Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 17 of 297
Found at i:5555040 original size:19 final size:19
Alignment explanation
Indices: 5555013--5555082 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
5555003 TGTGATAACA
5555013 AATACTAAAATTTTTAATT
1 AATACTAAAATTTTTAATT
* *
5555032 AATATTAAAATTTTTAATG
1 AATACTAAAATTTTTAATT
* * * * *
5555051 GAGACCAATATTTCTAATT
1 AATACTAAAATTTTTAATT
5555070 AATACTAAAATTT
1 AATACTAAAATTT
5555083 CGAGTACAAT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (19 bp):
AATACTAAAATTTTTAATT
Found at i:5555454 original size:16 final size:16
Alignment explanation
Indices: 5555418--5555448 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5555408 AACCATTTAA
*
5555418 AAAATTATAAAAATTG
1 AAAATTATAAAAAATG
5555434 AAAATTATAAAAAAT
1 AAAATTATAAAAAAT
5555449 ATAAATAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAATTATAAAAAATG
Found at i:5561972 original size:43 final size:42
Alignment explanation
Indices: 5561916--5562033 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 42
5561906 AGCTCGTACA
* *
5561916 ATGCCAACGTCCCATATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGATGTGGTCTTACATGTAATCAAATA-CG
* * * *
5561959 ATGCTACTGTCCCAGATAG-GGTCTTACACGAAATCAAATACG
1 ATGCCAATGTCCCAGAT-GTGGTCTTACATGTAATCAAATACG
*
5562001 ATGCCAATGTCCCAGACGTGGTCTTACATGTAA
1 ATGCCAATGTCCCAGATGTGGTCTTACATGTAA
5562034 ATTATAAGTC
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
41 1 0.02
42 28 0.45
43 32 0.52
44 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (42 bp):
ATGCCAATGTCCCAGATGTGGTCTTACATGTAATCAAATACG
Found at i:5562016 original size:42 final size:43
Alignment explanation
Indices: 5561916--5562075 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
5561906 AGCTCGTACA
* * * *
5561916 ATGCCAACGTCCCATATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGATGTGGTCTTACACGAAATCAAATATCG
* *
5561959 ATGCTACTGTCCCAGATAG-GGTCTTACACGAAATCAAATA-CG
1 ATGCCAATGTCCCAGAT-GTGGTCTTACACGAAATCAAATATCG
* * * *
5562001 ATGCCAATGTCCCAGACGTGGTCTTACATGTAAATTATAA-GTCG
1 ATGCCAATGTCCCAGATGTGGTCTTACACG-AAATCA-AATATCG
* * * *
5562045 ATGCCAACGTTCTAGACGTGGTCTTACACGA
1 ATGCCAATGTCCCAGATGTGGTCTTACACGA
5562076 TAACACATAT
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 26 0.27
43 38 0.40
44 31 0.32
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGATGTGGTCTTACACGAAATCAAATATCG
Found at i:5569031 original size:43 final size:43
Alignment explanation
Indices: 5568983--5569071 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
5568973 TTCAACCATA
5568983 ATTAAGCCATATCACATGGCTAAATATACACTTCTCAAAATAT
1 ATTAAGCCATATCACATGGCTAAATATACACTTCTCAAAATAT
5569026 ATTAAGCCATATCACATGGCTAAATATACACTTCTCAAAATAT
1 ATTAAGCCATATCACATGGCTAAATATACACTTCTCAAAATAT
5569069 ATT
1 ATT
5569072 CAACTACCTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (43 bp):
ATTAAGCCATATCACATGGCTAAATATACACTTCTCAAAATAT
Found at i:5569662 original size:42 final size:42
Alignment explanation
Indices: 5569582--5569719 Score: 145
Period size: 42 Copynumber: 3.2 Consensus size: 42
5569572 GTCCAGACAT
* * * *
5569582 GGTCTTACATGTACTCAAATATCGATGCCACTGTCCCAAATAG-
1 GGTCTTACACGAAATCAAATA-CGATGCCAATGTCCCAAAT-GC
5569625 GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAAATGC
1 GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAAATGC
* * * *
5569667 GGTCTTACACGTAAATCATAAGT-CGATGCCAACGTCCCAGACGT
1 GGTCTTACACG-AAATCA-AA-TACGATGCCAATGTCCCAAATGC
5569711 GGTCTTACA
1 GGTCTTACA
5569720 TGATAACACA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
41 1 0.01
42 29 0.35
43 24 0.29
44 28 0.34
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAAATGC
Found at i:5569715 original size:44 final size:42
Alignment explanation
Indices: 5569582--5569719 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 42
5569572 GTCCAGACAT
* * * *
5569582 GGTCTTACATGTACTCAAATATCGATGCC-ACTGTCCCAAATAG-
1 GGTCTTACACGAAATCAAATA-CGATGCCAAC-GTCCCAAA-CGC
* *
5569625 GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAAATGC
1 GGTCTTACACGAAATCAAATACGATGCCAACGTCCCAAACGC
* *
5569667 GGTCTTACACGTAAATCATAAGT-CGATGCCAACGTCCCAGACGT
1 GGTCTTACACG-AAATCA-AA-TACGATGCCAACGTCCCAAACGC
5569711 GGTCTTACA
1 GGTCTTACA
5569720 TGATAACACA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.01
42 26 0.32
43 25 0.31
44 28 0.35
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACGATGCCAACGTCCCAAACGC
Found at i:5573108 original size:21 final size:21
Alignment explanation
Indices: 5573082--5573145 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
5573072 ACTGAACGGA
5573082 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
5573103 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
5573124 TCAGCTCATACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
5573145 T
1 T
5573146 GACTTATTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.39
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:5573584 original size:77 final size:77
Alignment explanation
Indices: 5573488--5573798 Score: 613
Period size: 77 Copynumber: 4.0 Consensus size: 77
5573478 TAGCACCCAA
*
5573488 GTCACACTATCCAGCTTATCTCGGTAGTTTTTGAAATGTTAAATACGGTTTATATGGCATGTATA
1 GTCACACTATCCAGCTTATCTCTGTAGTTTTTGAAATGTTAAATACGGTTTATATGGCATGTATA
5573553 GGCTTTTGTATG
66 GGCTTTTGTATG
5573565 GTCACACTATCCAGCTTATCTCTGTAGTTTTTGAAATGTTAAATACGGTTTATATGGCATGTATA
1 GTCACACTATCCAGCTTATCTCTGTAGTTTTTGAAATGTTAAATACGGTTTATATGGCATGTATA
5573630 GGCTTTTGTATG
66 GGCTTTTGTATG
5573642 GTCACACTATCCAGCTTATCTCTGTAGTTTTTGAAATGTTAAATACGGTTTATATGGCATGTATA
1 GTCACACTATCCAGCTTATCTCTGTAGTTTTTGAAATGTTAAATACGGTTTATATGGCATGTATA
5573707 GGCTTTTGTATG
66 GGCTTTTGTATG
5573719 GTCACACTATCCAGCTTATCTCTGTAGTTTTTGAAATGTTAAATACGGTTTATATGGCATGTATA
1 GTCACACTATCCAGCTTATCTCTGTAGTTTTTGAAATGTTAAATACGGTTTATATGGCATGTATA
5573784 GGCTTTTGTATG
66 GGCTTTTGTATG
5573796 GTC
1 GTC
5573799 TTGGTCAAAG
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 233 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (77 bp):
GTCACACTATCCAGCTTATCTCTGTAGTTTTTGAAATGTTAAATACGGTTTATATGGCATGTATA
GGCTTTTGTATG
Found at i:5581488 original size:40 final size:40
Alignment explanation
Indices: 5581429--5581620 Score: 253
Period size: 40 Copynumber: 4.8 Consensus size: 40
5581419 CGGATGATAA
*
5581429 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
* * *
5581469 CCGAGCTAAGCCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
* * *
5581509 CCGGGCTAAGCCCCGAAGGAATTTGTGCGAGTTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-T
* * *
5581549 CCCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-T
*
5581589 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
5581621 AGCTATATCC
Statistics
Matches: 139, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 2 0.01
40 137 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
Found at i:5581564 original size:80 final size:79
Alignment explanation
Indices: 5581425--5581646 Score: 279
Period size: 80 Copynumber: 2.8 Consensus size: 79
5581415 TATTCGGATG
* * *
5581425 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGAGCTAAGCCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCG-GCTAAGTCCCGAAGGC
*
5581489 ATTTGTGCTAGTGACT
64 ATTTGTGCGAGTGACT
* * *
5581505 A-ATTCCGGGCTAAGCCCCGAAGGAATTTGTGCGAGTTACTATATCCCGGCTAAGTCCCGAAGGC
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT-CCGGCTAAGTCCCGAAGGC
*
5581569 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTGACT
* * *
5581585 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCCGACTAAATCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGCTAAGTCCCGAAGG
5581647 TACTTGGTTT
Statistics
Matches: 123, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
79 19 0.15
80 99 0.80
81 5 0.04
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCAT
TTGTGCGAGTGACT
Found at i:5581627 original size:40 final size:40
Alignment explanation
Indices: 5581429--5581646 Score: 234
Period size: 40 Copynumber: 5.5 Consensus size: 40
5581419 CGGATGATAA
*
5581429 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAG-CTATA-T
* * *
5581469 CCGAGCTAAGCCCCGAAGGCATTTGTGCTAGT-GACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAG-CTATA-T
* *
5581509 CCGGGCTAAGCCCCGAAGGAATTTGTGCGAGTTA-CTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATAT
* *
5581549 CCCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATAT
*
5581589 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATAT
* *
5581629 CC-GACTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
5581647 TACTTGGTTT
Statistics
Matches: 160, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 16 0.10
40 142 0.89
41 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATAT
Found at i:5584443 original size:225 final size:226
Alignment explanation
Indices: 5584042--5584490 Score: 641
Period size: 225 Copynumber: 2.0 Consensus size: 226
5584032 AGAACGAAAG
* * *
5584042 CCCTGTTTCTACAACAAATTCGGGAATTGCAAGATGATGATCCAAAGTTGATGTTCAAATGACAG
1 CCCTATTTCTACAACAAATTCGAGAATTGCAAGATGATGATCCAAAGTTCATGTTCAAATGACAG
*
5584107 ATAGTTCAAAATAATTTGAGTTCAGAGGAGAGGACAGTGTTGATGATAATGGTACATTGCGTTAT
66 ATAGTTCAAAATAATTTGAGTTC----GAGAGGACAGTGTTGATGATAATGGTACATTACGTTAT
** *
5584172 CGTTATAGAATTTGTGTTTCAACTAATTTAGATTTGAAAAATGATATTCTTTCTGAAGCTCACAG
127 CGCGATAGAATTTGTGTTTCAACTAATTTAGATTTGAAAAATGATATACTTTCTGAAGCTCACAG
* *
5584237 TAGCACGTACTTTATTCATCCGGGTAGCACAAAAC
192 TAGCACGTACTCTATTCATCCAGGTAGCACAAAAC
* * * **
5584272 CCCTATTTCTACAACGAATTCGAGAATTTCAAGATGATGATCCAAAGTTCATGTTGAAATGGTAG
1 CCCTATTTCTACAACAAATTCGAGAATTGCAAGATGATGATCCAAAGTTCATGTTCAAATGACAG
* * * * *
5584337 ATAGTTTAGAATAATTTGAGTTC-AGAGTACAGTGTTGATGATAGTGGTACATTATGTTATCGCG
66 ATAGTTCAAAATAATTTGAGTTCGAGAGGACAGTGTTGATGATAATGGTACATTACGTTATCGCG
**
5584401 ATAGAATTTGTGTTTCGAA-TAATTTAGATTTGAAAAATGATATACTTTCTGAATTTCACAGTAG
131 ATAGAATTTGTGTTTC-AACTAATTTAGATTTGAAAAATGATATACTTTCTGAAGCTCACAGTAG
*
5584465 CTCGTACTCTATTCATCCAGGTAGCA
195 CACGTACTCTATTCATCCAGGTAGCA
5584491 TGAAGATGTA
Statistics
Matches: 196, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
225 116 0.59
226 2 0.01
230 78 0.40
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (226 bp):
CCCTATTTCTACAACAAATTCGAGAATTGCAAGATGATGATCCAAAGTTCATGTTCAAATGACAG
ATAGTTCAAAATAATTTGAGTTCGAGAGGACAGTGTTGATGATAATGGTACATTACGTTATCGCG
ATAGAATTTGTGTTTCAACTAATTTAGATTTGAAAAATGATATACTTTCTGAAGCTCACAGTAGC
ACGTACTCTATTCATCCAGGTAGCACAAAAC
Found at i:5598519 original size:42 final size:42
Alignment explanation
Indices: 5598452--5598543 Score: 114
Period size: 43 Copynumber: 2.2 Consensus size: 42
5598442 GTTTTATGTA
* * * *
5598452 TAAGACCATGTCTGGACATTGGCATC-GTATTTGATTTCGTG
1 TAAGACCATGTCTGGACAGTGGCATCAATATTTGATTACATG
* *
5598493 TAAGACCCTGTCTAGGACAGTGGCATCAATGTTTGATTACATG
1 TAAGACCATGTCT-GGACAGTGGCATCAATATTTGATTACATG
5598536 TAAGACCA
1 TAAGACCA
5598544 CATCTGGTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 12 0.29
42 12 0.29
43 18 0.43
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (42 bp):
TAAGACCATGTCTGGACAGTGGCATCAATATTTGATTACATG
