Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007749.1 Hibiscus syriacus cultivar Beakdansim tig00110015_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: 1787532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:339665 original size:21 final size:20
Alignment explanation
Indices: 339639--339699 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
339629 GTTGCGAAAA
*
339639 AGAAATTCGCGTTGCGAATTC
1 AGAAA-TCGAGTTGCGAATTC
*
339660 AGAAATCGAGTTGCGAATTT
1 AGAAATCGAGTTGCGAATTC
* *
339680 GGAAAATCGTGTTGCGAATT
1 AG-AAATCGAGTTGCGAATT
339700 TGGAAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (20 bp):
AGAAATCGAGTTGCGAATTC
Found at i:339700 original size:21 final size:20
Alignment explanation
Indices: 339640--339741 Score: 96
Period size: 20 Copynumber: 5.0 Consensus size: 20
339630 TTGCGAAAAA
**
339640 GAAATTCGCGTTGCGAATTCA
1 GAAA-TCGCGTTGCGAATTTG
*
339661 GAAATCGAGTTGCGAATTTG
1 GAAATCGCGTTGCGAATTTG
*
339681 GAAAATCGTGTTGCGAATTTG
1 G-AAATCGCGTTGCGAATTTG
* * * *
339702 GAAATTGTGCTGCGAAATTG
1 GAAATCGCGTTGCGAATTTG
**
339722 GAGTTCGCGTTGCGAATTTG
1 GAAATCGCGTTGCGAATTTG
339742 TTGGTCATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
20 44 0.66
21 23 0.34
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.31
Consensus pattern (20 bp):
GAAATCGCGTTGCGAATTTG
Found at i:339706 original size:41 final size:41
Alignment explanation
Indices: 339640--339741 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 41
339630 TTGCGAAAAA
** * *
339640 GAAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTGGAAATCGAGCTGCGAAATTG
* * * *
339681 GAAAATCGTGTTGCGAATTTGGAAATTGTGCTGCGAAATTG
1 GAAATTCGCGTTGCGAATTTGGAAATCGAGCTGCGAAATTG
*
339722 G-AGTTCGCGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
339742 TTGGTCATTT
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
40 16 0.32
41 34 0.68
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.31
Consensus pattern (41 bp):
GAAATTCGCGTTGCGAATTTGGAAATCGAGCTGCGAAATTG
Found at i:339716 original size:81 final size:80
Alignment explanation
Indices: 339589--339739 Score: 187
Period size: 81 Copynumber: 1.9 Consensus size: 80
339579 CAAAATTTGT
* * *
339589 GTTGCGATTTAGAAAATCTTGTTGTGAAAAGGAAACTTGTGTTGCGAAAAAGAAATTCGCGTTGC
1 GTTGCGATTTAGAAAATCGTGTTGCGAAAAGGAAACTTGTGCTGCGAAAAAGAAATTCGCGTTGC
339654 GAATTCAGAAATCGA
66 GAATTCAGAAATCGA
* ** ** * *
339669 GTTGCGAATTTGGAAAATCGTGTTGCGAATTTGGAAA-TTGTGCTGCGAAATTGGAGTTCGCGTT
1 GTTGCG-ATTTAGAAAATCGTGTTGCGAA-AAGGAAACTTGTGCTGCGAAAAAGAAATTCGCGTT
339733 GCGAATT
64 GCGAATT
339740 TGTTGGTCAT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
80 6 0.10
81 48 0.81
82 5 0.08
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (80 bp):
GTTGCGATTTAGAAAATCGTGTTGCGAAAAGGAAACTTGTGCTGCGAAAAAGAAATTCGCGTTGC
GAATTCAGAAATCGA
Found at i:344032 original size:20 final size:20
Alignment explanation
Indices: 344004--344047 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
343994 ACATGGAAGA
*
344004 CTCCTAACCGATCAACAAGC
1 CTCCCAACCGATCAACAAGC
344024 CTCCCAACCGATCAACAAGC
1 CTCCCAACCGATCAACAAGC
344044 CTCC
1 CTCC
344048 ATACTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.45, G:0.09, T:0.14
Consensus pattern (20 bp):
CTCCCAACCGATCAACAAGC
Found at i:347143 original size:29 final size:29
Alignment explanation
Indices: 347097--347164 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
347087 ACATGACAGA
* * *
347097 GATTTAATCCCATATAGAATTAGGATGGG
1 GATTTAATCTCATATAGAATCAGGAAGGG
*
347126 GATTTAATCTCATGTAGAATCAGGAAGGG
1 GATTTAATCTCATATAGAATCAGGAAGGG
347155 GATTTAATCT
1 GATTTAATCT
347165 AGGGGTGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (29 bp):
GATTTAATCTCATATAGAATCAGGAAGGG
Found at i:347951 original size:142 final size:142
Alignment explanation
Indices: 347695--347989 Score: 491
Period size: 142 Copynumber: 2.1 Consensus size: 142
347685 ATCTCTAAAC
* *
347695 CGCAACACGATCTCCAGTATCGCAAATCAGTTTCCAGATTCACAACGCGATTTTGACTATCGCAT
1 CGCAACGCGATCTCCAGTATCACAAATCAGTTTCCAGATTCACAACGCGATTTTGACTATCGCAT
* * * *
347760 TGCGATTTTCCAAATTCGCGTTGCGATTTTCGAAAATCGAAATGTGAATATGTAAATCGCAACGC
66 TACGATTTTCCAAATTCGCGTTGCGATTTTAGAAAATCGAAATGTGAATATATAAATCACAACGC
347825 GATTCTGACTAT
131 GATTCTGACTAT
* *
347837 CGCAACGCGATCTCCAGTATCACAAATCAGTTTTCAGATTCGCAACGCGATTTTGACTATCGCAT
1 CGCAACGCGATCTCCAGTATCACAAATCAGTTTCCAGATTCACAACGCGATTTTGACTATCGCAT
* *
347902 TACGATTTTCCAAATTCGCGTTGCGATTTTAGAAAGTCGCAATGTGAATATATAAATCACAACGC
66 TACGATTTTCCAAATTCGCGTTGCGATTTTAGAAAATCGAAATGTGAATATATAAATCACAACGC
*
347967 GATTTTGACTAT
131 GATTCTGACTAT
347979 CGCAACGCGAT
1 CGCAACGCGAT
347990 AATACATAAT
Statistics
Matches: 142, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (142 bp):
CGCAACGCGATCTCCAGTATCACAAATCAGTTTCCAGATTCACAACGCGATTTTGACTATCGCAT
TACGATTTTCCAAATTCGCGTTGCGATTTTAGAAAATCGAAATGTGAATATATAAATCACAACGC
GATTCTGACTAT
Found at i:348003 original size:21 final size:21
Alignment explanation
Indices: 347977--348052 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
347967 GATTTTGACT
347977 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
*
347998 ATCGCAACGCTATAATACATA
1 ATCGCAACGCGATAATACATA
*
348019 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACATA
*
348040 ATCGCAATGCGAT
1 ATCGCAACGCGAT
348053 TTTTCAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:348450 original size:19 final size:19
Alignment explanation
Indices: 348426--348540 Score: 70
Period size: 19 Copynumber: 5.7 Consensus size: 19
348416 TTATTTTGGA
348426 TTTTTCACAATCGCAACAC
1 TTTTTCACAATCGCAACAC
*
348445 TTTTTCACTATCGCAACAACAC
1 TTTTTCACAATCG---CAACAC
348467 GTTTTTCA-AACTCTCGCAACAC
1 -TTTTTCACAA---TCGCAACAC
* * *
348489 ATTTTAACTATCGCAACAC
1 TTTTTCACAATCGCAACAC
* * **
348508 ATTTTAATTATCGCAACAC
1 TTTTTCACAATCGCAACAC
*
348527 ATTTTTCAAAATCG
1 -TTTTTCACAATCG
348541 TGTTGCGAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
19 39 0.51
20 9 0.12
21 5 0.06
22 14 0.18
23 7 0.09
25 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (19 bp):
TTTTTCACAATCGCAACAC
Found at i:348959 original size:18 final size:18
Alignment explanation
Indices: 348936--348990 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
348926 CAAAAACGTT
348936 AAAACCATCGACGATGGA
1 AAAACCATCGACGATGGA
*
348954 AAAA-C--CGAACG-T--T
1 AAAACCATCG-ACGATGGA
348967 AAAACCATCGACGATGGA
1 AAAACCATCGACGATGGA
348985 AAAACC
1 AAAACC
348991 GAGACCATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
13 4 0.14
14 1 0.04
15 6 0.21
16 6 0.21
17 1 0.04
18 10 0.36
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (18 bp):
AAAACCATCGACGATGGA
Found at i:348965 original size:31 final size:31
Alignment explanation
Indices: 348930--348992 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
348920 CTCCTCCAAA
348930 AACGTTAAAACCATCGACGATGGAAAAACCG
1 AACGTTAAAACCATCGACGATGGAAAAACCG
348961 AACGTTAAAACCATCGACGATGGAAAAACCG
1 AACGTTAAAACCATCGACGATGGAAAAACCG
348992 A
1 A
348993 GACCATCGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (31 bp):
AACGTTAAAACCATCGACGATGGAAAAACCG
Found at i:350366 original size:19 final size:20
Alignment explanation
Indices: 350342--350392 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
350332 AATGACCAAT
350342 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
350361 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
350381 AAAATCGCAACG
1 AAAATCGCAACG
350393 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:350402 original size:20 final size:20
Alignment explanation
Indices: 350379--350432 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
350369 AACGCGATTT
*
350379 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
350399 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
350419 AGAAAATCGCAACG
1 AGAAAATCGCAACG
350433 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:351513 original size:23 final size:24
Alignment explanation
Indices: 351481--351526 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
351471 AACAAAACTG
351481 AAATATGATAAA-AATAAAAATAAA
1 AAATATGATAAATAA-AAAAATAAA
351505 AAATA-GATAAATAAAAAAATAA
1 AAATATGATAAATAAAAAAATAA
351527 TTTATTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (24 bp):
AAATATGATAAATAAAAAAATAAA
Found at i:352921 original size:27 final size:27
Alignment explanation
Indices: 352886--352942 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
352876 AGAGGTGAGA
*
352886 AGAACGGAGAACGTGAAGGTGAAGAAG
1 AGAACGGAGAACGTGAACGTGAAGAAG
* * *
352913 AGAAGGGAGAATGTGAACGTGAAGATG
1 AGAACGGAGAACGTGAACGTGAAGAAG
352940 AGA
1 AGA
352943 CCTTCAGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.44, C:0.05, G:0.40, T:0.11
Consensus pattern (27 bp):
AGAACGGAGAACGTGAACGTGAAGAAG
Found at i:362062 original size:22 final size:22
Alignment explanation
Indices: 362037--362079 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
362027 TCAGGAGTTA
* *
362037 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
*
362059 CAGGGGTTATATGATATAATT
1 CAGGAGTTATATGATATAATT
362080 TTGGGAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:365177 original size:186 final size:185
Alignment explanation
Indices: 364845--365216 Score: 694
Period size: 186 Copynumber: 2.0 Consensus size: 185
364835 ATTTCTGAGA
364845 TAAATGATTTAGACTTCATTCAGATCCTATAGCTCAAATTTTCCTGTTAGAGAGGATCCTAAAAC
1 TAAATGATTTAGACTTCATTCAGATCC-ATAGCTCAAATTTTCCTGTTAGAGAGGATCCTAAAAC
