTTGCG-ATT-CTTG
375254 GAATCGCGTTGCGATTTTCTT-AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGA--TTCTTGAATCGCGTTGCGATTCTTG
* *
375294 GAAGATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCT-TGAATCGCGTTGCGATTCTTG
*
375336 GAAGATCGTGTTGCGAT
1 G-A-ATCGCGTTGCGAT
375353 CTTCTTTTCA
Statistics
Matches: 274, Mismatches: 4, Indels: 50
0.84 0.01 0.15
Matches are distributed among these distances:
38 2 0.01
39 8 0.03
40 124 0.45
41 12 0.04
42 115 0.42
43 3 0.01
44 10 0.04
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (39 bp):
GAATCGCGTTGCGATTCTTGAATCGCGTTGCGATTCTTG
Found at i:375370 original size:42 final size:40
Alignment explanation
Indices: 375256--375352 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 40
375246 GAATTACTGA
* *
375256 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTATCAAT--CGTTGCGATTCTTGGAAG
*
375298 ATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTATCAATCG--TTGCGATTCTTGGAAG
*
375340 ATCGTGTTGCGAT
1 ATCGCGTTGCGAT
375353 CTTCTTTTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 2 0.04
42 48 0.96
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.37
Consensus pattern (40 bp):
ATCGCGTTGCGATTTTATCAATCGTTGCGATTCTTGGAAG
Found at i:375387 original size:20 final size:20
Alignment explanation
Indices: 375364--375414 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
375354 TTCTTTTCAA
* *
375364 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTTCTGAATCG
*
375384 CGTTGCG-GTTT-TGATATCG
1 CGTTGCGATTTTCTGA-ATCG
375403 CGTTGCGATTTT
1 CGTTGCGATTTT
375415 GTTGGTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCTGAATCG
Found at i:379079 original size:33 final size:33
Alignment explanation
Indices: 379036--379135 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
379026 GTACGCCTAT
* *
379036 TTGGACGGAGAGCAGCTCATGAAGCACTTCCAG
1 TTGGATGGAGAGCAGGTCATGAAGCACTTCCAG
379069 TTGGATGGAGAGCAGGTCATGAAGCACTTCCAG
1 TTGGATGGAGAGCAGGTCATGAAGCACTTCCAG
*
379102 TTGGATGGAGAGCAGGTTATGAAGCACTTCCAG
1 TTGGATGGAGAGCAGGTCATGAAGCACTTCCAG
379135 T
1 T
379136 AGGTGCTATG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (33 bp):
TTGGATGGAGAGCAGGTCATGAAGCACTTCCAG
Found at i:384726 original size:48 final size:48
Alignment explanation
Indices: 384641--384738 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
384631 CTTTTAACTC
*
384641 TTCTACCTTCTAATAGAGAAAAAAAGTTCTAACATCAATCAACTACCA
1 TTCTACCTTCTAATAGAGAAAAAAAGTTCTAACATCAATCAACGACCA
* * * * * *
384689 TTCTACCTTCTAATAGAGAGAGAAGGTTTTGATATCAATCAACGACCA
1 TTCTACCTTCTAATAGAGAAAAAAAGTTCTAACATCAATCAACGACCA
384737 TT
1 TT
384739 AATAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (48 bp):
TTCTACCTTCTAATAGAGAAAAAAAGTTCTAACATCAATCAACGACCA
Found at i:391459 original size:2 final size:2
Alignment explanation
Indices: 391454--391523 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
391444 TTATGTAAAC
391454 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
391496 AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
391524 AAAGATAAAC
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:394309 original size:182 final size:182
Alignment explanation
Indices: 393981--394431 Score: 701
Period size: 182 Copynumber: 2.5 Consensus size: 182
393971 TTTTTACTAT
*
393981 CGGTTTTGTCATTTCGAGATCGATTTTGTCATA-TTTTACATGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAC
* * * * * *
394045 ATTTTTATAAGGTATCGATAC-TTATTTGCACTATAACTTTTTTTCTTTTAAATTTCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCACTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
* *
394109 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTTTAC
131 CGATACTTATAATAAAGTATCAACACTATCAACATATCCGGTAGCACTTTAC
* * *
394161 CGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAC
* *
394226 ATTTTTATAAAGTATCGACACTTTATTAGCGCTGT-ACATTCTTCTCTTTTAAATTCCAAAAGTG
66 ATTTTTATAAAGTATCGACACTTTATTAGCACTATAAC-TTCTTCTCTTTTAAATTCCAAAAGTG
394290 TCGATACTTATAATAAAGTATCAACACTATCAACATATCCGGTAGCACTTTAC
130 TCGATACTTATAATAAAGTATCAACACTATCAACATATCCGGTAGCACTTTAC
** ** *
394343 ATGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAC
394408 ATTTTTATAAAGTATCGACACTTT
66 ATTTTTATAAAGTATCGACACTTT
394432 CAATATATAC
Statistics
Matches: 246, Mismatches: 22, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
180 31 0.13
181 50 0.20
182 165 0.67
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACACTTTATTAGCACTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
CGATACTTATAATAAAGTATCAACACTATCAACATATCCGGTAGCACTTTAC
Found at i:394502 original size:112 final size:112
Alignment explanation
Indices: 394302--394687 Score: 554
Period size: 112 Copynumber: 3.5 Consensus size: 112
394292 GATACTTATA
* * * *
394302 ATAAAGTATCAACACTATCAACATATCCGGTAGC-ACTTTACATGTTTTGTCATTTATAGACC-G
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGA-TTTACCTGTTTTGTCATTTATAGACCAG
*
394365 ATTTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
65 -TTTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTT
*
394414 ATAAAGTATCGACACTTTCAATATATACGGTAGCGATTTACCTGTTTTGTCATTTATAGACCAGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATAGACCAGT
* *
394479 TTTGTCATTTTTTTACATTTTATAGTGTTATGGATAGATACATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTT
*
394526 ATAAAGTATCGACACTTTC-A-ATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGA-CATG
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATAGACCA-G
* * *
394588 TTTT-T-TTTTTTTTACCTGTTATATTGTTATGAATAGATACATTTTT
65 TTTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTT
* * *
394634 AT-AAGTATCGACACTTTTAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTT
394688 TTTACCTGTT
Statistics
Matches: 252, Mismatches: 17, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
107 15 0.06
108 39 0.15
109 35 0.14
110 41 0.16
111 1 0.00
112 119 0.47
113 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATAGACCAGT
TTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTT
Found at i:394738 original size:90 final size:88
Alignment explanation
Indices: 394595--394775 Score: 274
Period size: 90 Copynumber: 2.0 Consensus size: 88
394585 ATGTTTTTTT
*
394595 TTTTTTACCTGTTATATTGTTATGAATAGATACATTTTTATAAGTATCGACACTTTTAATATATC
1 TTTTTTACCTGTTATATTGTTATGAATAGATACATTTTTATAAGTATAGACAC-TTTAA-ATATC
*
394660 CGGTAGCGCTTTACTTGTTTTGTCA
64 CGGTAGCGCTTTACATGTTTTGTCA
* * * *
394685 TTTTTTACCTGTTATATTGTTATGGATAGATA-TTTTTTATAAAGTATAGACACTTTCAATATCT
1 TTTTTTACCTGTTATATTGTTATGAATAGATACATTTTTAT-AAGTATAGACACTTTAAATATCC
394749 GGTAGCGCTTTACATGTTTTGTCA
65 GGTAGCGCTTTACATGTTTTGTCA
394773 TTT
1 TTT
394776 ATAAACTAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
88 31 0.37
89 11 0.13
90 42 0.50
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (88 bp):
TTTTTTACCTGTTATATTGTTATGAATAGATACATTTTTATAAGTATAGACACTTTAAATATCCG
GTAGCGCTTTACATGTTTTGTCA
Found at i:394741 original size:197 final size:200
Alignment explanation
Indices: 394477--394845 Score: 543
Period size: 197 Copynumber: 1.9 Consensus size: 200
394467 TTATAGACCA
* *
394477 GTTTTGTCATTTTTTTACATTTTATAGTGTTATGGATAGATACATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACATGTTATAGTGTTATGGATAGATACATTTTTATAAAGTATAGACACT