Found at i:5603180 original size:57 final size:57
Alignment explanation
Indices: 5603113--5603224 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 57
5603103 CATTTTTGAA
* *
5603113 CCCTTAAAGCATGAGCTTTCAAATGAGGGTACTATTTTGCAAAATGGTTGAAAGTAC
1 CCCTTAAAGCATGAGCTTTCAAATGAGGGTACTATATTGCAAAATGATTGAAAGTAC
*
5603170 CCCTTGAAGCATGAGCTTTCAAATGAGGGTACTATATTGCAAAATGATTGAAAGT
1 CCCTTAAAGCATGAGCTTTCAAATGAGGGTACTATATTGCAAAATGATTGAAAGT
5603225 CTAAGGTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (57 bp):
CCCTTAAAGCATGAGCTTTCAAATGAGGGTACTATATTGCAAAATGATTGAAAGTAC
Found at i:5603677 original size:38 final size:38
Alignment explanation
Indices: 5603635--5603708 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
5603625 GGGGGAAAGC
*
5603635 TGTGACAACCCTAAATTGACCCTAGTCGGGAAGTGGAG
1 TGTGACAACCCAAAATTGACCCTAGTCGGGAAGTGGAG
*
5603673 TGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTGG
1 TGTGACAACCCAAAATTGACCCTAGTCGGGAAGTGG
5603709 TTTCGGGACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (38 bp):
TGTGACAACCCAAAATTGACCCTAGTCGGGAAGTGGAG
Found at i:5605392 original size:40 final size:40
Alignment explanation
Indices: 5605337--5605554 Score: 264
Period size: 40 Copynumber: 5.5 Consensus size: 40
5605327 CGGATGATAA
*
5605337 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-T
* * *
5605377 CCGGGCTAAGCCCCGAAGGCATTTGTTCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-T
* * *
5605417 CTGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
* * * *
5605457 CCGAGCTAAGTCACGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
*
5605497 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT-AGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGA-CTATAT
*
5605537 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
5605555 TACTTGGTTT
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 16 0.10
40 143 0.89
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
Found at i:5606331 original size:56 final size:56
Alignment explanation
Indices: 5606245--5606476 Score: 446
Period size: 56 Copynumber: 4.1 Consensus size: 56
5606235 ACAAGGGATG
5606245 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5606301 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5606357 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
5606413 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5606469 ATGGGCAA
1 ATGGGCAA
5606477 TAAACTAATA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 174 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:5613200 original size:56 final size:56
Alignment explanation
Indices: 5613114--5613401 Score: 558
Period size: 56 Copynumber: 5.1 Consensus size: 56
5613104 ACAAGGGATG
*
5613114 ATGGGAAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5613170 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5613226 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5613282 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
5613338 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5613394 ATGGGCAA
1 ATGGGCAA
5613402 TAAACTAATA
Statistics
Matches: 230, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 230 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:5616249 original size:963 final size:963
Alignment explanation
Indices: 5614288--5616287 Score: 3386
Period size: 963 Copynumber: 2.1 Consensus size: 963
5614278 GAAAGGATTG
* * *
5614288 TGCAAAGAAGTGATTTAAGTCTGCAAACCCCTCGTGTCCGACTCCGGCGACGGACTCGGGTACGG
1 TGCAAAGAAATGAATTAAGTCTGCAAACACCTCGTGTCCGACTCCGGCGACGGACTCGGGTACGG
5614353 GGTGTTACACGCCCACACTATCAAAGCCCTTTTGGTACTATTTTAGTTGAACTCTGATAATGGCA
66 GGTGTTACACGCCCACACTATCAAAGCCCTTTTGGTACTATTTTAGTTGAACTCTGATAATGGCA
5614418 TGTATAGGGCTGCCCTTTTGTTGTTAGTCAAGTACTTTGGTACTGTATATATTTGGATAGCCATG
131 TGTATAGGGCTGCCCTTTTGTTGTTAGTCAAGTACTTTGGTACTGTATATATTTGGATAGCCATG
5614483 CGAAAATGACTTATATATTTTGAGCATAACGTTATAATCATTTTGTATATATATGGTTATTGAGA
196 CGAAAATGACTTATATATTTTGAGCATAACGTTATAATCATTTTGTATATATATGGTTATTGAGA
5614548 GGTGTGGAAATGCTTGGCAATGATTAGCCATTGGAATGGTTAATCACGATCATATTTTTGTGCTA
261 GGTGTGGAAATGCTTGGCAATGATTAGCCATTGGAATGGTTAATCACGATCATATTTTTGTGCTA
5614613 TGTATGTTAAAGGGCTAGTTGAATCATGGAAATTATTAAATAGGTAAAGTCTACCTTAAAAACAG
326 TGTATGTTAAAGGGCTAGTTGAATCATGGAAATTATTAAATAGGTAAAGTCTACCTTAAAAACAG
5614678 ATACCGACAGCAGCAGTGATGTGAATATGAAAAATCACTAAAAATAGTAGGAATAGAATTAAATT
391 ATACCGACAGCAGCAGTGATGTGAATATGAAAAATCACTAAAAATAGTAGGAATAGAATTAAATT
5614743 GTGAATAAATTATGTAATCGAACCTTGATGAATCTATTTTCATATGAAAGTAACGAAACGATCAT
456 GTGAATAAATTATGTAATCGAACCTTGATGAATCTATTTTCATATGAAAGTAACGAAACGATCAT
5614808 ATGAGCCGTATTTTATGAGATGTTTAAGTTTTCGTGAAACAGGGCCAGAGCGAATTCTGGATTCC
521 ATGAGCCGTATTTTATGAGATGTTTAAGTTTTCGTGAAACAGGGCCAGAGCGAATTCTGGATTCC
* *
5614873 CTGTTCCGACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGAAGTAATTCCATATATGA
586 CTGATCCGACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGAAGTAATACCATATATGA
**
5614938 ATAGATTCCTTTTTGAGTCTAGTTTCTATAGAAACAAACGACATCAATATTGAAGCCCTGTACAG
651 ATAGATTCCTTTTCAAGTCTAGTTTCTATAGAAACAAACGACATCAATATTGAAGCCCTGTACAG
* * * * * * *
5615003 GGAGATATCCAAGTCGTAATGCGCAAAGGTTAGTGTAGTTGATCCCTGTAACATAGGAGACTTTG
716 GGAGATATCCAAGTCGTAATGCACAAAGATCAGAGTAGTCGAACCCTGTAACATAGGAGACTTTA
* * * *
5615068 ACTAATAAACTGTACTAATTGGCCGGACCAAAAATTCTAGAAAAAAATTTATAGATGTATATATG
781 ACTAATAAACTGTACTAAATGGCCAGACCAAAAATTCTAGAAAAAAATTTATAGATGAACATATG
5615133 AGTCTAGTTTCAGGGAAAAATCACGAAGCTGATTTTCGAGTTGTGAAACTAAAGATATGATTTTT
846 AGTCTAGTTTCAGGGAAAAATCACGAAGCTGATTTTCGAGTTGTGAAACTAAAGATATGATTTTT
* *
5615198 AAGGTGACAGTGACGCAGTTAGCCAGCTTGCCTAGAAAATTTAAAATGGATTG
911 AAGGTGACAGTGACGCAGTTAGCCAGCTTGCCTAGAAAATTTAAAATGGACTA
* * *
5615251 TGCAAAGAAGTGATTTAAGTCTGCAAACCCCTCGTGTCCGACTCCGGCGACGGACTCGGGTACGG
1 TGCAAAGAAATGAATTAAGTCTGCAAACACCTCGTGTCCGACTCCGGCGACGGACTCGGGTACGG
5615316 GGTGTTACACGCCCACACTATCAAAGCCCTTTTGGTACTATTTTAGTTGAACTCTGATAATGGCA
66 GGTGTTACACGCCCACACTATCAAAGCCCTTTTGGTACTATTTTAGTTGAACTCTGATAATGGCA
5615381 TGTATAGGGCTGCCCTTTTGTTGTTAGTCAAGTACTTTGGTACTGTATATATTTGGATAGCCATG
131 TGTATAGGGCTGCCCTTTTGTTGTTAGTCAAGTACTTTGGTACTGTATATATTTGGATAGCCATG
5615446 CGAAAATGACTTATATATTTTGAGCATAACGTTATAATCATTTTGTATATATATGGTTATTGAGA
196 CGAAAATGACTTATATATTTTGAGCATAACGTTATAATCATTTTGTATATATATGGTTATTGAGA
5615511 GGTGTGGAAATGCTTGGCAATGATTAGCCATTGGAATGGTTAATCACGATCATATTTTTGTGCTA
261 GGTGTGGAAATGCTTGGCAATGATTAGCCATTGGAATGGTTAATCACGATCATATTTTTGTGCTA
5615576 TGTATGTTAAAGGGCTAGTTGAATCATGGAAATTATTAAATAGGTAAAGTCTACCTTAAAAACAG
326 TGTATGTTAAAGGGCTAGTTGAATCATGGAAATTATTAAATAGGTAAAGTCTACCTTAAAAACAG
5615641 ATACCGACAGCAGCAGTGATGTGAATATGAAAAATCACTAAAAATAGTAGGAATAGAATTAAATT
391 ATACCGACAGCAGCAGTGATGTGAATATGAAAAATCACTAAAAATAGTAGGAATAGAATTAAATT
5615706 GTGAATAAATTATGTAATCGAACCTTGATGAATCTATTTTCATATGAAAGTAACGAAACGATCAT
456 GTGAATAAATTATGTAATCGAACCTTGATGAATCTATTTTCATATGAAAGTAACGAAACGATCAT
5615771 ATGAGCCGTATTTTATGAGATGTTTAAGTTTTCGTGAAACAGGGCCAGAGCGAATTCTGGATTCC
521 ATGAGCCGTATTTTATGAGATGTTTAAGTTTTCGTGAAACAGGGCCAGAGCGAATTCTGGATTCC
* * *
5615836 CTGATCTGACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGAAGTCATACCATATATGT
586 CTGATCCGACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGAAGTAATACCATATATGA
* * *
5615901 ATAGATTCCTTTTCAAGTCTAGTTTCTTTAGAAACAAAC-AGTAT-AAGTATTGAATCCCTGTAC
651 ATAGATTCCTTTTCAAGTCTAGTTTCTATAGAAACAAACGA-CATCAA-TATTGAAGCCCTGTAC
* **
5615964 AGGGAGATATCTAAGTCGTAATGCATGAAGATCAGAGTAGTCGAACCCTG-AA-ATAGGGGAGAC
714 AGGGAGATATCCAAGTCGTAATGCACAAAGATCAGAGTAGTCGAACCCTGTAACATA--GGAGAC
* * *
5616027 TTTAACTAATAAACTGTACTAAATGGCTCAG-CCAAAAATTCTATAAAAAAATTTGTATATGAAC
777 TTTAACTAATAAACTGTACTAAATGGC-CAGACCAAAAATTCTAGAAAAAAATTTATAGATGAAC
* * * * **
5616091 ATATGAGTCTAGTTTCA-GGAAAAATTTACGGAA-CTGGTTTTTCGAGTTTTGGAACTTGAGATA
841 ATATGAGTCTAGTTTCAGGGAAAAA-TCAC-GAAGCT-GATTTTCGAGTTGTGAAACTAAAGATA
* * *
5616154 TGATTTTTAAGGTGACAGTGACGCAGTTAGCCAGCTTGTCTGGAAATTTTAAAATGGACTA
903 TGATTTTTAAGGTGACAGTGACGCAGTTAGCCAGCTTGCCTAGAAAATTTAAAATGGACTA
* * **** * * * *
5616215 TGTAAATAAATGAATTAA-TCTGTTTGCACCTCGTGTTCAACTCCGGCAACGGTCTCGGGTACGG
1 TGCAAAGAAATGAATTAAGTCTGCAAACACCTCGTGTCCGACTCCGGCGACGGACTCGGGTACGG
5616279 GGTGTTACA
66 GGTGTTACA
5616288 AAAGCCAAGC
Statistics
Matches: 978, Mismatches: 51, Indels: 16
0.94 0.05 0.02
Matches are distributed among these distances:
961 3 0.00
962 12 0.01
963 866 0.89
964 97 0.10
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (963 bp):
TGCAAAGAAATGAATTAAGTCTGCAAACACCTCGTGTCCGACTCCGGCGACGGACTCGGGTACGG
GGTGTTACACGCCCACACTATCAAAGCCCTTTTGGTACTATTTTAGTTGAACTCTGATAATGGCA
TGTATAGGGCTGCCCTTTTGTTGTTAGTCAAGTACTTTGGTACTGTATATATTTGGATAGCCATG
CGAAAATGACTTATATATTTTGAGCATAACGTTATAATCATTTTGTATATATATGGTTATTGAGA
GGTGTGGAAATGCTTGGCAATGATTAGCCATTGGAATGGTTAATCACGATCATATTTTTGTGCTA
TGTATGTTAAAGGGCTAGTTGAATCATGGAAATTATTAAATAGGTAAAGTCTACCTTAAAAACAG
ATACCGACAGCAGCAGTGATGTGAATATGAAAAATCACTAAAAATAGTAGGAATAGAATTAAATT
GTGAATAAATTATGTAATCGAACCTTGATGAATCTATTTTCATATGAAAGTAACGAAACGATCAT
ATGAGCCGTATTTTATGAGATGTTTAAGTTTTCGTGAAACAGGGCCAGAGCGAATTCTGGATTCC
CTGATCCGACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGAAGTAATACCATATATGA
ATAGATTCCTTTTCAAGTCTAGTTTCTATAGAAACAAACGACATCAATATTGAAGCCCTGTACAG
GGAGATATCCAAGTCGTAATGCACAAAGATCAGAGTAGTCGAACCCTGTAACATAGGAGACTTTA
ACTAATAAACTGTACTAAATGGCCAGACCAAAAATTCTAGAAAAAAATTTATAGATGAACATATG
AGTCTAGTTTCAGGGAAAAATCACGAAGCTGATTTTCGAGTTGTGAAACTAAAGATATGATTTTT
AAGGTGACAGTGACGCAGTTAGCCAGCTTGCCTAGAAAATTTAAAATGGACTA
Found at i:5616583 original size:46 final size:47
Alignment explanation
Indices: 5616530--5616654 Score: 159
Period size: 46 Copynumber: 2.7 Consensus size: 47
5616520 ATTTAGATCT
*
5616530 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-C-GAGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTACAAAGA--TATAGCC
* *
5616576 AGTGTAAGACATATCTGGGACATGCATCGG-CTACAAAGATATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTACAAAGATATAGCC
5616622 AGTGTAAGACCATGTCTGGGACATAGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
5616655 ACCTTACCTC
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
45 4 0.06
46 42 0.61
47 16 0.23
48 7 0.10
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTACAAAGATATAGCC
Found at i:5619433 original size:28 final size:28
Alignment explanation
Indices: 5619364--5619433 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
5619354 CTGGGTTTTT
5619364 GGACACGGGTGTGTCTAGGCCATGTGAG
1 GGACACGGGTGTGTCTAGGCCATGTGAG
*
5619392 GGACACAGGTGTGTCTAGGCCATGTGAG
1 GGACACGGGTGTGTCTAGGCCATGTGAG
*
5619420 GGACACGGGCGTGT
1 GGACACGGGTGTGT
5619434 GTTTGGCCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.20
Consensus pattern (28 bp):
GGACACGGGTGTGTCTAGGCCATGTGAG
Found at i:5619555 original size:23 final size:23
Alignment explanation
Indices: 5619523--5619572 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
5619513 GTGTCCCAAG
5619523 CACACAGGCGTGTGCTTTGCCTC
1 CACACAGGCGTGTGCTTTGCCTC
*
5619546 CACACGGGCGTGTGCTTTGCCTC
1 CACACAGGCGTGTGCTTTGCCTC
5619569 CACA
1 CACA
5619573 AGGACGTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.26, T:0.24
