Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397277.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2651878
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 95949 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:1651908 original size:49 final size:49
Alignment explanation
Indices: 1651850--1651986 Score: 141
Period size: 49 Copynumber: 2.8 Consensus size: 49
1651840 TAATATAGTC
* *
1651850 CATAACATCGTCTGAAATCATCCATAGACGGAACATACATACCTCACAT
1 CATATCATCGTCTGAAATCATCCATGGACGGAACATACATACCTCACAT
* * *** * * *
1651899 CATATCATCGTTTGGAATCATCTGCGGACAGAACATACATATCTCATAT
1 CATATCATCGTCTGAAATCATCCATGGACGGAACATACATACCTCACAT
* * *
1651948 CATATCATTGTCT-AGAATCACCCATGGATGGAACATACA
1 CATATCATCGTCTGA-AATCATCCATGGACGGAACATACA
1651987 AAATCAACAT
Statistics
Matches: 68, Mismatches: 19, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (49 bp):
CATATCATCGTCTGAAATCATCCATGGACGGAACATACATACCTCACAT
Found at i:1654398 original size:2 final size:2
Alignment explanation
Indices: 1654391--1654422 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1654381 ACATGGATGC
1654391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1654423 GTACATGAGA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1655013 original size:12 final size:13
Alignment explanation
Indices: 1654996--1655024 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1654986 TGACTGCATA
1654996 AATTAATTAAT-T
1 AATTAATTAATGT
1655008 AATTAATTAATGT
1 AATTAATTAATGT
1655021 AATT
1 AATT
1655025 GTGGTTAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
AATTAATTAATGT
Found at i:1657101 original size:21 final size:21
Alignment explanation
Indices: 1657075--1657122 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1657065 TGGGTCAAAA
1657075 CAAACAAGGATTAAAACAGAT
1 CAAACAAGGATTAAAACAGAT
*
1657096 CAAACAAGGATTAAAACAGGT
1 CAAACAAGGATTAAAACAGAT
1657117 -AAACAA
1 CAAACAA
1657123 AATTAAGGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (21 bp):
CAAACAAGGATTAAAACAGAT
Found at i:1664758 original size:2 final size:2
Alignment explanation
Indices: 1664751--1664775 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1664741 ATTAAAAGTG
1664751 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1664776 TCCTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1675985 original size:18 final size:18
Alignment explanation
Indices: 1675950--1675985 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1675940 TTCTTCTCTT
*
1675950 TCTTTCTCTTTAATTTTC
1 TCTTTCTCTTTAACTTTC
*
1675968 TCTTTCTCTTTCACTTTC
1 TCTTTCTCTTTAACTTTC
1675986 CGTTTAGGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (18 bp):
TCTTTCTCTTTAACTTTC
Found at i:1677562 original size:2 final size:2
Alignment explanation
Indices: 1677555--1677589 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1677545 ATTATAATTG
1677555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1677590 GGCTAAATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1678237 original size:23 final size:23
Alignment explanation
Indices: 1678205--1678250 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1678195 TGTTAACTTA
* * *
1678205 TTAATGATTTGTATGAAGTGTTG
1 TTAATAATTTGTACGAAATGTTG
1678228 TTAATAATTTGTACGAAATGTTG
1 TTAATAATTTGTACGAAATGTTG
1678251 ATATACTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (23 bp):
TTAATAATTTGTACGAAATGTTG
Found at i:1678568 original size:27 final size:28
Alignment explanation
Indices: 1678538--1678751 Score: 188
Period size: 27 Copynumber: 7.8 Consensus size: 28
1678528 CTTACACACT
*
1678538 ATGTT-AAAAGTTTAATTGTTACATGTC
1 ATGTTGAAAAATTTAATTGTTACATGTC
*
1678565 ATGTTGAAAAATGTAATTGTTACATGT-
1 ATGTTGAAAAATTTAATTGTTACATGTC
* * **
1678592 -TGTGTCAAAAATTTAGTTGTTACACATC
1 ATGT-TGAAAAATTTAATTGTTACATGTC
* * * *
1678620 ATGTTG-AAGATTTTATTGTTACACGTT
1 ATGTTGAAAAATTTAATTGTTACATGTC
* * * * *
1678647 TTGTTAAAAAATGTAGTTGTTACACGTC
1 ATGTTGAAAAATTTAATTGTTACATGTC
1678675 ATGTTG-AAAATTTAATTGTTACATGTC
1 ATGTTGAAAAATTTAATTGTTACATGTC
* * *
1678702 ATATTGAAAAAATATAGTTGTTACATGTC
1 ATGTTG-AAAAATTTAATTGTTACATGTC
* *
1678731 ATGTTG-AAGATTTAGTTGTTA
1 ATGTTGAAAAATTTAATTGTTA
1678752 TACATACTAT
Statistics
Matches: 149, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
26 3 0.02
27 79 0.53
28 40 0.27
29 27 0.18
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (28 bp):
ATGTTGAAAAATTTAATTGTTACATGTC
Found at i:1678612 original size:55 final size:54
Alignment explanation
Indices: 1678537--1678751 Score: 225
Period size: 55 Copynumber: 3.9 Consensus size: 54
1678527 TCTTACACAC
* * * * *
1678537 TATGTTAAAAGTTTAATTGTTACATGTCATGTTGAAAAATGTAATTGTTACATGT
1 TATGTAAAAAATTTAGTTGTTACACGTCATGTTG-AAAATTTAATTGTTACATGT
* * * * * *
1678592 TGTGTCAAAAATTTAGTTGTTACACATCATGTTGAAGATTTTATTGTTACACGT
1 TATGTAAAAAATTTAGTTGTTACACGTCATGTTGAAAATTTAATTGTTACATGT
* *
1678646 TTTGTTAAAAAATGTAGTTGTTACACGTCATGTTGAAAATTTAATTGTTACATGT
1 TATG-TAAAAAATTTAGTTGTTACACGTCATGTTGAAAATTTAATTGTTACATGT
* * * *
1678701 CATAT-TGAAAAAATATAGTTGTTACATGTCATGTTGAAGATTTAGTTGTTA
1 --TATGT-AAAAAATTTAGTTGTTACACGTCATGTTGAAAATTTAATTGTTA
1678752 TACATACTAT
Statistics
Matches: 134, Mismatches: 22, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
54 19 0.14
55 73 0.54
56 40 0.30
57 2 0.01
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (54 bp):
TATGTAAAAAATTTAGTTGTTACACGTCATGTTGAAAATTTAATTGTTACATGT
Found at i:1678641 original size:82 final size:83
Alignment explanation
Indices: 1678552--1678738 Score: 205
Period size: 82 Copynumber: 2.3 Consensus size: 83
1678542 TAAAAGTTTA
* ** *
1678552 ATTGTTACATGTCATGTTGAAAAATGTAATTGTTACATGTTGTGTCAAAAATTTAGTTGTTACAC
1 ATTGTTACATGTCATGTTGAAAAATGTAATTGTTACACGTCATGTCAAAAATTTAATTGTTACAC
* * * *
1678617 ATCATGTTG-AAGATTTT
66 ATCATATTGAAAAAATAT
* ** * * ** *
1678634 ATTGTTACACGTTTTGTTAAAAAATGTAGTTGTTACACGTCATGTTGAAAATTTAATTGTTACAT
1 ATTGTTACATGTCATGTTGAAAAATGTAATTGTTACACGTCATGTCAAAAATTTAATTGTTACAC
*
1678699 GTCATATTGAAAAAATAT
66 ATCATATTGAAAAAATAT
1678717 AGTTGTTACATGTCATGTTGAA
1 A-TTGTTACATGTCATGTTGAA
1678739 GATTTAGTTG
Statistics
Matches: 82, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
82 60 0.73
83 6 0.07
84 16 0.20
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.42
Consensus pattern (83 bp):
ATTGTTACATGTCATGTTGAAAAATGTAATTGTTACACGTCATGTCAAAAATTTAATTGTTACAC
ATCATATTGAAAAAATAT
Found at i:1684400 original size:21 final size:21
Alignment explanation
Indices: 1684374--1684413 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1684364 TAAGTTACAT
*
1684374 AGAAATCTAAATTATGTATTG
1 AGAAATCTAAATTAGGTATTG
1684395 AGAAATCTAAATTAGGTAT
1 AGAAATCTAAATTAGGTAT
1684414 GTTAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (21 bp):
AGAAATCTAAATTAGGTATTG
Found at i:1687672 original size:2 final size:2
Alignment explanation
Indices: 1687665--1687697 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1687655 ATTTAATTTC
*
1687665 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1687698 TATCTTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1690940 original size:2 final size:2
Alignment explanation
Indices: 1690933--1690967 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
1690923 AAAATATTAT
*
1690933 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
1690968 GTTGTGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1695984 original size:22 final size:22
Alignment explanation
Indices: 1695954--1696009 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1695944 GCAAACTGCT
* *
1695954 ATGTGTTGAGGCCAAGTTACAG
1 ATGTATTGAGACCAAGTTACAG
*
1695976 ATGTATTGAGACCAAGTTATAG
1 ATGTATTGAGACCAAGTTACAG
*
1695998 ATGTATCGAGAC
1 ATGTATTGAGAC
1696010 ATGCTTCAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (22 bp):
ATGTATTGAGACCAAGTTACAG
Found at i:1703215 original size:27 final size:27
Alignment explanation
Indices: 1703185--1703246 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
1703175 TTAGTGATCA
1703185 AATTTGATTGGATCATGGTGACTAGTG
1 AATTTGATTGGATCATGGTGACTAGTG
1703212 AATTTGATTGGATCATGGTGACTAGTG
1 AATTTGATTGGATCATGGTGACTAGTG
1703239 AATTTGAT
1 AATTTGAT
1703247 AGACATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.39
Consensus pattern (27 bp):
AATTTGATTGGATCATGGTGACTAGTG
Found at i:1707467 original size:4 final size:4
Alignment explanation
Indices: 1707458--1707486 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1707448 GAGGGCAGGT
1707458 TTTC TTTC TTTC TTTC TTTC TTT- TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1707487 GAGAACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:1713994 original size:18 final size:18
Alignment explanation
Indices: 1713957--1713994 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1713947 AGACAATAAG
*
1713957 AAGAGAATTATGAAGTAT
1 AAGAGAATTATGAAGAAT
1713975 AAGAGAATTA-GAGAGAAT
1 AAGAGAATTATGA-AGAAT
1713993 AA
1 AA
1713995 CTCTAGAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (18 bp):
AAGAGAATTATGAAGAAT
Found at i:1714346 original size:58 final size:58
Alignment explanation
Indices: 1714277--1714420 Score: 261
Period size: 58 Copynumber: 2.5 Consensus size: 58
1714267 AAAGATACAA
*
1714277 AAGAAGTTGTATGTGAACAAGTATATGAAAAAAAATTATACATGAACAGGTATAAGAG
1 AAGAAGGTGTATGTGAACAAGTATATGAAAAAAAATTATACATGAACAGGTATAAGAG
*
1714335 AAGAAGGTGTATGTGAACAAGTATATGAAAAAAAGTTATACATGAACAGGTATAAGAG
1 AAGAAGGTGTATGTGAACAAGTATATGAAAAAAAATTATACATGAACAGGTATAAGAG
*
1714393 AAGAAGGTGTATGTGAACAAGCATATGA
1 AAGAAGGTGTATGTGAACAAGTATATGA
1714421 GAATAAGGTA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.23
Consensus pattern (58 bp):
AAGAAGGTGTATGTGAACAAGTATATGAAAAAAAATTATACATGAACAGGTATAAGAG
Found at i:1714409 original size:29 final size:29
