Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 101 of 141
Found at i:28721535 original size:25 final size:25
Alignment explanation
Indices: 28721522--28721647 Score: 75
Period size: 25 Copynumber: 5.2 Consensus size: 25
28721512 ACTTAATTTG
28721522 CATAATAAATAACTTACATAACTCA
1 CATAATAAATAACTTACATAACTCA
* *
28721547 CATAATACATAACTT--AT-AC-GA
1 CATAATAAATAACTTACATAACTCA
* * * * * **
28721568 CTTACATAACTTACATAGCATAATTTT
1 CATA-ATAAATAACTTA-CATAACTCA
* * **
28721595 CATAATAAAAAACTTACATAATTTT
1 CATAATAAATAACTTACATAACTCA
28721620 CATAATAAATAACTTACATAA-T-A
1 CATAATAAATAACTTACATAACTCA
28721643 CATAA
1 CATAA
28721648 CTTACATAGC
Statistics
Matches: 78, Mismatches: 17, Indels: 14
0.72 0.16 0.13
Matches are distributed among these distances:
21 4 0.05
22 9 0.12
23 7 0.09
24 1 0.01
25 45 0.58
26 9 0.12
27 3 0.04
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.33
Consensus pattern (25 bp):
CATAATAAATAACTTACATAACTCA
Found at i:28721631 original size:16 final size:16
Alignment explanation
Indices: 28721620--28721655 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28721610 ACATAATTTT
28721620 CATAATAAATAACTTA
1 CATAATAAATAACTTA
*
28721636 CATAATACATAACTTA
1 CATAATAAATAACTTA
28721652 CATA
1 CATA
28721656 GCTTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (16 bp):
CATAATAAATAACTTA
Found at i:28729161 original size:21 final size:21
Alignment explanation
Indices: 28729135--28729174 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28729125 CAGCAGCTTA
*
28729135 AAGCAGATGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
28729156 AAGCAGAGGCTGCAGCGAG
1 AAGCAGAGGCAGCAGCGAG
28729175 GGAATCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.40, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:28729186 original size:21 final size:21
Alignment explanation
Indices: 28729146--28729187 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28729136 AGCAGATGCA
*
28729146 GCAGCGAGAGAAGCAGAGGCT
1 GCAGCGAGAGAAGCAAAGGCT
* *
28729167 GCAGCGAGGGAATCAAAGGCT
1 GCAGCGAGAGAAGCAAAGGCT
28729188 AAAATGAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.40, T:0.07
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAAAGGCT
Found at i:28729896 original size:66 final size:65
Alignment explanation
Indices: 28729789--28729959 Score: 227
Period size: 66 Copynumber: 2.6 Consensus size: 65
28729779 GAGCAAATTA
* * * *
28729789 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
28729853 G
65 G
*
28729854 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
28729919 G
65 G
* * * *
28729920 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
28729960 CGGCAGCTAG
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.02
66 88 0.94
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:28729956 original size:21 final size:21
Alignment explanation
Indices: 28729930--28730042 Score: 82
Period size: 21 Copynumber: 5.4 Consensus size: 21
28729920 CAGCAGCTTA
*
28729930 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
*
28729951 AAGCAGAGGCGGCAGCTAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* * * * * *
28729972 AAGTACAGGCTGCAACGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
*** * *
28729993 AAGCAGAGGCTAAAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
* * *
28730014 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
28730035 AAGCAGAG
1 AAGCAGAG
28730043 CAGCGTCAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.35, C:0.18, G:0.42, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:28729997 original size:42 final size:42
Alignment explanation
Indices: 28729950--28730042 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
28729940 GGCAGCAAGA
** * *
28729950 GAAGCAGAGGCGGCAGCTAGAGAAGTACAGGCTGCAACGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCTGCAACGAGG
* * * *
28729992 GAAGCAGAGGCTAAAGCGAGGGAAGCAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCTGCAACGAGG
28730034 GAAGCAGAG
1 GAAGCAGAG
28730043 CAGCGTCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.17, G:0.43, T:0.05
Consensus pattern (42 bp):
GAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCTGCAACGAGG
Found at i:28730441 original size:43 final size:43
Alignment explanation
Indices: 28730394--28730579 Score: 196
Period size: 43 Copynumber: 4.3 Consensus size: 43
28730384 AGGTGTTGGC
28730394 CTTTAGTGGCGTCTT-TGGTAAAAGCGCCGCTAAAGATAAGGTT
1 CTTTAGTGGCGT-TTGTGGTAAAAGCGCCGCTAAAGATAAGGTT
* * * *
28730437 CTTTAGTGGCGTTTGTAGAAAAAGCGCCCCTAAAGATCATGG-T
1 CTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGAT-AAGGTT
* ** * *
28730480 CTTTAGCGGCGTTTGTGGGGAAAGTGCCGCTAAAGATTAGGTT
1 CTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGGTT
** * * *
28730523 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGGTT
* *
28730566 CGTTAGCGGCGTTT
1 CTTTAGTGGCGTTT
28730580 TAGGGAGAAG
Statistics
Matches: 118, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
42 4 0.03
43 111 0.94
44 3 0.03
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (43 bp):
CTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGGTT
Found at i:28730509 original size:86 final size:86
Alignment explanation
Indices: 28730414--28730593 Score: 245
Period size: 86 Copynumber: 2.1 Consensus size: 86
28730404 GTCTTTGGTA
*
28730414 AAAGCGCCGCTAAAGATAAGGTTCTTTAGTGGCGTTTGTAGAAAAAGCGCCCCTAAAGATCATGG
1 AAAGCGCCGCTAAAGATAAGGTTCTTTAGTGGCGTTTGTAGAAAAAGCGCCCCTAAAGATCAGGG
*
28730479 TCTTTAGCGGCGTTTGTGGGG
66 TCGTTAGCGGCGTTTGTGGGG
* * * *** * *
28730500 AAAGTGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATAAGGTTCTTTAGTGGCGTTTGTAGAAAAAGCGCCCCTAAAGATCAGGG
*
28730565 TCGTTAGCGGCGTTT-TAGGG
66 TCGTTAGCGGCGTTTGTGGGG
28730585 AGAAGCGCC
1 A-AAGCGCC
28730594 TAAAGACCCT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 5 0.06
86 76 0.94
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGATAAGGTTCTTTAGTGGCGTTTGTAGAAAAAGCGCCCCTAAAGATCAGGG
TCGTTAGCGGCGTTTGTGGGG
Found at i:28730646 original size:43 final size:43
Alignment explanation
Indices: 28730593--28730698 Score: 133
Period size: 43 Copynumber: 2.5 Consensus size: 43
28730583 GGAGAAGCGC
* *
28730593 CTAAAGACCCTAATCTTTAGCAGCACTTGTCGCAA-AAACGCCG
1 CTAAAGACCCTGATCTTTAGCAGCACTT-TCCCAACAAACGCCG
* * * *
28730636 CTAACGACCCTGGTCTATAGCAGCGCTTTCCCAACAAACGCCG
1 CTAAAGACCCTGATCTTTAGCAGCACTTTCCCAACAAACGCCG
*
28730679 CTAAAGACCATGATCTTTAG
1 CTAAAGACCCTGATCTTTAG
28730699 GGGCGTTTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 5 0.10
43 47 0.90
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (43 bp):
CTAAAGACCCTGATCTTTAGCAGCACTTTCCCAACAAACGCCG
Found at i:28731421 original size:18 final size:18
Alignment explanation
Indices: 28731389--28731433 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28731379 GTGCAATTTG
*
28731389 TAATAA-AATACAT-AAA
1 TAATAATAATAAATAAAA
28731405 TAGATAATAATAAATAAAA
1 TA-ATAATAATAAATAAAA
28731424 TAATAATAAT
1 TAATAATAAT
28731434 GATAGTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 4 0.16
18 14 0.56
19 5 0.20
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAATAATAATAAATAAAA
Found at i:28732839 original size:3 final size:3
Alignment explanation
Indices: 28732833--28732899 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
28732823 TTTGATGTTG
* * * *
28732833 TTA TTA TTA TTA TTA TTA TTA TCA ATA TCA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28732881 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
28732900 CATGTATTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28735406 original size:27 final size:27
Alignment explanation
Indices: 28735308--28735421 Score: 133
Period size: 27 Copynumber: 4.2 Consensus size: 27
28735298 TTTTGTTAAA
* *
28735308 AATTACCCGAATTACCCG-ATTAACCG
1 AATTAACCGAATTACCTGAATTAACCG
28735334 AATTAACCGAATTAACC-GAATTAACCG
1 AATTAACCGAATT-ACCTGAATTAACCG
* *
28735361 AATTAACCGAATTAACTGAATTAACTG
1 AATTAACCGAATTACCTGAATTAACCG
* *
28735388 AATTAATCGAATTACCTGAAAATTACCCG
1 AATTAACCGAATTACCTG--AATTAACCG
28735417 AATTA
1 AATTA
28735422 CCCAAAAAGT
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.20
27 49 0.64
29 12 0.16
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (27 bp):
AATTAACCGAATTACCTGAATTAACCG
Found at i:28735420 original size:9 final size:9
Alignment explanation
Indices: 28735308--28735401 Score: 136
Period size: 9 Copynumber: 10.6 Consensus size: 9
28735298 TTTTGTTAAA
*
28735308 AATTACCCG
1 AATTAACCG
*
28735317 AATTACCCG
1 AATTAACCG
28735326 -ATTAACCG
1 AATTAACCG
28735334 AATTAACCG
1 AATTAACCG
28735343 AATTAACCG
1 AATTAACCG
28735352 AATTAACCG
1 AATTAACCG
28735361 AATTAACCG
1 AATTAACCG
*
28735370 AATTAACTG
1 AATTAACCG
*
28735379 AATTAACTG
1 AATTAACCG
*
28735388 AATTAATCG
1 AATTAACCG
28735397 AATTA
1 AATTA
28735402 CCTGAAAATT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
8 7 0.09
9 73 0.91
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:28736612 original size:29 final size:29
Alignment explanation
Indices: 28736572--28736630 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
28736562 TCGTGGAAGA
* *
28736572 GGTGGAGAACTTATTCGTTGAGAGTTCGT
1 GGTGAAGAACTTATTCGTTGAGAATTCGT
* * *
28736601 GGTGAAGAACTTGTTTGTTGATAATTCGT
1 GGTGAAGAACTTATTCGTTGAGAATTCGT
28736630 G
1 G
28736631 TCAAGGTGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.22, C:0.08, G:0.32, T:0.37
Consensus pattern (29 bp):
GGTGAAGAACTTATTCGTTGAGAATTCGT
Found at i:28743841 original size:13 final size:14
Alignment explanation
Indices: 28743822--28743859 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
28743812 CAATGACATA
28743822 GAAATAATATAAAC
1 GAAATAATATAAAC
28743836 -AAATAA-ATAAAC
1 GAAATAATATAAAC
28743848 GAAACTAATATA
1 GAAA-TAATATA
28743860 CATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:28743870 original size:27 final size:26
Alignment explanation
Indices: 28743822--28743874 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
28743812 CAATGACATA
*
28743822 GAAATAATATAAACAAATAAATAAAC
1 GAAATAATATAAACAAAAAAATAAAC
* *
28743848 GAAACTAATATACATAAAAAAATAAAC
1 GAAA-TAATATAAACAAAAAAATAAAC
28743875 AATGACAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.68, C:0.09, G:0.04, T:0.19
Consensus pattern (26 bp):
GAAATAATATAAACAAAAAAATAAAC
Found at i:28744299 original size:28 final size:28
Alignment explanation
Indices: 28744267--28744321 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
28744257 TGTACATATA
28744267 TATAAAAAATAAAT-CTATATATATAAAT
1 TATAAAAAATAAATAC-ATATATATAAAT
*
28744295 TATAAAAAATAATTACATATATATAAA
1 TATAAAAAATAAATACATATATATAAA
28744322 AAATAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (28 bp):
TATAAAAAATAAATACATATATATAAAT
Found at i:28747248 original size:24 final size:24
Alignment explanation
Indices: 28747221--28747272 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
28747211 AATCAAAGTC
* * *
28747221 AAATATATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
28747245 AAATAAATTATACTCATAAATACT
1 AAATAAATTATACTAATAAATACT
28747269 AAAT
1 AAAT
