Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 5 of 202
Found at i:1556772 original size:25 final size:25
Alignment explanation
Indices: 1556694--1556778 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
1556684 AACTAGGAAT
*
1556694 CTCATGAGAGTCAAGTATCAAGAAG
1 CTCAAGAGAGTCAAGTATCAAGAAG
* * * *
1556719 CTCAAGAGAG-C-TGTTAACTAGGAAT
1 CTCAAGAGAGTCAAG-TATC-AAGAAG
*
1556744 CTCATGAGAGTCAAGTATCAAGAAG
1 CTCAAGAGAGTCAAGTATCAAGAAG
1556769 CTCAAGAGAG
1 CTCAAGAGAG
1556779 CTGTGGTACG
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
23 1 0.02
24 4 0.09
25 35 0.78
26 4 0.09
27 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (25 bp):
CTCAAGAGAGTCAAGTATCAAGAAG
Found at i:1556779 original size:50 final size:50
Alignment explanation
Indices: 1556665--1556782 Score: 227
Period size: 50 Copynumber: 2.4 Consensus size: 50
1556655 CAAATATCGG
*
1556665 GAAGCTCAAGAGAGATGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
1 GAAGCTCAAGAGAGCTGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
1556715 GAAGCTCAAGAGAGCTGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
1 GAAGCTCAAGAGAGCTGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
1556765 GAAGCTCAAGAGAGCTGT
1 GAAGCTCAAGAGAGCTGT
1556783 GGTACGTCTG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.21
Consensus pattern (50 bp):
GAAGCTCAAGAGAGCTGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
Found at i:1559821 original size:13 final size:14
Alignment explanation
Indices: 1559789--1559822 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1559779 GTTTGTTTCA
1559789 CTGAAAATGAATTT
1 CTGAAAATGAATTT
*
1559803 CGGAAAATG-ATTT
1 CTGAAAATGAATTT
1559816 CTGAAAA
1 CTGAAAA
1559823 ATGACTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (14 bp):
CTGAAAATGAATTT
Found at i:1559854 original size:19 final size:20
Alignment explanation
Indices: 1559813--1559857 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1559803 CGGAAAATGA
*
1559813 TTTCTGAAAAATGACTTATT
1 TTTCTGAAAAATGACTAATT
1559833 TTTCTGAAAAA-G-CTAATAT
1 TTTCTGAAAAATGACTAAT-T
1559852 TTTCTG
1 TTTCTG
1559858 GTGTTTGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 8 0.35
20 11 0.48
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (20 bp):
TTTCTGAAAAATGACTAATT
Found at i:1560419 original size:19 final size:18
Alignment explanation
Indices: 1560397--1560457 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
1560387 GAAATAAAAT
1560397 TTAAATATTAAATAATTTA
1 TTAAATATT-AATAATTTA
*
1560416 TTAAA-AATAATAAATTATA
1 TTAAATATTAAT-AATT-TA
1560435 TTAATTATATTAATAATTTA
1 TTAA--ATATTAATAATTTA
1560455 TTA
1 TTA
1560458 TATGATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 3 0.09
18 6 0.17
19 11 0.31
20 5 0.14
21 5 0.14
22 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATATTAATAATTTA
Found at i:1571226 original size:13 final size:13
Alignment explanation
Indices: 1571208--1571258 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
1571198 AAATTATAAA
1571208 ATTATAAAAAAAT
1 ATTATAAAAAAAT
*
1571221 ATTAT-AAAGAAT
1 ATTATAAAAAAAT
*
1571233 A-TATAAAAAATTT
1 ATTATAAAAAA-AT
*
1571246 ATTTTAAAAAAAT
1 ATTATAAAAAAAT
1571259 CCAAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
11 3 0.10
12 11 0.37
13 8 0.27
14 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
ATTATAAAAAAAT
Found at i:1571226 original size:21 final size:23
Alignment explanation
Indices: 1571200--1571247 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1571190 TTTTTAGAAA
*
1571200 ATTATAAA-ATTATA-AAAAAAT
1 ATTATAAAGAATATATAAAAAAT
1571221 ATTATAAAGAATATATAAAAAAT
1 ATTATAAAGAATATATAAAAAAT
1571244 -TTAT
1 ATTAT
1571248 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
ATTATAAAGAATATATAAAAAAT
Found at i:1571832 original size:24 final size:23
Alignment explanation
Indices: 1571784--1571833 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
1571774 TATGAGAGTG
*
1571784 AATACTCATTTTTATATAATTAA
1 AATACTCATTTTTATATAATAAA
*
1571807 AATATTCATATTTTATATTAA-AAA
1 AATACTCAT-TTTTATA-TAATAAA
1571831 AAT
1 AAT
1571834 TTATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 12 0.52
25 3 0.13
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (23 bp):
AATACTCATTTTTATATAATAAA
Found at i:1572010 original size:27 final size:29
Alignment explanation
Indices: 1571950--1572014 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 29
1571940 TTAAGCTTTA
1571950 TTATTAAAATAAAAATTTAATATTAAATATT
1 TTATTAAAATAAAAATTT-ATATT-AATATT
1571981 TTATTAAAATAATAAATTT-TATT-A-ATT
1 TTATTAAAATAA-AAATTTATATTAATATT
1572008 TTATTAA
1 TTATTAA
1572015 TAACTAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 10 0.30
28 1 0.03
30 4 0.12
31 12 0.36
32 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TTATTAAAATAAAAATTTATATTAATATT
Found at i:1572023 original size:25 final size:26
Alignment explanation
Indices: 1571978--1572029 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
1571968 AATATTAAAT
*
1571978 ATTTTATTAAAATAATAAATTTTATTA
1 ATTTTATT-AAATAATAAATTATATTA
1572005 ATTTTATT-AATAACT-AATTATATTA
1 ATTTTATTAAATAA-TAAATTATATTA
1572030 TTAAAAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 14 0.61
26 1 0.04
27 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTTATTAAATAATAAATTATATTA
Found at i:1573189 original size:5 final size:5
Alignment explanation
Indices: 1573181--1573205 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1573171 CCGAGCCCTG
1573181 CCCGA CCCGA CCCGA CCCGA CCCGA
1 CCCGA CCCGA CCCGA CCCGA CCCGA
1573206 ATATAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
CCCGA
Found at i:1573246 original size:13 final size:13
Alignment explanation
Indices: 1573214--1573247 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1573204 GAATATAATA
1573214 AATTTATATTTTTT
1 AATTT-TATTTTTT
*
1573228 ATTTTTATTTTTT
1 AATTTTATTTTTT
1573241 AATTTTA
1 AATTTTA
1573248 AAATACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
AATTTTATTTTTT
Found at i:1573910 original size:37 final size:37
Alignment explanation
Indices: 1573860--1573969 Score: 130
Period size: 37 Copynumber: 3.0 Consensus size: 37
1573850 CCTGGAAGAT
* * * *
1573860 AAAAGACGGAGATGAACAATAATGATTCTTTGCAAAG
1 AAAACACGAAGATGAACAGTAATGATTCTCTGCAAAG
* * *
1573897 AAAACACGAAGATGAATAGCAATGATTCCCTGCAAAG
1 AAAACACGAAGATGAACAGTAATGATTCTCTGCAAAG
* * *
1573934 AAAATACGAAGATGAACAGTAATCATTCTCTACAAA
1 AAAACACGAAGATGAACAGTAATGATTCTCTGCAAA
1573970 AATTCTCTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.20
Consensus pattern (37 bp):
AAAACACGAAGATGAACAGTAATGATTCTCTGCAAAG
Found at i:1585389 original size:12 final size:12
Alignment explanation
Indices: 1585367--1585401 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1585357 AGGAAGAGTA
1585367 GAGAGAAAAAATC
1 GAGA-AAAAAATC
*
1585380 GAGAAAAAAATT
1 GAGAAAAAAATC
1585392 GAGAAAAAAA
1 GAGAAAAAAA
1585402 AATATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (12 bp):
GAGAAAAAAATC
Found at i:1585688 original size:33 final size:33
Alignment explanation
Indices: 1585644--1585719 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
1585634 CCATTCAGTG
* *
1585644 AATTATTTTTTCACTATCACTACTATCAAGTTA
1 AATTTTTTTTTCACTATCACTACAATCAAGTTA
*
1585677 AATTTTTTTTTCACTATTACTACAATCAAGTTA
1 AATTTTTTTTTCACTATCACTACAATCAAGTTA
*
1585710 AAATTTTTTT
1 AATTTTTTTT
1585720 AATAGGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (33 bp):
AATTTTTTTTTCACTATCACTACAATCAAGTTA
Found at i:1585733 original size:21 final size:22
Alignment explanation
Indices: 1585709--1585758 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1585699 CAATCAAGTT
1585709 AAAATTTTTTTAATAGG-TGAA