Alignment explanation
Indices: 1714277--1714429 Score: 117
Period size: 29 Copynumber: 5.3 Consensus size: 29
1714267 AAAGATACAA
* * *
1714277 AAGAAGTTGTATGTGAACAAGTATATGAA
1 AAGAAGGTGTATGTGAACAAGTATAAGAG
* ** * ** *
1714306 AAAAAATTATACATGAACAGGTATAAGAG
1 AAGAAGGTGTATGTGAACAAGTATAAGAG
* *
1714335 AAGAAGGTGTATGTGAACAAGTATATGAA
1 AAGAAGGTGTATGTGAACAAGTATAAGAG
* * * ** *
1714364 AAAAAGTTATACATGAACAGGTATAAGAG
1 AAGAAGGTGTATGTGAACAAGTATAAGAG
* *
1714393 AAGAAGGTGTATGTGAACAAGCATATGAG
1 AAGAAGGTGTATGTGAACAAGTATAAGAG
*
1714422 AATAAGGT
1 AAGAAGGT
1714430 AAGAGAGAGA
Statistics
Matches: 90, Mismatches: 34, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.48, C:0.05, G:0.24, T:0.23
Consensus pattern (29 bp):
AAGAAGGTGTATGTGAACAAGTATAAGAG
Found at i:1714613 original size:18 final size:18
Alignment explanation
Indices: 1714590--1714644 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
1714580 ACTACCATCC
1714590 ATGTGAAATAGTTATTCT
1 ATGTGAAATAGTTATTCT
1714608 ATGTGAAATAGTTATTCT
1 ATGTGAAATAGTTATTCT
*
1714626 ATGTGAAATAGTTACTCT
1 ATGTGAAATAGTTATTCT
1714644 A
1 A
1714645 CTTGTATTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (18 bp):
ATGTGAAATAGTTATTCT
Found at i:1723695 original size:166 final size:167
Alignment explanation
Indices: 1723370--1723704 Score: 600
Period size: 166 Copynumber: 2.0 Consensus size: 167
1723360 GAATTTTAAG
*
1723370 GGACACCAATCTGAGATTCCTTTGAGAATGTTCCAAGACAACATTGCTTACTTCATCATTATGAT
1 GGACACCAATATGAGATTCCTTTGAGAATGTTCCAAGACAACATTGCTTACTTCATCATTATGAT
*
1723435 CAACTAAAAATTGCAAAAGCTTAAAAAAATTCCCTCTATTCTTTGAGTTTTTAGATTCATCACGT
66 CAACTAAAAATTG-AAAAGCTTAAAAAAATTCCCTCTATTCTTTGAGTTTTTAGATTCATCACAT
*
1723500 CCTTAGAAAGCTAGCCCTTGGTGCAAGAGAAACCTAAT
130 CCTTAGAAAGCTAGCCCTTGGTGCAAGAGAAACCAAAT
*
1723538 GGACACCAATATGAGATTCCTTTGAGAATGTTCCAAGACAACTTTGCTTACTTCATCATTATGAT
1 GGACACCAATATGAGATTCCTTTGAGAATGTTCCAAGACAACATTGCTTACTTCATCATTATGAT
* *
1723603 CAACTAAAAATTG-AAAGCTTAAGAAAATTCCCTCTATTCTTTGAGTTTTTAGATTCATCGCATC
66 CAACTAAAAATTGAAAAGCTTAAAAAAATTCCCTCTATTCTTTGAGTTTTTAGATTCATCACATC
1723667 CTTAGAAAGCTAGCCCTTGGTGCAAGAGAAACCAAAT
131 CTTAGAAAGCTAGCCCTTGGTGCAAGAGAAACCAAAT
1723704 G
1 G
1723705 CAGTCCATAA
Statistics
Matches: 161, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
166 85 0.53
168 76 0.47
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (167 bp):
GGACACCAATATGAGATTCCTTTGAGAATGTTCCAAGACAACATTGCTTACTTCATCATTATGAT
CAACTAAAAATTGAAAAGCTTAAAAAAATTCCCTCTATTCTTTGAGTTTTTAGATTCATCACATC
CTTAGAAAGCTAGCCCTTGGTGCAAGAGAAACCAAAT
Found at i:1735041 original size:2 final size:2
Alignment explanation
Indices: 1735034--1735059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1735024 GGCAAGTCAA
1735034 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1735060 GATCAATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1740117 original size:22 final size:20
Alignment explanation
Indices: 1740068--1740116 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1740058 ACAGCAACTC
*
1740068 ATTTCTCTCACCAGTTTTCT
1 ATTTCTCTCACCAATTTTCT
1740088 ATTTCTCTCACCAATTTTCT
1 ATTTCTCTCACCAATTTTCT
*
1740108 CTTTCTCTC
1 ATTTCTCTC
1740117 TCTACCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTCTCTCACCAATTTTCT
Found at i:1742654 original size:24 final size:23
Alignment explanation
Indices: 1742609--1742659 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
1742599 AAAAATCTAG
*
1742609 AAAACCCTAAAATTTTCCTATTTCA
1 AAAACCCTAAAATCTT-CTATTT-A
1742634 AAAACCCTAAAAGTCTT-TATTTA
1 AAAACCCTAAAA-TCTTCTATTTA
1742657 AAA
1 AAA
1742660 CCTAAAGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 5 0.21
25 12 0.50
26 3 0.12
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAACCCTAAAATCTTCTATTTA
Found at i:1743528 original size:2 final size:2
Alignment explanation
Indices: 1743521--1743550 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1743511 TTTATAGACT
1743521 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1743551 AACAATGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1748621 original size:2 final size:2
Alignment explanation
Indices: 1748614--1748645 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1748604 CATACATATT
1748614 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
1748646 TATTAATTCT
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:1752202 original size:29 final size:29
Alignment explanation
Indices: 1752169--1752462 Score: 260
Period size: 28 Copynumber: 10.2 Consensus size: 29
1752159 AAACAAGTAA
*
1752169 TTAATTTAAATAAGAAAACATGTTTTGTC
1 TTAATTTAGATAAGAAAACATGTTTTGTC
* *
1752198 TTAATTTAGACAAG-AAACATGTTATGTC
1 TTAATTTAGATAAGAAAACATGTTTTGTC
* ** * * * *
1752226 TTAATTTACACGAGAGAATATGCTTGGTC
1 TTAATTTAGATAAGAAAACATGTTTTGTC
* * * *
1752255 TTAATTT-GAACAAGAAAATAT-ATTTGTT
1 TTAATTTAG-ATAAGAAAACATGTTTTGTC
*
1752283 TTAATTTAAGATAAGAGAACATGTTTTGTC
1 TTAATTT-AGATAAGAAAACATGTTTTGTC
*
1752313 TTAATTTAGATAA-AAAATATGTTTTGTC
1 TTAATTTAGATAAGAAAACATGTTTTGTC
* *
1752341 TTAATTTAGATAAGAAAAGAT-ATTTGTC
1 TTAATTTAGATAAGAAAACATGTTTTGTC
* * * *
1752369 TTAGTTTAAGATAACAAAAATATATTTTGTC
1 TTAATTT-AGATAA-GAAAACATGTTTTGTC
* *
1752400 TTAATTTAGATAAGAAAACAT-ATTTATC
1 TTAATTTAGATAAGAAAACATGTTTTGTC
* *
1752428 TTAATTTAGACAAGATAAA-ATATTTTGTC
1 TTAATTTAGATAAGA-AAACATGTTTTGTC
1752457 TTAATT
1 TTAATT
1752463 AAAGACAAGA
Statistics
Matches: 217, Mismatches: 37, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
28 95 0.44
29 85 0.39
30 25 0.12
31 12 0.06
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (29 bp):
TTAATTTAGATAAGAAAACATGTTTTGTC
Found at i:1752398 original size:59 final size:57
Alignment explanation
Indices: 1752169--1752462 Score: 258
Period size: 57 Copynumber: 5.1 Consensus size: 57
1752159 AAACAAGTAA
* * * * * * *
1752169 TTAATTTAAATAAGAAAACATGTTTTGTCTTAATTTAGA-CAAGAAACATGTTATGTC
1 TTAATTTAGATAAGAAAACAT-ATTTGTCTTAATTTAGATAAAAAAATATATTTTGTC
* ** * * * * *
1752226 TTAATTTACACGAGAGAATATGCTTGGTCTTAATTT-GA-ACAAGAAAATATA-TTTGTT
1 TTAATTTAGATAAGAAAACAT-ATTTGTCTTAATTTAGATA-AA-AAAATATATTTTGTC
* * *
1752283 TTAATTTAAGATAAGAGAACATGTTTTGTCTTAATTTAGAT-AAAAAATATGTTTTGTC
1 TTAATTT-AGATAAGAAAACAT-ATTTGTCTTAATTTAGATAAAAAAATATATTTTGTC
* *
1752341 TTAATTTAGATAAGAAAAGATATTTGTCTTAGTTTAAGATAACAAAAATATATTTTGTC
1 TTAATTTAGATAAGAAAACATATTTGTCTTAATTT-AGATAA-AAAAATATATTTTGTC
* * *
1752400 TTAATTTAGATAAGAAAACATATTTATCTTAATTTAGACAAGATAAA-ATATTTTGTC
1 TTAATTTAGATAAGAAAACATATTTGTCTTAATTTAGATAA-AAAAATATATTTTGTC
1752457 TTAATT
1 TTAATT
1752463 AAAGACAAGA
Statistics
Matches: 196, Mismatches: 32, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
56 14 0.07
57 81 0.41
58 52 0.27
59 49 0.25
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (57 bp):
TTAATTTAGATAAGAAAACATATTTGTCTTAATTTAGATAAAAAAATATATTTTGTC
Found at i:1752433 original size:87 final size:85
Alignment explanation
Indices: 1752253--1752467 Score: 254
Period size: 87 Copynumber: 2.5 Consensus size: 85
1752243 ATATGCTTGG
* * * *
1752253 TCTTAATTT-GAACAAGAAAATATATTTGTTTTAATTTAAGATAAGAGAACATGTTTTGTCTTAA
1 TCTTAATTTAG-ACAAGAAAA-ATATTTGTCTTAATTTAAGATAAAAAAACATATTTTGTCTTAA
* * *
1752317 TTTAGATAAAAAATATGTTTTG
64 TTTAGATAAAAAACATGATTTA
* * *
1752339 TCTTAATTTAGATAAGAAAAGATATTTGTCTTAGTTTAAGATAACAAAAATATATTTTGTCTTAA
1 TCTTAATTTAGACAAGAAAA-ATATTTGTCTTAATTTAAGATAA-AAAAACATATTTTGTCTTAA
1752404 TTTAGATAAGAAAACAT-ATTTA
64 TTTAGATAA-AAAACATGATTTA
*
1752426 TCTTAATTTAGACAAGATAAAATATTTTGTCTTAATTAAAGA
1 TCTTAATTTAGACAAGA-AAAATA-TTTGTCTTAATTTAAGA
1752468 CAAGAGTTAT
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
86 38 0.35
87 48 0.44
88 24 0.22
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (85 bp):
TCTTAATTTAGACAAGAAAAATATTTGTCTTAATTTAAGATAAAAAAACATATTTTGTCTTAATT
TAGATAAAAAACATGATTTA
Found at i:1758867 original size:72 final size:70
Alignment explanation
Indices: 1758758--1758942 Score: 176
Period size: 70 Copynumber: 2.6 Consensus size: 70
1758748 GGGAAGTCAT
* * * * * *
1758758 ACATTTTGGCCCAAGGTCAACTATAGGCCCTTTATAGTCAATCTTG-GTAAGGAAAAATGGGA-G
1 ACATTTTGGTCCAAGATCGACTATAGACCCTCTATAGTCAATCTTGTG-AA-GAAAAAT-GGACC
1758821 AAAATATGA
63 AAAA-ATGA
* ** * *
1758830 ACATTTTGGTCCAAGATCGACTATAGACCCTCCATAGTTGATCTTGTGAAGCAAAATTGACCAAA
1 ACATTTTGGTCCAAGATCGACTATAGACCCTCTATAGTCAATCTTGTGAAGAAAAATGGACCAAA
*
1758895 AATGG
66 AATGA
* * **
1758900 ATATTCTGGTCCAAGATCGACTATAGATGCTCTATAGTCAATC
1 ACATTTTGGTCCAAGATCGACTATAGACCCTCTATAGTCAATC
1758943 CTATGAAGGG
Statistics
Matches: 92, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
70 41 0.45
71 10 0.11
72 40 0.43
73 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (70 bp):
ACATTTTGGTCCAAGATCGACTATAGACCCTCTATAGTCAATCTTGTGAAGAAAAATGGACCAAA
AATGA
Found at i:1759073 original size:21 final size:21
Alignment explanation
Indices: 1759049--1759092 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1759039 GGGCTCAAAA
1759049 TCCCCAAAATTGAAATTTCAT
1 TCCCCAAAATTGAAATTTCAT
1759070 TCCCCAAAATTGAAATTTCAT
1 TCCCCAAAATTGAAATTTCAT
1759091 TC
1 TC
1759093 GTTTTCCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (21 bp):
TCCCCAAAATTGAAATTTCAT
Found at i:1760445 original size:30 final size:30
Alignment explanation
Indices: 1760409--1760493 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 30
1760399 TACAATGCCA
*
1760409 TGATGCCGGCCATCAGGAGATTACTCCAAG
1 TGATGCCGGCCATCGGGAGATTACTCCAAG
* *
1760439 TGATGCC-GCCGAT-GGGATATTACTTCAAG
1 TGATGCCGGCC-ATCGGGAGATTACTCCAAG
* **
1760468 TGATGCCGACTGTCGGGAGATTACTC
1 TGATGCCGGCCATCGGGAGATTACTC
1760494 TGGTTAATGA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 24 0.55
30 20 0.45
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (30 bp):
TGATGCCGGCCATCGGGAGATTACTCCAAG