* * **
394542 TTCAATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGAC-ATGTTT-TTTTTTTTTTACCT
66 TTCAATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAAACAAT-TTTGTCATTTTTTTACCT
394605 GTTATATTGTTATGAAT-AGATACATTTT-TATAAGTATCGACACTTTTAATATATCCGGTAGCG
130 GTTATATTGTTATGAATCA-ATACATTTTATA-AAGTATCGACACTTTTAATATATCCGGTAGCG
394668 CTTTACTT
193 CTTTACTT
* * *
394676 GTTTTGTCA-TTTTTTACCTGTTATATTGTTATGGATAGATA-TTTTTTATAAAGTATAGACACT
1 GTTTTGTCATTTTTTTACATGTTATAGTGTTATGGATAGATACATTTTTATAAAGTATAGACACT
* *
394739 TTCAATATCTGGTAGCGCTTTACATGTTTTGTCATTTATAAACTAATTTTGTCATTTTTTTACTT
66 TTCAATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAAAC-AATTTTGTCATTTTTTTACCT
* *
394804 GTTATATTGTTATGGATCAATATATTTTATAAAGTATCGACA
130 GTTATATTGTTATGAATCAATACATTTTATAAAGTATCGACA
394846 TAAACCGACA
Statistics
Matches: 152, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
197 60 0.39
198 32 0.21
199 57 0.38
200 3 0.02
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (200 bp):
GTTTTGTCATTTTTTTACATGTTATAGTGTTATGGATAGATACATTTTTATAAAGTATAGACACT
TTCAATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAAACAATTTTGTCATTTTTTTACCTG
TTATATTGTTATGAATCAATACATTTTATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTT
TACTT
Found at i:395830 original size:21 final size:21
Alignment explanation
Indices: 395804--395853 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
395794 GCTACTTTAG
*
395804 ACTGTCATGTTAACACCGTGA
1 ACTGTCATGCTAACACCGTGA
* *
395825 ACTGTCATGCTAATATCGTGA
1 ACTGTCATGCTAACACCGTGA
*
395846 ACTATCAT
1 ACTGTCAT
395854 ATCAGTACTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (21 bp):
ACTGTCATGCTAACACCGTGA
Found at i:396287 original size:17 final size:17
Alignment explanation
Indices: 396265--396310 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
396255 TATAGAATTT
396265 TTGAATCATTCAGACCA
1 TTGAATCATTCAGACCA
396282 TTGAATCATTCAGACCA
1 TTGAATCATTCAGACCA
396299 TTGAATCATTCA
1 TTGAATCATTCA
396311 TGTCAACGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (17 bp):
TTGAATCATTCAGACCA
Found at i:396696 original size:31 final size:32
Alignment explanation
Indices: 396660--396719 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
396650 TTGCGATCAT
* *
396660 AAAATTTGAT-AAATTTACTGATAATTTTGTA
1 AAAATTTGATAAAAATTAATGATAATTTTGTA
396691 AAAATTTGATAAAAATTAATGATAATTTT
1 AAAATTTGATAAAAATTAATGATAATTTT
396720 TTAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (32 bp):
AAAATTTGATAAAAATTAATGATAATTTTGTA
Found at i:408182 original size:63 final size:63
Alignment explanation
Indices: 408105--408224 Score: 213
Period size: 63 Copynumber: 1.9 Consensus size: 63
408095 CTTTGATCAG
* *
408105 AATCCATCTGTTATATTTAAATTGTTAATTTAACTTATCTATCATATTATCTGTTACCTTGAC
1 AATCCATCTGTTATATTTAAATTATTAATTTAACTTATCTATCATATTATCTATTACCTTGAC
*
408168 AATCCATCTGTTATATTTGAATTATTAATTTAACTTATCTATCATATTATCTATTAC
1 AATCCATCTGTTATATTTAAATTATTAATTTAACTTATCTATCATATTATCTATTAC
408225 AGTTATCTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (63 bp):
AATCCATCTGTTATATTTAAATTATTAATTTAACTTATCTATCATATTATCTATTACCTTGAC
Found at i:408217 original size:25 final size:24
Alignment explanation
Indices: 408200--408261 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
408190 TATTAATTTA
408200 ACTTATCTATCATATTATCTATTAC
1 ACTTATCTATCATATTAT-TATTAC
*
408225 AGTTATCTATCATATTATTTATTAC
1 ACTTATCTATCATATTA-TTATTAC
* *
408250 AGTTATCAATCA
1 ACTTATCTATCA
408262 CAATAAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 33 0.97
26 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (24 bp):
ACTTATCTATCATATTATTATTAC
Found at i:408219 original size:12 final size:12
Alignment explanation
Indices: 408202--408242 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
408192 TTAATTTAAC
408202 TTATCTATCATA
1 TTATCTATCATA
* *
408214 TTATCTATTACA
1 TTATCTATCATA
408226 GTTATCTATCATA
1 -TTATCTATCATA
408239 TTAT
1 TTAT
408243 TTATTACAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.32, C:0.15, G:0.02, T:0.51
Consensus pattern (12 bp):
TTATCTATCATA
Found at i:408232 original size:13 final size:13
Alignment explanation
Indices: 408214--408256 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
408204 ATCTATCATA
408214 TTATCTATTACAG
1 TTATCTATTACAG
* *
408227 TTATCTATCATA-
1 TTATCTATTACAG
*
408239 TTATTTATTACAG
1 TTATCTATTACAG
408252 TTATC
1 TTATC
408257 AATCACAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (13 bp):
TTATCTATTACAG
Found at i:416765 original size:55 final size:55
Alignment explanation
Indices: 416601--416787 Score: 261
Period size: 56 Copynumber: 3.4 Consensus size: 55
416591 CCATATTTTC
* * * *
416601 TAGATATATTCGATTTCGGACCTTCTATTTTTATGCTTCTTAATGACAACAACTAA
1 TAGATATACTCGATTTCGG-GCTCCTATTTTTATGCTTCTTAATGACAACAACTGA
416657 T-GCATATACTCGATTTCGAGGC-CTCTATTTTTATGCTTCTTAATGACAACAACTGA
1 TAG-ATATACTCGATTTCG-GGCTC-CTATTTTTATGCTTCTTAATGACAACAACTGA
* *
416713 TAGATATACTCGATTTTGGGCTCCTATTTTTATGCTTATTAATGACAACAACTGA
1 TAGATATACTCGATTTCGGGCTCCTATTTTTATGCTTCTTAATGACAACAACTGA
*
416768 TAAATATACTCGATTTCGGG
1 TAGATATACTCGATTTCGGG
416788 GGTTCTATTT
Statistics
Matches: 118, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
55 53 0.45
56 63 0.53
57 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (55 bp):
TAGATATACTCGATTTCGGGCTCCTATTTTTATGCTTCTTAATGACAACAACTGA
Found at i:424090 original size:40 final size:41
Alignment explanation
Indices: 424014--424098 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 41
424004 GTGGGACTAT
* * *
424014 TTCATCAGTGTTCCCTTTTCCCTTCTACATTGATTCATGTTA
1 TTCATCAGTGTTCCC-TTTCCCTCCCACATTAATTCATGTTA
*
424056 TTCATCAGTTTTCCC-TTCCCTCCCACATTAATTCATGTTA
1 TTCATCAGTGTTCCCTTTCCCTCCCACATTAATTCATGTTA
424096 TTC
1 TTC
424099 TTCTGATGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 25 0.64
42 14 0.36
ACGTcount: A:0.18, C:0.29, G:0.07, T:0.46
Consensus pattern (41 bp):
TTCATCAGTGTTCCCTTTCCCTCCCACATTAATTCATGTTA
Found at i:432518 original size:56 final size:57
Alignment explanation
Indices: 432374--432522 Score: 176
Period size: 58 Copynumber: 2.6 Consensus size: 57
432364 AACGAGAGTT
* * * * *
432374 ATAATTTAGAGAAGAAATTGAAAT-ATTAAAAAATTCAAGGATTAGTTTACAATAAGTC
1 ATAATTTAAAGATGAAATTGAAATAATT-AAAAGTTCAAGGACTAATTTACAAT-AGTC
* * * * *
432432 ATAAATTAAGGATGAAATTGAAATATTTAAAAGTTCAAGGACTAATTTAGAAT-TTC
1 ATAATTTAAAGATGAAATTGAAATAATTAAAAGTTCAAGGACTAATTTACAATAGTC
432488 ATAATTTAAAGATGAAATTGAAATAATTAAAAGTT
1 ATAATTTAAAGATGAAATTGAAATAATTAAAAGTT
432523 TGAAAGTTGT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
56 34 0.44
58 41 0.53
59 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33
Consensus pattern (57 bp):
ATAATTTAAAGATGAAATTGAAATAATTAAAAGTTCAAGGACTAATTTACAATAGTC
Found at i:433035 original size:20 final size:20
Alignment explanation
Indices: 433006--433043 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
432996 TAGAAATTTA
*
433006 ATCCCAAACGGCTAGAAATC
1 ATCCCAAACGACTAGAAATC
*
433026 ATCCCTAACGACTAGAAA
1 ATCCCAAACGACTAGAAA
433044 CGACCACATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.29, G:0.13, T:0.16
Consensus pattern (20 bp):
ATCCCAAACGACTAGAAATC
Found at i:433636 original size:3 final size:3