28747273 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:28752001 original size:31 final size:29
Alignment explanation
Indices: 28751966--28752043 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 29
28751956 TCATAATTAC
* *
28751966 AAAAGTATAGGGACTAAAAGTGAGCAATTT
1 AAAAGTATAAGGACTAAAAGTGAGCAA-AT
* * * * *
28751996 GAAAAGTACATGGACTGAAATTGATCAAAT
1 -AAAAGTATAAGGACTAAAAGTGAGCAAAT
28752026 AAAAGTATAAGGACTAAA
1 AAAAGTATAAGGACTAAA
28752044 TTTGCAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 15 0.39
30 1 0.03
31 22 0.58
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.22
Consensus pattern (29 bp):
AAAAGTATAAGGACTAAAAGTGAGCAAAT
Found at i:28758253 original size:152 final size:152
Alignment explanation
Indices: 28758054--28758358 Score: 601
Period size: 152 Copynumber: 2.0 Consensus size: 152
28758044 AAGTTCTCTT
28758054 TAAAGCATTCAATAGATTTTATTCTTGTTAGCTTTCAAAAGTATAAAAATATCATCTTTGGTTGT
1 TAAAGCATTCAATAGATTTTATTCTTGTTAGCTTTCAAAAGTATAAAAATATCATCTTTGGTTGT
28758119 GGTTTCATCATCTTTCTTGTTGCCATCCTCTTCAACAAAGACTCCTTCAAGAGTCACTAAGAAAC
66 GGTTTCATCATCTTTCTTGTTGCCATCCTCTTCAACAAAGACTCCTTCAAGAGTCACTAAGAAAC
28758184 TCTAAATCTTGTCCATTTATGG
131 TCTAAATCTTGTCCATTTATGG
28758206 TAAAGCATTCAATAGATTTTATTCTTGTTAGCTTTCAAAAGTATAAAAATATCATCTTTGGTTGT
1 TAAAGCATTCAATAGATTTTATTCTTGTTAGCTTTCAAAAGTATAAAAATATCATCTTTGGTTGT
*
28758271 GGTTTCATCATCTTTCTTGTTGCCATCCTCTTCAACAGAGACTCCTTCAAGAGTCACTAAGAAAC
66 GGTTTCATCATCTTTCTTGTTGCCATCCTCTTCAACAAAGACTCCTTCAAGAGTCACTAAGAAAC
28758336 TCTAAATCTTGTCCATTTATGG
131 TCTAAATCTTGTCCATTTATGG
28758358 T
1 T
28758359 TATTTGATGA
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (152 bp):
TAAAGCATTCAATAGATTTTATTCTTGTTAGCTTTCAAAAGTATAAAAATATCATCTTTGGTTGT
GGTTTCATCATCTTTCTTGTTGCCATCCTCTTCAACAAAGACTCCTTCAAGAGTCACTAAGAAAC
TCTAAATCTTGTCCATTTATGG
Found at i:28762999 original size:50 final size:50
Alignment explanation
Indices: 28762890--28763186 Score: 321
Period size: 50 Copynumber: 5.8 Consensus size: 50
28762880 ATTTGGGTAA
*
28762890 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
28762946 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
28762996 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
28763046 AGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATA
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
28763096 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* *** *
28763145 AAACACCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28763187 TGTTATTATC
Statistics
Matches: 208, Mismatches: 30, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
49 38 0.18
50 124 0.60
51 1 0.00
53 3 0.01
55 2 0.01
56 40 0.19
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28765903 original size:3 final size:3
Alignment explanation
Indices: 28765895--28765919 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28765885 TAACATGTTT
28765895 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
28765920 CATCATCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:28765924 original size:3 final size:3
Alignment explanation
Indices: 28765918--28765955 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
28765908 AATAATAATA
28765918 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
28765956 TTTTCTTCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:28768477 original size:101 final size:101
Alignment explanation
Indices: 28768302--28768505 Score: 390
Period size: 101 Copynumber: 2.0 Consensus size: 101
28768292 CGGGCTTGAG
*
28768302 AGCTTCTGCTGTTTTGCTCCTTCCTTGGATGTCTGAGACTTTTTTTAACCCCGTAGTATAAATAT
1 AGCTTCTGCTGTTTTGCTCCTTCCTTGGATGGCTGAGACTTTTTTTAACCCCGTAGTATAAATAT
28768367 GTTTTTCTTTTATGTTAATTAAATCTGATTTTTACT
66 GTTTTTCTTTTATGTTAATTAAATCTGATTTTTACT
*
28768403 AGCTTCTGCTGTTTTGCTCCTTGCTTGGATGGCTGAGACTTTTTTTAACCCCGTAGTATAAATAT
1 AGCTTCTGCTGTTTTGCTCCTTCCTTGGATGGCTGAGACTTTTTTTAACCCCGTAGTATAAATAT
28768468 GTTTTTCTTTTATGTTAATTAAATCTGATTTTTACT
66 GTTTTTCTTTTATGTTAATTAAATCTGATTTTTACT
28768504 AG
1 AG
28768506 TCATCAACTT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (101 bp):
AGCTTCTGCTGTTTTGCTCCTTCCTTGGATGGCTGAGACTTTTTTTAACCCCGTAGTATAAATAT
GTTTTTCTTTTATGTTAATTAAATCTGATTTTTACT
Found at i:28769354 original size:288 final size:287
Alignment explanation
Indices: 28768715--28769409 Score: 1037
Period size: 288 Copynumber: 2.4 Consensus size: 287
28768705 TATAAAGTCG
*
28768715 ATGATGATAAGTTGTAAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGTCTAAGAGCTTTCGCCT
1 ATGATGATAAGTTGTAAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGACTAAGAGCTTTCGCCT
*
28768780 TTCGCCGGGCTTGAGAGCTTGTGCTGCTTCCTTCCTTCCTTGGATGTCTGAGACCTTTTATGACT
66 TTCGCCGGGCTTGAGAGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTTATGACT
* * *
28768845 TCTATATGGTTGTTGTTTTCACTATTTGTGCTTGAAAACCCAGTCACTTCCTCAGAAATCTGGTT
131 TCTATATAGTTGTTGTTTTCACTATTTGCGCTTGAAAACCCAATCACTTCCTCAGAAATCTGGTT
* *
28768910 GTACATTTTTTCCCCTTTTTTTTATTCAGTTCAATTGATAAACGATATTCTTAAAATTCAGTCAA
196 GTACATTTTTT-CCC-TTATTTTATTCAGTTCAATTGATAAACGATATTCATAAAATTCAGTCAA
**
28768975 AGGAAAATATATTTGTTGTGTATAGGTTT
259 AGGAAAATATATTTCATGTGTATAGGTTT
***
28769004 ATGATGATAA-TCCAAAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGACTAAGAGCTTTCGCCT
1 ATGATGATAAGTTGTAAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGACTAAGAGCTTTCGCCT
28769068 TTCGCCGGGCTTGAGAGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTTATGACT
66 TTCGCCGGGCTTGAGAGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTTATGACT
* * * * * *
28769133 TGTATATAGTTG-T-TTTTCATTATTTGCGCTTGAAAATCCAATTATTTTCTCAGAAATCTGGTT
131 TCTATATAGTTGTTGTTTTCACTATTTGCGCTTGAAAACCCAATCACTTCCTCAGAAATCTGGTT
* * * * *
28769196 GTATA-TTTTT-CC-TATTTT-TTCAGTTCCATTGATAAACGGTATTCATAAAATTGAGTCAAAT
196 GTACATTTTTTCCCTTATTTTATTCAGTTCAATTGATAAACGATATTCATAAAATTCAGTCAAAG
* *
28769257 GATAATATATTTCATGTGTATGGGTTT
261 GAAAATATATTTCATGTGTATAGGTTT
* * * *
28769284 ATGATGATAAGTTGTAAGGCTTGTTTCTCAAAACATTCGCAGGGGCCGCCTGAGAGCTTTCGCTT
1 ATGATGATAAGTTGTAAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGACTAAGAGCTTTCGCCT
*
28769349 TTCGCCGGGCTTGAGAGCTTGTGCTGCTT-TTATCCTTCCTTGGATGTCTGAGACCTTTTAT
66 TTCGCCGGGCTTGAGAGCTTGTGCTGCTTCAT-TCCTTCCTTGGATGTCTGAGACCTTTTAT
28769410 TATATCTTTA
Statistics
Matches: 371, Mismatches: 33, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
280 72 0.19
281 110 0.30
283 2 0.01
285 5 0.01
286 47 0.13
287 1 0.00
288 124 0.33
289 10 0.03
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (287 bp):
ATGATGATAAGTTGTAAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGACTAAGAGCTTTCGCCT
TTCGCCGGGCTTGAGAGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTTATGACT
TCTATATAGTTGTTGTTTTCACTATTTGCGCTTGAAAACCCAATCACTTCCTCAGAAATCTGGTT
GTACATTTTTTCCCTTATTTTATTCAGTTCAATTGATAAACGATATTCATAAAATTCAGTCAAAG
GAAAATATATTTCATGTGTATAGGTTT
Found at i:28769916 original size:18 final size:18
Alignment explanation
Indices: 28769877--28769919 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28769867 TTAAATTGGA
* *
28769877 TATTTCT-CTCAATTTGT
1 TATTTCTACTCAATATCT
*
28769894 AATTTCTACTCAATATCT
1 TATTTCTACTCAATATCT
28769912 TATTTCTA
1 TATTTCTA
28769920 TTGTTATGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (18 bp):
TATTTCTACTCAATATCT
Found at i:28789369 original size:24 final size:22
Alignment explanation
Indices: 28789330--28789373 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
28789320 TCCTCTGGCC
*
28789330 TTTTTTTGCGTTTTGCTGCTGT
1 TTTTTTTGCGTGTTGCTGCTGT
28789352 TTTTTTGTGCGTGGTTGCTGCT
1 TTTTTT-TGCGT-GTTGCTGCT
28789374 TGCGCTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 8 0.42
ACGTcount: A:0.00, C:0.14, G:0.27, T:0.59
Consensus pattern (22 bp):
TTTTTTTGCGTGTTGCTGCTGT
Found at i:28791314 original size:5 final size:5
Alignment explanation
Indices: 28791304--28791332 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28791294 TATTCAAATT
28791304 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
28791333 TATGAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:28793041 original size:5 final size:5
Alignment explanation
Indices: 28793031--28793058 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28793021 TGTCCCACAG
28793031 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
28793059 CCTTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:28794195 original size:51 final size:50
Alignment explanation
Indices: 28794120--28794256 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 50
28794110 TTTAATTGTT
* * * *
28794120 TTCAAATATGAT-ATTTTAAATAAATATAAATATTTATTTAATTTTTTTTG
1 TTCAGATATGATGTTTTTAAATAAATATAAATATTTATTT-ATATTATTTG
* * *
28794170 TTTAGATATGATGTTTTTACATAAATATAAATATTTGTTTATATTATTTG
1 TTCAGATATGATGTTTTTAAATAAATATAAATATTTATTTATATTATTTG
*
28794220 TTCAGATAT--TGTATTTAATATAAATATAAATATTTAT
1 TTCAGATATGATGTTTTTAA-ATAAATATAAATATTTAT
28794257 ATTTGTTCGC
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 7 0.09
49 17 0.23
50 26 0.35
51 24 0.32
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (50 bp):
TTCAGATATGATGTTTTTAAATAAATATAAATATTTATTTATATTATTTG
Found at i:28794227 original size:50 final size:49
Alignment explanation
Indices: 28794103--28794254 Score: 157
Period size: 50 Copynumber: 3.0 Consensus size: 49
28794093 TTTCAAGATC
* * *
28794103 TTGTTTATTTAATTGTTTTCAAATATGAT-ATTTTAAATAAATATAAATAT
1 TTGTTTATTT-ATT-TGTTCAGATATGATGTTTTTAAATAAATATAAATAT
* * * *
28794153 TTATTTAATTTTTTTTGTTTAGATATGATGTTTTTACATAAATATAAATAT
1 TTGTTT-A-TTTATTTGTTCAGATATGATGTTTTTAAATAAATATAAATAT
*
28794204 TTGTTTATATTATTTGTTCAGATAT--TGTATTTAATATAAATATAAATAT
1 TTGTTTAT-TTATTTGTTCAGATATGATGTTTTTAA-ATAAATATAAATAT
28794253 TT
1 TT
28794255 ATATTTGTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
48 7 0.08
49 17 0.20
50 31 0.36
51 27 0.32
52 3 0.04
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (49 bp):
TTGTTTATTTATTTGTTCAGATATGATGTTTTTAAATAAATATAAATAT
Found at i:28794630 original size:81 final size:82
Alignment explanation
Indices: 28794384--28794726 Score: 422
Period size: 81 Copynumber: 4.2 Consensus size: 82
28794374 AAAAAGTTAA
* * ** *
28794384 AATTAAATAATTCTGTTTCGGGATTTATTCCCGCTGTTTAACAGATTTTGTTTC-ATTTTGATTT
1 AATTGAATAATTCTGTTCCGGGATTTATTCCCGCCATTTAACAGATTTT-ATTCGATTTTGATTT
*
28794448 TGTTTCCAAACGAGAATT
65 TGTTTCCAAATGAGAATT
* * * ** * * * *
28794466 AATTGAATAATTCTATTTCAGGATTTATTCTTGCCATTTAACATATTTGATTTGATTTTTATTTT
1 AATTGAATAATTCTGTTCCGGGATTTATTCCCGCCATTTAACAGATTTTATTCGATTTTGATTTT
*
28794531 GTTTCCAGATGAGAATT
66 GTTTCCAAATGAGAATT
* * *
28794548 AATTGAATAATTCTGTTCCGGAATTTATTCCCGTCA-TTAATAGATTTTATTCGATTTTGATTTT
1 AATTGAATAATTCTGTTCCGGGATTTATTCCCGCCATTTAACAGATTTTATTCGATTTTGATTTT
28794612 GTTTCCAAATGAGAATT
66 GTTTCCAAATGAGAATT
* *
28794629 AATTGAATAATTCTGTTCCGGGA-TTATTCCTGCCATTTAACATATTTTATTCGATTTTGATTTT
1 AATTGAATAATTCTGTTCCGGGATTTATTCCCGCCATTTAACAGATTTTATTCGATTTTGATTTT
* * *
28794693 ATTTCCAAATAAGATTT
66 GTTTCCAAATGAGAATT
* *
28794710 AATTAAATAATTTTGTT
1 AATTGAATAATTCTGTT
28794727 TCGAGATTCA
Statistics
