Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold150
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1854615
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 196055 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:407064 original size:195 final size:194
Alignment explanation
Indices: 406732--407120 Score: 769
Period size: 195 Copynumber: 2.0 Consensus size: 194
406722 ATCATTTTGT
406732 GTGTAAGGAATATATCAATTTAAACAAAACTTTATTTTAAAATAATTATATTTCTTCATTCATAG
1 GTGTAAGGAATATATCAATTTAAACAAAACTTTATTTTAAAATAATTATATTTCTTCATTCATAG
406797 ATAACTAATGGTCTATTATCATCAGATAAAATACACTCAACACGTAGATTTTTTTTTTTTTGTTA
66 ATAACTAATGGTCTATTATCATCAGATAAAATACACTCAACACGTAGATTTTTTTTTTTTTGTTA
406862 AAACTTTAAAAAGTCTGACATTTCTGCTAAACATTGGTGACATTCTCTCTCTCTCTTTTTTCTC
131 AAACTTTAAAAAGTCTGACATTTCTGCTAAACATTGGTGACATTCTCTCTCTCTCTTTTTTCTC
406926 NGTGTAAGGAATATATCAATTTAAACAAAACTTTATTTTAAAATAATTATATTTCTTCATTCATA
1 -GTGTAAGGAATATATCAATTTAAACAAAACTTTATTTTAAAATAATTATATTTCTTCATTCATA
406991 GATAACTAATGGTCTATTATCATCAGATAAAATACACTCAACACGTAGATTTTTTTTTTTTTGTT
65 GATAACTAATGGTCTATTATCATCAGATAAAATACACTCAACACGTAGATTTTTTTTTTTTTGTT
407056 AAAACTTTAAAAAGTCTGACATTTCTGCTAAACATTGGTGACATTCTCTCTCTCTCTTTTTTCTC
130 AAAACTTTAAAAAGTCTGACATTTCTGCTAAACATTGGTGACATTCTCTCTCTCTCTTTTTTCTC
407121 TATCTGTGTC
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
195 194 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (194 bp):
GTGTAAGGAATATATCAATTTAAACAAAACTTTATTTTAAAATAATTATATTTCTTCATTCATAG
ATAACTAATGGTCTATTATCATCAGATAAAATACACTCAACACGTAGATTTTTTTTTTTTTGTTA
AAACTTTAAAAAGTCTGACATTTCTGCTAAACATTGGTGACATTCTCTCTCTCTCTTTTTTCTC
Found at i:407159 original size:2 final size:2
Alignment explanation
Indices: 407152--407184 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
407142 GCTAAGGATA
407152 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
407185 CAAAATATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:407440 original size:2 final size:2
Alignment explanation
Indices: 407433--407471 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
407423 TTCTTTTAAG
407433 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
407472 AACATTTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:407614 original size:12 final size:12
Alignment explanation
Indices: 407597--407623 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
407587 AAACACACAA
407597 TCTCTCTCTCTT
1 TCTCTCTCTCTT
407609 TCTCTCTCTCTT
1 TCTCTCTCTCTT
407621 TCT
1 TCT
407624 ACTTTGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTCTCTCTCTT
Found at i:407762 original size:2 final size:2
Alignment explanation
Indices: 407755--407807 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
407745 CAATAAACAT
407755 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
407797 TC TC TC TC TC T
1 TC TC TC TC TC T
407808 TAAAGATTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:408773 original size:2 final size:2
Alignment explanation
Indices: 408766--408804 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
408756 TGCTTTCTCT
408766 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
408805 TTTCATTGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:409101 original size:2 final size:2
Alignment explanation
Indices: 409094--409139 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
409084 TCTCTTTGCG
* *
409094 GA GA GA GA GA GA GA GA GA AA GA GA GA CA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
409136 GA GA
1 GA GA
409140 ACAAATGGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.02, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:409487 original size:47 final size:46
Alignment explanation
Indices: 409350--410597 Score: 1689
Period size: 47 Copynumber: 26.8 Consensus size: 46
409340 GGCTGATAGT
* *
409350 CTATGACTGGCTTTCTCCCTTTACCCTGGCCGAGTATTTGTCTGTGGC
1 CTATGACTGGCTTTC-CCC-TTACCCTGGCTGAGTATTTGACTGTGGC
*
409398 CTATGACTGGCTTT-CCCTAACCCTGGCTGAGTATTTGACTGTGGC
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* *
409443 CTATGACTGGCTTTCCCCCTTACCCTGGCCGAGTATTTGTCTGTGGC
1 CTATGACTGGCTTT-CCCCTTACCCTGGCTGAGTATTTGACTGTGGC
*
409490 CTATGACTGGCTTT-CCCTAACCCTGGCTGAGTATTTGACTGTGGC
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* *
409535 CTATGACTGGCTTTCCCCCTTACCCTGGCCGAGTATTTGTCTGTGGC
1 CTATGACTGGCTTT-CCCCTTACCCTGGCTGAGTATTTGACTGTGGC
*
409582 CTATGACTGGCTTT-CCCTAACCCTGGCTGAGTATTTGACTGTGGC
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
*
409627 CTATGACTGGCTTT-CCCTAACCCTGGCTGAGTATTTGACTGTGGC
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
*
409672 CTATGACTGGCTTT-CCCTAACCCTGGCTGAGTATTTGACTGTGGC
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* * *
409717 CTATGACTGGCTTTCTCCCCTTACCCTGGCCGAGTATTTGTCTGTGGA
1 CTATGACTGGC-TT-TCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* *
409765 CTATGACTGGCTTT-CGCTAACCCTGGCTGAGTATTTGACTGTGGC
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
409810 CTATGACTGGCTTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
1 CTATGACTGGC-TTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* **
409857 CTATGACTGGCTTTTCCCCTTACCCTGGCTGAGCATTTGACTACGGC
1 CTATGACTGGC-TTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
409904 CTATGACTGGCTTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
1 CTATGACTGGC-TTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* **
409951 CTATGACTGGCTTTTCCCCTTACCCTGGCTGAGCATTTGACTACGGC
1 CTATGACTGGC-TTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
**
409998 CTATGACTGGCTTTTCCCCTTACCCTGGCTGAGTATTTGACTACGGC
1 CTATGACTGGC-TTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
*
410045 CTATGACTGGCTTTTCCCCTTACCCTGGCTGAGCATTTGACTGTGGC
1 CTATGACTGGC-TTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
*
410092 CTATGACTGGCTTTCCCACTTACCCTGGCCGAGTATTTGACTGTGGC
1 CTATGACTGGCTTTCCC-CTTACCCTGGCTGAGTATTTGACTGTGGC
* * * * *
410139 ATAGGACTGGTTTTCCCACTTACCCTGGCCGAGTATTTGACTGTGGT
1 CTATGACTGGCTTTCCC-CTTACCCTGGCTGAGTATTTGACTGTGGC
* * * *
410186 CTATGACTGGTTTTCCCACTTACCCTGGCCGAGTATTTGACTGTTGT
1 CTATGACTGGCTTTCCC-CTTACCCTGGCTGAGTATTTGACTGTGGC
* * *
410233 CTATGACTAGCTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGT
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* * *
410279 CTATGACTAGCTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGT
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* * *
410325 CTATGACTAGCTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGT
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* * *
410371 CTATGACTAGCTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGT
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* * *
410417 CTATGACTAGCTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGT
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
** * *
410463 CTATGACTGGCTTTCCCAATGCCCTGGCTGAGTATTTGACTGTGGT
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* * *** * * *
410509 CTAAGTCTGGCCCCCCCCCCCCTCACCTTGGCTGAGTATTTGACTGTGGT
1 CTATGACTGG----CTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
* * * *
410559 CTATGACTGGCTTTCCCCTTTCCCAGGATGAGTGTTTGA
1 CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGA
410598 TTGTCCCTGG
Statistics
Matches: 1109, Mismatches: 77, Indels: 30
0.91 0.06 0.02
Matches are distributed among these distances:
45 247 0.22
46 296 0.27
47 478 0.43
48 52 0.05
50 36 0.03
ACGTcount: A:0.14, C:0.28, G:0.23, T:0.34
Consensus pattern (46 bp):
CTATGACTGGCTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGC
Found at i:409945 original size:94 final size:93
Alignment explanation
Indices: 409350--410578 Score: 1710
Period size: 92 Copynumber: 13.2 Consensus size: 93
409340 GGCTGATAGT
* *
409350 CTATGACTGGCTTTCTCCCTTTACCCTGGCCGAGTATTTGTCTGTGGCCTATGACTGGCTTT-CC
1 CTATGACTGGCTTT-TCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCC
*
409414 CTAACCCTGGCTGAGTATTTGACTGTGGC
65 CTTACCCTGGCTGAGTATTTGACTGTGGC
* *
409443 CTATGACTGGCTTTCCCCCTTACCCTGGCCGAGTATTTGTCTGTGGCCTATGACTGGCTTT-CCC
1 CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCCC
*
409507 TAACCCTGGCTGAGTATTTGACTGTGGC
66 TTACCCTGGCTGAGTATTTGACTGTGGC
* *
409535 CTATGACTGGCTTTCCCCCTTACCCTGGCCGAGTATTTGTCTGTGGCCTATGACTGGCTTT-CCC
1 CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCCC
*
409599 TAACCCTGGCTGAGTATTTGACTGTGGC
66 TTACCCTGGCTGAGTATTTGACTGTGGC
* *
409627 CTATGACTGGC-TTT-CCCTAACCCTGGCTGAGTATTTGACTGTGGCCTATGACTGGCTTT-CCC
1 CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCCC
*
409689 TAACCCTGGCTGAGTATTTGACTGTGGC
66 TTACCCTGGCTGAGTATTTGACTGTGGC
* * *
409717 CTATGACTGGCTTTCTCCCCTTACCCTGGCCGAGTATTTGTCTGTGGACTATGACTGGCTTT-CG
1 CTATGACTGGCTTT-TCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCC
*
409781 CTAACCCTGGCTGAGTATTTGACTGTGGC
65 CTTACCCTGGCTGAGTATTTGACTGTGGC
*
409810 CTATGACTGGCTTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGCCTATGACTGGCTTTTCCC
1 CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGC-TTTCCC
* **
409875 CTTACCCTGGCTGAGCATTTGACTACGGC
65 CTTACCCTGGCTGAGTATTTGACTGTGGC
*
409904 CTATGACTGGCTTTTCCCCTTACCCTGGCTGAGTATTTGACTGTGGCCTATGACTGGCTTTTCCC
1 CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGC-TTTCCC
* **
409969 CTTACCCTGGCTGAGCATTTGACTACGGC
65 CTTACCCTGGCTGAGTATTTGACTGTGGC
* **
409998 CTATGACTGGCTTTTCCCCTTACCCTGGCTGAGTATTTGACTACGGCCTATGACTGGCTTTTCCC
1 CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGC-TTTCCC
*
410063 CTTACCCTGGCTGAGCATTTGACTGTGGC
65 CTTACCCTGGCTGAGTATTTGACTGTGGC
* * *
410092 CTATGACTGGC-TTTCCCACTTACCCTGGCCGAGTATTTGACTGTGGCATAGGACTGGTTTTCCC
1 CTATGACTGGCTTTTCCC-CTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCC
* *
410156 ACTTACCCTGGCCGAGTATTTGACTGTGGT
65 -CTTACCCTGGCTGAGTATTTGACTGTGGC
* * *
410186 CTATGACTGG-TTTTCCCACTTACCCTGGCCGAGTATTTGACTGTTGTCTATGACTAGCTTTCCC
1 CTATGACTGGCTTTTCCC-CTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCC
* *
410250 CTTACCCTGGCCGAGTATTTGACTGTGGT
65 CTTACCCTGGCTGAGTATTTGACTGTGGC
* * *
410279 CTATGACTAGC-TTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGTCTATGACTAGCTTTCCCC
1 CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCCC
* *
410343 TTACCCTGGCCGAGTATTTGACTGTGGT
66 TTACCCTGGCTGAGTATTTGACTGTGGC
* * *
410371 CTATGACTAGC-TTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGTCTATGACTAGCTTTCCCC
1 CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCCC
* *
410435 TTACCCTGGCCGAGTATTTGACTGTGGT
66 TTACCCTGGCTGAGTATTTGACTGTGGC
** * * * * * ***
410463 CTATGACTGGC-TTTCCCAATGCCCTGGCTGAGTATTTGACTGTGGTCTAAGTCTGGCCCCCCCC
1 CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGG----CTTT
* * *
410527 CCCCTCACCTTGGCTGAGTATTTGACTGTGGT
62 CCCCTTACCCTGGCTGAGTATTTGACTGTGGC
410559 CTATGACTGGC-TTTCCCCTT
1 CTATGACTGGCTTTTCCCCTT
410579 TCCCAGGATG
Statistics
Matches: 1067, Mismatches: 56, Indels: 23
0.93 0.05 0.02
Matches are distributed among these distances:
90 84 0.08
91 4 0.00
92 435 0.41
93 158 0.15
94 338 0.32
96 48 0.04
ACGTcount: A:0.14, C:0.29, G:0.23, T:0.34
Consensus pattern (93 bp):
CTATGACTGGCTTTTCCCCTTACCCTGGCCGAGTATTTGACTGTGGCCTATGACTGGCTTTCCCC
TTACCCTGGCTGAGTATTTGACTGTGGC
Found at i:414331 original size:2 final size:2
Alignment explanation
Indices: 414326--414361 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
414316 CATAAGTACT
* *