Alignment explanation
Indices: 433628--433664 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
433618 ATTAGCAAAG
433628 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
433665 AAGTTAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:433770 original size:59 final size:60
Alignment explanation
Indices: 433693--433816 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
433683 GTCCTCAAAG
* * ** * *
433693 TATGACCCTTATTTTAAATTGGCCCT-AAACTTTTAAAT-GTTCCAATTTAATCCCTAAAC
1 TATGACCCTAATTATAAATTAACCCTCAAACATTTAAATAGTT-CAATTTAATCACTAAAC
* * *
433752 TATGACCCTAATTATAAATTAATCCTCAAACATTTGAATAGTTCAATTTCATCACTAAAC
1 TATGACCCTAATTATAAATTAACCCTCAAACATTTAAATAGTTCAATTTAATCACTAAAC
433812 TATGA
1 TATGA
433817 ATTTCATTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
59 21 0.39
60 30 0.56
61 3 0.06
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.37
Consensus pattern (60 bp):
TATGACCCTAATTATAAATTAACCCTCAAACATTTAAATAGTTCAATTTAATCACTAAAC
Found at i:434154 original size:60 final size:59
Alignment explanation
Indices: 434051--434167 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 59
434041 TATTCGTAGC
* * *
434051 TTAGAGATGAAATTAGAATGTTCAACAAGTTTAAGGAATAATTTAGAATGAGAGTCATAAT
1 TTAGAGATGAAATTAGAATATTCAACAAGTTTAAGGAAGAATTTAAAATG-G-GTCATAAT
* * * *
434112 TTAGGGATTAAATTAGAATATTTAA-AAGTTTAAGGACGAATTTAAAATGGGTCATA
1 TTAGAGATGAAATTAGAATATTCAACAAGTTTAAGGAAGAATTTAAAATGGGTCATA
434168 GTTTGAGGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 6 0.12
59 1 0.02
60 21 0.43
61 21 0.43
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (59 bp):
TTAGAGATGAAATTAGAATATTCAACAAGTTTAAGGAAGAATTTAAAATGGGTCATAAT
Found at i:440062 original size:20 final size:21
Alignment explanation
Indices: 440037--440075 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
440027 GTAATATCTA
440037 ATATATTTAT-AAAATTATAT
1 ATATATTTATAAAAATTATAT
*
440057 ATATATTTTTAAAAATTAT
1 ATATATTTATAAAAATTAT
440076 TGTCTTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATATTTATAAAAATTATAT
Found at i:451030 original size:3 final size:3
Alignment explanation
Indices: 451015--451094 Score: 72
Period size: 3 Copynumber: 26.0 Consensus size: 3
451005 AATTTTAATC
* * * *
451015 TTA TTA ATA TTA TTA TTA TTA ATG TTA TTA TTA TTA TTA TTA TT- TTGT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* *
451063 TTA TTT TTGT TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA -TTA TTA TTA TTA TTA TTA
451095 ATTACATATT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.03
3 54 0.84
4 8 0.12
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:451248 original size:24 final size:25
Alignment explanation
Indices: 451188--451247 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
451178 CATATAACTC
451188 TAACCCTAAAACAAATTAGGGGTTT
1 TAACCCTAAAACAAATTAGGGGTTT
451213 TAACCCTAAAACAAATTA-GGGTTT
1 TAACCCTAAAACAAATTAGGGGTTT
451237 TAAACCCTAAA
1 T-AACCCTAAA
451248 CCAATCTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 7 0.21
25 27 0.79
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (25 bp):
TAACCCTAAAACAAATTAGGGGTTT
Found at i:463038 original size:2 final size:2
Alignment explanation
Indices: 463033--463071 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
463023 ACACACACAC
463033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
463072 GCAAAAATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:473304 original size:165 final size:167
Alignment explanation
Indices: 473032--473373 Score: 474
Period size: 165 Copynumber: 2.0 Consensus size: 167
473022 AATAATGTCA
* * * *
473032 AAGTTTCAAGCTTTGTGAGGGCTTTTCTCTCAATAATTGTGAGAGAAGAAGAAGGGGGTAGCTAC
1 AAGTTTCAAACTTTGTGAGGGCTTTTCTCTCAAGAATTATGAGAAAAGAAGAAGGGGGTAGCTAC
**
473097 CATGTTAGAAAAATGGCAGAGTTAACTACCACATCATCAAAAAC-T-AGGTAATTGTAGGGGCCT
66 CATGTTAGAAAAATGGCAGAGTTAACTACCACATCATCAAAAACATGAGGTAACGGTAGGGGCCT
* ** *
473160 TACTAAAAATGAACTAAAAGTTCGATGATTGTATTGT
131 TAATAAAAACAAACTAAAAGTTCGATGATTGTATTAT
* * *
473197 AAGTTTCAAACTTTGTGAGGGTTTTTCTCTCAAGAATTATGAGAAAAGAAG-ATGGGGTATCTAC
1 AAGTTTCAAACTTTGTGAGGGCTTTTCTCTCAAGAATTATGAGAAAAGAAGAAGGGGGTAGCTAC
**
473261 CATGTTAGCAAAAATGGCAGAGTTAACTGTCACATCATCAAAAACTAATATGAGGTAACGGTAGG
66 CATGTTAG-AAAAATGGCAGAGTTAACTACCACATCATCAAAAAC----ATGAGGTAACGGTAGG
*
473326 GGCGTTAATAAAAACAAACTAAAAGTTCGATGATTGTATTAT
126 GGCCTTAATAAAAACAAACTAAAAGTTCGATGATTGTATTAT
473368 AAGTTT
1 AAGTTT
473374 TAAAAGTTAG
Statistics
Matches: 154, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
164 19 0.12
165 80 0.52
170 1 0.01
171 54 0.35
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (167 bp):
AAGTTTCAAACTTTGTGAGGGCTTTTCTCTCAAGAATTATGAGAAAAGAAGAAGGGGGTAGCTAC
CATGTTAGAAAAATGGCAGAGTTAACTACCACATCATCAAAAACATGAGGTAACGGTAGGGGCCT
TAATAAAAACAAACTAAAAGTTCGATGATTGTATTAT
Found at i:473584 original size:2 final size:2
Alignment explanation
Indices: 473577--473604 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
473567 TCTAACGCCT
473577 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
473605 CAAAACTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:486371 original size:59 final size:60
Alignment explanation
Indices: 486248--486376 Score: 161
Period size: 59 Copynumber: 2.2 Consensus size: 60
486238 AGAAGGATTA
* * ** * * * *
486248 TCATAGTTTAGGGATGAAATTGAAATATTTAAAAGTTTAATGACTAATTTATAATGATAG
1 TCATAATTTAAGGATGAAATCAAAATATTTAAAAGTTTAAGGACCAATTTATAATAAGAG
*
486308 TCATAATTTAAGGATGAAATCAAAATATTT-AAAGTTTAGGGACCAATTTATAATAAGAG
1 TCATAATTTAAGGATGAAATCAAAATATTTAAAAGTTTAAGGACCAATTTATAATAAGAG
*
486367 TCATACTTTA
1 TCATAATTTA
486377 TTTATATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
59 33 0.56
60 26 0.44
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (60 bp):
TCATAATTTAAGGATGAAATCAAAATATTTAAAAGTTTAAGGACCAATTTATAATAAGAG
Found at i:492983 original size:38 final size:38
Alignment explanation
Indices: 492941--493016 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
492931 GCTGAGCGGG
*
492941 AGAGCAACGGTCTAATTTTTCAAATTCAAAAATAAGAT
1 AGAGCAACGGTCTAATATTTCAAATTCAAAAATAAGAT
* ** *
492979 AGAGCAACGGTTTTGTATTTCAAATTCAAAATTAAGAT
1 AGAGCAACGGTCTAATATTTCAAATTCAAAAATAAGAT
493017 TACCGTTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (38 bp):
AGAGCAACGGTCTAATATTTCAAATTCAAAAATAAGAT
Found at i:513157 original size:313 final size:311
Alignment explanation
Indices: 512597--513217 Score: 892
Period size: 313 Copynumber: 2.0 Consensus size: 311
512587 ATATCAGTAG
512597 CGGATTGATGCTTAACGAGGCACGCACCCTTCTCGCTGGTTTTCTAAATCTCAAAATCCAATATG
1 CGGATTGATGCTTAACGAGGCACGCACCCTTCTC-C--G-TTTCTAAA-CTCAAAATCCAATATG
* *
512662 TGCACCGAGAAGCCAATCGGGTAGCACATACCCTCGCCTAATGTGTGATATAATGTATTTATACT
61 TGCACCAAGAAGCCAATCGGGTAGCACATACCCTCGCCCAATGTGTGATATAATGTATTTATACT
* * * * * * *
512727 CGTTCTCTATGTTTATAGTGGATTGTTGTTCATTTCACCCTTAGATGTAATCAAAATTGAACCAT
126 CGTTCTCTACGTTTATAATGAATTGTTGTTCATCTCACCCGTAGAAGTAATCAAAATTGAAACAT
* * *
512792 AATAAATCTCATCTATCTTACATGTATTATTTTATGTTGATATCGCTTTATTTATTTTTTCCTAT
191 AATAAATCTCATCTATCTTACATGTATTATCTCATGTTGATATCACTTTATTTATTTTTTCCTAT
* *
512857 CCTAGATTCTTAACAGAGCTCAGACAATCAATTAAACAT-CATTCAATCAGTAGTCGT
256 CCTAGATTCGTAACA-AACTCAGACAATCAATTAAACATAC-TTCAATCAGTAGTCGT
