Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold218
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: 1018737
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 45434 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:348594 original size:13 final size:13
Alignment explanation
Indices: 348576--348601 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
348566 TGAGTACAAG
348576 AGGGCTAAAGAAT
1 AGGGCTAAAGAAT
348589 AGGGCTAAAGAAT
1 AGGGCTAAAGAAT
348602 TCTGAGGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (13 bp):
AGGGCTAAAGAAT
Found at i:348857 original size:328 final size:328
Alignment explanation
Indices: 348254--348906 Score: 1083
Period size: 328 Copynumber: 2.0 Consensus size: 328
348244 ATAAAATTCG
* * *
348254 AAAGTATAGGGCTAAAGAATTCTGAGGTATAACTAAAGATGATCCAGAGAGATTCGAGTTCTGGT
1 AAAGAATAGGGCTAAAGAATTCTGAGGTATAACTAAAGATGATCCAGAGACAGTCGAGTTCTGGT
* * *
348319 TAAAAAACACAAATAGAGTTTTCAATGAATTGTCTTGTACACCAGTAGAATGCTTGAAATGTGTT
66 TAAAAAACACAAATAGAGTTTTCAATGAATCGTCGTGTACACCAGGAGAATGCTTGAAATGTGTT
* *
348384 GTTTCTCTATTAAAAGACTCAGCTTACTAGTGGTGGAACACGTTGATCACGGTGGTACCGAGGGA
131 GTTTCTATATTAAAAGACTCAGCTTACTAGTGGTGGAACACGTTGATCAAGGTGGTACCGAGGGA
* * * *
348449 TCAAGTAAATTGGGAATTCTTCCAGACAGAGTTCAAAAAGAAATATGTGAGTCAGAGGTTCCTAG
196 TCAAGTAAATTGGGAATTCTTCCAGACAGAGTTCAAAAAGAAATATGTGAGTAAAAGGTTCCAAA
*
348514 ATAAGAAACGCAAAGAGTTTCTTGAGTTGAAGCAATGACGTATGTCAGTAGCTGAGTACAAGAGG
261 ATAAGAAACGCAAAGAGTTTCTTGAGTTGAAGCAATGACGTATGTCAGTAGATGAGTACAAGAGG
348579 GCT
326 GCT
*
348582 AAAGAATAGGGCTAAAGAATTCTGAGGTATAACTGAAGATGATCCAGAGACAGTCGAGTTCTGGT
1 AAAGAATAGGGCTAAAGAATTCTGAGGTATAACTAAAGATGATCCAGAGACAGTCGAGTTCTGGT
* * * ** *
348647 TAGAAAACACAATTAGGGTTTTTGATGAATCGTCGTGTACACTAGGAGAATGCTTGAAATGTGTT
66 TAAAAAACACAAATAGAGTTTTCAATGAATCGTCGTGTACACCAGGAGAATGCTTGAAATGTGTT
*
348712 GTTTCTATATTAAAAGACTCAGCTTA-TCAGTGGTGGAACACGTTTATCAAGGTGGTACCGAGGG
131 GTTTCTATATTAAAAGACTCAGCTTACT-AGTGGTGGAACACGTTGATCAAGGTGGTACCGAGGG
348776 ATCAAGTAAATTGGGAATTCTTCCAGACAGAGTTCAAAAAGAAATATGTGAGTAAAAGGTTCCAA
195 ATCAAGTAAATTGGGAATTCTTCCAGACAGAGTTCAAAAAGAAATATGTGAGTAAAAGGTTCCAA
* *
348841 AATAAGAAATGCAAAGAGTTTCTTGAGTTGAAGCAATGATGTATGTCAGTAGATGAGTACAAGAG
260 AATAAGAAACGCAAAGAGTTTCTTGAGTTGAAGCAATGACGTATGTCAGTAGATGAGTACAAGAG
348906 G
325 G
348907 AAATTTATGA
Statistics
Matches: 301, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
327 1 0.00
328 300 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (328 bp):
AAAGAATAGGGCTAAAGAATTCTGAGGTATAACTAAAGATGATCCAGAGACAGTCGAGTTCTGGT
TAAAAAACACAAATAGAGTTTTCAATGAATCGTCGTGTACACCAGGAGAATGCTTGAAATGTGTT
GTTTCTATATTAAAAGACTCAGCTTACTAGTGGTGGAACACGTTGATCAAGGTGGTACCGAGGGA
TCAAGTAAATTGGGAATTCTTCCAGACAGAGTTCAAAAAGAAATATGTGAGTAAAAGGTTCCAAA
ATAAGAAACGCAAAGAGTTTCTTGAGTTGAAGCAATGACGTATGTCAGTAGATGAGTACAAGAGG
GCT
Found at i:359684 original size:19 final size:18
Alignment explanation
Indices: 359652--359687 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
359642 ATAGTAAATT
*
359652 ATTTTTATATTTTCTCAA
1 ATTTTTATACTTTCTCAA
359670 ATTTTTCATACTTTCTCA
1 ATTTTT-ATACTTTCTCA
359688 TGTCAGGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTATACTTTCTCAA
Found at i:360087 original size:26 final size:25
Alignment explanation
Indices: 360019--360093 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
360009 GAAGCTCCGG
*
360019 AGAGCCATTAATTAGGAAGCTCACAA
1 AGAGCCATTAA-TGGGAAGCTCACAA
**
360045 AGAGCTTTTAATCGGGAAGCTCACAA
1 AGAGCCATTAAT-GGGAAGCTCACAA
*
360071 AGAGCCATATAATGGGACGCTCA
1 AGAGCCAT-TAATGGGAAGCTCA
360094 TAAGAGCTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 1 0.02
26 36 0.88
27 4 0.10
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (25 bp):
AGAGCCATTAATGGGAAGCTCACAA
Found at i:364672 original size:126 final size:126
Alignment explanation
Indices: 364280--364664 Score: 531
Period size: 126 Copynumber: 3.1 Consensus size: 126
364270 GCCAAGCAAG
** * * * * *
364280 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGAGTTTTTCAATACTTTTGCTGATAGTACATCT
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGATGACAGTGCATCC
* * * * * *
364345 TGCTTGAAACATATTTGACATTATTTTTTTAGAACCGTCTTCTTAAATTTATTTTTTCAGA
66 TGCTTGAAGCATTTTTGACATTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGA
* * *
364406 AACTACTGTAGAAAAAGAGTGTCCACATGGGATCTTTTTT-AGTACTTTTGATGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGATGACAGTGCATCC
* *
364470 TGCTTGAAGCATTTTTGACATTATTTTTTCAGAA-CAGTCTTCTCAAAATTAGTTTTTCAAA
66 TGCTTGAAGCATTTTTGACATTATTTTTTCAGAACCA-TCTTCTCAAAATTATTTTTTCAGA
* * *
364531 AACTACTGCAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGTTGACAATGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGATGACAGTGCATCC
* * *
364596 TGCTTGAAGCGTTTTTGACACTATTTTTTCATAACCATCTTCTCAAAATTATTTTTTCAGA
66 TGCTTGAAGCATTTTTGACATTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGA
364657 AACTACTG
1 AACTACTG
364665 AACAAAAAAA
Statistics
Matches: 227, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
124 1 0.00
125 106 0.47
126 118 0.52
127 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (126 bp):
AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGATGACAGTGCATCC
TGCTTGAAGCATTTTTGACATTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGA
Found at i:364895 original size:33 final size:33
Alignment explanation
Indices: 364776--364887 Score: 161
Period size: 34 Copynumber: 3.3 Consensus size: 33
364766 TTAAAACCCT
364776 AAACCCTAAACCCTAATTTAATTTATTTTTAAAA
1 AAACCCTAAACCCTAATTTAATTTATTTTT-AAA
* *
364810 AAATCCTAAACCTTAATTTAATTTATTTTTAAA
1 AAACCCTAAACCCTAATTTAATTTATTTTTAAA
** *
364843 AAAATCTAAATCCTAATTTAATTTATTTGTTAAA
1 AAACCCTAAACCCTAATTTAATTTATTT-TTAAA
364877 AAACCCTAAAC
1 AAACCCTAAAC
364888 TTGATTTATT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 27 0.40
34 41 0.60
ACGTcount: A:0.45, C:0.15, G:0.01, T:0.39
Consensus pattern (33 bp):
AAACCCTAAACCCTAATTTAATTTATTTTTAAA
Found at i:364999 original size:24 final size:23
Alignment explanation
Indices: 364951--365014 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
364941 TTATTTTAAC
*
364951 AAAACCCT-AACACTAAACCCTT
1 AAAACCCTAAACACTAAACCCAT
*
364973 AAAACCCTAAAACTCTAAACCCAT
1 AAAACCCT-AAACACTAAACCCAT
**
364997 -AAACCCTAGGCACTAAAC
1 AAAACCCTAAACACTAAAC
365015 ATGCAAATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 16 0.46
23 7 0.20
24 12 0.34
ACGTcount: A:0.47, C:0.34, G:0.03, T:0.16
Consensus pattern (23 bp):
AAAACCCTAAACACTAAACCCAT
Found at i:371210 original size:18 final size:17
Alignment explanation
Indices: 371180--371221 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
371170 TTTTCAATTC
371180 TAATTTGACCCAAAATAAT
1 TAATTT-ACCCAAAA-AAT
371199 TAATTTACCCAAAAAAT
1 TAATTTACCCAAAAAAT
371216 T-ATTTA
1 TAATTTA
371222 AAACTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 4 0.17
18 8 0.35
19 6 0.26
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATTTACCCAAAAAAT
Found at i:372714 original size:13 final size:13
Alignment explanation
Indices: 372696--372722 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
372686 TACATAAAAC
372696 AAACAATTTTATA
1 AAACAATTTTATA
372709 AAACAATTTTATA
1 AAACAATTTTATA
372722 A
1 A
372723 GGGCAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
AAACAATTTTATA
Found at i:376348 original size:21 final size:22
Alignment explanation
Indices: 376322--376375 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
376312 TAGCGATGGC
*
376322 GGTGAGATTAGTTACTGTAG-A
1 GGTGAGATTAGATACTGTAGCA
*
376343 GGTGAGATTGGATACTGTAGCA
1 GGTGAGATTAGATACTGTAGCA
376365 -GTGAGATTAGA
1 GGTGAGATTAGA
376376 AACAATGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.35, T:0.30
Consensus pattern (22 bp):
GGTGAGATTAGATACTGTAGCA
Found at i:376638 original size:33 final size:32
Alignment explanation
Indices: 376584--376645 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
376574 AATGAATTAT
376584 ATAATTAATTTAAATTATTTATTAGTTAAAATG
1 ATAATTAATTTAAATTATTTA-TAGTTAAAATG
* * *
376617 ATAATTATTTTTAATTTTTTATAGTTAAA
1 ATAATTAATTTAAATTATTTATAGTTAAA
376646 TATTTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (32 bp):
ATAATTAATTTAAATTATTTATAGTTAAAATG
Found at i:381275 original size:18 final size:18
Alignment explanation
Indices: 381248--381288 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
381238 GGTTCGTGGG
*
381248 TATTGTAGGCAGAAGAGT
1 TATTGGAGGCAGAAGAGT
381266 TATTGGAGGCAGAAGAGT
1 TATTGGAGGCAGAAGAGT
381284 TATTG
1 TATTG
381289 CAAAAGATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (18 bp):
TATTGGAGGCAGAAGAGT
Found at i:385370 original size:30 final size:30
Alignment explanation
Indices: 385329--385386 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
385319 CGAATGAAAG
385329 AAATGAACCTATTTATAGCCTTCAGGTGAC
1 AAATGAACCTATTTATAGCCTTCAGGTGAC
*
385359 AAATGAGCCTATTTATAGCCTTCAGGTG
1 AAATGAACCTATTTATAGCCTTCAGGTG
385387 GTCATCGTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
AAATGAACCTATTTATAGCCTTCAGGTGAC
Found at i:387186 original size:23 final size:23
Alignment explanation
Indices: 387156--387206 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
387146 TAAACATAAG
387156 CAATCTATGTACATGCTCCTAAC
1 CAATCTATGTACATGCTCCTAAC
387179 CAATCTATGTACATGCTCCTAAC
1 CAATCTATGTACATGCTCCTAAC
387202 CAATC