414326 GA GA GA GA GA TA GA GA GA GA GA AA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414362 TATTAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (2 bp):
GA
Found at i:416077 original size:17 final size:16
Alignment explanation
Indices: 416052--416086 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
416042 CTGGCGTGCG
416052 ACCAGTTCTCGCCGAGT
1 ACCAGTTCTCGCC-AGT
*
416069 ACCATTTCTCGCCAGT
1 ACCAGTTCTCGCCAGT
416085 AC
1 AC
416087 ATTGTGACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26
Consensus pattern (16 bp):
ACCAGTTCTCGCCAGT
Found at i:416170 original size:17 final size:16
Alignment explanation
Indices: 416143--416177 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
416133 ACGTCACAAT
416143 GTACTGGCGAGAAATG
1 GTACTGGCGAGAAATG
*
416159 GTACTCGGCGAGAACTG
1 GTACT-GGCGAGAAATG
416176 GT
1 GT
416178 CGCACGCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.26, C:0.17, G:0.37, T:0.20
Consensus pattern (16 bp):
GTACTGGCGAGAAATG
Found at i:417002 original size:16 final size:16
Alignment explanation
Indices: 416981--417024 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
416971 CGCCTTAGTC
416981 CGTTCGCTCTAATTAT
1 CGTTCGCTCTAATTAT
* *
416997 CGTTCGCCCAAATTAT
1 CGTTCGCTCTAATTAT
417013 CGTTCGCTCTAA
1 CGTTCGCTCTAA
417025 ACCTCGTTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (16 bp):
CGTTCGCTCTAATTAT
Found at i:417178 original size:59 final size:59
Alignment explanation
Indices: 417102--417279 Score: 250
Period size: 59 Copynumber: 2.9 Consensus size: 59
417092 AATTTATTAA
*
417102 CTTT-TATTAATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTTCGGTTT
1 CTTTCTATT-ATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTACGGTTT
* *
417161 CTTTCTATTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTTTTGTTTTTCTACGGTTT
1 CTTTCTATTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTACGGTTT
417220 CTTTATTCTTATTATTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTA
1 C--T-TTC----TATTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTA
417280 TCGTTTTTTT
Statistics
Matches: 106, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
59 52 0.49
60 4 0.04
61 1 0.01
62 3 0.03
66 46 0.43
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.47
Consensus pattern (59 bp):
CTTTCTATTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTACGGTTT
Found at i:417698 original size:15 final size:16
Alignment explanation
Indices: 417678--417715 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
417668 TATTGATGTA
417678 TATAACGAA-CACGGC
1 TATAACGAATCACGGC
*
417693 TATAACGAATTTACGGC
1 TATAACGAA-TCACGGC
417710 TATAAC
1 TATAAC
417716 AAAGTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (16 bp):
TATAACGAATCACGGC
Found at i:418177 original size:13 final size:15
Alignment explanation
Indices: 418147--418178 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
418137 GCTTAATAAT
418147 AAAACTGCAAAGTTC
1 AAAACTGCAAAGTTC
418162 AAAA-TGCAAA-TTC
1 AAAACTGCAAAGTTC
418175 AAAA
1 AAAA
418179 AAATTTAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (15 bp):
AAAACTGCAAAGTTC
Found at i:419652 original size:168 final size:168
Alignment explanation
Indices: 419374--420039 Score: 1118
Period size: 168 Copynumber: 4.0 Consensus size: 168
419364 AAATACATTG
* *
419374 TATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATATTTACTATTTGGCCATATTG
1 TATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTG
*
419439 GCCCCACCCTAGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCT
66 GCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCT
*
419504 TCATGGACATCATAATCATGCATTTAGTATTTAACAAA
131 TCATGGACATCATAATCATGCATTTAGTTTTTAACAAA
419542 TATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTG
1 TATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTG
* * **
419607 GCCCCACCCTAGAGCCTGAACCCCAGACCCAGGGGTCATGAATTTCACAATTTAGGTTGAGGTAT
66 GCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCT
*
419672 TCATGGACATCATTATCATGCATTTAGTTTTTAACAAA
131 TCATGGACATCATAATCATGCATTTAGTTTTTAACAAA
** * *
419710 TATATATGATAGTAGAGAAAAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTG
1 TATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTG
* *
419775 GCCCCATCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCT
66 GCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCT
419840 TCATGGACATCATAATCATGCATTTAGTTTTTAACAAA
131 TCATGGACATCATAATCATGCATTTAGTTTTTAACAAA
*
419878 TATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTG
1 TATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTG
* * *
419943 GCCCCACCCTAGAGCCAGAACCCCTGACCCAGGGGCCATAAATTTCACAATTTTA-GTAGAGGGC
66 GCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAA-TTTAGGTAGAGGGC
* * *
420007 CTCATGGACATCATAACCATGCATTCAGTTTTT
130 TTCATGGACATCATAATCATGCATTTAGTTTTT
420040 TCCTCACATG
Statistics
Matches: 466, Mismatches: 31, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
168 462 0.99
169 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (168 bp):
TATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTG
GCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCT
TCATGGACATCATAATCATGCATTTAGTTTTTAACAAA
Found at i:421224 original size:33 final size:33
Alignment explanation
Indices: 421187--421414 Score: 203
Period size: 33 Copynumber: 6.8 Consensus size: 33
421177 GTCACTTTAT
* * *
421187 ATCATTTAATAAGGCCCCACTATCAGCCTTTTC
1 ATCATTGAATGAGGTCCCACTATCAGCCTTTTC
* * *
421220 ATCATTGAATGAGGTCCCATTATGAGCCTTTAC
1 ATCATTGAATGAGGTCCCACTATCAGCCTTTTC
* * *
421253 ATCATTGGATGAGGTCCAATTATCAGCCTTTAT-
1 ATCATTGAATGAGGTCCCACTATCAGCCTTT-TC
*
421286 ATCATTGGATGAGGTCCCACTATCAGCCTTTATACATGC
1 ATCATTGAATGAGGTCCCACTATCAGCC-TT-T---T-C
* * *
421325 ATCATTGAATGAGGTCCTGA-TATCAGACTTTAC
1 ATCATTGAATGAGGTCC-CACTATCAGCCTTTTC
** *
421358 ATCATTGAATGAGGTCCCTTTATGAGCCTTTAT-
1 ATCATTGAATGAGGTCCCACTATCAGCCTTT-TC
421391 ATCATTGAATGAGGT-CCACTATCA
1 ATCATTGAATGAGGTCCCACTATCA
421415 AACTTTACAT
Statistics
Matches: 161, Mismatches: 24, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
32 6 0.04
33 123 0.76
34 2 0.01
35 1 0.01
37 3 0.02
38 2 0.01
39 23 0.14
40 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (33 bp):
ATCATTGAATGAGGTCCCACTATCAGCCTTTTC
Found at i:421361 original size:105 final size:104
Alignment explanation
Indices: 421219--421414 Score: 295
Period size: 105 Copynumber: 1.9 Consensus size: 104
421209 TCAGCCTTTT
* * *
421219 CATCATTGAATGAGGTCCCATTATGAGCCTTTACATCATTGGATGAGGTCCAATTATCAGCCTTT
1 CATCATTGAATGAGGTCCCATTATCAGACTTTACATCATTGAATGAGGTCCAATTATCAGCCTTT
*
421284 ATATCATTGGATGAGGTCCCACTATCAGCCTTTATACATG
66 ATATCATTGAATGAGGT-CCACTATCAGCCTTTATACATG
* ** *
421324 CATCATTGAATGAGGTCCTGA-TATCAGACTTTACATCATTGAATGAGGTCCCTTTATGAGCCTT
1 CATCATTGAATGAGGTCC-CATTATCAGACTTTACATCATTGAATGAGGTCCAATTATCAGCCTT
421388 TATATCATTGAATGAGGTCCACTATCA
65 TATATCATTGAATGAGGTCCACTATCA
421415 AACTTTACAT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
104 9 0.11
105 72 0.88
106 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (104 bp):
CATCATTGAATGAGGTCCCATTATCAGACTTTACATCATTGAATGAGGTCCAATTATCAGCCTTT
ATATCATTGAATGAGGTCCACTATCAGCCTTTATACATG
Found at i:421487 original size:33 final size:33
Alignment explanation
Indices: 421438--421534 Score: 122
Period size: 34 Copynumber: 2.9 Consensus size: 33
421428 TGGTTCAGCT
* * *
421438 TTTACATCATTGAATGAGGTCCCACTATCAACC
1 TTTACACCATTAAATGAGGTCCCATTATCAACC
** *
421471 TTTACACCATTAAATGAGGTACCTTTTATCAGCC
1 TTTACACCATTAAATGAGGT-CCCATTATCAACC
*
421505 TTTATACCATTAAATGAGGTCCCATTATCA
1 TTTACACCATTAAATGAGGTCCCATTATCA
421535 GTCTGTATGT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 26 0.48
34 28 0.52
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (33 bp):
TTTACACCATTAAATGAGGTCCCATTATCAACC
Found at i:421507 original size:34 final size:33
Alignment explanation
Indices: 421432--421535 Score: 118
Period size: 33 Copynumber: 3.1 Consensus size: 33
421422 CATTATTGGT
* * *
421432 TCAGCTTTTACATCATTGAATGAGGTCCCACTA
1 TCAGCCTTTACACCATTAAATGAGGTCCCACTA
* ***
421465 TCAACCTTTACACCATTAAATGAGGTACCTTTTA
1 TCAGCCTTTACACCATTAAATGAGGT-CCCACTA
* *
421499 TCAGCCTTTATACCATTAAATGAGGTCCCATTA
1 TCAGCCTTTACACCATTAAATGAGGTCCCACTA
421532 TCAG
1 TCAG
421536 TCTGTATGTC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 31 0.53
34 28 0.47
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (33 bp):
TCAGCCTTTACACCATTAAATGAGGTCCCACTA
Found at i:425613 original size:4 final size:4
Alignment explanation
Indices: 425604--425660 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
425594 AATACATATT
* * * * * * *
425604 TCTC TCTC TCTC TCTC TCAC TCTC TGTC TGTC TCTG TCTG TCTG TCTG
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
425652 TCTC TCTC T
1 TCTC TCTC T
425661 GTGGGGCTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.02, C:0.39, G:0.11, T:0.49
Consensus pattern (4 bp):
TCTC
Found at i:425647 original size:18 final size:18
Alignment explanation
Indices: 425616--425662 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
425606 TCTCTCTCTC
* *
425616 TCTCTCACTCTCTGTCTG
1 TCTCTCTCTGTCTGTCTG
*
425634 TCTCTGTCTGTCTGTCTG
1 TCTCTCTCTGTCTGTCTG
425652 TCTCTCTCTGT
1 TCTCTCTCTGT
425663 GGGGCTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.34, G:0.15, T:0.49
Consensus pattern (18 bp):
TCTCTCTCTGTCTGTCTG
Found at i:425661 original size:10 final size:10
Alignment explanation
Indices: 425604--425662 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
425594 AATACATATT
*
425604 TCTCTCTCTC
1 TCTCTGTCTC
* *
425614 TCTCTCTCAC
1 TCTCTGTCTC
*
425624 TCTCTGTCTG
1 TCTCTGTCTC
425634 TCTCTGTCTGTC
1 TCTCTGTC--TC
*
425646 TGTCTGTCTC
1 TCTCTGTCTC
425656 TCTCTGT
1 TCTCTGT
425663 GGGGCTTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 32 0.80
12 8 0.20
ACGTcount: A:0.02, C:0.37, G:0.12, T:0.49
Consensus pattern (10 bp):
TCTCTGTCTC
Found at i:432624 original size:2 final size:2
Alignment explanation
Indices: 432619--432655 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
432609 AAAAAATCAA
*
432619 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
432656 ATGATTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:433204 original size:10 final size:11
Alignment explanation
Indices: 433169--433230 Score: 60
Period size: 10 Copynumber: 5.9 Consensus size: 11
433159 TAAAGACCGT
433169 ACAGGGG-ATG
1 ACAGGGGCATG
*
433179 TCAGGGGCATG
1 ACAGGGGCATG
433190 CACAGGGGCA-G
1 -ACAGGGGCATG
* *
433201 ACAGTGGC-TT
1 ACAGGGGCATG
433211 ACAGGGG-ATG
1 ACAGGGGCATG
433221 ACAGGGGCAT
1 ACAGGGGCAT
433231 AAAGGGGGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
10 27 0.66
11 6 0.15
12 8 0.20
ACGTcount: A:0.26, C:0.18, G:0.44, T:0.13
Consensus pattern (11 bp):
ACAGGGGCATG
Found at i:433223 original size:20 final size:20
Alignment explanation
Indices: 433168--433254 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
433158 TTAAAGACCG
*
433168 TACAGGGGATGTCAGGGGCAT
1 TACAGGGGATGACAGGGGC-T
* *
433189 GCACAGGGGCA-GACAGTGGCT
1 -TACAGGGG-ATGACAGGGGCT
*
433210 TACAGGGGATGACAGGGGCA
1 TACAGGGGATGACAGGGGCT
* * *
433230 TAAAGGGGGTGGCAGGGGCT
1 TACAGGGGATGACAGGGGCT
433250 TACAG
1 TACAG
433255 TGGCACACAG
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 35 0.67
21 1 0.02
22 14 0.27