1 AAAATTTTTTTAATAGGTTGAA
**
1585730 AAAA-TAATTTAATAGGTTGAA
1 AAAATTTTTTTAATAGGTTGAA
*
1585751 AATATTTT
1 AAAATTTT
1585759 AACTGGTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
20 10 0.45
21 11 0.50
22 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (22 bp):
AAAATTTTTTTAATAGGTTGAA
Found at i:1585759 original size:19 final size:19
Alignment explanation
Indices: 1585716--1585760 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1585706 GTTAAAATTT
1585716 TTTTAATAGGTGAAAAAATA
1 TTTTAATAGGTG-AAAAATA
*
1585736 ATTTAATAGGTTG-AAAATA
1 TTTTAATAGG-TGAAAAATA
1585755 TTTTAA
1 TTTTAA
1585761 CTGGTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 11 0.50
20 9 0.41
21 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTTAATAGGTGAAAAATA
Found at i:1603011 original size:23 final size:23
Alignment explanation
Indices: 1602985--1603039 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1602975 ATGTCGCCAG
*
1602985 GTCGTGACGCCAAGCATCACGCC
1 GTCGAGACGCCAAGCATCACGCC
1603008 GTCGAGACGCCAAGCATCACGCC
1 GTCGAGACGCCAAGCATCACGCC
1603031 GTCGAGACG
1 GTCGAGACG
1603040 ACGGTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.36, G:0.29, T:0.11
Consensus pattern (23 bp):
GTCGAGACGCCAAGCATCACGCC
Found at i:1604436 original size:16 final size:15
Alignment explanation
Indices: 1604415--1604444 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1604405 CCTTTTTTTA
1604415 TTTATTCATTTAATTG
1 TTTATTCA-TTAATTG
1604431 TTTATTCATTAATT
1 TTTATTCATTAATT
1604445 ATTCTTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTATTCATTAATTG
Found at i:1605825 original size:19 final size:21
Alignment explanation
Indices: 1605786--1605825 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1605776 TTGATGAAAC
1605786 AAGAAGTTTAAAAACTCAATT
1 AAGAAGTTTAAAAACTCAATT
*
1605807 AAGAA-TTTAGAAA-TCAATT
1 AAGAAGTTTAAAAACTCAATT
1605826 TGATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAGAAGTTTAAAAACTCAATT
Found at i:1608466 original size:27 final size:27
Alignment explanation
Indices: 1608436--1608497 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
1608426 CCTGTCAGGT
**
1608436 AGGCGCCACTAATTGTGCCTCATAGGG
1 AGGCGCCACTAAAAGTGCCTCATAGGG
*
1608463 AGGCGCCATTAAAAGTGCCTCATAGGG
1 AGGCGCCACTAAAAGTGCCTCATAGGG
1608490 AGGCGCCA
1 AGGCGCCA
1608498 ATGGATGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.31, T:0.18
Consensus pattern (27 bp):
AGGCGCCACTAAAAGTGCCTCATAGGG
Found at i:1608659 original size:3 final size:3
Alignment explanation
Indices: 1608653--1608699 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
1608643 GAGAGAAAGG
*
1608653 AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AG- AGA AGA AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1608699 A
1 A
1608700 AGAAAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1608663 original size:17 final size:17
Alignment explanation
Indices: 1608641--1608693 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
1608631 GAGAAAAAAA
1608641 AAGAGAGAAAGGAGAAG
1 AAGAGAGAAAGGAGAAG
*
1608658 AAGAGA-AGAAGAAGAAG
1 AAGAGAGA-AAGGAGAAG
1608675 AAGA-AG-AA-GAGAAG
1 AAGAGAGAAAGGAGAAG
1608689 AAGAG
1 AAGAG
1608694 GAAGAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 9 0.29
15 2 0.06
16 2 0.06
17 18 0.58
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (17 bp):
AAGAGAGAAAGGAGAAG
Found at i:1608683 original size:23 final size:23
Alignment explanation
Indices: 1608653--1608699 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1608643 GAGAGAAAGG
1608653 AGAAGAAGAGAAGAAGAAGAAGA
1 AGAAGAAGAGAAGAAGAAGAAGA
*
1608676 AGAAGAAGAGAAGAAGAGGAAGA
1 AGAAGAAGAGAAGAAGAAGAAGA
1608699 A
1 A
1608700 AGAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (23 bp):
AGAAGAAGAGAAGAAGAAGAAGA
Found at i:1608706 original size:17 final size:15
Alignment explanation
Indices: 1608655--1608707 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 15
1608645 GAGAAAGGAG
1608655 AAGAAGAGAAGAAG-
1 AAGAAGAGAAGAAGA
1608669 AAGAAGAAGAAGAAGA
1 AAGAAG-AGAAGAAGA
1608685 GAAGAAGAGGAAGAAAGA
1 -AAGAAGA-GAAG-AAGA
1608703 AAGAA
1 AAGAA
1608708 AAAATGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.18
15 8 0.24
16 1 0.03
17 15 0.44
18 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AAGAAGAGAAGAAGA
Found at i:1608707 original size:20 final size:19
Alignment explanation
Indices: 1608653--1608707 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
1608643 GAGAGAAAGG
1608653 AGAAGAAGAGAAGAAGAAGA
1 AGAAGAAGA-AAGAAGAAGA
1608673 AGAAGAAGAAGAGAAGAAGA
1 AGAAGAAGAA-AGAAGAAGA
*
1608693 GGAAGAAAGAAAGAA
1 AGAAG-AAGAAAGAA
1608708 AAAATGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 1 0.03
20 26 0.81
21 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
AGAAGAAGAAAGAAGAAGA
Found at i:1608866 original size:21 final size:21
Alignment explanation
Indices: 1608841--1608906 Score: 100
Period size: 19 Copynumber: 3.2 Consensus size: 21
1608831 TGGATTAGCA
*
1608841 TTTTGTATTAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
1608862 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
1608881 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
1608902 ATTTT
1 -TTTT
1608907 ATAATTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 19 0.46
21 18 0.44
22 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:1612979 original size:22 final size:21
Alignment explanation
Indices: 1612953--1612997 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1612943 CAAAAAAAAT
*
1612953 AAGAAGGAAGGAAGCAGAAGAA
1 AAGAAGGAAGGAA-AAGAAGAA
*
1612975 AAGAATGAAGGAAAAGAAGAA
1 AAGAAGGAAGGAAAAGAAGAA
1612996 AA
1 AA
1612998 AAATAAGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.64, C:0.02, G:0.31, T:0.02
Consensus pattern (21 bp):
AAGAAGGAAGGAAAAGAAGAA
Found at i:1612998 original size:22 final size:22
Alignment explanation
Indices: 1612953--1613005 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1612943 CAAAAAAAAT
* *
1612953 AAGAAGGAAGGAAGCAGAAGAA
1 AAGAATGAAGGAAGAAGAAGAA
1612975 AAGAATGAAGGAA-AAGAAGAA
1 AAGAATGAAGGAAGAAGAAGAA
*
1612996 AAAAAT-AAGG
1 AAGAATGAAGG
1613006 TATTTTGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 4 0.14
21 12 0.43
22 12 0.43
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.04
Consensus pattern (22 bp):
AAGAATGAAGGAAGAAGAAGAA
Found at i:1615353 original size:28 final size:27
Alignment explanation
Indices: 1615293--1615360 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
1615283 AAATTGTAAA
1615293 ATAAAAAAA-ATTATAATTTTATTTAC
1 ATAAAAAAACATTATAATTTTATTTAC
*
1615319 ATAAAAAACCATTATAATTTTATTTAC
1 ATAAAAAAACATTATAATTTTATTTAC
1615346 ATAAAAAAATCATTA
1 ATAAAAAAA-CATTA
1615361 CATAAATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 8 0.21
27 25 0.66
28 5 0.13
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.38
Consensus pattern (27 bp):
ATAAAAAAACATTATAATTTTATTTAC
Found at i:1615714 original size:6 final size:6
Alignment explanation
Indices: 1615684--1615736 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
1615674 AGAATGTGGT
* * * * *
1615684 TCTGTC TCTGGC ACTGGC ACTGGC TCTGGC TTTGGC TCTGGC TCTGGT
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
1615732 TCTGG
1 TCTGG
1615737 TGCATAATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.04, C:0.28, G:0.32, T:0.36
Consensus pattern (6 bp):
TCTGGC
Found at i:1617478 original size:38 final size:38
Alignment explanation
Indices: 1617435--1617516 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
1617425 AAAAAGTCAG
1617435 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
1617473 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1617511 TTATAA