Matches: 222, Mismatches: 37, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
80 10 0.05
81 118 0.53
82 94 0.42
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.48
Consensus pattern (82 bp):
AATTGAATAATTCTGTTCCGGGATTTATTCCCGCCATTTAACAGATTTTATTCGATTTTGATTTT
GTTTCCAAATGAGAATT
Found at i:28798118 original size:50 final size:50
Alignment explanation
Indices: 28798003--28798107 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 50
28797993 CAAAATTTTG
28798003 TTTATTTAA-TT-A-TT-TTTAGATATGATGTTTTAAATAAATATAAATA
1 TTTATTTAATTTGATTTGTTTAGATATGATGTTTTAAATAAATATAAATA
* * * *
28798049 TTTATTTAATTTGTTTTGTTTAGATCTGGTGTTTTTATATAAATATAAATA
1 TTTATTTAATTTGATTTGTTTAGATATGATG-TTTTAAATAAATATAAATA
*
28798100 TTTTTTTA
1 TTTATTTA
28798108 TATTATTTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
46 9 0.18
47 2 0.04
49 2 0.04
50 11 0.22
51 25 0.51
ACGTcount: A:0.33, C:0.01, G:0.09, T:0.57
Consensus pattern (50 bp):
TTTATTTAATTTGATTTGTTTAGATATGATGTTTTAAATAAATATAAATA
Found at i:28802216 original size:43 final size:43
Alignment explanation
Indices: 28802155--28802244 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
28802145 AAATACAAGG
*
28802155 GACACACGACCGTGTCACATGGCCGTGTGTCACACACGATTGA
1 GACACACGACCATGTCACATGGCCGTGTGTCACACACGATTGA
*
28802198 GACACACGACCATGTCACATGGCCGTGTGTCACACACGGTTGA
1 GACACACGACCATGTCACATGGCCGTGTGTCACACACGATTGA
28802241 GACA
1 GACA
28802245 TGCGTCCGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.18
Consensus pattern (43 bp):
GACACACGACCATGTCACATGGCCGTGTGTCACACACGATTGA
Found at i:28803231 original size:25 final size:24
Alignment explanation
Indices: 28803171--28803332 Score: 121
Period size: 25 Copynumber: 6.6 Consensus size: 24
28803161 ATACAAGTAT
28803171 GCTCATACGAG-CATGTAATCGGGAA
1 GCTCATACGAGCCAT-TAA-CGGGAA
* *
28803196 GCTCTTTCGAGCCATGTAACGGGAA
1 GCTCATACGAGCCAT-TAACGGGAA
*
28803221 GCTCATACGAGCCATAAACGGGAA
1 GCTCATACGAGCCATTAACGGGAA
* * * * *
28803245 GCTCAAAAGAGCCAAATATCGCGAA
1 GCTCATACGAGCC-ATTAACGGGAA
* * *
28803270 GCTCATGCGAGCCAATATCGGGAA
1 GCTCATACGAGCCATTAACGGGAA
* *
28803294 GCTC-TGAAGAGCCATTAATTGGGAA
1 GCTCAT-ACGAGCCATTAA-CGGGAA
* *
28803319 GCTTATAAGAGCCA
1 GCTCATACGAGCCA
28803333 ATTATCAAGA
Statistics
Matches: 111, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
23 1 0.01
24 41 0.37
25 61 0.55
26 8 0.07
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (24 bp):
GCTCATACGAGCCATTAACGGGAA
Found at i:28803257 original size:49 final size:48
Alignment explanation
Indices: 28803204--28803334 Score: 129
Period size: 49 Copynumber: 2.7 Consensus size: 48
28803194 AAGCTCTTTC
28803204 GAGCCATGTAACGGGAAGCTCATACGAGCC-ATAAACGGGAAGCTCAAAA
1 GAGCCAT-TAACGGGAAGCTCATACGAGCCAAT-AACGGGAAGCTCAAAA
* * * * * **
28803253 GAGCCAAATATCGCGAAGCTCATGCGAGCCAATATCGGGAAGCTCTGAA
1 GAGCC-ATTAACGGGAAGCTCATACGAGCCAATAACGGGAAGCTCAAAA
* * *
28803302 GAGCCATTAATTGGGAAGCTTATAAGAGCCAAT
1 GAGCCATTAA-CGGGAAGCTCATACGAGCCAAT
28803335 TATCAAGAAG
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
48 3 0.05
49 59 0.91
50 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (48 bp):
GAGCCATTAACGGGAAGCTCATACGAGCCAATAACGGGAAGCTCAAAA
Found at i:28803318 original size:74 final size:74
Alignment explanation
Indices: 28803188--28803396 Score: 181
Period size: 74 Copynumber: 2.8 Consensus size: 74
28803178 CGAGCATGTA
* * * * * *
28803188 ATCGGGAAGCTCTTTCGAGCCATGTAACGGGAAGCTCAT-ACGAGCCATAAACGGGAAGCTCAAA
1 ATCGAGAAGCTCATGCGAGCCA-ATATCGGGAAGCTCATGAAGAGCCATAAACGGGAAGCTCAAA
28803252 AGAGCCAAAT
65 AGAGCCAAAT
* ** * *
28803262 ATCGCGAAGCTCATGCGAGCCAATATCGGGAAGCTC-TGAAGAGCCATTAATTGGGAAGCTTATA
1 ATCGAGAAGCTCATGCGAGCCAATATCGGGAAGCTCATGAAGAGCCA-TAAACGGGAAGCTCAAA
*
28803326 AGAGCCAATT
65 AGAGCCAAAT
* ** * * * * *
28803336 ATCAAGAAGCTTGTGAGAGTCAATTATCAGGAAGCTCTTG-AGAGCCAAATAACGGGAAGCT
1 ATCGAGAAGCTCATGCGAGCCAA-TATCGGGAAGCTCATGAAGAGCCATA-AACGGGAAGCT
28803397 TGTGAGAGCC
Statistics
Matches: 109, Mismatches: 21, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
72 1 0.01
73 19 0.17
74 59 0.54
75 28 0.26
76 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (74 bp):
ATCGAGAAGCTCATGCGAGCCAATATCGGGAAGCTCATGAAGAGCCATAAACGGGAAGCTCAAAA
GAGCCAAAT
Found at i:28803344 original size:25 final size:25
Alignment explanation
Indices: 28803252--28803429 Score: 125
Period size: 25 Copynumber: 7.2 Consensus size: 25
28803242 GAAGCTCAAA
*
28803252 AGAGCCAAATATC-GCGAAGCTCATG
1 AGAGCCAAATATCAG-GAAGCTTATG
* * *
28803277 CGAGCC-AATATCGGGAAGC-TCTG
1 AGAGCCAAATATCAGGAAGCTTATG
* *
28803300 AAGAGCCATTAAT-T-GGGAAGCTTATA
1 -AGAGCCA--AATATCAGGAAGCTTATG
* * *
28803326 AGAGCCAATTATCAAGAAGCTTGTG
1 AGAGCCAAATATCAGGAAGCTTATG
* *
28803351 AGAGTCAATTATCAGGAAGCTCT-TG
1 AGAGCCAAATATCAGGAAGCT-TATG
* * *
28803376 AGAGCCAAATAACGGGAAGCTTGTG
1 AGAGCCAAATATCAGGAAGCTTATG
* *
28803401 AGAGCCAAATATCAGGACGCTTATA
1 AGAGCCAAATATCAGGAAGCTTATG
28803426 AGAG
1 AGAG
28803430 TTGTGGTGTG
Statistics
Matches: 121, Mismatches: 22, Indels: 20
0.74 0.13 0.12
Matches are distributed among these distances:
23 4 0.03
24 18 0.15
25 92 0.76
26 4 0.03
27 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (25 bp):
AGAGCCAAATATCAGGAAGCTTATG
Found at i:28803370 original size:50 final size:50
Alignment explanation
Indices: 28803315--28803429 Score: 142
Period size: 50 Copynumber: 2.3 Consensus size: 50
28803305 CCATTAATTG
* * * *
28803315 GGAAGCTTATAAGAGCCAATTATCAAGAAGCTTGTGAGAGTCAATTATCA
1 GGAAGCTTATAAGAGCCAAATAACAAGAAGCTTGTGAGAGCCAAATATCA
* **
28803365 GGAAGCTCT-TGAGAGCCAAATAACGGGAAGCTTGTGAGAGCCAAATATCA
1 GGAAGCT-TATAAGAGCCAAATAACAAGAAGCTTGTGAGAGCCAAATATCA
*
28803415 GGACGCTTATAAGAG
1 GGAAGCTTATAAGAG
28803430 TTGTGGTGTG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.02
50 52 0.96
51 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.22
Consensus pattern (50 bp):
GGAAGCTTATAAGAGCCAAATAACAAGAAGCTTGTGAGAGCCAAATATCA
Found at i:28803395 original size:75 final size:74
Alignment explanation
Indices: 28803229--28803414 Score: 189
Period size: 75 Copynumber: 2.5 Consensus size: 74
28803219 AAGCTCATAC
* * * ** * *
28803229 GAGCCATA-AACGGGAAGCTCAAAAGAGCCAAATATCGCGAAGCTCATGCGAGCCAATATCGGGA
1 GAGCCAAATAACGGGAAGCTTATAAGAGCCAAATATCAAGAAGCTCATGAGAGCCAATATCAGGA
28803293 AGCTCTGAA
66 AGCTCTGAA
* * * ** *
28803302 GAGCC-ATTAATTGGGAAGCTTATAAGAGCCAATTATCAAGAAGCTTGTGAGAGTCAATTATCAG
1 GAGCCAAATAA-CGGGAAGCTTATAAGAGCCAAATATCAAGAAGCTCATGAGAGCCAA-TATCAG
28803366 GAAGCTCTTG-A
64 GAAGCTC-TGAA
* *
28803377 GAGCCAAATAACGGGAAGCTTGTGAGAGCCAAATATCA
1 GAGCCAAATAACGGGAAGCTTATAAGAGCCAAATATCA
28803415 GGACGCTTAT
Statistics
Matches: 90, Mismatches: 18, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
73 7 0.08
74 36 0.40
75 41 0.46
76 6 0.07
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (74 bp):
GAGCCAAATAACGGGAAGCTTATAAGAGCCAAATATCAAGAAGCTCATGAGAGCCAATATCAGGA
AGCTCTGAA
Found at i:28816247 original size:18 final size:18
Alignment explanation
Indices: 28816224--28816260 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28816214 TCGAATTAGT
28816224 AGAAAATCATATACGAGC
1 AGAAAATCATATACGAGC
28816242 AGAAAATCATATACGAGC
1 AGAAAATCATATACGAGC
28816260 A
1 A
28816261 AGTGACGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (18 bp):
AGAAAATCATATACGAGC
Found at i:28818047 original size:13 final size:13
Alignment explanation
Indices: 28818029--28818072 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
28818019 CACATACAGT
28818029 CAGATACAGATA-G
1 CAGATA-AGATATG
28818042 CAGATATAGATATG
1 CAGATA-AGATATG
*
28818056 CAGATAAGATATA
1 CAGATAAGATATG
28818069 CAGA
1 CAGA
28818073 ATCCTACCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.20
Consensus pattern (13 bp):
CAGATAAGATATG
Found at i:28818734 original size:12 final size:12
Alignment explanation
Indices: 28818717--28818746 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
28818707 CCATGTCTCG
28818717 CACACGGCCAAC
1 CACACGGCCAAC
28818729 CACACGGCCAAC
1 CACACGGCCAAC
28818741 CACACG
1 CACACG
28818747 CCTGTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (12 bp):
CACACGGCCAAC
Found at i:28823195 original size:26 final size:26
Alignment explanation
Indices: 28823133--28823195 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
28823123 CCTATAAGTG
*
28823133 TTCTGAAACTCATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGATA
* *
28823159 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
*
28823185 TTCTAAAACTG
1 TTCTGAAACTG
28823196 TTGTAGGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Found at i:28828591 original size:22 final size:22
Alignment explanation
Indices: 28828555--28829065 Score: 655
Period size: 22 Copynumber: 23.2 Consensus size: 22
28828545 AGTAAAAAAT
28828555 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * * *
28828577 TATTGTTTGAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
28828599 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * * *
28828621 TATTGTTTGAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
28828643 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * *
28828665 TGTTGATTTAATGCTGTCTAAT
1 TGTTGATTAAATGCTGTCCAAA
* * *
28828687 TGTTGACTAAATGTTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
* *
28828709 TGTTGATTGAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
28828731 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * *
28828753 TGTTGATTTAATGCTGTCTAAT
1 TGTTGATTAAATGCTGTCCAAA
* * *
28828775 TGTTGACTAAATGTTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
* *
28828797 TGTTGATTGAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
28828819 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
*
28828841 TGTTGATTTAATGCTGT-CAAA
1 TGTTGATTAAATGCTGTCCAAA
*
28828862 TTATTGATTAAATGCTGTCCAAA
1 -TGTTGATTAAATGCTGTCCAAA
* *
28828885 TATTGATTGAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
28828907 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* *
28828929 TGTTGATTTAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
*
28828951 TGTTGATTAAATGCTATCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* *
28828973 TGTTGATTAAATGCTGTTCAAT
1 TGTTGATTAAATGCTGTCCAAA
* *
28828995 TGTTGATTTAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
28829017 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * **
28829039 TGTTAATTAAATGTTGTCTGAA
1 TGTTGATTAAATGCTGTCCAAA
28829061 TGTTG
1 TGTTG
28829066 GATAATTGCT
Statistics
Matches: 424, Mismatches: 63, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
21 4 0.01
22 416 0.98
23 4 0.01
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.41
Consensus pattern (22 bp):
TGTTGATTAAATGCTGTCCAAA
Found at i:28828663 original size:88 final size:88
Alignment explanation
Indices: 28828552--28829065 Score: 778
Period size: 88 Copynumber: 5.8 Consensus size: 88
28828542 TGAAGTAAAA
*
28828552 AATTGTTGATTAAATGCTGTCCAAATATTG-TTTGAATGCTGTCCAATTGTTGATTAAATGCTGT
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTT-AATGCTGTCCAATTGTTGATTAAATGCTGT
* *