23 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.45, T:0.14
Consensus pattern (20 bp):
TACAGGGGATGACAGGGGCT
Found at i:433308 original size:42 final size:43
Alignment explanation
Indices: 433261--433342 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
433251 ACAGTGGCAC
* * *
433261 ACAGGGGTTGTGTACAGCGGCGCACAGGGGATG-ACAGGGTAT
1 ACAGGGGCTCTGTACAGCGGCACACAGGGGATGTACAGGGTAT
*
433303 ACAGGGGCTCTGTACAGTGGCACACAGGGGATGTACAGGG
1 ACAGGGGCTCTGTACAGCGGCACACAGGGGATGTACAGGG
433343 GATGACAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 29 0.83
43 6 0.17
ACGTcount: A:0.24, C:0.18, G:0.41, T:0.16
Consensus pattern (43 bp):
ACAGGGGCTCTGTACAGCGGCACACAGGGGATGTACAGGGTAT
Found at i:433329 original size:23 final size:22
Alignment explanation
Indices: 433250--433340 Score: 82
Period size: 23 Copynumber: 4.2 Consensus size: 22
433240 GGCAGGGGCT
*
433250 TACAGTGGCACACAGGGGTTGTG
1 TACAGTGGCACACAGGGG-TATG
* *
433273 TACAGCGGCGCACAGGGG-ATG
1 TACAGTGGCACACAGGGGTATG
* * *
433294 -ACAG-GGTATACAGGGGCTCTG
1 TACAGTGGCACACAGGGG-TATG
433315 TACAGTGGCACACAGGGG-ATG
1 TACAGTGGCACACAGGGGTATG
433336 TACAG
1 TACAG
433341 GGGATGACAG
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
19 9 0.17
20 4 0.07
21 11 0.20
22 4 0.07
23 26 0.48
ACGTcount: A:0.25, C:0.20, G:0.38, T:0.16
Consensus pattern (22 bp):
TACAGTGGCACACAGGGGTATG
Found at i:438957 original size:34 final size:34
Alignment explanation
Indices: 438914--438980 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
438904 TGTGTAGAGC
** *
438914 TATAAACACACAGTTTGTTACATCATTGAATAAA
1 TATAAACACACAGTCCGTTACATCACTGAATAAA
*
438948 TATAAACACACGGTCCGTTACATCACTGAATAA
1 TATAAACACACAGTCCGTTACATCACTGAATAA
438981 GTTTGTGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (34 bp):
TATAAACACACAGTCCGTTACATCACTGAATAAA
Found at i:439015 original size:46 final size:46
Alignment explanation
Indices: 438948--439549 Score: 825
Period size: 46 Copynumber: 13.7 Consensus size: 46
438938 ATTGAATAAA
438948 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
438994 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
*
439040 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTGGAGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
439086 TATAAACACACGGTCCGTTACATCACTGAAT-A--------A-A--
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
439120 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
* *
439166 TATAAACACACGGTCCGTTACATCACTGAATAA------ATACATG-
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGA-GC
439206 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
439252 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
* *
439298 TATAAACACACGGTCCGTTACATCACTGAATATGTCTGTGTAGAGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
*
439344 TATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
* *
439390 TATAAACACACGGTCTGTTACATCATTGAAT-A--------A-A--
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
439424 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
* * * ** *
439470 TACAAACACACGGTCCGTTACATCACTCAATAAGTCTACGTAGGGC
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
* * *
439516 TATAAACACACGGTCAGTTATATCACGGAATAAG
1 TATAAACACACGGTCCGTTACATCACTGAATAAG
439550 ATACCGGTTA
Statistics
Matches: 500, Mismatches: 24, Indels: 64
0.85 0.04 0.11
Matches are distributed among these distances:
34 60 0.12
35 2 0.00
36 2 0.00
37 1 0.00
40 36 0.07
41 1 0.00
43 2 0.00
44 2 0.00
45 3 0.01
46 391 0.78
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (46 bp):
TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGC
Found at i:439129 original size:34 final size:34
Alignment explanation
Indices: 439086--439152 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
439076 TGTGTGGAGC
439086 TATAAACACACGGTCCGTTACATCACTGAATAAA
1 TATAAACACACGGTCCGTTACATCACTGAATAAA
439120 TATAAACACACGGTCCGTTACATCACTGAATAA
1 TATAAACACACGGTCCGTTACATCACTGAATAA
439153 GTTTGTGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (34 bp):
TATAAACACACGGTCCGTTACATCACTGAATAAA
Found at i:439355 original size:258 final size:252
Alignment explanation
Indices: 438904--439376 Score: 829
Period size: 258 Copynumber: 1.9 Consensus size: 252
438894 TGTGCAAAAA
** *
438904 TGTGTAGAGCTATAAACACACAGTTTGTTACATCATTGAATAAATATAAACACACGGTCCGTTAC
1 TGTGTAGAGCTATAAACACACAGTCCGTTACATCACTGAATAAATATAAACACACGGTCCGTTAC
438969 ATCACTGAATAAGTTTGTGTAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTG
66 ATCACTGAATAAGTTTGTGTAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTG
* *
439034 TAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTGGAGCTATAAACACACGG
131 TAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTATAAACACACGG
439099 TCCGTTACATCACTGAATAAATATAAACACACGGTCCGTTACATCACTGAATAAGTT
196 TCCGTTACATCACTGAATAAATATAAACACACGGTCCGTTACATCACTGAATAAGTT
*
439156 TGTGTAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAATACATGTATAAACACACGGTC
1 TGTGTAGAGCTATAAACACACAGTCCGTTACATCACTGAAT--A-A-A--TATAAACACACGGTC
439221 CGTTACATCACTGAATAAGTTTGTGTAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAG
60 CGTTACATCACTGAATAAGTTTGTGTAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAG
*
439286 TTTGTGTAGAGCTATAAACACACGGTCCGTTACATCACTGAATATGTCTGTGTAGAGCTATAAAC
125 TTTGTGTAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTATAAAC
439351 ACACGGTCCGTTACATCACTGAATAA
190 ACACGGTCCGTTACATCACTGAATAA
439377 GTCTGTGTAG
Statistics
Matches: 208, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
252 37 0.18
254 1 0.00
255 1 0.00
256 1 0.00
258 168 0.81
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (252 bp):
TGTGTAGAGCTATAAACACACAGTCCGTTACATCACTGAATAAATATAAACACACGGTCCGTTAC
ATCACTGAATAAGTTTGTGTAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTG
TAGAGCTATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTATAAACACACGG
TCCGTTACATCACTGAATAAATATAAACACACGGTCCGTTACATCACTGAATAAGTT
Found at i:439433 original size:34 final size:34
Alignment explanation
Indices: 439390--439456 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
439380 TGTGTAGAGC
* *
439390 TATAAACACACGGTCTGTTACATCATTGAATAAA
1 TATAAACACACGGTCCGTTACATCACTGAATAAA
439424 TATAAACACACGGTCCGTTACATCACTGAATAA
1 TATAAACACACGGTCCGTTACATCACTGAATAA
439457 GTTTGTGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (34 bp):
TATAAACACACGGTCCGTTACATCACTGAATAAA
Found at i:439477 original size:80 final size:80
Alignment explanation
Indices: 439344--439494 Score: 275
Period size: 80 Copynumber: 1.9 Consensus size: 80
439334 TGTGTAGAGC
* *
439344 TATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTATAAACACACGGTCTGTT
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTACAAACACACGGTCCGTT
439409 ACATCATTGAATAAA
66 ACATCATTGAATAAA
*
439424 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGCTACAAACACACGGTCCGTT
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTACAAACACACGGTCCGTT
439489 ACATCA
66 ACATCA
439495 CTCAATAAGT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (80 bp):
TATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTACAAACACACGGTCCGTT
ACATCATTGAATAAA
Found at i:439523 original size:126 final size:126
Alignment explanation
Indices: 439298--439540 Score: 405
Period size: 126 Copynumber: 1.9 Consensus size: 126
439288 TGTGTAGAGC
* *
439298 TATAAACACACGGTCCGTTACATCACTGAATATGTCTGTGTAGAGCTATAAACACACGGTCCGTT
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTACAAACACACGGTCCGTT
* ** *
439363 ACATCACTGAATAAGTCTGTGTAGAGCTATAAACACACGGTCTGTTACATCATTGAATAAA
66 ACATCACTCAATAAGTCTACGTAGAGCTATAAACACACGGTCAGTTACATCATTGAATAAA
*
439424 TATAAACACACGGTCCGTTACATCACTGAATAAGTTTGTGTAGAGCTACAAACACACGGTCCGTT
1 TATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTACAAACACACGGTCCGTT
* *
439489 ACATCACTCAATAAGTCTACGTAGGGCTATAAACACACGGTCAGTTATATCA
66 ACATCACTCAATAAGTCTACGTAGAGCTATAAACACACGGTCAGTTACATCA
439541 CGGAATAAGA
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 108 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (126 bp):
TATAAACACACGGTCCGTTACATCACTGAATAAGTCTGTGTAGAGCTACAAACACACGGTCCGTT
ACATCACTCAATAAGTCTACGTAGAGCTATAAACACACGGTCAGTTACATCATTGAATAAA
Found at i:441837 original size:30 final size:30
Alignment explanation
Indices: 441803--441877 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
441793 GTGCTTCTCA
*
441803 AAATTCAGTGTCTCAAGTGAATG-TCCTTTT
1 AAATTCAGTGTCTCAAGTGAATGTTCC-TTC
*
441833 AAATTCAGTGTCTCAAGTGAGTGTTCCTTC
1 AAATTCAGTGTCTCAAGTGAATGTTCCTTC
*
441863 AAATTCAGTGCCTCA
1 AAATTCAGTGTCTCA
441878 GATGCGTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 38 0.93
31 3 0.07
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (30 bp):
AAATTCAGTGTCTCAAGTGAATGTTCCTTC
Found at i:441889 original size:30 final size:30
Alignment explanation
Indices: 441776--441877 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
441766 CTACCTCGAT
**
441776 TTCAGTGCCTCAAGTTTGTGCTT-C-TCAAAA
1 TTCAGTGCCTCAAGTGAGTG-TTCCTTC-AAA
* * *
441806 TTCAGTGTCTCAAGTGAATG-TCCTTTTAAA
1 TTCAGTGCCTCAAGTGAGTGTTCC-TTCAAA
*
441836 TTCAGTGTCTCAAGTGAGTGTTCCTTCAAA
1 TTCAGTGCCTCAAGTGAGTGTTCCTTCAAA
441866 TTCAGTGCCTCA
1 TTCAGTGCCTCA
441878 GATGCGTGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 54 0.90
31 4 0.07
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (30 bp):
TTCAGTGCCTCAAGTGAGTGTTCCTTCAAA
Found at i:442969 original size:31 final size:31
Alignment explanation
Indices: 442931--443009 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
442921 TTCAGGCAAA
* * *
442931 GGGGTCATTGTTCTACGTAGAATAATGACCG
1 GGGGTCATTATTCTACGTAGAAAAATGACCC
*
442962 GGGGTCATTATTCTACGTCGAAAAATGACCC
1 GGGGTCATTATTCTACGTAGAAAAATGACCC
**
442993 CCGGTCATTATTCTACG
1 GGGGTCATTATTCTACG
443010 GGGGTCATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (31 bp):
GGGGTCATTATTCTACGTAGAAAAATGACCC
Found at i:452531 original size:18 final size:18
Alignment explanation
Indices: 452456--452536 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
452446 TCACAAACAA
* *
452456 CACCAACAACAACGCCAT
1 CACCAACAACAACGACAG
* *
452474 CATCAACAACAACAACA-
1 CACCAACAACAACGACAG
* * *
452491 CTATCAACAGCAACGGCTTCAG
1 C-ACCAACAACAAC-G--ACAG
452513 CACCAACAACAACGACAG
1 CACCAACAACAACGACAG
452531 CACCAA
1 CACCAA
452537 AGACAAATGA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
17 1 0.02
18 34 0.69
20 1 0.02
21 12 0.24
22 1 0.02
ACGTcount: A:0.46, C:0.38, G:0.09, T:0.07
Consensus pattern (18 bp):
CACCAACAACAACGACAG
Found at i:457129 original size:23 final size:23
Alignment explanation
Indices: 457087--457130 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
457077 TTAGTTATAG
* *
457087 TACAACTTTTGAATGTATCATCA
1 TACAACTTTTGAACGGATCATCA
457110 TACAACTTTTGAACGGATCAT
1 TACAACTTTTGAACGGATCAT
457131 TGTAGCAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (23 bp):
TACAACTTTTGAACGGATCATCA
Found at i:465300 original size:20 final size:19
Alignment explanation
Indices: 465254--465309 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
465244 CTTCTGTAAC
465254 TTGTGTCTTAGTGACTTGA
1 TTGTGTCTTAGTGACTTGA
* *
465273 TAGTGTCTTTGTGACTTCGA
1 TTGTGTCTTAGTGACTT-GA
*
465293 TTGTGTCTTGGTGACTT
1 TTGTGTCTTAGTGACTT
465310 TCGACTGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.48
Consensus pattern (19 bp):
TTGTGTCTTAGTGACTTGA
Found at i:471146 original size:2 final size:2