1 TTATAA
1617517 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:1617626 original size:60 final size:60
Alignment explanation
Indices: 1617550--1617671 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
1617540 ATACTAAACT
* * * * * *
1617550 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATT-AATTATAAAATAATTAC
*
1617610 AAACACAAAAATTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
1617670 AA
1 AA
1617672 TATTCATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:1617699 original size:8 final size:8
Alignment explanation
Indices: 1617686--1617776 Score: 56
Period size: 8 Copynumber: 10.4 Consensus size: 8
1617676 CATACAAAAA
1617686 ATTACAAT
1 ATTACAAT
1617694 ATTACAAT
1 ATTACAAT
* * *
1617702 ATATCCCGAC
1 AT-T-ACAAT
1617712 ATTACAAT
1 ATTACAAT
*
1617720 ATTCATACAAA
1 A-T--TACAAT
*
1617731 ATTATAAT
1 ATTACAAT
1617739 ATTACAAT
1 ATTACAAT
*
1617747 ATTTATACAAA
1 A--T-TACAAT
1617758 ATTACAAT
1 ATTACAAT
1617766 ATTACAAT
1 ATTACAAT
1617774 ATT
1 ATT
1617777 CACACAAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
8 41 0.65
9 4 0.06
10 6 0.10
11 12 0.19
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.36
Consensus pattern (8 bp):
ATTACAAT
Found at i:1617748 original size:27 final size:26
Alignment explanation
Indices: 1617712--1617855 Score: 162
Period size: 27 Copynumber: 5.8 Consensus size: 26
1617702 ATATCCCGAC
1617712 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
*
1617739 ATTACAATATTTATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
*
1617766 ATTACAATATTCACAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
1617788 ATTGCAAAATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
1617815 ATTACAATATTCATAC--AA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
1617836 ATTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
1617856 AACTAATCCA
Statistics
Matches: 101, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
21 16 0.16
22 15 0.15
23 8 0.08
24 1 0.01
25 3 0.03
26 5 0.05
27 53 0.52
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAT
Found at i:1617783 original size:19 final size:19
Alignment explanation
Indices: 1617689--1617783 Score: 51
Period size: 19 Copynumber: 5.2 Consensus size: 19
1617679 ACAAAAAATT
1617689 ACAATATTACAATATATC-C
1 ACAATATTACAATAT-TCAC
* * *
1617708 -CGACATTACAATATTCAT
1 ACAATATTACAATATTCAC
* *
1617726 ACAAAATTATAATATT-AC
1 ACAATATTACAATATTCAC
* *
1617744 A-ATATTTATACAAAATT---
1 ACA-ATAT-TACAATATTCAC
1617761 ACAATATTACAATATTCAC
1 ACAATATTACAATATTCAC
1617780 ACAA
1 ACAA
1617784 AAAAATTGCA
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
16 8 0.15
17 7 0.13
18 17 0.31
19 23 0.42
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (19 bp):
ACAATATTACAATATTCAC
Found at i:1617816 original size:76 final size:73
Alignment explanation
Indices: 1617665--1617846 Score: 242
Period size: 76 Copynumber: 2.4 Consensus size: 73
1617655 TTATAAAATA
* * *
1617665 ATTACAATATTCATACAAAAAATTACAATATTACAATATATCCCGACATTACAATATTCATACAA
1 ATTACAATATTCATAC-AAAAATTACAATATTACAATATATCCCAAAATTACAAAATTCATACAA
1617730 AATTATAAT
65 AATTATAAT
* *
1617739 ATTACAATATTTATAC-AAAATTACAATATTACAATAT-TCACACAAAAAAATTGCAAAATTCAT
1 ATTACAATATTCATACAAAAATTACAATATTACAATATATC-C-C---AAAATTACAAAATTCAT
1617802 ACAAAATTATAAT
61 ACAAAATTATAAT
1617815 ATTACAATATTCATACAAAAAATTACAATATT
1 ATTACAATATTCATAC-AAAAATTACAATATT
1617847 CATACAAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
71 2 0.02
72 22 0.23
73 1 0.01
74 15 0.16
76 41 0.43
78 14 0.15
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.32
Consensus pattern (73 bp):
ATTACAATATTCATACAAAAATTACAATATTACAATATATCCCAAAATTACAAAATTCATACAAA
ATTATAAT
Found at i:1617819 original size:49 final size:48
Alignment explanation
Indices: 1617739--1617855 Score: 171
Period size: 49 Copynumber: 2.4 Consensus size: 48
1617729 AAATTATAAT
* *
1617739 ATTACAATATTTATACAAAATTACAATATTACAATATTCACACAAAAAA
1 ATTACAAAATTCATACAAAATTACAATATTACAATATTCACAC-AAAAA
* * *
1617788 ATTGCAAAATTCATACAAAATTATAATATTACAATATTCATACAAAAA
1 ATTACAAAATTCATACAAAATTACAATATTACAATATTCACACAAAAA
*
1617836 ATTACAATATTCATACAAAA
1 ATTACAAAATTCATACAAAA
1617856 AACTAATCCA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
48 23 0.38
49 38 0.62
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.31
Consensus pattern (48 bp):
ATTACAAAATTCATACAAAATTACAATATTACAATATTCACACAAAAA
Found at i:1617841 original size:21 final size:22
Alignment explanation
Indices: 1617815--1617857 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
1617805 AAATTATAAT
1617815 ATTACAATATTCATAC-AAAAA
1 ATTACAATATTCATACAAAAAA
1617836 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
1617858 CTAATCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:1617921 original size:19 final size:19
Alignment explanation
Indices: 1617896--1617978 Score: 112
Period size: 19 Copynumber: 4.2 Consensus size: 19
1617886 ATTATAAAAT
1617896 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* *
1617915 CATTACAATATTCATAAAA
1 AATTACAATATTCATACAA
1617934 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
*
1617955 AAGTTAGAATATTCATACAA
1 AA-TTACAATATTCATACAA
1617975 AATT
1 AATT
1617979 CTAATCTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
19 34 0.61
20 4 0.07
21 4 0.07
22 14 0.25
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:1617965 original size:22 final size:21
Alignment explanation
Indices: 1617930--1617976 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
1617920 CAATATTCAT
1617930 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
1617951 AAAAAAGTTAGAATATTCATAC
1 AAAAAA-TTACAATATTCATAC
1617973 AAAA
1 AAAA
1617977 TTCTAATCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.60, C:0.11, G:0.04, T:0.26
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:1617966 original size:41 final size:38
Alignment explanation
Indices: 1617889--1617978 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 38
1617879 AAATTTAATT
*
1617889 ATAAAATAATTACAATATTCATACAACATTACAATATTC
1 ATAAAA-AATTACAATATTCATACAAAATTACAATATTC
*
1617928 ATAAAAAATTACAATATTCATACAAAAAAGTTAGAATATTC
1 ATAAAAAATTACAATATTCATAC--AAAA-TTACAATATTC
*
1617969 ATACAAAATT
1 ATAAAAAATT
1617979 CTAATCTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 17 0.38
39 6 0.13
40 3 0.07
41 19 0.42
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.31
Consensus pattern (38 bp):
ATAAAAAATTACAATATTCATACAAAATTACAATATTC
Found at i:1618062 original size:12 final size:12
Alignment explanation
Indices: 1618045--1618070 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1618035 AAAAATTCAC
1618045 AATATCTTCTAA
1 AATATCTTCTAA
1618057 AATATCTTCTAA
1 AATATCTTCTAA
1618069 AA
1 AA
1618071 AATTCACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATCTTCTAA
Found at i:1620517 original size:60 final size:60
Alignment explanation
Indices: 1620390--1620518 Score: 147
Period size: 60 Copynumber: 2.1 Consensus size: 60
1620380 TTTTGGTGCA
* * *
1620390 TGAACTTAGCTTTAAGGTTCAAATTGGTATCTAATATTTTTTTTTGGTTCAATTAAGTACT
1 TGAACTT-GCTTTAAGGTTCAAATTGGTATCTAATAATTTATTTTGGTCCAATTAAGTACT
* * *
1620451 TAAACTTGCCTTTAGGGTTCAATTTGGTA-CTTAA-AATTTATTTTGGTCCAATT-AGATACT
1 TGAACTTG-CTTTAAGGTTCAAATTGGTATC-TAATAATTTATTTTGGTCCAATTAAG-TACT
1620511 TGAACTTG
1 TGAACTTG
1620519 GCTTCTTAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
59 2 0.03
60 29 0.50
61 27 0.47
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (60 bp):
TGAACTTGCTTTAAGGTTCAAATTGGTATCTAATAATTTATTTTGGTCCAATTAAGTACT
Found at i:1628111 original size:22 final size:22
Alignment explanation