1 CAATC
387207 ACTTGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.29
Consensus pattern (23 bp):
CAATCTATGTACATGCTCCTAAC
Found at i:389131 original size:20 final size:19
Alignment explanation
Indices: 389079--389140 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
389069 ACTCCCCCTA
* *
389079 TTTACTTTCCCTC-AAACT
1 TTTACTTCCCCCCAAAACT
389097 TTTA-TT--CCCCAAAACTT
1 TTTACTTCCCCCCAAAAC-T
*
389114 TTTACTTCCCCCCTAAACT
1 TTTACTTCCCCCCAAAACT
389133 TTTACTTC
1 TTTACTTC
389141 TCACCCTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 3 0.08
16 4 0.11
17 7 0.19
18 6 0.16
19 9 0.24
20 8 0.22
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTACTTCCCCCCAAAACT
Found at i:389135 original size:19 final size:18
Alignment explanation
Indices: 389087--389140 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
389077 TATTTACTTT
389087 CCCTCAAACTTTTA-TT-C
1 CCCT-AAACTTTTACTTCC
*
389104 CCCAAAACTTTTTACTTCCC
1 CCCTAAAC-TTTTACTT-CC
389124 CCCTAAACTTTTACTTC
1 CCCTAAACTTTTACTTC
389141 TCACCCTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 4 0.13
17 8 0.26
18 3 0.10
19 8 0.26
20 8 0.26
ACGTcount: A:0.24, C:0.37, G:0.00, T:0.39
Consensus pattern (18 bp):
CCCTAAACTTTTACTTCC
Found at i:389147 original size:20 final size:20
Alignment explanation
Indices: 389108--389147 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
389098 TTATTCCCCA
*
389108 AAACTTTTTACTTCCCCCCT
1 AAACTTTTTACTTCCACCCT
389128 AAAC-TTTTACTTCTCACCCT
1 AAACTTTTTACTTC-CACCCT
389148 TTACTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.40
Consensus pattern (20 bp):
AAACTTTTTACTTCCACCCT
Found at i:392762 original size:76 final size:76
Alignment explanation
Indices: 392636--392787 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
392626 GGACTCAATT
*
392636 TACCCTTCCGACCAAATCTCAAAATCTTCTTCCACGGAGACACTTTCCAAAACACTTTATCGCCA
1 TACCCTTCCGACCAAATCTCAAAATCTTCTTCCACAGAGACACTTTCCAAAACACTTTATCGCCA
392701 ACTTGAAACTC
66 ACTTGAAACTC
392712 TACCCTTCCGACCAAATCTCAAAATCTTCTTCCACAGAGACACTTTCCAAAACACTTTATCGCCA
1 TACCCTTCCGACCAAATCTCAAAATCTTCTTCCACAGAGACACTTTCCAAAACACTTTATCGCCA
392777 ACTTGAAACTC
66 ACTTGAAACTC
392788 AATGTCTTTC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.32, C:0.34, G:0.07, T:0.26
Consensus pattern (76 bp):
TACCCTTCCGACCAAATCTCAAAATCTTCTTCCACAGAGACACTTTCCAAAACACTTTATCGCCA
ACTTGAAACTC
Found at i:405947 original size:40 final size:41
Alignment explanation
Indices: 405868--405960 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 41
405858 ACGTATGTGT
* * *
405868 AATTCAGGGGTACCAAAGTACATATAGGGGCACAAAAGTGC
1 AATTTAGGGGTACCAAAGTAAAAATAGGGGCACAAAAGTGC
* * *
405909 AATTTAGGGGTACCAGAG-AAAAATAGGGGCATATAAGTGC
1 AATTTAGGGGTACCAAAGTAAAAATAGGGGCACAAAAGTGC
405949 AATTTAGGGGTA
1 AATTTAGGGGTA
405961 TCGAAGTACA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 30 0.65
41 16 0.35
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (41 bp):
AATTTAGGGGTACCAAAGTAAAAATAGGGGCACAAAAGTGC
Found at i:405967 original size:21 final size:21
Alignment explanation
Indices: 405942--405994 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
405932 TAGGGGCATA
*
405942 TAAGTGCAATTTAGGGGTATCG
1 TAAGTGCAATTCAGGGGTA-CG
*
405964 -AAGTAC-A-TCAGGGGTACG
1 TAAGTGCAATTCAGGGGTACG
405982 TAAGTGCAATTCA
1 TAAGTGCAATTCA
405995 ATGTATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
18 2 0.08
19 13 0.52
20 2 0.08
21 8 0.32
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.26
Consensus pattern (21 bp):
TAAGTGCAATTCAGGGGTACG
Found at i:405977 original size:40 final size:38
Alignment explanation
Indices: 405868--405992 Score: 106
Period size: 40 Copynumber: 3.1 Consensus size: 38
405858 ACGTATGTGT
* *
405868 AATTCAGGGGTACCAAAGTACATATAGGGGCACAAAAGTGC
1 AATTTAGGGGTA-CAAAGTAC--ATAGGGGCACATAAGTGC
* * * *
405909 AATTTAGGGGTACCAGAGAAAAATAGGGGCATATAAGTGC
1 AATTTAGGGGTA-CAAAG-TACATAGGGGCACATAAGTGC
* * *
405949 AATTTAGGGGTATCGAAGTACATCAGGGGTACGTAAGTGC
1 AATTTAGGGGTA-CAAAGTACAT-AGGGGCACATAAGTGC
405989 AATT
1 AATT
405993 CAATGTATAA
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.04
40 48 0.71
41 16 0.24
42 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.22
Consensus pattern (38 bp):
AATTTAGGGGTACAAAGTACATAGGGGCACATAAGTGC
Found at i:413280 original size:40 final size:41
Alignment explanation
Indices: 413194--413287 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
413184 AGGCACTTAT
* * *
413194 GTGCAATTCAGGGGTACTGAAGTACAAACAGGGGCATGTAA
1 GTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGAAA
*
413235 GTGCAATTCAGGTGTACCGAAGTACAATA-A-GGGCACGAAA
1 GTGCAATTCAGGGGTACCGAAGTACAA-ACAGGGGCACGAAA
*
413275 GTGCAATTTAGGG
1 GTGCAATTCAGGG
413288 TATAATTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 19 0.41
41 26 0.57
42 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (41 bp):
GTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGAAA
Found at i:417670 original size:45 final size:45
Alignment explanation
Indices: 417606--417773 Score: 176
Period size: 45 Copynumber: 3.7 Consensus size: 45
417596 ATATCGTTGG
* * * * **
417606 AAATATAGGTGGATGCTATGTGCTGATTCCACCCTATATTAATGA
1 AAATAAAGGTGGTTGCTATGTGCTGATTTCACCCGATACCAATGA
* * * *
417651 AAATAAAGGTGGTTGCTATGTGTTGATTTTACCGGATACCAATGG
1 AAATAAAGGTGGTTGCTATGTGCTGATTTCACCCGATACCAATGA
** * *
417696 TTATATAGGTGGTTGCTATGTGCTGATTTCACCCGGA-ACCATTGA
1 AAATAAAGGTGGTTGCTATGTGCTGATTTCACCC-GATACCAATGA
**
417741 GTATAAAGGTGGTTGCTATGTGCTGATTTCACC
1 AAATAAAGGTGGTTGCTATGTGCTGATTTCACC
417774 AAGTACTCTT
Statistics
Matches: 102, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
45 100 0.98
46 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (45 bp):
AAATAAAGGTGGTTGCTATGTGCTGATTTCACCCGATACCAATGA
Found at i:417791 original size:45 final size:44
Alignment explanation
Indices: 417653--417798 Score: 159
Period size: 45 Copynumber: 3.2 Consensus size: 44
417643 ATTAATGAAA
* * * **
417653 ATAAAGGTGGTTGCTATGTGTTGATTTTACCGGATACCAATGGTT
1 ATAAAGGTGGTTGCTATGTGCTGATTTCACCGG-TACCATTGACT
* * *
417698 ATATAGGTGGTTGCTATGTGCTGATTTCACCCGGAACCATTGAGT
1 ATAAAGGTGGTTGCTATGTGCTGATTTCA-CCGGTACCATTGACT
*
417743 ATAAAGGTGGTTGCTATGTGCTGATTTCACCAAGTACTC-TTGACT
1 ATAAAGGTGGTTGCTATGTGCTGATTTCACC-GGTAC-CATTGACT
*
417788 ATAAGGGTGGT
1 ATAAAGGTGGT
417799 GTTGTGTACT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
44 2 0.02
45 79 0.92
46 5 0.06
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (44 bp):
ATAAAGGTGGTTGCTATGTGCTGATTTCACCGGTACCATTGACT
Found at i:433757 original size:27 final size:27
Alignment explanation
Indices: 433710--433811 Score: 150
Period size: 27 Copynumber: 3.8 Consensus size: 27
433700 ACAAGAAAAT
*
433710 GGAAGCCTTTGTGGCAGTCTATGATAA
1 GGAAGCCTTTGTGGCAATCTATGATAA
* *
433737 GGATGCCTTTGTGGAAATCTATGATAA
1 GGAAGCCTTTGTGGCAATCTATGATAA
* *
433764 GGAAGCTTTTGTGGCAATCTATGAAAA
1 GGAAGCCTTTGTGGCAATCTATGATAA
*
433791 TGAAGCCTTTGTGGCAATCTA
1 GGAAGCCTTTGTGGCAATCTA
433812 CGAAGAGAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.31
Consensus pattern (27 bp):
GGAAGCCTTTGTGGCAATCTATGATAA
Found at i:434195 original size:8 final size:8
Alignment explanation
Indices: 434182--434207 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
434172 TATAAACTAA
434182 AAAGAAAT
1 AAAGAAAT
434190 AAAGAAAT
1 AAAGAAAT
434198 AAAGAAAT
1 AAAGAAAT
434206 AA
1 AA
434208 TGAGAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAGAAAT
Found at i:454039 original size:43 final size:43
Alignment explanation
Indices: 454005--454254 Score: 331
Period size: 43 Copynumber: 5.8 Consensus size: 43
453995 AGGCCATGTT
* *
454005 CTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGAACATGAC
1 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATGAC
* * * *
454048 CTTTAGCGGTGCTTTTATCACAATCGCCACTAAAGAACATGAT
1 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATGAC
*
454091 CTTTAGCGGCGCTTTTATCACAAACGCCGATAAAGAACATGAC
1 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATGAC
* *
454134 CTTTAGCGGTC-CTTTTATCACAAACACCACTAAAGAACATGAC
1 CTTTAGCGG-CGCTTTTATCACAAACGCCGCTAAAGAACATGAC
* * *
454177 CTTTAGCAGCGCCTTTTTTCACAAACGCTGCTAAAGAACATGAC
1 CTTTAGCGGCG-CTTTTATCACAAACGCCGCTAAAGAACATGAC
* * * *
454221 ATTTAGCGACGTTTTTTTCACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAA
454255 AGTACCATTC
Statistics
Matches: 180, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.01
43 142 0.79
44 37 0.21
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATGAC
Found at i:454268 original size:130 final size:128
Alignment explanation
Indices: 454003--454273 Score: 323
Period size: 130 Copynumber: 2.1 Consensus size: 128
453993 AAAGGCCATG
* * * *
454003 TTCTTTAGCGG-CGCTTTTATAAAAAACGCCGCTAAAGAACATGACCTTTAGCGGTGCTTTTATC
1 TTCTTTAGCGGTCGCTTTTATAAAAAACACCACTAAAGAACATGACCTTTAGCAGCGCTTTTATC
* *
454067 ACAATCGCCACTAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGATAAAGAACA
66 ACAAACGCCACTAAAGAACATGATCTTTAGCGACGCTTTTATCACAAACGCCGATAAAGAACA
* * *
454130 TGACCTTTAGCGGTC-CTTTTATCACAAACACCACTAAAGAACATGACCTTTAGCAGCGCCTTTT
1 T--TCTTTAGCGGTCGCTTTTATAAAAAACACCACTAAAGAACATGACCTTTAGCAGCG-CTTTT
* ** * * *
454194 TTCACAAACGCTGCTAAAGAACATGA-CATTTAGCGACGTTTTTTTCACAAACGCCGCTAAAAGT
63 ATCACAAACGCCACTAAAGAACATGATC-TTTAGCGACGCTTTTATCACAAACGCCGAT-AAAG-