364910 TTTTGAAGAAGCTATAAGATCTATCGATGCTAGTTTTGGAAAAACGCTGTTAATGATGAACTAGA
65 TTTTGAAGAAGCTATAAGATCTATCGATGCTAGTTTTGGAAAAACGCTGTTAATGATGAACTAGA
364975 ATCGATAATGTCTAATCATACTTGGGAATTAGTTGACTTGCCTAAGGTATTCAAAC
130 ATCGATAATGTCTAATCATACTTGGGAATTAGTTGACTTGCCTAAGGTATTCAAAC
365031 TAAA-GATTTAGACTTCATTTCAGATCC-TAGCTCAAATTTTCCTGTTAGATGAGGATCCTAAAA
1 TAAATGATTTAGACTTCA-TTCAGATCCATAGCTCAAATTTTCCTGTTAGA-GAGGATCCTAAAA
365094 CTTTTGAAGAAGCTATAAGATCTATCGATGCTAGATTTTGGAAAAACGCTGTTAATGATGAACTA
64 CTTTTGAAGAAGCTATAAGATCTATCGATGCTAG-TTTTGGAAAAACGCTGTTAATGATGAACTA
365159 GAATCGATAATGTCTAATCATACTTGGGAATTAGTTGACTTGCCTAAGGTATTCAAAC
128 GAATCGATAATGTCTAATCATACTTGGGAATTAGTTGACTTGCCTAAGGTATTCAAAC
365217 CAATCTCCAA
Statistics
Matches: 183, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
184 22 0.12
185 60 0.33
186 101 0.55
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (185 bp):
TAAATGATTTAGACTTCATTCAGATCCATAGCTCAAATTTTCCTGTTAGAGAGGATCCTAAAACT
TTTGAAGAAGCTATAAGATCTATCGATGCTAGTTTTGGAAAAACGCTGTTAATGATGAACTAGAA
TCGATAATGTCTAATCATACTTGGGAATTAGTTGACTTGCCTAAGGTATTCAAAC
Found at i:367988 original size:22 final size:22
Alignment explanation
Indices: 367963--368017 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
367953 TCAGGAGTTA
* *
367963 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* *
367985 CAGGGGTTATATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
368007 CGGGAGTTATA
1 CAGGAGTTATA
368018 ACATCTTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:381755 original size:156 final size:156
Alignment explanation
Indices: 381471--381782 Score: 624
Period size: 156 Copynumber: 2.0 Consensus size: 156
381461 TGACATGCCA
381471 CTTTATTTGGAGACTCAATCTCTCGAGGAGTTTCCAAAACTGTGTAATTCTGGAAGATTGGGGTT
1 CTTTATTTGGAGACTCAATCTCTCGAGGAGTTTCCAAAACTGTGTAATTCTGGAAGATTGGGGTT
381536 GTCATTGTGGGGTGCCTTGTGCTTATGAACATGAAATCAACCTTGGGTCCAAACGCATTGCTTAG
66 GTCATTGTGGGGTGCCTTGTGCTTATGAACATGAAATCAACCTTGGGTCCAAACGCATTGCTTAG
381601 AAAACCATGTAAAGATTCTAAAGAGG
131 AAAACCATGTAAAGATTCTAAAGAGG
381627 CTTTATTTGGAGACTCAATCTCTCGAGGAGTTTCCAAAACTGTGTAATTCTGGAAGATTGGGGTT
1 CTTTATTTGGAGACTCAATCTCTCGAGGAGTTTCCAAAACTGTGTAATTCTGGAAGATTGGGGTT
381692 GTCATTGTGGGGTGCCTTGTGCTTATGAACATGAAATCAACCTTGGGTCCAAACGCATTGCTTAG
66 GTCATTGTGGGGTGCCTTGTGCTTATGAACATGAAATCAACCTTGGGTCCAAACGCATTGCTTAG
381757 AAAACCATGTAAAGATTCTAAAGAGG
131 AAAACCATGTAAAGATTCTAAAGAGG
381783 TGGCACATAT
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 156 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (156 bp):
CTTTATTTGGAGACTCAATCTCTCGAGGAGTTTCCAAAACTGTGTAATTCTGGAAGATTGGGGTT
GTCATTGTGGGGTGCCTTGTGCTTATGAACATGAAATCAACCTTGGGTCCAAACGCATTGCTTAG
AAAACCATGTAAAGATTCTAAAGAGG
Found at i:382313 original size:81 final size:81
Alignment explanation
Indices: 382184--382545 Score: 293
Period size: 81 Copynumber: 4.4 Consensus size: 81
382174 AGGGTGTTTT
* * * * *
382184 GAAGCAGAGGTTTTGTGAAAGTAAGCCGCT-GCATACTTAT-TATTCAAACGCTTCATTACCTCG
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAG-TAGCATACTTGTCT-TCCAAACTCTTCATTACCTCG
* *
382247 TCTCTGTCAACGTTCTCA
64 TCTCTGTCAAGGTTTTCA
** * * * *
382265 GAATTAGAGGTTTTGTGGAAGTAAGCGGTAGCATACTTGTCTTCCAAACTCTTCATCATCTTGTT
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCATTACCTCG--
* * *
382330 ATCCCTGTCGAGGTTTTTA
64 -TCTCTGTCAAGGTTTTCA
* * * *
382349 GCAGCAGAGTTTTTGTGGAAGTAAGCAGTGGCATACTTGTCTTCCAAACTCTTCACCTT--CTCC
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCA--TTACCTCG
* * * *
382412 TCTTTGCCATGGTTTTTA
64 TCTCTGTCAAGGTTTTCA
* * * * *
382430 GCAGCAGTGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCATCATCTCCTCCTC
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCAT-T--ACCTC
*
382495 GTCTCT-TCCATGGTTTTCA
63 GTCTCTGT-CAAGGTTTTCA
** *
382514 GAATTAGAGGTTTTGTGAAAGTAAGCAGTAGC
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGC
382546 GAATTTTCTT
Statistics
Matches: 225, Mismatches: 43, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
79 1 0.00
80 2 0.01
81 113 0.50
82 1 0.00
84 107 0.48
86 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (81 bp):
GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCATTACCTCGTC
TCTGTCAAGGTTTTCA
Found at i:382372 original size:84 final size:82
Alignment explanation
Indices: 382270--382545 Score: 295
Period size: 84 Copynumber: 3.3 Consensus size: 82
382260 TCTCAGAATT
* * * *
382270 AGAGGTTTTGTGGAAGTAAGCGGTAGCATACTTGTCTTCCAAACTCTTCATCATCTTGTTATCCC
1 AGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCATC--CTTCTCATCCC
*
382335 TGTCGA-GGTTTTTAGCAGC
64 TG-CCATGGTTTTTAGCAGC
* * * **
382354 AGAGTTTTTGTGGAAGTAAGCAGTGGCATACTTGTCTTCCAAACTCTTCA-CCTTCTCCTCTTTG
1 AGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCATCCTTCTCATCCCTG
382418 CCATGGTTTTTAGCAGC
66 CCATGGTTTTTAGCAGC
* * * * *
382435 AGTGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCATCATCTCCTCCTCGTCTC
1 AGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCA--TCCTTCTCATCCC
* * * **
382500 TTCCATGGTTTTCAGAATT
64 TGCCATGGTTTTTAGCAGC
* *
382519 AGAGGTTTTGTGAAAGTAAGCAGTAGC
1 AGAGCTTTTGTGGAAGTAAGCAGTAGC
382546 GAATTTTCTT
Statistics
Matches: 164, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
80 2 0.01
81 67 0.41
83 1 0.01
84 94 0.57
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (82 bp):
AGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCATCCTTCTCATCCCTG
CCATGGTTTTTAGCAGC
Found at i:385912 original size:33 final size:33
Alignment explanation
Indices: 385822--385904 Score: 166
Period size: 33 Copynumber: 2.5 Consensus size: 33
385812 CCTAATCCAT
385822 TGCATCGAGAGGTGAGTGATATTGTGTGAGTAC
1 TGCATCGAGAGGTGAGTGATATTGTGTGAGTAC
385855 TGCATCGAGAGGTGAGTGATATTGTGTGAGTAC
1 TGCATCGAGAGGTGAGTGATATTGTGTGAGTAC
385888 TGCATCGAGAGGTGAGT
1 TGCATCGAGAGGTGAGT
385905 ACCATTGTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.24, C:0.10, G:0.37, T:0.29
Consensus pattern (33 bp):
TGCATCGAGAGGTGAGTGATATTGTGTGAGTAC
Found at i:394092 original size:6 final size:6
Alignment explanation
Indices: 394081--394105 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
394071 GAAGACACGT
394081 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
394106 CGACCACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:394111 original size:6 final size:6
Alignment explanation
Indices: 394102--394132 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
394092 CATTACCATT
394102 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
394133 GCCGAGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:394140 original size:5 final size:5
Alignment explanation
Indices: 394130--394178 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
394120 ACCACGACCA
* * * *
394130 CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
394179 ACGGATGGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.20, C:0.35, G:0.41, T:0.04
Consensus pattern (5 bp):
CGAGC
Found at i:396327 original size:29 final size:29
Alignment explanation
Indices: 396253--396334 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
396243 GTCTCTATTA
*
396253 TAATTTATAAAAGGTTTTATCCTTAATTT
1 TAATTTATAAAAGGTTTTTTCCTTAATTT
*
396282 TAATTTATAAAATGTTTTTTCCTTAATTT
1 TAATTTATAAAAGGTTTTTTCCTTAATTT
*
396311 TAATTTATTTAAA-GTTTTTTCCTT
1 TAATTTA-TAAAAGGTTTTTTCCTT
396335 TTACTAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (29 bp):
TAATTTATAAAAGGTTTTTTCCTTAATTT
Found at i:396344 original size:50 final size:48
Alignment explanation
Indices: 396285--396383 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 48
396275 TTAATTTTAA
* * * * * *
396285 TTTATAAAATGTTTTTTCCTTAATTTTAATTTATTTAAAGTTTTTTCCT
1 TTTATAAAATATTTTGTCCTTAAGTGTAATTTA-TAAAAGTTTTGTCCT
*
396334 TTTACTAAAATATTTTGTCCTTTAGTGTAATTTATAAAAGTTTTGTCCT
1 TTTA-TAAAATATTTTGTCCTTAAGTGTAATTTATAAAAGTTTTGTCCT
396383 T
1 T
396384 AAATGTGATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 18 0.43
50 24 0.57
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.57
Consensus pattern (48 bp):
TTTATAAAATATTTTGTCCTTAAGTGTAATTTATAAAAGTTTTGTCCT
Found at i:396380 original size:28 final size:28
Alignment explanation
Indices: 396346--396400 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
396336 TACTAAAATA
* *
396346 TTTTGTCCTTTAGTGTAATTTATAAAAG
1 TTTTGTCCTTAAATGTAATTTATAAAAG
*
396374 TTTTGTCCTTAAATGTGATTTATAAAA
1 TTTTGTCCTTAAATGTAATTTATAAAA
396401 AGCTGTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (28 bp):
TTTTGTCCTTAAATGTAATTTATAAAAG
Found at i:406959 original size:32 final size:32
Alignment explanation
Indices: 406901--406969 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
406891 CCTAAGGTAG
* *
406901 CCCTTGGGGAGACTCTTAGGCACCAAGTTACT
1 CCCTTGGGGAGACTCTAAGGCACCAAGGTACT
* *
406933 CCCTTGGGTAGGCTCTAAGG-ACCCAAGGTACT
1 CCCTTGGGGAGACTCTAAGGCA-CCAAGGTACT
406965 CCCTT
1 CCCTT
406970 ATGTTGGCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 1 0.03
32 31 0.97
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (32 bp):
CCCTTGGGGAGACTCTAAGGCACCAAGGTACT
Found at i:407455 original size:59 final size:60
Alignment explanation
Indices: 407362--407483 Score: 221
Period size: 59 Copynumber: 2.0 Consensus size: 60
407352 ATTTTTATTG
407362 TGGGTCACTCAGGTGGCCCTAATGTGACACCTCGGATTGGATTGGGTCA-CCATATTAGTC
1 TGGGTCACTCAGGTGGCCCTAATGTGACACCTCGGA-TGGATTGGGTCACCCATATTAGTC
407422 TGGGTCACTCAGG-GGCCCTAATGTGACACCTCGGATGGATTGGGTCACCCATATTAGTC
1 TGGGTCACTCAGGTGGCCCTAATGTGACACCTCGGATGGATTGGGTCACCCATATTAGTC