Indices: 1628085--1628137 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1628075 TAACATGACT
1628085 TTAAATAAAATATTAAATTCAA
1 TTAAATAAAATATTAAATTCAA
* * * *
1628107 TTAAACAGATTATTAAATTTAA
1 TTAAATAAAATATTAAATTCAA
1628129 --AAATAAAAT
1 TTAAATAAAAT
1628138 GAAATAGTGT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 6 0.25
22 18 0.75
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAAATAAAATATTAAATTCAA
Found at i:1628227 original size:15 final size:15
Alignment explanation
Indices: 1628180--1628228 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1628170 ACCAAATTAC
*
1628180 AAAAAATTTAAATATA
1 AAAAAATTGAAA-ATA
* **
1628196 AAAAAATAGAATCTA
1 AAAAAATTGAAAATA
1628211 AAAAAATTGAAAATA
1 AAAAAATTGAAAATA
1628226 AAA
1 AAA
1628229 GCAAAATCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (15 bp):
AAAAAATTGAAAATA
Found at i:1629372 original size:16 final size:15
Alignment explanation
Indices: 1629333--1629375 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1629323 AAAGTGCAGG
1629333 GATTAAAATATTAAC
1 GATTAAAATATTAAC
** *
1629348 TTTTCAAATATATAAC
1 GATTAAAATAT-TAAC
1629364 GATTAAAATATT
1 GATTAAAATATT
1629376 CCTTTTAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (15 bp):
GATTAAAATATTAAC
Found at i:1630260 original size:16 final size:16
Alignment explanation
Indices: 1630239--1630272 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1630229 TGCAAACCGT
* *
1630239 TTATTTTTATTTTTTA
1 TTATTTTCATTTTCTA
1630255 TTATTTTCATTTTCTA
1 TTATTTTCATTTTCTA
1630271 TT
1 TT
1630273 CTTTCCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCATTTTCTA
Found at i:1631400 original size:27 final size:27
Alignment explanation
Indices: 1631108--1631423 Score: 388
Period size: 27 Copynumber: 11.7 Consensus size: 27
1631098 CCCCAAACTA
*
1631108 TTATAAAATAACTGTTATG-CCCTCATG
1 TTATAAAATGACTGTTATGCCCCT-ATG
** * *
1631135 TGGTAAAATAACTATTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
* *
1631162 TTATAAAATAACGGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
* *
1631189 TTATAAAATTACAGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
* * *
1631216 TTATAAAATAACTATTATGCCCTTATG
1 TTATAAAATGACTGTTATGCCCCTATG
*
1631243 TTATAAAATGACTGTTATG-CCCTCACG
1 TTATAAAATGACTGTTATGCCCCT-ATG
** *
1631270 TGGTAAAATGACTATTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
*
1631297 TTATAAAATGACGGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
1631324 TTATAAAATGACTGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
*
1631351 TTATAAAATGACTGTTATGCCCTTATG
1 TTATAAAATGACTGTTATGCCCCTATG
*
1631378 TTATAAAATAACTGTTATG-CCCTCATG
1 TTATAAAATGACTGTTATGCCCCT-ATG
**
1631405 TGGTAAAATGACTG-TATGC
1 TTATAAAATGACTGTTATGC
1631424 TTAATGCTAT
Statistics
Matches: 252, Mismatches: 32, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
26 10 0.04
27 234 0.93
28 8 0.03
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (27 bp):
TTATAAAATGACTGTTATGCCCCTATG
Found at i:1631751 original size:34 final size:32
Alignment explanation
Indices: 1631703--1631765 Score: 99
Period size: 34 Copynumber: 1.9 Consensus size: 32
1631693 TTATTGTCAC
1631703 TGTAATGGGATAAGGCCCACACTGATACTGATAT
1 TGTAATGGGATAAGGCCCA-ACTGA-ACTGATAT
*
1631737 TGTAATGGGCTAAGGCCCAACTGAACTGA
1 TGTAATGGGATAAGGCCCAACTGAACTGA
1631766 ACTGTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 5 0.18
33 5 0.18
34 18 0.64
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (32 bp):
TGTAATGGGATAAGGCCCAACTGAACTGATAT
Found at i:1635508 original size:17 final size:17
Alignment explanation
Indices: 1635465--1635557 Score: 86
Period size: 17 Copynumber: 5.7 Consensus size: 17
1635455 CCGATATAAT
* * *
1635465 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
1635482 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
*
1635499 AAATA-CTTT--TTTTA
1 AAATATTTTTAATTTTA
**
1635513 TTAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
1635529 AAATATTTTTAATTTTA
1 AAATATTTTTAATTTTA
*
1635546 AAACATTTTTAA
1 AAATATTTTTAA
1635558 AATACTTTGT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
14 10 0.17
16 10 0.17
17 40 0.67
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:1635511 original size:30 final size:29
Alignment explanation
Indices: 1635474--1635538 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
1635464 TAAATATATT
*
1635474 TATTTTTTAAAT-TTTTTTAATTTTAAAA
1 TATTTTTTTAATATTTTTTAATTTTAAAA
*
1635502 TACTTTTTTTATTATTTTTTAATTTTAAAA
1 TA-TTTTTTTAATATTTTTTAATTTTAAAA
1635532 TATTTTT
1 TATTTTT
1635539 AATTTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 2 0.06
29 13 0.39
30 18 0.55
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
TATTTTTTTAATATTTTTTAATTTTAAAA
Found at i:1640298 original size:3 final size:3
Alignment explanation
Indices: 1640290--1640381 Score: 80
Period size: 3 Copynumber: 30.3 Consensus size: 3
1640280 CAATAACATA
** *
1640290 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TGT ACT ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * *
1640339 GCCAT CAT AAT ATT AA- CAT AA- AAT AAT AAT AAT AAT AAT AAT A
1 --AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1640382 TGTGTGATAC
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
2 3 0.04
3 67 0.92
4 1 0.01
5 2 0.03
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1641435 original size:9 final size:10
Alignment explanation
Indices: 1641386--1641443 Score: 53
Period size: 10 Copynumber: 5.3 Consensus size: 10
1641376 TTTATTCTCT
1641386 AAAAAAATAGA
1 AAAAAAATA-A
1641397 TAAAAGAAATAA
1 -AAAA-AAATAA
* *
1641409 ATAAAACTAA
1 AAAAAAATAA
1641419 GTAAAAAAATAA
1 --AAAAAAATAA
1641431 AAAAAAATAA
1 AAAAAAATAA
1641441 AAA
1 AAA
1641444 GACCACCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 18 0.46
11 3 0.08
12 13 0.33
13 5 0.13
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:1641676 original size:16 final size:15
Alignment explanation
Indices: 1641645--1641685 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
1641635 GGTACTAGGC
*
1641645 GCGTGGAGGATGGCGT
1 GCGTGGTGG-TGGCGT
1641661 GCGGTGGTGGTGGCGT
1 GC-GTGGTGGTGGCGT
1641677 GCGTGGTGG
1 GCGTGGTGG
1641686 CAGCTAGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.05, C:0.12, G:0.61, T:0.22
Consensus pattern (15 bp):
GCGTGGTGGTGGCGT
Found at i:1652837 original size:77 final size:77
Alignment explanation
Indices: 1652710--1652940 Score: 444
Period size: 77 Copynumber: 3.0 Consensus size: 77
1652700 ATAAAAGCAG
*
1652710 ATCACTATCGTATACACATTTCAATCACATCATCTTTACGATTTATCATAATTAATAGATTAAAC
1 ATCACTATCGTATACACATTTCAATCACATCATCTTTACGACTTATCATAATTAATAGATTAAAC
1652775 ATTGAAATTCAA
66 ATTGAAATTCAA
1652787 ATCACTATCGTATACACATTTCAATCACATCATCTTTACGACTTATCATAATTAATAGATTAAAC
1 ATCACTATCGTATACACATTTCAATCACATCATCTTTACGACTTATCATAATTAATAGATTAAAC
1652852 ATTGAAATTCAA
66 ATTGAAATTCAA
*
1652864 ATCACTATCGTATACACATTTCAATCACATCATCTTTACTACTTATCATAATTAATAGATTAAAC
1 ATCACTATCGTATACACATTTCAATCACATCATCTTTACGACTTATCATAATTAATAGATTAAAC
1652929 ATTGAAATTCAA
66 ATTGAAATTCAA
1652941 CTGTGAATGA
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 152 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (77 bp):
ATCACTATCGTATACACATTTCAATCACATCATCTTTACGACTTATCATAATTAATAGATTAAAC
ATTGAAATTCAA
Found at i:1653421 original size:16 final size:17
Alignment explanation
Indices: 1653384--1653422 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1653374 GATAAAAATT
1653384 TAATTTTATTATTTTAA
1 TAATTTTATTATTTTAA
*
1653401 T-ATTTTA-TATTTTTA
1 TAATTTTATTATTTTAA
1653416 TAATTTT
1 TAATTTT
1653423 TACTTATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 11 0.55