* *
512914 CGGATTGATGCTTAACGTGGCACGCACCCTTCT-C-TTTCT-AA-TCAAAATCCAATATGTGCAT
1 CGGATTGATGCTTAACGAGGCACGCACCCTTCTCCGTTTCTAAACTCAAAATCCAATATGTGCAC
* * *
512975 CAAGAAGCCAATCGGGTAGTACATACCCTCGCCCAATGTGTGATATCATGTATTTATATTTTTCG
66 CAAGAAGCCAATCGGGTAGCACATACCCTCGCCCAATGTGTGATATAATGTATTTATA---CTC-
* * *
513040 TGTTCTCTACGTTTATAATGAATTGTTGTTCATCTCACTCGTAGAAGTAATCAAAATTTAAATAT
127 -GTTCTCTACGTTTATAATGAATTGTTGTTCATCTCACCCGTAGAAGTAATCAAAATTGAAACAT
*
513105 AATAAATCTCATCTATTTTACATGTATTATCTCATGTTGATATCACTTTATTTATTTTTTCCTAT
191 AATAAATCTCATCTATCTTACATGTATTATCTCATGTTGATATCACTTTATTTATTTTTTCCTAT
513170 CCTAGATTCGTAACAAACTCAGACAATCAATTAAACATACTTCAATCA
256 CCTAGATTCGTAACAAACTCAGACAATCAATTAAACATACTTCAATCA
513218 CTATACCTTA
Statistics
Matches: 275, Mismatches: 23, Indels: 17
0.87 0.07 0.05
Matches are distributed among these distances:
308 73 0.27
310 2 0.01
311 7 0.03
312 30 0.11
313 130 0.47
315 1 0.00
317 32 0.12
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (311 bp):
CGGATTGATGCTTAACGAGGCACGCACCCTTCTCCGTTTCTAAACTCAAAATCCAATATGTGCAC
CAAGAAGCCAATCGGGTAGCACATACCCTCGCCCAATGTGTGATATAATGTATTTATACTCGTTC
TCTACGTTTATAATGAATTGTTGTTCATCTCACCCGTAGAAGTAATCAAAATTGAAACATAATAA
ATCTCATCTATCTTACATGTATTATCTCATGTTGATATCACTTTATTTATTTTTTCCTATCCTAG
ATTCGTAACAAACTCAGACAATCAATTAAACATACTTCAATCAGTAGTCGT
Found at i:515419 original size:237 final size:239
Alignment explanation
Indices: 515004--515481 Score: 942
Period size: 237 Copynumber: 2.0 Consensus size: 239
514994 CAGAAGGTCA
515004 ATTGGCATAAATTAGTTTGGTTTCCATTGCATATTCCAAAATATAGTTTAATTGCTTGGATGACA
1 ATTGGCATAAATTAGTTTGGTTTCCATTGCATATTCCAAAATATAGTTTAATTGCTTGGATGACA
515069 ATTCTCAACAGGCTGCCTACTAGAGATCGGCTCATTAAAATGGGAATTTGCTCAGAAGTTCACTG
66 ATTCTCAACAGGCTGCCTACTAGAGATCGGCTCATTAAAATGGGAATTTGCTCAGAAGTTCACTG
515134 TGTAAACTACAATTTGAATCAAGAAACAAGGGACCACCTTTTCTTGCATTGTTCGCTGGCAGCAA
131 TGTAAACTACAATTTGAATCAAGAAACAAGGGACCACCTTTTCTTGCATTGTTCGCTGGCAGCAA
515199 CTCTCTGAAAATCTG-TTTGAACCTTAATGGGATGAAGCCA-CG
196 CTCTCTGAAAATCTGTTTTGAACCTTAATGGGATGAAGCCATCG
515241 ATTGGCATAAATTAGTTTGGTTTCCATTGCATATTCCAAAATATAGTTTAATTGCTTGGATGACA
1 ATTGGCATAAATTAGTTTGGTTTCCATTGCATATTCCAAAATATAGTTTAATTGCTTGGATGACA
515306 ATTCTCAACAGGCTGCCTACTAGAGATCGGCTCATTAAAATGGGAATTTGCTCAGAAGTTCACTG
66 ATTCTCAACAGGCTGCCTACTAGAGATCGGCTCATTAAAATGGGAATTTGCTCAGAAGTTCACTG
515371 TGTAAACTACAATTTGAATCAAGAAACAAGGGACCACCTTTTCTTGCATTGTTCGCTGGCAGCAA
131 TGTAAACTACAATTTGAATCAAGAAACAAGGGACCACCTTTTCTTGCATTGTTCGCTGGCAGCAA
515436 CTCTCTGAAAATCTGTTTTGAACCTTAATGGGATGAAGCCATCG
196 CTCTCTGAAAATCTGTTTTGAACCTTAATGGGATGAAGCCATCG
515480 AT
1 AT
515482 CATGTCATGG
Statistics
Matches: 239, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
237 210 0.88
238 25 0.10
239 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (239 bp):
ATTGGCATAAATTAGTTTGGTTTCCATTGCATATTCCAAAATATAGTTTAATTGCTTGGATGACA
ATTCTCAACAGGCTGCCTACTAGAGATCGGCTCATTAAAATGGGAATTTGCTCAGAAGTTCACTG
TGTAAACTACAATTTGAATCAAGAAACAAGGGACCACCTTTTCTTGCATTGTTCGCTGGCAGCAA
CTCTCTGAAAATCTGTTTTGAACCTTAATGGGATGAAGCCATCG
Found at i:517861 original size:41 final size:39
Alignment explanation
Indices: 517804--517922 Score: 130
Period size: 39 Copynumber: 3.0 Consensus size: 39
517794 CGTGACGCAT
*
517804 CGAAGTGCTTACGCATAAGGTTGTGTCGACCCTTCTTGCAC
1 CGAAGTGCTTACGCATAAGGTTGCGTCGACCC-T-TTGCAC
* * * * *
517845 CGAAGTGCCTACGCATAAGGATACGTTGATCCTTTGCAC
1 CGAAGTGCTTACGCATAAGGTTGCGTCGACCCTTTGCAC
* * **
517884 CAAAGTGCTTACGCATAAGGTTGCATCGATTCTTTGCAC
1 CGAAGTGCTTACGCATAAGGTTGCGTCGACCCTTTGCAC
517923 TCAATTGTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 38 0.58
40 1 0.02
41 26 0.40
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (39 bp):
CGAAGTGCTTACGCATAAGGTTGCGTCGACCCTTTGCAC
Found at i:523342 original size:75 final size:74
Alignment explanation
Indices: 523213--523354 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 74
523203 GTAATGGCCT
*
523213 TGTTATTGAGTTATCAACAACTACGTTACTTCAACTTGGTTGTAGGAGTCGGTTATGGGTATGCT
1 TGTTATTGAGTTATCAACAACTACGTTACTTCAACTTGGTAGTAGGAGTCGGTTATGGGTATG-T
523278 TTTTGCCTCA
65 TTTTGCCTCA
* * * ** *
523288 TGTTATTGAGTTGTTAACAACTATGTTACTTGGACTTGGTAGTAGGCGAT-GGTTATGGGTATGT
1 TGTTATTGAGTTATCAACAACTACGTTACTTCAACTTGGTAGTAGGAG-TCGGTTATGGGTATGT
523352 TTT
65 TTT
523355 CTACACCGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 4 0.07
75 54 0.92
76 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (74 bp):
TGTTATTGAGTTATCAACAACTACGTTACTTCAACTTGGTAGTAGGAGTCGGTTATGGGTATGTT
TTTGCCTCA
Found at i:525343 original size:39 final size:39
Alignment explanation
Indices: 525267--525343 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
525257 GATTGTAACC
*
525267 GAAAATATTATTAAAAAATAATATTTTTTATTGTTAATT
1 GAAAATATTATTAAAAAATAATATTTTTTAGTGTTAATT
* *
525306 GAAAATATTATTAATAATATAATATTTTTTGGT-TTAAT
1 GAAAATATTATTAA-AAAATAATATTTTTTAGTGTTAAT
525344 AAAAAATGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 19 0.56
40 15 0.44
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (39 bp):
GAAAATATTATTAAAAAATAATATTTTTTAGTGTTAATT
Found at i:528167 original size:5 final size:5
Alignment explanation
Indices: 528159--528190 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
528149 AATCCCAGGA
528159 TCTTG TCTTG TCTTG TCTTG TCTTG TC-TG TCT
1 TCTTG TCTTG TCTTG TCTTG TCTTG TCTTG TCT
528191 GTGTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.22, G:0.19, T:0.59
Consensus pattern (5 bp):
TCTTG
Found at i:529513 original size:21 final size:21
Alignment explanation
Indices: 529487--529526 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
529477 CACTAGAAAG
529487 TAAATTTAAA-ATAAATAAAAT
1 TAAA-TTAAATATAAATAAAAT
*
529508 TAAATTAAATTTAAATAAA
1 TAAATTAAATATAAATAAA
529527 TTATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATTAAATATAAATAAAAT
Found at i:531114 original size:11 final size:12
Alignment explanation
Indices: 531091--531122 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
531081 TATACACTTA
531091 TAAAAATATATT
1 TAAAAATATATT
531103 TAAAAATA-ATT
1 TAAAAATATATT
531114 TAAAAATAT
1 TAAAAATAT
531123 TTTTTATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAAATATATT
Found at i:533158 original size:19 final size:19
Alignment explanation
Indices: 533108--533165 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
533098 CAAAGAAAAT
533108 AATAATATAATAATAATGAATA
1 AATAATATAA-AATAAT-AA-A
*
533130 AA-AA-ACAAAATAATAAA
1 AATAATATAAAATAATAAA
*
533147 AATAATATAAAATTATAAA
1 AATAATATAAAATAATAAA
533166 GTTATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 3 0.10
18 4 0.13
19 17 0.55
20 3 0.10
21 2 0.06
22 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATATAAAATAATAAA
Found at i:533424 original size:15 final size:14
Alignment explanation
Indices: 533395--533432 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
533385 TATATCATAT
*
533395 AATAATAATACATG
1 AATAATAATAAATG
533409 AATAATAAATAAATG
1 AATAAT-AATAAATG
533424 AATAA-AATA
1 AATAATAATA
533433 TTCATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 6 0.27
15 12 0.55
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (14 bp):
AATAATAATAAATG
Found at i:533440 original size:60 final size:55