*
454258 ACCA
125 AACA
454262 TTCTTTAGCGGT
1 TTCTTTAGCGGT
454274 GTTTGTGAAT
Statistics
Matches: 120, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
127 1 0.01
129 47 0.39
130 64 0.53
131 4 0.03
132 4 0.03
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (128 bp):
TTCTTTAGCGGTCGCTTTTATAAAAAACACCACTAAAGAACATGACCTTTAGCAGCGCTTTTATC
ACAAACGCCACTAAAGAACATGATCTTTAGCGACGCTTTTATCACAAACGCCGATAAAGAACA
Found at i:460071 original size:9 final size:9
Alignment explanation
Indices: 460057--460115 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
460047 TAAGTATAAT
460057 TAAGTTATG
1 TAAGTTATG
460066 TAAGTTATG
1 TAAGTTATG
* * *
460075 ATATGATATA
1 -TAAGTTATG
*
460085 T-ATTTATG
1 TAAGTTATG
460093 T-A-TTATG
1 TAAGTTATG
460100 TAAGTTATG
1 TAAGTTATG
460109 TAAGTTA
1 TAAGTTA
460116 CAAACATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
7 6 0.15
8 6 0.15
9 22 0.55
10 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:460181 original size:28 final size:27
Alignment explanation
Indices: 460117--460181 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
460107 TGTAAGTTAC
*
460117 AAACATAATTTATTCAATTAAATCGAA
1 AAACATAATTTATTCAATTAAACCGAA
*
460144 AATCGATAATTTATTCACATTAAACCGAA
1 AAAC-ATAATTTATTCA-ATTAAACCGAA
460173 TAAAC-TAAT
1 -AAACATAAT
460182 CAAACATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.09
28 16 0.50
29 10 0.31
30 3 0.09
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (27 bp):
AAACATAATTTATTCAATTAAACCGAA
Found at i:460191 original size:66 final size:66
Alignment explanation
Indices: 460116--460665 Score: 983
Period size: 66 Copynumber: 8.3 Consensus size: 66
460106 ATGTAAGTTA
*
460116 CAAACATAATTTATTCAATTAAATCGAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
1 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
460181 T
66 T
*
460182 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCTAATAAACTAA
1 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
460247 T
66 T
* * *
460248 CAAACATAATTTATTCAATTAAATCGAAAATCGATAATTTATTCACATTAAATCAAATAAACTAA
1 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
460313 T
66 T
* *
460314 CAAACATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCGAATAAACTAA
1 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
460379 T
66 T
*
460380 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCTAATAAACTAA
1 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
460445 T
66 T
*
460446 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCTAATAAACTAA
1 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
460511 T
66 T
* * *
460512 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATAAAATCAAATAAACTAA
1 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
460577 T
66 T
*
460578 CAAACATAATTTATTCAATTAAATCGAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
1 CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
460643 T
66 T
460644 CAAACATAATTTATTCAATTAA
1 CAAACATAATTTATTCAATTAA
460666 TCTAATATAT
Statistics
Matches: 466, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 466 1.00
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (66 bp):
CAAACATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCGAATAAACTAA
T
Found at i:460204 original size:28 final size:28
Alignment explanation
Indices: 460173--460247 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 28
460163 TTAAACCGAA
460173 TAAACTAATCAAACATAATTTATTCA-AT
1 TAAACTAAT-AAACATAATTTATTCACAT
460201 TAAA-TCAA-AAATCGATAATTTATTCACAT
1 TAAACT-AATAAA-C-ATAATTTATTCACAT
460230 TAAACCTAATAAAC-TAAT
1 TAAA-CTAATAAACATAAT
460248 CAAACATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
26 3 0.08
27 2 0.05
28 22 0.55
29 6 0.15
30 3 0.08
31 4 0.10
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.33
Consensus pattern (28 bp):
TAAACTAATAAACATAATTTATTCACAT
Found at i:460577 original size:28 final size:27
Alignment explanation
Indices: 460513--460577 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
460503 TAAACTAATC
*
460513 AAACATAATTTATTCAATTAAATCAAA
1 AAACATAATTTATTCAATAAAATCAAA
*
460540 AATCGATAATTTATTCACATAAAATCAAA
1 AAAC-ATAATTTATTCA-ATAAAATCAAA
460569 TAAAC-TAAT
1 -AAACATAAT
460578 CAAACATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.09
28 16 0.50
29 10 0.31
30 3 0.09
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (27 bp):
AAACATAATTTATTCAATAAAATCAAA
Found at i:460643 original size:28 final size:27
Alignment explanation
Indices: 460579--460643 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
460569 TAAACTAATC
*
460579 AAACATAATTTATTCAATTAAATCGAA
1 AAACATAATTTATTCAATTAAACCGAA
*
460606 AATCGATAATTTATTCACATTAAACCGAA
1 AAAC-ATAATTTATTCA-ATTAAACCGAA
460635 TAAAC-TAAT
1 -AAACATAAT
460644 CAAACATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.09
28 16 0.50
29 10 0.31
30 3 0.09
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (27 bp):
AAACATAATTTATTCAATTAAACCGAA
Found at i:463501 original size:36 final size:36
Alignment explanation
Indices: 463444--463513 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
463434 ACTAACTAAT
* *
463444 GTAAACCATAAACCCCTAACCCCTATCCCCTAAATC
1 GTAAAACATAAACCCCTAACCCCTAACCCCTAAATC
* *
463480 GTAAAACATAAA-CCGTAAACCCCTAACCCTTAAA
1 GTAAAACATAAACCCCT-AACCCCTAACCCCTAAA
463514 CCCCAACCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.10
36 26 0.90
ACGTcount: A:0.41, C:0.36, G:0.04, T:0.19
Consensus pattern (36 bp):
GTAAAACATAAACCCCTAACCCCTAACCCCTAAATC
Found at i:463522 original size:14 final size:15
Alignment explanation
Indices: 463495--463525 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
463485 ACATAAACCG
463495 TAAACCCCTAACCCT
1 TAAACCCCTAACCCT
463510 TAAACCCC-AACCCT
1 TAAACCCCTAACCCT
463524 TA
1 TA
463526 TAACTGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAACCCCTAACCCT
Found at i:463902 original size:14 final size:14
Alignment explanation
Indices: 463864--463902 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
463854 CCTTATCCTT
463864 TAAACCCTAAATCA
1 TAAACCCTAAATCA
* * *
463878 TAAAACATAAATTA
1 TAAACCCTAAATCA
463892 TAAACCCTAAA
1 TAAACCCTAAA
463903 CCCCTAACCC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:463911 original size:14 final size:14
Alignment explanation
Indices: 463894--463932 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
463884 ATAAATTATA
463894 AACCC-TAAACCCC
1 AACCCTTAAACCCC
463907 TAACCCTTAAACCCC
1 -AACCCTTAAACCCC
463922 AACCCTTAAAC
1 AACCCTTAAAC
463933 AATAAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (14 bp):
AACCCTTAAACCCC
Found at i:463960 original size:57 final size:57
Alignment explanation
Indices: 463750--463975 Score: 192
Period size: 57 Copynumber: 3.9 Consensus size: 57
463740 CTCAATCCCT
* * * * * *
463750 AACCCTTAAATCACAAACCATAAACCATAATCCCTAAACATCTTAACCCATACACCCC
1 AACCCTTAAATCATAAACAATAAACCATAATCCCTAAAC-CCCTAACCCTTAAACCCC
* * * * * * **
463808 AACACTTAAAACATAACCCATAAACCATAATCCTTAAACCCCTAACCCTT-ATCCTTTA
1 AACCCTTAAATCATAAACAATAAACCATAATCCCTAAACCCCTAACCCTTAAACC--CC
** *
463866 AACCC-TAAATCATAAA-ACATAAATTATAAACCCTAAACCCCTAACCCTTAAACCCC
1 AACCCTTAAATCATAAACA-ATAAACCATAATCCCTAAACCCCTAACCCTTAAACCCC
* *
463922 AACCCTTAAA-CAATAAACAATAAACCATAATCCTTAAACCCATAATCCC-TAAAC
1 AACCCTTAAATC-ATAAACAATAAACCATAATCCCTAAACCCCTAA-CCCTTAAAC
463976 TGCTAATACC
Statistics
Matches: 132, Mismatches: 28, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
56 8 0.06
57 79 0.60
58 45 0.34
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (57 bp):
AACCCTTAAATCATAAACAATAAACCATAATCCCTAAACCCCTAACCCTTAAACCCC
Found at i:463966 original size:15 final size:15
Alignment explanation
Indices: 463942--463975 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
463932 CAATAAACAA
*
463942 TAAA-CCATAATCCT
1 TAAACCCATAATCCC
463956 TAAACCCATAATCCC
1 TAAACCCATAATCCC
463971 TAAAC
1 TAAAC
463976 TGCTAATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAACCCATAATCCC
Found at i:464242 original size:40 final size:40
Alignment explanation
Indices: 464198--464312 Score: 115
Period size: 40 Copynumber: 2.9 Consensus size: 40
464188 CACTTTTGGG
*
464198 AAAGCGCCGCTAATGCTTGACCTATAGCGGCGTTT-TACAA
1 AAAGCGCCGCTAATGCTTGATCTATAGCGGCGTTTCT-CAA
* * ** * *
464238 AAAGCACCACTAATGCTCAATCTTTAGTGGCGTTTCTCAA
1 AAAGCGCCGCTAATGCTTGATCTATAGCGGCGTTTCTCAA
* * * *
464278 TAAGCGGCGCTAATGATTGATCTATTGCGGCGTTT
1 AAAGCGCCGCTAATGCTTGATCTATAGCGGCGTTT
464313 GTCAGTAAGC
Statistics
Matches: 57, Mismatches: 17, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
40 56 0.98
41 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (40 bp):
AAAGCGCCGCTAATGCTTGATCTATAGCGGCGTTTCTCAA
Found at i:464561 original size:196 final size:192
Alignment explanation
Indices: 464051--464646 Score: 533
Period size: 196 Copynumber: 3.1 Consensus size: 192
464041 CAAAAAACGT
*** * * **
464051 CGCTATTGCTCGATGATTAGCGGCGTTTCTAAATAAGCGCCGCTAATGCTCAATCTATTGCGGCG
1 CGCTATTGCTCGAACTTTAGCGGCGTTTCTCAATAAGCGCCGCTAATGATTGATCTATTGCGGCG
* * * ** *
464116 TTTATTGAAAAGCG-CGCTAATGTCGCTAGAGCTCAACAAAAAATGACACCATTTTGCTTAACTT
66 TTTGTT-AAAACCGCCGCTAATGTC-CTAAAGCTCAAC-AAAAATGACGTCGTTTTGCTTAACTT
* **
464180 TTTTGCGGCACTTTTGGGAAAGCGCCGCTAATGCTTGACCTATAGCGGCGTTTTACAAAAAGCAC
128 TTTTGCAGCACTTTTAAGAAAGCGCCGCTAATGCTTGACCTATAGCGGCGTTTTACAAAAAGCAC