Found at i:1761889 original size:29 final size:29
Alignment explanation
Indices: 1761852--1762069 Score: 230
Period size: 29 Copynumber: 7.6 Consensus size: 29
1761842 GGAAGTTTTT
* *
1761852 ACATA-TTTGTCTTAATTGAGATAAGAAA
1 ACATATTTTGTCTTAATTTAGACAAGAAA
* *
1761880 ATATATTTTGTCTTAATTTAGACAAGAAT
1 ACATATTTTGTCTTAATTTAGACAAGAAA
* *
1761909 ACAT-GTTTGTTTTAATTTAGACAAGAAA
1 ACATATTTTGTCTTAATTTAGACAAGAAA
* * *
1761937 ACATGTTTTGCCTTAATTTAAACAAGAAA
1 ACATATTTTGTCTTAATTTAGACAAGAAA
1761966 ACATA-TTTGTCTTAATTTAAGACAAGAAA
1 ACATATTTTGTCTTAATTT-AGACAAGAAA
* * *
1761995 AAATGTTTTGTGC-TAATCTAGACAAGAAA
1 ACATATTTTGT-CTTAATTTAGACAAGAAA
* * * *
1762024 ACAT-GTTTGTCTCAATTTAGATAAGATA
1 ACATATTTTGTCTTAATTTAGACAAGAAA
*
1762052 ACATGTTTTGTCTTAATT
1 ACATATTTTGTCTTAATT
1762070 AAAGACAATA
Statistics
Matches: 157, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
27 1 0.01
28 62 0.39
29 83 0.53
30 10 0.06
31 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (29 bp):
ACATATTTTGTCTTAATTTAGACAAGAAA
Found at i:1761924 original size:57 final size:57
Alignment explanation
Indices: 1761852--1762069 Score: 276
Period size: 57 Copynumber: 3.8 Consensus size: 57
1761842 GGAAGTTTTT
* * * * *
1761852 ACATATTTGTCTTAATTGAGATAAGAAAATATATTTTGTCTTAATTTAGACAAGAAT
1 ACATATTTGTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACAAGAAA
* * * *
1761909 ACATGTTTGTTTTAATTTAGACAAGAAAACATGTTTTGCCTTAATTTAAACAAGAAA
1 ACATATTTGTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACAAGAAA
* *
1761966 ACATATTTGTCTTAATTTAAGACAAGAAAAAATGTTTTGTGC-TAATCTAGACAAGAAA
1 ACATATTTGTCTTAATTT-AGACAAGAAAACATGTTTTGT-CTTAATTTAGACAAGAAA
* * * *
1762024 ACATGTTTGTCTCAATTTAGATAAGATAACATGTTTTGTCTTAATT
1 ACATATTTGTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATT
1762070 AAAGACAATA
Statistics
Matches: 137, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
56 1 0.01
57 86 0.63
58 49 0.36
59 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (57 bp):
ACATATTTGTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACAAGAAA
Found at i:1768821 original size:2 final size:2
Alignment explanation
Indices: 1768778--1768804 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1768768 TGTGTGTGTG
1768778 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1768805 TTGTGTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1785638 original size:20 final size:19
Alignment explanation
Indices: 1785596--1785638 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1785586 CTCAGTTTCT
*
1785596 TTTTATCTTTTTGTTGTGT
1 TTTTATCTTTTTGTTGTGG
* *
1785615 TTTTATTTTTTTAGTTTTGG
1 TTTTATCTTTTT-GTTGTGG
1785635 TTTT
1 TTTT
1785639 GATGATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.07, C:0.02, G:0.14, T:0.77
Consensus pattern (19 bp):
TTTTATCTTTTTGTTGTGG
Found at i:1789996 original size:240 final size:243
Alignment explanation
Indices: 1789534--1790020 Score: 675
Period size: 240 Copynumber: 2.0 Consensus size: 243
1789524 AACAGTTATA
* *
1789534 AAAACTGGCATAATATTCTTTGAAAAATGTTCATTTCATGGAAAATATCATTTTTGAAATAATTA
1 AAAACTCGCATAATATTCTTTGAAAAATGTTCATTTCATGGAAAATATCATTTTTGAAACAATTA
* *
1789599 AAATTGAATAAATGAAATCCACAAACAGTTAAATAAAAGGAAACATAATAGACAGACAAAAATAC
66 AAATTAAATAAATGAAATCCACAAACAGTCAAATAAAAGGAAACATAATAGACAGACAAAAATAC
* *
1789664 AAGACCAATATGCTAACAAAGAAAGAAAGATAAATAAACTAAACTAACAATTAGAAAAACACCAT
131 AAGACCAATATGCTAAAAAAGAAAGAAAGATAAATAAACTAAACTAACAATAAGAAAAACACCAT
* *
1789729 TTCTTAAACATTTGAAATTGAATAAATGAAATCCCCA-AACAATGAAAT
196 TTCTTAAACATTTAAAATTGAATAAATGAAAT-CCCATAACAATCAAAT
* ** * *
1789777 AAAACTCGTATAATATTCTTTGAGCAATGTTCATTTCATGGAAAATA-CTATTTTTTAAACATTT
1 AAAACTCGCATAATATTCTTTGAAAAATGTTCATTTCATGGAAAATATC-ATTTTTGAAACAATT
* * *
1789841 AAGATTAAATAAATGAAATCTC-CAAACAGTCAAATAAATGGAAACAT-A-A-ATAGACAAAAAT
65 AAAATTAAATAAATGAAATC-CACAAACAGTCAAATAAAAGGAAACATAATAGACAGACAAAAAT
* * * *
1789902 ATAAGA-CATATATGCTAAAAAAGAAAGAAAGATAAATAAACTAATCTAACAATAAGCAAAATAC
129 ACAAGACCA-ATATGCTAAAAAAGAAAGAAAGATAAATAAACTAAACTAACAATAAGAAAAACAC
* *
1789966 CATTT-TTAAAATATTTAAAATTGAATAAATGAAATCCCATAACACTCAAAT
193 CATTTCTT-AAACATTTAAAATTGAATAAATGAAATCCCATAACAATCAAAT
1790017 AAAA
1 AAAA
1790021 GGAAACATAA
Statistics
Matches: 217, Mismatches: 22, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
239 8 0.04
240 109 0.50
241 1 0.00
242 2 0.01
243 96 0.44
244 1 0.00
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.26
Consensus pattern (243 bp):
AAAACTCGCATAATATTCTTTGAAAAATGTTCATTTCATGGAAAATATCATTTTTGAAACAATTA
AAATTAAATAAATGAAATCCACAAACAGTCAAATAAAAGGAAACATAATAGACAGACAAAAATAC
AAGACCAATATGCTAAAAAAGAAAGAAAGATAAATAAACTAAACTAACAATAAGAAAAACACCAT
TTCTTAAACATTTAAAATTGAATAAATGAAATCCCATAACAATCAAAT
Found at i:1790087 original size:144 final size:142
Alignment explanation
Indices: 1789818--1790253 Score: 565
Period size: 144 Copynumber: 3.0 Consensus size: 142
1789808 CATTTCATGG
* * * * * *
1789818 AAAATACTATTTTTTAAACATTTAAGATTAAATAAATGAAATCTCCAAACAGTCAAATAAATGGA
1 AAAATACCATTTTTAAAACATTTAAAATTGAATAAATGAAATC-CCAAACACTCAAATAAAAGGA
* * *
1789883 AAC--ATAAATAGACAAAAATATAAGACATATATGCTAAAAAAGAAAGAAAGATAAATAAACTAA
65 AACTAATAAATAGACAAAAATATTAGACAGATATGCTAACAAAGAAAGAAAGATAAATAAACTAA
*
1789946 TCTAACAATAAGC
130 ACTAACAATAAGC
*
1789959 AAAATACCATTTTTAAAATATTTAAAATTGAATAAATGAAATCCCATAACACTCAAATAAAAGGA
1 AAAATACCATTTTTAAAACATTTAAAATTGAATAAATGAAATCCCA-AACACTCAAATAAAAGGA
*
1790024 AACATAATAAATAGACAAAAATATTAGACAGATAAGCTAACAAAGAAAGAAAGATAAATAAACTA
65 AAC-TAATAAATAGACAAAAATATTAGACAGATATGCTAACAAAGAAAGAAAGATAAATAAACTA
**
1790089 AACTAACAATTTGC
129 AACTAACAATAAGC
*
1790103 AAAATACCATTTTTAAAACATTTAAAATTGAATAAATGAAATCCCCAAACAGC-GAAATAAAAGG
1 AAAATACCATTTTTAAAACATTTAAAATTGAATAAATGAAAT-CCCAAACA-CTCAAATAAAAGG
* * *
1790167 AAAGGTAATAAATAGACAAAAGTA-TAGAACAGGTATGCTAACAAAGAAAGAAAGAAAGATAAAT
64 AAA-CTAATAAATAGACAAAAATATTAG-ACAGATATGCTAAC----AAAGAAAGAAAGATAAAT
* *
1790231 CAACTAAACTAACAATCAGC
123 AAACTAAACTAACAATAAGC
1790251 AAA
1 AAA
1790254 TAAAGTATTT
Statistics
Matches: 260, Mismatches: 23, Indels: 17
0.87 0.08 0.06
Matches are distributed among these distances:
140 3 0.01
141 57 0.22
143 3 0.01
144 154 0.59
145 5 0.02
148 38 0.15
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.22
Consensus pattern (142 bp):
AAAATACCATTTTTAAAACATTTAAAATTGAATAAATGAAATCCCAAACACTCAAATAAAAGGAA
ACTAATAAATAGACAAAAATATTAGACAGATATGCTAACAAAGAAAGAAAGATAAATAAACTAAA
CTAACAATAAGC
Found at i:1798469 original size:53 final size:52
Alignment explanation
Indices: 1798400--1798507 Score: 153
Period size: 53 Copynumber: 2.1 Consensus size: 52
1798390 TAGAAAGAAG
* * *
1798400 TTTTGTAAAAATAATAGAGATTTATATTTGATACATTGTCAATGACTATAAA
1 TTTTGTAAAAATAATAGAGATTTATATTTAATACATTGTCAATGAATACAAA
* * *
1798452 TTTTGTGAAAAGTAATAGAGATTTGTATTTAATACATTGTCCATGAATACAAA
1 TTTTGT-AAAAATAATAGAGATTTATATTTAATACATTGTCAATGAATACAAA
1798505 TTT
1 TTT
1798508 CCTTTTTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 6 0.12
53 43 0.88
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (52 bp):
TTTTGTAAAAATAATAGAGATTTATATTTAATACATTGTCAATGAATACAAA
Found at i:1801813 original size:25 final size:26
Alignment explanation
Indices: 1801775--1801823 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1801765 AATGGTCAAA
1801775 TTGGTTAAAATGTGATG-CCTTTTTT
1 TTGGTTAAAATGTGATGTCCTTTTTT
* *
1801800 TTGGTTATAGTGTGATGTCCTTTT
1 TTGGTTAAAATGTGATGTCCTTTT
1801824 ATTATTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.16, C:0.08, G:0.22, T:0.53
Consensus pattern (26 bp):
TTGGTTAAAATGTGATGTCCTTTTTT
Found at i:1807023 original size:26 final size:26
Alignment explanation
Indices: 1806987--1807048 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
1806977 ACTCCGTGAC
*
1806987 ACAACTAAGAAAAGCTTAAGACTTTT
1 ACAACTTAGAAAAGCTTAAGACTTTT
1807013 ACAACTTAGAAAAGCTTAAGACTTTT
1 ACAACTTAGAAAAGCTTAAGACTTTT
1807039 ACAACTTAGA
1 ACAACTTAGA
1807049 GCTCTGATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (26 bp):
ACAACTTAGAAAAGCTTAAGACTTTT
Found at i:1807374 original size:21 final size:22
Alignment explanation
Indices: 1807349--1807392 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1807339 AAGTGATTAA
1807349 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
1807370 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1807392 T
1 T
1807393 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1810137 original size:68 final size:67
Alignment explanation
Indices: 1809988--1810217 Score: 185
Period size: 68 Copynumber: 3.4 Consensus size: 67
1809978 CCCAATCCAT
* * * * * *
1809988 CCTTGTGGTATACTTACCCCCACACCGGGCTGTAGGATGGGAAAGGATAGGAATATTCACCCAAA
1 CCTTGTGGTATTCTTACCCCCACACCGAGCTCTA--AAGGGAAAAGATGGGAATATTCACCCAAA
1810053 TAAA
64 TAAA
* * *** *
1810057 CCTTATGGTATTCTTACCCCCACACCGAGCTCTAAAGGAGAAAAGATGGGTATATTCATGTAACT
1 CCTTGTGGTATTCTTACCCCCACACCGAGCTCTAAAGG-GAAAAGATGGGAATATTCACCCAAAT
1810122 AAA
65 AAA
* *** * *
1810125 TCTTGTGGTATTCTTACCCCTGTACC-AGGCTCTAAAGGGGAAAAGAT-GGATACATCCACCCAA
1 CCTTGTGGTATTCTTACCCCCACACCGA-GCTCTAAA-GGGAAAAGATGGGA-ATATTCACCCAA
* *
1810188 CTATA
63 ATAAA
* *
1810193 CCCTATGGTATTCTTATCCCCCACA
1 CCTTGTGGTATTCTTA-CCCCCACA
1810218 TCAAGCTTTA
Statistics
Matches: 126, Mismatches: 30, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
67 6 0.05
68 83 0.66
69 37 0.29
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (67 bp):
CCTTGTGGTATTCTTACCCCCACACCGAGCTCTAAAGGGAAAAGATGGGAATATTCACCCAAATA
AA
Found at i:1820776 original size:21 final size:22
Alignment explanation
Indices: 1820737--1820777 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1820727 CATGCTAAAG
*
1820737 CCTAAGAATCGACTTCTTGGTT
1 CCTAACAATCGACTTCTTGGTT
1820759 CCTAACAATCGA-TTCTTGG