407481 TGG
1 TGG
407484 AGGTGTTACA
Statistics
Matches: 61, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
58 12 0.20
59 36 0.59
60 13 0.21
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.27
Consensus pattern (60 bp):
TGGGTCACTCAGGTGGCCCTAATGTGACACCTCGGATGGATTGGGTCACCCATATTAGTC
Found at i:410025 original size:21 final size:22
Alignment explanation
Indices: 410001--410044 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
409991 AAACATTTTC
410001 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
410022 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
410044 T
1 T
410045 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:411745 original size:3 final size:3
Alignment explanation
Indices: 411739--411801 Score: 90
Period size: 3 Copynumber: 21.0 Consensus size: 3
411729 ATAATATATT
* *
411739 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
411787 TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
411802 ACGAAAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:411750 original size:18 final size:17
Alignment explanation
Indices: 411727--411801 Score: 100
Period size: 18 Copynumber: 4.4 Consensus size: 17
411717 ATTGGGCTTG
411727 TAATAATATATTTAATAA
1 TAATAATA-ATTTAATAA
411745 TAATAATAA--TAATAA
1 TAATAATAATTTAATAA
*
411760 TAATAATATTTATAATAA
1 TAATAATAATT-TAATAA
411778 TAATAATAATTTTAATAA
1 TAATAATAA-TTTAATAA
411796 TAATAA
1 TAATAA
411802 ACGAAAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
15 14 0.27
17 1 0.02
18 34 0.67
19 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATAATTTAATAA
Found at i:413557 original size:147 final size:146
Alignment explanation
Indices: 413269--413564 Score: 533
Period size: 147 Copynumber: 2.0 Consensus size: 146
413259 TCTTGTAATT
*
413269 TTGGTTCTATAATCTTAATTTTCTGATTATACAACAATTAAAGTACATGGACACGTTCTACAAGT
1 TTGGTTCTATAATCTTAATTTTCTGATTATACAACAATTAAAGTACATGGACAAGTTCTACAAGT
413334 TAAGTATACAGATTAATTCAGGGAGTTCAGAACCTGTAAATTCAATTTTGATTTATTATAGGTTG
66 TAAGTATACAGATTAATTCAGGGAGTTCAGAACCTGTAAATTCAATTTTGATTTATTATAGGTTG
413399 TGTGTTAGCTTCATTG
131 TGTGTTAGCTTCATTG
413415 TTGGTTCTATAATTCTTAATTTTCTGATTATACAACAATTAAAGTACATGGACAAGTTCTACAAG
1 TTGGTTCTATAA-TCTTAATTTTCTGATTATACAACAATTAAAGTACATGGACAAGTTCTACAAG
413480 TTAAGTATACAGA-TAATTCAGGGAGTTCAGAACCTGTAAATTCAATTTTGATTTATTATAGGGG
65 TTAAGTATACAGATTAATTCAGGGAGTTCAGAACCTGTAAATTCAATTTTGATTTATTATA--GG
*
413544 TTGTGTG-TGGCTTCATTG
128 TTGTGTGTTAGCTTCATTG
413562 TTG
1 TTG
413565 TATCTGTAAT
Statistics
Matches: 145, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
146 59 0.41
147 77 0.53
148 9 0.06
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (146 bp):
TTGGTTCTATAATCTTAATTTTCTGATTATACAACAATTAAAGTACATGGACAAGTTCTACAAGT
TAAGTATACAGATTAATTCAGGGAGTTCAGAACCTGTAAATTCAATTTTGATTTATTATAGGTTG
TGTGTTAGCTTCATTG
Found at i:414091 original size:3 final size:3
Alignment explanation
Indices: 414077--414110 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
414067 AAATTTTCGA
*
414077 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
414111 TCTCCTGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:415042 original size:36 final size:37
Alignment explanation
Indices: 414992--415112 Score: 192
Period size: 37 Copynumber: 3.3 Consensus size: 37
414982 ATGGAGTAGG
*
414992 TGGAGTAGGGGGCAATAATG-ATGACTATCAATTTAA
1 TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
415028 TGGAGTAGGTGGCAATAATGGAATG-CTATCAATTTAA
1 TGGAGTAGGTGGCAATAAT-GAATGACTATCAATTTAA
* *
415065 TGGAGTAGGTGGCAATAATGTATGACTAGCAATTTAA
1 TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
415102 TGGAGTAGGTG
1 TGGAGTAGGTG
415113 AAGTAGGTGG
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
36 22 0.28
37 54 0.68
38 3 0.04
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.29
Consensus pattern (37 bp):
TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
Found at i:415046 original size:18 final size:18
Alignment explanation
Indices: 415025--415084 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
415015 ACTATCAATT
415025 TAATGGAGTAGGTGGCAA
1 TAATGGAGTAGGTGGCAA
* * **
415043 TAATGGAAT-GCTATCAA
1 TAATGGAGTAGGTGGCAA
415060 TTTAATGGAGTAGGTGGCAA
1 --TAATGGAGTAGGTGGCAA
415080 TAATG
1 TAATG
415085 TATGACTAGC
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
17 5 0.16
18 13 0.42
19 8 0.26
20 5 0.16
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (18 bp):
TAATGGAGTAGGTGGCAA
Found at i:419491 original size:46 final size:45
Alignment explanation
Indices: 419441--419561 Score: 144
Period size: 46 Copynumber: 2.8 Consensus size: 45
419431 TGAAAGTTTC
*
419441 TCAATTAAATGGAGTAGGTGGAGTAGGTGGCAATAATGAATGACTA
1 TCAATT-AATGGAGTAGGTGGAGTAAGTGGCAATAATGAATGACTA
*
419487 TCAATTTAATGGAGTAGGT--AGTAAGTGGC---AATGTATGACTA
1 TCAA-TTAATGGAGTAGGTGGAGTAAGTGGCAATAATGAATGACTA
* * *
419528 ACAATTAATGGAGTAGGTGGAGTATGTGGTAATA
1 TCAATTAATGGAGTAGGTGGAGTAAGTGGCAATA
419562 TATGGCTAGG
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
40 14 0.22
41 14 0.22
42 8 0.12
44 9 0.14
45 1 0.02
46 16 0.25
47 2 0.03
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.29
Consensus pattern (45 bp):
TCAATTAATGGAGTAGGTGGAGTAAGTGGCAATAATGAATGACTA
Found at i:422983 original size:19 final size:19
Alignment explanation
Indices: 422959--423021 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 19
422949 TTTTATCATA
422959 TAAAATTTTATTTTTTATT
1 TAAAATTTTATTTTTTATT
* **
422978 TAAAA---TATTATCGA--
1 TAAAATTTTATTTTTTATT
422992 TAAAATTTTATTTTTTATT
1 TAAAATTTTATTTTTTATT
*
423011 TAAAATATTAT
1 TAAAATTTTAT
423022 CGTATAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
14 5 0.16
16 6 0.19
17 6 0.19
19 15 0.47
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TAAAATTTTATTTTTTATT
Found at i:423000 original size:33 final size:33
Alignment explanation
Indices: 422944--423035 Score: 148
Period size: 33 Copynumber: 2.7 Consensus size: 33
422934 ATTTAAAAAA
* *
422944 TAAAATTTTATCATATAAAATTTTATTTTTTATT
1 TAAAATATTATC-GATAAAATTTTATTTTTTATT
422978 TAAAATATTATCGATAAAATTTTATTTTTTATT
1 TAAAATATTATCGATAAAATTTTATTTTTTATT
423011 TAAAATATTATCGTATAAAATTTTA
1 TAAAATATTATCG-ATAAAATTTTA
423036 ATTAATATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 33 0.60
34 22 0.40
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (33 bp):
TAAAATATTATCGATAAAATTTTATTTTTTATT
Found at i:424107 original size:22 final size:22
Alignment explanation
Indices: 424079--424120 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
424069 GAAATGTGTA
*
424079 AATAAGGATTAAATGTGTAAAT
1 AATAAGGATTAAATATGTAAAT
424101 AATAAGGATTAAATATGTAA
1 AATAAGGATTAAATATGTAA
424121 TTATACCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (22 bp):
AATAAGGATTAAATATGTAAAT
Found at i:431965 original size:23 final size:23
Alignment explanation
Indices: 431939--431998 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
431929 TATTTTATAT
*
431939 GGCACTACGGTG-TATTCCTACGC
1 GGCACTACGGTGCAATT-CTACGC
* *
431962 GGCACTTCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
431985 GGCACTTA-GGTGCA
1 GGCAC-TACGGTGCA
431999 TTTATACGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:432006 original size:23 final size:23
Alignment explanation
Indices: 431957--432006 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
431947 GGTGTATTCC
* *
431957 TACGCGGCACTTCGGTGCAATTC
1 TACGCGGCACTTAGGTGCAATTA
* *
431980 TACGTGGCACTTAGGTGCATTTA
1 TACGCGGCACTTAGGTGCAATTA
432003 TACG
1 TACG
432007 AGTTGTGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TACGCGGCACTTAGGTGCAATTA
Found at i:437443 original size:29 final size:30
Alignment explanation
Indices: 437395--437453 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
437385 CATGATATGA
*
437395 TATATGACATGAATTCATAT-TATATGCAT
1 TATATGACATGAATTCATATGAATATGCAT
*
437424 TATATGACAATG-ATTTATATGAATATGCAT
1 TATATGAC-ATGAATTCATATGAATATGCAT
437454 GAGAAGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (30 bp):
TATATGACATGAATTCATATGAATATGCAT
Found at i:437787 original size:23 final size:23
Alignment explanation
Indices: 437719--437787 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
437709 ACATTTTATA
*
437719 TGGCACTAT-GGTGCATTCCTACG
1 TGGCACT-TCGGTGCATTTCTACG
* * *
437742 CGGCTCTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
437765 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
437788 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:448206 original size:15 final size:15
Alignment explanation
Indices: 448186--448219 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
448176 TTCATATGTG
*
448186 ATGTAATGTATGAGA
1 ATGTAATGTATAAGA
*
448201 ATGTAATGTTTAAGA
1 ATGTAATGTATAAGA
448216 ATGT
1 ATGT
448220 TATTCTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (15 bp):
ATGTAATGTATAAGA
Found at i:452213 original size:32 final size:32
Alignment explanation
Indices: 452166--452252 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
452156 CCTAAGGTGA
* *
452166 CCCTTGGGGAAGCTCTTAGGCCCCAA-GTTACT
1 CCCTTGGGTAGGCTCTTAGGCCCCAATG-TACT
*
452198 CCCTTGGGTAGGCTCTAAGGCCCCAATGTACT
1 CCCTTGGGTAGGCTCTTAGGCCCCAATGTACT
* * *
452230 CCCTTAGGTTGGCTCTTACGCCC
1 CCCTTGGGTAGGCTCTTAGGCCC
452253 ATTGGGCCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 46 0.98
33 1 0.02
ACGTcount: A:0.16, C:0.33, G:0.24, T:0.26
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTTAGGCCCCAATGTACT
Found at i:454513 original size:24 final size:24
Alignment explanation
Indices: 454476--454545 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
454466 ACAGAGATAT
*
454476 CAGAAATCAAAACATAATTCAGAA
1 CAGAAATCAGAACATAATTCAGAA
* * * * *
454500 CAGATATTAGAACATAATCCATAT
1 CAGAAATCAGAACATAATTCAGAA
*
454524 CAGAAATCAGAACAGAATTCAG
1 CAGAAATCAGAACATAATTCAG
454546 GTCATGTATC
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.20
Consensus pattern (24 bp):
CAGAAATCAGAACATAATTCAGAA
Found at i:454545 original size:12 final size:12
Alignment explanation
Indices: 454476--454568 Score: 55
Period size: 12 Copynumber: 7.8 Consensus size: 12
454466 ACAGAGATAT
* *
454476 CAGAAATCAAAA
1 CAGAATTCAGAA
*
454488 CATAATTCAGAA
1 CAGAATTCAGAA
454500 CAGATATT-AGAA
1 CAGA-ATTCAGAA
* * * *
454512 CATAATCCATAT
1 CAGAATTCAGAA
*
454524 CAGAAATCAGAA
1 CAGAATTCAGAA
**
454536 CAGAATTCAGGT
1 CAGAATTCAGAA
*
454548 CATGTA-TCAGAA
1 CA-GAATTCAGAA
454560 CAGAATTCA
1 CAGAATTCA
454569 AGTCGAAAAT
Statistics
Matches: 57, Mismatches: 20, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
11 4 0.07
12 48 0.84
13 5 0.09
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:454580 original size:24 final size:24
Alignment explanation
Indices: 454527--454582 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
454517 TCCATATCAG
*
454527 AAATCAGAACAGAATTCAGGTCAT
1 AAATCAGAACAGAATTCAAGTCAT
**
454551 GTATCAGAACAGAATTCAAGTCGA-
1 AAATCAGAACAGAATTCAAGTC-AT
454575 AAATCAGA
1 AAATCAGA
454583 TAAAATAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAT
Found at i:455730 original size:18 final size:18
Alignment explanation
Indices: 455707--455742 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
455697 CTTCCATCCG
*
455707 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
455725 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
455743 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:457076 original size:13 final size:14
Alignment explanation
Indices: 457052--457082 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
457042 GTCAACGCCA
457052 GTCAACGTCAACGG
1 GTCAACGTCAACGG
457066 GTCAA-GTCAACGG
1 GTCAACGTCAACGG
457079 GTCA
1 GTCA
457083 GGTCGGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (14 bp):
GTCAACGTCAACGG
Found at i:457092 original size:18 final size:18
Alignment explanation
Indices: 457071--457126 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
457061 AACGGGTCAA
*
457071 GTCAACGGGTCAGGTCGG
1 GTCAACGGGTCGGGTCGG
457089 GTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
457107 GTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
457125 GT
1 GT
457127 TACGACCGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.12, C:0.21, G:0.48, T:0.18
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGG
Found at i:458574 original size:21 final size:21
Alignment explanation
Indices: 458550--458622 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
458540 ATATAACATT
*
458550 AAATGGTTATGAGTGAATAAA
1 AAATGCTTATGAGTGAATAAA
*
458571 AAATGCTTAT-AAT--ATAACA
1 AAATGCTTATGAGTGAATAA-A
458590 TTAAATG-TGTATGAGTGAATAAA
1 --AAATGCT-TATGAGTGAATAAA
458613 AAATGCTTAT
1 AAATGCTTAT
458623 ACATTTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
18 4 0.10
19 1 0.02
20 3 0.07
21 25 0.61
22 3 0.07
23 1 0.02
24 4 0.10
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (21 bp):
AAATGCTTATGAGTGAATAAA
Found at i:458603 original size:42 final size:42
Alignment explanation
Indices: 458540--458623 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
458530 TGTAAGTATG
458540 ATATAACATTAAATGGTTATGAGTGAATAAAAAATGCTTATA
1 ATATAACATTAAATGGTTATGAGTGAATAAAAAATGCTTATA
458582 ATATAACATTAAAT-GTGTATGAGTGAATAAAAAATGCTTATA
1 ATATAACATTAAATGGT-TATGAGTGAATAAAAAATGCTTATA
458624 CATTTAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (42 bp):
ATATAACATTAAATGGTTATGAGTGAATAAAAAATGCTTATA
Found at i:458611 original size:24 final size:24
Alignment explanation
Indices: 458542--458611 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 24
458532 TAAGTATGAT
458542 ATAACATTAAATG-GTTATGAGTGA
1 ATAACATTAAATGTG-TATGAGTGA
*
458566 ATAA-A--AAATGCT-TAT-AAT--
1 ATAACATTAAATG-TGTATGAGTGA
458584 ATAACATTAAATGTGTATGAGTGA
1 ATAACATTAAATGTGTATGAGTGA
458608 ATAA
1 ATAA
458612 AAAATGCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 18
0.64 0.04 0.33
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 3 0.09
21 16 0.46
22 2 0.06
23 1 0.03
24 8 0.23
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (24 bp):
ATAACATTAAATGTGTATGAGTGA
Found at i:460981 original size:3 final size:3
Alignment explanation
Indices: 460973--461022 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
460963 AAATTTTAGA
460973 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
461021 TA
1 TA
461023 ACAAAGCCTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:464455 original size:67 final size:70
Alignment explanation
Indices: 464330--464459 Score: 180
Period size: 70 Copynumber: 1.9 Consensus size: 70
464320 TACCCTCTCA
*
464330 AACGAGAAAATTTCAGAATGTCATAGGGTTACCGATACCCCCCAGTTGGGTACCATACCCCCTCC
1 AACGAGAAAATTACAGAATGTCATAGGGTTACCGATA-CCCCCAGTTGGGTACCATACCCCCTCC
464395 CCCTTG
65 CCCTTG
*
464401 AACGA-AAAATTACAGAATGTCATGAGGG-TA-CGATA-CCCCAG-TGGGTATCGATACCCCCT
1 AACGAGAAAATTACAGAATGTCAT-AGGGTTACCGATACCCCCAGTTGGGTA-CCATACCCCCT
464460 AAAGGAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
66 6 0.11
67 16 0.29
69 5 0.09
70 19 0.35
71 9 0.16
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (70 bp):
AACGAGAAAATTACAGAATGTCATAGGGTTACCGATACCCCCAGTTGGGTACCATACCCCCTCCC
CCTTG
Found at i:466272 original size:23 final size:23
Alignment explanation
Indices: 466237--466304 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
466227 AATCTTATAT
*
466237 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
466260 GGCA-TTACGGTGCAATTCTACGT
1 GGCACTT-CGGTGCATTTCTACGC
* *
466283 GGCACTTTGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
466305 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 2 0.05
23 33 0.89
24 2 0.05
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:470958 original size:14 final size:14
Alignment explanation
Indices: 470939--470967 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
470929 ACTTATATAA
470939 TCACATGAATTATT
1 TCACATGAATTATT
470953 TCACATGAATTATT
1 TCACATGAATTATT
470967 T
1 T
470968 ATACTGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (14 bp):
TCACATGAATTATT
Found at i:472400 original size:20 final size:20
Alignment explanation
Indices: 472375--472452 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
472365 AATATGTATG
472375 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
472395 GCATCCTTTTCATGCATTTTCAATTAT
1 GCATCC-TTTCATGC--CTT--A--AT
*
472422 GGCATCCGTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
472443 GCATCCTTTC
1 GCATCCTTTC
472453 CTGTATTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
20 15 0.33
21 10 0.22
23 3 0.07
25 3 0.07
27 9 0.20
28 6 0.13
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:472435 original size:27 final size:27
Alignment explanation
Indices: 472403--472530 Score: 86
Period size: 27 Copynumber: 5.3 Consensus size: 27
472393 ATGCATCCTT
472403 TTCATGCATTTTCAATTATGGCATCCG
1 TTCATGCATTTTCAATTATGGCATCCG
* *
472430 TTCATGC--CTT--A--AT-GCATCCT
1 TTCATGCATTTTCAATTATGGCATCCG
* *
472450 TTCCTGTATTTTCAATTATGGCATCCG
1 TTCATGCATTTTCAATTATGGCATCCG
* * *
472477 TTCATGC--CTT--A--AT-GTATCCT
1 TTCATGCATTTTCAATTATGGCATCCG
*
472497 TTCCTGCATTTTCAATTATGGCATCCG
1 TTCATGCATTTTCAATTATGGCATCCG
472524 TTCATGC
1 TTCATGC
472531 CTTACATCCT
Statistics
Matches: 71, Mismatches: 16, Indels: 28
0.62 0.14 0.24
Matches are distributed among these distances:
20 22 0.31
21 4 0.06
22 4 0.06
23 2 0.03
24 2 0.03
25 4 0.06
26 4 0.06
27 29 0.41
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (27 bp):
TTCATGCATTTTCAATTATGGCATCCG
Found at i:472478 original size:47 final size:47
Alignment explanation
Indices: 472347--472698 Score: 534
Period size: 47 Copynumber: 7.5 Consensus size: 47
472337 CGTATTAACT
* *
472347 CATCCATTT-ATGCATTTTAATATGTATGGCATCCTTTCATGCCTTAATG
1 CATCC-TTTCATGCATTTTCA-AT-TATGGCATCCGTTCATGCCTTAATG
472396 CATCCTTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
1 CATCC-TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
* *
472444 CATCCTTTCCTGTATTTTCAATTATGGCATCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
* *
472491 TATCCTTTCCTGCATTTTCAATTATGGCATCCGTTCATGCCTT-A--
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
*
472535 CATCCTTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
*
472582 CATCATTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
* *
472629 CATCCGTTCATG-ACTTTTCAATTATGGCATTCGTTCATGCCTTAATG
1 CATCCTTTCATGCA-TTTTCAATTATGGCATCCGTTCATGCCTTAATG
472676 CATCCTTTCATGCATTTTCAATT
1 CATCCTTTCATGCATTTTCAATT
472699 TTGCATTTGA
Statistics
Matches: 281, Mismatches: 16, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
44 40 0.14
45 1 0.00
46 2 0.01
47 188 0.67
48 30 0.11
49 10 0.04
50 10 0.04
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
Found at i:472564 original size:27 final size:27
Alignment explanation
Indices: 472534--472668 Score: 84
Period size: 27 Copynumber: 5.5 Consensus size: 27
472524 TTCATGCCTT
*
472534 ACATCCTTTCATGCATTTTCAATTATG
1 ACATCCGTTCATGCATTTTCAATTATG
*