17 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TAATTTTATTATTTTAA
Found at i:1660352 original size:11 final size:11
Alignment explanation
Indices: 1660332--1660450 Score: 78
Period size: 11 Copynumber: 11.4 Consensus size: 11
1660322 TTATAATTAA
1660332 AAAAAGTATTTT
1 AAAAA-TATTTT
1660344 AAAAATATTTT
1 AAAAATATTTT
*
1660355 TAAAATATTTT
1 AAAAATATTTT
1660366 --AAA-A--TT
1 AAAAATATTTT
* **
1660372 AAAAAAATTAA
1 AAAAATATTTT
1660383 AAAAAGTATTTT
1 AAAAA-TATTTT
1660395 AAAAATATTTT
1 AAAAATATTTT
1660406 --AAA-A--TT
1 AAAAATATTTT
* *
1660412 AAAAAAATTTAA
1 AAAAATATTT-T
1660424 AAAAAGTATTTT
1 AAAAA-TATTTT
1660436 AAAAATATTTT
1 AAAAATATTTT
1660447 AAAA
1 AAAA
1660451 TTTAAAAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 27
0.70 0.07 0.22
Matches are distributed among these distances:
6 4 0.05
8 8 0.09
9 8 0.09
11 38 0.45
12 23 0.27
13 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1660393 original size:40 final size:40
Alignment explanation
Indices: 1660344--1660499 Score: 246
Period size: 40 Copynumber: 3.9 Consensus size: 40
1660334 AAAGTATTTT
*
1660344 AAAAA-TATTTTTAAAATATTTTAAAATTAAAAAAATTAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
1660383 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA-TTAA
1660424 AAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATT-A
1 AAAAAGTATTTTAAAAATATTTTAAAA-TTAAAAAAATTAA
* *
1660464 AAAAAGTA-TGTAAAAATATTTTTAAATTAAAAAAAT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAT
1660500 AAATATATTT
Statistics
Matches: 111, Mismatches: 3, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
38 10 0.09
39 21 0.19
40 38 0.34
41 33 0.30
42 9 0.08
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (40 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
Found at i:1660417 original size:41 final size:41
Alignment explanation
Indices: 1660320--1660498 Score: 240
Period size: 41 Copynumber: 4.4 Consensus size: 41
1660310 CCCGGCCTAT
* ** *
1660320 TTTTATAATTAAAAAAAGTATTTTAAAAA-TATTTTTAAAATA
1 TTTTAAAATTAAAAAAA--ATTAAAAAAAGTATTTTAAAAATA
1660362 TTTTAAAATT-AAAAAAATTAAAAAAAGTATTTTAAAAATA
1 TTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATA
*
1660402 TTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATA
1 TTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATA
* *
1660443 TTTTAAAATTTAAAAAAATT-AAAAAAGTA-TGTAAAAATA
1 TTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATA
*
1660482 TTTTTAAATTAAAAAAA
1 TTTTAAAATTAAAAAAA
1660499 TAAATATATT
Statistics
Matches: 125, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
39 32 0.26
40 31 0.25
41 53 0.42
42 9 0.07
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (41 bp):
TTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATA
Found at i:1660426 original size:17 final size:17
Alignment explanation
Indices: 1660393--1660426 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1660383 AAAAAGTATT
* *
1660393 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAA
1660410 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
1660427 AAGTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:1662891 original size:76 final size:76
Alignment explanation
Indices: 1662810--1663233 Score: 356
Period size: 76 Copynumber: 5.6 Consensus size: 76
1662800 TACGGTCCAC
* * * * * * * *
1662810 TGATTTAATATCGTGACTTTCAATTTTTTAACAATTCGCTTGATTTAATCTCGTGACTGTCATTT
1 TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
*
1662875 TTATAATCTGT
66 TTATGATCTGT
* * * * * *
1662886 TGATTTAAGATCGAGACCATCCGTTTTCTAACAGTTTGC-TGATTTAATATCGTAACTGTCATTT
1 TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
* *
1662950 TTACGATCCGCT
66 TTATGATCTG-T
* * * *
1662962 T-ATCTAAGATCGCAACCTTCAGTTTTTCTAACAGTTTGCTTGATTTAATCTTGTGACTAACATT
1 TGATTTAAGATCGCGACCTTCAG-TTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATT
* *
1663026 TTTATGGT-TCGC
65 TTTATGATCT-GT
* * * * *
1663038 TGATTTAAGATCGTGACCTTCGGTTTTCTAACAATTTGCTTGATTTAATCTTGCGACTATCATTT
1 TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
* * *
1663103 TTACGATCCGC
66 TTATGATCTGT
* * * * * * **
1663114 TAATTTAATATCGCAACCTTCAATTTTCTAATAGTTCGCTTGATTTAATCTCGCAACTATCATTT
1 TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
*
1663179 TTATG-GCTTGT
66 TTATGATC-TGT
* * * * *
1663190 TGATTTAATAGCACAACCTT-TGATTTTCTAACAGTTTGC-TGATT
1 TGATTTAAGATCGCGACCTTCAG-TTTTCTAACAGTTTGCTTGATT
1663234 CACGATCACG
Statistics
Matches: 280, Mismatches: 60, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
75 52 0.19
76 185 0.66
77 43 0.15
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (76 bp):
TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
TTATGATCTGT
Found at i:1663209 original size:152 final size:149
Alignment explanation
Indices: 1662762--1663256 Score: 513
Period size: 152 Copynumber: 3.3 Consensus size: 149
1662752 TCATTTAAGA
* * * * * * * **
1662762 TAACAGTTTACTTGATTTAATATCGCGATTATCCTCTTTACGGTCCACTGATTTAATATCGTGAC
1 TAACAGTTTGC-TGATTTAATATCGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAAC
* * * * **
1662827 TTTCAATTTTTTAACAATTCGCTTGATTTAATCTCGTGACTGTCATTTTTATAATCTGTTGATTT
65 CTTCAATTTTCTAACAGTTCGCTTGATTTAATCTCGTGACTATCATTTTTATGGT-TGTTGATTT
* *
1662892 AAGATCGAGACCATCCGTTTTC
129 AAGATC-AGACCTTCGGTTTTC
** * * * *
1662914 TAACAGTTTGCTGATTTAATATCGTAACTGTCATTTTTACGATCCGCTTATCTAAGATCGCAACC
1 TAACAGTTTGCTGATTTAATATCGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAACC
* * * * *
1662979 TTCAGTTTTTCTAACAGTTTGCTTGATTTAATCTTGTGACTAACATTTTTATGGTTCGCTGATTT
66 TTCA-ATTTTCTAACAGTTCGCTTGATTTAATCTCGTGACTATCATTTTTATGGTT-GTTGATTT
*
1663044 AAGATCGTGACCTTCGGTTTTC
129 AAGATC-AGACCTTCGGTTTTC
* * *
1663066 TAACAATTTGCTTGATTTAATCTTGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAAC
1 TAACAGTTTGC-TGATTTAATATCGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAAC
* **
1663131 CTTCAATTTTCTAATAGTTCGCTTGATTTAATCTCGCAACTATCATTTTTATGGCTTGTTGATTT
65 CTTCAATTTTCTAACAGTTCGCTTGATTTAATCTCGTGACTATCATTTTTATGG-TTGTTGATTT
* * * * *
1663196 AATAGCACAACCTTTGATTTTC
129 AAGATCA-GACCTTCGGTTTTC
* ** *
1663218 TAACAGTTTGCTGATTCACGATCACGACTATCATTTTTA
1 TAACAGTTTGCTGATTTAATATCGCGACTATCATTTTTA
1663257 AAGCTCGCTA
Statistics
Matches: 280, Mismatches: 58, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
151 67 0.24
152 161 0.57
153 52 0.19
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (149 bp):
TAACAGTTTGCTGATTTAATATCGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAACC
TTCAATTTTCTAACAGTTCGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTGTTGATTTAA
GATCAGACCTTCGGTTTTC
Found at i:1663219 original size:228 final size:227
Alignment explanation
Indices: 1662809--1663233 Score: 489
Period size: 228 Copynumber: 1.9 Consensus size: 227
1662799 TTACGGTCCA
* * * * *
1662809 CTGATTTAATATCGTGACTTTCAATTTTTTAACAATTCGCTTGATTTAATCTCGTGACTGTCATT
1 CTGATTTAAGATCGTGACCTTCAATTTTCTAACAATTCGCTTGATTTAATCTCGCGACTATCATT
* * * * ** * *
1662874 TTTATAATCTGTTGATTTAAGATCGAGACCATCCGTTTTCTAACAGTTTGCTGATTTAATATCGT
66 TTTACAATCCGCTAATTTAAGATCGAGACCATCAATTTTCTAACAGTTCGCTGATTTAATATCGC
* * * *
1662939 AACTGTCATTTTTACGATCCGCTTATCTAAGATCGCAACCTTCAGTTTTTCTAACAGTTTGCTTG
131 AACTATCATTTTTACGATCCGCTTATCTAAGAGCACAACCTTCAGATTTTCTAACAGTTTGC-TG
1663004 ATTTAATCTTGTGACTAACATTTTTATGGTTCG
195 ATTTAATCTTGTGACTAACATTTTTATGGTTCG
** * *
1663037 CTGATTTAAGATCGTGACCTTCGGTTTTCTAACAATTTGCTTGATTTAATCTTGCGACTATCATT
1 CTGATTTAAGATCGTGACCTTCAATTTTCTAACAATTCGCTTGATTTAATCTCGCGACTATCATT
* * * * *
1663102 TTTACGATCCGCTAATTTAATATCGCA-ACCTTCAATTTTCTAATAGTTCGCTTGATTTAATCTC
66 TTTACAATCCGCTAATTTAAGATCG-AGACCATCAATTTTCTAACAGTTCGC-TGATTTAATATC
* * * * * *