Consensus pattern (23 bp):
CACACAGGCGTGTGCTTTGCCTC
Found at i:5625982 original size:47 final size:48
Alignment explanation
Indices: 5625912--5626134 Score: 244
Period size: 46 Copynumber: 4.8 Consensus size: 48
5625902 GGGTAAGTTA
*
5625912 CCGATGCTATGTCCCAGACATGGTCTTACACTGGCTCACATCT-AAAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAAG
* ** **
5625959 TCGATGCCATGTCCCAGACATGGTCTTACAC-AACT-ATCATCTCGTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA-CATCTCAAAG
* * ** * *
5626006 CCGATG-CATGTCCCAGACAT-GTCTTACATTGGCTTATGTCTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAAG
* * *
5626052 TCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCAAAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAAG
*
5626098 CCGATGCCATGTCCCAGACATGGTCTTTCACTGGCTC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
5626135 TCATAATGTG
Statistics
Matches: 144, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
45 9 0.06
46 71 0.49
47 51 0.35
48 13 0.09
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAAG
Found at i:5626156 original size:47 final size:45
Alignment explanation
Indices: 5625912--5626175 Score: 201
Period size: 46 Copynumber: 5.7 Consensus size: 45
5625902 GGGTAAGTTA
* * **
5625912 CCGATGCTATGTCCCAGACATGGTCTTACACTGGCTCACATCTAAAG
1 CCGATGC-ATGTCCCAGACAT-GTCTTACACTGGCTCTCATATGTAG
* ** * *
5625959 TCGATGCCATGTCCCAGACATGGTCTTACAC-AACTATCATCTCGTAG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAT-GTAG
* * *
5626006 CCGATGCATGTCCCAGACATGTCTTACATTGGCT-T-ATGTCTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATGT--A-G
* * * **
5626052 TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAAG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAT-GTAG
* *
5626098 CCGATGCCATGTCCCAGACATGGTCTTTCACTGGCTCTCATAATGTGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-ATGTAG
* **
5626146 CTGATGCATGTCTTAGACATGTCTTACACT
1 CCGATGCATGTCCCAGACATGTCTTACACT
5626176 AGCCAACAAC
Statistics
Matches: 175, Mismatches: 30, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.02
45 10 0.06
46 70 0.40
47 63 0.36
48 27 0.15
49 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (45 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATGTAG
Found at i:5634725 original size:25 final size:27
Alignment explanation
Indices: 5634696--5634755 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
5634686 TTTTACTGTA
5634696 TTTATTATTACGA-ATATTT-T-AAATT
1 TTTATTATTA-GATATATTTATAAAATT
*
5634721 TTTATGATTAGATATATTTATAAAATT
1 TTTATTATTAGATATATTTATAAAATT
*
5634748 ATTATTAT
1 TTTATTAT
5634756 AATTATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.07
25 15 0.52
26 1 0.03
27 11 0.38
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (27 bp):
TTTATTATTAGATATATTTATAAAATT
Found at i:5635724 original size:5 final size:5
Alignment explanation
Indices: 5635706--5635737 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
5635696 AGGATTCAGT
5635706 TTTTC TTCTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC T
5635738 CTTCATCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:5635734 original size:15 final size:16
Alignment explanation
Indices: 5635706--5635761 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
5635696 AGGATTCAGT
5635706 TTTTCTTCTTCTTTTC
1 TTTTCTTCTTCTTTTC
5635722 TTTTCTT-TTCTTTTC
1 TTTTCTTCTTCTTTTC
* * *
5635737 TCTTCATCTAC-TTTC
1 TTTTCTTCTTCTTTTC
*
5635752 TCTTCTTCTT
1 TTTTCTTCTT
5635762 TTCCCCCATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 25 0.74
16 9 0.26
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTCTTCTTCTTTTC
Found at i:5639570 original size:40 final size:40
Alignment explanation
Indices: 5639511--5639874 Score: 602
Period size: 40 Copynumber: 9.1 Consensus size: 40
5639501 GAGCATTGGA
*
5639511 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
5639551 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
5639591 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
5639631 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
5639671 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
5639711 ATATATCCGGGCTAAGACCCGAAAGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
5639751 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
5639791 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
5639831 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
5639871 ATAT
1 ATAT
5639875 NNNNNNNNNN
Statistics
Matches: 310, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 310 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:5649163 original size:39 final size:39
Alignment explanation
Indices: 5648999--5649181 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
5648989 TTGAATGCTG
* * * * * * *
5648999 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
5649039 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
5649079 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
5649119 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
5649158 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
5649182 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:5649201 original size:79 final size:80
Alignment explanation
Indices: 5649035--5649216 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
5649025 GCTAAGTGAA
* * * *
5649035 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
5649099 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
5649115 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
5649179 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
5649194 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
5649217 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:5654657 original size:94 final size:93
Alignment explanation
Indices: 5654490--5654946 Score: 554
Period size: 94 Copynumber: 4.9 Consensus size: 93
5654480 TGATTTGTGC
* *
5654490 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACAT-TATGATAGCCAGTGTAAGACCATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-AGCA-TTCTATGATAGCCAGTGTAAGACCATGT
* * *
5654554 CTGGAACATGGCATCGGCATCA-AGACGAGG
64 CTGGGACATGGCATCGGCA-CAGAGATGAGT
*
5654584 GCTAGTGTAAGACATGTCTGGGACATGCATCAGTCATTCTATGATAGCCAGTGTAAGACCATGTC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAG-CATTCTATGATAGCCAGTGTAAGACCATGTC
*
5654649 TGGGACATGGCATCGGCACAGAGTTGAGT
65 TGGGACATGGCATCGGCACAGAGATGAGT
* * *
5654678 GCCAGTGTAAGACATGTCTGGGACATGCATCTGCAATACTATGATAGCTAGTGTAAGACCATGTC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGC-ATTCTATGATAGCCAGTGTAAGACCATGTC
*
5654743 TGGGACATGGCACCGGCACAGAGATGAGT
65 TGGGACATGGCATCGGCACAGAGATGAGT
* * * * *
5654772 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-CTCGACAGAGATAGCCAGTGTAAGA-CGTG
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCATTC--TA-TGATAGCCAGTGTAAGACCATG
* *
5654835 TCTGGGACA-CGCATTGGCTA-AGAGAT--GT
63 TCTGGGACATGGCATCGGC-ACAGAGATGAGT
* * *
5654863 GCTAGTGTAAGACAT-TCTGGGACATGCATCAGCACGCTTATATGAGAGCCAGTGTAAGACCATG
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCA---TTCTATGATAGCCAGTGTAAGACCATG
5654927 TCTGGGACATGGCATCGGCA
63 TCTGGGACATGGCATCGGCA
5654947 ATATATCCCA
Statistics
Matches: 316, Mismatches: 33, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
90 17 0.05
91 31 0.10
92 15 0.05
93 24 0.08
94 214 0.68
95 15 0.05
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (93 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCATTCTATGATAGCCAGTGTAAGACCATGTCT
GGGACATGGCATCGGCACAGAGATGAGT
Found at i:5654952 original size:47 final size:45
Alignment explanation
Indices: 5654490--5654952 Score: 366
Period size: 47 Copynumber: 9.9 Consensus size: 45
5654480 TGATTTGTGC
* *
5654490 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACAT-TATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCG-GCA-ATATATGAGA
* * * *
5654536 GCCAGTGTAAGACCATGTCTGGAACATGGCATCGGC-ATCAAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAAT--ATATGAGA
* * * * *
5654584 GCTAGTGTAAGACATGTCTGGGACATGCATCAGTCATTCTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GGCAATATATGAGA
* *
5654630 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGT-TGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-ATA-TATGAGA
* *
5654678 GCCAGTGTAAGACATGTCTGGGACATGCATCTGCAATACTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCAATA-TATGAGA
* * * * *
5654724 GCTAGTGTAAGACCATGTCTGGGACATGGCACCGGCACAGAGATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-ATATATGAGA
* *
5654772 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-CTCGACA-GAGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCAAT--ATATGAG--A
* * * * * *
5654819 GCCAGTGTAAGACGTGTCTGGGACACGCATTGGCTA-AGA-GATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCAATATATGA-GA
* * *
5654863 GCTAGTGTAAGACAT-TCTGGGACATGCATCAGCACGCTTATATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCA---ATATATGAGA
5654910 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAATATAT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAATATAT
5654953 CCCATGTTGA
Statistics
Matches: 330, Mismatches: 58, Indels: 57
0.74 0.13 0.13
Matches are distributed among these distances:
43 15 0.05
44 13 0.04
45 12 0.04
46 63 0.19
47 138 0.42
48 68 0.21
49 13 0.04
50 8 0.02
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCAATATATGAGA
Found at i:5665922 original size:40 final size:40
Alignment explanation
Indices: 5665875--5666120 Score: 402
Period size: 40 Copynumber: 6.2 Consensus size: 40
5665865 AACTAAGATT
* *
5665875 CGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
5665915 CGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
1 CGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
*
5665955 CGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
* * * * *
5665995 CAAAGGCATTTGTGCTAGTTACTATATCTGGACTAAGTCC
1 CGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
*
5666035 CGAAGGCATTTGTGCTAGTTGGTATATCCGGGCTAAATCC
1 CGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
*
5666075 CGAAGGCATTTGTGCTAGTTGCTGTATCCGGGCTAAATCC
1 CGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
5666115 CGAAGG
1 CGAAGG
5666121 TACTTGGGTT
Statistics
Matches: 191, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 191 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (40 bp):
CGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
Found at i:5669605 original size:40 final size:40
Alignment explanation
Indices: 5669575--5669746 Score: 199
Period size: 40 Copynumber: 4.3 Consensus size: 40
5669565 GCTACTCGTT
* *
5669575 CAAATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCA
*
5669615 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-TTATAGTAACTCGCA
* *
5669655 CAAATGCCTTCGGGACTTAACCCAGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCC-GGTTATAGTAACTCGCA
* * * * *
5669695 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGTTA-TAGTAACTCGCA
5669734 CAAATGCCTTCGG
1 CAAATGCCTTCGG
5669747 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
38 1 0.01
39 30 0.25