472561 ACATCCGTTCATGC--CTT--A--ATG
1 ACATCCGTTCATGCATTTTCAATTATG
**
472582 -CATCATTTCATGCATTTTCAATTATG
1 ACATCCGTTCATGCATTTTCAATTATG
* *
472608 GCATCCGTTCATGC--CTT--A--ATG
1 ACATCCGTTCATGCATTTTCAATTATG
472629 -CATCCGTTCATG-ACTTTTCAATTATG
1 ACATCCGTTCATGCA-TTTTCAATTATG
* *
472655 GCATTCGTTCATGC
1 ACATCCGTTCATGC
472669 CTTAATGCAT
Statistics
Matches: 82, Mismatches: 10, Indels: 31
0.67 0.08 0.25
Matches are distributed among these distances:
20 23 0.28
21 6 0.07
22 4 0.05
23 2 0.02
24 2 0.02
25 4 0.05
26 6 0.07
27 35 0.43
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (27 bp):
ACATCCGTTCATGCATTTTCAATTATG
Found at i:472623 original size:138 final size:140
Alignment explanation
Indices: 472347--472698 Score: 521
Period size: 138 Copynumber: 2.5 Consensus size: 140
472337 CGTATTAACT
* * * *
472347 CATCCATTTATGCATTTTAATATGTATGGCATCCTTTCATGCCTTAATGCATCCTTTTCATGCAT
1 CATCCGTTCATGCATTTTCA-AT-TATGGCATCCGTTCATGCCTTAA-GCATCC-TTTCATGCAT
* * * *
472412 TTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCCTGTATTTTCAATTATGGCATCCG
62 TTTCAATTATGACATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTCAATTATGGCATCCG
472477 TTCATGCCTTAATG
127 TTCATGCCTTAATG
* * *
472491 TATCCTTTCCTGCATTTTCAATTATGGCATCCGTTCATGCCTT-A-CATCCTTTCATGCATTTTC
1 CATCCGTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAAGCATCCTTTCATGCATTTTC
472554 AATTATGACATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTCAATTATGGCATCCGTTCA
66 AATTATGACATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTCAATTATGGCATCCGTTCA
472619 TGCCTTAATG
131 TGCCTTAATG
*
472629 CATCCGTTCATG-ACTTTTCAATTATGGCATTCGTTCATGCCTTAATGCATCCTTTCATGCATTT
1 CATCCGTTCATGCA-TTTTCAATTATGGCATCCGTTCATGCCTTAA-GCATCCTTTCATGCATTT
472693 TCAATT
64 TCAATT
472699 TTGCATTTGA
Statistics
Matches: 190, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
137 1 0.01
138 122 0.64
139 6 0.03
141 24 0.13
142 20 0.11
143 2 0.01
144 15 0.08
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (140 bp):
CATCCGTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAAGCATCCTTTCATGCATTTTC
AATTATGACATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTCAATTATGGCATCCGTTCA
TGCCTTAATG
Found at i:472633 original size:20 final size:20
Alignment explanation
Indices: 472562--472688 Score: 74
Period size: 20 Copynumber: 5.7 Consensus size: 20
472552 TCAATTATGA
472562 CATCCGTTCATGCCTTAATG
1 CATCCGTTCATGCCTTAATG
** *
472582 CATCATTTCATGCATTTTCAATTATGG
1 CATCCGTTCATGC--CTT--A--AT-G
472609 CATCCGTTCATGCCTTAATG
1 CATCCGTTCATGCCTTAATG
*
472629 CATCCGTTCATGACTTTTCAATTATGG
1 CATCCGTTCATG-C-CTT--A--AT-G
*
472656 CATTCGTTCATGCCTTAATG
1 CATCCGTTCATGCCTTAATG
*
472676 CATCCTTTCATGC
1 CATCCGTTCATGC
472689 ATTTTCAATT
Statistics
Matches: 82, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
20 36 0.44
21 5 0.06
22 4 0.05
23 2 0.02
24 2 0.02
25 4 0.05
26 5 0.06
27 24 0.29
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.39
Consensus pattern (20 bp):
CATCCGTTCATGCCTTAATG
Found at i:472695 original size:185 final size:188
Alignment explanation
Indices: 472347--472698 Score: 570
Period size: 185 Copynumber: 1.9 Consensus size: 188
472337 CGTATTAACT
* * *
472347 CATCCATTTATGCATTTTAATATGTATGGCATCCTTTCATGCCTTAATGCATCCTTTTCATGCAT
1 CATCCATTTATGCATTTTAATATGTATGACATCCGTTCATGCCTTAATGCATCCATTTCATGCAT
* *
472412 TTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCCTGTATTTTCAATTATGGCATCCG
66 TTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCGTTCATGTATTTTCAATTATGGCATCCG
* *
472477 TTCATGCCTTAATGTATCCTTTCCTGCATTTTCAATTATGGCATCCGTTCATGCCTTA
131 TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTA
*
472535 CATCC-TTTCATGCATTTTCA-AT-TATGACATCCGTTCATGCCTTAATGCAT-CATTTCATGCA
1 CATCCATTT-ATGCATTTTAATATGTATGACATCCGTTCATGCCTTAATGCATCCATTTCATGCA
*
472596 TTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCGTTCATG-ACTTTTCAATTATGGCATT
65 TTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCGTTCATGTA-TTTTCAATTATGGCATC
472660 CGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATT
129 CGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATT
472699 TTGCATTTGA
Statistics
Matches: 153, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
184 1 0.01
185 106 0.69
186 26 0.17
187 5 0.03
188 15 0.10
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (188 bp):
CATCCATTTATGCATTTTAATATGTATGACATCCGTTCATGCCTTAATGCATCCATTTCATGCAT
TTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCGTTCATGTATTTTCAATTATGGCATCCG
TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTA
Found at i:473253 original size:95 final size:95
Alignment explanation
Indices: 473129--473309 Score: 292
Period size: 95 Copynumber: 1.9 Consensus size: 95
473119 TCCTAGTACT
* ** *
473129 GATACTTCTATACATGGTACTGATACCCCCTTCTGGTATCGATACCAAAATTAGCTTCGATGTTT
1 GATACTACTATACATGGTACTGATACCCCCTTAAGGTATCGATACCAAAATTAGATTCGATGTTT
473194 -CATGGTATCGATACCCTTACCACGATATC
66 GCATGGTATCGATACCCTTACCACGATATC
* *
473223 GATACTACTATATTATGGTACTGATACCCCCTTAAGGTATCGATAGCAAAATTAGATTCGATGTT
1 GATACTACTATA-CATGGTACTGATACCCCCTTAAGGTATCGATACCAAAATTAGATTCGATGTT
473288 TGCATGGTATCGATACCCTTAC
65 TGCATGGTATCGATACCCTTAC
473310 AACGGTATTG
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 11 0.14
95 48 0.61
96 20 0.25
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (95 bp):
GATACTACTATACATGGTACTGATACCCCCTTAAGGTATCGATACCAAAATTAGATTCGATGTTT
GCATGGTATCGATACCCTTACCACGATATC
Found at i:480335 original size:23 final size:23
Alignment explanation
Indices: 480305--480353 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
480295 CTGCTCGTGG
480305 CTCAAGAAGAGGTTCTTCTGTGA
1 CTCAAGAAGAGGTTCTTCTGTGA
480328 CTCAAGAAGAGGTTCTTCTGTGA
1 CTCAAGAAGAGGTTCTTCTGTGA
480351 CTC
1 CTC
480354 TGATGTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (23 bp):
CTCAAGAAGAGGTTCTTCTGTGA
Found at i:481050 original size:8 final size:8
Alignment explanation
Indices: 481037--481098 Score: 67
Period size: 8 Copynumber: 7.9 Consensus size: 8
481027 TCATTTTCTT
481037 AGTTTGAG
1 AGTTTGAG
481045 AGTTTGAG
1 AGTTTGAG
*
481053 AGATTT-AA
1 AG-TTTGAG
*
481061 AGTTTGAA
1 AGTTTGAG
481069 AGTTTGA-
1 AGTTTGAG
481076 ACGTTTGAG
1 A-GTTTGAG
481085 AGTTTGAG
1 AGTTTGAG
481093 A-TTTGA
1 AGTTTGA
481099 AAGATATAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
7 9 0.18
8 36 0.73
9 4 0.08
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.39
Consensus pattern (8 bp):
AGTTTGAG
Found at i:481433 original size:83 final size:83
Alignment explanation
Indices: 481172--481701 Score: 550
Period size: 83 Copynumber: 6.4 Consensus size: 83
481162 GTAATGTGAA
** *
481172 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACATGTCTTTCATTTCGGAT
1 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGTCTTTCATTTTGGAT
*
481237 AGGATAGAACACTATGAC
66 AGGATGGAACACTATGAC
* * * * *
481255 ATGACAGAGATTCTCTAAATAATAATGG-AAATGCTTCTCCTGGAACACG-CTTTTCATTTTGGA
1 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGTC-TTTCATTTTGGA
* ** *
481318 TGGGATTAAACACTAT-ATT
65 TAGGATGGAACACTATGA-C
* * * * * * * * *
481337 GTGGCATATATTCTCTAAATAATAATGGAAAACACGTCCCCTGAAACTCTTCTTTCATTTCT-GA
1 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGTCTTTCATTT-TGGA
* *
481401 TAGAATTGAACACTATGAC
65 TAGGATGGAACACTATGAC
* * ***
481420 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGTTTCCCCTGGAACGCGCCTTTCATTTCATAT
1 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGTCTTTCATTTTGGAT
* *
481485 CGGATGGTACACTATGAC
66 AGGATGGAACACTATGAC
* * * * * * *
481503 AT-GCAAGAGATTATCTAAATAATAATAGAAAATGTTTCCCCTGGAACGCGCCTATCATTTTGGA
1 ATGGC-AGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGTCTTTCATTTTGGA
481567 TAGGATGGAACACTATGAC
65 TAGGATGGAACACTATGAC
* * ** * * *
481586 ATGGCATAGATTCTCTGAATAATAATGGAAAATGCTTCCTTTGGAACGTGCCTTTTATTTTGGAT
1 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGTCTTTCATTTTGGAT
*
481651 -GTGATGGAATACTATGAC
66 AG-GATGGAACACTATGAC
*
481669 ATGGCAGAGATTCTATGAATAATAATGGAAAAC
1 ATGGCAGAGATTCTCTGAATAATAATGGAAAAC
481702 ACTATGACAT
Statistics
Matches: 371, Mismatches: 66, Indels: 20
0.81 0.14 0.04
Matches are distributed among these distances:
81 2 0.01
82 69 0.19
83 295 0.80
84 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (83 bp):
ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGTCTTTCATTTTGGAT
AGGATGGAACACTATGAC
Found at i:481694 original size:249 final size:247
Alignment explanation
Indices: 481172--481701 Score: 647
Period size: 249 Copynumber: 2.1 Consensus size: 247
481162 GTAATGTGAA
* * *
481172 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACATGTCTTTCATTTCGGAT
1 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACACGCCTTTCATTTCAGAT
* * *
481237 AGGATAGAACACTATGACATGACAGAGATTCTCTAAATAATAATGGAAATGCTTCTCCTGGAACA
66 AGGATAGAACACTATGACATGACAGAGATTATCTAAATAATAATGAAAATGCTTCCCCTGGAACA
* * * * ** *
481302 CGCTTTTCATTTTGGATGGGATTAAACACTATATTGTGGCATATATTCTCTAAATAATAATGGAA
131 CGCCTATCATTTTGGATAGGATGAAACACTATATCATGGCATAGATTCTCTAAATAATAATGGAA
*
481367 AACACGTCCCCTGAAACTCTTCTTTCATTTCTGATAGAATTGAACACTATGAC
196 AACACGTCCCCTGAAACTC-TCTTTCATTTCTGATAGAATGGAACACTATGAC
* * *
481420 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGTTTCCCCTGGAACGCGCCTTTCATTTCATAT
1 ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACACGCCTTTCATTTCAGAT
* * * *
481485 CGGATGGTACACTATGACATG-CAAGAGATTATCTAAATAATAATAGAAAATGTTTCCCCTGGAA