1 CCTAACAATCGACTTCTTGG
1820778 AATTCCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (22 bp):
CCTAACAATCGACTTCTTGGTT
Found at i:1825923 original size:53 final size:51
Alignment explanation
Indices: 1825865--1825974 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 51
1825855 GTAGACATAA
*
1825865 TTGATTTGGAC-TATGAATATTCGTTTCACTTTGATGTTCTAAATTTGTTACAT
1 TTGATTTGGACAT-TGAATATTCGTTTCACTTTGATGTT-TAAA-TTGATACAT
* * ** *
1825918 TTGATTTGGACATTGGATATTTGTTTGGCTTTGATGTTTGAATTGATACAT
1 TTGATTTGGACATTGAATATTCGTTTCACTTTGATGTTTAAATTGATACAT
1825969 TTGATT
1 TTGATT
1825975 AAGACTTTGG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
51 14 0.28
52 3 0.06
53 32 0.64
54 1 0.02
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (51 bp):
TTGATTTGGACATTGAATATTCGTTTCACTTTGATGTTTAAATTGATACAT
Found at i:1825985 original size:51 final size:52
Alignment explanation
Indices: 1825893--1826015 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 52
1825883 ATTCGTTTCA
* * **
1825893 CTTTGATGTTCTAAATTTGTTACATTTGATTTGGACATTGGATATTTGTTTGG
1 CTTTGATGTT-TGAATTTGATACATTTGATTAAGACATTGGATATTTGTTTGG
*
1825946 CTTTGATGTTTGAA-TTGATACATTTGATTAAGACTTTGGATATTTGTTTGG
1 CTTTGATGTTTGAATTTGATACATTTGATTAAGACATTGGATATTTGTTTGG
*
1825997 --TTGATGTTTGGACTTTGAT
1 CTTTGATGTTT-GAATTTGAT
1826016 TATTCCATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
49 9 0.15
50 2 0.03
51 38 0.61
52 3 0.05
53 10 0.16
ACGTcount: A:0.21, C:0.07, G:0.22, T:0.50
Consensus pattern (52 bp):
CTTTGATGTTTGAATTTGATACATTTGATTAAGACATTGGATATTTGTTTGG
Found at i:1829259 original size:43 final size:42
Alignment explanation
Indices: 1829202--1829404 Score: 137
Period size: 42 Copynumber: 4.8 Consensus size: 42
1829192 TCCGTGATAG
* *
1829202 TTGTTGTGATGTGGATTGAGAAGGTCTCCACATTCCTC-CGAAT
1 TTGTTGTAAAGTGGATTGAGAAGGTCTCCAC-TT-CTCACGAAT
* * * *
1829245 TTGTTGTAAAGTGGATTGAGTATGTCTCCACTTCTCATGATT
1 TTGTTGTAAAGTGGATTGAGAAGGTCTCCACTTCTCACGAAT
** ** * * * *
1829287 TTGTTGTAAAG-GGAATTGATTATTTCTCCGCTTCCCATGAGT
1 TTGTTGTAAAGTGG-ATTGAGAAGGTCTCCACTTCTCACGAAT
* * * *
1829329 TTGTGGTAAAGTGGATTGA-ATAGGTCTCCA-TCTCCCATGAGT
1 TTGTTGTAAAGTGGATTGAGA-AGGTCTCCACT-TCTCACGAAT
* *
1829371 TTGTTGTAAAGTGGACTGA-ATAAGTCTCCACTTC
1 TTGTTGTAAAGTGGATTGAGA-AGGTCTCCACTTC
1829405 CCATGATTTT
Statistics
Matches: 135, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
41 6 0.04
42 99 0.73
43 30 0.22
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGTTGTAAAGTGGATTGAGAAGGTCTCCACTTCTCACGAAT
Found at i:1829305 original size:42 final size:42
Alignment explanation
Indices: 1829244--1829416 Score: 215
Period size: 42 Copynumber: 4.1 Consensus size: 42
1829234 TTCCTCCGAA
* * *
1829244 TTTGTTGTAAAGTGGATTGAGTATGTCTCCACTTCTCATGAT
1 TTTGTTGTAAAGTGGATTGAATATGTCTCCACTTCCCATGAG
* * *
1829286 TTTGTTGTAAAG-GGAATTGATTATTTCTCCGCTTCCCATGAG
1 TTTGTTGTAAAGTGG-ATTGAATATGTCTCCACTTCCCATGAG
* *
1829328 TTTGTGGTAAAGTGGATTGAATAGGTCTCCA-TCTCCCATGAG
1 TTTGTTGTAAAGTGGATTGAATATGTCTCCACT-TCCCATGAG
* * *
1829370 TTTGTTGTAAAGTGGACTGAATAAGTCTCCACTTCCCATGAT
1 TTTGTTGTAAAGTGGATTGAATATGTCTCCACTTCCCATGAG
1829412 TTTGT
1 TTTGT
1829417 ATATTAACTT
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
41 3 0.03
42 107 0.95
43 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (42 bp):
TTTGTTGTAAAGTGGATTGAATATGTCTCCACTTCCCATGAG
Found at i:1829745 original size:35 final size:34
Alignment explanation
Indices: 1829650--1829774 Score: 126
Period size: 34 Copynumber: 3.6 Consensus size: 34
1829640 GTGGTTGAGC
*
1829650 CCATTAAAA-ACCATTATAAGGATTGTGCTTGCTT
1 CCATTAAAAGA-CATTGTAAGGATTGTGCTTGCTT
* ** *
1829684 TCATTAAAAGTTATTGTAAGGGTTGTGCTTGCTT
1 CCATTAAAAGACATTGTAAGGATTGTGCTTGCTT
*
1829718 CCATTAAAAGACATTTGTAAGGATTGTGATTGCTCT
1 CCATTAAAAGACA-TTGTAAGGATTGTGCTTGCT-T
** **
1829754 TAAAAAAAAGACATTGTAAGG
1 CCATTAAAAGACATTGTAAGG
1829775 GTTTAATGAT
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
34 38 0.51
35 26 0.35
36 10 0.14
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (34 bp):
CCATTAAAAGACATTGTAAGGATTGTGCTTGCTT
Found at i:1834286 original size:15 final size:16
Alignment explanation
Indices: 1834266--1834298 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1834256 CAATGCTCAG
1834266 GTCATTT-AGGTGCAA
1 GTCATTTCAGGTGCAA
*
1834281 GTCATTTCAGGTTCAA
1 GTCATTTCAGGTGCAA
1834297 GT
1 GT
1834299 AGATGACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (16 bp):
GTCATTTCAGGTGCAA
Found at i:1834336 original size:32 final size:32
Alignment explanation
Indices: 1834300--1834362 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1834290 GGTTCAAGTA
*
1834300 GATGACTTTT-AAAGTCAAATTGAGTAGGATTT
1 GATGACTTTTAAAAAT-AAATTGAGTAGGATTT
1834332 GATGACTTTTAAAAATAAATTGAGTAGGATT
1 GATGACTTTTAAAAATAAATTGAGTAGGATT
1834363 CAAGCAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.37
Consensus pattern (32 bp):
GATGACTTTTAAAAATAAATTGAGTAGGATTT
Found at i:1843576 original size:7 final size:7
Alignment explanation
Indices: 1843564--1843595 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1843554 AAAGAAACCA
1843564 ATAGTCC
1 ATAGTCC
1843571 ATAGTCC
1 ATAGTCC
1843578 ATAGTCC
1 ATAGTCC
*
1843585 ATGGTCC
1 ATAGTCC
1843592 ATAG
1 ATAG
1843596 CTGATTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (7 bp):
ATAGTCC
Found at i:1843858 original size:23 final size:22
Alignment explanation
Indices: 1843810--1843859 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
1843800 GTATGAATAA
* *
1843810 AATAT-AAAATTAATTTACATT
1 AATATAAAAATAAATTTAAATT
1843831 AATATAAAAATAAATATTAAATT
1 AATATAAAAATAAAT-TTAAATT
1843854 AATATA
1 AATATA
1843860 TTATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.20
22 8 0.32
23 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AATATAAAAATAAATTTAAATT
Found at i:1850306 original size:27 final size:27
Alignment explanation
Indices: 1850263--1850315 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1850253 AGGTAAGAAT
1850263 TTAGTTATTCTTAGTGACTT-TTTTAA
1 TTAGTTATTCTTAGTGACTTATTTTAA
* * *
1850289 TTAGTTTATTTTTTGTGAGTTATTTTA
1 TTAG-TTATTCTTAGTGACTTATTTTA
1850316 TTTTATGCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 13 0.59
28 5 0.23
ACGTcount: A:0.21, C:0.04, G:0.13, T:0.62
Consensus pattern (27 bp):
TTAGTTATTCTTAGTGACTTATTTTAA
Found at i:1857019 original size:33 final size:33
Alignment explanation
Indices: 1856974--1857046 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
1856964 TAACATATAT
* *
1856974 AATATATGAGATTATATTAAAAAATGAAAATAA
1 AATATATAAGATTATAATAAAAAATGAAAATAA
* *
1857007 AATATATAAGATTGTAATAAGAAATGAAAATAA
1 AATATATAAGATTATAATAAAAAATGAAAATAA
1857040 AATATAT
1 AATATAT
1857047 TTAAGAGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (33 bp):
AATATATAAGATTATAATAAAAAATGAAAATAA
Found at i:1860045 original size:21 final size:21
Alignment explanation
Indices: 1860019--1860069 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1860009 AGAACCGATA
*
1860019 TCTTCTTCATGTCGAATCAAT
1 TCTTCTTCATCTCGAATCAAT
*
1860040 TCTTCTTCATCTTGAATCAAT
1 TCTTCTTCATCTCGAATCAAT
1860061 TCTTTCTTC
1 TC-TTCTTC
1860070 TTTGCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.20, C:0.25, G:0.06, T:0.49
Consensus pattern (21 bp):
TCTTCTTCATCTCGAATCAAT
Found at i:1864219 original size:21 final size:22
Alignment explanation
Indices: 1864184--1864227 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1864174 CTCTTAAAGT
1864184 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
1864206 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
1864227 A
1 A
1864228 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:1868254 original size:21 final size:20
Alignment explanation
Indices: 1868226--1868267 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1868216 TATGTTATGT
*
1868226 TTCAAATGAATTGATACATA
1 TTCAAATGAATCGATACATA
*
1868246 TTCATAATGTATCGATACATA
1 TTCA-AATGAATCGATACATA
1868267 T
1 T
1868268 GATTATGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (20 bp):
TTCAAATGAATCGATACATA
Found at i:1877014 original size:221 final size:215
Alignment explanation
Indices: 1876565--1877021 Score: 605
Period size: 215 Copynumber: 2.1 Consensus size: 215
1876555 TAAACATTAT
* * *
1876565 ATATATTTAATTTATATATAAGCATTACTATAAGTTATAATTAACTTTATTTATATGATTACACT
1 ATATATTTAATTTATATATAAGCATTACTACAACTTATAATTAACTTTATTTATATAATTACACT
* *
1876630 TAATAACGTTATTAATTATCACCTTAGTTTTATAACATATTCTTTTTAATTAGTTATTATTTATA
66 TAATAACGTTATTAATTATCACCTTAGTTTTACAACATATTCTTTATAATTAGTTATTATTTATA
** * *
1876695 CAAACTTTGATATAAAACATTATAACATATAAGTTGTGTCATTAATTATATATATATATAATAAA
131 CAAACTAAGATATAAAAAATTATAACATATAAGTTATGTCATTAATTATATATATATATAATAAA
*
1876760 GTAATATATTATACATATAT
196 GTAATATATTATACATATAC
* * *
1876780 ATATATTTAATTTATACATAAGCATTATTGCAACTTATAA-TAGACTTTATTTATATAATTACAC
1 ATATATTTAATTTATATATAAGCATTACTACAACTTATAATTA-ACTTTATTTATATAATTACAC
** * ** * * *
1876844 TTAATAATTTTATTAGTTATCGTCTTAATTTTTACAACATATTGTTTATAATTAGTTATTATTTT
65 TTAATAACGTTATTAATTATCACCTT-AGTTTTACAACATATTCTTTATAATTAGTTATTATTTA
*
1876909 TACAAACTAAGATATAAAAAATAAAATATTAAAATATATAAGTTATGTCATTAA-T-TATATATA
129 TACAAACTAAGATATAAAAAAT----TA-T--AACATATAAGTTATGTCATTAATTATATATATA
*
1876972 TATAATAAAGTAATATATTATAGATATAC
187 TATAATAAAGTAATATATTATACATATAC
1877001 ATATATTTAATTTATATATAA
1 ATATATTTAATTTATATATAA
1877022 TTTGTATATT
Statistics
Matches: 209, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
214 2 0.01
215 76 0.36
216 52 0.25
220 2 0.01
221 56 0.27
222 1 0.00
223 20 0.10
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (215 bp):
ATATATTTAATTTATATATAAGCATTACTACAACTTATAATTAACTTTATTTATATAATTACACT
TAATAACGTTATTAATTATCACCTTAGTTTTACAACATATTCTTTATAATTAGTTATTATTTATA