* * * *
464245 CACTAATGCTC-AATCTTTAGTGGCGTTTCTCAATAAGCGGCGCTAATGATTGATCTATTGCGGC
1 CGCTATTGCTCGAA-CTTTAGCGGCGTTTCTCAATAAGCGCCGCTAATGATTGATCTATTGCGGC
* * * * * * ** * *
464309 GTTTGTCAGTAAGCC-CTGCTAAT-TCCAGGAAAGCACAAAAAGGAAACAAGGTCGTTTTGCTAA
65 GTTTGTTA--AAACCGCCGCTAATGTCC--TAAAGCTCAACAA--AAATGACGTCGTTTTGCTTA
* * * * * *
464372 ACTTTTTTGCAGC-GTTTTCCAAGAAA-CGCCGCTAATGCTTGACCTTTAGTGGCTTTTTATAGA
124 ACTTTTTTGCAGCACTTTT--AAGAAAGCGCCGCTAATGCTTGACCTATAGCGGCGTTTTACAAA
*
464435 AATCAC
187 AAGCAC
* * *
464441 CGCTATTGCTCGAACTTTAGCGGCGTTTCTCAACAGGCGCCGCTAATGATTGATCTATTGCGGTG
1 CGCTATTGCTCGAACTTTAGCGGCGTTTCTCAATAAGCGCCGCTAATGATTGATCTATTGCGGCG
464506 TTTGTTAAAACTCGCCGCTAATGTCCTTAAAGCTCAACAACAATATGACGTCGTTTTGCTTAACT
66 TTTGTTAAAAC-CGCCGCTAATGTCC-TAAAGCTCAACAA-AA-ATGACGTCGTTTTGCTTAACT
* * * * * * * * *
464571 TTTTTG-TGGAGCTTTCACA-AAAGCACCGCTAATGCTCGATCTATTGCGGTGTTTTAGAAAAAG
127 TTTTTGCAGCA-CTTTTA-AGAAAGCGCCGCTAATGCTTGACCTATAGCGGCGTTTTACAAAAAG
464634 CAC
190 CAC
464637 CGCTATTGCT
1 CGCTATTGCT
464647 TACCTATTGC
Statistics
Matches: 312, Mismatches: 71, Indels: 36
0.74 0.17 0.09
Matches are distributed among these distances:
193 3 0.01
194 63 0.20
195 28 0.09
196 206 0.66
197 12 0.04
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (192 bp):
CGCTATTGCTCGAACTTTAGCGGCGTTTCTCAATAAGCGCCGCTAATGATTGATCTATTGCGGCG
TTTGTTAAAACCGCCGCTAATGTCCTAAAGCTCAACAAAAATGACGTCGTTTTGCTTAACTTTTT
TGCAGCACTTTTAAGAAAGCGCCGCTAATGCTTGACCTATAGCGGCGTTTTACAAAAAGCAC
Found at i:473038 original size:19 final size:19
Alignment explanation
Indices: 472994--473044 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
472984 TATTCAGAAC
*
472994 CAATTTCACCATTTCATATT
1 CAATTTCA-CATCTCATATT
*
473014 CAATTTCACATCTCATTTT
1 CAATTTCACATCTCATATT
* *
473033 CCATTTCTCATC
1 CAATTTCACATC
473045 CTTATCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.45
Consensus pattern (19 bp):
CAATTTCACATCTCATATT
Found at i:493027 original size:20 final size:20
Alignment explanation
Indices: 492985--493051 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
492975 TATATTCTTT
*
492985 ATTTTTTTAATAT-TTTTATA
1 ATTTTTTTAAAATATTTTA-A
*
493005 ATTTTTTTAAAATATTTTGA
1 ATTTTTTTAAAATATTTTAA
*
493025 A--TTTTAAAAATTATTTTAA
1 ATTTTTTTAAAA-TATTTTAA
493044 ATTTTTTT
1 ATTTTTTT
493052 GTAATTTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 8 0.21
19 8 0.21
20 14 0.37
21 8 0.21
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (20 bp):
ATTTTTTTAAAATATTTTAA
Found at i:493029 original size:18 final size:19
Alignment explanation
Indices: 493008--493049 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
492998 TTTTATAATT
*
493008 TTTTTAAAA-TATTTTGAA
1 TTTTTAAAATTATTTTAAA
*
493026 TTTTAAAAATTATTTTAAA
1 TTTTTAAAATTATTTTAAA
493045 TTTTT
1 TTTTT
493050 TTGTAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTAAAATTATTTTAAA
Found at i:495050 original size:106 final size:107
Alignment explanation
Indices: 494859--495072 Score: 412
Period size: 106 Copynumber: 2.0 Consensus size: 107
494849 TAATGTTATA
494859 AGAATAGTATGAATGCTGACAATTGATTATGATTGATGTTTAACTTTTTATTACCATACATTAAT
1 AGAATAGTATGAATGCTGACAATTGATTATGATTGATGTTTAACTTTTTATTACCATACATTAAT
*
494924 AAAATATGTGATAATTTTTTAAAATTACTTATAAAATAAAAT
66 AAAATATGTGATAATTTTTTAAAATTAATTATAAAATAAAAT
494966 AGAATAGTAT-AATGCTGACAATTGATTATGATTGATGTTTAACTTTTTATTACCATACATTAAT
1 AGAATAGTATGAATGCTGACAATTGATTATGATTGATGTTTAACTTTTTATTACCATACATTAAT
495030 AAAATATGTGATAATTTTTTAAAATTAATTATAAAATAAAAT
66 AAAATATGTGATAATTTTTTAAAATTAATTATAAAATAAAAT
495072 A
1 A
495073 TATATATATT
Statistics
Matches: 106, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
106 96 0.91
107 10 0.09
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (107 bp):
AGAATAGTATGAATGCTGACAATTGATTATGATTGATGTTTAACTTTTTATTACCATACATTAAT
AAAATATGTGATAATTTTTTAAAATTAATTATAAAATAAAAT
Found at i:519425 original size:18 final size:17
Alignment explanation
Indices: 519398--519444 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
519388 GCCACCGCTG
*
519398 CCTTTTTTTTCTTCTCCT
1 CCTTTATTTTCTTCT-CT
*
519416 CCTTTATTTTGTTCTCT
1 CCTTTATTTTCTTCTCT
*
519433 TC-TTATTTTCTT
1 CCTTTATTTTCTT
519445 TTTCACTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 9 0.36
17 3 0.12
18 13 0.52
ACGTcount: A:0.04, C:0.26, G:0.02, T:0.68
Consensus pattern (17 bp):
CCTTTATTTTCTTCTCT
Found at i:533462 original size:30 final size:29
Alignment explanation
Indices: 533428--533489 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
533418 ACTTAACAAG
533428 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAA-AAAATTAA
*
533458 CAAATGCCTTTAAAATAATAAAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAATTAA
533487 CAA
1 CAA
533490 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (29 bp):
CAAATGCCTCTAAAATAATAAAAAATTAA
Found at i:540361 original size:28 final size:28
Alignment explanation
Indices: 540296--540363 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
540286 TTATGAAATC
* *
540296 GAAGCCTTTGTGCCAATCTATGAAAAGA
1 GAAGCCTTTGTGGCAATCTAAGAAAAGA
* *
540324 G-AGCCTTTGTGGCAATCTAAGGAAAGG
1 GAAGCCTTTGTGGCAATCTAAGAAAAGA
*
540351 GAAGCCCTTGTGG
1 GAAGCCTTTGTGG
540364 AAAAGGATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (28 bp):
GAAGCCTTTGTGGCAATCTAAGAAAAGA
Found at i:544342 original size:15 final size:13
Alignment explanation
Indices: 544310--544352 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
544300 TGTCGTCATC
*
544310 CTTTTTCTTCTCCT
1 CTTTTT-TTCTTCT
544324 CTTTTATTTCATTCT
1 CTTTT-TTTC-TTCT
544339 CTTTTTTTCTTCT
1 CTTTTTTTCTTCT
544352 C
1 C
544353 ACTTCACCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 9 0.35
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (13 bp):
CTTTTTTTCTTCT
Found at i:545261 original size:39 final size:39
Alignment explanation
Indices: 545218--545292 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
545208 TATTAAATAG
* * *
545218 CATGCCACTGATTGTATCCTATATTGATTGCATGTATAA
1 CATGCCACTGACTGAAACCTATATTGATTGCATGTATAA
* *
545257 CATGCCATTGACTGAAACGTATATTGATTGCATGTA
1 CATGCCACTGACTGAAACCTATATTGATTGCATGTA
545293 CGCATACAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (39 bp):
CATGCCACTGACTGAAACCTATATTGATTGCATGTATAA
Found at i:545555 original size:24 final size:24
Alignment explanation
Indices: 545528--545599 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
545518 TATTTGCATA
545528 TCTGGTGGCTTGTCCACATATATT
1 TCTGGTGGCTTGTCCACATATATT
** *
545552 TCTGGCAGCTTGAATGCA-AT-TA--
1 TCTGGTGGCTTG--TCCACATATATT
545574 T-TGGTGGCTTGTCCACATATATT
1 TCTGGTGGCTTGTCCACATATATT
545597 TCT
1 TCT
545600 AACAGCTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 10 0.29
22 1 0.03
23 1 0.03
24 13 0.37
25 2 0.06
26 3 0.09
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (24 bp):
TCTGGTGGCTTGTCCACATATATT
Found at i:545590 original size:45 final size:45
Alignment explanation
Indices: 545475--545640 Score: 157
Period size: 45 Copynumber: 3.7 Consensus size: 45
545465 TCTGGCAGTA
* *
545475 TAACTACAATTACTGGTGGCTTGTCCACATAT-TTT-TGACA--T
1 TAACTGCAATTACTGGTGGCTTGTCCACATATATTTCTAACAGCT
* **
545516 TATATTTGC-A-TATCTGGTGGCTTGTCCACATATATTTCTGGCAGCT
1 TA-A-CTGCAATTA-CTGGTGGCTTGTCCACATATATTTCTAACAGCT
*
545562 TGAA-TGCAATTATTGGTGGCTTGTCCACATATATTTCTAACAGCT
1 T-AACTGCAATTACTGGTGGCTTGTCCACATATATTTCTAACAGCT
* * *
545607 TAACTTCAATTACTAGTGACTTGTCCACAATATA
1 TAACTGCAATTACTGGTGGCTTGTCCAC-ATATA
545641 GTGTGTTTTT
Statistics
Matches: 103, Mismatches: 10, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
41 4 0.04
42 22 0.21
43 5 0.05
44 9 0.09
45 52 0.50
46 10 0.10
47 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (45 bp):
TAACTGCAATTACTGGTGGCTTGTCCACATATATTTCTAACAGCT
Found at i:546931 original size:2 final size:2
Alignment explanation
Indices: 546924--546990 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
546914 TTGCTTAATG
546924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
546966 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
546991 GGTTGAAAAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:548859 original size:21 final size:21
Alignment explanation
Indices: 548835--548893 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
548825 CTACTAGTAG
*
548835 AACTGGGAGTTCTATCGATAC
1 AACTAGGAGTTCTATCGATAC
* *
548856 AACTCTGG-GTTCTACCGATAC
1 AACT-AGGAGTTCTATCGATAC
* *
548877 AACCAGGACTTCTATCG
1 AACTAGGAGTTCTATCG
548894 GTATAACGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (21 bp):
AACTAGGAGTTCTATCGATAC
Found at i:550303 original size:12 final size:12
Alignment explanation
Indices: 550286--550313 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
550276 CTTTTGATTT
550286 CTTTAATTTTAA
1 CTTTAATTTTAA
550298 CTTTAATTTTAA
1 CTTTAATTTTAA
550310 CTTT
1 CTTT
550314 TTAGTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (12 bp):
CTTTAATTTTAA
Found at i:560639 original size:2 final size:2
Alignment explanation
Indices: 560634--560659 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
560624 AAACCAGCTG
560634 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
560660 CTTTTACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:563575 original size:1 final size:1
Alignment explanation