Alignment explanation
Indices: 471134--471177 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
471124 TAAGGTAATA
*
471134 TC TC AC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
471176 TC
1 TC
471178 ATGATAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:474814 original size:2 final size:2
Alignment explanation
Indices: 474807--474848 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
474797 GTTGAAACAA
474807 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
474849 ATGATATCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:474907 original size:2 final size:2
Alignment explanation
Indices: 474900--474932 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
474890 TAAATTTGAA
474900 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
474933 ACACACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:474962 original size:88 final size:88
Alignment explanation
Indices: 474812--474987 Score: 271
Period size: 88 Copynumber: 2.0 Consensus size: 88
474802 AACAATCTCT
* * ** *
474812 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATGATATCATATTACTAAAAGTTTTGTT
1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACAATATCATATTACTAAAACTTTTGTT
*
474877 TTTACTTTTATTGTAAATTTGAA
66 TTTACTTTGATTGTAAATTTGAA
* * *
474900 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACAATATTATTTTATTAAAACTTTTGTT
1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACAATATCATATTACTAAAACTTTTGTT
474965 TTTACTTTGATTGTAAATTTGAA
66 TTTACTTTGATTGTAAATTTGAA
474988 ATTCATTTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.49
Consensus pattern (88 bp):
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACAATATCATATTACTAAAACTTTTGTT
TTTACTTTGATTGTAAATTTGAA
Found at i:478508 original size:202 final size:201
Alignment explanation
Indices: 478162--478565 Score: 799
Period size: 202 Copynumber: 2.0 Consensus size: 201
478152 ATGTATACAT
478162 TGTTTAATTTTGGTTTTAAAATTGTACTCAGGACAGTGGCTTGAGATGATGATAATCGTCTATCT
1 TGTTTAATTTTGGTTTTAAAATTGTACTCAGGACAGTGGCTTGAGATGATGATAATCGTCTATCT
478227 CCTTAATTAATTCAAACGGGAACGAGCTGGAAACAACATAGAGACGTATAAAACATTGCAAGTAC
66 CCTTAATTAATTCAAACGGGAACGAGCTGGAAACAACATAGAGACGTATAAAACATTGCAAGTAC
478292 AACAACTCATGCAATACATTACGTAAAATTGCATACTATGTATATTGACACTAACAGGTATACTA
131 AACAACTCATGCAATACATTACGTAAAATTGCATACTATGTATATTGACACTAACAGGTATACTA
478357 ATAATA
196 ATAATA
478363 NTGTTTAATTTTGGTTTTAAAATTGTACTCAGGACAGTGGCTTGAGATGATGATAATCGTCTATC
1 -TGTTTAATTTTGGTTTTAAAATTGTACTCAGGACAGTGGCTTGAGATGATGATAATCGTCTATC
478428 TCCTTAATTAATTCAAACGGGAACGAGCTGGAAACAACATAGAGACGTATAAAACATTGCAAGTA
65 TCCTTAATTAATTCAAACGGGAACGAGCTGGAAACAACATAGAGACGTATAAAACATTGCAAGTA
478493 CAACAACTCATGCAATACATTACGTAAAATTGCATACTATGTATATTGACACTAACAGGTATACT
130 CAACAACTCATGCAATACATTACGTAAAATTGCATACTATGTATATTGACACTAACAGGTATACT
478558 AATAATA
195 AATAATA
478565 T
1 T
478566 ATGGAAGTGT
Statistics
Matches: 202, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
201 1 0.00
202 201 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (201 bp):
TGTTTAATTTTGGTTTTAAAATTGTACTCAGGACAGTGGCTTGAGATGATGATAATCGTCTATCT
CCTTAATTAATTCAAACGGGAACGAGCTGGAAACAACATAGAGACGTATAAAACATTGCAAGTAC
AACAACTCATGCAATACATTACGTAAAATTGCATACTATGTATATTGACACTAACAGGTATACTA
ATAATA
Found at i:497319 original size:2 final size:2
Alignment explanation
Indices: 497314--497339 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
497304 GAGAAAGAAA
497314 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
497340 TAAATTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:498464 original size:21 final size:21
Alignment explanation
Indices: 498438--498506 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
498428 ACGCTTTGCC
498438 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
** ** *
498459 CGAAACGCTTCAC-AATCACA
1 CGAAACGCTAAACGGTTTACA
498479 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
498500 CGAAACG
1 CGAAACG
498507 TTTCTCGCAC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (21 bp):
CGAAACGCTAAACGGTTTACA
Found at i:502265 original size:2 final size:2
Alignment explanation
Indices: 502258--502298 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
502248 CCTTATTAGT
*
502258 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
502299 TTACCTCTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:502381 original size:2 final size:2
Alignment explanation
Indices: 502376--502430 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
502366 CCTTTTTTGT
502376 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
502418 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
502431 TTGAAACCGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:508099 original size:18 final size:18
Alignment explanation
Indices: 508076--508113 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
508066 ACTTATCAAA
508076 TTGAGAAAGAGAGAGAGT
1 TTGAGAAAGAGAGAGAGT
*
508094 TTGAGAGAGAGAGAGAGT
1 TTGAGAAAGAGAGAGAGT
508112 TT
1 TT
508114 ATTACCGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (18 bp):
TTGAGAAAGAGAGAGAGT
Found at i:511347 original size:63 final size:62
Alignment explanation
Indices: 511244--511368 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 62
511234 AAAAAAAAAA
* *
511244 AATAATAATAAGAAACAGTAGAATAACAGAAGGGTTTTCCGTTGAAAAACGGAAAACCCTAAT
1 AATAATAATAAGAAACAGTACAATAACAGAAGGGTCTTCCGTTG-AAAACGGAAAACCCTAAT
* * * * * *
511307 AATAATAATAAGAAACATTACAATCACTATAA-GGTCTTCCGTTGGAAACGGAAGACCTTAAT
1 AATAATAATAAGAAACAGTACAATAAC-AGAAGGGTCTTCCGTTGAAAACGGAAAACCCTAAT
511369 TATACATCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 15 0.28
63 35 0.66
64 3 0.06
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.23
Consensus pattern (62 bp):
AATAATAATAAGAAACAGTACAATAACAGAAGGGTCTTCCGTTGAAAACGGAAAACCCTAAT
Found at i:518833 original size:2 final size:2
Alignment explanation
Indices: 518826--518877 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
518816 TTTTAACATT
518826 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
518868 GA GA GA GA GA
1 GA GA GA GA GA
518878 TTGATTGTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:522323 original size:96 final size:95
Alignment explanation
Indices: 522194--522366 Score: 319
Period size: 96 Copynumber: 1.8 Consensus size: 95
522184 ATGTAACCAA
* *
522194 AACATTTTTAAAAACGTTATTACAACGTGAATCTGTGTGGTTTTTTTTACGTTATAATAACATTT
1 AACATTTTTAAAAACGTTATTACAACGTAAATCTGTGTGGTTTTTGTTACGTTATAATAACATTT
522259 TCTAAAAACATTTGTAAGAAATGTTTATAG
66 TCTAAAAACATTTGTAAGAAATGTTTATAG
522289 AACATTTTTAAAAAACGTTATTACAACGTAAATCTGTGTGGTTTTTGTTACGTTATAATAACATT
1 AACATTTTT-AAAAACGTTATTACAACGTAAATCTGTGTGGTTTTTGTTACGTTATAATAACATT
522354 TTCTAAAAACATT
65 TTCTAAAAACATT
522367 CCTATGAAAT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
95 9 0.12
96 66 0.88
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (95 bp):
AACATTTTTAAAAACGTTATTACAACGTAAATCTGTGTGGTTTTTGTTACGTTATAATAACATTT
TCTAAAAACATTTGTAAGAAATGTTTATAG
Found at i:524087 original size:11 final size:11
Alignment explanation
Indices: 524073--524107 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
524063 ACAACAAAAA
524073 TAAAATGTTTT
1 TAAAATGTTTT
* *
524084 TAAAACGTTCT
1 TAAAATGTTTT
524095 TAAAATGTTTT
1 TAAAATGTTTT
524106 TA
1 TA
524108 TGAAAACGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (11 bp):
TAAAATGTTTT
Found at i:525527 original size:3 final size:3
Alignment explanation
Indices: 525519--525584 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
525509 AGTATTACCC
* * * *
525519 ATT ATT ATT -TT ATT ATT ATC AAT ATT ATT ATT -TT ATT ATC ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
525565 ATCT ATT ATT ATTT ATT ATT
1 AT-T ATT ATT A-TT ATT ATT
525585 TTCCTGGTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:525546 original size:20 final size:20
Alignment explanation
Indices: 525521--525559 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
525511 TATTACCCAT
525521 TATTATT-TTATTATTATCAA
1 TATTATTATT-TTATTATCAA
525541 TATTATTATTTTATTATCA
1 TATTATTATTTTATTATCA
525560 TTAATATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATTATTTTATTATCAA
Found at i:525548 original size:23 final size:23
Alignment explanation
Indices: 525519--525584 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 23
525509 AGTATTACCC
525519 ATTATTATTTTATTATTATCAAT
1 ATTATTATTTTATTATTATCAAT
* *
525542 ATTATTATTTTATTATCATTAAT
1 ATTATTATTTTATTATTATCAAT
525565 ATCTATTATTATTTATTATT
1 AT-TATTA-T-TTTATTATT
525585 TTCCTGGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.62
24 5 0.14
25 1 0.03
26 8 0.22
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTATTATTTTATTATTATCAAT
Found at i:535813 original size:8 final size:8
Alignment explanation
Indices: 535800--535829 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
535790 TTTACTTATG
535800 TTTTTGTT
1 TTTTTGTT
535808 TTTTTGTTT
1 TTTTTG-TT
535817 TTTTTGTT
1 TTTTTGTT
535825 TTTTT
1 TTTTT
535830 TTCTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (8 bp):
TTTTTGTT
Found at i:535831 original size:10 final size:9
Alignment explanation
Indices: 535800--535830 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
535790 TTTACTTATG
535800 TTTTTG-TT
1 TTTTTGTTT
535808 TTTTTGTTT
1 TTTTTGTTT
535817 TTTTTGTTT
1 TTTTTGTTT
535826 TTTTT
1 TTTTT
535831 TCTATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:544992 original size:1 final size:1
Alignment explanation
Indices: 544986--545013 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
544976 GCTGATTATG
544986 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
545014 AAAGGAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:560649 original size:21 final size:21
Alignment explanation
Indices: 560613--560885 Score: 235
Period size: 21 Copynumber: 13.0 Consensus size: 21
560603 AAAATATTTT
* *
560613 TTTCGCAAATAAACGCTAAAC
1 TTTCGCGAATAAACGCGAAAC
* *
560634 TTACGCGAATATACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
**
560655 TTTCGCGATATAAA-GCGTTAC
1 TTTCGCGA-ATAAACGCGAAAC
*
560676 CTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
* *
560697 TTTCGCGAATAAACGTGTAAC
1 TTTCGCGAATAAACGCGAAAC
* * *
560718 TTTTGCGAATTAACGGGAAAC
1 TTTCGCGAATAAACGCGAAAC
* *
560739 TTTCGCGAATTAACGCGTAAC
1 TTTCGCGAATAAACGCGAAAC
* *
560760 TTTCGCGAATTAACGTGAAAC
1 TTTCGCGAATAAACGCGAAAC
** ** *
560781 TTTCGCGAATAATTGCGTTAG
1 TTTCGCGAATAAACGCGAAAC
* *
560802 TGTCGCGAATAAACGCGTAAC
1 TTTCGCGAATAAACGCGAAAC
* **
560823 TTTCGCGAAAAAACGCGTCAC
1 TTTCGCGAATAAACGCGAAAC
*
560844 TTTCGCGAA-ATAACGCAAAAC
1 TTTCGCGAATA-AACGCGAAAC
* * * *
560865 TTTTGCGTATTAACGCAAAAC
1 TTTCGCGAATAAACGCGAAAC
560886 CATTTTATAA
Statistics
Matches: 204, Mismatches: 44, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
20 6 0.03
21 194 0.95
22 4 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (21 bp):
TTTCGCGAATAAACGCGAAAC
Found at i:561842 original size:21 final size:21
Alignment explanation
Indices: 561772--561842 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
561762 AAAAAAAACC
* *
561772 CGCGTTTTATCGCGAAAGTTT
1 CGCGTTTTATCGCAAAAGTTA
* *
561793 CGCATTTGT-TTGCAAAAG-TA
1 CGCGTTT-TATCGCAAAAGTTA
*
561813 TCGCTTTTTATCGCAAAAGTTA
1 -CGCGTTTTATCGCAAAAGTTA
561835 CGCGTTTT
1 CGCGTTTT
561843 TTTGCTAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 2 0.05