CAAACTAAGATATAAAAAATTATAACATATAAGTTATGTCATTAATTATATATATATATAATAAA
GTAATATATTATACATATAC
Found at i:1877789 original size:15 final size:15
Alignment explanation
Indices: 1877769--1877800 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1877759 AATGCTAGTG
1877769 CAGTTGTCACAGGGT
1 CAGTTGTCACAGGGT
1877784 CAGTTGTCACAGGGT
1 CAGTTGTCACAGGGT
1877799 CA
1 CA
1877801 TTACCCTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (15 bp):
CAGTTGTCACAGGGT
Found at i:1878331 original size:29 final size:28
Alignment explanation
Indices: 1878299--1878353 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
1878289 TTTTAATAAA
*
1878299 ATTTAAATAAATTTTGATTTTTTTATTAT
1 ATTTAAATAAATTTTG-TCTTTTTATTAT
* *
1878328 ATTTAATTAAGTTTTGTCTTTTTATT
1 ATTTAAATAAATTTTGTCTTTTTATT
1878354 TTAGATCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (28 bp):
ATTTAAATAAATTTTGTCTTTTTATTAT
Found at i:1896473 original size:15 final size:14
Alignment explanation
Indices: 1896455--1896510 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 14
1896445 TAAAATAAAA
1896455 AATAATAATTTAATT
1 AATAATAA-TTAATT
1896470 AATAATAATTAATT
1 AATAATAATTAATT
1896484 -A-AAT-ATTAATT
1 AATAATAATTAATT
* *
1896495 -ATAAAAATTATTT
1 AATAATAATTAATT
1896508 AAT
1 AAT
1896511 TTAAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 8 0.22
12 5 0.14
13 7 0.19
14 8 0.22
15 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAATAATTAATT
Found at i:1896478 original size:18 final size:17
Alignment explanation
Indices: 1896453--1896540 Score: 68
Period size: 15 Copynumber: 5.6 Consensus size: 17
1896443 TATAAAATAA
1896453 AAAATAATAATTTAATT
1 AAAATAATAATTTAATT
1896470 --AATAATAA-TTAATT
1 AAAATAATAATTTAATT
*
1896484 -AAATATTAA-TT-A-T
1 AAAATAATAATTTAATT
*
1896497 -AAA-AATTATTTAATTT
1 AAAATAATAATTTAA-TT
*
1896513 AAAATAAAAATTTAATT
1 AAAATAATAATTTAATT
1896530 AAATATAATAA
1 AAA-ATAATAA
1896541 AAAATAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
12 3 0.05
13 6 0.11
14 8 0.14
15 17 0.30
16 1 0.02
17 8 0.14
18 14 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAATAATTTAATT
Found at i:1896522 original size:22 final size:21
Alignment explanation
Indices: 1896444--1896545 Score: 64
Period size: 21 Copynumber: 4.7 Consensus size: 21
1896434 ATCAGATGGT
*
1896444 ATAAAATAAAAAATAATAATTTA
1 ATAAAATAAAAAAT--TAATTAA
* *
1896467 AT-TAAT-AATAATTAATTAA
1 ATAAAATAAAAAATTAATTAA
* *
1896486 ATATTAATTATAAAAATTATTTAA
1 ATA--AAATA-AAAAATTAATTAA
* *
1896510 TTTAAAATAAAAATTTAATTAA
1 -ATAAAATAAAAAATTAATTAA
*
1896532 ATATAATAAAAAAT
1 ATAAAATAAAAAAT
1896546 AAAAAATAAT
Statistics
Matches: 59, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
19 8 0.14
21 16 0.27
22 16 0.27
23 6 0.10
24 11 0.19
25 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAAATAAAAAATTAATTAA
Found at i:1899206 original size:11 final size:10
Alignment explanation
Indices: 1899167--1899206 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1899157 ATATAATTAA
1899167 AAAATTATTT
1 AAAATTATTT
*
1899177 -AAATTTTTT
1 AAAATTATTT
1899186 AAAATTATTT
1 AAAATTATTT
1899196 AAAAGTTATTT
1 AAAA-TTATTT
1899207 GAGTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 8 0.31
10 12 0.46
11 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (10 bp):
AAAATTATTT
Found at i:1900885 original size:29 final size:30
Alignment explanation
Indices: 1900843--1900911 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
1900833 TTTATCATGT
*
1900843 TCAATTAAATTTTTATAATTTTATTTTAAG
1 TCAAATAAATTTTTATAATTTTATTTTAAG
* *
1900873 TTAAATAAATTTTTATATTTTTATTTTAAG
1 TCAAATAAATTTTTATAATTTTATTTTAAG
1900903 TCAAATAAA
1 TCAAATAAA
1900912 CTCTTATGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (30 bp):
TCAAATAAATTTTTATAATTTTATTTTAAG
Found at i:1905975 original size:14 final size:15
Alignment explanation
Indices: 1905956--1905985 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1905946 TAAATTTTAG
1905956 ATTAGTTTTA-TTTT
1 ATTAGTTTTAGTTTT
1905970 ATTAGTTTTAGTTTT
1 ATTAGTTTTAGTTTT
1905985 A
1 A
1905986 ATTTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (15 bp):
ATTAGTTTTAGTTTT
Found at i:1917603 original size:21 final size:19
Alignment explanation
Indices: 1917579--1917618 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
1917569 ATTAGTATAA
1917579 TATTTAAATAAAATTTTAAAT
1 TATTTAAAT-AAA-TTTAAAT
1917600 TATTTAAATAAATTTAAAT
1 TATTTAAATAAATTTAAAT
1917619 AAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 3 0.16
21 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTTAAATAAATTTAAAT
Found at i:1917614 original size:10 final size:10
Alignment explanation
Indices: 1917575--1917624 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
1917565 CTATATTAGT
1917575 ATAATATTTAA
1 ATAA-ATTTAA
1917586 ATAAAATTTTAA
1 AT-AAA-TTTAA
*
1917598 AT-TATTTAA
1 ATAAATTTAA
1917607 ATAAATTTAA
1 ATAAATTTAA
1917617 ATAAATTT
1 ATAAATTT
1917625 TTTTACTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 7 0.21
10 15 0.44
11 3 0.09
12 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATAAATTTAA
Found at i:1918013 original size:30 final size:29
Alignment explanation
Indices: 1917946--1918014 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
1917936 TAATCACAAG
1917946 GATTTATTTGATTCAAAATAAAAATAGAA
1 GATTTATTTGATTCAAAATAAAAATAGAA
* *
1917975 GAACTTATTTGATTTAAAATAAAAGTATA-AA
1 G-ATTTATTTGATTCAAAATAAAA--ATAGAA
1918006 GATTTATTT
1 GATTTATTT
1918015 AAATTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 1 0.03
30 27 0.79
31 3 0.09
32 3 0.09
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (29 bp):
GATTTATTTGATTCAAAATAAAAATAGAA
Found at i:1918283 original size:18 final size:19
Alignment explanation
Indices: 1918256--1918293 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1918246 ATTTGTATTA
*
1918256 ATATTATAATATTTAAATT
1 ATATTATAATATTAAAATT
1918275 ATATT-TAATATTAAAATT
1 ATATTATAATATTAAAATT
1918293 A
1 A
1918294 AATAAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATTATAATATTAAAATT
Found at i:1920618 original size:18 final size:18
Alignment explanation
Indices: 1920595--1920638 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1920585 CTGTTGTAAT
1920595 GATTGAGAGGCATT-T-GAA
1 GATTGAGA-GCATTCTAG-A
1920613 GATTGAGAGCATTCTAGA
1 GATTGAGAGCATTCTAGA
1920631 GATTGAGA
1 GATTGAGA
1920639 AGAGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.21
18 18 0.75
19 1 0.04
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (18 bp):
GATTGAGAGCATTCTAGA
Found at i:1920749 original size:25 final size:25
Alignment explanation
Indices: 1920721--1920776 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1920711 AAGTTTGTGT
*
1920721 TCAAGCCATCAAGTGA-AGTTCATGA
1 TCAAGACATCAAGT-ATAGTTCATGA
*
1920746 TCAAGATATCAAGTATAGTTCATGA
1 TCAAGACATCAAGTATAGTTCATGA
*
1920771 TTAAGA
1 TCAAGA
1920777 TCAAGTCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (25 bp):
TCAAGACATCAAGTATAGTTCATGA
Found at i:1920777 original size:25 final size:25
Alignment explanation
Indices: 1920728--1920777 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1920718 TGTTCAAGCC
1920728 ATCAAGTGAAGTTCATGATCAAGAT
1 ATCAAGTGAAGTTCATGATCAAGAT
*
1920753 ATCAAGT-ATAGTTCATGATTAAGAT
1 ATCAAGTGA-AGTTCATGATCAAGAT
1920778 CAAGTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (25 bp):
ATCAAGTGAAGTTCATGATCAAGAT
Found at i:1932773 original size:36 final size:34
Alignment explanation
Indices: 1932685--1932775 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 34
1932675 ACAAATTGTG
*
1932685 TGCTATTATAAAGAGCAC-CCAAAAGATCGCAAG
1 TGCTATTATAAAGAGCACTCCAAAAGATCGCAAA
* * * *
1932718 TGCTATTGTAAAGAGCACTCTCCAAGGATTGACAAA
1 TGCTATTATAAAGAGCACTC-CAAAAGATCG-CAAA
*
1932754 TGTTATTATAAAGAGCACTCCA
1 TGCTATTATAAAGAGCACTCCA
1932776 CAAAATGCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
33 17 0.36
34 1 0.02
35 8 0.17
36 21 0.45
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (34 bp):
TGCTATTATAAAGAGCACTCCAAAAGATCGCAAA
Found at i:1933810 original size:33 final size:31
Alignment explanation
Indices: 1933715--1933865 Score: 134
Period size: 28 Copynumber: 4.9 Consensus size: 31
1933705 ATACCAATTT
*
1933715 CAATATACCTCTTCAAAGATTATAGTTTTATTG
1 CAATATACTTCTTC-AAGA-TATAGTTTTATTG
* * * *
1933748 TAATATACTTCTT--TGA-ACAATTTTATTG
1 CAATATACTTCTTCAAGATATAGTTTTATTG
1933776 CAATATACTTCTTCAAAGATTATAGTTTTATTG
1 CAATATACTTCTTC-AAGA-TATAGTTTTATTG
1933809 CAATATACTTCTTC-A-A-ATAGTTTTATTG
1 CAATATACTTCTTCAAGATATAGTTTTATTG
* * *
1933837 CAATACACATCTTCCAAGATCATAATTTT
1 CAATATACTTCTT-CAAGAT-ATAGTTTT
1933866 CTTACTTATG
Statistics
Matches: 96, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
28 45 0.47
29 1 0.01
30 4 0.04
31 4 0.04
33 42 0.44
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (31 bp):
CAATATACTTCTTCAAGATATAGTTTTATTG
Found at i:1933814 original size:61 final size:61
Alignment explanation
Indices: 1933715--1933865 Score: 203
Period size: 61 Copynumber: 2.5 Consensus size: 61
1933705 ATACCAATTT
* * **
1933715 CAATATACCTCTTCAAAGATTATAGTTTTATTGTAATATACTTCTTTGAACAATTTTATTG
1 CAATATACATCTTCAAAGATTATAGTTTTATTGCAATATACTTCTTCAAACAATTTTATTG
* * *
1933776 CAATATACTTCTTCAAAGATTATAGTTTTATTGCAATATACTTCTTCAAATAGTTTTATTG
1 CAATATACATCTTCAAAGATTATAGTTTTATTGCAATATACTTCTTCAAACAATTTTATTG
* * * *
1933837 CAATACACATCTTCCAAGATCATAATTTT
1 CAATATACATCTTCAAAGATTATAGTTTT
1933866 CTTACTTATG
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 79 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (61 bp):
CAATATACATCTTCAAAGATTATAGTTTTATTGCAATATACTTCTTCAAACAATTTTATTG
Found at i:1938475 original size:18 final size:18
Alignment explanation