Alignment explanation
Indices: 533325--533440 Score: 137
Period size: 57 Copynumber: 2.0 Consensus size: 55
533315 TATTAAATAA
* *
533325 ATATATATATAATAATAATAATATAGTAAAAAAATAAATGAAAATAATTTTATAT
1 ATATATATATAATAATAATAATACAGTAAAAAAATAAATGAAAATAATTTCATAT
533380 ATATATATATCATATAATAATAATACA-TGAATAATAAATAAATGAATAA-AATATTCATAT
1 ATATATATAT-A-ATAATAATAATACAGT-AA-AA-AAATAAATGAA-AATAAT-TTCATAT
533440 A
1 A
533441 ATAAATAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
55 10 0.19
56 2 0.04
57 15 0.29
58 2 0.04
59 14 0.27
60 9 0.17
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (55 bp):
ATATATATATAATAATAATAATACAGTAAAAAAATAAATGAAAATAATTTCATAT
Found at i:533902 original size:34 final size:35
Alignment explanation
Indices: 533824--533924 Score: 152
Period size: 34 Copynumber: 2.9 Consensus size: 35
533814 ATAGTAGAAC
533824 TCTATCCTATTTTTAGGAGTTTGAATCCTAACAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCT-A-AAAAT
*
533861 T-TCATCCTATTTTTAGGAGTTTGAATCCT-GAAAT
1 TCT-ATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
533895 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
533925 GTAGGACGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
34 31 0.52
35 1 0.02
36 1 0.02
37 27 0.45
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:534853 original size:105 final size:105
Alignment explanation
Indices: 534471--535227 Score: 1090
Period size: 105 Copynumber: 7.3 Consensus size: 105
534461 CATTGTTCCA
* * * ** * *
534471 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAG
** * * *
534536 CAGCCTTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
534577 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
* *
534637 AGTGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
534677 AGTCCAATATCCTTCG-T-T---GTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
*
534737 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
534777 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
* * **
534842 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTAA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
534882 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
534947 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
534987 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAG-T-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GGAAGTTGTTGTTGACAAG
* *
535050 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
535091 AGTCCAATATCCTTCATTGTGAA-ATGAAATTAGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
*
535155 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
535195 AGTCCAATATCCTTCATTGTGAAGTTGAAATTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
535228 CGTTATCTGG
Statistics
Matches: 595, Mismatches: 42, Indels: 29
0.89 0.06 0.04
Matches are distributed among these distances:
95 14 0.02
96 1 0.00
97 1 0.00
98 1 0.00
99 6 0.01
100 125 0.21
101 1 0.00
102 10 0.02
103 20 0.03
104 145 0.24
105 233 0.39
106 38 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:535209 original size:43 final size:43
Alignment explanation
Indices: 535162--535270 Score: 173
Period size: 43 Copynumber: 2.5 Consensus size: 43
535152 GGCAGCGGTC
* * *
535162 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAAATTGCGTTATCTGAAGTCCAATAT
* *
535205 CCTTCATTGTGAAGTTGAAATTGCGTTATCTGGAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAAATTGCGTTATCTGAAGTCCAATAT
535248 CCTTCGTTGTGAAGTTGAAATTG
1 CCTTCGTTGTGAAGTTGAAATTG
535271 GCTCTGAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
CCTTCGTTGTGAAGTTGAAATTGCGTTATCTGAAGTCCAATAT
Found at i:536112 original size:67 final size:66
Alignment explanation
Indices: 535979--536136 Score: 187
Period size: 68 Copynumber: 2.4 Consensus size: 66
535969 AAGATATATG
* * **
535979 TTGTTTCATGAGAAA-TGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGA
1 TTGTTTCAAGAGAAACT-GCCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
536043 TTT
65 -TT
* *
536046 TGTGTTTCAAGAGTAACTGCCTCAAGGGAGACAAAATT-TGTTTT-AGGAGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACTGCCTCAAGGGAAACAAAATTATGTTTTAAGG-GAAATAAATTCAAAG
536109 ATT
64 ATT
* *
536112 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGCCTCAAG
536137 ATAGAAAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
65 21 0.27
66 6 0.08
67 21 0.27
68 30 0.38
69 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGCCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:536212 original size:15 final size:15
Alignment explanation
Indices: 536117--536172 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
536107 AGATTTTGTT
*
536117 TCAAGGGAAACTGTC
1 TCAAGAGAAACTGTC
* *
536132 TCAAGATAGAAAATTGTT
1 TCAAG--AG-AAACTGTC
536150 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
536165 TCAAGAGA
1 TCAAGAGA
536173 GACAAAACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 19 0.58
16 2 0.06
17 1 0.03
18 11 0.33
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:536240 original size:135 final size:136
Alignment explanation
Indices: 536101--536346 Score: 370
Period size: 135 Copynumber: 1.8 Consensus size: 136
536091 GGAGAAATAA
* *
536101 ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGATAG-AAAA-TTGTTTCAAGAGAAACTGT
1 ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAATTTATTTCAAGAGAAACTGT
536164 CTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAAACGGTATTTGTTTCAAAG
66 CTCAAGAGAGACAAAA-TTAGTTCCAAAAGAAACTGTCTCAAGAGAAACGGTATTTGTTTCAAAG
536229 AAAACAT
130 AAAACAT
* * *
536236 ATTCAAATATTTTGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAATTTATTTCAAGGGAAACTG
1 ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-AAAATTTATTTCAAGAGAAACTG
* * * * *
536301 TCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
65 TCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGA
536347 GACAAAATTT
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
135 37 0.38
137 30 0.31
138 31 0.32
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (136 bp):
ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAATTTATTTCAAGAGAAACTGT
CTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGAAACGGTATTTGTTTCAAAGA
AAACAT
Found at i:536274 original size:102 final size:102
Alignment explanation
Indices: 536145--536333 Score: 272
Period size: 102 Copynumber: 1.9 Consensus size: 102
536135 AGATAGAAAA
536145 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGA
**
536210 AACGGTATTTGTTTCAA-AGAAAACATATTCAAATATT
65 AACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * * ** * *
536247 TTGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAA
536312 ACGAAATTTGTTTCAAGAGAAA
66 ACGAAATTTGTTTCAAGAGAAA
536334 CTGTCTCAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
101 35 0.46
102 41 0.54
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAA
ACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:536297 original size:36 final size:36
Alignment explanation
Indices: 536246--536389 Score: 243
Period size: 36 Copynumber: 4.0 Consensus size: 36
536236 ATTCAAATAT
*
536246 TTTGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
536282 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