40 84 0.71
41 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCA
Found at i:5669687 original size:80 final size:79
Alignment explanation
Indices: 5669575--5669799 Score: 267
Period size: 80 Copynumber: 2.8 Consensus size: 79
5669565 GCTACTCGTT
* * * *
5669575 CAAATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
5669640 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* *
5669655 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
5669719 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * *
5669734 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAG-CCCGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
5669797 GGA
63 GGA
5669800 CATCATTCGA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.02
79 54 0.43
80 65 0.52
81 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:5669759 original size:119 final size:120
Alignment explanation
Indices: 5669577--5669792 Score: 287
Period size: 119 Copynumber: 1.8 Consensus size: 120
5669567 TACTCGTTCA
* *
5669577 AATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
5669642 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACC
* * **
5669697 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
5669759 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
5669793 GCCCGGACAT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.05
119 60 0.72
120 19 0.23
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACC
Found at i:5669783 original size:79 final size:79
Alignment explanation
Indices: 5669575--5669799 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 79
5669565 GCTACTCGTT
* * * * * * *
5669575 CAAATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCGG
*
5669640 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * *
5669655 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGG
*
5669719 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
** * * *
5669734 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAACCCAGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCG
5669798 GA
64 GA
5669800 CATCATTCGA
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
78 3 0.02
79 59 0.48
80 58 0.47
81 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:5674741 original size:47 final size:45
Alignment explanation
Indices: 5674627--5674987 Score: 194
Period size: 47 Copynumber: 7.7 Consensus size: 45
5674617 CGATTTGTGC
* *
5674627 GCCAGTGTAAGA-CATGTCTGGGACATCCATCTGCCACAT-TATGATA-
1 GCCAGTGTAAGACCATGTCTGGGACATGCATC-G--ACATCCA-GATAG
* *
5674673 GCCAGTCTAAGACCATATCTGGGACATGGCATCGACATCCAGACTAGG
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGACATCCAGA-TA-G
* * *
5674721 GCTAGTGTAAGA-CATGTCTGGGACATGCATCAGCCATACTATGATA-
1 GCCAGTGTAAGACCATGTCTGGGACATGCATC-GACAT-CCA-GATAG
* *
5674767 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CAGAGATGAG
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGACATC-CAGAT-AG
* *
5674814 TGCCAGTGTAAGA-CATGTCTGGGACATGCATCGGCCTCGACAGAGATA-
1 -GCCAGTGTAAGACCATGTCTGGGACATGCATCGACATC--C--AGATAG
* ** * *
5674862 GCCAGTGTAAGA-CGTGTCTTTGACATGCATC-AGC-T-AAGAGATG
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCGA-CATCCAGATA-G
* *
5674905 TGCTAGTGTAAGA-CATGTCTGGGACATGCATC-AGCA-CGCATATATGAG
1 -GCCAGTGTAAGACCATGTCTGGGACATGCATCGA-CATC-C--AGAT-AG
*
5674953 AGCCAGTTTAAGACCATGTCTGGGACATGGCATCG
1 -GCCAGTGTAAGACCATGTCTGGGACAT-GCATCG
5674988 GTAATATATC
Statistics
Matches: 253, Mismatches: 30, Indels: 59
0.74 0.09 0.17
Matches are distributed among these distances:
41 4 0.02
44 30 0.12
45 10 0.04
46 41 0.16
47 92 0.36
48 49 0.19
49 18 0.07
50 9 0.04
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACCATGTCTGGGACATGCATCGACATCCAGATAG
Found at i:5674791 original size:94 final size:92
Alignment explanation
Indices: 5674630--5674987 Score: 381
Period size: 94 Copynumber: 3.8 Consensus size: 92
5674620 TTTGTGCGCC
* * * * * *
5674630 AGTGTAAGACATGTCTGGGACATCCATCTGCCACATTATGATAGCCAGTCTAAGACCATATCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGATAGCCAGTGTAAGACCATGTCTGG
*
5674695 GACATGGCATCGACATCCAGACTAGGGCT
66 GACATGGCATCGACAT-CAGA-TAGTGCT
5674724 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGATAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGATAGCCAGTGTAAGACCATGTCTGG
* *
5674789 GACATGGCATCGGCACA-GAGATGAGTGCC
66 GACATGGCATC-G-ACATCAGAT-AGTGCT
* * *
5674818 AGTGTAAGACATGTCTGGGACATGCATCGGCC-TCGAC-AGAGATAGCCAGTGTAAGA-CGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAT--ACTA-TGATAGCCAGTGTAAGACCATGTC
** * *
5674880 TTTGACAT-GCATC-AGC-TAAGAGATGTGCT
63 TGGGACATGGCATCGA-CATCAGATA-GTGCT
* *
5674909 AGTGTAAGACATGTCTGGGACATGCATCAGCACGCATA-TATGAGAGCCAGTTTAAGACCATGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAG--C-CATACTATGATAGCCAGTGTAAGACCATGTC
5674973 TGGGACATGGCATCG
63 TGGGACATGGCATCG
5674988 GTAATATATC
Statistics
Matches: 223, Mismatches: 24, Indels: 33
0.80 0.09 0.12
Matches are distributed among these distances:
90 2 0.01
91 37 0.17
92 14 0.06
93 21 0.09
94 126 0.57
95 20 0.09
96 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGATAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGACATCAGATAGTGCT
Found at i:5674880 original size:141 final size:136
Alignment explanation
Indices: 5674627--5674988 Score: 374
Period size: 141 Copynumber: 2.6 Consensus size: 136
5674617 CGATTTGTGC
* * * *
5674627 GCCAGTGTAAGACATGTCTGGGACATCCATCTGCCACATTATGA-TAGCCAGTCTAAGACCATAT
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GGCACAATATGAGT-GCCAGTCTAAGACCATGT
* * *
5674691 CTGGGACATGGCATCGACATCCAGACTAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCC
64 CTGGGACATGGCATCGGCATCCAGAATA-GGCCAGTGTAAGACATGTCTGGGACATGCATCAG-C
**
5674756 ATACTATGAT-A
127 -TAAGA-GATGA
* *
5674767 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGATGAGTGCCAGTGTAAGA-CATG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACA-ATATGAGTGCCAGTCTAAGACCATG
* * **
5674831 TCTGGGACAT-GCATCGGCCTCGACAGAGATA-GCCAGTGTAAGACGTGTCTTTGACATGCATCA
63 TCTGGGACATGGCATCGGCATC--CAGA-ATAGGCCAGTGTAAGACATGTCTGGGACATGCATCA
*
5674894 GCTAAGAGATGT
125 GCTAAGAGATGA
* * * *
5674906 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCATATATGAGAGCCAGTTTAAGACCATG
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCA--CA-ATATGAGTGCCAGTCTAAGACCATG
5674971 TCTGGGACATGGCATCGG
63 TCTGGGACATGGCATCGG
5674989 TAATATATCC
Statistics
Matches: 188, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
137 8 0.04
138 17 0.09
139 33 0.18
140 36 0.19
141 68 0.36
142 23 0.12
143 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (136 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAATATGAGTGCCAGTCTAAGACCATGTCT
GGGACATGGCATCGGCATCCAGAATAGGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTAAG
AGATGA
Found at i:5677970 original size:24 final size:24
Alignment explanation
Indices: 5677939--5678082 Score: 91
Period size: 24 Copynumber: 6.0 Consensus size: 24
5677929 TACCAATATA
* *
5677939 TCAGCTCGTAAGAGTTTACTGTTT
1 TCAGCTCGTAAGAGCTTACTGTTC
* * *
5677963 TCATCTCGTTAGAGCTTATTGTTC
1 TCAGCTCGTAAGAGCTTACTGTTC
*
5677987 TCAGCTCGTATGAGCTTACTGGTT-
1 TCAGCTCGTAAGAGCTTACT-GTTC
** * *
5678011 T-AGCTTATCAGAGCTTACCGTT-
1 TCAGCTCGTAAGAGCTTACTGTTC
* *
5678033 TCAGCTC-AATAGAGCTTACTGTCC
1 TCAGCTCGTA-AGAGCTTACTGTTC
*
5678057 ATAAGCTCAG-AAGGAGCTTACTGTTC
1 -TCAGCTC-GTAA-GAGCTTACTGTTC
5678083 ATAGCTCAAA
Statistics
Matches: 91, Mismatches: 21, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
22 4 0.04
23 28 0.31
24 36 0.40
25 10 0.11
26 13 0.14
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (24 bp):
TCAGCTCGTAAGAGCTTACTGTTC
Found at i:5678024 original size:23 final size:24
Alignment explanation
Indices: 5677949--5678053 Score: 67
Period size: 23 Copynumber: 4.5 Consensus size: 24
5677939 TCAGCTCGTA
* * * **
5677949 AGAGTTTACTGTTTTCATCTCGTT
1 AGAGCTTACTGGTTTCAGCTCAAT
* *
5677973 AGAGCTTA-TTGTTCTCAGCTC-GT
1 AGAGCTTACTGGTT-TCAGCTCAAT
*
5677996 ATGAGCTTACTGGTTT-AGCT-TAT
1 A-GAGCTTACTGGTTTCAGCTCAAT
*
5678019 CAGAGCTTAC-CGTTTCAGCTCAAT
1 -AGAGCTTACTGGTTTCAGCTCAAT
5678043 AGAGCTTACTG
1 AGAGCTTACTG
5678054 TCCATAAGCT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
22 4 0.06
23 31 0.49
24 24 0.38
25 4 0.06
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
AGAGCTTACTGGTTTCAGCTCAAT
Found at i:5678160 original size:27 final size:27
Alignment explanation
Indices: 5678122--5678174 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
5678112 AATTGACAGA
5678122 GTACTGATGTATATCACCCGAGTATCT
1 GTACTGATGTATATCACCCGAGTATCT
5678149 GTACTGATGTATATCACCCGAGTATC
1 GTACTGATGTATATCACCCGAGTATC
5678175 CTTTGAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (27 bp):
GTACTGATGTATATCACCCGAGTATCT
Found at i:5687672 original size:43 final size:42
Alignment explanation
Indices: 5687526--5687673 Score: 140
Period size: 43 Copynumber: 3.5 Consensus size: 42
5687516 TGAGACAACG
* *
5687526 TGTAAGACCGTGTCTGGGACACAGGCTTCG-ATTGAGATTTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCGTATTGA-A-TTACA
** * *
5687569 -GATAAGACCATGTCTGGGACATC-GGCATCGTATTTTATTTCG
1 TG-TAAGACCATGTCTGGGACA-CAGGCATCGTATTGAATTACA
* * *
5687611 TGTAAGAACTTGTCTGGGACAGAGGCATCGATATTGAATTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCG-TATTGAATTACA
*
5687654 TGTAAGACCACGTCTGGGAC
1 TGTAAGACCATGTCTGGGAC
5687674 GTCAACATTG
Statistics
Matches: 83, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
42 28 0.34
43 51 0.61
44 4 0.05
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACACAGGCATCGTATTGAATTACA
Found at i:5694081 original size:25 final size:25
Alignment explanation
Indices: 5694008--5694082 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
5693998 ATACATGTAT
* *
5694008 GCTCATATGAGCT-ATGAATAGGTAT
1 GCTCATACGAGCTGA-GAATAGGTAA
*
5694033 GCTC-TCACGAGCTGTA-AATCGGTAA
1 GCTCAT-ACGAGCTG-AGAATAGGTAA
*
5694058 GCTCATACGAGCTGAGAATTGGTAA
1 GCTCATACGAGCTGAGAATAGGTAA
5694083 CCCTAATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 2 0.05
25 37 0.90
26 1 0.02
27 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTGAGAATAGGTAA
Found at i:5695162 original size:27 final size:26
Alignment explanation
Indices: 5695116--5695221 Score: 122
Period size: 27 Copynumber: 4.0 Consensus size: 26
5695106 CATGGCTGCT
* * *
5695116 AGAACAGATATTCTGACAGAGTCACC
1 AGAACAGATATTGTGGCAGAGCCACC
5695142 AGATACAGATATTGTGGCAGAGCCACC
1 AGA-ACAGATATTGTGGCAGAGCCACC
*
5695169 AGAACAGATATTTGTGGCATAGCCACC
1 AGAACAGATA-TTGTGGCAGAGCCACC
* * *
5695196 AGAAATAGATAATGTGGCAAAGCCAC
1 AG-AACAGATATTGTGGCAGAGCCAC
5695222 TTAACAGAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.14
27 53 0.76
28 7 0.10
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (26 bp):
AGAACAGATATTGTGGCAGAGCCACC
Found at i:5695577 original size:27 final size:26
Alignment explanation
Indices: 5695525--5695603 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 26
5695515 TCGATCGGTC
* * *
5695525 AACAGATATTGTGACAAAGTCGCCAG
1 AACAGATATTGTGGCAAAGCCACCAG
* *
5695551 ATATAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAAAGCCACCAG
*
5695578 AACAGATATTTGTGGCATAGCCACCA
1 AACAGATA-TTGTGGCAAAGCCACCA
5695604 AAACGCTTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 7 0.16
27 37 0.84
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
AACAGATATTGTGGCAAAGCCACCAG
Found at i:5695925 original size:27 final size:27
Alignment explanation
Indices: 5695831--5695945 Score: 158
Period size: 27 Copynumber: 4.3 Consensus size: 27
5695821 GAGGTAAAAT
* * *
5695831 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
5695858 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
5695885 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
5695912 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
5695939 AGTAATT
1 GGTAATT
5695946 TGGTAAACGA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:5719904 original size:18 final size:17
Alignment explanation
Indices: 5719877--5719911 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5719867 NNNNNNTTAA
*
5719877 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5719895 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5719912 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5720001 original size:18 final size:17
Alignment explanation
Indices: 5719978--5720014 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
5719968 AAATATTATT
5719978 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
5719994 AAATATATGATTTAATA
1 AAATATATGATTTAATA
5720011 AAAT
1 AAAT
5720015 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:5720086 original size:25 final size:26
Alignment explanation
Indices: 5720058--5720107 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
5720048 ATAATAATAT
5720058 ATGA-TACTATAAAATATAATTTAAC
1 ATGATTACTATAAAATATAATTTAAC
* * *
5720083 ATGATTATTATTAAATATATTTTAA
1 ATGATTACTATAAAATATAATTTAA
5720108 TTAAAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (26 bp):
ATGATTACTATAAAATATAATTTAAC
Found at i:5720118 original size:18 final size:17
Alignment explanation
Indices: 5720095--5720131 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
5720085 GATTATTATT
5720095 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
5720111 AAATATATGATTTAATA
1 AAATATATGATTTAATA
5720128 AAAT
1 AAAT
5720132 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:5720134 original size:28 final size:28
Alignment explanation
Indices: 5719986--5720135 Score: 76
Period size: 31 Copynumber: 5.2 Consensus size: 28
5719976 TTAAATATAT
5719986 TTTAATTAAAATATATGATTTAATAAAA
1 TTTAATTAAAATATATGATTTAATAAAA
* * *
5720014 -TT-CTTAATAATCA-AT-ATTCTTATATGAA
1 TTTAATTAA-AAT-ATATGATT-TAATA-AAA
* *
5720042 TTTCATATAATAATATATGATACT-ATAAAA
1 TTTAAT-TAA-AATATATGAT-TTAATAAAA
* * * * * *
5720072 TATAATTTAACATGATTATTATTAAATATAT
1 TTTAA-TTAAAAT-A-TATGATTTAATAAAA
5720103 TTTAATTAAAATATATGATTTAATAAAA
1 TTTAATTAAAATATATGATTTAATAAAA
5720131 TTTAA
1 TTTAA
5720136 AATAATTATT
Statistics
Matches: 88, Mismatches: 20, Indels: 28
0.65 0.15 0.21
Matches are distributed among these distances:
26 7 0.08
27 11 0.12
28 19 0.22
29 5 0.06
30 17 0.19
31 26 0.30
32 3 0.03
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (28 bp):
TTTAATTAAAATATATGATTTAATAAAA
Found at i:5720182 original size:47 final size:46
Alignment explanation
Indices: 5720114--5720281 Score: 161
Period size: 47 Copynumber: 3.7 Consensus size: 46
5720104 TTAATTAAAA
*
5720114 TATATG-ATTTAATAAAATTTAAAATAATTATTACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATTA-TAATAAATTTTCT
* * *
5720161 TATTTGAATTTGTATAATTTAAAATAATTATTAT--TAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT
* * *
5720206 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT
5720252 TATATGAATTTATATAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
5720282 ATATTAAATA
Statistics
Matches: 96, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
43 3 0.03
44 21 0.22
45 10 0.10
46 9 0.09
47 46 0.48
48 7 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATTATAATAAATTTTCT
Found at i:5720223 original size:44 final size:43
Alignment explanation
Indices: 5720173--5720315 Score: 139
Period size: 44 Copynumber: 3.2 Consensus size: 43
5720163 TTTGAATTTG
5720173 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
* * * *
5720217 TATAATTTCATAA-AATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-AT--TAAATATAAT-TTA-AT-AATATA
*
5720264 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
5720308 TATAATTT
1 TATAATTT
5720316 TATAAATTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
43 3 0.04
44 31 0.39
45 10 0.13
46 10 0.13
47 22 0.28
48 3 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (43 bp):
TATAATTTAAAATAATTATTATTAAATATAATTTAATAATATA
Found at i:5720250 original size:91 final size:91
Alignment explanation
Indices: 5720139--5720354 Score: 342
Period size: 91 Copynumber: 2.4 Consensus size: 91
5720129 AATTTAAAAT
* * * * *
5720139 AATTATTACTAATAAATTTTCTTATTTGAATTTGTATAATTTAAAATAATTATTATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
5720204 TTTAATAATAATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
*
5720230 AATTCTTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
* *
5720295 TTTAATAATGATATATAATTTTATAA
66 TTTAATAATAATATATAATTTCATAA
* *
5720321 ATTTCTTAATAATAAATATTCTTATATGAATTTA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTA
5720355 CTAAAATCAT
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 114 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (91 bp):
AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
TTTAATAATAATATATAATTTCATAA
Found at i:5720337 original size:47 final size:45
Alignment explanation
Indices: 5720195--5720339 Score: 136
Period size: 47 Copynumber: 3.2 Consensus size: 45
5720185 TAATTATTAT
* *
5720195 TAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAA
1 TAAATATAATTTAATAAT-ATATATAATTTTAT-AAATTCTTAATAA
* * ** *
5720242 TAAAT-T-TTCTTATATGAATTTATATAA-TTTA-AAATAATTAATAT
1 TAAATATAAT-TTA-AT-AATATATATAATTTTATAAATTCTTAATAA
5720286 TAAATATAATTTAATAATGATATATAATTTTATAAATTTCTTAATAA
1 TAAATATAATTTAATAAT-ATATATAATTTTATAAA-TTCTTAATAA
5720333 TAAATAT
1 TAAATAT
5720340 TCTTATATGA
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
43 3 0.04
44 23 0.30
45 9 0.12
46 11 0.14
47 28 0.36
48 3 0.04
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (45 bp):
TAAATATAATTTAATAATATATATAATTTTATAAATTCTTAATAA
Found at i:5726792 original size:40 final size:40
Alignment explanation
Indices: 5726420--5726782 Score: 500
Period size: 40 Copynumber: 9.1 Consensus size: 40
5726410 AACCCAAGTA
* *
5726420 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
5726459 CCTTCGGGACTTAACCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
5726499 CCTTCGGGACTTAGCCCGAATGTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* * *
5726539 CCTTTGGGACTTAGCCCTGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
5726579 CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
** * *
5726619 CCTTC-GGATCTTATTCCGGTTATAGTAACTAGCACAAATG
1 CCTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATG
*
5726659 CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
** * *
5726699 CCTTC-GGATCTTATTCCGGTTATAGTAACTAGCACAAATG
1 CCTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATG
5726739 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
5726779 CCTT
1 CCTT
5726783 TGGATCTTAG
Statistics
Matches: 282, Mismatches: 36, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
39 18 0.06
40 257 0.91
41 7 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:5726797 original size:80 final size:80
Alignment explanation
Indices: 5726420--5726801 Score: 554
Period size: 80 Copynumber: 4.8 Consensus size: 80
5726410 AACCCAAGTA
* * * ** *
5726420 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATGCCTTC-GGATCTTAGTCCGGTTATA
* *
5726483 ATCACTAGCACAAATG
65 GTAACTAGCACAAATG
* * * * * * *
5726499 CCTTCGGGACTTAGCCCGAATGTAGTCACTAGCACAAATGCCTTTGGGA-CTTAGCCCTGATATA
1 CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATGCC-TTCGGATCTTAGTCCGGTTATA
5726563 GTAACTAGCACAAATG
65 GTAACTAGCACAAATG
*
5726579 CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATGCCTTCGGATCTTATTCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTATAG
5726644 TAACTAGCACAAATG
66 TAACTAGCACAAATG
*
5726659 CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATGCCTTCGGATCTTATTCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTATAG
5726724 TAACTAGCACAAATG
66 TAACTAGCACAAATG
* *
5726739 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTTGGATCTTAGTCCGGTTAT
1 CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTAT
5726802 CATCCGAATA
Statistics
Matches: 278, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
79 18 0.06
80 258 0.93
81 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCCACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTATAG
TAACTAGCACAAATG
Found at i:5727827 original size:24 final size:24
Alignment explanation
Indices: 5727783--5727828 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
5727773 ACAATTTTAG
* *
5727783 AACATCTAAACGACACTTGTTCAA
1 AACATCTAAACAACACATGTTCAA
5727807 AACAT-TAAACAACTACATGTTC
1 AACATCTAAACAAC-ACATGTTC
5727829 GACTACTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (24 bp):
AACATCTAAACAACACATGTTCAA
Found at i:5728193 original size:13 final size:13
Alignment explanation
Indices: 5728177--5728204 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5728167 TTTATTATTT
5728177 TTAACACAAAATA
1 TTAACACAAAATA
5728190 TTAACACAAAATA
1 TTAACACAAAATA
5728203 TT
1 TT
5728205 TATAATATGT
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:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAACACAAAATA
Found at i:5728987 original size:28 final size:28
Alignment explanation
Indices: 5728956--5729167 Score: 130
Period size: 28 Copynumber: 7.5 Consensus size: 28
5728946 GTGAACATAG
*
5728956 GCACTGTGTGTGTGAGTTTCGTAACCGA
1 GCACTGTGTGTGCGAGTTTCGTAACCGA
*
5728984 GCACTGTGTGTGCAAGATCGGTT-GTTAA--G-
1 GCACTGTGTGTGC--GA--GTTTCG-TAACCGA
* * *
5729013 GCACTGTGTGTGCAAGTTCCGTAACCAA
1 GCACTGTGTGTGCGAGTTTCGTAACCGA
* ****
5729041 GCACTGTGTGTGCGAG-ATCGGTTGTTGA
1 GCACTGTGTGTGCGAGTTTC-GTAACCGA
* *
5729069 GGCACTGTGTGTGTGAGTTCCGTAACCGA
1 -GCACTGTGTGTGCGAGTTTCGTAACCGA
* ****
5729098 GCACTGTGTGTGCGAG-ATCGGTTGTTGA
1 GCACTGTGTGTGCGAGTTTC-GTAACCGA
* *
5729126 GGCACTGTGTGTGCGAGTTCCGTAACCAA
1 -GCACTGTGTGTGCGAGTTTCGTAACCGA
5729155 GCACTGTGTGTGC
1 GCACTGTGTGTGC
5729168 AAGATCGGTT
Statistics
Matches: 134, Mismatches: 35, Indels: 30
0.67 0.18 0.15
Matches are distributed among these distances:
25 5 0.04
26 1 0.01
27 3 0.02
28 62 0.46
29 51 0.38
30 5 0.04
31 1 0.01
32 6 0.04
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (28 bp):
GCACTGTGTGTGCGAGTTTCGTAACCGA
Found at i:5729023 original size:29 final size:28
Alignment explanation
Indices: 5728983--5729180 Score: 144
Period size: 29 Copynumber: 7.0 Consensus size: 28
5728973 TTCGTAACCG
*
5728983 AGCACTGTGTGTGCAAGATCGGTTGTTA
1 AGCACTGTGTGTGCGAGATCGGTTGTTA