21 34 0.87
22 3 0.08
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (21 bp):
CGCGTTTTATCGCAAAAGTTA
Found at i:561873 original size:83 final size:84
Alignment explanation
Indices: 561773--561953 Score: 213
Period size: 83 Copynumber: 2.2 Consensus size: 84
561763 AAAAAAACCC
* * * * * * *
561773 GCGTTTTATCGCGAAAGTTTCGCATTTGTTTGCAAAAGTATCGCTTTTTATCGCAAAAGTTACGC
1 GCGTTTTTTCGCGAAAGTTTCGCATTTATTCGCAAAAGCAACGCGTTATATCGCAAAAGTTACGC
* *
561838 GTTTTTTTGC-TAAATTTT
66 GTTTATTTGCGGAAATTTT
* * * *
561856 GCGTTTATTT-GCGAAAGTTTCGCGTTTATTCGCGAAAGCAACGCGTTATATCTCGAAAGTTACG
1 GCGTTT-TTTCGCGAAAGTTTCGCATTTATTCGCAAAAGCAACGCGTTATATCGCAAAAGTTACG
*
561920 CGTTTATTTGCGGAAGTTTT
65 CGTTTATTTGCGGAAATTTT
561940 GCGTTTTTTCGCGA
1 GCGTTTTTTCGCGA
561954 GAAAAAATAT
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
83 63 0.78
84 18 0.22
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (84 bp):
GCGTTTTTTCGCGAAAGTTTCGCATTTATTCGCAAAAGCAACGCGTTATATCGCAAAAGTTACGC
GTTTATTTGCGGAAATTTT
Found at i:561881 original size:21 final size:21
Alignment explanation
Indices: 561783--561953 Score: 118
Period size: 21 Copynumber: 8.2 Consensus size: 21
561773 GCGTTTTATC
* *
561783 GCGAAAGTTTCGCATTTGTTT
1 GCGAAAGTTTCGCGTTTATTT
* *
561804 GCAAAAGTATCGC-TTT-TTAT
1 GCGAAAGTTTCGCGTTTATT-T
* * *
561824 CGCAAAAGTTACGCGTTTTTTT
1 -GCGAAAGTTTCGCGTTTATTT
* *
561846 GCTAAA-TTTTGCGTTTATTT
1 GCGAAAGTTTCGCGTTTATTT
*
561866 GCGAAAGTTTCGCGTTTATTC
1 GCGAAAGTTTCGCGTTTATTT
*** *
561887 GCGAAAGCAACGCGTTATATCT
1 GCGAAAGTTTCGCGTT-TATTT
*
561909 -CGAAAGTTACGCGTTTATTT
1 GCGAAAGTTTCGCGTTTATTT
* *
561929 GCGGAAGTTTTGCGTTT-TTT
1 GCGAAAGTTTCGCGTTTATTT
561949 CGCGA
1 -GCGA
561954 GAAAAAATAT
Statistics
Matches: 119, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.02
20 27 0.23
21 81 0.68
22 7 0.06
23 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (21 bp):
GCGAAAGTTTCGCGTTTATTT
Found at i:561944 original size:42 final size:42
Alignment explanation
Indices: 561777--561945 Score: 130
Period size: 42 Copynumber: 4.1 Consensus size: 42
561767 AAACCCGCGT
* * * * * * *
561777 TTTATC-GCGAAAGTTTCGCATTTGTTTGCAAAAGTATCGCTT
1 TTTATCTGCGAAAGTTACGCGTTTATTTGCGAAAGTTTTGC-G
* * *
561819 TTTATC-GCAAAAGTTACGCGTTTTTTTGCTAAA-TTTTGCG
1 TTTATCTGCGAAAGTTACGCGTTTATTTGCGAAAGTTTTGCG
* * * ****
561859 TTTATTTGCGAAAGTTTCGCGTTTATTCGCGAAAGCAACGCG
1 TTTATCTGCGAAAGTTACGCGTTTATTTGCGAAAGTTTTGCG
*
561901 TTATATCT-CGAAAGTTACGCGTTTATTTGCGGAAGTTTTGCG
1 TT-TATCTGCGAAAGTTACGCGTTTATTTGCGAAAGTTTTGCG
561943 TTT
1 TTT
561946 TTTCGCGAGA
Statistics
Matches: 98, Mismatches: 26, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
40 5 0.05
41 27 0.28
42 62 0.63
43 4 0.04
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (42 bp):
TTTATCTGCGAAAGTTACGCGTTTATTTGCGAAAGTTTTGCG
Found at i:574020 original size:97 final size:98
Alignment explanation
Indices: 573801--574013 Score: 302
Period size: 97 Copynumber: 2.2 Consensus size: 98
573791 TGATAGACCT
* **
573801 CTGATGTCCTCTGTCCTACATGCTCTGTTGTATATTGAATAATCTCACTCTGTACATTTGTAGGG
1 CTGATGTCCTCAGTCCTACATGCTCTGTTACATATTGAATAA-CTCACTCTGTACATTTGTAGGG
* * * *
573866 AATTGTGGTCCTCATGAGAAGCGCTCTATCTCCT
65 AATGGTGGTCCTCATGAGAAGCGCCCTATCCCCA
*
573900 CTGATGTCCTCAGTCCTACATGCTCTGTTACATATTGAATCA-TCACTCTGTACATTTGTAGGGA
1 CTGATGTCCTCAGTCCTACATGCTCTGTTACATATTGAATAACTCACTCTGTACATTTGTAGGGA
* * * *
573964 GTGGTTGTCCTCATGAGCAGTGCCCTATCCCCA
66 ATGGTGGTCCTCATGAGAAGCGCCCTATCCCCA
573997 CTGATGTCCTCAGTCCT
1 CTGATGTCCTCAGTCCT
574014 CGATGCTGTG
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
97 64 0.63
99 38 0.37
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (98 bp):
CTGATGTCCTCAGTCCTACATGCTCTGTTACATATTGAATAACTCACTCTGTACATTTGTAGGGA
ATGGTGGTCCTCATGAGAAGCGCCCTATCCCCA
Found at i:575727 original size:2 final size:2
Alignment explanation
Indices: 575722--575753 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
575712 CCCCCAACTT
575722 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
575754 AATCAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:580425 original size:16 final size:16
Alignment explanation
Indices: 580404--580434 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
580394 ATATTGAGAT
*
580404 GAAACAGTTCGAAAAA
1 GAAACAGTACGAAAAA
580420 GAAACAGTACGAAAA
1 GAAACAGTACGAAAA
580435 CAATAAGGTC
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:0.58, C:0.13, G:0.19, T:0.10
Consensus pattern (16 bp):
GAAACAGTACGAAAAA
Found at i:580480 original size:52 final size:54
Alignment explanation
Indices: 580418--580532 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 54
580408 CAGTTCGAAA
580418 AAGAAACAGTACGAAAACAATAAGGTCTTCTG-TTGGAAACGGAAGAT-TTAAT
1 AAGAAACAGTACGAAAACAATAAGGTCTTCTGATTGGAAACGGAAGATCTTAAT
* *
580470 AAGAAACAGTACGAAAACAGTAAGGTCTTTTGTTAATTGGAAACGGAAGATCTTAAT
1 AAGAAACAGTACGAAAACAATAAGGTCTTCTG---ATTGGAAACGGAAGATCTTAAT
580527 AAGAAA
1 AAGAAA
580533 TGCAAAAAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
52 30 0.54
56 15 0.27
57 11 0.20
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.23
Consensus pattern (54 bp):
AAGAAACAGTACGAAAACAATAAGGTCTTCTGATTGGAAACGGAAGATCTTAAT
Found at i:586777 original size:13 final size:14
Alignment explanation
Indices: 586745--586785 Score: 75
Period size: 13 Copynumber: 3.0 Consensus size: 14
586735 ATGTCAACTG
586745 ATATAGATACAAAC
1 ATATAGATACAAAC
586759 ATATAGATACAAA-
1 ATATAGATACAAAC
586772 ATATAGATACAAAC
1 ATATAGATACAAAC
586786 TTCTATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.59, C:0.12, G:0.07, T:0.22
Consensus pattern (14 bp):
ATATAGATACAAAC
Found at i:590560 original size:15 final size:15
Alignment explanation
Indices: 590536--590569 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
590526 TTCTGATCAC
590536 CTGTTGTCCGT-CGT
1 CTGTTGTCCGTCCGT
590550 CTGTCTGTCCGTCCGT
1 CTGT-TGTCCGTCCGT
590566 CTGT
1 CTGT
590570 AAACTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 7 0.39
16 7 0.39
ACGTcount: A:0.00, C:0.32, G:0.26, T:0.41
Consensus pattern (15 bp):
CTGTTGTCCGTCCGT
Found at i:592964 original size:160 final size:160
Alignment explanation
Indices: 592571--593034 Score: 680
Period size: 160 Copynumber: 2.9 Consensus size: 160
592561 TAACAACAGA
* * * *
592571 TTCCGTTCATATTCTTTGCATAGGATTAACATATTGAAATGAAATTTGGTATACAGGTTTATCAT
1 TTCCGCTCATTTTCTTCGCATAGGATAAACATATTGAAATGAAATTTGGTATACAGGTTTATCAT
* * * * * *
592636 GATAATGTCTAGGTGAAATTTGATATTGGGTACGATCAAGCAATTTTCAACAGAGTTATGGTCCT
66 GATAATATCTAGGTCAAGTTTGATATTTGGTACGATCGAGCAATTTTCAACAGAGTTATGGCCCT
*
592701 TGGACTTAGAAAAATTGGAGTTATTTGCAGT
131 TGGACTTAG-AAAATTCGAGTTATTTGCAGT
* * *
592732 TTCCGCTCATTTTTTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCAT
1 TTCCGCTCATTTTCTTCGCATAGGATAAACATATTGAAATGAAATTTGGTATACAGGTTTATCAT
592797 GATAATATCTAGGTCAAGTTTGATATTTGGTACGATCGAGCAATTTTCAACAGAGTTATGGCCCT
66 GATAATATCTAGGTCAAGTTTGATATTTGGTACGATCGAGCAATTTTCAACAGAGTTATGGCCCT
592862 TGGACTTAGAAAATTCGAGTTATTTGCAGT
131 TGGACTTAGAAAATTCGAGTTATTTGCAGT
* *
592892 TTCTGCTCATTTTCTTCGCATAGGATAAACATATTGAAATGAAATTTGATATAC-GTGTTTATCA
1 TTCCGCTCATTTTCTTCGCATAGGATAAACATATTGAAATGAAATTTGGTATACAG-GTTTATCA
* * * ** *
592956 TGATAATATCTAGGTCAAGTTTGAT-TTTGGGTATGATAGAGCAATTTCCGTCAGAGTTATGCCC
65 TGATAATATCTAGGTCAAGTTTGATATTT-GGTACGATCGAGCAATTTTCAACAGAGTTATGGCC
*
593020 CTTGGACTTAAAAAA
129 CTTGGACTTAGAAAA
593035 AATCAAAATA
Statistics
Matches: 276, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
159 4 0.01
160 145 0.53
161 127 0.46
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (160 bp):
TTCCGCTCATTTTCTTCGCATAGGATAAACATATTGAAATGAAATTTGGTATACAGGTTTATCAT
GATAATATCTAGGTCAAGTTTGATATTTGGTACGATCGAGCAATTTTCAACAGAGTTATGGCCCT
TGGACTTAGAAAATTCGAGTTATTTGCAGT
Found at i:598309 original size:51 final size:50
Alignment explanation
Indices: 598194--598336 Score: 189
Period size: 51 Copynumber: 2.8 Consensus size: 50
598184 TCTGGTTAGC
* *
598194 TTATCTGTAGGTGTAAAAACATGTATTAAATCTACAGAGAGTAAGTTAAA
1 TTATCTGTAGGTGTGAAAACATGTATTAAATCTACAGAGAGTAACTTAAA
** * *
598244 TTATCTGTTTGTGTGAAAACATGTTTTAAATCTTCAGAGAAGTAACTTAAA
1 TTATCTGTAGGTGTGAAAACATGTATTAAATCTACAGAG-AGTAACTTAAA
* *
598295 TTATCTGTAGGTGTGAAAACCTGTATTGAATCT-CGAGAGAGT
1 TTATCTGTAGGTGTGAAAACATGTATTAAATCTAC-AGAGAGT
598337 GAAATCTGTA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 38 0.47
51 42 0.52
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.35
Consensus pattern (50 bp):
TTATCTGTAGGTGTGAAAACATGTATTAAATCTACAGAGAGTAACTTAAA
Found at i:601315 original size:25 final size:25
Alignment explanation
Indices: 601265--601315 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
601255 ATTTTCATTA
**
601265 GTAAAACACAACCCAATTTTTATAT
1 GTAAAACACAACCCAATTCCTATAT
601290 GTAAAACACAACCCATATTCCT-TAT
1 GTAAAACACAACCCA-ATTCCTATAT
601315 G
1 G
601316 ACAAATTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (25 bp):
GTAAAACACAACCCAATTCCTATAT
Found at i:602970 original size:54 final size:54
Alignment explanation
Indices: 602901--603270 Score: 486
Period size: 54 Copynumber: 7.0 Consensus size: 54
602891 CAGAAATTAG
* * * *
602901 ACATTGGAGAACTGAGATGTTAGGGTTCTACATCTTATCTCAGTCTCGGAAAAT
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCTATCTCAGACTCAGAAAAT
* * *
602955 ACATTGGGGATCTGAGATGTCAGGGTTCTATATCCTATCTCAGACTCAGAAAAT
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCTATCTCAGACTCAGAAAAT
* *
603009 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCTTATCTCAG--TC-GAAATT
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCTATCTCAGACTCAGAAAAT
* * * *
603060 ACATTTGAGAACTGAGATGTCAGAGTCCTACATCCCATCTCCA-ACTCAGAAAAT
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCTATCT-CAGACTCAGAAAAT
* * *
603114 ACATTGGAGAACTGAGATGTCAGGGTTCTAAATCTTATCTCAG--TC-GAAATT
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCTATCTCAGACTCAGAAAAT
* *
603165 ACATTGGAGAACTGAGATGTCAGAGTCCTACATCCTATCTCAGACTCAGAAAAT
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCTATCTCAGACTCAGAAAAT
* *
603219 ACATTGGAG-ACTTGAGATGTCAGGGTTCTACATCCCATCTCAGTCTCAGAAA
1 ACATTGGAGAAC-TGAGATGTCAGGGTTCTACATCCTATCTCAGACTCAGAAA
603271 TTATGATTTG
Statistics
Matches: 273, Mismatches: 34, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
51 84 0.31
52 6 0.02
53 8 0.03
54 175 0.64
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (54 bp):
ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCTATCTCAGACTCAGAAAAT
Found at i:603123 original size:105 final size:105
Alignment explanation
Indices: 602901--603263 Score: 559
Period size: 105 Copynumber: 3.4 Consensus size: 105
602891 CAGAAATTAG
* * * *
602901 ACATTGGAGAACTGAGATGTTAGGGTTCTACATCTTATCTCAGTCTCGGAAAATACATTGGGGAT
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCTTATCTCAG--TC-GAAATTACATTGGAGAA
* * *
602966 CTGAGATGTCAGGGTTCTATATCCTATCTCAGACTCAGAAAAT
63 CTGAGATGTCAGAGTCCTACATCCTATCTCAGACTCAGAAAAT
*
603009 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCTTATCTCAGTCGAAATTACATTTGAGAACTG
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCTTATCTCAGTCGAAATTACATTGGAGAACTG
*
603074 AGATGTCAGAGTCCTACATCCCATCTCCA-ACTCAGAAAAT
66 AGATGTCAGAGTCCTACATCCTATCT-CAGACTCAGAAAAT
*
603114 ACATTGGAGAACTGAGATGTCAGGGTTCTAAATCTTATCTCAGTCGAAATTACATTGGAGAACTG
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCTTATCTCAGTCGAAATTACATTGGAGAACTG