536318 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
536354 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
536390 CTCTTCTAGT
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 99 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:537299 original size:22 final size:22
Alignment explanation
Indices: 537274--537329 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
537264 TTGTGTTTGG
537274 TCAAAGGTTTCG-CATTTGATGC
1 TCAAAGGTTT-GACATTTGATGC
*
537296 TCAAAGGTTTGATATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
537318 TCAAAGGATTGA
1 TCAAAGGTTTGA
537330 TGGGGTAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:537330 original size:22 final size:22
Alignment explanation
Indices: 537287--537330 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
537277 AAGGTTTCGC
*
537287 ATTTGATGCTCAAAGGTTTGAT
1 ATTTGATGCTCAAAGGATTGAT
537309 ATTTGATGCTCAAAGGATTGAT
1 ATTTGATGCTCAAAGGATTGAT
537331 GGGGTAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (22 bp):
ATTTGATGCTCAAAGGATTGAT
Found at i:542254 original size:18 final size:17
Alignment explanation
Indices: 542231--542273 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
542221 ATATATACAT
542231 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
542249 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
542266 ATAA-AATA
1 ATAATAATA
542274 TTCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:542281 original size:56 final size:54
Alignment explanation
Indices: 542152--542266 Score: 133
Period size: 56 Copynumber: 2.0 Consensus size: 54
542142 ACTTATAAGT
* * *
542152 AAAAT-ATTAAATAATATATATATATAATAATAATAAAATAGTAAAAAATAAATG
1 AAAATAATTATAT-ATATATACATATAATAATAATAAAATAATAAAAAATAAATG
*
542206 AAAATAATTTTATATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG
1 AAAATAA--TTATATATATATACATATAATAATAATAAAAT-AAT-A-AAAAATAAATG
542265 AA
1 AA
542267 TAAAATATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
54 5 0.10
55 1 0.02
56 24 0.47
57 7 0.14
58 1 0.02
59 13 0.25
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (54 bp):
AAAATAATTATATATATATACATATAATAATAATAAAATAATAAAAAATAAATG
Found at i:542744 original size:34 final size:35
Alignment explanation
Indices: 542666--542766 Score: 152
Period size: 34 Copynumber: 2.9 Consensus size: 35
542656 ATAGTAGAAC
542666 TCTATCCTATTTTTAGGAGTTTGAATCCTAACAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCT-A-AAAAT
*
542703 T-TCATCCTATTTTTAGGAGTTTGAATCCT-GAAAT
1 TCT-ATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
542737 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
542767 GTAGGACGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
34 31 0.52
35 1 0.02
36 1 0.02
37 27 0.45
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:544076 original size:13 final size:13
Alignment explanation
Indices: 544030--544076 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
544020 CGACCCGTTT
*
544030 ACCCGTTTACCCG
1 ACCCGTTGACCCG
544043 ACCCGTTGACCCG
1 ACCCGTTGACCCG
544056 ACCC---GACCCG
1 ACCCGTTGACCCG
544066 ACCCGTTGACC
1 ACCCGTTGACC
544077 GTTGACCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.17, C:0.49, G:0.19, T:0.15
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:544145 original size:29 final size:29
Alignment explanation
Indices: 544084--544150 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
544074 ACCGTTGACC
*** *
544084 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
*
544113 GGTGTTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
544142 GGTGCTATT
1 GGTGCTATT
544151 TTTGGTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:548831 original size:75 final size:75
Alignment explanation
Indices: 548708--549007 Score: 411
Period size: 75 Copynumber: 4.0 Consensus size: 75
548698 TGATTCGCGG
* * * *
548708 GGGCTAACCGGCTTCTTCTCGGGAATTTCAGGCTTCGTTGTTGCTGGTTGTCCAGAACCAACACC
1 GGGCTAACCGGCTTCTTCTCAGGAATTTCAGGCTTCGCTGTGGCTGGTTGTCCCGAACCAACACC
*
548773 TTTAACAGAA
66 TTTGACAGAA
* *
548783 GGGCTAACTGGCTTCTTCTCGGGAATTTCAGGCTTCGCTGTGGCTGGTTGTCCCGAACCAACACC
1 GGGCTAACCGGCTTCTTCTCAGGAATTTCAGGCTTCGCTGTGGCTGGTTGTCCCGAACCAACACC
548848 TTTGACAGAA
66 TTTGACAGAA
* * * * * *
548858 GGGGTAGCCGGCTTCTTCTCAGGAGTTTCAGGCTTCACTGAGGCTGTTTGTCCCGAACCAACACC
1 GGGCTAACCGGCTTCTTCTCAGGAATTTCAGGCTTCGCTGTGGCTGGTTGTCCCGAACCAACACC
*
548923 TTTGGCAGAA
66 TTTGACAGAA
* * * * **
548933 GGGCTAACCGGCTTCTTCTCAGGAATTTCAGGCTTCCCTTTGGTTGGTCGTCCCGAACCAAGTCC
1 GGGCTAACCGGCTTCTTCTCAGGAATTTCAGGCTTCGCTGTGGCTGGTTGTCCCGAACCAACACC
*
548998 TTTGGCAGAA
66 TTTGACAGAA
549008 CTTGATGATG
Statistics
Matches: 200, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 200 1.00
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (75 bp):
GGGCTAACCGGCTTCTTCTCAGGAATTTCAGGCTTCGCTGTGGCTGGTTGTCCCGAACCAACACC
TTTGACAGAA
Found at i:552630 original size:15 final size:15
Alignment explanation
Indices: 552612--552648 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
552602 CTGAAGTGGC
552612 TCTTCCTCCTGTTCT
1 TCTTCCTCCTGTTCT
* *
552627 TCTTCTTCTTGTTCT
1 TCTTCCTCCTGTTCT
552642 TCTTCCT
1 TCTTCCT
552649 TCGTGACCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.35, G:0.05, T:0.59
Consensus pattern (15 bp):
TCTTCCTCCTGTTCT
Found at i:557031 original size:2 final size:2
Alignment explanation
Indices: 557024--557064 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
557014 TTTTTCATCT
*
557024 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
557065 TCGTGTCCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:558516 original size:31 final size:30
Alignment explanation
Indices: 558434--558527 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 30
558424 GTTTAAATAA
*
558434 ATAAAATAATCATTAAATTTATTAAACTATT
1 ATAAAAT-ATCATTAAATTTATTAAACTTTT
* *
558465 AAAAAACTATCATCAAATTTATTAAACTTTT
1 ATAAAA-TATCATTAAATTTATTAAACTTTT
* * * *
558496 ATAAAATGATTATTAGATTTATCAAAATTTT
1 ATAAAAT-ATCATTAAATTTATTAAACTTTT
558527 A
1 A
558528 CTTATTATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 1 0.02
31 50 0.96
32 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (30 bp):
ATAAAATATCATTAAATTTATTAAACTTTT
Found at i:564851 original size:2 final size:2
Alignment explanation
Indices: 564846--564874 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
564836 TACCAATAAT
564846 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
564875 TAATACTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:567195 original size:35 final size:35
Alignment explanation
Indices: 567149--567219 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
567139 ATATCGTTGT
567149 CGTCGAACTCTCCTAAGGAAATAGCGCATTCTAGG
1 CGTCGAACTCTCCTAAGGAAATAGCGCATTCTAGG
* *
567184 CGTCGAACTCTCCTAAGGAACTAGCGCATTGTAGG
1 CGTCGAACTCTCCTAAGGAAATAGCGCATTCTAGG
567219 C
1 C
567220 CATACTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.23
Consensus pattern (35 bp):
CGTCGAACTCTCCTAAGGAAATAGCGCATTCTAGG
Found at i:568248 original size:23 final size:23
Alignment explanation
Indices: 568196--568248 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
568186 TTGTTGTTGT
*
568196 TTATGTTCGTTTACGTTCATTTA
1 TTATGTTCGATTACGTTCATTTA
* * *
568219 TTGTGTTCGATTATGTTCATTTG
1 TTATGTTCGATTACGTTCATTTA