1663166 GCAACTATCATTTTTATG-GCTTG-TTGATTTAATAGCACAACCTT-TGATTTTCTAACAGTTTG
129 GCAACTATCATTTTTACGATC-CGCTT-ATCTAAGAGCACAACCTTCAGATTTTCTAACAGTTTG
1663228 CTGATT
192 CTGATT
1663234 CACGATCACG
Statistics
Matches: 161, Mismatches: 32, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
227 5 0.03
228 114 0.71
229 42 0.26
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (227 bp):
CTGATTTAAGATCGTGACCTTCAATTTTCTAACAATTCGCTTGATTTAATCTCGCGACTATCATT
TTTACAATCCGCTAATTTAAGATCGAGACCATCAATTTTCTAACAGTTCGCTGATTTAATATCGC
AACTATCATTTTTACGATCCGCTTATCTAAGAGCACAACCTTCAGATTTTCTAACAGTTTGCTGA
TTTAATCTTGTGACTAACATTTTTATGGTTCG
Found at i:1663642 original size:18 final size:19
Alignment explanation
Indices: 1663616--1663653 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1663606 CTCTCTTTGT
*
1663616 TTTTGAAATTTTAAA-ATA
1 TTTTAAAATTTTAAATATA
1663634 TTTTAAAATTTTAAATATA
1 TTTTAAAATTTTAAATATA
1663653 T
1 T
1663654 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTAAAATTTTAAATATA
Found at i:1666095 original size:13 final size:13
Alignment explanation
Indices: 1666061--1666102 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1666051 AAAGTCAAAT
*
1666061 TAAATAA-AAAAT
1 TAAATAATAAAAA
1666073 TAAAATTAATAAAAA
1 T-AAA-TAATAAAAA
1666088 TAAATAATAAAAA
1 TAAATAATAAAAA
1666101 TA
1 TA
1666103 TATTGATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 14 0.54
14 6 0.23
15 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:1669982 original size:19 final size:20
Alignment explanation
Indices: 1669958--1669996 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
1669948 AAATTGGTTA
1669958 GTGTAATTTA-ATTTTTTTC
1 GTGTAATTTAGATTTTTTTC
1669977 GTGTAATTTAGTATTTTTTT
1 GTGTAATTTAG-ATTTTTTT
1669997 TTATAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.13, T:0.64
Consensus pattern (20 bp):
GTGTAATTTAGATTTTTTTC
Found at i:1671807 original size:15 final size:15
Alignment explanation
Indices: 1671751--1671808 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1671741 CTTTATACTA
*
1671751 TAAAATATTTAGTAT
1 TAAAATATTTATTAT
* *
1671766 TAATATATTTATAATT
1 TAAAATATTTATTA-T
1671782 GTAATAAATATTTATTAT
1 -T-A-AAATATTTATTAT
1671800 TAAAATATT
1 TAAAATATT
1671809 AATATTGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 18 0.53
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAAATATTTATTAT
Found at i:1673073 original size:54 final size:54
Alignment explanation
Indices: 1673009--1673114 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
1672999 CCGTGTGACC
*
1673009 CAAGTCAGTGAGTTACACGGGCAGGGACACGAGCTGGGACACAATCATGTGTTT
1 CAAGTCAGTGAGTTACACGGGCAGAGACACGAGCTGGGACACAATCATGTGTTT
* * * * *
1673063 CAAGTCAGTGAGTTACACGGGCAGAGACATGGGTTGGGACACGATCGTGTGT
1 CAAGTCAGTGAGTTACACGGGCAGAGACACGAGCTGGGACACAATCATGTGT
1673115 CCCAACTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (54 bp):
CAAGTCAGTGAGTTACACGGGCAGAGACACGAGCTGGGACACAATCATGTGTTT
Found at i:1673448 original size:48 final size:48
Alignment explanation
Indices: 1673389--1673481 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
1673379 TCAAGAGGGA
*
1673389 ATAAATAGTGATAAGACTGTAGACAGTGGAAGACCAAGCTTAGCAATG
1 ATAAATAGTGATAAGACTGTAGACACTGGAAGACCAAGCTTAGCAATG
* * * *
1673437 ATAAATAGTGATAAGAGTGTAGGCACTGGAAGATCAAGTTTAGCA
1 ATAAATAGTGATAAGACTGTAGACACTGGAAGACCAAGCTTAGCA
1673482 TTGCATAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.23
Consensus pattern (48 bp):
ATAAATAGTGATAAGACTGTAGACACTGGAAGACCAAGCTTAGCAATG
Found at i:1674461 original size:19 final size:21
Alignment explanation
Indices: 1674420--1674463 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
1674410 AAGGTTCAAA
1674420 AATGATGTTAATTGCATTAATT
1 AATGATGTTAATTGCA-TAATT
1674442 AATGATGTTAA-TGC-TAATT
1 AATGATGTTAATTGCATAATT
1674461 AAT
1 AAT
1674464 CCAATTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
21 3 0.14
22 11 0.50
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (21 bp):
AATGATGTTAATTGCATAATT
Found at i:1676656 original size:26 final size:28
Alignment explanation
Indices: 1676590--1676664 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 28
1676580 TATAGATACG
*
1676590 TACATATATGTATGAATAAATTATAAAAAA
1 TACATATATGTAT--ATATATTATAAAAAA
* * *
1676620 TATACACATGTATATATATTA-AAAAAA
1 TACATATATGTATATATATTATAAAAAA
*
1676647 -ACATATATGTGTATATAT
1 TACATATATGTATATATAT
1676665 ATGACTACGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 14 0.38
27 6 0.16
28 7 0.19
30 10 0.27
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (28 bp):
TACATATATGTATATATATTATAAAAAA
Found at i:1677655 original size:3 final size:3
Alignment explanation
Indices: 1677647--1677676 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1677637 TAATGGTAAT
1677647 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1677677 ATAACATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1681896 original size:17 final size:18
Alignment explanation
Indices: 1681876--1681913 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1681866 TTTTTTATAA
1681876 TTATTAAGTA-TTTTAAG
1 TTATTAAGTAGTTTTAAG
* *
1681893 TTATTTAGTAGTTTTATG
1 TTATTAAGTAGTTTTAAG
1681911 TTA
1 TTA
1681914 ACAAGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
TTATTAAGTAGTTTTAAG
Found at i:1695411 original size:16 final size:16
Alignment explanation
Indices: 1695329--1695411 Score: 62
Period size: 16 Copynumber: 5.2 Consensus size: 16
1695319 CTTAAACACT
1695329 AATGACCTAAACTCAA
1 AATGACCTAAACTCAA
* * *
1695345 AAT-AACTCAACCTTAA
1 AATGACCT-AAACTCAA
* *
1695361 AATGACATGAACTCAA
1 AATGACCTAAACTCAA
* *
1695377 ACTAACCTAAACT-AGA
1 AATGACCTAAACTCA-A
*
1695393 AATGATCTAAACTCAA
1 AATGACCTAAACTCAA
1695409 AAT
1 AAT
1695412 TCATATAAAT
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
15 4 0.08
16 41 0.85
17 3 0.06
ACGTcount: A:0.51, C:0.22, G:0.06, T:0.22
Consensus pattern (16 bp):
AATGACCTAAACTCAA
Found at i:1704468 original size:23 final size:25
Alignment explanation
Indices: 1704413--1704495 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
1704403 ACCTAATATT
* * *
1704413 TATAAAATATCATATTTTATAAAAAAA
1 TATAAAATATGAT-TTATAT-AAAATA
* *
1704440 TATAAAATAT-ATTTGTCT-AAATA
1 TATAAAATATGATTTATATAAAATA
*
1704463 TATAAAATATGTTTTATATAAAATA
1 TATAAAATATGATTTATATAAAATA
1704488 TATAAAAT
1 TATAAAAT
1704496 CTAAAAACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
23 14 0.29
24 5 0.10
25 17 0.35
26 2 0.04
27 10 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
TATAAAATATGATTTATATAAAATA
Found at i:1704492 original size:25 final size:24
Alignment explanation
Indices: 1704427--1704495 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
1704417 AAATATCATA
*
1704427 TTTTATA-AAAAAATATAAAATAT
1 TTTTATATAAAATATATAAAATAT
* * *
1704450 ATTTGTCT-AAATATATAAAATAT
1 TTTTATATAAAATATATAAAATAT
1704473 GTTTTATATAAAATATATAAAAT
1 -TTTTATATAAAATATATAAAAT
1704496 CTAAAAACAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 18 0.50
24 5 0.14
25 13 0.36
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (24 bp):
TTTTATATAAAATATATAAAATAT
Found at i:1707605 original size:24 final size:25
Alignment explanation
Indices: 1707572--1707625 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
1707562 CCTTAGCGCT
* *
1707572 CTCTCTGATTATTAGCACGTTA-TG
1 CTCTCCGATTATTAGCACATTAGTG
1707596 CTCTCCGATTATTAGCACATTAGTG
1 CTCTCCGATTATTAGCACATTAGTG
1707621 CTCTC
1 CTCTC
1707626 TGTTTAGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (25 bp):
CTCTCCGATTATTAGCACATTAGTG
Found at i:1707638 original size:22 final size:22
Alignment explanation
Indices: 1707607--1707671 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