603179 AGATGTCAGAGTCCTACATCCTATCTCAGACTCAGAAAAT
66 AGATGTCAGAGTCCTACATCCTATCTCAGACTCAGAAAAT
**
603219 ACATTGGAG-ACTTGAGATGTCAGGGTTCTACATCCCATCTCAGTC
1 ACATTGGAGAAC-TGAGATGTCAGGGTTCTACATCTTATCTCAGTC
603264 TCAGAAATTA
Statistics
Matches: 237, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
104 4 0.02
105 187 0.79
106 4 0.02
108 42 0.18
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (105 bp):
ACATTGGAGAACTGAGATGTCAGGGTTCTACATCTTATCTCAGTCGAAATTACATTGGAGAACTG
AGATGTCAGAGTCCTACATCCTATCTCAGACTCAGAAAAT
Found at i:603222 original size:159 final size:159
Alignment explanation
Indices: 602901--603270 Score: 491
Period size: 159 Copynumber: 2.3 Consensus size: 159
602891 CAGAAATTAG
* ** * * *
602901 ACATTGGAGAACTGAGATGTTAGGGTTCTACATCTTATCT-CAGTCTCGGAAAATACATTGGGGA
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCCATCTCCAGACTCAGAAAATACATTGGAGA
* *
602965 TCTGAGATGTCAGGGTTCTATATCCTATCTCAGACTCAGAAAATACATTGGAGAACTGAGATGTC
66 ACTGAGATGTCAGGGTTCTAAATCCTATCTCAGA-TCAGAAAATACATTGGAGAACTGAGATGTC
* * * *
603030 AGGGTTCTACATCTTATCTCAGTCGAAATT
130 AGAGTCCTACATCCTATCTCAGTCGAAAAT
* * *
603060 ACATTTGAGAACTGAGATGTCAGAGTCCTACATCCCATCTCCA-ACTCAGAAAATACATTGGAGA
1 ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCCATCTCCAGACTCAGAAAATACATTGGAGA
* *
603124 ACTGAGATGTCAGGGTTCTAAATCTTATCTCAG-TC-GAAATTACATTGGAGAACTGAGATGTCA
66 ACTGAGATGTCAGGGTTCTAAATCCTATCTCAGATCAGAAAATACATTGGAGAACTGAGATGTCA
603187 GAGTCCTACATCCTATCTCAGACTCAGAAAAT
131 GAGTCCTACATCCTATCTCAG--TC-GAAAAT
*
603219 ACATTGGAG-ACTTGAGATGTCAGGGTTCTACATCCCATCT-CAGTCTCAGAAA
1 ACATTGGAGAAC-TGAGATGTCAGGGTTCTACATCCCATCTCCAGACTCAGAAA
603271 TTATGATTTG
Statistics
Matches: 184, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
156 45 0.24
157 2 0.01
158 6 0.03
159 129 0.70
160 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (159 bp):
ACATTGGAGAACTGAGATGTCAGGGTTCTACATCCCATCTCCAGACTCAGAAAATACATTGGAGA
ACTGAGATGTCAGGGTTCTAAATCCTATCTCAGATCAGAAAATACATTGGAGAACTGAGATGTCA
GAGTCCTACATCCTATCTCAGTCGAAAAT
Found at i:610625 original size:28 final size:28
Alignment explanation
Indices: 610580--611607 Score: 408
Period size: 28 Copynumber: 35.8 Consensus size: 28
610570 CATAGGATAT
* * * *
610580 ACTTCATACTAGTTTAAGCTTAAGGAAT
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* ** *
610608 ACTTCTAACTGGTGTAAGCACAGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
*
610636 ACTTCTTACTGGTGTAAG-TTTAGAGAAG
1 ACTTCTTACTGGTGTAAGCTTAAG-GAAG
* * **
610664 ACTTCTAACTGGTGTAAGCCTGGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* * *
610692 ATTTCTAACTGGTGAAAGCTT-AGGTAAG
1 ACTTCTTACTGGTGTAAGCTTAAGG-AAG
* *
610720 ACTTCTTACTGGTGTAAGCATAGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* * **
610748 ACTTCTTATTGGTGTTAGCTTTGGGAA-
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* * *
610775 TCATTCTTACTGGTGTAATCTTAGGGAAG
1 AC-TTCTTACTGGTGTAAGCTTAAGGAAG
* * ** *
610804 ACTTCTTACAGGTGTAAGCCTGGGGAAA
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
*
610832 ATTTCTTACTGGTGTAAGCTTAAGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* * * ** *
610860 ATTTCTCATTGGCATAAGCAT-AGGAAGG
1 ACTTCTTACTGGTGTAAGCTTAAGGAA-G
** *
610888 ACTTCAAACTGGTGTAAGCAT-AGGAAAG
1 ACTTCTTACTGGTGTAAGCTTAAGG-AAG
* *
610916 ACTTCTTACTGGTGAAAGCTTACTGGTGTAAG
1 ACTTCTTACTGGTGTAAGCTTA--AG-G-AAG
*** ** * * *
610948 -CTTGGGGAAGACTTCT-TACTGGTGTAAGCATAGGGAAT
1 ACTT----CTTACTGGTGTA-AGCT-TAA------GGAAG
*
610986 ACTTCTTACTGGTG-AAGCAT-AGGAAAG
1 ACTTCTTACTGGTGTAAGCTTAAGG-AAG
* * *
611013 ACTTCTTACTTGTGAAAGCTTACTGGTGTAAG
1 ACTTCTTACTGGTGTAAGCTTA--AG-G-AAG
*** ** * *
611045 -CTTGGGGAAGACTTCT-TACTGGTGTAAGCATAGGAAAG
1 ACTT----CTTACTGGTGTA-AGCT-TAA-----GG-AAG
* *
611083 ACTTCTTACTGGTGTAGGCTTATGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
*
611111 ACTTCTTACTGGTG-AAGGCTTATGGAAG
1 ACTTCTTACTGGTGTAA-GCTTAAGGAAG
* * *
611139 ATTTCTTACTGGTGTAAGTTTAGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* ** *
611167 A-TTTTTCACTGGCATAAGCAT-AGGAAAG
1 ACTTCTT-ACTGGTGTAAGCTTAAGG-AAG
*
611195 ACTTCTTACTGGTGTAAGCTTAGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* * * *
611223 ACTACTTACTGGTGTAAGCATAGGGAAT
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* * ** *
611251 ACTTCTTTCTGATGTAAGCTTGTGAAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
** * * *
611279 -C-TAATACTGGTGTAAGCCTAGGGAAT
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* *
611305 ACTTCTTACTGGTGTAGGCTTATGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* *
611333 ATTTCTTACTGGTGTAAGCTTAGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* ** * *
611361 A-TTTTTCACTGGCATAGGCAT-AGGAAAG
1 ACTTCTT-ACTGGTGTAAGCTTAAGG-AAG
* ** *
611389 ACTTCTTACTGGTGTAAGAATATAAAAAAAT
1 ACTTCTTACTGGTGTAAG-CT-T-AAGGAAG
611420 ACTTCTTACTGGTGTAAGCTT-AGGAAAG
1 ACTTCTTACTGGTGTAAGCTTAAGG-AAG
* *
611448 ACTACTTACTGGTGTAAGCTTAGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* * * *
611476 ACTACTTATTGGTGTAAG-TATAGGGAAT
1 ACTTCTTACTGGTGTAAGCT-TAAGGAAG
* * ** *
611504 ACTTCTTTCTGATGTAAGCTTGTGAAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
** * * *
611532 -C-TAATACTGGTGTAAGCCTAGGGAAT
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
* **
611558 ACTTCTAACTGGTGTAAGCTTTTGGAAG
1 ACTTCTTACTGGTGTAAGCTTAAGGAAG
611586 ACTTCTTACTGGTGTAAGCTTA
1 ACTTCTTACTGGTGTAAGCTTA
611608 CTGGTGTAAG
Statistics
Matches: 737, Mismatches: 197, Indels: 132
0.69 0.18 0.12
Matches are distributed among these distances:
26 34 0.05
27 43 0.06
28 544 0.74
29 25 0.03
30 2 0.00
31 28 0.04
32 10 0.01
33 1 0.00
34 5 0.01
35 24 0.03
36 6 0.01
38 6 0.01
39 8 0.01
40 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.32
Consensus pattern (28 bp):
ACTTCTTACTGGTGTAAGCTTAAGGAAG
Found at i:610675 original size:56 final size:55
Alignment explanation
Indices: 610580--611607 Score: 452
Period size: 56 Copynumber: 18.4 Consensus size: 55
610570 CATAGGATAT
* * * * *
610580 ACTTCATACTAGTTTAAGCTTAAGGAATACTTCTAACTGGTGTAAGCACAGGGAAG
1 ACTTCTTACTGGTGTAAGCTT-AGGAAGACTTCTAACTGGTGTAAGCATAGGGAAG
* * *
610636 ACTTCTTACTGGTGTAAGTTTAGAGAAGACTTCTAACTGGTGTAAGCCTGGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAG-GAAGACTTCTAACTGGTGTAAGCATAGGGAAG
* * * *
610692 ATTTCTAACTGGTGAAAGCTTAGGTAAGACTTCTTACTGGTGTAAGCATAGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAGG-AAGACTTCTAACTGGTGTAAGCATAGGGAAG
* * * * * * *
610748 ACTTCTTATTGGTGTTAGCTTTGGGAA-TCATTCTTACTGGTGTAATCTTAGGGAAG
1 ACTTCTTACTGGTGTAAGC-TTAGGAAGAC-TTCTAACTGGTGTAAGCATAGGGAAG
* ** * * * * *
610804 ACTTCTTACAGGTGTAAGCCTGGGGAAAATTTCTTACTGGTGTAAGCTTAAGGAAG
1 ACTTCTTACTGGTGTAAG-CTTAGGAAGACTTCTAACTGGTGTAAGCATAGGGAAG
* * * ** * * *
610860 ATTTCTCATTGGCATAAGCATAGGAAGGACTTCAAACTGGTGTAAGCATAGGAAAG
1 ACTTCTTACTGGTGTAAGCTTAGGAA-GACTTCTAACTGGTGTAAGCATAGGGAAG
* * * **
610916 ACTTCTTACTGGTGAAAGCTTACTG--G---TGTAAGCTTGG-G---G-A-A--GACT
1 ACTTCTTACTGGTGTAAGCTTA-GGAAGACTTCTAA-C-TGGTGTAAGCATAGGGAAG
* ** * *** ** * * * * * *****
610961 TCTTAC-TGGT-GT-AAGCATAGGGAATACTTCTTACTGGTGAAGCATAGGAAAGACTTCTT
1 ACTT-CTTACTGGTGTAAGCTTAGGAAGACTTCTAACTGGT---GTA-AGCATAG--GGAAG
* * *
611020 ACTTGTGAAAGCTTACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAGCATAGGAAAG
1 AC-T-T-----CTTACTGGTGTAAGCTT-AGGAAGACTTCTAACTGGTGTAAGCATAGGGAAG
* * * *
611083 ACTTCTTACTGGTGTAGGCTTATGGAAGACTTCTTACTGGTG-AAGGCTTATGGAAG
1 ACTTCTTACTGGTGTAAGCTTA-GGAAGACTTCTAACTGGTGTAA-GCATAGGGAAG
* * * * * ** *
611139 ATTTCTTACTGGTGTAAGTTTAGGGAAGATTTTTCACTGGCATAAGCATAGGAAAG
1 ACTTCTTACTGGTGTAAGCTTA-GGAAGACTTCTAACTGGTGTAAGCATAGGGAAG
* * *
611195 ACTTCTTACTGGTGTAAGCTTAGGGAAGACTACTTACTGGTGTAAGCATAGGGAAT
1 ACTTCTTACTGGTGTAAGCTTA-GGAAGACTTCTAACTGGTGTAAGCATAGGGAAG
* * ** * *
611251 ACTTCTTTCTGATGTAAGCTT-GTGAA-AGCTAAT-ACTGGTGTAAGCCTAGGGAAT
1 ACTTCTTACTGGTGTAAGCTTAG-GAAGA-CTTCTAACTGGTGTAAGCATAGGGAAG
* * * *
611305 ACTTCTTACTGGTGTAGGCTTATGGAAGATTTCTTACTGGTGTAAGCTTAGGGAAG
1 ACTTCTTACTGGTGTAAGCTTA-GGAAGACTTCTAACTGGTGTAAGCATAGGGAAG
* ** * * * * *** *
611361 A-TTTTTCACTGGCATAGGCATAGGAAAGACTTCTTACTGGTGTAAGAATATAAAAAAAT
1 ACTTCTT-ACTGGTGTAAGCTTAGG-AAGACTTCTAACTGGTGTAAG--CAT-AGGGAAG
* * *
611420 ACTTCTTACTGGTGTAAGCTTAGGAAAGACTACTTACTGGTGTAAGCTTAGGGAAG
1 ACTTCTTACTGGTGTAAGCTTAGG-AAGACTTCTAACTGGTGTAAGCATAGGGAAG
* * * ** * * *
611476 ACTACTTATTGGTGTAAG-TATAGGGAATACTTCTTTCTGATGTAAGC-TTGTGAA-
1 ACTTCTTACTGGTGTAAGCT-TA-GGAAGACTTCTAACTGGTGTAAGCATAGGGAAG
** * * * **
611530 AGC-TAATACTGGTGTAAGCCTAGGGAATACTTCTAACTGGTGTAAGCTTTTGGAAG
1 A-CTTCTTACTGGTGTAAGCTTA-GGAAGACTTCTAACTGGTGTAAGCATAGGGAAG
611586 ACTTCTTACTGGTGTAAGCTTA
1 ACTTCTTACTGGTGTAAGCTTA
611608 CTGGTGTAAG
Statistics
Matches: 733, Mismatches: 177, Indels: 124
0.71 0.17 0.12
Matches are distributed among these distances:
42 1 0.00
43 3 0.00
44 2 0.00
45 9 0.01
46 2 0.00
47 4 0.01
48 1 0.00
49 2 0.00
51 3 0.00
52 2 0.00
53 4 0.01
54 78 0.11
55 43 0.06
56 485 0.66
57 11 0.02
58 1 0.00
59 40 0.05
60 5 0.01
61 2 0.00
62 1 0.00
63 2 0.00
65 6 0.01
66 4 0.01
67 2 0.00
68 2 0.00
69 18 0.02
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.32
Consensus pattern (55 bp):
ACTTCTTACTGGTGTAAGCTTAGGAAGACTTCTAACTGGTGTAAGCATAGGGAAG
Found at i:610939 original size:14 final size:14
Alignment explanation
Indices: 610920--610950 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
610910 GGAAAGACTT
610920 CTTACTGGTGAAAG
1 CTTACTGGTGAAAG
*
610934 CTTACTGGTGTAAG
1 CTTACTGGTGAAAG
610948 CTT
1 CTT
610951 GGGGAAGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (14 bp):
CTTACTGGTGAAAG
Found at i:610959 original size:42 final size:42
Alignment explanation
Indices: 610895--610976 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
610885 AGGACTTCAA
610895 ACTGGTGTAAGCATAGGAAAGACTTCTTACTGGTGAAAGCTT
1 ACTGGTGTAAGCATAGGAAAGACTTCTTACTGGTGAAAGCTT
* * * *
610937 ACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAGC
1 ACTGGTGTAAGCATAGGAAAGACTTCTTACTGGTGAAAGC
610977 ATAGGGAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (42 bp):
ACTGGTGTAAGCATAGGAAAGACTTCTTACTGGTGAAAGCTT
Found at i:611045 original size:97 final size:98
Alignment explanation
Indices: 610836--611132 Score: 420
Period size: 97 Copynumber: 3.0 Consensus size: 98
610826 GGGAAAATTT
** * * * ** **
610836 CTTACTGGTGTAAGCTTAAGGAAGATTTCTCATTGGCATAAGCATA-GGAAGGACTTCAAACTGG
1 CTTACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAGCATAGGGAA-GACTTCTTACTGG
610900 TGTAAGCATAGGAAAGACTTCTTACTGGTGAAAG
65 TGTAAGCATAGGAAAGACTTCTTACTGGTGAAAG
*
610934 CTTACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAGCATAGGGAATACTTCTTACTGGT
1 CTTACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGT
*
610999 G-AAGCATAGGAAAGACTTCTTACTTGTGAAAG
66 GTAAGCATAGGAAAGACTTCTTACTGGTGAAAG
*
611031 CTTACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAGCATAGGAAAGACTTCTTACTGGT
1 CTTACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGT
* * *
611096 GTAGGCTTATGG-AAGACTTCTTACTGGTGAAGG
66 GTAAGCATA-GGAAAGACTTCTTACTGGTGAAAG
611129 CTTA
1 CTTA
611133 TGGAAGATTT
Statistics
Matches: 179, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
97 94 0.53
98 79 0.44
99 6 0.03
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (98 bp):
CTTACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGT
GTAAGCATAGGAAAGACTTCTTACTGGTGAAAG
Found at i:611053 original size:69 final size:70