568242 TTATGTT
1 TTATGTT
568249 TGTGCATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.15, C:0.09, G:0.17, T:0.58
Consensus pattern (23 bp):
TTATGTTCGATTACGTTCATTTA
Found at i:568889 original size:60 final size:60
Alignment explanation
Indices: 568785--568967 Score: 153
Period size: 60 Copynumber: 3.0 Consensus size: 60
568775 TTCCTTAATG
* ** **
568785 TATGATCC-TCATTTTAAATTAGT-CTATAAACTTTTAAATGTTTCAATTTT-ATCCTTAAAC
1 TATGA-CCATCATTTTAAATTAGTCCT-CAAACTTTTAAACATTTC-ATTTTCATCCCCAAAC
* * *
568845 TATGACTATCATTTTAAATTAGTCCTCAAACTTTTCAACATTTCATTTTCATCCCCAAGC
1 TATGACCATCATTTTAAATTAGTCCTCAAACTTTTAAACATTTCATTTTCATCCCCAAAC
* * * * *
568905 TATGACCACCATTCTAAATTGGTACC-CAAACTTTTTGAACA-TTCTAATTTCAT-CCCAAAC
1 TATGACCATCATTTTAAATTAGT-CCTCAAAC-TTTTAAACATTTC-ATTTTCATCCCCAAAC
568965 TAT
1 TAT
568968 ACATATATAC
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
59 6 0.06
60 77 0.75
61 19 0.19
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.40
Consensus pattern (60 bp):
TATGACCATCATTTTAAATTAGTCCTCAAACTTTTAAACATTTCATTTTCATCCCCAAAC
Found at i:569222 original size:60 final size:59
Alignment explanation
Indices: 569097--569244 Score: 170
Period size: 60 Copynumber: 2.5 Consensus size: 59
569087 TGAATTTAGG
* * * * ** *
569097 GATGAAATTGGAATATCCAAAAGTTTAGGGACTAATTTAGAAAGGGAGTCATAGTTTGT
1 GATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAACCATAATTTGT
* * * *
569156 GAATGAAATTAGAATGTTTAAAAGTTTAAGGACTAATTTAGCATGAGAACCATAATTTGAT
1 G-ATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAACCATAATTTG-T
*
569217 GATGAAATTTGAATATTCAAAAGTTTAA
1 GATGAAATTAGAATATTCAAAAGTTTAA
569245 TAATCAATTT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.01
60 70 0.96
61 2 0.03
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.32
Consensus pattern (59 bp):
GATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAACCATAATTTGT
Found at i:573004 original size:23 final size:20
Alignment explanation
Indices: 572954--573007 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 20
572944 AAAACGTAAC
572954 ATAAAAAT-AAAATTATTAA
1 ATAAAAATAAAAATTATTAA
572973 A-AAATAATAAATAATTATATAA
1 ATAAA-AATAAA-AATTAT-TAA
572995 TATAAAAATAAAA
1 -ATAAAAATAAAA
573008 GATATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 3 0.10
19 4 0.14
20 2 0.07
21 6 0.21
22 4 0.14
23 7 0.24
24 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAAATAAAAATTATTAA
Found at i:573245 original size:9 final size:10
Alignment explanation
Indices: 573212--573244 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
573202 TTTTATTACA
*
573212 TTTTAATATT
1 TTTTAAAATT
573222 TTTTAAAATT
1 TTTTAAAATT
573232 TTTTAAAATT
1 TTTTAAAATT
573242 TTT
1 TTT
573245 AGTGACTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:574187 original size:16 final size:16
Alignment explanation
Indices: 574166--574198 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
574156 TAAAAAACAT
574166 AAAAAATTAAATACTAA
1 AAAAAATTAAA-ACTAA
574183 AAAAAATTAAAACTAA
1 AAAAAATTAAAACTAA
574199 TAGTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAATTAAAACTAA
Found at i:579960 original size:36 final size:35
Alignment explanation
Indices: 579879--580018 Score: 194
Period size: 36 Copynumber: 3.9 Consensus size: 35
579869 AGATGAACAA
579879 TTGAATCGAAAGTG-CTGATGCTTCC-TTCAGTTCAC
1 TTGAATCGAAAGTGTC-GATGCTTCCTTTC-GTTCAC
*
579914 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC-AC
* *
579950 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCAC
*
579985 TTTGAATCGAAAGTGTTGATGCTTCCTTTCGTTC
1 -TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC
580019 TTCTTATTCA
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
35 28 0.30
36 66 0.70
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCAC
Found at i:580021 original size:72 final size:71
Alignment explanation
Indices: 579879--580023 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 71
579869 AGATGAACAA
*
579879 TTGAATCGAAAGTGCTGATGCTTCCTTCAGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCCTTCAGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
579944 TTCTTC
66 TTCTTC
* *
579950 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGTTGATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCAGTTCAC-TTGAATCGAAAGTGTCGATGCTTCCTTTC
580015 GTTCTTC
65 GTTCTTC
580022 TT
1 TT
580024 ATTCACCTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 33 0.47
72 37 0.53
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (71 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCAGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
TTCTTC
Found at i:582302 original size:29 final size:29
Alignment explanation
Indices: 582260--582322 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
582250 TGCAGAGAGG
582260 TTGGGGTATGTGATTGTCCCCCATGTTGT
1 TTGGGGTATGTGATTGTCCCCCATGTTGT
*
582289 TTGGGGTATGTGATTGTCTCCCATGTTGT
1 TTGGGGTATGTGATTGTCCCCCATGTTGT
582318 TTGGG
1 TTGGG
582323 CAGTGTTGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.10, C:0.14, G:0.33, T:0.43
Consensus pattern (29 bp):
TTGGGGTATGTGATTGTCCCCCATGTTGT
Found at i:586923 original size:19 final size:19
Alignment explanation
Indices: 586899--586936 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
586889 ATTAGGAATT
*
586899 AATTATCTAAATGATTAAA
1 AATTATCTAAATAATTAAA
*
586918 AATTATCTCAATAATTAAA
1 AATTATCTAAATAATTAAA
586937 TAAATCGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (19 bp):
AATTATCTAAATAATTAAA
Found at i:592412 original size:20 final size:21
Alignment explanation
Indices: 592387--592428 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
592377 TTGTTGGTGT
592387 TGATAA-TTACGGTATTAATG
1 TGATAATTTACGGTATTAATG
*
592407 TGATAATTTACGGTGTTAATG
1 TGATAATTTACGGTATTAATG
592428 T
1 T
592429 ATATTCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
TGATAATTTACGGTATTAATG
Found at i:594553 original size:32 final size:30
Alignment explanation
Indices: 594481--594553 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 30
594471 AGGTTTAATT
*
594481 TTTTAATTTAATCACTTAACTTTCAAATTAC
1 TTTT-ATTTAATCACTTAACTTTCAAATTAA
* *
594512 TCATAATTTAATCACTCTAACTTTCAAATTTAA
1 T-TTTATTTAATCACT-TAACTTTCAAA-TTAA
594545 TTTTATTTA
1 TTTTATTTA
594554 TTTTTAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
31 12 0.35
32 18 0.53
33 4 0.12
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTTATTTAATCACTTAACTTTCAAATTAA
Found at i:597764 original size:40 final size:38
Alignment explanation
Indices: 597715--597793 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 38
597705 ATACATAAAA
* *
597715 TTTAATTTTTGTTTCATTTTAGTATTTTGTCGTTAAAATT
1 TTTAATTTTTGTTTCAATTTAGTATCTTGT--TTAAAATT
*
597755 TTTAGTTTTTGTTTCAATTTAGTATCTTGTTTAAAATT
1 TTTAATTTTTGTTTCAATTTAGTATCTTGTTTAAAATT
597793 T
1 T
597794 GAAAAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 9 0.25
40 27 0.75
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (38 bp):
TTTAATTTTTGTTTCAATTTAGTATCTTGTTTAAAATT
Found at i:597863 original size:29 final size:30
Alignment explanation
Indices: 597798--597863 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
597788 AAATTTGAAA
*
597798 AAAATTGAGAGTTTAGGTATTAAAATGAATT