66 AGGATAGAACACTATGACATGAC-AGAGATTATCTAAATAATAAT-GAAAATGCTTCCCCTGGAA
* * *
481549 CGCGCCTATCATTTTGGATAGGATGGAACACTATGA-CATGGCATAGATTCTCTGAATAATAATG
129 CACGCCTATCATTTTGGATAGGATGAAACACTAT-ATCATGGCATAGATTCTCTAAATAATAATG
** * ** * * * *
481613 GAAAATGCTTCCTTTGGAACGTGC-CTTTTATTT-TGGAT-GTGATGGAATACTATGAC
193 GAAAACACGTCCCCTGAAAC-T-CTCTTTCATTTCT-GATAG-AATGGAACACTATGAC
*
481669 ATGGCAGAGATTCTATGAATAATAATGGAAAAC
1 ATGGCAGAGATTCTCTGAATAATAATGGAAAAC
481702 ACTATGACAT
Statistics
Matches: 241, Mismatches: 34, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
247 1 0.00
248 99 0.41
249 138 0.57
250 2 0.01
251 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (247 bp):
ATGGCAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACACGCCTTTCATTTCAGAT
AGGATAGAACACTATGACATGACAGAGATTATCTAAATAATAATGAAAATGCTTCCCCTGGAACA
CGCCTATCATTTTGGATAGGATGAAACACTATATCATGGCATAGATTCTCTAAATAATAATGGAA
AACACGTCCCCTGAAACTCTCTTTCATTTCTGATAGAATGGAACACTATGAC
Found at i:482740 original size:32 final size:33
Alignment explanation
Indices: 482677--482751 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 33
482667 TCTTTCACAG
*
482677 ACCTTAAACACTAAATAAAAAACATACACATAC
1 ACCTAAAACACTAAATAAAAAACATACACATAC
* *
482710 ACCTAAAACAGTAAAT-AAAAGCATACACATAC
1 ACCTAAAACACTAAATAAAAAACATACACATAC
482742 ACCTAAAACA
1 ACCTAAAACA
482752 AACTTTTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 25 0.64
33 14 0.36
ACGTcount: A:0.57, C:0.24, G:0.03, T:0.16
Consensus pattern (33 bp):
ACCTAAAACACTAAATAAAAAACATACACATAC
Found at i:484708 original size:2 final size:2
Alignment explanation
Indices: 484701--484728 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
484691 TTTAATATCA
484701 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
484729 GTCATTCTAT
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):
AT
Found at i:485563 original size:14 final size:14
Alignment explanation
Indices: 485544--485574 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
485534 CAAAATTATT
485544 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
485558 TAAATAAATTCTAA
1 TAAATAAATTCAAA
485572 TAA
1 TAA
485575 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:485812 original size:16 final size:15
Alignment explanation
Indices: 485793--485836 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
485783 AATTAATTAC
485793 TTAAATAATAAAAAA
1 TTAAATAATAAAAAA
*
485808 TTTAATGAATAAAAAA
1 TTAAAT-AATAAAAAA
*
485824 -TAAATTATAAAAA
1 TTAAATAATAAAAA
485837 CAATTATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 7 0.28
15 9 0.36
16 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
TTAAATAATAAAAAA
Found at i:485819 original size:35 final size:35
Alignment explanation
Indices: 485748--485812 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
485738 ATAAGTTTAC
485748 AATTAATTAATCAAATAAAAAATAAATATTAAAAT
1 AATTAATTAATCAAATAAAAAATAAATATTAAAAT
* * *
485783 AATTAATTACTTAAATAATAAA-AAAT-TTAA
1 AATTAATTAATCAAATAAAAAATAAATATTAA
485813 TGAATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 4 0.15
35 19 0.70
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (35 bp):
AATTAATTAATCAAATAAAAAATAAATATTAAAAT
Found at i:488570 original size:35 final size:35
Alignment explanation
Indices: 488524--488598 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
488514 AAAATACTTC
*
488524 AATTTAGGGTTTAGAATGTAATTGAAGTTTTTTGG
1 AATTTAGGGTTTAGAATGTAATTGAAGTGTTTTGG
*
488559 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATGTAATTGAAGTGTTTTGG
488594 AATTT
1 AATTT
488599 TAAACATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATGTAATTGAAGTGTTTTGG
Found at i:492184 original size:219 final size:220
Alignment explanation
Indices: 491791--492228 Score: 844
Period size: 219 Copynumber: 2.0 Consensus size: 220
491781 GTACCTTCAA
491791 ACAATAATAATTTATCAGCTCCAAATCTTACTTAATTGTTCAAAGCTAAAATTCTTAAGTATATA
1 ACAATAATAATTTATCAGCTCCAAATCTTACTTAATTGTTCAAAGCTAAAATTCTTAAGTATATA
491856 AGCATTTCAGAGTTTGACTATCAATGTGGAGGATTTCGGGTTTGAATTTGGCCAAACGGATTGCG
66 AGCATTTCAGAGTTTGACTATCAATGTGGAGGATTTCGGGTTTGAATTTGGCCAAACGGATTGCG
491921 GATCGGAATCAGGACGTCAAAAAACCATAAAGTATGTCATTTCGAAAATTTAAATTCTTGGTCAA
131 GATCGGAATCAGGACGTCAAAAAACCATAAAGTATGTCATTTCGAAAATTTAAATTCTTGGTCAA
491986 AGTCAAAGTCAACCACTTTGACCGC
196 AGTCAAAGTCAACCACTTTGACCGC
492011 ACAATAATAATTT-TCAGCTCCAAATCTTACTTAATTGTTCAAAGCTAAAATTCTTAAGTATATA
1 ACAATAATAATTTATCAGCTCCAAATCTTACTTAATTGTTCAAAGCTAAAATTCTTAAGTATATA
*
492075 AGCATTTTCAGAGTTTGACTATCAATTTGGAGGATTTCGGGTTTGAATTTGGCCAAACGGATTGC
66 AGCA-TTTCAGAGTTTGACTATCAATGTGGAGGATTTCGGGTTTGAATTTGGCCAAACGGATTGC
492140 GGATCGGAATCAGGACGTCAAAAAA-CATAAAGTATGTCATTTCGAAAATTTAAATTCTTGGTCA
130 GGATCGGAATCAGGACGTCAAAAAACCATAAAGTATGTCATTTCGAAAATTTAAATTCTTGGTCA
492204 AAGTCAAAGTCAACCACTTTGACCG
195 AAGTCAAAGTCAACCACTTTGACCG
492229 TCGATTTGGA
Statistics
Matches: 216, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
219 119 0.55
220 97 0.45
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (220 bp):
ACAATAATAATTTATCAGCTCCAAATCTTACTTAATTGTTCAAAGCTAAAATTCTTAAGTATATA
AGCATTTCAGAGTTTGACTATCAATGTGGAGGATTTCGGGTTTGAATTTGGCCAAACGGATTGCG
GATCGGAATCAGGACGTCAAAAAACCATAAAGTATGTCATTTCGAAAATTTAAATTCTTGGTCAA
AGTCAAAGTCAACCACTTTGACCGC
Found at i:499566 original size:5 final size:5
Alignment explanation
Indices: 499556--499597 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
499546 CTGTCAACGA
499556 TCGGG TCGGG TC-GG TC-GG TC-GG TCGGG TCGGG TC-GG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG T
499598 TGAGTCAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 16 0.46
5 19 0.54
ACGTcount: A:0.00, C:0.21, G:0.55, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:505094 original size:131 final size:131
Alignment explanation
Indices: 504714--505096 Score: 491
Period size: 131 Copynumber: 2.9 Consensus size: 131
504704 GGAAAAAGGA
* * * * * * *
504714 AATATTTAATTATCTT-CTATCGAGAAGAAACAACATCTCATGCCTTAAAGCAATCATCTCTTAC
1 AATATCTAATTAT-TTCCAATCGAGAATAAATAACATCTCATGCCTTAAAGCAGTCATTTATTAC
* * * * * * ** * *
504778 TCCAAGCAAAAT-AAAGAAATATCACTATTTCCTTCTAAAATTTGATATTAAGTCAAGAGAAAAC
65 TCCAACCGAAATGAAA-AGATATTACTATTTCATCCTAAAATTCAATATTAATTCGAGAGAAAAC
504842 GAT
129 GAT
* * *
504845 AATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTACTACT
1 AATATCTAATTATTTCCAATCGAGAATAAATAACATCTCATGCCTTAAAGCAGTCATTTATTACT
* * * * *
504910 CCAATCGAAATGAAGAGATGTTACTATTTCGTCCTAAAATTCAATATTGATTCGAGAGAAAACGA
66 CCAACCGAAATGAAAAGATATTACTATTTCATCCTAAAATTCAATATTAATTCGAGAGAAAACGA
504975 T
131 T
* *
504976 AATATCTAATTATTTCCAATCGAGAATAAATAACATGTTATGCCTTAAAGCAGTCATTTATTACT
1 AATATCTAATTATTTCCAATCGAGAATAAATAACATCTCATGCCTTAAAGCAGTCATTTATTACT
505041 CCAACCGAAATGAAAAGATATTACTATTTCATCCTAAAATTCAATATTAATTCGAG
66 CCAACCGAAATGAAAAGATATTACTATTTCATCCTAAAATTCAATATTAATTCGAG
505097 TGTTACTATT
Statistics
Matches: 217, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
130 2 0.01
131 213 0.98
132 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (131 bp):
AATATCTAATTATTTCCAATCGAGAATAAATAACATCTCATGCCTTAAAGCAGTCATTTATTACT
CCAACCGAAATGAAAAGATATTACTATTTCATCCTAAAATTCAATATTAATTCGAGAGAAAACGA
T
Found at i:505567 original size:24 final size:24
Alignment explanation
Indices: 505540--505589 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
505530 ATTAGTGACT
*
505540 AAAA-TAAAATAAAAGCAACATGCA
1 AAAATTAAAATAAAA-CAAAATGCA
505564 AAAATTAAAATAAAACAAAATGCA
1 AAAATTAAAATAAAACAAAATGCA
505588 AA
1 AA
505590 TAGAACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.70, C:0.10, G:0.06, T:0.14
Consensus pattern (24 bp):
AAAATTAAAATAAAACAAAATGCA
Found at i:508041 original size:3 final size:3
Alignment explanation
Indices: 508033--508084 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
508023 TTTTTCATCC
* * *
508033 TAT TAT TAT TAT TAT TAT TAT TAA TA- TAA TAA TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
508079 TAT TAT
1 TAT TAT
508085 ATATAATTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:508075 original size:26 final size:26
Alignment explanation
Indices: 508039--508091 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
508029 ATCCTATTAT
508039 TATTATTATTATTATTAATATA-ATAA
1 TATTATTATTATT-TTAATATATATAA
*
508065 TATTATTATTATTTTATTATATATAA
1 TATTATTATTATTTTAATATATATAA
508091 T
1 T
508092 TACAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTATTATTATTTTAATATATATAA
Found at i:508088 original size:29 final size:29
Alignment explanation
Indices: 508036--508091 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
508026 TTCATCCTAT
508036 TATTATTATTATTATTATTAATATAATAA
1 TATTATTATTATTATTATTAATATAATAA
508065 TATTATTATTATT-TTATTATATATAAT
1 TATTATTATTATTATTATTA-ATATAAT
508092 TACAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TATTATTATTATTATTATTAATATAATAA
Found at i:508806 original size:54 final size:54
Alignment explanation
Indices: 508741--508904 Score: 217
Period size: 54 Copynumber: 3.0 Consensus size: 54
508731 ATGGAAAGAA
* * * *
508741 ATGTTCATAAAACATGTGACAATACATTCATCATTTCTCGTGGTTTCTG-CATAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCATTTCTCGTGGTTTCTGAC-CAG
* * *
508795 ATGTTCGTAAAACATTTGATAACACATTCATCCTTTCTTGTGGTTTCTGACCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCATTTCTCGTGGTTTCTGACCAG
508849 ATGTTCGTAAAACATTTGACAACACATTCATCATTT-TCTGTGGTTTCT-ACACAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCATTTCTC-GTGGTTTCTGAC-CAG
508903 AT
1 AT