Alignment explanation
Indices: 610962--611092 Score: 228
Period size: 69 Copynumber: 1.9 Consensus size: 70
610952 GGGAAGACTT
*
610962 CTTACTGGTGTAAGCATAGGGAATACTTCTTACTGGTG-AAGCATAGGAAAGACTTCTTACTTGT
1 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCATAGGAAAGACTTCTTACTTGT
611026 GAAAG
66 GAAAG
* *
611031 CTTACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAGCATAGGAAAGACTTCTTACT
1 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCATAGGAAAGACTTCTTACT
611093 GGTGTAGGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (70 bp):
CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCATAGGAAAGACTTCTTACTTGT
GAAAG
Found at i:611061 original size:42 final size:41
Alignment explanation
Indices: 610990--611073 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
610980 GGGAATACTT
*
610990 CTTACTGGTGAAGCATAGGAAAGACTTCTTACTTGTGAAAG
1 CTTACTGGTGAAGCATAGGAAAGACTTCTTACTGGTGAAAG
* * * *
611031 CTTACTGGTGTAAGCTTGGGGAAGACTTCTTACTGGTGTAAG
1 CTTACTGGTG-AAGCATAGGAAAGACTTCTTACTGGTGAAAG
611073 C
1 C
611074 ATAGGAAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 10 0.27
42 27 0.73
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.31
Consensus pattern (41 bp):
CTTACTGGTGAAGCATAGGAAAGACTTCTTACTGGTGAAAG
Found at i:611612 original size:42 final size:42
Alignment explanation
Indices: 611565--611730 Score: 251
Period size: 42 Copynumber: 4.0 Consensus size: 42
611555 AATACTTCTA
**
611565 ACTGGTGTAAGCTTTTGGAAGACTTCTTACTGGTGTAAGCTT
1 ACTGGTGTAAGCTTAGGGAAGACTTCTTACTGGTGTAAGCTT
* * *
611607 ACTGGTGTAAGCTTGGGGAAGATTTCTTACTGATGTAAGCTT
1 ACTGGTGTAAGCTTAGGGAAGACTTCTTACTGGTGTAAGCTT
*
611649 ACTGGTGTAAGCTTAGGGAAGACTTCTCACTGGTGTAAGCTT
1 ACTGGTGTAAGCTTAGGGAAGACTTCTTACTGGTGTAAGCTT
* * *
611691 ATTGGTGCAAGCTTATGGAAGACTTCTTACTGGTGTAAGC
1 ACTGGTGTAAGCTTAGGGAAGACTTCTTACTGGTGTAAGC
611731 ATAGGGAAGA
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 112 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.34
Consensus pattern (42 bp):
ACTGGTGTAAGCTTAGGGAAGACTTCTTACTGGTGTAAGCTT
Found at i:611663 original size:28 final size:28
Alignment explanation
Indices: 611590--611663 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 28
611580 TGGAAGACTT
*
611590 CTTACTGGTGTAAGCTTACTGGTGTAAG
1 CTTACTGGTGTAAGCTTACTGATGTAAG
*
611618 C-T--TGG-GGAAGATTTCTTACTGATGTAAG
1 CTTACTGGTGTAAG----CTTACTGATGTAAG
611646 CTTACTGGTGTAAGCTTA
1 CTTACTGGTGTAAGCTTA
611664 GGGAAGACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 16
0.65 0.06 0.30
Matches are distributed among these distances:
24 4 0.11
25 3 0.09
27 1 0.03
28 19 0.54
29 1 0.03
31 3 0.09
32 4 0.11
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (28 bp):
CTTACTGGTGTAAGCTTACTGATGTAAG
Found at i:611681 original size:112 final size:111
Alignment explanation
Indices: 611536--611870 Score: 424
Period size: 112 Copynumber: 3.0 Consensus size: 111
611526 TGAAAGCTAA
* *
611536 TACTGGTGTAAGCCTAGGGAATACTTCTAACTGGTGTAAGCTTTTGGAAGACTTCTTACTGGTGT
1 TACTGGTGTAAGCTTAGGGAAGACTTCTAACTGGTGTAAGCTTTTGGAAGACTTCTTA-TGGTGT
* *
611601 AAGCTTACTGGTGTAAGCTTGGGGAAGATTTCTTACTGATGTAAGCT
65 AAGCTTACTGGTGTAAGCTTAGGGAAGACTTCTTACTGATGTAAGCT
* * ** *
611648 TACTGGTGTAAGCTTAGGGAAGACTTCTCACTGGTGTAAGCTTATTGG-TG-CAAGCTTATGGAA
1 TACTGGTGTAAGCTTAGGGAAGACTTCTAACTGGTGTAAGCTT-TTGGAAGAC-TTCTTATGG-T
** * *
611711 G-ACTTCTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCT
63 GTA-AGCTTACTGGTGTAAGCTTAGGGAAGACTTCTTACTGATGTAAGCT
* * * **
611760 TACTGGTGTAGGCTTATGGAAGACTTCTTACTGGTGTAAGCTTAGGGAAGACTTCTTATTGGTGT
1 TACTGGTGTAAGCTTAGGGAAGACTTCTAACTGGTGTAAGCTTTTGGAAGACTTCTTA-TGGTGT
*
611825 AAGCTTACTGGTGTAAGCTTAGGGAAGACTTCTTACTGTTGTAAGC
65 AAGCTTACTGGTGTAAGCTTAGGGAAGACTTCTTACTGATGTAAGC
611871 ATAGGGAAGA
Statistics
Matches: 189, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
111 7 0.04
112 173 0.92
113 9 0.05
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.34
Consensus pattern (111 bp):
TACTGGTGTAAGCTTAGGGAAGACTTCTAACTGGTGTAAGCTTTTGGAAGACTTCTTATGGTGTA
AGCTTACTGGTGTAAGCTTAGGGAAGACTTCTTACTGATGTAAGCT
Found at i:611725 original size:70 final size:70
Alignment explanation
Indices: 611646--611900 Score: 420
Period size: 70 Copynumber: 3.6 Consensus size: 70
611636 CTGATGTAAG
* * * *
611646 CTTACTGGTGTAAGCTTAGGGAAGACTTCTCACTGGTGTAAGCTTATTGGTGCAAGCTTATGGAA
1 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCTTACTGGTGTAAGCTTATGGAA
611711 GACTT
66 GACTT
*
611716 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCTTACTGGTGTAGGCTTATGGAA
1 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCTTACTGGTGTAAGCTTATGGAA
611781 GACTT
66 GACTT
* * *
611786 CTTACTGGTGTAAGCTTAGGGAAGACTTCTTATTGGTGTAAGCTTACTGGTGTAAGCTTAGGGAA
1 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCTTACTGGTGTAAGCTTATGGAA
611851 GACTT
66 GACTT
* *
611856 CTTACTGTTGTAAGCATAGGGAAGACTTCTTACTGGTGTTAGCTT
1 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCTT
611901 TGGGATAAAT
Statistics
Matches: 172, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 172 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (70 bp):
CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAGCTTACTGGTGTAAGCTTATGGAA
GACTT
Found at i:611730 original size:28 final size:28
Alignment explanation
Indices: 611688--611761 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
611678 CTGGTGTAAG
* * *
611688 CTTATTGGTGCAAGCTTATGGAAGACTT
1 CTTACTGGTGTAAGCTTAGGGAAGACTT
*
611716 CTTACTGGTGTAAGCATAGGGAAGACTT
1 CTTACTGGTGTAAGCTTAGGGAAGACTT
611744 CTTACTGGTGTAAGCTTA
1 CTTACTGGTGTAAGCTTA
611762 CTGGTGTAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (28 bp):
CTTACTGGTGTAAGCTTAGGGAAGACTT
Found at i:611762 original size:42 final size:42
Alignment explanation
Indices: 611716--611803 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
611706 TGGAAGACTT
611716 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAG
1 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAG
* * *
611758 CTTACTGGTGTAGGCTTATGGAAGACTTCTTACTGGTGTAAG
1 CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAG
611800 CTTA
1 CTTA
611804 GGGAAGACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (42 bp):
CTTACTGGTGTAAGCATAGGGAAGACTTCTTACTGGTGTAAG
Found at i:611790 original size:28 final size:28
Alignment explanation
Indices: 611758--611831 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
611748 CTGGTGTAAG
* *
611758 CTTACTGGTGTAGGCTTATGGAAGACTT
1 CTTACTGGTGTAAGCTTAGGGAAGACTT
611786 CTTACTGGTGTAAGCTTAGGGAAGACTT
1 CTTACTGGTGTAAGCTTAGGGAAGACTT
*
611814 CTTATTGGTGTAAGCTTA
1 CTTACTGGTGTAAGCTTA
611832 CTGGTGTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (28 bp):
CTTACTGGTGTAAGCTTAGGGAAGACTT
Found at i:611818 original size:42 final size:43
Alignment explanation
Indices: 611735--611859 Score: 127
Period size: 42 Copynumber: 3.0 Consensus size: 43
611725 GTAAGCATAG
* *
611735 GGAAGACTTCTTACTGGTGTAAGCTTACTGGTGTAG---GCTTA-T
1 GGAAGACTTCTTACTGGTGTAAGCTTA--GG-GAAGACTTCTTATT
611777 GGAAGACTTCTTACTGGTGTAAGCTTAGGGAAGACTTCTTATT
1 GGAAGACTTCTTACTGGTGTAAGCTTAGGGAAGACTTCTTATT
* **
611820 GG-TGTA-AGCTTACTGGTGTAAGCTTAGGGAAGACTTCTTA
1 GGAAG-ACTTCTTACTGGTGTAAGCTTAGGGAAGACTTCTTA
611860 CTGTTGTAAG
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
39 3 0.04
40 2 0.03
42 64 0.88
43 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (43 bp):
GGAAGACTTCTTACTGGTGTAAGCTTAGGGAAGACTTCTTATT
Found at i:611860 original size:28 final size:28
Alignment explanation
Indices: 611828--612041 Score: 261
Period size: 28 Copynumber: 7.6 Consensus size: 28
611818 TTGGTGTAAG
611828 CTTACTGGTGTAAGCTTAGGGAAGACTT
1 CTTACTGGTGTAAGCTTAGGGAAGACTT
* *
611856 CTTACTGTTGTAAGCATAGGGAAGACTT
1 CTTACTGGTGTAAGCTTAGGGAAGACTT
* * *
611884 CTTACTGGTGTTAGCTTTGGGATA-AATT
1 CTTACTGGTGTAAGCTTAGGGA-AGACTT
*
611912 CTTACTGGTGTAATCTTAGGGAAGACTT
1 CTTACTGGTGTAAGCTTAGGGAAGACTT
* * ** *
611940 CTTACTGGTGTTAGCTTTGGGATTAATT
1 CTTACTGGTGTAAGCTTAGGGAAGACTT
*
611968 CTTACTGGTGTAATCTTAGGGAAGACTT
1 CTTACTGGTGTAAGCTTAGGGAAGACTT
* *
611996 CTTACTGGTGTTAA-TTTAGGAAAGACTT
1 CTTACTGGTG-TAAGCTTAGGGAAGACTT
*
612024 CTTTCTGGTGTAAGCTTA
1 CTTACTGGTGTAAGCTTA
612042 CATACTGGTG
Statistics
Matches: 155, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.03
28 147 0.95
29 4 0.03
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (28 bp):
CTTACTGGTGTAAGCTTAGGGAAGACTT
Found at i:611868 original size:42 final size:42
Alignment explanation
Indices: 611786--611870 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
611776 TGGAAGACTT
*
611786 CTTACTGGTGTAAGCTTAGGGAAGACTTCTTATTGGTGTAAG
1 CTTACTGGTGTAAGCTTAGGGAAGACTTCTTACTGGTGTAAG
*
611828 CTTACTGGTGTAAGCTTAGGGAAGACTTCTTACTGTTGTAAG
1 CTTACTGGTGTAAGCTTAGGGAAGACTTCTTACTGGTGTAAG
611870 C
1 C
611871 ATAGGGAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (42 bp):
CTTACTGGTGTAAGCTTAGGGAAGACTTCTTACTGGTGTAAG
Found at i:623780 original size:43 final size:43
Alignment explanation
Indices: 623741--624399 Score: 933
Period size: 43 Copynumber: 15.3 Consensus size: 43
623731 ACAGGGCTCC
*
623741 TGCTCCTGTTGACCAATCAAAGACTATTGTAACATAGGGCACT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
* *
623784 TGCTCCTGTTGACCAATCATAGATTATTATAACATAGGGCACT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
* *
623827 TGCTCCTGTTGACCAATCATAGATTATTATAACATAGGGCACT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
* *
623870 TGCTCCTGTTGACCAATCATAGATTATTATAACATAGGGCACT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
*
623913 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGACACT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
*
623956 TGCTCCAGTTGACCAATCATAGACTATTGTAACATAGGGCACT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
* *
623999 TGCTCCTGTTGACCAATCATAGATTATTATAACATAGGGCACT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
* * *
624042 TGCTCCTGTTGACCAATCATAGATTATTATAACATAGGGCATT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
*
624085 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACA
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
* *
624128 TGCTCCTGTTGACCAATCATATACTATTGTAACATAGGGCACA
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
* * *
624171 TGCTCCTGTTGACCAATCATAGATTATTATAACATAGGACACT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
* * * *
624214 TGCTCCAGTTGACCAATCTTAGACTATTGTAACATTA-GACACA
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACA-TAGGGCACT
*** * * *
624257 TGCTCCTGTTGACTTTTCATTGACTATTGTAACGTAGGGAACT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
* * * * * *
624300 TGCCCCAGCTGACCAACCGTAGACTATTGTAACATAGGGCTCT
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
** * * *
624343 TGCTCCAATTGACCAATCATAGACTTTTGAAACATAGGGCACA
1 TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
624386 TGCTCCTGTTGACC
1 TGCTCCTGTTGACC
624400 TTTCTTAGAT
Statistics
Matches: 554, Mismatches: 60, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
42 2 0.00
43 550 0.99
44 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (43 bp):
TGCTCCTGTTGACCAATCATAGACTATTGTAACATAGGGCACT
Found at i:626503 original size:12 final size:12
Alignment explanation
Indices: 626486--626525 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
626476 AGGTGGGTTT
626486 GAGAAA-AGAGCA
1 GAGAAAGAGAG-A
626498 GAGAAAGAGAGA
1 GAGAAAGAGAGA