1707597 TCTCCGATTA
1707607 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
1707629 TTAGCTCATTTGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* * * *
1707651 ATAACACTTTAGTGTTCTCTG
1 TTAGCACATTAGTGCTCTCTG
1707672 CTTAATAGTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.45
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:1710296 original size:23 final size:23
Alignment explanation
Indices: 1710253--1710311 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1710243 AAAAATAGTG
*
1710253 AAATTATATATTAATACATAATA
1 AAATTATATATTAATACATAAAA
* * **
1710276 AATTTATATTTTAATTTATAAAA
1 AAATTATATATTAATACATAAAA
1710299 AAATTATA-ATTAA
1 AAATTATATATTAA
1710312 ATACTGACCC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTATATATTAATACATAAAA
Found at i:1712656 original size:11 final size:11
Alignment explanation
Indices: 1712640--1712664 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1712630 TGTTCCGTTG
1712640 GTTGTTCAATC
1 GTTGTTCAATC
1712651 GTTGTTCAATC
1 GTTGTTCAATC
1712662 GTT
1 GTT
1712665 CTTCGACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (11 bp):
GTTGTTCAATC
Found at i:1713035 original size:20 final size:20
Alignment explanation
Indices: 1713023--1713062 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1713013 CTGACTGCAC
1713023 TTACTGCTAACTGCTAAACT
1 TTACTGCTAACTGCTAAACT
1713043 TTACTGCTAACTGCTAAACT
1 TTACTGCTAACTGCTAAACT
1713063 AACCATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (20 bp):
TTACTGCTAACTGCTAAACT
Found at i:1734390 original size:46 final size:46
Alignment explanation
Indices: 1734323--1734731 Score: 432
Period size: 46 Copynumber: 9.6 Consensus size: 46
1734313 TTTGAGTACT
* * *
1734323 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
1734369 TCTGATCAAGTGAAAAAGTGATAA---GT-G-C-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
1734405 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTATCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
1734451 TCTGATCAAGTGAAAAAGTGATAA---GT-G-C-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
1734487 TCTGATCAAGTGAAAAAGTGATAA---GT-G-C-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
1734523 TCTGATCAAGTGACACAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* * *
1734569 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTTAGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
1734615 ACTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
1734661 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
1734707 TCTGATC-AGGGAC-AAGTAATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
1734732 ATCATACGTA
Statistics
Matches: 319, Mismatches: 24, Indels: 42
0.83 0.06 0.11
Matches are distributed among these distances:
36 91 0.29
38 2 0.01
39 2 0.01
40 6 0.02
41 3 0.01
42 6 0.02
43 3 0.01
44 13 0.04
45 5 0.02
46 188 0.59
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:1734405 original size:36 final size:36
Alignment explanation
Indices: 1734359--1734549 Score: 256
Period size: 36 Copynumber: 5.0 Consensus size: 36
1734349 GGTAGCTTTA
*
1734359 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
1734395 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGTT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAA--G-T
1734434 AGCCTTATCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -G-C-TA--T--ACTTATCTGATCAAGTGAAAAAGTGATAAGT
1734477 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
1734513 GCTATACTTATCTGATCAAGTGACACAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1734549 G
1 G
1734550 TTAGCCTTAG
Statistics
Matches: 140, Mismatches: 5, Indels: 20
0.85 0.03 0.12
Matches are distributed among these distances:
36 98 0.70
38 2 0.01
39 1 0.01
40 3 0.02
41 2 0.01
42 3 0.02
43 1 0.01
44 2 0.01
46 28 0.20
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:1734426 original size:82 final size:88
Alignment explanation
Indices: 1734323--1734714 Score: 423
Period size: 82 Copynumber: 4.6 Consensus size: 88
1734313 TTTGAGTACT
* * *
1734323 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1734388 GATAA-GT-G-C-TA-T-ACTTA
66 GATAAGGTAGCCTTACTAACTTA
* *
1734405 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTATCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1734470 GATAA-GT-G-C-TA-T-ACTTA
66 GATAAGGTAGCCTTACTAACTTA
* * *
1734487 TCTGATCAAGTGAAAAAGTGATAA---GT-G-C-TA--T--ACTTATCTGATCAAGTGACACAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1734542 GATAAGTGTTAGCCTTAGCTACACTTA
66 GATAAG-G-TAGCCTTA-CTA-ACTTA
* * * * *
1734569 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTTAGCTATACTTAACTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1734634 GATAAGTGGTAGCCTTAGCTACACTTA
66 GATAA--GGTAGCCTTA-CTA-ACTTA
* *
1734661 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTATACTTATCTGATCA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCA
1734715 GGGACAAGTA
Statistics
Matches: 271, Mismatches: 17, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
72 27 0.10
74 2 0.01
75 1 0.00
76 3 0.01
77 2 0.01
78 3 0.01
79 1 0.00
80 1 0.00
82 128 0.47
85 2 0.01
86 1 0.00
88 2 0.01
90 1 0.00
92 95 0.35
93 1 0.00
94 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (88 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGGTAGCCTTACTAACTTA
Found at i:1734497 original size:21 final size:20
Alignment explanation
Indices: 1734469--1734534 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
1734459 AGTGAAAAAG
1734469 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
1734489 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
1734505 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
1734525 TGATCAAGTG
1 TGAT-AAGTG
1734535 ACACAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:1743922 original size:18 final size:18
Alignment explanation
Indices: 1743901--1743937 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1743891 TAAACCCTTA
*
1743901 AAAAATCCTAACCCTAAC
1 AAAAATCCTAAACCTAAC
1743919 AAAAATCCTAAACCTAAC
1 AAAAATCCTAAACCTAAC
1743937 A
1 A
1743938 TAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAATCCTAAACCTAAC
Found at i:1744144 original size:35 final size:35
Alignment explanation
Indices: 1744105--1744176 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1744095 ATAAAAACAG
1744105 ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
1 ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
1744140 ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
1 ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
1744175 AT
1 AT
1744177 GATTTGCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.26
Consensus pattern (35 bp):
ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
Found at i:1745990 original size:18 final size:19
Alignment explanation
Indices: 1745953--1745990 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1745943 TTTAAAATAA
* *
1745953 TATAAATTATAAATTATTT
1 TATAAAATATAAAATATTT
1745972 TATAAAATA-AAAATATTT
1 TATAAAATATAAAATATTT
1745990 T
1 T
1745991 TATCATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAAAATATAAAATATTT
Found at i:1750597 original size:16 final size:16
Alignment explanation
Indices: 1750576--1750611 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1750566 TTTGGTTCGC
1750576 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAAG
*
1750592 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAAG
1750608 TGTA
1 TGTA
1750612 ATAGCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAAG
Found at i:1761305 original size:20 final size:21
Alignment explanation
Indices: 1761269--1761307 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1761259 TTTGTATTTT