508905 TTCTGATCAA
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
53 3 0.03
54 93 0.96
55 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (54 bp):
ATGTTCGTAAAACATTTGACAACACATTCATCATTTCTCGTGGTTTCTGACCAG
Found at i:509959 original size:31 final size:33
Alignment explanation
Indices: 509899--509960 Score: 85
Period size: 31 Copynumber: 1.9 Consensus size: 33
509889 TTATATTTCT
*
509899 TTAATTTTAGTCATATTAATATATATTATTTGA
1 TTAATTTTAGTCAAATTAATATATATTATTTGA
509932 TTAATTTT-GT-AAATTAATA-ATATTTATTT
1 TTAATTTTAGTCAAATTAATATATA-TTATTT
509961 TTAAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 3 0.11
31 14 0.52
32 2 0.07
33 8 0.30
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (33 bp):
TTAATTTTAGTCAAATTAATATATATTATTTGA
Found at i:510041 original size:24 final size:24
Alignment explanation
Indices: 510014--510060 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
510004 TTTTTTGATA
510014 TTTT-TAAATAAGTAAATATTTTAC
1 TTTTATAAATAA-TAAATATTTTAC
* *
510038 TTTTATAAATTATATATATTTTA
1 TTTTATAAATAATAAATATTTTA
510061 ATTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTTATAAATAATAAATATTTTAC
Found at i:516616 original size:38 final size:38
Alignment explanation
Indices: 516574--516655 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
516564 AAAATTCACT
* *
516574 AAATAATAAACTCGTTCGCTTCAATTAAGTAATAAACA
1 AAATAATAAAATCATTCGCTTCAATTAAGTAATAAACA
* *
516612 AAATAATAAAATCATTCGCTTGAATTAAGTAATATACA
1 AAATAATAAAATCATTCGCTTCAATTAAGTAATAAACA
516650 AAATAA
1 AAATAA
516656 ATTAAGTCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (38 bp):
AAATAATAAAATCATTCGCTTCAATTAAGTAATAAACA
Found at i:516982 original size:27 final size:27
Alignment explanation
Indices: 516951--517008 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
516941 TAATTTAATA
* * * * *
516951 AATATTATAGAAATTAATATATAAACT
1 AATATTAAACAAATAAATAAATAAAAT
516978 AATATTAAACAAATAAATAAATAAAAT
1 AATATTAAACAAATAAATAAATAAAAT
517005 AATA
1 AATA
517009 CCAATAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (27 bp):
AATATTAAACAAATAAATAAATAAAAT
Found at i:525162 original size:71 final size:71
Alignment explanation
Indices: 525043--525177 Score: 193
Period size: 71 Copynumber: 1.9 Consensus size: 71
525033 TCGTGTATGT
* *
525043 GTTTTAACTAATTTGTTTTTTGTTCTCTTCATTCTATTCTCATCC-TTTTTTGCTTTGTAACTAG
1 GTTTTAACTAATTTGTTTTTTATTCTCTTCATACTATTCTCATCCTTTTTTTGCTTTGTAACTAG
525107 TATCTC
66 TATCTC
** *
525113 GTTTTAACTAATTTGTTTTTTTATTCGT-TTTGTACTATTCTCATGCTTTTTTTGCTTTGTAACT
1 GTTTTAACTAATTTG-TTTTTTATTC-TCTTCATACTATTCTCATCCTTTTTTTGCTTTGTAACT
525177 A
64 A
525178 ATAAGTATCT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
70 15 0.26
71 23 0.40
72 19 0.33
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.59
Consensus pattern (71 bp):
GTTTTAACTAATTTGTTTTTTATTCTCTTCATACTATTCTCATCCTTTTTTTGCTTTGTAACTAG
TATCTC
Found at i:548086 original size:13 final size:13
Alignment explanation
Indices: 548049--548087 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
548039 ATTTAAAAAT
548049 CAAAAGAAAATAA
1 CAAAAGAAAATAA
548062 CAATAA-AAAATAA
1 CAA-AAGAAAATAA
*
548075 CAAAAGATAATAA
1 CAAAAGAAAATAA
548088 TAAATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 2 0.09
13 19 0.83
14 2 0.09
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (13 bp):
CAAAAGAAAATAA
Found at i:548861 original size:21 final size:21
Alignment explanation
Indices: 548819--548859 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
548809 TTAAATTATA
548819 ATTAAAATATATAAAATATTT
1 ATTAAAATATATAAAATATTT
548840 ATTAAAA-ATA-AATAATATTT
1 ATTAAAATATATAA-AATATTT
548860 TAATAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 10 0.53
21 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAAAATATATAAAATATTT
Found at i:552090 original size:3 final size:3
Alignment explanation
Indices: 552082--552122 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
552072 ATGCTACCAT
552082 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA T
552123 TAAAATCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:552245 original size:14 final size:14
Alignment explanation
Indices: 552226--552258 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
552216 CTATCATGAA
552226 CATGCTTCATAACT
1 CATGCTTCATAACT
552240 CATGCTTCATAACT
1 CATGCTTCATAACT
552254 CATGC
1 CATGC
552259 AACCTACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.33
Consensus pattern (14 bp):
CATGCTTCATAACT
Found at i:553730 original size:26 final size:26
Alignment explanation
Indices: 553701--553753 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
553691 TTTATAAAGA
553701 AGCCAGTGAGGAAAGAGGTAAAATTT
1 AGCCAGTGAGGAAAGAGGTAAAATTT
553727 AGCCAGTGAGGAAAGAGGTAAAATTT
1 AGCCAGTGAGGAAAGAGGTAAAATTT
553753 A
1 A
553754 TAGGTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.30, T:0.19
Consensus pattern (26 bp):
AGCCAGTGAGGAAAGAGGTAAAATTT
Found at i:554642 original size:6 final size:6
Alignment explanation
Indices: 554631--554658 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
554621 ATTTAAAATA
554631 AATTGT AATTGT AATTGT AATTGT AATT
1 AATTGT AATTGT AATTGT AATTGT AATT
554659 AATTTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (6 bp):
AATTGT
Found at i:557014 original size:20 final size:19
Alignment explanation
Indices: 556988--557037 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
556978 TAGACTATCA
*
556988 CAACGCGAATCTGAAAATCG
1 CAACGCGAAT-GGAAAATCG
*
557008 TAACGCGAAATGGAAAATCG
1 CAACGCG-AATGGAAAATCG
557028 CAACGCGAAT
1 CAACGCGAAT
557038 TTAAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 20 0.77
21 3 0.12
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (19 bp):
CAACGCGAATGGAAAATCG
Found at i:563795 original size:23 final size:22
Alignment explanation
Indices: 563751--563795 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
563741 AATGCCAGAG
*
563751 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
563773 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
563796 AAATTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:564838 original size:24 final size:25
Alignment explanation
Indices: 564784--564830 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 25
564774 ATTTATTATG
*
564784 AGAATTATAATGGAGCTATATGAAA
1 AGAATTATAATGGAGATATATGAAA
564809 AG-ATTATAAT-GA-ATATATGAAA
1 AGAATTATAATGGAGATATATGAAA
564831 TTGAATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 2 0.10
24 8 0.38
25 2 0.10
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.30
Consensus pattern (25 bp):
AGAATTATAATGGAGATATATGAAA
Found at i:565502 original size:100 final size:101
Alignment explanation
Indices: 565267--565583 Score: 539
Period size: 100 Copynumber: 3.1 Consensus size: 101
565257 GTCGAGGGTC
565267 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTC--GTGAGACACATAC
565332 TTGATCCTTGGCATATGT-TATGATTCTTAAGGAATGA
64 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
565369 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTC-TGAGACACATACTT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGTGAGACACATACTT
565433 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
565469 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTC--GTGAGACACATAC
* * *
565534 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
64 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
565572 TATGTAGTCCTT
1 TATGTGGTCCTT
565584 ATGGATATTA
Statistics
Matches: 205, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
99 30 0.15
100 68 0.33
102 50 0.24
103 57 0.28
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (101 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGTGAGACACATACTT
GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:565655 original size:23 final size:23
Alignment explanation
Indices: 565599--565658 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
565589 TATTATTATA
565599 TGGCACTAC-GTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
565621 CGGCGCTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
565644 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
565659 TTTATATGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:569323 original size:24 final size:24
Alignment explanation
Indices: 569289--569342 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
569279 TCGTTAAAAT
*
569289 GATAAACGAACACAAATGAACGAA
1 GATAAACGAACACAAAAGAACGAA
* *
569313 GATAAATGAACATAAAAGAACGAA
1 GATAAACGAACACAAAAGAACGAA
*
569337 CATAAA
1 GATAAA
569343 ATTAATTGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.61, C:0.13, G:0.15, T:0.11
Consensus pattern (24 bp):
GATAAACGAACACAAAAGAACGAA
Found at i:569564 original size:14 final size:14
Alignment explanation
Indices: 569522--569566 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
569512 TGGGTCTGAA
*
569522 GAACATAAACGAAC
1 GAACATAAACGAAT
* **
569536 GTACATAAATAAAT
1 GAACATAAACGAAT
569550 GAACATAAACGAAT
1 GAACATAAACGAAT
569564 GAA
1 GAA
569567 TTACCGAATG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (14 bp):
GAACATAAACGAAT
Found at i:582605 original size:20 final size:20
Alignment explanation
Indices: 582580--582618 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
582570 GGGAACCTAT
582580 ACCTTCTAATGTTCGGATGA
1 ACCTTCTAATGTTCGGATGA
582600 ACCTTCTAATGTTCGGATG
1 ACCTTCTAATGTTCGGATG
582619 GGGATAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
ACCTTCTAATGTTCGGATGA