Indices: 1938452--1938491 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1938442 TTTTTTTTTT
*
1938452 AAAATTGTATTCTTTAAA
1 AAAATTATATTCTTTAAA
* *
1938470 AAAATTATTTTTTTTAAA
1 AAAATTATATTCTTTAAA
1938488 AAAA
1 AAAA
1938492 ACTTTTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
AAAATTATATTCTTTAAA
Found at i:1941748 original size:110 final size:110
Alignment explanation
Indices: 1941572--1941791 Score: 361
Period size: 110 Copynumber: 2.0 Consensus size: 110
1941562 ATATTCATAC
* * * *
1941572 ATAAGTTAAAAGAGATTGAAATAAACTATCAAAATCATCATCAAAATATAAGAATTAAGACTAAT
1 ATAAGATAAAAGAAATTGAAACAAACTATCAAAATCATCATCAAAATATAAGAATCAAGACTAAT
1941637 TCTCAT-TCATGTTTACAATAAAAAATGTTAACAAAAACAAGCCAT
66 TCTCATAT-ATGTTTACAATAAAAAATGTTAACAAAAACAAGCCAT
*
1941682 ATAAGATAAAGGAAATTGAAACAAACTATCAAAATCATCATCAAAATATAAGAATCAAGACTAAT
1 ATAAGATAAAAGAAATTGAAACAAACTATCAAAATCATCATCAAAATATAAGAATCAAGACTAAT
* *
1941747 TCTCATATATTTTTACAATAAAAAATGTTAACAAAAACATGCCAT
66 TCTCATATATGTTTACAATAAAAAATGTTAACAAAAACAAGCCAT
1941792 TCTAACATAC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
110 101 0.99
111 1 0.01
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (110 bp):
ATAAGATAAAAGAAATTGAAACAAACTATCAAAATCATCATCAAAATATAAGAATCAAGACTAAT
TCTCATATATGTTTACAATAAAAAATGTTAACAAAAACAAGCCAT
Found at i:1942780 original size:28 final size:28
Alignment explanation
Indices: 1942736--1942792 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
1942726 TGCACATTAG
1942736 TAATGCCTATTTATTATTAAGTGGCAAC
1 TAATGCCTATTTATTATTAAGTGGCAAC
1942764 TAATGCCTAGTTT-TTATTAAGTGGCAAC
1 TAATGCCTA-TTTATTATTAAGTGGCAAC
1942792 T
1 T
1942793 TATAGATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (28 bp):
TAATGCCTATTTATTATTAAGTGGCAAC
Found at i:1947868 original size:5 final size:5
Alignment explanation
Indices: 1947852--1947892 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
1947842 GGAAATGGCG
*
1947852 TCATT TCCTT TCATT TCATT TCAATT TGCATT TCATT TCAT
1 TCATT TCATT TCATT TCATT TC-ATT T-CATT TCATT TCAT
1947893 CTTTTTTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 23 0.72
6 8 0.25
7 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (5 bp):
TCATT
Found at i:1950096 original size:2 final size:2
Alignment explanation
Indices: 1950089--1950113 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1950079 ACAATCAAGC
1950089 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1950114 GTCATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1953212 original size:14 final size:14
Alignment explanation
Indices: 1953190--1953221 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1953180 ATCATTATCA
*
1953190 ATTTGGCCTTACTC
1 ATTTAGCCTTACTC
1953204 ATTTAGCCTTACTC
1 ATTTAGCCTTACTC
1953218 ATTT
1 ATTT
1953222 TGACCCTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.25, G:0.09, T:0.47
Consensus pattern (14 bp):
ATTTAGCCTTACTC
Found at i:1954113 original size:22 final size:24
Alignment explanation
Indices: 1954061--1954117 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
1954051 TCAACAAAAT
1954061 TTAAACATTTTATTTTATTATTAATA
1 TTAAAC-TTTTA-TTTATTATTAATA
* *
1954087 ATAAACTTTTA-TTA-TATTTATA
1 TTAAACTTTTATTTATTATTAATA
1954109 TTAAACTTT
1 TTAAACTTT
1954118 ACTATATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 15 0.54
23 3 0.11
25 5 0.18
26 5 0.18
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAAACTTTTATTTATTATTAATA
Found at i:1954123 original size:21 final size:22
Alignment explanation
Indices: 1954079--1954124 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1954069 TTTATTTTAT
*
1954079 TATTAATAATAAACTTTTATTA
1 TATTAATAATAAACTTTTACTA
* *
1954101 TATTTATATTAAAC-TTTACTA
1 TATTAATAATAAACTTTTACTA
1954122 TAT
1 TAT
1954125 AAACTATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTAATAATAAACTTTTACTA
Found at i:1955216 original size:37 final size:37
Alignment explanation
Indices: 1955146--1955217 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
1955136 CTATTACGAA
*
1955146 ATATTATTATTATAGATATAAGTCTAATAATTATAAC
1 ATATTAATATTATAGATATAAGTCTAATAATTATAAC
*
1955183 ATATTAATA-TATATATATAATGT-TAATATATTATA
1 ATATTAATATTATAGATATAA-GTCTAATA-ATTATA
1955218 TTACAATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 15 0.48
37 16 0.52
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (37 bp):
ATATTAATATTATAGATATAAGTCTAATAATTATAAC
Found at i:1958257 original size:17 final size:17
Alignment explanation
Indices: 1958225--1958268 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1958215 TTTTATTAAT
* *
1958225 TATTTTTTACTTTTATA
1 TATTTTTAATTTTTATA
1958242 -ATTTTATAATTTTTATA
1 TATTTT-TAATTTTTATA
1958259 TATTTTTAAT
1 TATTTTTAAT
1958269 ATAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTTAATTTTTATA
Found at i:1958434 original size:20 final size:20
Alignment explanation
Indices: 1958409--1958451 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1958399 TGTATTTCCC
*
1958409 TTTATAATAAAAATAATTAA
1 TTTATAATAAAAAGAATTAA
1958429 TTTATAATAAAAAGAATTAA
1 TTTATAATAAAAAGAATTAA
1958449 TTT
1 TTT
1958452 TGTTTGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TTTATAATAAAAAGAATTAA
Found at i:1959128 original size:26 final size:26
Alignment explanation
Indices: 1959092--1959153 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
1959082 ACTCTTTGGC
1959092 TTCTTTGAAAATTTTGGTGCTCATAA
1 TTCTTTGAAAATTTTGGTGCTCATAA
1959118 TTCTTTGAAAATTTTGGTGCTCATAA
1 TTCTTTGAAAATTTTGGTGCTCATAA
1959144 TTCTTTGAAA
1 TTCTTTGAAA
1959154 GTCATACTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (26 bp):
TTCTTTGAAAATTTTGGTGCTCATAA
Found at i:1960570 original size:44 final size:43
Alignment explanation
Indices: 1960461--1960590 Score: 172
Period size: 44 Copynumber: 3.0 Consensus size: 43
1960451 TGGAGCCAAC
* * *
1960461 CATAACACAATCATGGGAA-GTGGAGACCTTTTTAATCCACTT
1 CATAACACAATCATGGGAATGTGGAGACCTTCTCAATCCACAT
* * * * *
1960503 TACAACACAATCATGCGAATGTGGATACCTTCTCAATCCGCAT
1 CATAACACAATCATGGGAATGTGGAGACCTTCTCAATCCACAT
1960546 CATAACACTAATCATGGGAATGTGGAGACCTTCTCAATCCACAT
1 CATAACAC-AATCATGGGAATGTGGAGACCTTCTCAATCCACAT
1960590 C
1 C
1960591 CACAAAACTC
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 16 0.22
43 24 0.33
44 33 0.45
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (43 bp):
CATAACACAATCATGGGAATGTGGAGACCTTCTCAATCCACAT
Found at i:1963427 original size:64 final size:63
Alignment explanation
Indices: 1963325--1963543 Score: 225
Period size: 64 Copynumber: 3.5 Consensus size: 63
1963315 TAATCATTAA
* * *
1963325 TATTTTAAAATATTAATATTTTATTTAATTTAAATATTATTATGATCAATTATTTTATTTTATTT
1 TATTTTAAAATATTAATAATTGA--TAATTTAAATATTATTATGATTAATTATTTTATTTTATTT
* * * * *
1963390 TATTTTCAAAATATTAATAATTGATAATTTAAATATTAATAT-TTTATTTATAATTTA-ATCATT
1 TATTTT-AAAATATTAATAATTGATAATTTAAATATTATTATGATTAATTAT--TTTATTTTATT
*
1963453 AA
63 -T
* **
1963455 TATTTTAAAATATTAATATTTTTTAATTTAAATATTATTATGATTAATTATTTTATTTTA--T
1 TATTTTAAAATATTAATAATTGATAATTTAAATATTATTATGATTAATTATTTTATTTTATTT
*
1963516 T-TTTT-AAATATTAATAATTGATAGTTTA
1 TATTTTAAAATATTAATAATTGATAATTTA
1963544 TTTAAAATAT
Statistics
Matches: 126, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
59 19 0.15
60 4 0.03
61 1 0.01
63 10 0.08
64 54 0.43
65 23 0.18
66 15 0.12
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (63 bp):
TATTTTAAAATATTAATAATTGATAATTTAAATATTATTATGATTAATTATTTTATTTTATTT
Found at i:1963558 original size:128 final size:128
Alignment explanation
Indices: 1963265--1963543 Score: 435
Period size: 130 Copynumber: 2.2 Consensus size: 128
1963255 TAGAATTTAA
* **
1963265 TTAAAATATTAATAATTAAGCATTTAAATA-TAACTATTTCATTTATAATTTAATCATTAATATT
1 TTAAAATATTAATAATTGATAATTTAAATATTAA-TATTTCATTTATAATTTAATCATTAATATT
1963329 TTAAAATATTAATATTTTATTTAATTTAAATATTATTATGATCAATTATTTTATTTTATTTTATT
65 TTAAAATATTAATATTTTATTTAATTTAAATATTATTATGATCAATTATTTTATTTTA-TTTATT
*
1963394 TTCAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATT
1 TT-AAAATATTAATAATTGATAATTTAAATATTAATATTTCATTTATAATTTAATCATTAATATT
*
1963459 TTAAAATATTAATA-TTT-TTTAATTTAAATATTATTATGATTAATTATTTTATTTTA-TT-TT
65 TTAAAATATTAATATTTTATTTAATTTAAATATTATTATGATCAATTATTTTATTTTATTTATT
*
1963519 TT-AAATATTAATAATTGATAGTTTA
1 TTAAAATATTAATAATTGATAATTTA
1963544 TTTAAAATAT
Statistics
Matches: 142, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
123 22 0.15
125 4 0.03
126 2 0.01
128 38 0.27
129 5 0.04
130 68 0.48
131 3 0.02
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (128 bp):
TTAAAATATTAATAATTGATAATTTAAATATTAATATTTCATTTATAATTTAATCATTAATATTT
TAAAATATTAATATTTTATTTAATTTAAATATTATTATGATCAATTATTTTATTTTATTTATT
Found at i:1963570 original size:27 final size:25
Alignment explanation
Indices: 1963514--1963570 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
1963504 ATTTTATTTT
*
1963514 ATTT-TTTAAATATTAATAATTGAT
1 ATTTATTTAAATATTAATAATTGAC
1963538 AGTTTATTTAAAATATTAATAATTGACC
1 A-TTTATTT-AAATATTAATAATTGA-C
1963566 ATTTA
1 ATTTA
1963571 AATATTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.04
25 3 0.11
26 3 0.11
27 20 0.71
28 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (25 bp):
ATTTATTTAAATATTAATAATTGAC
Found at i:1963644 original size:128 final size:122
Alignment explanation
Indices: 1963530--1963846 Score: 312
Period size: 130 Copynumber: 2.5 Consensus size: 122
1963520 TAAATATTAA
* *
1963530 TAATTGATAGTTTA-TTTAAAATATTAATAATTGACCATTTAAATATTAATATTTATTTATAATT
1 TAATT-ATAGTTTATTTTAAAATATTAATAATTGACCATTT--AT-TTAA-A-ATATTAATAATT
*
1963594 TAGTCATTAATATAATAAAATATTAATATTTAATTTAATTTAAATATTATTATGATAAATTATT
60 TAATCATTAATATAATAAAATATTAATATTTAATTTAATTT-AATATTATTATGATAAATTATT
* * * * **
1963658 TTATTTTATTTTATTTTTAAATATTAATAATTGATTATTTATTTAAAATATTAATAATTTAATCA