Indices: 563569--563601 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
563559 CAAATTAAGG
563569 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
563602 AACAACTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:563857 original size:150 final size:150
Alignment explanation
Indices: 563602--563888 Score: 574
Period size: 150 Copynumber: 1.9 Consensus size: 150
563592 TTTTTTTTTT
563602 AACAACTTAGAATGATTGATACTATAATAAAGGGGTGTACTTCATAAAGGCAGGTGCTTTAAATT
1 AACAACTTAGAATGATTGATACTATAATAAAGGGGTGTACTTCATAAAGGCAGGTGCTTTAAATT
563667 AACATCGGAGTGAATTTGGGGTATCTTTTTTACATGGTGTAATAACTAGTTGAGGTGTTTGGCAT
66 AACATCGGAGTGAATTTGGGGTATCTTTTTTACATGGTGTAATAACTAGTTGAGGTGTTTGGCAT
563732 CCTATTTTTTTCCTTTCTGA
131 CCTATTTTTTTCCTTTCTGA
563752 AACAACTTAGAATGATTGATACTATAATAAAGGGGTGTACTTCATAAAGGCAGGTGCTTTAAATT
1 AACAACTTAGAATGATTGATACTATAATAAAGGGGTGTACTTCATAAAGGCAGGTGCTTTAAATT
563817 AACATCGGAGTGAATTTGGGGTATCTTTTTTACATGGTGTAATAACTAGTTGAGGTGTTTGGCAT
66 AACATCGGAGTGAATTTGGGGTATCTTTTTTACATGGTGTAATAACTAGTTGAGGTGTTTGGCAT
563882 CCTATTT
131 CCTATTT
563889 AAGTGTCTTA
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 137 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (150 bp):
AACAACTTAGAATGATTGATACTATAATAAAGGGGTGTACTTCATAAAGGCAGGTGCTTTAAATT
AACATCGGAGTGAATTTGGGGTATCTTTTTTACATGGTGTAATAACTAGTTGAGGTGTTTGGCAT
CCTATTTTTTTCCTTTCTGA
Found at i:567138 original size:141 final size:141
Alignment explanation
Indices: 566838--567223 Score: 516
Period size: 141 Copynumber: 2.8 Consensus size: 141
566828 GATTCCATTG
* *
566838 GCATTAGTTGTGGCATGTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGTGGTTCT-TTTGC
1 GCATTAGTTGTGGCATTTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGCGGTTCTGTTT-C
* * *
566902 AAAAGACATCTGTGGTTCGAGCTCTTTGGTTCGTAGATC------TTCAGGTTGCTTAACTTCAA
65 AAAAGATATCTGTGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGTTCAGGTTGCTTAACTTCAA
566961 TGTGGACATTCT
130 TGTGGACATTCT
* * * * *
566973 GCATTAGTTGTGGCATTTCAGAACTTCCTATTTCCATTTTTGATTTCTCATGCGGTTCTGTTTCA
1 GCATTAGTTGTGGCATTTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGCGGTTCTGTTTCA
* * *
567038 AAAGATGTCTGCGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGTTGAGGTTGCTTAACTTCAAT
66 AAAGATATCTGTGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGTTCAGGTTGCTTAACTTCAAT
567103 GTGGACATTCT
131 GTGGACATTCT
* * ** * * * *
567114 GCGTTAGTTGTGGCATTTGAGAACTTTCTGTCGCCATTTCAGATTTCTTATGCTGCTCTGCTGCA
1 GCATTAGTTGTGGCATTTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGCGGTTCTGTTTCA
*
567179 AAAGATATCTGTGGTTTGAGCTCTTTAGTTCGTAGTTCTTGAGGT
66 AAAGATATCTGTGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGT
567224 CTCTTAACTT
Statistics
Matches: 215, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
135 87 0.40
136 3 0.01
141 125 0.58
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (141 bp):
GCATTAGTTGTGGCATTTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGCGGTTCTGTTTCA
AAAGATATCTGTGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGTTCAGGTTGCTTAACTTCAAT
GTGGACATTCT
Found at i:570903 original size:14 final size:16
Alignment explanation
Indices: 570874--570905 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
570864 ACATACATTT
570874 TAATATACTAAATTAC
1 TAATATACTAAATTAC
570890 TAAT-TACT-AATTAC
1 TAATATACTAAATTAC
570904 TA
1 TA
570906 TTGATGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATATACTAAATTAC
Found at i:571564 original size:14 final size:15
Alignment explanation
Indices: 571532--571571 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
571522 ACCTTTTCTA
571532 TTCATTAGCATTACAT
1 TTCATTA-CATTACAT
571548 TTCATTACATT-CAT
1 TTCATTACATTACAT
571562 TTCATTACAT
1 TTCATTACAT
571572 GAAAAGTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 13 0.54
15 4 0.17
16 7 0.29
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (15 bp):
TTCATTACATTACAT
Found at i:580467 original size:21 final size:21
Alignment explanation
Indices: 580443--580484 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
580433 TACACGTGTC
*
580443 AAATCAGAAGAAATAATACAA
1 AAATCAGAAAAAATAATACAA
580464 AAATCAGAAAAAATAATACAA
1 AAATCAGAAAAAATAATACAA
580485 CGATTCTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.69, C:0.10, G:0.07, T:0.14
Consensus pattern (21 bp):
AAATCAGAAAAAATAATACAA
Found at i:581193 original size:16 final size:16
Alignment explanation
Indices: 581174--581206 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
581164 AAAATTATAT
581174 TAATTATTAATGTCAA
1 TAATTATTAATGTCAA
581190 TAATTATTAATGTCAA
1 TAATTATTAATGTCAA
581206 T
1 T
581207 TATGGTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATTATTAATGTCAA
Found at i:588524 original size:20 final size:20
Alignment explanation
Indices: 588499--588576 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
588489 CAGCTGCACG
588499 AAGGAGAAGAAAGAAAAGGA
1 AAGGAGAAGAAAGAAAAGGA
* *
588519 AAGGAGAA-AAGGAAAAAGA
1 AAGGAGAAGAAAGAAAAGGA
*
588538 AGAAGAGAAGAAGAAGAAGAAGGA
1 A-AGGAGAAG-A-AAGAA-AAGGA
*
588562 GAAGGAGGAGAAAGA
1 -AAGGAGAAGAAAGA
588577 GAGGGCAGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
19 10 0.22
20 14 0.31
22 5 0.11
23 5 0.11
24 10 0.22
25 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
AAGGAGAAGAAAGAAAAGGA
Found at i:588570 original size:9 final size:9
Alignment explanation
Indices: 588498--588573 Score: 55
Period size: 9 Copynumber: 8.0 Consensus size: 9
588488 TCAGCTGCAC
588498 GAAGGAGAA
1 GAAGGAGAA
* *
588507 GAAAGAAAA
1 GAAGGAGAA
588516 GGAAAGGAGAA
1 -G-AAGGAGAA
*
588527 -AAGGAAAAA
1 GAAGG-AGAA
588536 GAAGAAGAGAA
1 GAAG--GAGAA
*
588547 GAAGAAGAA
1 GAAGGAGAA
588556 GAAGGAGAA
1 GAAGGAGAA
*
588565 GGAGGAGAA
1 GAAGGAGAA
588574 AGAGAGGGCA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
8 4 0.08
9 30 0.58
10 4 0.08
11 13 0.25
12 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (9 bp):
GAAGGAGAA
Found at i:588999 original size:37 final size:38
Alignment explanation
Indices: 588952--589038 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 38
588942 TAGTTTTTAT
*
588952 ACTA-TATTATTGTTAG-T-TATTATTTCTAGTAAAAC
1 ACTATTATTATTGTTAGTTATATTATTTCTAGTAAAAA
* *
588987 CCTAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAA
1 ACT-ATTATTATTGTTAGTTA-TATTATTTCTAGTAAAAA
589027 ACTATTATTATT
1 ACTATTATTATT
589039 ATTATTGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
35 2 0.05
36 1 0.02
37 12 0.28
38 1 0.02
39 9 0.21
40 18 0.42
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (38 bp):
ACTATTATTATTGTTAGTTATATTATTTCTAGTAAAAA
Found at i:589036 original size:76 final size:78
Alignment explanation
Indices: 588831--589038 Score: 228
Period size: 76 Copynumber: 2.6 Consensus size: 78
588821 GTTTAGTTAT
* *
588831 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-TGGTTAGTTAT
588896 TAGGATTAGTAAAAACCC
61 TAGGATTAGTAAAAACCC
* *** * *
588914 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTATACTA-TATTATT-GTTAGTTATTA-T
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGGTTAGTTATTAGG
*
588975 TTCTAGT-AAAACCC
65 AT-TAGTAAAAACCC
*
588989 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATT
589039 ATTATTGTGT
Statistics
Matches: 106, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
75 25 0.24
76 40 0.38
77 1 0.01
78 1 0.01
79 5 0.05
80 2 0.02
82 18 0.17
83 14 0.13
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.50
Consensus pattern (78 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGGTTAGTTATTAGGA
TTAGTAAAAACCC
Found at i:593379 original size:114 final size:114
Alignment explanation
Indices: 593170--593399 Score: 397
Period size: 114 Copynumber: 2.0 Consensus size: 114
593160 CAGCTAATAG
593170 AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACCGAGCATCAGTACTCCCCCTATAATAT
1 AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACCGAGCATCAGTACTCCCCCTATAATAT
* *
593235 GCATGATGTACGCTCGAGCAACGCACATCAACTCTCCTTCAGTGGCATT
66 GCATGATATACGCTCGAGCAACGCACATCAACTCTCATTCAGTGGCATT
*
593284 AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACCGGGCATCAGTACTCCCCCTATAATAT
1 AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACCGAGCATCAGTACTCCCCCTATAATAT
* * * *
593349 GCATGATATATGCTCGAGCAGCGCATATCAACTCTCATTCAGTTGCATT
66 GCATGATATACGCTCGAGCAACGCACATCAACTCTCATTCAGTGGCATT
593398 AG
1 AG
593400 CTGATAAGTG
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (114 bp):
AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACCGAGCATCAGTACTCCCCCTATAATAT
GCATGATATACGCTCGAGCAACGCACATCAACTCTCATTCAGTGGCATT
Found at i:594025 original size:17 final size:17
Alignment explanation
Indices: 594005--594043 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
593995 ATTTCAATGT
* *
594005 ATTTTTCTTATTTTCGG
1 ATTTTTCTTAATTTCGA
594022 ATTTTTCTTAATTTCGA
1 ATTTTTCTTAATTTCGA
594039 ATTTT
1 ATTTT
594044 ATTACTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.64
Consensus pattern (17 bp):
ATTTTTCTTAATTTCGA
Found at i:594082 original size:16 final size:15
Alignment explanation
Indices: 594061--594090 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
594051 TCAAAAAATA
594061 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
594077 TATTATTTTATATT
1 TATTATTTTATATT
594091 ATTTTAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:594241 original size:16 final size:15