*
626510 GAGAGAGAGAGA
1 GAGAAAGAGAGA
626522 GAGA
1 GAGA
626526 GAGATGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.55, C:0.03, G:0.42, T:0.00
Consensus pattern (12 bp):
GAGAAAGAGAGA
Found at i:626545 original size:2 final size:2
Alignment explanation
Indices: 626492--626529 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
626482 GTTTGAGAAA
*
626492 AG AG CAG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
626530 TGGAAAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:655053 original size:25 final size:25
Alignment explanation
Indices: 655025--655074 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
655015 TGATAGTATA
*
655025 TTAGTAGTATATAAGTACTCGGGAC
1 TTAGTAGTATATAAGTACTCAGGAC
*
655050 TTAGTAGTATATTAGTACTCAGGAC
1 TTAGTAGTATATAAGTACTCAGGAC
655075 ACGTAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (25 bp):
TTAGTAGTATATAAGTACTCAGGAC
Found at i:657027 original size:18 final size:18
Alignment explanation
Indices: 657004--657061 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
656994 TCCAAAGTCG
657004 AAATGCATGAAAGTCCTA
1 AAATGCATGAAAGTCCTA
*
657022 AAATGCGTGAAAGTCCTA
1 AAATGCATGAAAGTCCTA
*
657040 AAATGCATGATAGTCCTA
1 AAATGCATGAAAGTCCTA
657058 AAAT
1 AAAT
657062 ATATTTTACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (18 bp):
AAATGCATGAAAGTCCTA
Found at i:657953 original size:54 final size:54
Alignment explanation
Indices: 657893--657997 Score: 167
Period size: 54 Copynumber: 1.9 Consensus size: 54
657883 GCCTGAATTT
* *
657893 TAAAATATTTCTTTTTATGATAAGATTATTCCATGTAGTACTAA-AATAATTGTA
1 TAAAATATTTCATTTTATGATAAGATTATTCCATGTAGCA-TAATAATAATTGTA
*
657947 TAAAATATTTCATTTTATGATCAGATTATTCCATGTAGCATAATAATAATT
1 TAAAATATTTCATTTTATGATAAGATTATTCCATGTAGCATAATAATAATT
657998 ATTATCATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
53 3 0.06
54 44 0.94
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (54 bp):
TAAAATATTTCATTTTATGATAAGATTATTCCATGTAGCATAATAATAATTGTA
Found at i:663931 original size:59 final size:59
Alignment explanation
Indices: 663790--663906 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 59
663780 GGCAGGTGAA
* *
663790 GACCAAGAACTTACTGAAAACAAAGAAAACCATTGATTGAACAGTGTGTACTATACATT
1 GACCAAGGACTTACTGAAAATAAAGAAAACCATTGATTGAACAGTGTGTACTATACATT
663849 GACCAAGGACTTACTGAAAATAAAGAAAACCATTGATTGAACAGTGTGTACTATACAT
1 GACCAAGGACTTACTGAAAATAAAGAAAACCATTGATTGAACAGTGTGTACTATACAT
663907 ACCCAATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (59 bp):
GACCAAGGACTTACTGAAAATAAAGAAAACCATTGATTGAACAGTGTGTACTATACATT
Found at i:666450 original size:16 final size:16
Alignment explanation
Indices: 666429--666467 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
666419 GTCAAGTCGT
* *
666429 ACCCAACCCGACTCGC
1 ACCCAAACCAACTCGC
*
666445 ACCCAAACCAACTCGT
1 ACCCAAACCAACTCGC
666461 ACCCAAA
1 ACCCAAA
666468 TATTTGAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.49, G:0.08, T:0.08
Consensus pattern (16 bp):
ACCCAAACCAACTCGC
Found at i:668221 original size:21 final size:22
Alignment explanation
Indices: 668186--668227 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
668176 CTGCTATAGC
* *
668186 TGTCCGATGCTTGGT-AAATAT
1 TGTCCGATCCATGGTGAAATAT
668207 TGTCCGATCCATGGTGAAATA
1 TGTCCGATCCATGGTGAAATA
668228 GTTCAACACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (22 bp):
TGTCCGATCCATGGTGAAATAT
Found at i:672683 original size:32 final size:32
Alignment explanation
Indices: 672647--672708 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
672637 TGTATGTGTA
672647 GTTTTAAATCTCAACCTCTCTATTATATGGAT
1 GTTTTAAATCTCAACCTCTCTATTATATGGAT
672679 GTTTTAAATCTCAACCTCTCTATTATATGG
1 GTTTTAAATCTCAACCTCTCTATTATATGG
672709 GACACCAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (32 bp):
GTTTTAAATCTCAACCTCTCTATTATATGGAT
Found at i:682866 original size:34 final size:34
Alignment explanation
Indices: 682822--682894 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
682812 GTTTATTTTG
* *
682822 TCAAATAAATAGAACCCATAAAAATGAAGAATTT
1 TCAAAAAAATAGAACCCATAAAAATGAACAATTT
*
682856 TCAAAAAAATAGAACCCATTAAAATGAACAATTT
1 TCAAAAAAATAGAACCCATAAAAATGAACAATTT
*
682890 ACAAA
1 TCAAA
682895 TATATATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.58, C:0.14, G:0.07, T:0.22
Consensus pattern (34 bp):
TCAAAAAAATAGAACCCATAAAAATGAACAATTT
Found at i:683873 original size:14 final size:14
Alignment explanation
Indices: 683854--683902 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
683844 GGCTACAGTA
683854 CTCTCTCCCCCTCT
1 CTCTCTCCCCCTCT
*** *
683868 CTCTCTCTTTCGCT
1 CTCTCTCCCCCTCT
*
683882 CTCTCTCCCCCTTT
1 CTCTCTCCCCCTCT
683896 CTCTCTC
1 CTCTCTC
683903 TCTTCCCTCT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.00, C:0.55, G:0.02, T:0.43
Consensus pattern (14 bp):
CTCTCTCCCCCTCT
Found at i:683885 original size:18 final size:18
Alignment explanation
Indices: 683864--683915 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
683854 CTCTCTCCCC
*
683864 CTCTCTCTCTCTTTCGCT
1 CTCTCTCCCTCTTTCGCT
* *
683882 CTCTCTCCCCCTTTCTCT
1 CTCTCTCCCTCTTTCGCT
683900 CTCTCTTCCCTCTTTC
1 CTCTC-TCCCTCTTTC
683916 TCTCAAAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 20 0.69
19 9 0.31
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (18 bp):
CTCTCTCCCTCTTTCGCT
Found at i:692039 original size:2 final size:2
Alignment explanation
Indices: 692034--692064 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
692024 ACATACAATA
692034 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
692065 ACAAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:693472 original size:78 final size:80
Alignment explanation
Indices: 693370--693527 Score: 266
Period size: 78 Copynumber: 2.0 Consensus size: 80
693360 ATATAGCAAA
*
693370 GTTTTTTTCGAGTTCCTGGCAAAATTCTTAACAAATCTTTGCAAAATTCTACAGTCAAAATGAAC
1 GTTTTTTTCGAGTTCCCGGCAAAATTCTTAACAAATCTTTGCAAAATTCTACAGTCAAAATGAAC
693435 TTGGTTATAACGAAT
66 TTGGTTATAACGAAT
* *
693450 GTTTTTTT-GAG-TCCCGGTAAAATTCTTAACAAATCTTTGCAAAATTCTACGGTCAAAATGAAC
1 GTTTTTTTCGAGTTCCCGGCAAAATTCTTAACAAATCTTTGCAAAATTCTACAGTCAAAATGAAC
*
693513 TTGGTTATTACGAAT
66 TTGGTTATAACGAAT
693528 TTACTGATAT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
78 63 0.85
79 3 0.04
80 8 0.11
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (80 bp):
GTTTTTTTCGAGTTCCCGGCAAAATTCTTAACAAATCTTTGCAAAATTCTACAGTCAAAATGAAC
TTGGTTATAACGAAT
Found at i:697622 original size:14 final size:14
Alignment explanation
Indices: 697603--697634 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
697593 TAATTTCATG
697603 TTTTTTTTTG-TTT
1 TTTTTTTTTGATTT
697616 TTTTTTTTTGATTT
1 TTTTTTTTTGATTT
697630 TTTTT
1 TTTTT
697635 GCAATAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (14 bp):
TTTTTTTTTGATTT
Found at i:739593 original size:8 final size:7
Alignment explanation
Indices: 739568--739678 Score: 54
Period size: 8 Copynumber: 15.6 Consensus size: 7
739558 GCCTTTAGGT
739568 CGAAGATG
1 CGAAG-TG
739576 CGAGAGTG
1 CGA-AGTG
739584 CGAAGTTG
1 CGAAG-TG
739592 CGAAG-G
1 CGAAGTG
739598 CGAGAGTG
1 CGA-AGTG
* *
739606 TGACG-G
1 CGAAGTG
*
739612 CGAAGGAG
1 CGAA-GTG
739620 CGAAAGTG
1 CG-AAGTG
739628 CGAAGATG
1 CGAAG-TG
*
739636 CGACG-G
1 CGAAGTG
*
739642 CGAAGCG
1 CGAAGTG
739649 CGAAGATG
1 CGAAG-TG
*
739657 CGATG-G
1 CGAAGTG
739663 CGAAG-G
1 CGAAGTG
739669 CGAAG-G
1 CGAAGTG
739675 CGAA
1 CGAA
739679 TGAGCGATAC
Statistics
Matches: 83, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
6 28 0.34
7 15 0.18
8 36 0.43
9 4 0.05
ACGTcount: A:0.31, C:0.16, G:0.44, T:0.09
Consensus pattern (7 bp):
CGAAGTG
Found at i:739601 original size:22 final size:21
Alignment explanation
Indices: 739575--739673 Score: 78
Period size: 22 Copynumber: 4.6 Consensus size: 21
739565 GGTCGAAGAT
*
739575 GCGAGAGTGCGAAGTTGCGAAG
1 GCGA-AGTGCGAAGATGCGAAG
* *
739597 GCGAGAGTGTGACG--GCGAAGG
1 GCGA-AGTGCGAAGATGCGAA-G
*
739618 AGCGAAAGTGCGAAGATGCGACG
1 -GCG-AAGTGCGAAGATGCGAAG
* *
739641 GCGAAGCGCGAAGATGCGATG
1 GCGAAGTGCGAAGATGCGAAG
739662 GCGAAG-GCGAAG
1 GCGAAGTGCGAAG
739674 GCGAATGAGC
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
20 11 0.17
21 23 0.35
22 25 0.38
23 2 0.03
24 4 0.06
ACGTcount: A:0.29, C:0.16, G:0.45, T:0.09
Consensus pattern (21 bp):
GCGAAGTGCGAAGATGCGAAG
Found at i:739652 original size:21 final size:20
Alignment explanation
Indices: 739627--739673 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
739617 GAGCGAAAGT
739627 GCGAAGATGCGACGGCGAAG
1 GCGAAGATGCGACGGCGAAG
*
739647 CGCGAAGATGCGATGGCGAAG
1 -GCGAAGATGCGACGGCGAAG
739668 GCGAAG
1 GCGAAG
739674 GCGAATGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.30, C:0.19, G:0.45, T:0.06
Consensus pattern (20 bp):
GCGAAGATGCGACGGCGAAG
Found at i:739665 original size:27 final size:26
Alignment explanation
Indices: 739635--739686 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
739625 GTGCGAAGAT
*
739635 GCGACGGCGAAGCGCGAA-GATGCGATG
1 GCGAAGGCGAAG-GCGAATGA-GCGATG
739662 GCGAAGGCGAAGGCGAATGAGCGAT
1 GCGAAGGCGAAGGCGAATGAGCGAT
739687 ACTACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.29, C:0.19, G:0.44, T:0.08
Consensus pattern (26 bp):
GCGAAGGCGAAGGCGAATGAGCGATG
Found at i:740433 original size:22 final size:22
Alignment explanation
Indices: 740408--740469 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
740398 TTATAAAAAG
*
740408 GCGAAGGCAAAATTGCGAAGAT
1 GCGAAGGCAAAAGTGCGAAGAT
* * *
740430 GCGAAGGCGAGAGTGCGAAGTT
1 GCGAAGGCAAAAGTGCGAAGAT
* * *
740452 GCGATGGCGAAGGTGCGA
1 GCGAAGGCAAAAGTGCGA
740470 TAGTAGTATC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.42, T:0.13
Consensus pattern (22 bp):
GCGAAGGCAAAAGTGCGAAGAT
Found at i:748150 original size:28 final size:28
Alignment explanation
Indices: 748110--748249 Score: 271
Period size: 28 Copynumber: 5.0 Consensus size: 28
748100 AAGCGTCCAT
*
748110 CAAATGCAAGATTATGCAGTATATAAGA
1 CAAATACAAGATTATGCAGTATATAAGA
748138 CAAATACAAGATTATGCAGTATATAAGA
1 CAAATACAAGATTATGCAGTATATAAGA
748166 CAAATACAAGATTATGCAGTATATAAGA
1 CAAATACAAGATTATGCAGTATATAAGA
748194 CAAATACAAGATTATGCAGTATATAAGA
1 CAAATACAAGATTATGCAGTATATAAGA
748222 CAAATACAAGATTATGCAGTATATAAGA
1 CAAATACAAGATTATGCAGTATATAAGA
748250 GGATTAAAAC
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 111 1.00
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (28 bp):
CAAATACAAGATTATGCAGTATATAAGA
Found at i:749045 original size:20 final size:23
Alignment explanation
Indices: 748997--749045 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
748987 TACTTATATG
* *
748997 ATTTTATCATTGTACAAGGAATA
1 ATTTTATCATTGTAAAAGAAATA
749020 ATTTTATCA-T-TAAAAGAAAT-
1 ATTTTATCATTGTAAAAGAAATA
749040 ATTTTA
1 ATTTTA
749046 AGGTCAGGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 8 0.33
22 1 0.04
23 9 0.38
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (23 bp):
ATTTTATCATTGTAAAAGAAATA
Found at i:752239 original size:21 final size:21
Alignment explanation
Indices: 752215--752272 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
752205 TATTATTATC
*
752215 GCGAATAAACGGGAAACTTTT
1 GCGAATAAACGCGAAACTTTT
**
752236 GCGAATAAACGCGTTACTTTT
1 GCGAATAAACGCGAAACTTTT
752257 GCGAATAAACGCGAAA
1 GCGAATAAACGCGAAA
752273 GTTCATCTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (21 bp):
GCGAATAAACGCGAAACTTTT
Done.