* * * ****
5729011 AGGCACTGTGTGTGCAAGTTCCGTAACCA
1 A-GCACTGTGTGTGCGAGATCGGTTGTTA
5729040 AGCACTGTGTGTGCGAGATCGGTTGTTGA
1 AGCACTGTGTGTGCGAGATCGGTTGTT-A
* * * * *****
5729069 GGCACTGTGTGTGTGAGTTCCGTAACCG
1 AGCACTGTGTGTGCGAGATCGGTTGTTA
5729097 AGCACTGTGTGTGCGAGATCGGTTGTTGA
1 AGCACTGTGTGTGCGAGATCGGTTGTT-A
* * * ****
5729126 GGCACTGTGTGTGCGAGTTCCGTAACCA
1 AGCACTGTGTGTGCGAGATCGGTTGTTA
*
5729154 AGCACTGTGTGTGCAAGATCGGTTGTT
1 AGCACTGTGTGTGCGAGATCGGTTGTT
5729181 GGGGAACTAA
Statistics
Matches: 121, Mismatches: 46, Indels: 6
0.70 0.27 0.03
Matches are distributed among these distances:
28 59 0.49
29 62 0.51
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (28 bp):
AGCACTGTGTGTGCGAGATCGGTTGTTA
Found at i:5729195 original size:57 final size:57
Alignment explanation
Indices: 5728954--5729181 Score: 375
Period size: 57 Copynumber: 4.0 Consensus size: 57
5728944 AAGTGAACAT
* * * *
5728954 AGGCACTGTGTGTGTGAGTTTCGTAACCGAGCACTGTGTGTGCAAGATCGGTTGTTA
1 AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTG
* *
5729011 AGGCACTGTGTGTGCAAGTTCCGTAACCAAGCACTGTGTGTGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTG
* * *
5729068 AGGCACTGTGTGTGTGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTG
5729125 AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTG
5729182 GGGAACTAAG
Statistics
Matches: 159, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 159 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (57 bp):
AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTG
Found at i:5734166 original size:28 final size:28
Alignment explanation
Indices: 5734135--5734198 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 28
5734125 GCAATCAAAT
*
5734135 ATGGTACTCAGTGCACGAAATATTGAGA
1 ATGGCACTCAGTGCACGAAATATTGAGA
* ** * *
5734163 ATGGCACTTAGTGTGCGAGATATTTAGA
1 ATGGCACTCAGTGCACGAAATATTGAGA
*
5734191 ATGACACT
1 ATGGCACT
5734199 TAATGTGCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (28 bp):
ATGGCACTCAGTGCACGAAATATTGAGA
Found at i:5734213 original size:28 final size:28
Alignment explanation
Indices: 5734152--5734213 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
5734142 TCAGTGCACG
* * *
5734152 AAATATTGAGAATGGCACTTAGTGTGCG
1 AAATATTGAGAATGACACTTAATGTGCA
* *
5734180 AGATATTTAGAATGACACTTAATGTGCA
1 AAATATTGAGAATGACACTTAATGTGCA
5734208 AAATAT
1 AAATAT
5734214 CGAATGATTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.31
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAATGTGCA
Found at i:5741074 original size:21 final size:21
Alignment explanation
Indices: 5741042--5741092 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
5741032 ATTACATTAA
* *
5741042 AAATTCA-GAAAATTTTTATC
1 AAATTCATAAAAAATTTTATC
5741062 AAATTCATAAAAAATTTTATC
1 AAATTCATAAAAAATTTTATC
5741083 AAATTCATAA
1 AAATTCATAA
5741093 CGACATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATTCATAAAAAATTTTATC
Found at i:5741635 original size:5 final size:5
Alignment explanation
Indices: 5741625--5741653 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5741615 CAAGTAATTT
5741625 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5741654 TATATGCATA
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:5743211 original size:21 final size:21
Alignment explanation
Indices: 5743179--5743229 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
5743169 ATTACATTAA
* *
5743179 AAATTCA-GAAAATTTTTATC
1 AAATTCATAAAAAATTTTATC
5743199 AAATTCATAAAAAATTTTATC
1 AAATTCATAAAAAATTTTATC
5743220 AAATTCATAA
1 AAATTCATAA
5743230 CGACATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATTCATAAAAAATTTTATC
Found at i:5743772 original size:5 final size:5
Alignment explanation
Indices: 5743762--5743790 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5743752 CAAGTAATTT
5743762 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5743791 TATATGCATA
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:5744710 original size:18 final size:18
Alignment explanation
Indices: 5744687--5744722 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5744677 CATAGCATCA
5744687 ATAGGCATTCAAACCAAT
1 ATAGGCATTCAAACCAAT
5744705 ATAGGCATTCAAACCAAT
1 ATAGGCATTCAAACCAAT
5744723 CTCATCTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (18 bp):
ATAGGCATTCAAACCAAT
Found at i:5747614 original size:29 final size:29
Alignment explanation
Indices: 5747551--5747618 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
5747541 TAATCAACCG
5747551 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
5747580 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
5747609 CGCACACTTA
1 CGCACACTTA
5747619 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:5747730 original size:174 final size:174
Alignment explanation
Indices: 5747440--5747767 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
5747430 AACTCAAGGT
* *
5747440 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
5747505 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
5747570 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
5747614 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
5747679 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
5747744 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
5747768 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:5747759 original size:29 final size:30
Alignment explanation
Indices: 5747720--5747798 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
5747710 CTTAATAATC
5747720 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
5747750 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
5747779 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
5747799 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:5749853 original size:19 final size:19
Alignment explanation
Indices: 5749829--5749868 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5749819 TGTGTTATCA
*
5749829 TAAATTCATAGGCATAACT
1 TAAATTCATAGACATAACT
**
5749848 TAAATTTGTAGACATAACT
1 TAAATTCATAGACATAACT
5749867 TA
1 TA
5749869 CACAATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGACATAACT
Found at i:5750639 original size:16 final size:18
Alignment explanation
Indices: 5750618--5750651 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5750608 CAAATTCACC
5750618 TTATTC-AATCA-TCAAA
1 TTATTCAAATCAGTCAAA
5750634 TTATTCAAATCAGTCAAA
1 TTATTCAAATCAGTCAAA
5750652 AAAATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (18 bp):
TTATTCAAATCAGTCAAA
Found at i:5752908 original size:22 final size:22
Alignment explanation
Indices: 5752883--5752924 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5752873 ATAGGTTACG
*
5752883 GTACTATTTTCTCATAGCTTCT
1 GTACCATTTTCTCATAGCTTCT
5752905 GTACCATTTTCTCATAGCTT
1 GTACCATTTTCTCATAGCTT
5752925 TTTTGGGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.48
Consensus pattern (22 bp):
GTACCATTTTCTCATAGCTTCT
Found at i:5755063 original size:42 final size:41
Alignment explanation
Indices: 5755004--5755158 Score: 175
Period size: 42 Copynumber: 3.7 Consensus size: 41
5754994 CTAAGTCTAT
* * * *
5755004 GTGTAAGACCGTATCTGGGATATGGCATCAATATGGGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATAAGAGA-TTC
*
5755046 GTGTAAGACCATATCTGGGATATGGCATCGATAAGACATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATAAGAGA-TTC
* * * * *
5755088 GTGTAAGACAATAGCTAGGCTATTGGCATCGATACGAGATTAC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATAAGAGATT-C
*
5755131 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
5755159 TGGCATGGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 62 0.66
43 32 0.34
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (41 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTC
Found at i:5759334 original size:40 final size:40
Alignment explanation
Indices: 5759201--5759327 Score: 236
Period size: 40 Copynumber: 3.2 Consensus size: 40
5759191 AACCCAAGTA
5759201 CCTTCGGGATTTAGCCCGGATATAGCAACTAGCACAAATG
1 CCTTCGGGATTTAGCCCGGATATAGCAACTAGCACAAATG
5759241 CCTTCGGGATTTAGCCCGGATATAGCAACTAGCACAAATG
1 CCTTCGGGATTTAGCCCGGATATAGCAACTAGCACAAATG
* *
5759281 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGATTTAGCCCGGATATAGCAACTAGCACAAATG
5759321 CCTTCGG
1 CCTTCGG
5759328 ATCTTAGTTC
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGATTTAGCCCGGATATAGCAACTAGCACAAATG
Found at i:5760141 original size:19 final size:19
Alignment explanation
Indices: 5760089--5760144 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
5760079 ATAAGTATAA
*
5760089 GTTCAATATAAACTCACAT
1 GTTCAATATAAATTCACAT
* *
5760108 G-T-AA-CTAAATACACAT
1 GTTCAATATAAATTCACAT
5760124 GTTCAATATAAATTCACAT
1 GTTCAATATAAATTCACAT
5760143 GT
1 GT
5760145 AATCGAATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.34
17 3 0.10
18 3 0.10
19 13 0.45
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (19 bp):
GTTCAATATAAATTCACAT
Found at i:5761636 original size:28 final size:25
Alignment explanation
Indices: 5761612--5761663 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 25
5761602 AGTACTGTGT
5761612 TAGTGGCTTTGCCACGTAATTACTGCTC
1 TAGTGGCTTTGCCACGT--TTACTG-TC
*
5761640 TGGTGGCTTTGCCACGTTTACTGT
1 TAGTGGCTTTGCCACGTTTACTGT
5761664 TATTAGTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 1 0.04
26 6 0.26
28 16 0.70
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.38
Consensus pattern (25 bp):
TAGTGGCTTTGCCACGTTTACTGTC
Found at i:5761842 original size:28 final size:27
Alignment explanation
Indices: 5761811--5761863 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
5761801 ATACTAAATT
* *
5761811 GGGCTTAGGCCCATACTGTTACTGTATA
1 GGGCTAAGGCCCAGACTG-TACTGTATA
*
5761839 GGGCTAAGGCCGAGACTGTACTGTA
1 GGGCTAAGGCCCAGACTGTACTGTA
5761864 CTGAATAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (27 bp):
GGGCTAAGGCCCAGACTGTACTGTATA
Found at i:5761872 original size:32 final size:33
Alignment explanation
Indices: 5761824--5761887 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
5761814 CTTAGGCCCA
*
5761824 TACTGTTACTGTATAGGGCTAAGGCCGAGACTG
1 TACTGTTACTGAATAGGGCTAAGGCCGAGACTG
* *
5761857 TACTG-TACTGAATAGGGCTCAGGCCTAGACT
1 TACTGTTACTGAATAGGGCTAAGGCCGAGACT
5761888 ATTACTGCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (33 bp):
TACTGTTACTGAATAGGGCTAAGGCCGAGACTG
Found at i:5767407 original size:43 final size:42
Alignment explanation
Indices: 5767285--5767435 Score: 187
Period size: 42 Copynumber: 3.6 Consensus size: 42
5767275 TAAGTCTATG
** * * *
5767285 TGTAAGACCATATCTGGGATATGATATCAATATGAGACTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTTCA
*
5767327 TGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTTCA
* * *
5767369 TGTAAGACCATAGCT-GGACTATTGGCATCGATACGAGATTACA
1 TGTAAGACCATATCTGGGA-TA-TGGCATCGATAAGAGATTTCA
*
5767412 TGTAAGACCATATCTGGTATATGG
1 TGTAAGACCATATCTGGGATATGG
5767436 TATTGGTATG
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 3 0.03
42 55 0.59
43 34 0.36
44 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTTCA
Found at i:5773479 original size:19 final size:19