Alignment explanation
Indices: 594220--594249 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
594210 TCAAAAAATA
594220 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
594236 TATTATTTTATATT
1 TATTATTTTATATT
594250 ATTTTAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:594311 original size:159 final size:159
Alignment explanation
Indices: 594017--594397 Score: 685
Period size: 159 Copynumber: 2.4 Consensus size: 159
594007 TTTTCTTATT
* *
594017 TTCGGATTTTTCTTAATTTCGAATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTA
1 TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTA
594082 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATT
66 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATT
594147 TAGTAAATAACCCTTATTTTGGCCCTTTG
131 TAGTAAATAACCCTTATTTTGGCCCTTTG
594176 TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTA
1 TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTA
594241 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATT
66 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATT
594306 TAGTAAATAACCCTTATTTTGGCCCTTTG
131 TAGTAAATAACCCTTATTTTGGCCCTTTG
** * *
594335 TTCGTATTTTTCTTATTTTC-AGATTTTATTACTTTCAGTAAATATACTATTTTCGT-TTTTATT
1 TTCGTATTTTTCTTATTTTCGA-ATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATT
594398 TCTTTTCGTA
Statistics
Matches: 215, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
158 8 0.04
159 207 0.96
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.55
Consensus pattern (159 bp):
TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTA
TTTTATATTATTTTAGTACATAATATTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATT
TAGTAAATAACCCTTATTTTGGCCCTTTG
Found at i:594405 original size:16 final size:17
Alignment explanation
Indices: 594384--594415 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
594374 AAATATACTA
594384 TTTTCGT-TTTTATTTC
1 TTTTCGTATTTTATTTC
594400 TTTTCGTATTTTATTT
1 TTTTCGTATTTTATTT
594416 TTTCATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTCGTATTTTATTTC
Found at i:594574 original size:19 final size:20
Alignment explanation
Indices: 594550--594588 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
594540 TTTTTTACAC
594550 AAATAATA-CAAAAAAATTA
1 AAATAATACCAAAAAAATTA
594569 AAATAATACCAAAAAAATTA
1 AAATAATACCAAAAAAATTA
594589 CCTTTCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAATACCAAAAAAATTA
Found at i:594645 original size:6 final size:6
Alignment explanation
Indices: 594628--594719 Score: 51
Period size: 6 Copynumber: 14.5 Consensus size: 6
594618 TTTCCTCCCT
* * * * *
594628 CTTCTT CTTCTC CTTCTC TTTCTC TTTTTC CTGTGCCTC CTTCTC CTTCTT
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CT-T--CTC CTTCTC CTTCTC
* * *
594679 CTTCTT CTTCTT CTTCTT CTTCCTC TTCTTCTC CTT-TC CTT
1 CTTCTC CTTCTC CTTCTC CTT-CTC --CTTCTC CTTCTC CTT
594720 TTCTTTCTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
5 5 0.07
6 54 0.74
7 3 0.04
8 4 0.05
9 7 0.10
ACGTcount: A:0.00, C:0.39, G:0.02, T:0.59
Consensus pattern (6 bp):
CTTCTC
Found at i:594679 original size:9 final size:9
Alignment explanation
Indices: 594667--594714 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
594657 CCTGTGCCTC
594667 CTTCTCCTT
1 CTTCTCCTT
*
594676 CTTCTTCTT
1 CTTCTCCTT
*
594685 CTTCTTCTT
1 CTTCTCCTT
594694 CTTCTTCCTCTT
1 CTTC-T-C-CTT
594706 CTTCTCCTT
1 CTTCTCCTT
594715 TCCTTTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 24 0.71
10 2 0.06
11 1 0.03
12 7 0.21
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (9 bp):
CTTCTCCTT
Found at i:594731 original size:10 final size:10
Alignment explanation
Indices: 594712--594788 Score: 82
Period size: 10 Copynumber: 7.7 Consensus size: 10
594702 TCTTCTTCTC
*
594712 CTTTCCTTTT
1 CTTTCTTTTT
594722 CTTTCTTTTT
1 CTTTCTTTTT
* *
594732 CTTTCTTCTC
1 CTTTCTTTTT
*
594742 CTTTCCTTTT
1 CTTTCTTTTT
594752 CTTTCTTTTT
1 CTTTCTTTTT
* *
594762 CTTTCTTCTC
1 CTTTCTTTTT
*
594772 CTTTCCTTTT
1 CTTTCTTTTT
*
594782 CTATCTT
1 CTTTCTT
594789 CTCCTTCATC
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 53 1.00
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:594738 original size:30 final size:30
Alignment explanation
Indices: 594704--594788 Score: 161
Period size: 30 Copynumber: 2.8 Consensus size: 30
594694 CTTCTTCCTC
594704 TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
1 TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
594734 TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
1 TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
*
594764 TTCTTCTCCTTTCCTTTTCTATCTT
1 TTCTTCTCCTTTCCTTTTCTTTCTT
594789 CTCCTTCATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (30 bp):
TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
Found at i:594789 original size:20 final size:20
Alignment explanation
Indices: 594664--594794 Score: 97
Period size: 20 Copynumber: 6.3 Consensus size: 20
594654 TTTCCTGTGC
594664 CTCCTTCTCCTTCTTC-TTCTT
1 CTCCTT-TCCTT-TTCTTTCTT
* *
594685 CTTCTTCTTCTTCTTCCTCTTCTT
1 CTCCTT-TCCTT-TT-CT-TTCTT
594709 CTCCTTTCCTTTTCTTTCTT
1 CTCCTTTCCTTTTCTTTCTT
* * *
594729 TTTCTTT-CTTCTCCTTTCCTT
1 CTCCTTTCCTT-TTCTTT-CTT
* *
594750 -TTCTTTCTTTTTCTTTCTT
1 CTCCTTTCCTTTTCTTTCTT
*
594769 CTCCTTTCCTTTTCTATCTT
1 CTCCTTTCCTTTTCTTTCTT
594789 CTCCTT
1 CTCCTT
594795 CATCTATTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.07
20 48 0.53
21 20 0.22
22 3 0.03
23 4 0.04
24 10 0.11
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (20 bp):
CTCCTTTCCTTTTCTTTCTT
Found at i:594937 original size:12 final size:12
Alignment explanation
Indices: 594920--594950 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
594910 GAATGTACAG
594920 AACATAAATAAT
1 AACATAAATAAT
594932 AACATAAATAAT
1 AACATAAATAAT
*
594944 AAAATAA
1 AACATAA
594951 TAAGACATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (12 bp):
AACATAAATAAT
Found at i:595276 original size:14 final size:14
Alignment explanation
Indices: 595193--595277 Score: 61
Period size: 13 Copynumber: 6.3 Consensus size: 14
595183 CCCTCCCTCT
*
595193 TCTTCTTCTCCTTC
1 TCTTCTTCTTCTTC
* *
595207 TCTTTTTCTTTTTC
1 TCTTCTTCTTCTTC
*
595221 -CTTTTTCTTCTT-
1 TCTTCTTCTTCTTC
* * *
595233 TCTGCTCCTCCTTCC
1 TCTTCTTCTTCTT-C
*
595248 CCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
595262 TCTTCTT-TTCTT-
1 TCTTCTTCTTCTTC
595274 TCTT
1 TCTT
595278 GCAGCTTCAT
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
12 4 0.07
13 24 0.44
14 18 0.33
15 9 0.16
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.64
Consensus pattern (14 bp):
TCTTCTTCTTCTTC
Found at i:596371 original size:21 final size:22
Alignment explanation
Indices: 596341--596381 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
596331 ATATCTAAAT
596341 TACCACACACACATA-TATATA
1 TACCACACACACATACTATATA
*
596362 TACCATACACACATACTATA
1 TACCACACACACATACTATA
596382 AAACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (22 bp):
TACCACACACACATACTATATA
Found at i:596481 original size:28 final size:28
Alignment explanation
Indices: 596441--596495 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
596431 ATAAGTATCA
*
596441 TTTCTATTTCATCGTTTATCAATTATAC
1 TTTCTATTTCATCGCTTATCAATTATAC
*
596469 TTTCTATTTCATCGCTTATTAATTATA
1 TTTCTATTTCATCGCTTATCAATTATA
596496 ATCGAACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (28 bp):
TTTCTATTTCATCGCTTATCAATTATAC
Found at i:600107 original size:21 final size:19
Alignment explanation
Indices: 600063--600137 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
600053 AATCATATAT
*
600063 TCTAAGATTGCATATTATA
1 TCTAAGATTGCATATCATA
600082 TCTAAGATTGCACATATCATA
1 TCTAAGATTG--CATATCATA
*
600103 ACTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
600122 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
600138 CTCAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 34 0.67
21 17 0.33
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:611148 original size:2 final size:2
Alignment explanation
Indices: 611141--611178 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
611131 CCACATCTAA
*
611141 AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
611179 TGAAATCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:614257 original size:19 final size:19
Alignment explanation
Indices: 614224--614271 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
614214 CCAAATCAAG
* * *
614224 CTTAAGTACGCTTAAGTAA
1 CTTAAGTAAGGTTAACTAA
* *
614243 GTTAATTAAGGTTAACTAA
1 CTTAAGTAAGGTTAACTAA
614262 CTTAAGTAAG
1 CTTAAGTAAG
614272 CTAATTATAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (19 bp):
CTTAAGTAAGGTTAACTAA
Found at i:615615 original size:2 final size:2
Alignment explanation
Indices: 615570--615597 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
615560 ATTCATCAAC
615570 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
615598 GGCACGGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:615728 original size:2 final size:2
Alignment explanation
Indices: 615721--615747 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
615711 TGGCAATTGT
615721 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
615748 TTGGCACGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:618193 original size:11 final size:11