1 TAATTATAGTTTATTTTAAAATATTAATAATTGACCATTTATTTAAAATATTAATAATTTAATCA
** * *
1963723 TTAATATTTTAAAATATTAATATTTTATTTAATTTAATATTATTATGATTAATTTTTTATTT
66 TTAATATAATAAAATATTAATATTTAATTTAATTTAATATTATTATGA-TAA---ATTA-TT
* * * * ***
1963785 TATTTTTTAAATTTTATTTTTAAATATTAATAATTGGTAATTTATTTAAAATATTAATAATT
1 TA---ATTATAGTTTATTTTAAAATATTAATAATTGACCATTTATTTAAAATATTAATAATT
1963847 GATGATTTAA
Statistics
Matches: 161, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
122 13 0.08
123 50 0.31
124 1 0.01
125 4 0.02
126 5 0.03
127 9 0.06
128 27 0.17
130 52 0.32
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (122 bp):
TAATTATAGTTTATTTTAAAATATTAATAATTGACCATTTATTTAAAATATTAATAATTTAATCA
TTAATATAATAAAATATTAATATTTAATTTAATTTAATATTATTATGATAAATTATT
Found at i:1963663 original size:151 final size:152
Alignment explanation
Indices: 1963388--1963716 Score: 513
Period size: 155 Copynumber: 2.1 Consensus size: 152
1963378 TTTATTTTAT
*
1963388 TTTATTTTCAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATT
1 TTTA-TTT-AAAATATTAATAATTGACAATTTAAATATTAATATTTTATTTATAATTTAATCATT
** *
1963453 AATATTTTAAAATATTAATATTTTTTAATTTAAATATTATTATGATTAATTATTTTATTTTA-T-
64 AATATAATAAAATATTAATATTTTTTAATTTAAATATTATTATGATAAATTATTTTATTTTATTA
1963516 TTTTTAAATATTAATAATTGA-TA
129 TTTTTAAATATTAATAATTGATTA
* *
1963539 GTTTATTTAAAATATTAATAATTGACCATTTAAATATTAATA-TTTATTTATAATTTAGTCATTA
1 -TTTATTTAAAATATTAATAATTGACAATTTAAATATTAATATTTTATTTATAATTTAATCATTA
1963603 ATATAATAAAATATTAATATTTAATTTAATTTAAATATTATTATGATAAATTATTTTATTTTATT
65 ATATAATAAAATATTAATATTT--TTTAATTTAAATATTATTATGATAAATTATTTTATTTTA--
1963668 TTATTTTTAAATATTAATAATTGATTA
126 TTATTTTTAAATATTAATAATTGATTA
1963695 TTTATTTAAAATATTAATAATT
1 TTTATTTAAAATATTAATAATT
1963717 TAATCATTAA
Statistics
Matches: 164, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
149 41 0.25
150 32 0.20
151 41 0.25
152 4 0.02
154 1 0.01
155 43 0.26
156 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (152 bp):
TTTATTTAAAATATTAATAATTGACAATTTAAATATTAATATTTTATTTATAATTTAATCATTAA
TATAATAAAATATTAATATTTTTTAATTTAAATATTATTATGATAAATTATTTTATTTTATTATT
TTTAAATATTAATAATTGATTA
Found at i:1963711 original size:27 final size:27
Alignment explanation
Indices: 1963667--1963855 Score: 112
Period size: 27 Copynumber: 7.1 Consensus size: 27
1963657 TTTATTTTAT
*
1963667 TTTATTTTTAAATATTAATAATTGATTA
1 TTTA-TTTAAAATATTAATAATTGATTA
* *
1963695 TTTATTTAAAATATTAATAATTTAATCA
1 TTTATTTAAAATATTAATAA-TTGATTA
1963723 TTAATATTTTAAAATATTAAT-ATT--TTA
1 TT--TA-TTTAAAATATTAATAATTGATTA
* * * *
1963750 TTTAATTTAATATTATT-ATGATTAATTT
1 TTT-ATTTAA-AATATTAATAATTGATTA
* * * *
1963778 TTTATTT-TATTTTTTA-AATT--TTA
1 TTTATTTAAAATATTAATAATTGATTA
* *
1963801 -TT-TTT-AAATATTAATAATTGGTAA
1 TTTATTTAAAATATTAATAATTGATTA
*
1963825 TTTATTTAAAATATTAATAATTGATGA
1 TTTATTTAAAATATTAATAATTGATTA
1963852 TTTA
1 TTTA
1963856 ATTATTAATA
Statistics
Matches: 128, Mismatches: 17, Indels: 33
0.72 0.10 0.19
Matches are distributed among these distances:
21 8 0.06
22 6 0.05
23 2 0.02
24 2 0.02
25 18 0.14
26 13 0.10
27 44 0.34
28 16 0.12
29 2 0.02
30 3 0.02
31 14 0.11
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTATTTAAAATATTAATAATTGATTA
Found at i:1963717 original size:16 final size:16
Alignment explanation
Indices: 1963698--1963749 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
1963688 TTGATTATTT
1963698 ATTTAAAATATTAATA
1 ATTTAAAATATTAATA
1963714 ATTT--AATCATTAATA
1 ATTTAAAAT-ATTAATA
*
1963729 TTTTAAAATATTAATA
1 ATTTAAAATATTAATA
*
1963745 TTTTA
1 ATTTA
1963750 TTTAATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.09
15 10 0.31
16 16 0.50
17 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAAAATATTAATA
Found at i:1963737 original size:31 final size:29
Alignment explanation
Indices: 1963667--1963749 Score: 98
Period size: 31 Copynumber: 2.9 Consensus size: 29
1963657 TTTATTTTAT
* * *
1963667 TTTATTTTTAAATATTAATAA-TTGATTA
1 TTTATTTTAAAATATTAATAATTTAATCA
1963695 TTTA-TTTAAAATATTAATAATTTAATCA
1 TTTATTTTAAAATATTAATAATTTAATCA
*
1963723 TTAATATTTTAAAATATTAATATTTTA
1 TT--TATTTTAAAATATTAATAATTTA
1963750 TTTAATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 15 0.32
28 11 0.23
30 2 0.04
31 19 0.40
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTATTTTAAAATATTAATAATTTAATCA
Found at i:1963739 original size:123 final size:126
Alignment explanation
Indices: 1963583--1963846 Score: 383
Period size: 123 Copynumber: 2.1 Consensus size: 126
1963573 TATTAATATT
* *
1963583 TATTTATAATTTAGTCATTAATATAATAAAATATTAATATTTAATTTAATTTAAATATTATTATG
1 TATTAATAATTTAATCATTAATATAATAAAATATTAATATTTAATTTAATTT-AATATTATTATG
*
1963648 A-TAA-ATTATTTTA-TTTT-ATTTTATTTTTAAATATTAATAATTGATTATTTATTTAAAA
65 ATTAATATTATTTTATTTTTAATTTTATTTTTAAATATTAATAATTGATAATTTATTTAAAA
** *
1963706 TATTAATAATTTAATCATTAATATTTTAAAATATTAATATTTTATTTAATTTAATATTATTATGA
1 TATTAATAATTTAATCATTAATATAATAAAATATTAATATTTAATTTAATTTAATATTATTATGA
* *
1963771 TTAATTTTTTATTTTATTTTTTAAATTTTATTTTTAAATATTAATAATTGGTAATTTATTTAAAA
66 TTAA--TATTATTTTA-TTTTT-AATTTTATTTTTAAATATTAATAATTGATAATTTATTTAAAA
1963836 TATTAATAATT
1 TATTAATAATT
1963847 GATGATTTAA
Statistics
Matches: 125, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
122 13 0.10
123 50 0.40
126 8 0.06
128 4 0.03
130 50 0.40
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (126 bp):
TATTAATAATTTAATCATTAATATAATAAAATATTAATATTTAATTTAATTTAATATTATTATGA
TTAATATTATTTTATTTTTAATTTTATTTTTAAATATTAATAATTGATAATTTATTTAAAA
Found at i:1963755 original size:151 final size:148
Alignment explanation
Indices: 1963388--1963761 Score: 436
Period size: 151 Copynumber: 2.5 Consensus size: 148
1963378 TTTATTTTAT
* ** * * *
1963388 TTTATTTTCAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATT
1 TTTA-TTT-AAAATATTAATAATTAACCATTTAAATATTAATA-TATATTAATAATTTAGT-ATT
** *
1963453 AATATTTTAAAATATTAATATTTTTTAATTTAAATATTATTATGATTAATTATTTTATTTTATTT
62 AATATAATAAAATATTAATATTTTTTAATTTAAATATTATTATGATAAATTATTTTATTTTATTT
1963518 TTTAAATATTAATAATTGATAG
127 TTTAAATATTAATAATTGATAG
* * *
1963540 TTTATTTAAAATATTAATAATTGACCATTTAAATATTAATATTTATTTATAATTTAGTCATTAAT
1 TTTATTTAAAATATTAATAATTAACCATTTAAATATTAATATATATTAATAATTTAGT-ATTAAT
1963605 ATAATAAAATATTAATATTTAATTTAATTTAAATATTATTATGATAAATTATTTTATTTTATTTT
65 ATAATAAAATATTAATATTT--TTTAATTTAAATATTATTATGATAAATTATTTTATTTTA---T
1963670 ATTTTTAAATATTAATAATTGATTA-
125 -TTTTTAAATATTAATAATTGA-TAG
* * *
1963695 TTTATTTAAAATATTAATAATTTAATCA-TTAATATTTTAA-A-ATATTAATATTTTA-T-TTAA
1 TTTATTTAAAATATTAATAA-TTAACCATTTAA-ATATTAATATATATTAATAATTTAGTATTAA
*
1963755 TTTAATA
64 TATAATA
1963762 TTATTATGAT
Statistics
Matches: 200, Mismatches: 13, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
149 41 0.20
150 32 0.16
151 51 0.25
152 4 0.02
153 1 0.00
154 12 0.06
155 46 0.23
156 13 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (148 bp):
TTTATTTAAAATATTAATAATTAACCATTTAAATATTAATATATATTAATAATTTAGTATTAATA
TAATAAAATATTAATATTTTTTAATTTAAATATTATTATGATAAATTATTTTATTTTATTTTTTA
AATATTAATAATTGATAG
Found at i:1963774 original size:20 final size:17
Alignment explanation
Indices: 1963739--1963803 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 17
1963729 TTTTAAAATA
1963739 TTAATATTTTATTTAAT
1 TTAATATTTTATTTAAT
1963756 TTAATATTATTATGATTAAT
1 TTAATATT-TTAT--TTAAT
**
1963776 TTTTTATTTTATTT--T
1 TTAATATTTTATTTAAT
1963791 TTAA-ATTTTATTT
1 TTAATATTTTATTT
1963804 TTAAATATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 9 0.22
15 3 0.07
17 10 0.24
18 4 0.10
19 4 0.10
20 11 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTAATATTTTATTTAAT
Found at i:1963804 original size:13 final size:14
Alignment explanation
Indices: 1963781--1963809 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1963771 TTAATTTTTT
1963781 ATTTTATTTTTTAA
1 ATTTTATTTTTTAA
1963795 ATTTTA-TTTTTAA
1 ATTTTATTTTTTAA
1963808 AT
1 AT
1963810 ATTAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTATTTTTTAA
Found at i:1963971 original size:23 final size:23
Alignment explanation
Indices: 1963926--1964001 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
1963916 TTTAAATAAG
* ***
1963926 AATAATTTATAAGTTATTTTATT
1 AATAATTTATAATTTAAAATATT
1963949 AATAATTTATAATTTAAAATATT
1 AATAATTTATAATTTAAAATATT
1963972 AATATTTTATTTATAATTT-AAATATT
1 AATA----ATTTATAATTTAAAATATT
1963998 AATA
1 AATA
1964002 TGTTAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
23 23 0.51
26 11 0.24
27 11 0.24
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
AATAATTTATAATTTAAAATATT
Found at i:1969153 original size:40 final size:40
Alignment explanation
Indices: 1969098--1969208 Score: 123
Period size: 46 Copynumber: 2.6 Consensus size: 40
1969088 CGTTATCAGC
*
1969098 ACGATCCTTTAATCTCTCACCCTCAAGCTTCACAAAGTCG
1 ACGATCCTATAATCTCTCACCCTCAAGCTTCACAAAGTCG
* *
1969138 ACGATCCTATAATCTCTCACCTTCACCCCCAAGCTTTACAAAGTCG
1 ACGATCCTATAA--TCT---C-TCACCCTCAAGCTTCACAAAGTCG
* *
1969184 ACAATCTTATAATCTCTCACCCTCA
1 ACGATCCTATAATCTCTCACCCTCA
1969209 CCTTCACCCT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
40 19 0.32
41 1 0.02
42 3 0.05
44 3 0.05
45 1 0.02
46 32 0.54
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.28
Consensus pattern (40 bp):
ACGATCCTATAATCTCTCACCCTCAAGCTTCACAAAGTCG
Found at i:1969181 original size:46 final size:46
Alignment explanation
Indices: 1969113--1969260 Score: 188
Period size: 46 Copynumber: 3.1 Consensus size: 46
1969103 CCTTTAATCT
* *
1969113 CTCACCCTCAAGCTTCACAAAGTCGACGATCCTATAATCTCTCACC
1 CTCACCCCCAAGCTTCACAAAGTCGACGATCTTATAATCTCTCACC
* * *
1969159 TTCACCCCCAAGCTTTACAAAGTCGACAATCTTATAATCTCTCACC
1 CTCACCCCCAAGCTTCACAAAGTCGACGATCTTATAATCTCTCACC
*
1969205 CTCACCTTCACCCTTAAACTTCACAAAGTCGACGATCTTATAATCTCTCACC
1 CTCA-C--C-CCC--AAGCTTCACAAAGTCGACGATCTTATAATCTCTCACC