Alignment explanation
Indices: 5773435--5773481 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
5773425 AAAACTTTGG
*
5773435 AAAAATATTAGAATACATA
1 AAAAATTTTAGAATACATA
5773454 AAAAATTTTAGCAA-ACATA
1 AAAAATTTTAG-AATACATA
5773473 AAAAATTTT
1 AAAAATTTT
5773482 TAAAATACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAAATTTTAGAATACATA
Found at i:5784980 original size:23 final size:22
Alignment explanation
Indices: 5784938--5784982 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5784928 TATTTATTTA
5784938 TTTTTATATTAAATAAATATAAT
1 TTTTTATATTAAAT-AATATAAT
5784961 TTTTTATATATACAAT-ATATAA
1 TTTTTATAT-TA-AATAATATAA
5784983 ATATAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 15 0.75
24 2 0.10
25 3 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTTATATTAAATAATATAAT
Found at i:5785010 original size:12 final size:12
Alignment explanation
Indices: 5784995--5785020 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5784985 ATAAAATTTG
5784995 TTATATTAATAA
1 TTATATTAATAA
5785007 TTATATTAATAA
1 TTATATTAATAA
5785019 TT
1 TT
5785021 TTAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTATATTAATAA
Found at i:5785093 original size:29 final size:27
Alignment explanation
Indices: 5785040--5785116 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 27
5785030 TTAATCAAAT
5785040 TAAAATTTTATATATAAAATTATATAAAAA
1 TAAAA-TTTATATAT--AATTATATAAAAA
* *
5785070 TAAAATTTATATATAATTAGATATTAAAT
1 TAAAATTTATATATAATT--ATATAAAAA
* *
5785099 TATAATTCATATATAATT
1 TAAAATTTATATATAATT
5785117 TTAATATTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.10
29 32 0.78
30 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
TAAAATTTATATATAATTATATAAAAA
Found at i:5786051 original size:17 final size:17
Alignment explanation
Indices: 5786031--5786072 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5786021 TTTGAAGAGT
5786031 TTTTATTTTTTTCATAA
1 TTTTATTTTTTTCATAA
*
5786048 TTTT-TTATTTTTCATAT
1 TTTTATT-TTTTTCATAA
5786065 TTTTATTT
1 TTTTATTT
5786073 AAAATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTTTTTCATAA
Found at i:5786069 original size:15 final size:17
Alignment explanation
Indices: 5786038--5786072 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
5786028 AGTTTTTATT
5786038 TTTTTCATAATTTTTTA
1 TTTTTCATAATTTTTTA
5786055 TTTTTCAT-A-TTTTTA
1 TTTTTCATAATTTTTTA
5786070 TTT
1 TTT
5786073 AAAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCATAATTTTTTA
Found at i:5786872 original size:64 final size:64
Alignment explanation
Indices: 5786771--5786904 Score: 259
Period size: 64 Copynumber: 2.1 Consensus size: 64
5786761 TTTCTCACCA
*
5786771 AAATTTTTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
1 AAATTATTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
5786835 AAATTATTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
1 AAATTATTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
5786899 AAATTA
1 AAATTA
5786905 ATGTATATTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (64 bp):
AAATTATTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
Found at i:5791514 original size:20 final size:20
Alignment explanation
Indices: 5791489--5791526 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5791479 GAAACATATA
5791489 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
5791509 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
5791527 TAGTTCCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:5791768 original size:9 final size:9
Alignment explanation
Indices: 5791754--5791780 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5791744 ACATGCAATA
5791754 TTAAAGTAT
1 TTAAAGTAT
5791763 TTAAAGTAT
1 TTAAAGTAT
5791772 TTAAAGTAT
1 TTAAAGTAT
5791781 GGTACATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (9 bp):
TTAAAGTAT
Found at i:5795241 original size:40 final size:40
Alignment explanation
Indices: 5795197--5795272 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
5795187 CGGCTAAGAA
* *
5795197 TGGCACTTAGTGTGCGGTTTGAAATAGCTTCGGCTAAATG
1 TGGCACTTAGTGTACGATTTGAAATAGCTTCGGCTAAATG
* *
5795237 TGGCACTTGGTGTACGATTTGAGATAGCTTCGGCTA
1 TGGCACTTAGTGTACGATTTGAAATAGCTTCGGCTA
5795273 TATATGCGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (40 bp):
TGGCACTTAGTGTACGATTTGAAATAGCTTCGGCTAAATG
Found at i:5795314 original size:28 final size:28
Alignment explanation
Indices: 5795277--5795345 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
5795267 CGGCTATATA
* * *
5795277 TGCGAAATATTGAGAATGGCACTTGGTG
1 TGCGAGATATTGAGAATGGAACTTAGTG
* *
5795305 TGCGAGATATTTAGTATGGAACTTAGTG
1 TGCGAGATATTGAGAATGGAACTTAGTG
*
5795333 TGTGAGATATTGA
1 TGCGAGATATTGA
5795346 AGATGCAACG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.29, C:0.07, G:0.30, T:0.33
Consensus pattern (28 bp):
TGCGAGATATTGAGAATGGAACTTAGTG
Found at i:5803413 original size:56 final size:56
Alignment explanation
Indices: 5803327--5803558 Score: 446
Period size: 56 Copynumber: 4.1 Consensus size: 56
5803317 ACAAGGGATG
5803327 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5803383 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5803439 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
5803495 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5803551 ATGGGCAA
1 ATGGGCAA
5803559 TAAACTAATA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 174 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:5813895 original size:27 final size:27
Alignment explanation
Indices: 5813857--5813919 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
5813847 TGTCTCCAGG
5813857 CCGTGTCTCTCATGTTGAGACACACGA
1 CCGTGTCTCTCATGTTGAGACACACGA
5813884 CCGTGTCTCTCATGTTGAGACACACGA
1 CCGTGTCTCTCATGTTGAGACACACGA
*
5813911 TCGTGTCTC
1 CCGTGTCTC
5813920 AGCCCGTGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.29
Consensus pattern (27 bp):
CCGTGTCTCTCATGTTGAGACACACGA
Found at i:5815803 original size:49 final size:44
Alignment explanation
Indices: 5815746--5815865 Score: 141
Period size: 44 Copynumber: 2.6 Consensus size: 44
5815736 CTAAGTTGAT
* * *
5815746 GCCATGTCCCAGACAGGTCTTACATTGACTTCCATATATCGAGGCCAAA
1 GCCATGTCCCAGACAGGTCTTACACTGA----CACATATC-AAGCCAAA
* * *
5815795 GCCATGTCCCAGACATGTCTTACACTGACACATGTCAAGCCAAT
1 GCCATGTCCCAGACAGGTCTTACACTGACACATATCAAGCCAAA
5815839 GCCATGTCCCAGACAGGTCTTACACTG
1 GCCATGTCCCAGACAGGTCTTACACTG
5815866 GATTGCATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
44 32 0.50
45 6 0.09
49 26 0.41
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (44 bp):
GCCATGTCCCAGACAGGTCTTACACTGACACATATCAAGCCAAA
Found at i:5815852 original size:44 final size:45
Alignment explanation
Indices: 5815744--5815967 Score: 159
Period size: 49 Copynumber: 4.8 Consensus size: 45
5815734 ATCTAAGTTG
* * * * *
5815744 ATGCCATGTCCCAGACAGGTCTTACATTGACTTCCATATATCGAGGCCA
1 ATGCCATGTCCCAGACATGTCTTACACTGA----CACATGTCGAAGCCA
*
5815793 AAGCCATGTCCCAGACATGTCTTACACTGACACATGTC-AAGCCA
1 ATGCCATGTCCCAGACATGTCTTACACTGACACATGTCGAAGCCA
* * * *
5815837 ATGCCATGTCCCAGACAGGTCTTACACTGGATTGCATATCTCGAAGCCG
1 ATGCCATGTCCCAGACATGTCTTACACT-GA---CACATGTCGAAGCCA
* * * * * *
5815886 ATG-CATGTCCCAGGCATGTTTTACACTGGCTC-TCGTCTTAATGCCG
1 ATGCCATGTCCCAGACATGTCTTACACTGACACAT-GTC-GAA-GCCA
5815932 ATG-CATGTCCCAGACATGTCTTACACTAGCACACAT
1 ATGCCATGTCCCAGACATGTCTTACACT-G-ACACAT
5815968 ATCACCCAAA
Statistics
Matches: 141, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 34 0.24
45 10 0.07
46 29 0.21
47 2 0.01
48 29 0.21
49 36 0.26
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (45 bp):
ATGCCATGTCCCAGACATGTCTTACACTGACACATGTCGAAGCCA
Found at i:5815861 original size:93 final size:94
Alignment explanation
Indices: 5815744--5815958 Score: 251
Period size: 93 Copynumber: 2.3 Consensus size: 94
5815734 ATCTAAGTTG
* *
5815744 ATGCCATGTCCCAGACAGGTCTTACA-TTGACTTCCATATATCGAGGCCAAAGCCATGTCCCAGA
1 ATGCCATGTCCCAGACAGGTCTTACACTGGA-TTCCATATATCGAAGCCAAAG-CATGTCCCAGA
5815808 CATGTCTTACACTGACACAT-GTC-AA-GCCA
64 CATGTCTTACACTGACAC-TCGTCTAATGCCA
* * * * *
5815837 ATGCCATGTCCCAGACAGGTCTTACACTGGATTGCATATCTCGAAGCCGATGCATGTCCCAGGCA
1 ATGCCATGTCCCAGACAGGTCTTACACTGGATTCCATATATCGAAGCCAAAGCATGTCCCAGACA
* * * *
5815902 TGTTTTACACTGGCTCTCGTCTTAATGCCG
66 TGTCTTACACTGACACTCGTC-TAATGCCA
*
5815932 ATG-CATGTCCCAGACATGTCTTACACT
1 ATGCCATGTCCCAGACAGGTCTTACACT
5815959 AGCACACATA
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
91 1 0.01
92 28 0.27
93 42 0.40
94 28 0.27
95 6 0.06
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (94 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGGATTCCATATATCGAAGCCAAAGCATGTCCCAGACA
TGTCTTACACTGACACTCGTCTAATGCCA
Found at i:5816648 original size:20 final size:18
Alignment explanation
Indices: 5816611--5816661 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
5816601 CTATAGCAAC
5816611 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
5816628 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
5816648 TTACAACTTTACAA
1 TCACAA-TTTACAA
5816662 AATAGCCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 4 0.14
20 16 0.55
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:5826062 original size:20 final size:20
Alignment explanation
Indices: 5826037--5826082 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5826027 ATTGGGCCTT
5826037 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
5826057 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
5826076 GCCCATA
1 GCCCATA
5826083 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:5826091 original size:19 final size:20
Alignment explanation
Indices: 5826049--5826092 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5826039 CCATATTAAC
** *
5826049 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
5826069 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
5826088 ACAGT
1 ACAGT
5826093 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:5829722 original size:43 final size:43
Alignment explanation
Indices: 5829664--5829829 Score: 199
Period size: 43 Copynumber: 3.9 Consensus size: 43
5829654 ATTATCGAGA
* * *
5829664 TGTGATTGCATGTAAGAACATGCCTGGGACATTGGCATTGTAT
1 TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCATTGTAT
* * *
5829707 TGTGCTTACGTGTAAGAACATGTCGGGGACACTGGCATTGTAT
1 TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCATTGTAT
* * *
5829750 TGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGT-T
1 TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCATTGTAT
* * * *
5829792 ATATGATTTCGTGGAAGACCATGTCTGGGACATTGGCA
1 -TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCA
5829830 CCGATATGTG
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 1 0.01
43 105 0.99
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCATTGTAT
Found at i:5829855 original size:43 final size:43
Alignment explanation
Indices: 5829760--5829856 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 43
5829750 TGTGATTATG
* * ** *
5829760 TGTAAGACCATGTCTGGGACATTGGCATCGTTATATGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCACCGATATATGATAACA
* *