Alignment explanation
Indices: 618158--618240 Score: 61
Period size: 11 Copynumber: 7.9 Consensus size: 11
618148 ACCAAAAATT
618158 TATTTT-AAAA
1 TATTTTAAAAA
*
618168 -ATTTAAAAAA
1 TATTTTAAAAA
618178 GTATTTTAAAAA
1 -TATTTTAAAAA
618190 TATTTT--AAA
1 TATTTTAAAAA
**
618199 -ATTAAAAAAA
1 TATTTTAAAAA
* *
618209 TA-ATAAAAAA
1 TATTTTAAAAA
618219 GTATTTTAAAAA
1 -TATTTTAAAAA
618231 TATTTTAAAA
1 TATTTTAAAA
618241 TTAAAAAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 3 0.05
9 7 0.12
10 13 0.23
11 19 0.33
12 15 0.26
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:618206 original size:30 final size:31
Alignment explanation
Indices: 618158--618229 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
618148 ACCAAAAATT
* * *
618158 TATTTTAAAAATTTAAAAAAGTATTTTAAAAA-
1 TATTTT-AAAATTTAAAAAAATA-ATAAAAAAG
618190 TATTTTAAAA-TTAAAAAAATAATAAAAAAG
1 TATTTTAAAATTTAAAAAAATAATAAAAAAG
618220 TATTTTAAAA
1 TATTTTAAAA
618230 ATATTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 6 0.17
30 20 0.56
31 4 0.11
32 6 0.17
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (31 bp):
TATTTTAAAATTTAAAAAAATAATAAAAAAG
Found at i:618223 original size:41 final size:42
Alignment explanation
Indices: 618171--618260 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 42
618161 TTTAAAAATT
618171 TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAT-AA
1 TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAA
618212 TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAA
1 TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAA
618254 TAAAAAA
1 TAAAAAA
618261 TAAAAGAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 39 0.81
42 9 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (42 bp):
TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAA
Found at i:618275 original size:51 final size:53
Alignment explanation
Indices: 618203--618314 Score: 167
Period size: 51 Copynumber: 2.2 Consensus size: 53
618193 TTTAAAATTA
*
618203 AAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA-ATAAAT
1 AAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAAAAT
*
618255 AAAAAATAA-AAGAAAA-TATTTTAAAAGTATTTTAAAATTAAAAAATAAAAAT
1 AAAAAATAATAA-AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAAAAT
*
618307 AAAGAATA
1 AAAAAATA
618315 TATATTTAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
51 30 0.55
52 25 0.45
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (53 bp):
AAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAAAAT
Found at i:619685 original size:15 final size:15
Alignment explanation
Indices: 619653--619681 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
619643 ATTTTGTGTG
619653 TTTAATATGTGTGAA
1 TTTAATATGTGTGAA
619668 TTTAAT-TGTGTGAA
1 TTTAATATGTGTGAA
619682 ATTTTCGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
TTTAATATGTGTGAA
Found at i:627334 original size:16 final size:17
Alignment explanation
Indices: 627313--627347 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
627303 CTCATTCTAT
*
627313 AAAGGCC-ACAAAATCA
1 AAAGGCCAACAAAACCA
627329 AAAGGCCAACAAAACCA
1 AAAGGCCAACAAAACCA
627346 AA
1 AA
627348 TCTTCCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.60, C:0.26, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAGGCCAACAAAACCA
Found at i:635481 original size:69 final size:68
Alignment explanation
Indices: 635360--635512 Score: 173
Period size: 69 Copynumber: 2.2 Consensus size: 68
635350 ATAGCATTTT
* * *
635360 TTGTCATATTAAGGCTCACAGACGAAGAACTGCAACCTCCAACACAGATAGTGAGAGCAAA-ACT
1 TTGTTATATTAAGGCTCACAGACGAAGAACCGCAACCTCCAACACAGATAGTGAGAGCAAAGCCT
635424 CCTAG
66 -C-AG
** * * * ** *
635429 TTGTTATATTAAGGCTCGTAGGCGAAGAGCCGCACCCTCCAACGTAGTTAGTGAGAGCAAAGCCT
1 TTGTTATATTAAGGCTCACAGACGAAGAACCGCAACCTCCAACACAGATAGTGAGAGCAAAGCCT
635494 CAG
66 CAG
*
635497 CTGTTATATTAAGGCT
1 TTGTTATATTAAGGCT
635513 TACAAGCGAA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
68 17 0.24
69 52 0.73
70 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (68 bp):
TTGTTATATTAAGGCTCACAGACGAAGAACCGCAACCTCCAACACAGATAGTGAGAGCAAAGCCT
CAG
Found at i:635603 original size:69 final size:69
Alignment explanation
Indices: 635450--635840 Score: 259
Period size: 69 Copynumber: 5.7 Consensus size: 69
635440 AGGCTCGTAG
* * * * * * * * * *
635450 GCGAAGAGCCGCACCCTCCAACGTAGTTAGTGAGAGCAAAGC-CTCAGCTGTTATATTAAGGCTT
1 GCGAAGAGCCACAGCCTCCAACATAATTAGCGAGAGAAAAGCTCCCAACTATCATATTAAGGCTT
635514 ACAA
66 ACAA
* * * * *
635518 GCGAAGAGCCATAGCCTCCAATA-AAGTTAGCGAGAGAAAAGTTCCCAATTGTCATATTAAGGCT
1 GCGAAGAGCCACAGCCTCCAACATAA-TTAGCGAGAGAAAAGCTCCCAACTATCATATTAAGGCT
*
635582 TACAG
65 TACAA
* * * * * * *
635587 GTGAATAGCCGCAGCCTTCAACATAATTAGCGAGAGCAGAGCTCCCAACTATTATATTAAGGCTC
1 GCGAAGAGCCACAGCCTCCAACATAATTAGCGAGAGAAAAGCTCCCAACTATCATATTAAGGCT-
635652 T-CAA
65 TACAA
* * * * * ** *
635656 GCAAACAGCCGCAGCCTCTAAC-TCAATTAGCAAGATCAAAGCTCCCAGCTATCATATTAAGGCT
1 GCGAAGAGCCACAGCCTCCAACAT-AATTAGCGAGAGAAAAGCTCCCAACTATCATATTAAGGCT
*
635720 CACAA
65 TACAA
** * * * ** * *
635725 ATGAAGTGCTACAGCCTCCAACATAGTTAGCGAGATCAAAGCTCCCAACTATCATGTTAAAGCTT
1 GCGAAGAGCCACAGCCTCCAACATAATTAGCGAGAGAAAAGCTCCCAACTATCATATTAAGGCTT
* *
635790 GCAG
66 ACAA
* * ** ** * * *
635794 GCGAAAAGTCTTAGCCTCCAACGCAGTTAGTGAGAGGAAAGCTCCCA
1 GCGAAGAGCCACAGCCTCCAACATAATTAGCGAGAGAAAAGCTCCCA
635841 GCTGCCATAT
Statistics
Matches: 249, Mismatches: 67, Indels: 13
0.76 0.20 0.04
Matches are distributed among these distances:
67 1 0.00
68 32 0.13
69 212 0.85
70 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (69 bp):
GCGAAGAGCCACAGCCTCCAACATAATTAGCGAGAGAAAAGCTCCCAACTATCATATTAAGGCTT
ACAA
Found at i:635810 original size:138 final size:138
Alignment explanation
Indices: 635598--635853 Score: 300
Period size: 138 Copynumber: 1.9 Consensus size: 138
635588 TGAATAGCCG
* * * *
635598 CAGCCTTCAACATAATTAGCGAGAGCAGAGCTCCCAACTATTATATTAAGGCTCTCAAGCAAACA
1 CAGCCTCCAACATAATTAGCGAGAGCAAAGCTCCCAACTATCATATTAAAGCTCTCAAGCAAACA
* * * *
635663 GCCGCAGCCTCTAACTCAATTAGCAAGATCAAAGCTCCCAGCTATCATATTAAGGCTCACAAATG
66 GCCGCAGCCTCCAACGCAATTAGCAAGAGCAAAGCTCCCAGCTACCATATTAAGGCTCACAAATG
635728 AAGTGCTA
131 AAGTGCTA
* * * *
635736 CAGCCTCCAACATAGTTAGCGAGATCAAAGCTCCCAACTATCATGTTAAAGCT-TGCAGGCGAAA
1 CAGCCTCCAACATAATTAGCGAGAGCAAAGCTCCCAACTATCATATTAAAGCTCT-CAAGC-AAA
* ** * ** * *
635800 -AGTCTTAGCCTCCAACGCAGTTAGTGAGAGGAAAGCTCCCAGCTGCCATATTAA
64 CAGCCGCAGCCTCCAACGCAATTAGCAAGAGCAAAGCTCCCAGCTACCATATTAA
635854 AGCTACTAGG
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
137 1 0.01
138 92 0.96
139 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (138 bp):
CAGCCTCCAACATAATTAGCGAGAGCAAAGCTCCCAACTATCATATTAAAGCTCTCAAGCAAACA
GCCGCAGCCTCCAACGCAATTAGCAAGAGCAAAGCTCCCAGCTACCATATTAAGGCTCACAAATG
AAGTGCTA
Found at i:636017 original size:56 final size:55
Alignment explanation
Indices: 635941--636102 Score: 222
Period size: 55 Copynumber: 2.9 Consensus size: 55
635931 TTTTCTAAAT
*
635941 ATAAAATAGCTCTCA-G-ATTCACATTTCCAGCTTATTATTTTAGAAAAATTTTAAGG
1 ATAAAATAG-T-TCACGAATTCACATTCCCAGCTTATTATTTTAG-AAAATTTTAAGG
* *
635997 ATAAAATAGTTCACGAATTCACATTCCCAACTTATTATTTTAGAAAATTTCCAAGG
1 ATAAAATAGTTCACGAATTCACATTCCCAGCTTATTATTTTAGAAAATTT-TAAGG
* *
636053 ATAAAA-AGTTCACAAATCCACATTCCCAGCTTATTATTTTAGAAAATTTT
1 ATAAAATAGTTCACGAATTCACATTCCCAGCTTATTATTTTAGAAAATTTT
636103 CCCAAGTACA
Statistics
Matches: 96, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
54 3 0.03
55 49 0.51
56 44 0.46
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.36
Consensus pattern (55 bp):
ATAAAATAGTTCACGAATTCACATTCCCAGCTTATTATTTTAGAAAATTTTAAGG
Found at i:640497 original size:18 final size:18
Alignment explanation
Indices: 640466--640510 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
640456 AATAATAAAG
*
640466 TAAATAAACATAAAAGAAA
1 TAAAGAAACATAAAAG-AA
640485 TAAAGAAAC-TAAAAGAA
1 TAAAGAAACATAAAAGAA
640502 TAAAAGAAA
1 T-AAAGAAA
640511 GAAATGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 3 0.12
18 13 0.54
19 8 0.33
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (18 bp):
TAAAGAAACATAAAAGAA
Found at i:641905 original size:67 final size:67
Alignment explanation
Indices: 641797--641928 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 67
641787 TTTCCAATTC
*
641797 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
641862 CA
66 CA
* * * *
641864 AGAGAGCACACTCCCGCGAACTTCATTTCTTACAATGGGATTATCAGTCTAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
641929 TAATATAAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:645593 original size:126 final size:126
Alignment explanation
Indices: 645363--645606 Score: 398
Period size: 126 Copynumber: 1.9 Consensus size: 126
645353 AAATTATTAG
*
645363 TTAAATTAAAAATTATTTATGAATGATCAAGTAGATAAATTGTTAAATCAATGTTGTAGGCATAA
1 TTAAATTAAAAATTATTTATGAATGATCAAGTAGATAAATTGTTAAATCAATATTGTAGGCATAA
* * *
645428 TTAGGCATGTTTGATTGCGGAGATATATAGGTTGTTATATTGGTTGCAAATTGAATATATT
66 TTAGGCATGTTTGAGTACGGAGATAGATAGGTTGTTATATTGGTTGCAAATTGAATATATT
* *
645489 TTAATTTAAAAATTATTTATGAATGATCAAGTAGATAAATTGTTAAATTAATATTGTAGGCATAA
1 TTAAATTAAAAATTATTTATGAATGATCAAGTAGATAAATTGTTAAATCAATATTGTAGGCATAA
* * * *
645554 TTAGGCGTGTTTGAGTATGGAGATGGATAGGTTGTTATATTGGTTGTAAATTG
66 TTAGGCATGTTTGAGTACGGAGATAGATAGGTTGTTATATTGGTTGCAAATTG