28828616 CCAAATATTGTTTGAATGCTGTCC
65 CCAAATGTTGATTGAATGCTGTCC
* * *
28828640 AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCTAATTGTTGACTAAATGTTGTC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCCAATTGTTGATTAAATGCTGTC
*
28828705 CAATTGTTGATTGAATGCTGTCC
66 CAAATGTTGATTGAATGCTGTCC
* * *
28828728 AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCTAATTGTTGACTAAATGTTGTC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCCAATTGTTGATTAAATGCTGTC
*
28828793 CAATTGTTGATTGAATGCTGTCC
66 CAAATGTTGATTGAATGCTGTCC
* *
28828816 AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCAAATTATTGATTAAATGCTGTC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCCAATTGTTGATTAAATGCTGTC
*
28828881 CAAATATTGATTGAATGCTGTCC
66 CAAATGTTGATTGAATGCTGTCC
* *
28828904 AAATGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCCAATTGTTGATTAAATGCTATC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCCAATTGTTGATTAAATGCTGTC
* *
28828969 CAAATGTTGATTAAATGCTGTTC
66 CAAATGTTGATTGAATGCTGTCC
* * * * * *
28828992 AATTGTTGATTTAATGCTGTCCAATTGTTGATTAAATGCTGTCCAAATGTTAATTAAATGTTGTC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCCAATTGTTGATTAAATGCTGTC
**
28829057 TGAATGTTG
66 CAAATGTTG
28829066 GATAATTGCT
Statistics
Matches: 395, Mismatches: 30, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
88 392 0.99
89 3 0.01
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.41
Consensus pattern (88 bp):
AATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGCTGTCCAATTGTTGATTAAATGCTGTC
CAAATGTTGATTGAATGCTGTCC
Found at i:28831740 original size:53 final size:53
Alignment explanation
Indices: 28831671--28831825 Score: 231
Period size: 53 Copynumber: 2.9 Consensus size: 53
28831661 ATGGCACTAA
* *
28831671 AAGATCATATCATGTAAGACCGTAATTGGTGGGTTATGGCATCATATGGTAAG
1 AAGAACATATCATGTAAGACCGTAATTGGTGGGTTATGGCATCATATGGGAAG
* **
28831724 AAGAACATATCGTGTAAGACCGTAATTGGCAGGTTATGGCATCATATGGGAAG
1 AAGAACATATCATGTAAGACCGTAATTGGTGGGTTATGGCATCATATGGGAAG
* *
28831777 AA-AACCATATCATGTAAGACCGTAATTGGTGAGTTATTGCATCATATGG
1 AAGAA-CATATCATGTAAGACCGTAATTGGTGGGTTATGGCATCATATGG
28831826 AAAAAGTTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 2 0.02
53 89 0.98
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (53 bp):
AAGAACATATCATGTAAGACCGTAATTGGTGGGTTATGGCATCATATGGGAAG
Found at i:28833900 original size:58 final size:60
Alignment explanation
Indices: 28833855--28833971 Score: 157
Period size: 61 Copynumber: 2.0 Consensus size: 60
28833845 AATCACTTTA
* * *
28833855 ATATTATATTAATATAACACTTA-T-CAAGATAAATATTACATTAAATTTAATATTAAAT
1 ATATTAAATTAATAGAACACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAAT
* * *
28833913 ATATTAAATTACTAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTAA
1 ATATTAAATTAATAGAACACTTA-CTACAAGATAAATATTAAATTAAATTTAATATTAA
28833972 GACAATCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 18 0.36
60 1 0.02
61 31 0.62
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (60 bp):
ATATTAAATTAATAGAACACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAAT
Found at i:28835735 original size:21 final size:21
Alignment explanation
Indices: 28835709--28835766 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
28835699 GAAAACAATT
28835709 ACATTTCCCAACAATATGGAC
1 ACATTTCCCAACAATATGGAC
28835730 ACATTTCCCAACAATATGGAC
1 ACATTTCCCAACAATATGGAC
28835751 ACATTTCCCAACAATA
1 ACATTTCCCAACAATA
28835767 ATATAGTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (21 bp):
ACATTTCCCAACAATATGGAC
Found at i:28838347 original size:30 final size:30
Alignment explanation
Indices: 28838301--28838809 Score: 667
Period size: 30 Copynumber: 16.9 Consensus size: 30
28838291 GTATATGTTT
* * *
28838301 TATATATTGTCGAATTGGTTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
28838331 TATACATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* * *
28838361 CATACATTGTCGAATTGATTTATATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* **
28838391 TATACATTGTCGAATTGATTTGTATATGTTT
1 TATACATTGCCGAATTGATTTGTATATG-GA
*
28838422 TATATATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* * *
28838452 CATACATTGTCGAATTGATTTATATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
28838482 TATACATTGCCGAATTGATTTCTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* **
28838512 TATACATTGCCAAATTGATTTGTATATGTTT
1 TATACATTGCCGAATTGATTTGTATATG-GA
* * * *
28838543 TATATATTGCAGAATTGATTTGTACATAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
28838573 CATACATTGCGGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
28838603 CATACATTGCGGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
28838633 CATACATTGCCGAATTGATTTGTATATGGG
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
28838663 CATACATTGCTGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* **
28838693 TATACATTGCTGAATTGATTTGTATATGTTT
1 TATACATTGCCGAATTGATTTGTATATG-GA
* *
28838724 TATATATTGCCGCATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
28838754 TATACATTGCCAAATTGATTTGTATATTGA
1 TATACATTGCCGAATTGATTTGTATATGGA
28838784 TATACATTGCCGAATTGATTTGTATA
1 TATACATTGCCGAATTGATTTGTATA
28838810 CATATACATA
Statistics
Matches: 422, Mismatches: 54, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
30 348 0.82
31 74 0.18
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:28838444 original size:121 final size:121
Alignment explanation
Indices: 28838290--28838809 Score: 720
Period size: 121 Copynumber: 4.3 Consensus size: 121
28838280 TGAATTCAAA
* * *
28838290 TGTATATGTTTTATATATTGTCGAATTGGTTTGTATATGGATATACATTGCCGAATTGATTTGTA
1 TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGACATACATTGCCGAATTGATTTGTA
* * * *
28838355 TATGGACATACATTGTCGAATTGATTTATATATGGATATACATTGTCGAATTGATT
66 TATGGACATACATTGCCGAATTGATTTGTATATGGATATACATTGCCAAATTGATT
* *
28838411 TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGACATACATTGTCGAATTGATTTATA
1 TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGACATACATTGCCGAATTGATTTGTA
* *
28838476 TATGGATATACATTGCCGAATTGATTTCTATATGGATATACATTGCCAAATTGATT
66 TATGGACATACATTGCCGAATTGATTTGTATATGGATATACATTGCCAAATTGATT
* * * *
28838532 TGTATATGTTTTATATATTGCAGAATTGATTTGTACATAGACATACATTGCGGAATTGATTTGTA
1 TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGACATACATTGCCGAATTGATTTGTA
* * *
28838597 TATGGACATACATTGCGGAATTGATTTGTATATGGACATACATTGCCGAATTGATT
66 TATGGACATACATTGCCGAATTGATTTGTATATGGATATACATTGCCAAATTGATT
*** * * * *
28838653 TGTATATG-GGCATACATTGCTGAATTGATTTGTATATGGATATACATTGCTGAATTGATTTGTA
1 TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGACATACATTGCCGAATTGATTTGTA
*** * *
28838717 TATGTTTTATATATTGCCGCATTGATTTGTATATGGATATACATTGCCAAATTGATT
66 TATG-GACATACATTGCCGAATTGATTTGTATATGGATATACATTGCCAAATTGATT
** *
28838774 TGTATAT-TGATATACATTGCCGAATTGATTTGTATA
1 TGTATATGTTTTATATATTGCCGAATTGATTTGTATA
28838810 CATATACATA
Statistics
Matches: 356, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
120 51 0.14
121 305 0.86
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (121 bp):
TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGACATACATTGCCGAATTGATTTGTA
TATGGACATACATTGCCGAATTGATTTGTATATGGATATACATTGCCAAATTGATT
Found at i:28838499 original size:151 final size:150
Alignment explanation
Indices: 28838306--28838809 Score: 719
Period size: 151 Copynumber: 3.3 Consensus size: 150
28838296 TGTTTTATAT
*
28838306 ATTGTCGAATTGGTTTGTATATGGATATACATTGCCGAATTGATTTGTATATGGACATACATTGT
1 ATTGTCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATGGACATACATTG-
*
28838371 CGAATTGATTTATATATGGATATACATTGTC-GAATTGATTTGTATATGTTTTATATATTGCCGA
65 CGAATTGATTTGTATATGGATATACATTG-CAGAATTGATTTGTATATGTTTTATATATTGCCGA
28838435 ATTGATTTGTATATGGACATAC
129 ATTGATTTGTATATGGACATAC
* * *
28838457 ATTGTCGAATTGATTTATATATGGATATACATTGCCGAATTGATTTCTATATGGATATACATTGC
1 ATTGTCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATGGACATACATTG-
* ** * * ** * *
28838522 CAAATTGATTTGTATATGTTTTATATATTGCAGAATTGATTTGTACATAG--ACATACATTGCGG
65 CGAATTGATTTGTATATG-GATATACATTGCAGAATTGATTTGTATAT-GTTTTATATATTGCCG
28838585 AATTGATTTGTATATGGACATAC
128 AATTGATTTGTATATGGACATAC
* *
28838608 ATTG-CGGAATTGATTTGTATATGGACATACATTGCCGAATTGATTTGTATATGGGCATACATTG
1 ATTGTC-GAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATGGACATACATTG
* *
28838672 CTGAATTGATTTGTATATGGATATACATTGCTGAATTGATTTGTATATGTTTTATATATTGCCGC
65 C-GAATTGATTTGTATATGGATATACATTGCAGAATTGATTTGTATATGTTTTATATATTGCCGA
*
28838737 ATTGATTTGTATATGGATATAC
129 ATTGATTTGTATATGGACATAC
* * *
28838759 ATTGCCAAATTGATTTGTATATTGATATACATTGCCGAATTGATTTGTATA
1 ATTGTCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATA
28838810 CATATACATA
Statistics
Matches: 310, Mismatches: 35, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
149 1 0.00
150 26 0.08
151 258 0.83
152 24 0.08
153 1 0.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (150 bp):
ATTGTCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATGGACATACATTGC
GAATTGATTTGTATATGGATATACATTGCAGAATTGATTTGTATATGTTTTATATATTGCCGAAT
TGATTTGTATATGGACATAC
Found at i:28845866 original size:30 final size:30
Alignment explanation
Indices: 28845820--28846278 Score: 580
Period size: 30 Copynumber: 15.2 Consensus size: 30
28845810 GTATATGTTT
* *
28845820 TATATATTTCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
28845850 TATACATTGTCGAATTGATTTGTCTATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
**
28845880 TATACATTGCCGAATTGATTTGTATATGTTT
1 TATACATTGCCGAATTGATTTGTATATG-GA
* *
28845911 TATATATTGCTGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* * *
28845941 CATATATTGCCGAATTGATTTGTATACGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
28845971 TATACATTGCCAAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
28846001 TATAAATTGCCGAATTGATTTGTATACGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
28846031 CATACATTACCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* * **
28846061 TATACTTTGCCGAATTTATTTGTATATGTTT
1 TATACATTGCCGAATTGATTTGTATATG-GA
* *
28846092 TATATATTGTCGAATATGATTTGTATATGGA
1 TATACATTGCCGAAT-TGATTTGTATATGGA
* *
28846123 TATAAATTGCCGAATTGATTTGTATATGAA
1 TATACATTGCCGAATTGATTTGTATATGGA
**
28846153 TATACATTGCCGAATTGATTTGTATATGTTT
1 TATACATTGCCGAATTGATTTGTATATG-GA
* **
28846184 TATATATTGCCGAATTGATTTGTATACAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
28846214 TATACATTGTCAAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
28846244 TATACATTGCCGAATTGATGTGTATAT-G-
1 TATACATTGCCGAATTGATTTGTATATGGA
28846272 TATACAT
1 TATACAT
28846279 ATATATTGCC
Statistics
Matches: 368, Mismatches: 57, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
28 7 0.02
29 1 0.00
30 272 0.74
31 76 0.21
32 12 0.03
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:28845918 original size:91 final size:91
Alignment explanation
Indices: 28845809--28846299 Score: 705
Period size: 91 Copynumber: 5.4 Consensus size: 91
28845799 TGAATTCAAA
* * *
28845809 TGTATATGTTTTATATATTTCCGAATTGATTTGTATATGGATATACATTGTCGAATTGATTTGTC
1 TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTA
28845874 TATGGATATACATTGCCGAATTGATT
66 TATGGATATACATTGCCGAATTGATT
* * *
28845900 TGTATATGTTTTATATATTGCTGAATTGATTTGTATATGGACATATATTGCCGAATTGATTTGTA
1 TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTA
* *
28845965 TACGGATATACATTGCCAAATTGATT
66 TATGGATATACATTGCCGAATTGATT
** * * * *
28845991 TGTATATG-GATATAAATTGCCGAATTGATTTGTATACGGACATACATTACCGAATTGATTTGTA
1 TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTA
* *
28846055 TATGGATATACTTTGCCGAATTTATT
66 TATGGATATACATTGCCGAATTGATT
* *
28846081 TGTATATGTTTTATATATTGTCGAATATGATTTGTATATGGATATAAATTGCCGAATTGATTTGT
1 TGTATATGTTTTATATATTGCCGAAT-TGATTTGTATATGGATATACATTGCCGAATTGATTTGT
*
28846146 ATATGAATATACATTGCCGAATTGATT
65 ATATGGATATACATTGCCGAATTGATT
** * *
28846173 TGTATATGTTTTATATATTGCCGAATTGATTTGTATACAGATATACATTGTCAAATTGATTTGTA
1 TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTA
*
28846238 TATGGATATACATTGCCGAATTGATG
66 TATGGATATACATTGCCGAATTGATT
* *
28846264 TGTATATGTATACATATATATTGCCAAATTGATTTG
1 TGTATATGT-T--TTATATATTGCCGAATTGATTTG
28846300 AGCATTAGAT
Statistics
Matches: 355, Mismatches: 40, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
90 79 0.22
91 171 0.48
92 84 0.24
94 21 0.06
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (91 bp):
TGTATATGTTTTATATATTGCCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTA
TATGGATATACATTGCCGAATTGATT
Found at i:28853173 original size:21 final size:21
Alignment explanation
Indices: 28853149--28853216 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
28853139 TCATGAAAGC
28853149 TAAACGGAAACCCATAAGGGT
1 TAAACGGAAACCCATAAGGGT
* * * * *
28853170 TAAACGGAAGCTCGTAAGAGC
1 TAAACGGAAACCCATAAGGGT
* * *
28853191 TGAACGAAAACCTATAAGGGT
1 TAAACGGAAACCCATAAGGGT
28853212 TAAAC
1 TAAAC
28853217 TGAAGCTCAA
Statistics
Matches: 33, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
TAAACGGAAACCCATAAGGGT
Found at i:28853260 original size:42 final size:41
Alignment explanation
Indices: 28853146--28853262 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 41
28853136 AACTCATGAA
* * **
28853146 AGCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTCGTAAG
1 AGCTGAAC-GAAACCCATAAGGGTTAAACTGAAGCTCAAAAG
*
28853188 AGCTGAACGAAAACCTATAAGGGTTAAACTGAAGCTCAAAAG
1 AGCTGAACG-AAACCCATAAGGGTTAAACTGAAGCTCAAAAG
* * *
28853230 AGCTGATCAGAAACCCATTAGGGTTTAACTGAA
1 AGCTGAAC-GAAACCCATAAGGGTTAAACTGAA
28853263 ACTTATATGA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.02
42 62 0.97
43 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (41 bp):
AGCTGAACGAAACCCATAAGGGTTAAACTGAAGCTCAAAAG
Found at i:28853396 original size:25 final size:24
Alignment explanation
Indices: 28853339--28853425 Score: 111
Period size: 24 Copynumber: 3.6 Consensus size: 24
28853329 TGCTGAAACT
*
28853339 TCAATTCATCCTTTGCATATACTG
1 TCAATTCATCCTTTGCATATACCG
* * *
28853363 TCAATTCATCGTTTTCATTTTACCG
1 TCAATTCATCCTTTGCA-TATACCG
* *
28853388 TCAATTCATCCTTTGCATATATCA
1 TCAATTCATCCTTTGCATATACCG
28853412 TCAATTCATCCTTT
1 TCAATTCATCCTTT
28853426 ACTCTTTACT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 33 0.62
25 20 0.38
ACGTcount: A:0.24, C:0.25, G:0.06, T:0.45
Consensus pattern (24 bp):
TCAATTCATCCTTTGCATATACCG
Found at i:28853416 original size:49 final size:49
Alignment explanation
Indices: 28853339--28853447 Score: 141
Period size: 49 Copynumber: 2.2 Consensus size: 49
28853329 TGCTGAAACT
* * *
28853339 TCAATTCATCCTTTGCATATACTGTCAATTCATCGTTTTCAT-TTTACCG
1 TCAATTCATCCTTTGCATATACTATCAATTCATCCTTTAC-TCTTTACCG
**
28853388 TCAATTCATCCTTTGCATATA-TCATCAATTCATCCTTTACTCTTTACTT
1 TCAATTCATCCTTTGCATATACT-ATCAATTCATCCTTTACTCTTTACCG
28853437 TCAATTCATCC
1 TCAATTCATCC
28853448 ATTTTTCACA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
48 2 0.04
49 51 0.96
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.45
Consensus pattern (49 bp):
TCAATTCATCCTTTGCATATACTATCAATTCATCCTTTACTCTTTACCG
Found at i:28857302 original size:24 final size:24
Alignment explanation
Indices: 28857274--28857321 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28857264 AAATATGGGT
28857274 TAAAAACCATGAAAGTCCAAAACC
1 TAAAAACCATGAAAGTCCAAAACC
28857298 TAAAAACCATGAAAGTCCAAAACC
1 TAAAAACCATGAAAGTCCAAAACC
28857322 GTGGTCACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.25, G:0.08, T:0.12
Consensus pattern (24 bp):
TAAAAACCATGAAAGTCCAAAACC
Found at i:28857968 original size:15 final size:15
Alignment explanation
Indices: 28857948--28857977 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28857938 ATGATGCTTA
28857948 CCGACCCTATAGTAG
1 CCGACCCTATAGTAG
28857963 CCGACCCTATAGTAG
1 CCGACCCTATAGTAG
28857978 GTTCACAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (15 bp):
CCGACCCTATAGTAG
Found at i:28864378 original size:16 final size:16
Alignment explanation
Indices: 28864359--28864402 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
28864349 ATTTTATATG
28864359 TTATTTTAAAATTATT
1 TTATTTTAAAATTATT
** *
28864375 TTATTTTTTATTTATT
1 TTATTTTAAAATTATT
28864391 TTA-TTTAAAATT
1 TTATTTTAAAATT
28864403 TCTCGTATGC
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTAAAATTATT
Found at i:28870702 original size:15 final size:15
Alignment explanation
Indices: 28870678--28870721 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
28870668 AAATGAAAAT
*
28870678 GAAAATGAAAAAAGA
1 GAAAAGGAAAAAAGA
28870693 GAAAAGGAAAAAAGA
1 GAAAAGGAAAAAAGA
*
28870708 AAAAAGGAAAAAAG
1 GAAAAGGAAAAAAG
28870722 GAGAGGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (15 bp):
GAAAAGGAAAAAAGA
Found at i:28870711 original size:7 final size:7
Alignment explanation
Indices: 28870679--28870721 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
28870669 AATGAAAATG
*
28870679 AAAATGA
1 AAAAAGA
28870686 AAAAAGA
1 AAAAAGA
*
28870693 GAAAAGGA
1 -AAAAAGA
28870701 AAAAAGA
1 AAAAAGA
28870708 AAAAAGGA
1 AAAAA-GA
28870716 AAAAAG
1 AAAAAG
28870722 GAGAGGTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:28870722 original size:8 final size:8
Alignment explanation
Indices: 28870679--28870723 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
28870669 AATGAAAATG
*
28870679 AAAATGAA
1 AAAAGGAA
*
28870687 AAAA-GAG
1 AAAAGGAA
28870694 AAAAGGAA
1 AAAAGGAA
28870702 AAAA-GAA
1 AAAAGGAA
28870709 AAAAGGAA
1 AAAAGGAA
28870717 AAAAGGA
1 AAAAGGA
28870724 GAGGTCAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 13 0.39
8 20 0.61
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (8 bp):
AAAAGGAA
Found at i:28871917 original size:7 final size:6
Alignment explanation
Indices: 28871894--28871929 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
28871884 TTAAGTCAAA
28871894 AAAATG AAAATG AAAATG AGAAATG AAAAATG AAAA
1 AAAATG AAAATG AAAATG A-AAATG -AAAATG AAAA
28871930 AGTAAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 17 0.61
7 10 0.36
8 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:28871917 original size:13 final size:12
Alignment explanation
Indices: 28871894--28871929 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
28871884 TTAAGTCAAA
28871894 AAAATGAAAATG
1 AAAATGAAAATG
28871906 AAAATGAGAAATG
1 AAAATGA-AAATG
28871919 AAAAATGAAAA
1 -AAAATGAAAA
28871930 AGTAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 8 0.36
14 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (12 bp):
AAAATGAAAATG
Found at i:28871930 original size:7 final size:7
Alignment explanation
Indices: 28871893--28871939 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
28871883 TTTAAGTCAA
28871893 AAAAATG
1 AAAAATG
28871900 -AAAATG
1 AAAAATG
28871906 -AAAATG
1 AAAAATG
*
28871912 AGAAATG
1 AAAAATG
28871919 AAAAATG
1 AAAAATG
28871926 AAAAA-G
1 AAAAATG
28871932 TAAAAATG
1 -AAAAATG
28871940 GAGAGGCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 13 0.37
7 21 0.60
8 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:28872244 original size:87 final size:87
Alignment explanation
Indices: 28872001--28872246 Score: 357
Period size: 87 Copynumber: 2.8 Consensus size: 87
28871991 GAGTTGAAAA
* * * * * *
28872001 CAGTGGAGCGGGTTAAAAATATCAGATCTTGCCTTCCTGCATTAACAGCAAAGCATATCAAAAAC
1 CAGTGGAGCGGGTTAAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAAC
* *
28872066 AAAGACTTGCCTCCATCGGTTG
66 AAAGCCTTGCCTCCATCAGTTG
*
28872088 CAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAAC
1 CAGTGGAGCGGGTTAAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAAC
28872153 AAAGCCTTGCCTCCATCAGTTG
66 AAAGCCTTGCCTCCATCAGTTG
* ** * * *
28872175 CGGTGGAGCTAGTTAAAGATAACAGATCTTGTCTTCCTACATTGACAGTGAAGCAGATCGAAAAC
1 CAGTGGAGCGGGTTAAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAAC
28872240 AAAGCCT
66 AAAGCCT
28872247 CACGAAAAAT
Statistics
Matches: 144, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 144 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (87 bp):
CAGTGGAGCGGGTTAAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAAC
AAAGCCTTGCCTCCATCAGTTG
Found at i:28872489 original size:87 final size:88
Alignment explanation
Indices: 28872343--28872697 Score: 403
Period size: 88 Copynumber: 4.1 Consensus size: 88
28872333 CCTGAAAAGC
** * *
28872343 TCGAAAACAAAGCCTCACCTCCATCGGTTGCAGTGGAACT-GGTTAAAGATAGCAGATCTTGCCT
1 TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGGTTAAAGATAACAGATCTTGCCT
**
28872407 TCCTGCATTGACAATGAAGCAGA
66 TCCTGCATTGACAGCGAAGCAGA
* *
28872430 TCGAAAACAAAGCCTTGCCTCCATCGGCTGCAGTGGAGCTA-GTTAAAGATAGCAGATCTTGCCT
1 TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGGTTAAAGATAACAGATCTTGCCT
* * *
28872494 TCCTGCATAGATAGCAAAGCAGA
66 TCCTGCATTGACAGCGAAGCAGA
* ** *
28872517 TCGAAGACCCCAGCCTTGCCTCCCTCGGTTGCAGTGGAGC-AGGTTAAAGATAACAGATCTTGCC
1 TCGAA-AACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGGTTAAAGATAACAGATCTTGCC
* * * * *
28872581 TTCCTGTATCGACGGTGAAACAGA
65 TTCCTGCATTGACAGCGAAGCAGA
* * * * * * *
28872605 TCTAAGACACAATCCTTGCCTCCCTCGGTTGTAGTGGAG-TAGGTTGAAGATAACAGATCTTACC
1 TCGAAAACA-AAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGGTTAAAGATAACAGATCTTGCC
**
28872669 TTCCTGCGCTGACAGCGAAGCAGA
65 TTCCTGCATTGACAGCGAAGCAGA
28872693 TCGAA
1 TCGAA
28872698 GATACCAGCC
Statistics
Matches: 224, Mismatches: 39, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
87 84 0.38
88 140 0.62
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (88 bp):
TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGGTTAAAGATAACAGATCTTGCCT
TCCTGCATTGACAGCGAAGCAGA
Found at i:28872579 original size:44 final size:43
Alignment explanation
Indices: 28872531--28872665 Score: 107
Period size: 44 Copynumber: 3.1 Consensus size: 43
28872521 AGACCCCAGC
28872531 CTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGCAGGTT-AAGATAACAGAT
* * * * * *
28872575 CTTGCCTTCCT--GTATCGACGGTGAAACAGATCTAAGA-CACA-AT
1 CTTGCCTCCCTCGGT-T-G-CAGTGGAGCAGGT-TAAGATAACAGAT
* *
28872618 CCTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTGAAGATAACAGAT
1 -CTTGCCTCCCTCGGTTGCAGTGGAGCAGGTT-AAGATAACAGAT
28872663 CTT
1 CTT
28872666 ACCTTCCTGC