5829803 TGGAAGACCATGTCTGGGACATTGGCACCGATATGTGATAACA
1 TGTAAGACCATGTCTGGGACATTGGCACCGATATATGATAACA
*
5829846 TGTACGACCAT
1 TGTAAGACCAT
5829857 ATTTGGGATA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCACCGATATATGATAACA
Found at i:5829855 original size:86 final size:85
Alignment explanation
Indices: 5829663--5829856 Score: 201
Period size: 86 Copynumber: 2.3 Consensus size: 85
5829653 TATTATCGAG
* * * * * *
5829663 ATGTGATTGCATGTAAGAACATGCCTGGGACATTGGCATTGTATTGTGCTTACGTGTAAGAACAT
1 ATGTGATTACATGTAAGACCATGCCTGGGACATTGGCATCGTATTATGATTACGTGGAAGAACAT
**
5829728 GTCGGGGACACTGGCATTGT
66 GTCGGGGACACTGGCACCGT
** * * *
5829748 ATTGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGT-TATATGATTTCGTGGAAGACC
1 A-TGTGATTACATGTAAGACCATGCCTGGGACATTGGCATCGTAT-TATGATTACGTGGAAGAAC
* *
5829812 ATGTCTGGGACATTGGCACCGAT
64 ATGTCGGGGACACTGGCACCG-T
* *
5829835 ATGTGATAACATGTACGACCAT
1 ATGTGATTACATGTAAGACCAT
5829857 ATTTGGGATA
Statistics
Matches: 87, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
85 2 0.02
86 83 0.95
87 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (85 bp):
ATGTGATTACATGTAAGACCATGCCTGGGACATTGGCATCGTATTATGATTACGTGGAAGAACAT
GTCGGGGACACTGGCACCGT
Found at i:5830236 original size:13 final size:13
Alignment explanation
Indices: 5830218--5830244 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5830208 GAAGTAATCG
5830218 CACACGGGCGTGT
1 CACACGGGCGTGT
5830231 CACACGGGCGTGT
1 CACACGGGCGTGT
5830244 C
1 C
5830245 CCTGCTGAGC
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:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:5842928 original size:40 final size:40
Alignment explanation
Indices: 5842861--5843147 Score: 456
Period size: 40 Copynumber: 7.2 Consensus size: 40
5842851 CCTTCGGAGT
* *
5842861 TTAG-CCGGATATAGGT-ACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATA-GTAACTCGCACAAATGCCTTCGGGAC
*
5842900 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
5842940 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGAT
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
5842980 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
5843020 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
*
5843060 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG-C
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
5843099 TTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGAC
5843139 TTAGCCCGG
1 TTAGCCCGG
5843148 TTATCAATCC
Statistics
Matches: 232, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.00
39 40 0.17
40 191 0.82
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:5844351 original size:14 final size:14
Alignment explanation
Indices: 5844332--5844358 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5844322 AACATGAGAG
5844332 CTTTTTCTTTCTTT
1 CTTTTTCTTTCTTT
5844346 CTTTTTCTTTCTT
1 CTTTTTCTTTCTT
5844359 CTATTCGGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
CTTTTTCTTTCTTT
Found at i:5844362 original size:53 final size:55
Alignment explanation
Indices: 5844286--5844406 Score: 201
Period size: 53 Copynumber: 2.2 Consensus size: 55
5844276 CAAAGCTCTT
*
5844286 TTTCCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGC-T-TTTTC
1 TTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTCTTTTC
*
5844339 TTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAGCAACATGAGAGCTTCTTTTC
1 TTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTCTTTTC
*
5844394 TTTCTTTTTTTTT
1 TTTCTTTCTTTTT
5844407 TCATCATCAT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
53 45 0.71
54 1 0.02
55 17 0.27
ACGTcount: A:0.16, C:0.22, G:0.11, T:0.51
Consensus pattern (55 bp):
TTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTCTTTTC
Found at i:5866301 original size:40 final size:40
Alignment explanation
Indices: 5866264--5866446 Score: 214
Period size: 40 Copynumber: 4.6 Consensus size: 40
5866254 GCTACTCGTT
*
5866264 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
5866304 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
5866344 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * *
5866383 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
5866424 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
5866447 TACATCATTC
Statistics
Matches: 123, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 76 0.62
41 14 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:5866375 original size:79 final size:81
Alignment explanation
Indices: 5866264--5866446 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
5866254 GCTACTCGTT
* *
5866264 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
5866328 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
5866344 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
5866407 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
5866424 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
5866447 TACATCATTC
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 4 0.04
79 55 0.61
80 31 0.34
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:5869721 original size:46 final size:46
Alignment explanation
Indices: 5869671--5870032 Score: 372
Period size: 46 Copynumber: 7.8 Consensus size: 46
5869661 TGATTGAGCA
5869671 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5869717 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
5869762 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5869810 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
5869855 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5869903 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
5869948 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5869996 -CTTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5870033 GCGGGTTACA
Statistics
Matches: 266, Mismatches: 22, Indels: 56
0.77 0.06 0.16
Matches are distributed among these distances:
42 6 0.02
43 15 0.06
45 10 0.04
46 119 0.45
47 87 0.33
48 9 0.03
50 14 0.05
51 6 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5869827 original size:93 final size:93
Alignment explanation
Indices: 5869668--5870025 Score: 673
Period size: 93 Copynumber: 3.8 Consensus size: 93
5869658 GGATGATTGA
5869668 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
5869733 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
5869761 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
5869826 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
5869854 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
5869919 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
5869947 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC-CGAACTCGTTGAG
5870011 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
5870026 CTTATGGGCG
Statistics
Matches: 261, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 1 0.00
93 260 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5871597 original size:39 final size:39
Alignment explanation
Indices: 5871553--5871676 Score: 146
Period size: 39 Copynumber: 3.2 Consensus size: 39
5871543 CCTTCGGAGT
* *
5871553 TTAGCCAGATATAGCT-ACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCGGATATAG-TAACTAGCACAAATGCCTTCGGGAC
*
5871592 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-C
1 TTAG-CCGGATATAGTAACTAGCACAAATGCCTTCGGGAC
* *
5871631 TTATCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGAC
1 TTA-GCCGGATA-TAGTAACTAGCACAAATGCCTTCGGGAC
5871671 TTAGCC
1 TTAGCC
5871677 CGGTTATCAA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
38 1 0.01
39 40 0.55
40 32 0.44
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
TTAGCCGGATATAGTAACTAGCACAAATGCCTTCGGGAC
Found at i:5871620 original size:40 final size:40
Alignment explanation
Indices: 5871569--5871679 Score: 163
Period size: 39 Copynumber: 2.8 Consensus size: 40
5871559 AGATATAGCT
*
5871569 ACTAGCTCAAATGCCTTCGGGACTTAGCCCGG-ATATAGTA
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
* * *
5871609 ACTCGCACAAATGCCTTCGGG-CTTATCCCGGAATTAGTC
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
5871648 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
5871680 TTATCAATCC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
39 33 0.52
40 30 0.48
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:5872890 original size:54 final size:55
Alignment explanation
Indices: 5872814--5872938 Score: 198
Period size: 54 Copynumber: 2.3 Consensus size: 55
5872804 CTCAAAGCTC
*
5872814 TTTTTCCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTT-TTT
1 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTCTTT
*
5872868 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAGCAACATGAGAGCTTCTTT
1 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTCTTT
* *
5872923 TCTTTCCTTTTTTTTT
1 T-TTTTCTTTCTTTTT
5872939 TCATCATCAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
54 49 0.75
55 4 0.06
56 12 0.18
ACGTcount: A:0.15, C:0.22, G:0.10, T:0.53
Consensus pattern (55 bp):
TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTCTTT
Found at i:5876153 original size:46 final size:46
Alignment explanation
Indices: 5876030--5876228 Score: 185
Period size: 45 Copynumber: 4.4 Consensus size: 46
5876020 TCTTCTCAAT
* * **
5876030 GCCGAGGCCATGTCCAACATGGTCTTACACTGGCTCAC--AAT-CA
1 GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCGTAATGTG
* ** * *
5876073 ACACTGATTTCATGTCTAGCATGGTCTTACACTGGCTCTCGTAATGTG
1 GC-C-GATGCCATGTCCAACATGGTCTTACACTGGCTCTCGTAATGTG
* * *
5876121 GCCGATGCCATGTCCAACATGGTCTTATACTGGCTCACAGTCAACGT-
1 GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCTC-GT-AATGTG
* * *
5876168 --CGATGCCATGTGCAACATGGTCTTACACTGACTCTCGTAATATG
1 GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCGTAATGTG
5876212 GCCGATGCCATGTCCAA
1 GCCGATGCCATGTCCAA
5876229 TGTGGTTTAA
Statistics
Matches: 122, Mismatches: 24, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
43 4 0.03
44 3 0.02
45 61 0.50
46 43 0.35
47 6 0.05
48 5 0.04
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (46 bp):
GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCGTAATGTG
Found at i:5876156 original size:91 final size:91
Alignment explanation
Indices: 5876030--5876228 Score: 285
Period size: 91 Copynumber: 2.2 Consensus size: 91
5876020 TCTTCTCAAT
* ** *
5876030 GCCGAGGCCATGTCCAACATGGTCTTACACTGGCTCACAATCAACACT-GATTTCATGT-CTAGC
1 GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCACAATCAAC-CTCGATGCCATGTGC-AAC
* *
5876093 ATGGTCTTACACTGGCTCTCGTAATGTG
64 ATGGTCTTACACTGACTCTCGTAATATG
* * *
5876121 GCCGATGCCATGTCCAACATGGTCTTATACTGGCTCACAGTCAACGTCGATGCCATGTGCAACAT
1 GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCACAATCAACCTCGATGCCATGTGCAACAT
5876186 GGTCTTACACTGACTCTCGTAATATG
66 GGTCTTACACTGACTCTCGTAATATG
5876212 GCCGATGCCATGTCCAA
1 GCCGATGCCATGTCCAA
5876229 TGTGGTTTAA
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
90 1 0.01
91 95 0.98
92 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (91 bp):
GCCGATGCCATGTCCAACATGGTCTTACACTGGCTCACAATCAACCTCGATGCCATGTGCAACAT
GGTCTTACACTGACTCTCGTAATATG
Done.