645607 GTTATGGTTT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 108 1.00
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (126 bp):
TTAAATTAAAAATTATTTATGAATGATCAAGTAGATAAATTGTTAAATCAATATTGTAGGCATAA
TTAGGCATGTTTGAGTACGGAGATAGATAGGTTGTTATATTGGTTGCAAATTGAATATATT
Found at i:647581 original size:2 final size:2
Alignment explanation
Indices: 647574--647606 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
647564 GACAAATAAA
*
647574 AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
647607 GACAGAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:649424 original size:16 final size:17
Alignment explanation
Indices: 649384--649429 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
649374 CATATATCAA
649384 CCCTTTTTGTTTATTAT
1 CCCTTTTTGTTTATTAT
649401 CCCTTTTTGTTTATTAT
1 CCCTTTTTGTTTATTAT
*
649418 CCCTTTTCGTTT
1 CCCTTTTTGTTT
649430 TCGCAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.09, C:0.22, G:0.07, T:0.63
Consensus pattern (17 bp):
CCCTTTTTGTTTATTAT
Found at i:656327 original size:25 final size:25
Alignment explanation
Indices: 656263--656351 Score: 72
Period size: 25 Copynumber: 3.3 Consensus size: 25
656253 TATTTTTCTC
*
656263 ATAAAAATGATTAAATAATAATTATAAAT
1 ATAAAAA-AATTAAATAATAA--A-AAAT
656292 ATTAAACAAAATTTTAAA-AATAAAAAAT
1 A-TAAA-AAAA--TTAAATAATAAAAAAT
*
656320 ATAAAAAAATTAAATATTAAAAAAT
1 ATAAAAAAATTAAATAATAAAAAAT
*
656345 ATGAAAA
1 ATAAAAA
656352 TTTATATAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
24 5 0.10
25 15 0.29
26 4 0.08
27 4 0.08
28 5 0.10
29 2 0.04
30 5 0.10
31 7 0.13
32 5 0.10
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (25 bp):
ATAAAAAAATTAAATAATAAAAAAT
Found at i:657838 original size:19 final size:19
Alignment explanation
Indices: 657816--657856 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
657806 TTTATATCAA
* * *
657816 TTTAATATTTTTATTATTT
1 TTTAATAATTCTAATATTT
657835 TTTAATAATTCTAATATTT
1 TTTAATAATTCTAATATTT
657854 TTT
1 TTT
657857 TAAATTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATAATTCTAATATTT
Found at i:657864 original size:27 final size:27
Alignment explanation
Indices: 657814--657866 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
657804 AGTTTATATC
**
657814 AATTTAATATTTTTATTATTTTTTAAT
1 AATTTAATATTTTTATTAAATTTTAAT
657841 AATTCTAATATTTTT-TTAAATTTTAA
1 AATT-TAATATTTTTATTAAATTTTAA
657867 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
AATTTAATATTTTTATTAAATTTTAAT
Found at i:658779 original size:16 final size:15
Alignment explanation
Indices: 658754--658785 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
658744 AGTTTATATC
658754 AATATTAATATTTTT
1 AATATTAATATTTTT
658769 AATATTTAATATTTTT
1 AATA-TTAATATTTTT
658785 A
1 A
658786 TTTTCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATTAATATTTTT
Found at i:661862 original size:33 final size:33
Alignment explanation
Indices: 661794--661862 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
661784 TGAACTATTA
* * * *
661794 GGAGAGGAAACACTGTGAGGGCTAGTGTTTTTT
1 GGAGAGGAAACACTATGAGGACTAGTATTTGTT
*
661827 GGAGAGGAAACACTATGAGGATTAGTATTTGTT
1 GGAGAGGAAACACTATGAGGACTAGTATTTGTT
661860 GGA
1 GGA
661863 ACATCATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.07, G:0.35, T:0.29
Consensus pattern (33 bp):
GGAGAGGAAACACTATGAGGACTAGTATTTGTT
Found at i:663795 original size:63 final size:63
Alignment explanation
Indices: 663666--663796 Score: 163
Period size: 63 Copynumber: 2.1 Consensus size: 63
663656 ATGAGTTCCT
* * * * **
663666 CCACCATTCGGGCCAAGATATTGTTGCCTATACTCATGATTTTCAACAATAGGCCTTTGCCAA
1 CCACCATTCGGGCCAAGAGATTGTGGCCTATACTCATGACTTTCAACAATAGACCTGGGCCAA
* * * * *
663729 CCACCATTCGGGCCAAGAGATTGTGGCCTATACTCATGACTTTGAATATTTGACCTGGGCCCA
1 CCACCATTCGGGCCAAGAGATTGTGGCCTATACTCATGACTTTCAACAATAGACCTGGGCCAA
663792 CCACC
1 CCACC
663797 TATCGGTGCT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (63 bp):
CCACCATTCGGGCCAAGAGATTGTGGCCTATACTCATGACTTTCAACAATAGACCTGGGCCAA
Found at i:665855 original size:27 final size:23
Alignment explanation
Indices: 665823--665884 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 23
665813 GTATAGGGAC
665823 ATATGACATATTTTAATCTAGTATAAA
1 ATATGA-ATATTTTAAT-TA-TAT-AA
*
665850 ATATGAATGTTTTAATTATATAA
1 ATATGAATATTTTAATTATATAA
*
665873 ATATGAGTATTT
1 ATATGAATATTT
665885 GTTTAAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 12 0.38
24 3 0.09
25 2 0.06
26 9 0.28
27 6 0.19
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (23 bp):
ATATGAATATTTTAATTATATAA
Found at i:665864 original size:26 final size:24
Alignment explanation
Indices: 665823--665878 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
665813 GTATAGGGAC
665823 ATATGACATATTTTAATCTAGTATAAA
1 ATATGACATATTTTAAT-TA-TAT-AA
*
665850 ATATGA-ATGTTTTAATTATATAA
1 ATATGACATATTTTAATTATATAA
665873 ATATGA
1 ATATGA
665879 GTATTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.29
24 3 0.11
25 2 0.07
26 9 0.32
27 6 0.21
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (24 bp):
ATATGACATATTTTAATTATATAA
Found at i:678658 original size:29 final size:27
Alignment explanation
Indices: 678598--678657 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 27
678588 TGCAACAATC
678598 AAAAGAAAGCAAAATAAAATAAAAAGGT
1 AAAAGAAAGCAAAATAAAATAAAAA-GT
*
678626 AAAATGAAAGGAAAATTAAAATAAAAA-T
1 AAAA-GAAAGCAAAA-TAAAATAAAAAGT
678654 AAAA
1 AAAA
678658 AAGGATCTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.31
29 9 0.31
30 11 0.38
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (27 bp):
AAAAGAAAGCAAAATAAAATAAAAAGT
Found at i:678961 original size:30 final size:30
Alignment explanation
Indices: 678901--678963 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
678891 TGGCCATGTC
* *
678901 TTTAGCCCTTGTGGTTCAGATGACCGTGTT
1 TTTAGCCCCTGTGGTTCAGATAACCGTGTT
* *
678931 TTTAGCCCCTGTGGTTTTAG-TAACCTTGTT
1 TTTAGCCCCTGTGG-TTCAGATAACCGTGTT
678961 TTT
1 TTT
678964 TTCATGACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (30 bp):
TTTAGCCCCTGTGGTTCAGATAACCGTGTT
Found at i:688111 original size:37 final size:38
Alignment explanation
Indices: 688038--688111 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
688028 TATTTATTTG
*
688038 TTCTTTGTTCTCAAATTTCTTCTTTTCTTCCTTTCGAT
1 TTCTTTGTTATCAAATTTCTTCTTTTCTTCCTTTCGAT
* *
688076 TTCTTTGTTATTAAATTT-TT-TATTTCTTCTTTTCGA
1 TTCTTTGTTATCAAATTTCTTCT-TTTCTTCCTTTCGA
688112 GTTGAACAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.03
37 15 0.47
38 16 0.50
ACGTcount: A:0.14, C:0.18, G:0.05, T:0.64
Consensus pattern (38 bp):
TTCTTTGTTATCAAATTTCTTCTTTTCTTCCTTTCGAT
Found at i:692423 original size:2 final size:2
Alignment explanation
Indices: 692416--692440 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
692406 TGGTAAAAGA
692416 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
692441 CCGTCTATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:696006 original size:3 final size:3
Alignment explanation
Indices: 695998--696155 Score: 316
Period size: 3 Copynumber: 52.7 Consensus size: 3
695988 CAACTAATTT
695998 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
696046 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
696094 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
696142 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
696156 TTGACAAATG
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 155 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:699523 original size:10 final size:10
Alignment explanation
Indices: 699510--699542 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
699500 AATTTATTCT
699510 GAAATCATAA
1 GAAATCATAA
699520 GAAATCAT-A
1 GAAATCATAA
*
699529 GATATCATAA
1 GAAATCATAA
699539 GAAA
1 GAAA
699543 ATTAATTCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (10 bp):
GAAATCATAA
Found at i:701377 original size:63 final size:62
Alignment explanation
Indices: 701293--701482 Score: 229
Period size: 63 Copynumber: 3.0 Consensus size: 62
701283 AGTGTTACAC
* * * * * * *
701293 CGCCTAGACACACGCCTGTGTCTCTGGCTCGTATGATTTATAGTGGCCAACAGTGAA-TCATA
1 CGCCTGGACACACGCCCGTGTCTCTGGCCCGTGTGATCTATAGTGGCAAACAGT-AAGTCACA
*
701355 CAGCCTGGACACACGCCCGTGTCTCTGGCCCGTGTGATCAATAGTGGCAAACAGTAAGTCACA
1 C-GCCTGGACACACGCCCGTGTCTCTGGCCCGTGTGATCTATAGTGGCAAACAGTAAGTCACA
* * * * *
701418 CGACCTGGACACGCGCCCGTGTCTCTAGCCCGTGTGATCTATAGTGGCAAGCACTGAGTCACA
1 CG-CCTGGACACACGCCCGTGTCTCTGGCCCGTGTGATCTATAGTGGCAAACAGTAAGTCACA
701481 CG
1 CG
701483 GCCTAACACA
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
62 4 0.04
63 107 0.96
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.22
Consensus pattern (62 bp):
CGCCTGGACACACGCCCGTGTCTCTGGCCCGTGTGATCTATAGTGGCAAACAGTAAGTCACA
Found at i:701686 original size:18 final size:17
Alignment explanation
Indices: 701631--701695 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
701621 GAATGCAATC
*
701631 AAAAAGAAAATAAAAAGA
1 AAAAAGAAAAGAAAAA-A
*
701649 AAAGAGAAACAGGAAGAAAA
1 AAAAAGAAA-A-GAA-AAAA
*
701669 AGAAAGAAAAGAAAAAA
1 AAAAAGAAAAGAAAAAA
701686 AATAAAGAAA
1 AA-AAAGAAA
701696 GAAGGAATAC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
17 5 0.13
18 18 0.47
19 2 0.05
20 10 0.26
21 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAA
Done.