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
42 3 0.04
43 14 0.21
44 31 0.46
45 16 0.24
46 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (43 bp):
CTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAGATAACAGAT
Found at i:28872579 original size:88 final size:87
Alignment explanation
Indices: 28872343--28872751 Score: 389
Period size: 88 Copynumber: 4.7 Consensus size: 87
28872333 CCTGAAAAGC
* ** * * * *
28872343 TCGAAAACA-AAGCCTCACCTCCATCGGTTGCAGTGGAACTGGTTAAAGATAGCAGATCTTGCCT
1 TCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGATCTTGCCT
***
28872407 TCCTGCATTGACAATGAAGCAGA
66 TCCTGCA-TGACAGCAAAGCAGA
* * * *
28872430 TCGAAAACA-AAGCCTTGCCTCCATCGGCTGCAGTGGAGCTA-GTTAAAGATAGCAGATCTTGCC
1 TCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGC-AGGTTAAAGATAACAGATCTTGCC
*
28872493 TTCCTGCATAGATAGCAAAGCAGA
65 TTCCTGCAT-GACAGCAAAGCAGA
* *
28872517 TCGAAGACCCCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGATCTTGCCT
1 TCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGATCTTGCCT
* * *
28872582 TCCTGTATCGACGGTGAAA-CAGA
66 TCCTGCAT-GACAG-CAAAGCAGA
* * * * * *
28872605 TCTAAGACACAATCCTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTGAAGATAACAGATCTTACCT
1 TCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGATCTTGCCT
* *
28872670 TCCTGCGCTGACAGCGAAGCAGA
66 TCCTGC-ATGACAGCAAAGCAGA
* * ** * * *
28872693 TCGAAGATACCAGCCTTATCTCCCT-GAGATTACAGTGGAGCAGATTAAA-ATAAAAGATC
1 TCGAAGACACAAGCCTTGCCTCCCTCG-G-TTGCAGTGGAGCAGGTTAAAGATAACAGATC
28872752 CTGCGGCTCA
Statistics
Matches: 268, Mismatches: 45, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
86 1 0.00
87 86 0.32
88 162 0.60
89 19 0.07
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (87 bp):
TCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGATCTTGCCT
TCCTGCATGACAGCAAAGCAGA
Found at i:28872693 original size:176 final size:175
Alignment explanation
Indices: 28872353--28872751 Score: 464
Period size: 176 Copynumber: 2.3 Consensus size: 175
28872343 TCGAAAACAA
* * * * * *
28872353 AGCCTCACCTCCATCGGTTGCAGTGGAACTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGA
1 AGCCTTACCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGATCTTGCCTTCCTGCATCGA
* *
28872418 CAATGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGCTGCAGTGGAGCTAGTTAAAGATAGC
66 CAATGAAACAGATCGAAAACAAAGCCTTGCCTCCATCGGCTGCAGTGGAGCTAGTTAAAGATAAC
* * *
28872483 AGATCTTGCCTTCCTGCATAGATAGCAAAGCAGATCGAAGACCCC
131 AGATCTTACCTTCCTGCATAGACAGCAAAGCAGATCGAAGACACC
* *
28872528 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGATCTTGCCTTCCTGTATCGA
1 AGCCTTACCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGATCTTGCCTTCCTGCATCGA
** * * * * * * *
28872593 CGGTGAAACAGATCTAAGACACAATCCTTGCCTCCCTCGGTTGTAGTGGAG-TAGGTTGAAGATA
66 CAATGAAACAGATCGAAAACA-AAGCCTTGCCTCCATCGGCTGCAGTGGAGCTA-GTTAAAGATA
* * *
28872657 ACAGATCTTACCTTCCTGCGCT-GACAGCGAAGCAGATCGAAGATACC
129 ACAGATCTTACCTTCCTGC-ATAGACAGCAAAGCAGATCGAAGACACC
* * * *
28872704 AGCCTTATCTCCCT-GAGATTACAGTGGAGCAGATTAAA-ATAAAAGATC
1 AGCCTTACCTCCCTCG-G-TTGCAGTGGAGCAGGTTAAAGATAACAGATC
28872752 CTGCGGCTCA
Statistics
Matches: 189, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
175 76 0.40
176 94 0.50
177 19 0.10
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (175 bp):
AGCCTTACCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAACAGATCTTGCCTTCCTGCATCGA
CAATGAAACAGATCGAAAACAAAGCCTTGCCTCCATCGGCTGCAGTGGAGCTAGTTAAAGATAAC
AGATCTTACCTTCCTGCATAGACAGCAAAGCAGATCGAAGACACC
Found at i:28873087 original size:44 final size:41
Alignment explanation
Indices: 28873039--28873146 Score: 101
Period size: 41 Copynumber: 2.6 Consensus size: 41
28873029 ATACCAGCCT
28873039 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAAGATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGA-TAAAAT--AAGATCC
* * * * * * * *
28873083 TATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAGGTCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATAAAATAAGATCC
28873124 TATCTCCCTGAGATTACAGTGGA
1 TATCTCCCTGAGATTACAGTGGA
28873147 ATAAACCGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
41 23 0.44
42 1 0.02
43 5 0.10
44 23 0.44
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATAAAATAAGATCC
Found at i:28873567 original size:134 final size:131
Alignment explanation
Indices: 28873375--28873784 Score: 339
Period size: 134 Copynumber: 3.1 Consensus size: 131
28873365 GAATTTTAGA
* * * * ** * *
28873375 TCTTGTCTTCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATTCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAACAAACCGAAGATAGTAATCCTATCTCCCTGAGATTACA
28873440 GTGGAGCGGATTAAAACAATAAAGGATTTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
66 GTGGAGCGGATTAAAACAAT-AAGGATTTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
28873505 GG
130 GG
* * * ** *
28873507 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTTAGATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGCGGAACAAACCGAAG-ATAGTA-ATCCTATCTCCCTGAGATTA
* ** * * * * * * *
28873572 CAGCGGAGCATATTAAAGC--T-AGTAATTCTATCTCCCTG-AGATTACAGTGGAATAGACCGAA
64 CAGTGGAGCGGATTAAAACAATAAG-GATTTTATCTCTCTGAAG-TTACAGTAGAGTAGATC---
* *
28873633 GAATTTCAGA
124 GCA--TCAGG
* ** *
28873643 TCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAACAAACCGAAGATAGTAATCCTATCTCCCTGAGATTACA
* * * ** * *
28873708 GTGGAGCGGATTAAAAAAAT-A-GATCTTATCTCTCTGAGGTTGTAGTAGAGTAGGTCGCACCAG
66 GTGGAGCGGATTAAAACAATAAGGATTTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
28873771 G
131 G
28873772 TCTTA-CTTCCCTG
1 TCTTATC-TCCCTG
28873785 GCGGCGTAGT
Statistics
Matches: 212, Mismatches: 53, Indels: 29
0.72 0.18 0.10
Matches are distributed among these distances:
128 1 0.00
129 14 0.07
130 4 0.02
131 28 0.13
132 31 0.15
133 3 0.01
134 90 0.42
135 4 0.02
136 37 0.17
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (131 bp):
TCTTATCTCCCTGAGATTACAGCGGAACAAACCGAAGATAGTAATCCTATCTCCCTGAGATTACA
GTGGAGCGGATTAAAACAATAAGGATTTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
G
Found at i:28873574 original size:46 final size:46
Alignment explanation
Indices: 28873507--28873664 Score: 187
Period size: 46 Copynumber: 3.5 Consensus size: 46
28873497 TCGCATCAGG
28873507 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTTAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTTAGA
* ** * *** * **
28873553 TCTTATCTCCCTGAGATTACAGCGGAGCATATTAAAG-CTAGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTTAGA
*
28873597 T-TCTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGA
1 TCT-TATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTTAGA
28873643 TCTTATCTCCCTGAGATTACAG
1 TCTTATCTCCCTGAGATTACAG
28873665 CGGAGCAAAT
Statistics
Matches: 87, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
43 1 0.01
44 29 0.33
45 5 0.06
46 51 0.59
47 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (46 bp):
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTTAGA
Found at i:28873620 original size:90 final size:90
Alignment explanation
Indices: 28873300--28873712 Score: 505
Period size: 90 Copynumber: 4.6 Consensus size: 90
28873290 ATTGTTTAAN
* *
28873300 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGGAATAGACCGAA
1 ATTACAGCGGAGCAGATTGAAGCTAGTAATTCTATCTCCCTGAGATTACAGTGGAATAGACCGAA
* *
28873365 GAATTTTAGATCTTGTCTTCCTGAG
66 GAATTTTAGATCTTATCTCCCTGAG
*** **
28873390 ATTACAGCGGAGCAGATTGAAGCTAGTAATTCTATCTCCCTGAGATTACAGTGGAGCGGA-TTAA
1 ATTACAGCGGAGCAGATTGAAGCTAGTAATTCTATCTCCCTGAGATTACAGTGGAATAGACCGAA
* * ** * *
28873454 AACAATAAAGGATTTTATCTCTCTGA-
66 GA-ATTTTA-GATCTTATCTCCCTGAG
** * * * * *
28873480 AGTTACAGTAGAGTAGATCGCATC-AG---GTCTTATCTCCCTGAGATTACAGTGGAATAGACCG
1 A-TTACAGCGGAGCAGATTGAAGCTAGTAATTC-TATCTCCCTGAGATTACAGTGGAATAGACCG
28873541 AAGAATTTTAGATCTTATCTCCCTGAG
64 AAGAATTTTAGATCTTATCTCCCTGAG
* *
28873568 ATTACAGCGGAGCATATTAAAGCTAGTAATTCTATCTCCCTGAGATTACAGTGGAATAGACCGAA
1 ATTACAGCGGAGCAGATTGAAGCTAGTAATTCTATCTCCCTGAGATTACAGTGGAATAGACCGAA
*
28873633 GAATTTCAGATCTTATCTCCCTGAG
66 GAATTTTAGATCTTATCTCCCTGAG
* *
28873658 ATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGA
1 ATTACAGCGGAGCAGATTGAAGCTAGTAATTCTATCTCCCTGAGATTACAGTGGA
28873713 GCGGATTAAA
Statistics
Matches: 267, Mismatches: 46, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
87 30 0.11
88 31 0.12
89 6 0.02
90 170 0.64
91 30 0.11
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (90 bp):
ATTACAGCGGAGCAGATTGAAGCTAGTAATTCTATCTCCCTGAGATTACAGTGGAATAGACCGAA
GAATTTTAGATCTTATCTCCCTGAG
Found at i:28873738 original size:44 final size:44
Alignment explanation
Indices: 28873371--28873745 Score: 149
Period size: 44 Copynumber: 8.4 Consensus size: 44
28873361 CGAAGAATTT
* * ***
28873371 TAGATCTTGTCTTCCTGAGATTACAGCGGAGCAGATTGAAGCTAG
1 TAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAAAAG
* *
28873416 TA-AT-TCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAA-
1 TAGATCT-TATCTCCCTGAGATTACAGCGGAGCAGATTAAAA-AAG
* * ** * *** **
28873459 TAAAGGATTTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAG
1 T--A-GATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTAAAAAAG
* ** ** ***
28873506 --G-TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTT
1 TAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TTAA-AAAAG
* **
28873549 TAGATCTTATCTCCCTGAGATTACAGCGGAGCATATTAAAGCTAG
1 TAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAA-AAAG
* ** ** * **
28873594 TA-AT-TCTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATT
1 TAGATCT-TATCTCCCTGAGATTACAGCGGAGCAGA-TTAAAAAAG
* ***
28873638 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAG
1 T-AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAAAAG
* * * *
28873684 TA-ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAAAAA
1 TAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAG
*
28873727 TAGATCTTATCTCTCTGAG
1 TAGATCTTATCTCCCTGAG
28873746 GTTGTAGTAG
Statistics
Matches: 239, Mismatches: 68, Indels: 47
0.68 0.19 0.13
Matches are distributed among these distances:
41 25 0.10
42 2 0.01
43 11 0.05
44 101 0.42
45 13 0.05
46 59 0.25
47 27 0.11
48 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
TAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAG
Found at i:28873739 original size:178 final size:180
Alignment explanation
Indices: 28873300--28873712 Score: 539
Period size: 178 Copynumber: 2.3 Consensus size: 180
28873290 ATTGTTTAAN
*
28873300 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGGAATAGACCGAA
1 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAATAGACCGAA
* * *
28873365 GAATTTTAGATCTTGTCTTCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATTCTATCTCCC
66 GAATTTTAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCTAGTAATTCTATCTCCC
* * ** * *
28873430 TGAGATTACAGTGGAGCGGATTAAAACAATAAAGGATTTTATCTCTCTGA
131 TGAGATTACAGTGGAACAGACGAAAACAATAAAGGATCTTATCTCCCTGA
** * * * * * *
28873480 AGTTACAGTAGAGTAGATCGCATC-AG--GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGA
1 A-TTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAATAGACCGA
*
28873542 AGAATTTTAGATCTTATCTCCCTGAGATTACAGCGGAGCATATTAAAGCTAGTAATTCTATCTCC
65 AGAATTTTAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCTAGTAATTCTATCTCC
* * * **
28873607 CTGAGATTACAGTGGAATAGACCGAAGA-ATTTCA-GATCTTATCTCCCTGA
130 CTGAGATTACAGTGGAACAGA-CGAAAACAATAAAGGATCTTATCTCCCTGA
*
28873657 GATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGA
1 -ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGA
28873713 GCGGATTAAA
Statistics
Matches: 194, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
177 29 0.15
178 118 0.61
179 3 0.02
180 28 0.14
181 16 0.08
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (180 bp):
ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAATAGACCGAA
GAATTTTAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCTAGTAATTCTATCTCCC
TGAGATTACAGTGGAACAGACGAAAACAATAAAGGATCTTATCTCCCTGA
Found at i:28875513 original size:16 final size:16
Alignment explanation
Indices: 28875494--28875537 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
28875484 ATTTTATATG
28875494 TTATTTTAAAATTATT
1 TTATTTTAAAATTATT
** *
28875510 TTATTTTTTATTTATT
1 TTATTTTAAAATTATT
28875526 TTA-TTTAAAATT
1 TTATTTTAAAATT
28875538 TCTCGTATGC
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTAAAATTATT
Found at i:28875637 original size:27 final size:27
Alignment explanation
Indices: 28875581--28875668 Score: 96
Period size: 25 Copynumber: 3.4 Consensus size: 27
28875571 TTCGTTTATG
*
28875581 ATTATTTTAACTTGCTTTATA-A-ATT
1 ATTATTTTAACTTACTTTATATATATT
28875606 ATTATTTTAACTTACTTTATATATCATT
1 ATTATTTTAACTTACTTTATATAT-ATT
* *
28875634 -TTATTTTAAGTTA-TTT-TACATATT
1 ATTATTTTAACTTACTTTATATATATT
28875658 ACTTATTTTAA
1 A-TTATTTTAA
28875669 AATTAACCTA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
24 3 0.05
25 24 0.44
26 13 0.24
27 12 0.22
28 3 0.05
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTATTTTAACTTACTTTATATATATT
Found at i:28877667 original size:19 final size:19
Alignment explanation
Indices: 28877643--28877681 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28877633 TTAATTAAAT
28877643 AAAAGA-AATAAAAGATAGA
1 AAAAGAGAATAAAA-ATAGA
*
28877662 AAAAGAGAATAGAAATAGA
1 AAAAGAGAATAAAAATAGA
28877681 A
1 A
28877682 TAGCAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAAGAGAATAAAAATAGA
Found at i:28877733 original size:27 final size:26
Alignment explanation
Indices: 28877686--28877741 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
28877676 ATAGAATAGC
*
28877686 AAAAAGAAAACAAGGCAGAAAGGAAAG
1 AAAAAGAAAACAAGGAAGAAA-GAAAG
*
28877713 AAAAAGAAAA-AGGGAAGGAAAGAAAG
1 AAAAAGAAAACAAGGAA-GAAAGAAAG
28877739 AAA
1 AAA
28877742 GAAAATTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.70, C:0.04, G:0.27, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAACAAGGAAGAAAGAAAG
Found at i:28878632 original size:25 final size:23
Alignment explanation
Indices: 28878604--28878705 Score: 100
Period size: 22 Copynumber: 4.3 Consensus size: 23
28878594 ACTTTAGCGC
*
28878604 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTG--TATTAGCACGTTAGT
*
28878629 GCTCTCTGATTACTAGCACGTTAGT
1 GCTCTCTG--TATTAGCACGTTAGT
* * *
28878654 GCTCTCCGT-TTAGCACATTTGT
1 GCTCTCTGTATTAGCACGTTAGT
*
28878676 GCTCTCTGTA-TAGCACTTTAGT
1 GCTCTCTGTATTAGCACGTTAGT
28878698 GCTCTCTG
1 GCTCTCTG
28878706 CTCATTAGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
22 36 0.54
23 1 0.01
25 30 0.45
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.39
Consensus pattern (23 bp):
GCTCTCTGTATTAGCACGTTAGT
Found at i:28878633 original size:23 final size:24
Alignment explanation
Indices: 28878607--28878655 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
28878597 TTAGCGCGCT
* *
28878607 CTCTGATTATTAGCACGTTGGTGC
1 CTCTGATTACTAGCACGTTAGTGC
28878631 TCTCTGATTACTAGCACGTTAGTGC
1 -CTCTGATTACTAGCACGTTAGTGC
28878656 TCTCCGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (24 bp):
CTCTGATTACTAGCACGTTAGTGC
Found at i:28878678 original size:47 final size:44
Alignment explanation
Indices: 28878616--28878703 Score: 122
Period size: 47 Copynumber: 1.9 Consensus size: 44
28878606 TCTCTGATTA
*
28878616 TTAGCACGTTGGTGCTCTCTGATTACTAGCACGTTAGTGCTCTCCGT
1 TTAGCACATTGGTGCTCTCTG--TA-TAGCACGTTAGTGCTCTCCGT
* *
28878663 TTAGCACATTTGTGCTCTCTGTATAGCACTTTAGTGCTCTC
1 TTAGCACATTGGTGCTCTCTGTATAGCACGTTAGTGCTCTC
28878704 TGCTCATTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 17 0.45
45 2 0.05
47 19 0.50
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (44 bp):
TTAGCACATTGGTGCTCTCTGTATAGCACGTTAGTGCTCTCCGT
Found at i:28888445 original size:18 final size:19
Alignment explanation
Indices: 28888424--28888459 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28888414 TTTTTTAAAA
28888424 TATAAAT-TTTGGAATTTC
1 TATAAATATTTGGAATTTC
*
28888442 TATAAATATTTTGAATTT
1 TATAAATATTTGGAATTT
28888460 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (19 bp):
TATAAATATTTGGAATTTC
Found at i:28888459 original size:19 final size:18
Alignment explanation
Indices: 28888424--28888472 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
28888414 TTTTTTAAAA
*
28888424 TATAAAT-TTTGGAATTT
1 TATAAATATTTTGAATTT
28888441 CTATAAATATTTTGAATTT
1 -TATAAATATTTTGAATTT
*
28888460 TAAAAATTATTTT
1 TATAAA-TATTTT
28888473 CAAAATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:28888695 original size:14 final size:14
Alignment explanation
Indices: 28888678--28888732 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
28888668 ATAATTCGAA
28888678 TAACTCAATTTGAT
1 TAACTCAATTTGAT
*
28888692 TAACTCAAAATAATTCGAA
1 TAACTC--AAT--TT-GAT
28888711 TAACTCAATTTGAT
1 TAACTCAATTTGAT
28888725 TAACTCAA
1 TAACTCAA
28888733 AATTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.24
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (14 bp):
TAACTCAATTTGAT
Found at i:28888709 original size:33 final size:33
Alignment explanation
Indices: 28888667--28888735 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
28888657 AGTTGACTCT
28888667 AATAATTCGAATAACTCAATTTGATTAACTCAA
1 AATAATTCGAATAACTCAATTTGATTAACTCAA
28888700 AATAATTCGAATAACTCAATTTGATTAACTCAA
1 AATAATTCGAATAACTCAATTTGATTAACTCAA
28888733 AAT
1 AAT
28888736 TTAAATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (33 bp):
AATAATTCGAATAACTCAATTTGATTAACTCAA
Found at i:28888714 original size:19 final size:19
Alignment explanation
Indices: 28888667--28888718 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
28888657 AGTTGACTCT
28888667 AATAATTCGAATAACTC--
1 AATAATTCGAATAACTCAA
*
28888684 AAT--TT-GATTAACTCAA
1 AATAATTCGAATAACTCAA
28888700 AATAATTCGAATAACTCAA
1 AATAATTCGAATAACTCAA
28888719 TTTGATTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.29
15 2 0.07
16 3 0.11
17 3 0.11
18 2 0.07
19 10 0.36
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (19 bp):
AATAATTCGAATAACTCAA
Found at i:28890706 original size:21 final size:21
Alignment explanation
Indices: 28890680--28890741 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
28890670 TTCTTAAATC
* *
28890680 AAGAAAAAATAAAGAAGAAAA
1 AAGAAAAAATAAACAACAAAA
28890701 AAGAAAAAATAAACAACAAAA
1 AAGAAAAAATAAACAACAAAA
*
28890722 CA-AAAAAATAAAC--CAAAA
1 AAGAAAAAATAAACAACAAAA
28890740 AA
1 AA
28890742 TAGAGAGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 6 0.16
20 11 0.30
21 20 0.54
ACGTcount: A:0.81, C:0.08, G:0.06, T:0.05
Consensus pattern (21 bp):
AAGAAAAAATAAACAACAAAA
Found at i:28896332 original size:18 final size:17
Alignment explanation
Indices: 28896309--28896342 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28896299 GTTGGGTCGA
28896309 AATGGGCCGTGTGGGCCC
1 AATGGG-CGTGTGGGCCC
*
28896327 AATGGGCTTGTGGGCC
1 AATGGGCGTGTGGGCC
28896343 TCACATGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.12, C:0.24, G:0.44, T:0.21
Consensus pattern (17 bp):
AATGGGCGTGTGGGCCC
Found at i:28896626 original size:27 final size:27
Alignment explanation
Indices: 28896567--28896633 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
28896557 CCCAAACTGA
*
28896567 TATAAAATGATTGTTATGCCCCCACGT
1 TATAAAATGACTGTTATGCCCCCACGT
** ** *
28896594 GGTAAAATGACTGTTATGCCCTTATGT
1 TATAAAATGACTGTTATGCCCCCACGT
28896621 TATAAAATGACTG
1 TATAAAATGACTG
28896634 CATACTCTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (27 bp):
TATAAAATGACTGTTATGCCCCCACGT
Found at i:28898915 original size:27 final size:27
Alignment explanation
Indices: 28898885--28898952 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
28898875 CCCAAACTGA
*
28898885 TATAAAATGACTGTTGTGCCCCTATGT
1 TATAAAATGACTGTTATGCCCCTATGT
28898912 TATAAAATGACTGTTATGCCCCTATGT
1 TATAAAATGACTGTTATGCCCCTATGT
28898939 TATAAAATGACTGT
1 TATAAAATGACTGT
28898953 ATATTTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (27 bp):
TATAAAATGACTGTTATGCCCCTATGT
Found at i:28899198 original size:22 final size:22
Alignment explanation
Indices: 28899154--28899198 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28899144 TCCCCACATG
*
28899154 GAGTGTTGGGCTGGATGGAGTA
1 GAGTGTAGGGCTGGATGGAGTA
*
28899176 GAGTGTAGAGGCTGGTTGG-GTA
1 GAGTGTAG-GGCTGGATGGAGTA
28899198 G
1 G
28899199 GATTTCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.18, C:0.04, G:0.51, T:0.27
Consensus pattern (22 bp):
GAGTGTAGGGCTGGATGGAGTA
Found at i:28899263 original size:34 final size:32
Alignment explanation
Indices: 28899216--28899290 Score: 132
Period size: 34 Copynumber: 2.3 Consensus size: 32
28899206 TATTGCATGT
28899216 CTGAACTGATACTGTAATGGGCTAAGGCCCACA
1 CTGAACTGATACTGTAATGGGCTAAGGCCCA-A
28899249 CTGATACTGATACTGTAATGGGCTAAGGCCCAA
1 CTGA-ACTGATACTGTAATGGGCTAAGGCCCAA
28899282 CTGAACTGA
1 CTGAACTGA
28899291 ACTATTACTG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
32 5 0.12
33 9 0.22
34 27 0.66
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (32 bp):
CTGAACTGATACTGTAATGGGCTAAGGCCCAA
Found at i:28906279 original size:18 final size:18
Alignment explanation
Indices: 28906239--28906279 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28906229 AGACCAATTT
28906239 TGGGCTATGTGGGCCACA
1 TGGGCTATGTGGGCCACA
*
28906257 CGGGC-ATGTGGGCCCACA
1 TGGGCTATGTGGG-CCACA
28906275 TGGGC
1 TGGGC
28906280 CCGCATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.15, C:0.27, G:0.41, T:0.17
Consensus pattern (18 bp):
TGGGCTATGTGGGCCACA
Found at i:28906434 original size:27 final size:27
Alignment explanation
Indices: 28906396--28906477 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
28906386 CCTAAACTGA
28906396 TATAAAATGATTGTTATGCTCCTATGT
1 TATAAAATGATTGTTATGCTCCTATGT
*
28906423 TATAAAATGATTGTTATGCCCCTATGT
1 TATAAAATGATTGTTATGCTCCTATGT
* * *
28906450 TATAAAACGTTTG-TATGCT-TTATGT
1 TATAAAATGATTGTTATGCTCCTATGT
28906475 TAT
1 TAT
28906478 GTATGATTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
25 8 0.16
26 5 0.10
27 37 0.74
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (27 bp):
TATAAAATGATTGTTATGCTCCTATGT
Found at i:28909514 original size:20 final size:21
Alignment explanation