Found at i:584115 original size:15 final size:16
Alignment explanation
Indices: 584095--584125 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
584085 GTTCATGCAT
584095 TTAATTTT-TGTTAAA
1 TTAATTTTATGTTAAA
584110 TTAATTTTATGTTAAA
1 TTAATTTTATGTTAAA
584126 ATTCAGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TTAATTTTATGTTAAA
Found at i:585968 original size:24 final size:24
Alignment explanation
Indices: 585917--585982 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
585907 CAATCTTATA
* *
585917 TGGCACTACGGTGT-ATTTCTATG
1 TGGCACTACGGTGTAAATTCTACG
* *
585940 CGGCACTTCGGTGTAAATTCTACG
1 TGGCACTACGGTGTAAATTCTACG
*
585964 TGGCACTACGGTGCAAATT
1 TGGCACTACGGTGTAAATT
585983 TATACGATCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
23 12 0.34
24 23 0.66
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (24 bp):
TGGCACTACGGTGTAAATTCTACG
Found at i:592927 original size:19 final size:20
Alignment explanation
Indices: 592903--592940 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
592893 GCAAAATTTA
592903 TCAACT-ACATAATCAAAAG
1 TCAACTGACATAATCAAAAG
*
592922 TCAACTGACATATTCAAAA
1 TCAACTGACATAATCAAAA
592941 AGTGGGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (20 bp):
TCAACTGACATAATCAAAAG
Found at i:594625 original size:120 final size:119
Alignment explanation
Indices: 594413--594658 Score: 483
Period size: 120 Copynumber: 2.1 Consensus size: 119
594403 AGGAAAGGCT
594413 AGTTTGCTGCTGATAGTTTCATTTACATGTGTGTCTGTCTACTTGTTTCTTATGGTTCTGAATAT
1 AGTTTGCTGCTGATAGTTTCATTTACATGTGTGTCTGTCTACTTGTTTCTTATGGTTCTGAATAT
594478 GTCCTTTCTCCTATGGCTGCCTTCTTGAAATAAAAAAATGATCATTTTAAGTTG
66 GTCCTTTCTCCTATGGCTGCCTTCTTGAAATAAAAAAATGATCATTTTAAGTTG
594532 AGTTTGCTGCTGATAGTTTTCATTTACATGTGTGTCTGTCTACTTGTTTCTTATGGTTCTGAATA
1 AGTTTGCTGCTGATAG-TTTCATTTACATGTGTGTCTGTCTACTTGTTTCTTATGGTTCTGAATA
594597 TGTCCTTTCTCCTATGGCTGCCTTCTTGAAATAAAAAAATGATCATTTTAAGTTG
65 TGTCCTTTCTCCTATGGCTGCCTTCTTGAAATAAAAAAATGATCATTTTAAGTTG
594652 AGTTTGC
1 AGTTTGC
594659 AGCTAGATCG
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 16 0.13
120 110 0.87
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.45
Consensus pattern (119 bp):
AGTTTGCTGCTGATAGTTTCATTTACATGTGTGTCTGTCTACTTGTTTCTTATGGTTCTGAATAT
GTCCTTTCTCCTATGGCTGCCTTCTTGAAATAAAAAAATGATCATTTTAAGTTG
Found at i:604669 original size:53 final size:53
Alignment explanation
Indices: 604611--604716 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
604601 CAATAGCACT
*
604611 ATAGCAGTGTTGTTGTCATGACTGAACCTG-ATTTATCATGCGAGGACTAAGCA
1 ATAGCAGTATTGTTGTCATGACTGAACCTGAATTT-TCATGCGAGGACTAAGCA
604664 ATAGCAGTATTGTTGTCATGACTGAACCTGAATTTTCATGCGAGGACTAAGCA
1 ATAGCAGTATTGTTGTCATGACTGAACCTGAATTTTCATGCGAGGACTAAGCA
604717 TGTTGAATTG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
53 47 0.92
54 4 0.08
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (53 bp):
ATAGCAGTATTGTTGTCATGACTGAACCTGAATTTTCATGCGAGGACTAAGCA
Found at i:605948 original size:22 final size:23
Alignment explanation
Indices: 605913--605972 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
605903 GAACTCATGT
605913 GCCCAAT-ATATGCACTTCAAT-A
1 GCCCAATGAT-TGCACTTCAATAA
* * *
605935 GCCCCATGCTTGCACTTTAATAA
1 GCCCAATGATTGCACTTCAATAA
605958 GCCCAATGATTGCAC
1 GCCCAATGATTGCAC
605973 CAATGGTGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (23 bp):
GCCCAATGATTGCACTTCAATAA
Found at i:607425 original size:47 final size:47
Alignment explanation
Indices: 607374--607472 Score: 180
Period size: 47 Copynumber: 2.1 Consensus size: 47
607364 ATACACATCC
607374 TATCAAATCATCTCACTCATATGCTTTTCATATAACAATTACATACA
1 TATCAAATCATCTCACTCATATGCTTTTCATATAACAATTACATACA
* *
607421 TATCAAATCATCTCACTCATATGTTTTTCATATAACAATTACATACG
1 TATCAAATCATCTCACTCATATGCTTTTCATATAACAATTACATACA
607468 TATCA
1 TATCA
607473 TCATTTATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (47 bp):
TATCAAATCATCTCACTCATATGCTTTTCATATAACAATTACATACA
Found at i:607837 original size:23 final size:23
Alignment explanation
Indices: 607803--607871 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
607793 CATCGCAACT
*
607803 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
607826 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
607849 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
607872 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:609579 original size:24 final size:20
Alignment explanation
Indices: 609525--609562 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
609515 TTCCCCTTGA
609525 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
609545 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
609563 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:610763 original size:20 final size:20
Alignment explanation
Indices: 610734--610785 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
610724 ACAGACTGAA
*
610734 AGTATAGATACTAGCCCAAG
1 AGTATCGATACTAGCCCAAG
610754 AGTATCGATACTAGCCCAAG
1 AGTATCGATACTAGCCCAAG
610774 AGTATCGATACT
1 AGTATCGATACT
610786 CCTGCAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
AGTATCGATACTAGCCCAAG
Found at i:615114 original size:162 final size:163
Alignment explanation
Indices: 614847--615172 Score: 645
Period size: 162 Copynumber: 2.0 Consensus size: 163
614837 CTACATAATC
614847 AGTGTAATAAATGTTATGTTTCTTTAAGTATGCAATCATTCAAACTTTTTCGAGTTTGTTTTTGG
1 AGTGTAATAAATGTTATGTTTCTTTAAGTATGCAATCATTCAAACTTTTTCGAGTTTGTTTTTGG
614912 TCTATACCGGTTAAGTTCTTTTGTAGCTAGATGTTTTCTAACGTTAAATAA-TGGTTGAAGAACT
66 TCTATACCGGTTAAGTTCTTTTGTAGCTAGATGTTTTCTAACGTTAAATAATTGGTTGAAGAACT
614976 GAAGAACATTGTCTGCAAATCAATTATTGATGG
131 GAAGAACATTGTCTGCAAATCAATTATTGATGG
615009 AGTGTAATAAATGTTATGTTTCTTTAAGTATGCAATCATTCAAACTTTTTCGAGTTTGTTTTTGG
1 AGTGTAATAAATGTTATGTTTCTTTAAGTATGCAATCATTCAAACTTTTTCGAGTTTGTTTTTGG
615074 TCTATACCGGTTAAGTTCTTTTGTAGCTAGATGTTTTCTAACGTTAAATAATTGGTTGAAGAACT
66 TCTATACCGGTTAAGTTCTTTTGTAGCTAGATGTTTTCTAACGTTAAATAATTGGTTGAAGAACT
615139 GAAGAACATTGTCTGCAAATCAATTATTGATGG
131 GAAGAACATTGTCTGCAAATCAATTATTGATGG
615172 A
1 A
615173 AACATTGCTC
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 116 0.71
163 47 0.29
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.41
Consensus pattern (163 bp):
AGTGTAATAAATGTTATGTTTCTTTAAGTATGCAATCATTCAAACTTTTTCGAGTTTGTTTTTGG
TCTATACCGGTTAAGTTCTTTTGTAGCTAGATGTTTTCTAACGTTAAATAATTGGTTGAAGAACT
GAAGAACATTGTCTGCAAATCAATTATTGATGG
Found at i:616425 original size:24 final size:24
Alignment explanation
Indices: 616398--616476 Score: 158
Period size: 24 Copynumber: 3.3 Consensus size: 24
616388 TTTCATTTTT
616398 GTTCTGCAAACTATTTTTAGTTCA
1 GTTCTGCAAACTATTTTTAGTTCA
616422 GTTCTGCAAACTATTTTTAGTTCA
1 GTTCTGCAAACTATTTTTAGTTCA
616446 GTTCTGCAAACTATTTTTAGTTCA
1 GTTCTGCAAACTATTTTTAGTTCA
616470 GTTCTGC
1 GTTCTGC
616477 TATCCTTAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (24 bp):
GTTCTGCAAACTATTTTTAGTTCA
Found at i:620067 original size:30 final size:30
Alignment explanation
Indices: 620022--620099 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
620012 AAACAAGGGC
620022 TTAAAAGATCTAAAAT-G-ACAAAAACAAAAAT
1 TTAAAAGA-CTAAAATAGTAC--AAACAAAAAT
*
620053 TTAAAAGACTAAAATAGTACAAACAAGAAT
1 TTAAAAGACTAAAATAGTACAAACAAAAAT
*
620083 TTAAAGGACTAAAATAG
1 TTAAAAGACTAAAATAG
620100 CACTTAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 32 0.74
31 9 0.21
32 2 0.05
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (30 bp):
TTAAAAGACTAAAATAGTACAAACAAAAAT
Found at i:622416 original size:63 final size:65
Alignment explanation
Indices: 622343--622536 Score: 214
Period size: 68 Copynumber: 2.9 Consensus size: 65
622333 AAAGAGACAA
* *
622343 AATTCGTTTCAAGCG-AATGA-CTCAAAGATG-GTATTGTTTCAAGAGAAACAGACTTAAAGATT
1 AATTCGTTTCAAG-GAAACGATCTCAAAGATGTGTATTGTTTCAAGAGAAACAGACTCAAAGATT
622405 T
65 T
* * * *
622406 AATTCATTTCAAGGTAAACGATCTCAAAGATGTTTGTTTTGTTTCAAGGGAAATAGACTCAAAGA
1 AATTCGTTTCAAGG-AAACGATCTCAAAGATG--TGTATTGTTTCAAGAGAAACAGACTCAAAGA
622471 TTT
63 TTT
* * * *
622474 AATTCGTTTCAAGGGAAACTATCTCAAAGATGTTTGTTTTGTTTCAAGGGAAACAAACTCAAA
1 AATTCGTTTCAA-GGAAACGATCTCAAAGATG--TGTATTGTTTCAAGAGAAACAGACTCAAA
622537 TATGGATATT
Statistics
Matches: 114, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
62 1 0.01
63 12 0.11
64 4 0.04
65 10 0.09
68 85 0.75
69 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (65 bp):
AATTCGTTTCAAGGAAACGATCTCAAAGATGTGTATTGTTTCAAGAGAAACAGACTCAAAGATTT
Found at i:622417 original size:33 final size:33
Alignment explanation
Indices: 622343--622536 Score: 139
Period size: 35 Copynumber: 5.8 Consensus size: 33
622333 AAAGAGACAA
* * *
622343 AATTCGTTTCAAGCG-AA-TGACTCAAAGATGGT
1 AATTCGTTTCAAGGGAAACAGACTCAAAGAT-TT
* *
622375 -ATT-GTTTCAAGAGAAACAGACTTAAAGATTT
1 AATTCGTTTCAAGGGAAACAGACTCAAAGATTT
* *
622406 AATTCATTTCAAGGTAAAC-GATCTCAAAGATGTTT
1 AATTCGTTTCAAGGGAAACAGA-CTCAAAGA--TTT
** * *
622441 GTTTTGTTTCAAGGGAAATAGACTCAAAGATTT
1 AATTCGTTTCAAGGGAAACAGACTCAAAGATTT
*
622474 AATTCGTTTCAAGGGAAACTA-TCTCAAAGATGTTT
1 AATTCGTTTCAAGGGAAAC-AGACTCAAAGA--TTT
** * *
622509 GTTTTGTTTCAAGGGAAACAAACTCAAA
1 AATTCGTTTCAAGGGAAACAGACTCAAA
622537 TATGGATATT
Statistics
Matches: 127, Mismatches: 23, Indels: 21
0.74 0.13 0.12
Matches are distributed among these distances:
30 9 0.07
31 6 0.05
32 15 0.12
33 44 0.35
34 2 0.02
35 49 0.39
36 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (33 bp):
AATTCGTTTCAAGGGAAACAGACTCAAAGATTT
Done.