1969257 CTCA
1 CTCA
1969261 AGTGTCACAA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
46 44 0.51
47 1 0.01
49 1 0.01
50 3 0.03
52 38 0.44
ACGTcount: A:0.29, C:0.37, G:0.07, T:0.27
Consensus pattern (46 bp):
CTCACCCCCAAGCTTCACAAAGTCGACGATCTTATAATCTCTCACC
Found at i:1969231 original size:52 final size:49
Alignment explanation
Indices: 1969113--1969260 Score: 194
Period size: 52 Copynumber: 3.0 Consensus size: 49
1969103 CCTTTAATCT
* *
1969113 CTCACCCTCAAGCTTCACAAAGTCGACGATCCTATAATCTCTCACCTTCA
1 CTCACCCT-AAGCTTCACAAAGTCGACGATCTTATAATCTCTCACCCTCA
* *
1969163 C-C-CCC-AAGCTTTACAAAGTCGACAATCTTATAATCTCTCACCCTCA
1 CTCACCCTAAGCTTCACAAAGTCGACGATCTTATAATCTCTCACCCTCA
*
1969209 CCTTCACCCTTAAACTTCACAAAGTCGACGATCTTATAATCTCTCACCCTCA
1 -C-TCACCC-TAAGCTTCACAAAGTCGACGATCTTATAATCTCTCACCCTCA
1969261 AGTGTCACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
46 37 0.44
47 1 0.01
48 3 0.04
49 2 0.02
50 4 0.05
52 38 0.45
ACGTcount: A:0.29, C:0.37, G:0.07, T:0.27
Consensus pattern (49 bp):
CTCACCCTAAGCTTCACAAAGTCGACGATCTTATAATCTCTCACCCTCA
Found at i:1979527 original size:16 final size:14
Alignment explanation
Indices: 1979506--1979603 Score: 53
Period size: 15 Copynumber: 6.9 Consensus size: 14
1979496 CCTATTGAAT
1979506 AAAATACAAAGAAGCA
1 AAAATACAAA-AAG-A
*
1979522 AAAATATAAAAAGA
1 AAAATACAAAAAGA
1979536 AAAATAACAAAAA-A
1 AAAAT-ACAAAAAGA
*
1979550 ATAAATA-AAAACGATA
1 A-AAATACAAAA--AGA
*
1979566 AAAATA-AAAAATA
1 AAAATACAAAAAGA
* *
1979579 CAAATAGAAAATA-A
1 AAAATACAAAA-AGA
1979593 AAAATA-AAAAA
1 AAAATACAAAAA
1979604 AAATTAATAA
Statistics
Matches: 71, Mismatches: 4, Indels: 18
0.76 0.04 0.19
Matches are distributed among these distances:
12 1 0.01
13 16 0.23
14 19 0.27
15 24 0.34
16 11 0.15
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (14 bp):
AAAATACAAAAAGA
Found at i:1979539 original size:15 final size:14
Alignment explanation
Indices: 1979506--1979603 Score: 67
Period size: 14 Copynumber: 6.8 Consensus size: 14
1979496 CCTATTGAAT
*
1979506 AAAATACAAAGAAGCA
1 AAAATA-AAA-AAGAA
1979522 AAAATATAAAAAG-A
1 AAAATA-AAAAAGAA
1979536 AAAATAACAAAA-AA
1 AAAATAA-AAAAGAA
*
1979550 ATAAATAAAAACGATA
1 A-AAATAAAAAAGA-A
*
1979566 AAAATAAAAAA-TA
1 AAAATAAAAAAGAA
* * *
1979579 CAAATAGAAAATAA
1 AAAATAAAAAAGAA
1979593 AAAATAAAAAA
1 AAAATAAAAAA
1979604 AAATTAATAA
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
13 11 0.16
14 26 0.39
15 19 0.28
16 11 0.16
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (14 bp):
AAAATAAAAAAGAA
Found at i:1979574 original size:6 final size:6
Alignment explanation
Indices: 1979522--1979622 Score: 62
Period size: 6 Copynumber: 15.8 Consensus size: 6
1979512 CAAAGAAGCA
* * *
1979522 AAAATAT AAAAAG AAAAAT AACAA- AAAAAT AAATAA- AAACGAT AAAAAT
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAA-AAT AAA-AAT AAAAAT
* * *
1979571 AAAAAAT ACAAAT AGAAAAT AAAAAAT AAAAAA AAATTAAT AATAAT AAAAA
1 -AAAAAT AAAAAT A-AAAAT -AAAAAT AAAAAT AAA--AAT AAAAAT AAAAA
1979623 AGGGAAGGTC
Statistics
Matches: 73, Mismatches: 13, Indels: 17
0.71 0.13 0.17
Matches are distributed among these distances:
5 4 0.05
6 40 0.55
7 24 0.33
8 5 0.07
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:1979574 original size:27 final size:26
Alignment explanation
Indices: 1979527--1979604 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
1979517 AAGCAAAAAT
* * *
1979527 ATAAAAAGAAAAATAACAAAAAAATAA
1 ATAAAAAGATAAA-AATAAAAAAACAA
1979554 ATAAAAACGATAAAAATAAAAAATACAA
1 ATAAAAA-GATAAAAATAAAAAA-ACAA
*
1979582 ATAGAAA-ATAAAAAATAAAAAAA
1 ATAAAAAGAT-AAAAATAAAAAAA
1979605 AATTAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
26 3 0.07
27 27 0.61
28 14 0.32
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (26 bp):
ATAAAAAGATAAAAATAAAAAAACAA
Found at i:1979577 original size:7 final size:7
Alignment explanation
Indices: 1979521--1979603 Score: 66
Period size: 7 Copynumber: 11.7 Consensus size: 7
1979511 ACAAAGAAGC
1979521 AAAAATA
1 AAAAATA
*
1979528 TAAAAA-G
1 -AAAAATA
1979535 AAAAATA
1 AAAAATA
1979542 ACAAAA-A
1 A-AAAATA
1979549 AATAAATA
1 AA-AAATA
1979557 AAAACGAT-
1 AAAA--ATA
1979565 AAAAATA
1 AAAAATA
1979572 AAAAAT-
1 AAAAATA
*
1979578 ACAAATA
1 AAAAATA
*
1979585 GAAAATA
1 AAAAATA
1979592 AAAAATA
1 AAAAATA
1979599 AAAAA
1 AAAAA
1979604 AAATTAATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
6 13 0.21
7 30 0.49
8 16 0.26
9 2 0.03
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:1979583 original size:13 final size:13
Alignment explanation
Indices: 1979521--1979603 Score: 76
Period size: 14 Copynumber: 5.9 Consensus size: 13
1979511 ACAAAGAAGC
*
1979521 AAAAATATAAAAAG
1 AAAAATA-AAAAAT
*
1979535 AAAAATAACAAAAA
1 AAAAATAA-AAAAT
1979549 AATAAATAAAAACGAT
1 AA-AAATAAAAA--AT
1979565 AAAAATAAAAAAT
1 AAAAATAAAAAAT
* *
1979578 ACAAATAGAAAAT
1 AAAAATAAAAAAT
1979591 AAAAAATAAAAAA
1 -AAAAATAAAAAA
1979604 AAATTAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
13 14 0.24
14 26 0.45
15 15 0.26
16 3 0.05
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.13
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:1980378 original size:19 final size:19
Alignment explanation
Indices: 1980354--1980413 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 19
1980344 ATAAAAAATA
1980354 TATAAATATTATAATCAAT
1 TATAAATATTATAATCAAT
**
1980373 TATAAATTAGAATTGCAAGTCAAT
1 TATAAA-T---ATTATAA-TCAAT
1980397 TATAAATATTATAATCA
1 TATAAATATTATAATCA
1980414 CCTAATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
19 9 0.28
20 6 0.19
23 6 0.19
24 11 0.34
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (19 bp):
TATAAATATTATAATCAAT
Found at i:1981837 original size:22 final size:20
Alignment explanation
Indices: 1981806--1981904 Score: 85
Period size: 22 Copynumber: 4.7 Consensus size: 20
1981796 ACAAAAAAGC
*
1981806 AAAAATATAAAAAGATAAATA
1 AAAAAAATAAAAAGA-AAATA
1981827 ACAAAAAATAAATAA-AAATGATA
1 A-AAAAAATAAA-AAGAAA--ATA
1981850 AAAAAAATACAAATAGAAAATA
1 AAAAAAATA-AAA-AGAAAATA
1981872 AAAAAAAT-AAAAGAAAATTA
1 AAAAAAATAAAAAGAAAA-TA
* *
1981892 ATAATAATAAAAA
1 AAAAAAATAAAAA
1981905 AGGGAAGGTC
Statistics
Matches: 66, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
19 6 0.09
20 11 0.17
21 7 0.11
22 30 0.45
23 9 0.14
24 3 0.05
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (20 bp):
AAAAAAATAAAAAGAAAATA
Found at i:1981862 original size:31 final size:33
Alignment explanation
Indices: 1981806--1981889 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 33
1981796 ACAAAAAAGC
*
1981806 AAAAATATAAAAAGATAAATAACAAA-AAATAAATA
1 AAAAAAAT-AAAAGA-AAATAACAAATAAA-AAATA
** *
1981841 AAAATGATAAAA-AAAAT-ACAAATAGAAAATA
1 AAAAAAATAAAAGAAAATAACAAATAAAAAATA
1981872 AAAAAAATAAAAGAAAAT
1 AAAAAAATAAAAGAAAAT
1981890 TAATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
31 20 0.48
32 11 0.26
33 1 0.02
34 4 0.10
35 6 0.14
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.15
Consensus pattern (33 bp):
AAAAAAATAAAAGAAAATAACAAATAAAAAATA
Found at i:1981883 original size:14 final size:14
Alignment explanation
Indices: 1981788--1981905 Score: 64
Period size: 14 Copynumber: 8.0 Consensus size: 14
1981778 AGCCCTATTG
1981788 AATAAAATACAAAAA
1 AATAAAATA-AAAAA
1981803 AGCA-AAAATATAAAAA
1 A--ATAAAATA-AAAAA
*
1981819 GAT-AAATAACAAAA
1 AATAAAATAA-AAAA
*
1981833 AAT-AAATAAAAAT
1 AATAAAATAAAAAA
*
1981846 GATAAAA-AAAATACA
1 AATAAAATAAAA-A-A
1981861 AATAGAAAATAAAAAA
1 AAT--AAAATAAAAAA
* **
1981877 AATAAAAGAAAATT
1 AATAAAATAAAAAA
1981891 AATAATAATAAAAAA
1 AATAA-AATAAAAAA
1981906 GGGAAGGTCG
Statistics
Matches: 79, Mismatches: 13, Indels: 22
0.69 0.11 0.19
Matches are distributed among these distances:
13 10 0.13
14 35 0.44
15 9 0.11
16 15 0.19
17 6 0.08
18 4 0.05
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.16
Consensus pattern (14 bp):
AATAAAATAAAAAA
Found at i:1982929 original size:23 final size:23
Alignment explanation
Indices: 1982893--1982950 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
1982883 TATTTGAATA
1982893 ATAAAAAATATAAA-AAG-GAAACT
1 ATAAAAAA-ATAAATAAGAGAAA-T
*
1982916 CATAAATAAATAAATAAGAGAAAT
1 -ATAAAAAAATAAATAAGAGAAAT
*
1982940 ATAAACAAATA
1 ATAAAAAAATA
1982951 TGAAGTCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 15 0.50
24 11 0.37
25 4 0.13
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (23 bp):
ATAAAAAAATAAATAAGAGAAAT
Found at i:1984654 original size:21 final size:22
Alignment explanation
Indices: 1984630--1984682 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
1984620 TGATTTTGTT
1984630 TTAGGCATTAGGTTTA-GGGTA
1 TTAGGCATTAGGTTTAGGGGTA
* *
1984651 TTAGGCATTGGGTTTAGGGGTT
1 TTAGGCATTAGGTTTAGGGGTA
1984673 TTAGGCATTA
1 TTAGGCATTA
1984683 CATGACGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.21, C:0.06, G:0.34, T:0.40
Consensus pattern (22 bp):
TTAGGCATTAGGTTTAGGGGTA
Found at i:1984868 original size:23 final size:23
Alignment explanation
Indices: 1984758--1984871 Score: 81
Period size: 23 Copynumber: 5.0 Consensus size: 23
1984748 ATTAGTTGAC
*
1984758 AAGGTATTATGTGATTGA-TTTT
1 AAGGTATTACGTGATTGATTTTT
* * * *
1984780 GAGGTTATTGCATGACTGATTTTT
1 AAGG-TATTACGTGATTGATTTTT
* * * *
1984804 -AGGCATCACGTAATTG-GTTTT
1 AAGGTATTACGTGATTGATTTTT
* ** *
1984825 AGGGTATTACGTGGCTAATTTTT
1 AAGGTATTACGTGATTGATTTTT
1984848 AAGGTATTACGTGATTGATTTTT
1 AAGGTATTACGTGATTGATTTTT
1984871 A
1 A
1984872 GGCATTGAGT
Statistics
Matches: 64, Mismatches: 24, Indels: 7
0.67 0.25 0.07
Matches are distributed among these distances:
21 4 0.06
22 19 0.30
23 37 0.58
24 4 0.06
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.45
Consensus pattern (23 bp):
AAGGTATTACGTGATTGATTTTT
Done.