Indices: 28909489--28909527 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28909479 TGGTTCAACT
28909489 ATTTT-GGAAATGGAGGTTCA
1 ATTTTGGGAAATGGAGGTTCA
*
28909509 ATTTTGGGTAATGGAGGTT
1 ATTTTGGGAAATGGAGGTT
28909528 TCGTTCAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.33, T:0.38
Consensus pattern (21 bp):
ATTTTGGGAAATGGAGGTTCA
Found at i:28912540 original size:11 final size:11
Alignment explanation
Indices: 28912469--28912540 Score: 57
Period size: 11 Copynumber: 6.8 Consensus size: 11
28912459 ATTTTAAAAA
*
28912469 TAATATTATTT
1 TAATATTAATT
28912480 TAATA-T-ATT
1 TAATATTAATT
28912489 TAATATTTAATT
1 TAATA-TTAATT
28912501 TAATACTT-ATCT
1 TAATA-TTAAT-T
*
28912513 TAATAGT-ATT
1 TAATATTAATT
28912523 T--TATTAATT
1 TAATATTAATT
28912532 TAATATTAA
1 TAATATTAA
28912541 ATTGATTATC
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
8 3 0.06
9 11 0.22
10 3 0.06
11 17 0.34
12 16 0.32
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (11 bp):
TAATATTAATT
Found at i:28912554 original size:25 final size:25
Alignment explanation
Indices: 28912526--28912576 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
28912516 TAGTATTTTA
28912526 TTAAT-TTAATATTAAAT-TGATTATC
1 TTAATATTAA-ATTAAATCT-ATTATC
*
28912551 TTAATATTAAATTTAATCTATTATC
1 TTAATATTAAATTAAATCTATTATC
28912576 T
1 T
28912577 ATCTTGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (25 bp):
TTAATATTAAATTAAATCTATTATC
Found at i:28916543 original size:16 final size:16
Alignment explanation
Indices: 28916500--28916544 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
28916490 TTGAAATTAG
28916500 ACTCATTAATAATTTAA
1 ACTCA-TAATAATTTAA
28916517 A--CAT-ATAAATTTAA
1 ACTCATAAT-AATTTAA
28916531 ACTCATAATAATTT
1 ACTCATAATAATTT
28916545 TTTTTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 2 0.08
16 8 0.33
17 3 0.12
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (16 bp):
ACTCATAATAATTTAA
Found at i:28920569 original size:3 final size:3
Alignment explanation
Indices: 28920561--28920585 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28920551 TGTGAATCTA
28920561 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
28920586 TTTGGTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:28923760 original size:19 final size:19
Alignment explanation
Indices: 28923736--28923773 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28923726 TTGAATGGGG
*
28923736 CAGGGTGAGATTTGTGAGA
1 CAGGGTAAGATTTGTGAGA
28923755 CAGGGTAAGATTTGTGAGA
1 CAGGGTAAGATTTGTGAGA
28923774 GAAACAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.39, T:0.26
Consensus pattern (19 bp):
CAGGGTAAGATTTGTGAGA
Found at i:28930158 original size:7 final size:7
Alignment explanation
Indices: 28930148--28930179 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
28930138 ATGTTAAGTA
28930148 TATATAT
1 TATATAT
28930155 TATATAT
1 TATATAT
28930162 TATATAT
1 TATATAT
28930169 TATATAT
1 TATATAT
28930176 TATA
1 TATA
28930180 ATAAAGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:28930167 original size:14 final size:14
Alignment explanation
Indices: 28930105--28930179 Score: 66
Period size: 14 Copynumber: 5.3 Consensus size: 14
28930095 AAAGTTAAAA
28930105 TATATATTATAATAT
1 TATATATTAT-ATAT
*
28930120 TATAATATTA-AAACT
1 TAT-ATATTATATA-T
* *
28930135 TAAATGTTA-AGTA-
1 TATATATTATA-TAT
28930148 TATATATTATATAT
1 TATATATTATATAT
28930162 TATATATTATATAT
1 TATATATTATATAT
28930176 TATA
1 TATA
28930180 ATAAAGAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
13 9 0.18
14 27 0.55
15 7 0.14
16 6 0.12
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (14 bp):
TATATATTATATAT
Found at i:28930227 original size:4 final size:4
Alignment explanation
Indices: 28930218--28930249 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
28930208 AACACAAAGG
28930218 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAA
28930250 GGAGAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:28930237 original size:13 final size:13
Alignment explanation
Indices: 28930219--28930246 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28930209 ACACAAAGGG
28930219 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
28930232 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
28930245 AA
1 AA
28930247 GAAGGAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:28930249 original size:17 final size:17
Alignment explanation
Indices: 28930182--28930246 Score: 69
Period size: 17 Copynumber: 3.6 Consensus size: 17
28930172 ATATTATAAT
28930182 AAAGAAAGAAACAAAAG
1 AAAGAAAGAAACAAAAG
*
28930199 CAAA-AACGAAACACAAAGGG
1 -AAAGAAAGAAACA-AAA--G
*
28930219 AAAGAAAGAAAGAAAAG
1 AAAGAAAGAAACAAAAG
28930236 AAAGAAAGAAA
1 AAAGAAAGAAA
28930247 GAAGGAGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 20 0.50
18 6 0.15
19 6 0.15
20 8 0.20
ACGTcount: A:0.72, C:0.08, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAACAAAAG
Found at i:28931271 original size:40 final size:40
Alignment explanation
Indices: 28931139--28931276 Score: 129
Period size: 40 Copynumber: 3.5 Consensus size: 40
28931129 ACTTCGAGTT
* * * *
28931139 GATGAGACAGTGGGTGTCAATTTACTACTTCGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTATTACTTAGGATT-ATCC
* * * * * *
28931180 GATGAGGCACTGGGTGCCAA--T-TCACTTTGGTTTAGCC
1 GATGAGACACTGGGTGTCAATTTATTACTTAGGATTATCC
* *
28931217 GATGAGACATTGGGTGTCAATTTATTACTTAGAATTATCC
1 GATGAGACACTGGGTGTCAATTTATTACTTAGGATTATCC
*
28931257 GATGAGGCACTGGGTGTCAA
1 GATGAGACACTGGGTGTCAA
28931277 ACTGGTGTGT
Statistics
Matches: 75, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
37 19 0.25
38 8 0.11
39 2 0.03
40 29 0.39
41 17 0.23
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATTACTTAGGATTATCC
Found at i:28934844 original size:16 final size:16
Alignment explanation
Indices: 28934824--28934861 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28934814 AAAATCCTAA
*
28934824 AAAAATTAATTTTTTTT
1 AAAAATTAA-TTATTTT
28934841 AAAAA-TAATTATTTT
1 AAAAATTAATTATTTT
28934856 AAAAAT
1 AAAAAT
28934862 CAGCTCTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATTAATTATTTT
Found at i:28934909 original size:32 final size:32
Alignment explanation
Indices: 28934873--28934937 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
28934863 AGCTCTAGGA
28934873 TGAACCAAGACAAAACAT-TGTCCAGATTCATT
1 TGAACCAAGAC-AAACATATGTCCAGATTCATT
** * *
28934905 TGAACCTGGACAATCATATGTCTAGATTCATT
1 TGAACCAAGACAAACATATGTCCAGATTCATT
28934937 T
1 T
28934938 TATTTGTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (32 bp):
TGAACCAAGACAAACATATGTCCAGATTCATT
Found at i:28935049 original size:20 final size:19
Alignment explanation
Indices: 28934987--28935050 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
28934977 AAAAAATATA
28934987 TAAAATTTATTAGAAATTAT
1 TAAAATTTATTA-AAATTAT
* *
28935007 TAATACTTA-TAATAAGTTA-
1 TAAAATTTATTAA-AA-TTAT
28935026 TAAAATTTTATTAAAATTAT
1 TAAAA-TTTATTAAAATTAT
28935046 TAAAA
1 TAAAA
28935051 ATCAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 1 0.03
19 11 0.31
20 20 0.57
21 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (19 bp):
TAAAATTTATTAAAATTAT
Found at i:28935078 original size:10 final size:10
Alignment explanation
Indices: 28934977--28935080 Score: 54
Period size: 10 Copynumber: 10.4 Consensus size: 10
28934967 TAAAATTACA
*
28934977 AAAAAATATAT
1 AAAAATTAT-T
*
28934988 AAAATTTATT
1 AAAAATTATT
*
28934998 AGAAATTATT
1 AAAAATTATT
* *
28935008 AATACTTA-T
1 AAAAATTATT
*
28935017 AATAAGTTA-T
1 AA-AAATTATT
*
28935027 AAAATTTTATT
1 AAAA-ATTATT
28935038 -AAAATTATT
1 AAAAATTATT
* *
28935047 AAAAATCAATA
1 AAAAAT-TATT
*
28935058 AAAAAGT-TT
1 AAAAATTATT
28935067 AAAAATTATT
1 AAAAATTATT
28935077 AAAA
1 AAAA
28935081 GCCACCCCTG
Statistics
Matches: 70, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
9 17 0.24
10 38 0.54
11 15 0.21
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (10 bp):
AAAAATTATT
Found at i:28937377 original size:17 final size:17
Alignment explanation
Indices: 28937350--28937395 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
28937340 CCGATATAAT
* * *
28937350 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
28937367 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
28937384 AAATATTTTTAA
1 AAATATTTTTAA
28937396 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:28937393 original size:11 final size:11
Alignment explanation
Indices: 28937379--28937448 Score: 67
Period size: 11 Copynumber: 6.6 Consensus size: 11
28937369 ATTTTTTTAA
28937379 TTTTAAAATAT
1 TTTTAAAATAT
28937390 TTTTAAAATACT
1 TTTTAAAATA-T
** *
28937402 TTTTTTATTAT
1 TTTTAAAATAT
*
28937413 TTTT----TAA
1 TTTTAAAATAT
28937420 TTTTAAAATAT
1 TTTTAAAATAT
28937431 TTTTAAAATAT
1 TTTTAAAATAT
28937442 TTTTAAA
1 TTTTAAA
28937449 TACTTTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
7 6 0.12
11 35 0.71
12 8 0.16
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:28937413 original size:51 final size:50
Alignment explanation
Indices: 28937358--28937459 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 50
28937348 ATAAATATAT
**
28937358 TTATTTTTTAAATTTT-TTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 TTATTTTTT-AATTTTAAATAATTTTAAAATATTTTT-AAATACTTTTTTTA
*
28937409 TTATTTTTTAATTTTAAAATATTTTTAAAATATTTTTAAATACTTTTTTTA
1 TTATTTTTTAATTTT-AAATAATTTTAAAATATTTTTAAATACTTTTTTTA
28937460 ATTTTTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
50 6 0.13
51 23 0.50
52 17 0.37
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (50 bp):
TTATTTTTTAATTTTAAATAATTTTAAAATATTTTTAAATACTTTTTTTA
Found at i:28937416 original size:41 final size:40
Alignment explanation
Indices: 28937362--28937471 Score: 145
Period size: 41 Copynumber: 2.7 Consensus size: 40
28937352 ATATATTTAT
28937362 TTTTTAAAT--TTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTAAATACTTTTTTAATTTTAAAATATTTTTAAAATA
* *
28937400 CTTTTTTTATTA-TTTTTTAATTTTAAAATATTTTTAAAATA
1 --TTTTTAAATACTTTTTTAATTTTAAAATATTTTTAAAATA
28937441 TTTTTAAATACTTTTTTTAATTTTTAAAATA
1 TTTTTAAATAC-TTTTTTAA-TTTTAAAATA
28937472 AATTTTTGGT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
39 8 0.13
40 7 0.11
41 37 0.60
42 10 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (40 bp):
TTTTTAAATACTTTTTTAATTTTAAAATATTTTTAAAATA
Found at i:28937455 original size:11 final size:10
Alignment explanation
Indices: 28937362--28937456 Score: 56
Period size: 10 Copynumber: 9.5 Consensus size: 10
28937352 ATATATTTAT
28937362 TTTTTAAAT-
1 TTTTTAAATA
*
28937371 TTTTT-TA-A
1 TTTTTAAATA
*
28937379 TTTTAAAATA
1 TTTTTAAATA
28937389 TTTTTAAAATA
1 TTTTT-AAATA
* *
28937400 CTTTTTTTATTA
1 --TTTTTAAATA
*
28937412 TTTTT-TA-A
1 TTTTTAAATA
*
28937420 TTTTAAAATA
1 TTTTTAAATA
28937430 TTTTTAAAATA
1 TTTTT-AAATA
28937441 TTTTTAAATA
1 TTTTTAAATA
28937451 CTTTTT
1 -TTTTT
28937457 TTAATTTTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
8 10 0.15
9 7 0.11
10 20 0.31
11 20 0.31
12 3 0.05
13 5 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTAAATA
Done.