1 AAAATTGAGAGTTTAGGTACTAAAATG-ATT
*
597829 GAAATTGA-AGTTTAGGTACTAAATATG-TT
1 AAAATTGAGAGTTTAGGTACTAAA-ATGATT
597858 AAAATT
1 AAAATT
597864 TTAACGATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 7 0.23
30 14 0.45
31 10 0.32
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (30 bp):
AAAATTGAGAGTTTAGGTACTAAAATGATT
Found at i:597915 original size:26 final size:26
Alignment explanation
Indices: 597880--597929 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
597870 ATTGAATACG
*
597880 AAAATGAAAGTTTTAA-TATTAAAATT
1 AAAATAAAAG-TTTAAGTATTAAAATT
597906 AAAATAAAAGTTTAAGTATTAAAA
1 AAAATAAAAGTTTAAGTATTAAAA
597930 CGGATTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (26 bp):
AAAATAAAAGTTTAAGTATTAAAATT
Found at i:601150 original size:192 final size:194
Alignment explanation
Indices: 600823--601208 Score: 758
Period size: 192 Copynumber: 2.0 Consensus size: 194
600813 TTTTTAATAG
600823 TTGAGGGACTCAACAGAGCAACTCTCTATAATTAGAGGACCATTTTATAACTTTTAATAGTTGAG
1 TTGAGGGACTCAACAGAGCAACTCTCTATAATTAGAGGACCATTTTATAACTTTTAATAGTTGAG
600888 GAATTTAATAAAACAATATCTTATTGTCAAGGGACCATTTGTGTACCTTATCCTAAAAATAGTTT
66 GAATTTAATAAAACAATATCTTATTGTCAAGGGACCATTTGTGTACCTTATCCTAAAAATAGTTT
600953 CGTTAGAATTAGTGTAATTTCAAAAGTGGATATTGTCCCCGGAAATT-AGAGA-TCCAAATTTC
131 CGTTAGAATTAGTGTAATTTCAAAAGTGGATATTGTCCCCGGAAATTAAGAGATTCCAAATTTC
601015 TTGAGGGACTCAACAGAGCAACTCTCTATAATTAGAGGACCATTTTATAACTTTTAATAGTTGAG
1 TTGAGGGACTCAACAGAGCAACTCTCTATAATTAGAGGACCATTTTATAACTTTTAATAGTTGAG
601080 GAATTTAATAAAACAATATCTTATTGTCAAGGGACCATTTGTGTACCTTATCCTAAAAATAGTTT
66 GAATTTAATAAAACAATATCTTATTGTCAAGGGACCATTTGTGTACCTTATCCTAAAAATAGTTT
601145 CGTTAGAATTAGTGTAATTTCAAAAGTGGATATTGTCCCCGGAAATTAAGAGATTCCAAATTTC
131 CGTTAGAATTAGTGTAATTTCAAAAGTGGATATTGTCCCCGGAAATTAAGAGATTCCAAATTTC
601209 ATAACTCTAA
Statistics
Matches: 192, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
192 177 0.92
193 5 0.03
194 10 0.05
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (194 bp):
TTGAGGGACTCAACAGAGCAACTCTCTATAATTAGAGGACCATTTTATAACTTTTAATAGTTGAG
GAATTTAATAAAACAATATCTTATTGTCAAGGGACCATTTGTGTACCTTATCCTAAAAATAGTTT
CGTTAGAATTAGTGTAATTTCAAAAGTGGATATTGTCCCCGGAAATTAAGAGATTCCAAATTTC
Found at i:603635 original size:23 final size:23
Alignment explanation
Indices: 603605--603651 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
603595 GGTTTAATTT
603605 ATTTTAGGTCCTTACCAATATTA
1 ATTTTAGGTCCTTACCAATATTA
603628 ATTTTAGGTCCTTACCAATATTA
1 ATTTTAGGTCCTTACCAATATTA
603651 A
1 A
603652 CGATGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (23 bp):
ATTTTAGGTCCTTACCAATATTA
Found at i:604532 original size:44 final size:44
Alignment explanation
Indices: 604383--604938 Score: 750
Period size: 44 Copynumber: 12.8 Consensus size: 44
604373 ACAATAAATT
** *
604383 TTTTAAAATAAATCATT-CAT-TTTAAAAATAAATCAATCCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
***
604425 TTTT-AAAT-AATCAATCCATATTTT-AAATAAATCAATCCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
* **
604466 -TTTAAAATAACTTTTTTTATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
* ***
604509 TTTTAAAATAACTCAATCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
*** * ***
604553 TTTTAAAATAAATCAATCCATATTTTAAAATAATTTTTTCCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
* *
604597 TTTTAAAATACATTTTTTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
* *
604641 TTTTAAAAT-AATTTTTCCATATTTTAAAATAAATAAATTCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
* *
604684 TTTTAAAATAATTTTTTTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
* *
604728 TTTTAAAATAAAATTTTCCATATTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
604772 TTTTAAAATAAAATTTTT-CATATTTTAAAATAAATCAATCCATA
1 TTTTAAAAT-AAATTTTTCCATATTTTAAAATAAATCAATCCATA
*
604816 TTTTAAAATAAATTTTTTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
*
604860 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
* **
604904 TTTTAAAATAATTTTTTTTATATTTTAAAATAAAT
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAAT
604939 TTTAAAATAG
Statistics
Matches: 459, Mismatches: 46, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
40 9 0.02
41 28 0.06
42 17 0.04
43 64 0.14
44 334 0.73
45 7 0.02
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (44 bp):
TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCATA
Found at i:604941 original size:22 final size:22
Alignment explanation
Indices: 604383--604939 Score: 565
Period size: 22 Copynumber: 25.6 Consensus size: 22
604373 ACAATAAATT
* *
604383 TTTTAAAATAAA-TCATTCAT-
1 TTTTAAAATAAATTAATCCATA
* *
604403 TTTAAAAATAAATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
*
604425 TTTT-AAAT-AATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
*
604445 TTTT-AAATAAATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
* ** **
604466 -TTTAAAATAACTTTTTTTATA
1 TTTTAAAATAAATTAATCCATA
*
604487 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
* *
604509 TTTTAAAATAACTCAATCCATA
1 TTTTAAAATAAATTAATCCATA
*
604531 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
*
604553 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
* **
604575 TTTTAAAATAATTTTTTCCATA
1 TTTTAAAATAAATTAATCCATA
* ** *
604597 TTTTAAAATACATTTTTTCATA
1 TTTTAAAATAAATTAATCCATA
*
604619 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
**
604641 TTTTAAAAT-AATTTTTCCATA
1 TTTTAAAATAAATTAATCCATA
* *
604662 TTTTAAAATAAATAAATTCATA
1 TTTTAAAATAAATTAATCCATA
* ** *
604684 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATTAATCCATA
*
604706 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
*
604728 TTTTAAAATAAAATT-TTCCATA
1 TTTTAAAAT-AAATTAATCCATA
* *
604750 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATTAATCCATA
* *
604772 TTTTAAAATAAAATT-TTTCATA
1 TTTTAAAAT-AAATTAATCCATA
*
604794 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
** *
604816 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATTAATCCATA
*
604838 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTAATCCATA
**
604860 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATTAATCCATA
* *
604882 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATTAATCCATA
* ** **
604904 TTTTAAAATAATTTTTTTTATA
1 TTTTAAAATAAATTAATCCATA
604926 TTTTAAAATAAATT
1 TTTTAAAATAAATT
604940 TTAAAATAGA
Statistics
Matches: 449, Mismatches: 78, Indels: 18
0.82 0.14 0.03
Matches are distributed among these distances:
20 34 0.08
21 58 0.13
22 349 0.78
23 8 0.02
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTAAAATAAATTAATCCATA
Found at i:613559 original size:2 final size:2
Alignment explanation
Indices: 613552--613587 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
613542 TGTCTCTTAA
613552 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
613588 GAGATATGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:617087 original size:3 final size:3
Alignment explanation
Indices: 617076--617144 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
617066 TTAAATAATA
*
617076 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * *
617120 TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
617145 TTTGCAGACT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Done.