1761269 TATTTATAATATAATTATTAA
1 TATTTATAATATAATTATTAA
*
1761290 TATTTAT-ATTTAATTATT
1 TATTTATAATATAATTATT
1761308 TTATATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTATAATATAATTATTAA
Found at i:1761313 original size:21 final size:22
Alignment explanation
Indices: 1761263--1761313 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
1761253 TTTTGATTTG
1761263 TATTTT-TATTTATAATATAAT
1 TATTTTATATTTATAATATAAT
* *
1761284 TA-TTAATATTTAT-ATTTAAT
1 TATTTTATATTTATAATATAAT
1761304 TATTTTATAT
1 TATTTTATAT
1761314 CTAAAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTATATTTATAATATAAT
Found at i:1762818 original size:10 final size:10
Alignment explanation
Indices: 1762780--1762826 Score: 62
Period size: 9 Copynumber: 4.9 Consensus size: 10
1762770 AAATTAATAA
1762780 ATAAAAAATT
1 ATAAAAAATT
1762790 -TAAAAAATT
1 ATAAAAAATT
* *
1762799 ATTAATAATT
1 ATAAAAAATT
1762809 ATAAAAAATT
1 ATAAAAAATT
1762819 -TAAAAAAT
1 ATAAAAAAT
1762827 ATTACGAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 17 0.53
10 15 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:1762823 original size:28 final size:29
Alignment explanation
Indices: 1762772--1762840 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 29
1762762 GGCTAAACAA
*
1762772 ATTAATAA--ATAAAAAATTTAAAAAATT
1 ATTAATAATTATAAAAAATTTAAAAAAAT
1762799 ATTAATAATTATAAAAAATTT-AAAAAAT
1 ATTAATAATTATAAAAAATTTAAAAAAAT
**
1762827 ATTACGAATTATAA
1 ATTAATAATTATAA
1762841 GAAAGGTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.22
28 18 0.49
29 11 0.30
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (29 bp):
ATTAATAATTATAAAAAATTTAAAAAAAT
Found at i:1763154 original size:2 final size:2
Alignment explanation
Indices: 1763147--1763171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1763137 ACTTCTAAAA
1763147 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1763172 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1772834 original size:184 final size:183
Alignment explanation
Indices: 1772522--1772889 Score: 413
Period size: 184 Copynumber: 2.0 Consensus size: 183
1772512 TAATTGTAAC
* * * ***
1772522 AATTATTATTTATTATATTTTATTTCGGGACACTTAGACTTGAGTGTGGTGGTTCAAAAATATTT
1 AATTATTATTTATTATATTTCATTTCGGGACACTTAGACTTGAGTATAGTGCCCCAAAAATATTT
* * *
1772587 TTAAGATTTTCTGTGATACTTATAAAAATTATCATTTATTATAATTCAATTTCAAGGCACTTGAG
66 TTAAGATTTTCTGAGATACTTATAAAAATTATCATTGATTATAATTCAATTTCAAGACACTTGAG
* * * * * *
1772652 TTTGAGTATGGTGGTGCAAAAGTATTTTTAAAAATTTTT-AGGATAGCTATAAA
131 CTTAAGTATGGTGATGAAAAAATATTTTTAAAAATTTTTGAGG-TAACTATAAA
* *
1772705 AATTATTGTTTATTATATTTCATTTTCGGTG-CACTTGAGA-TTGAGTATAGTGCCCCCAAAATA
1 AATTATTATTTATTATATTTCA-TTTCGG-GACACTT-AGACTTGAGTATAGTGCCCCAAAAATA
** * * * * * *
1772768 TTTTTAATTTTTTTTGAGATAAC-TGTAAAAATTATTATTGATTATATTTTATTTTCCAA-ACAC
63 TTTTTAAGATTTTCTGAGAT-ACTTATAAAAATTATCATTGATTATAATTCAATTT-CAAGACAC
*
1772831 TTGAGCTTAAGTATGGTGATGAAAAAATATTTTTAAAATTTTTTGAGGTAACTATAAA
126 TTGAGCTTAAGTATGGTGATGAAAAAATATTTTTAAAAATTTTTGAGGTAACTATAAA
1772889 A
1 A
1772890 GGGCCACAAT
Statistics
Matches: 153, Mismatches: 26, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
183 20 0.13
184 121 0.79
185 12 0.08
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (183 bp):
AATTATTATTTATTATATTTCATTTCGGGACACTTAGACTTGAGTATAGTGCCCCAAAAATATTT
TTAAGATTTTCTGAGATACTTATAAAAATTATCATTGATTATAATTCAATTTCAAGACACTTGAG
CTTAAGTATGGTGATGAAAAAATATTTTTAAAAATTTTTGAGGTAACTATAAA
Found at i:1772873 original size:92 final size:92
Alignment explanation
Indices: 1772522--1772889 Score: 332
Period size: 92 Copynumber: 4.0 Consensus size: 92
1772512 TAATTGTAAC
* *** * *
1772522 AATTATTATTTATTATATTTTA-TTTCGGGACACTT-AGACTTGAGTGTGGTGGTTCAAAAATAT
1 AATTATTATTTATTATATTTCATTTTCCAAACACTTGAG-CTTGAGTATGGTGGTGCAAAAATAT
* * *
1772585 TTTTAAGATTTTCTGTGAT-ACTTATAAA
65 TTTTAAAATTTTTTGAGATAAC-TATAAA
* * * * * *
1772613 AATTATCATTTATTATAATTCAATTT-CAAGGCACTTGAGTTTGAGTATGGTGGTGCAAAAGTAT
1 AATTATTATTTATTATATTTCATTTTCCAA-ACACTTGAGCTTGAGTATGGTGGTGCAAAAATAT
* *
1772677 TTTTAAAAATTTTT-AGGATAGCTATAAA
65 TTTTAAAATTTTTTGA-GATAACTATAAA
* **** * * *** *
1772705 AATTATTGTTTATTATATTTCATTTTCGGTGCACTTGAGATTGAGTATAGTGCCCCCAAAATATT
1 AATTATTATTTATTATATTTCATTTTCCAAACACTTGAGCTTGAGTATGGTGGTGCAAAAATATT
** *
1772770 TTTAATTTTTTTTGAGATAACTGTAAA
66 TTTAAAATTTTTTGAGATAACTATAAA
* * * * *
1772797 AATTATTATTGATTATATTTTATTTTCCAAACACTTGAGCTTAAGTATGGTGATGAAAAAATATT
1 AATTATTATTTATTATATTTCATTTTCCAAACACTTGAGCTTGAGTATGGTGGTGCAAAAATATT
*
1772862 TTTAAAATTTTTTGAGGTAACTATAAA
66 TTTAAAATTTTTTGAGATAACTATAAA
1772889 A
1 A
1772890 GGGCCACAAT
Statistics
Matches: 216, Mismatches: 54, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
91 19 0.09
92 193 0.89
93 4 0.02
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (92 bp):
AATTATTATTTATTATATTTCATTTTCCAAACACTTGAGCTTGAGTATGGTGGTGCAAAAATATT
TTTAAAATTTTTTGAGATAACTATAAA
Found at i:1773687 original size:20 final size:20
Alignment explanation
Indices: 1773657--1773699 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1773647 AACTGATGAA
1773657 TTTTATAATTTT-TAAATAT
1 TTTTATAATTTTGTAAATAT
*
1773676 TTTTATTAATTTTGTGAATAT
1 TTTTA-TAATTTTGTAAATAT
1773697 TTT
1 TTT
1773700 AAATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 7 0.33
21 9 0.43
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTATAATTTTGTAAATAT
Found at i:1773700 original size:20 final size:18
Alignment explanation
Indices: 1773656--1773700 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
1773646 GAACTGATGA
1773656 ATTTTATAATTTTTAAAT
1 ATTTTATAATTTTTAAAT
*
1773674 ATTTTTATTAATTTTGTGAAT
1 A-TTTTA-TAATTTT-TAAAT
1773695 ATTTTA
1 ATTTTA
1773701 AATATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 5 0.22
20 12 0.52
21 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
ATTTTATAATTTTTAAAT
Found at i:1774528 original size:18 final size:19
Alignment explanation
Indices: 1774494--1774531 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1774484 TTTCAATTTC
*
1774494 AATTAAATAAATTATTAAA
1 AATTAAATAAATAATTAAA
1774513 AATTAAA-AAATAATTAAA
1 AATTAAATAAATAATTAAA
1774531 A
1 A
1774532 TATCATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTAAATAAATAATTAAA
Found at i:1781254 original size:141 final size:141
Alignment explanation
Indices: 1781000--1781278 Score: 427
Period size: 141 Copynumber: 2.0 Consensus size: 141
1780990 TAAATAAGAA
** * * *
1781000 TAAGTTTGCATAGGTCCACGACCTCTATCAGTTTCGACTATTAGTAATGAAAGGGGCCTTTCGCC
1 TAAGTTTGCATAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGACCTGTCGCC
* * * *
1781065 AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTTTTTCTCTGGCAAGGGAGTAATATTTTGGGC
66 AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGGGC
1781130 TGAATCTATAC
131 TGAATCTATAC
1781141 TAAGTTTGTC-TAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGACCTAGT-G
1 TAAGTTTG-CATAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGACCT-GTCG
* *
1781204 CCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTGATCTTATGG
64 CCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGG
1781269 GCTGAATCTA
129 GCTGAATCTA
1781279 CGTTAGGAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
141 123 0.98
142 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (141 bp):
TAAGTTTGCATAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGACCTGTCGCC
AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGGGC
TGAATCTATAC
Found at i:1781730 original size:129 final size:133
Alignment explanation
Indices: 1781491--1781873 Score: 452
Period size: 129 Copynumber: 2.8 Consensus size: 133
1781481 CACGAACCCT
* ** *
1781491 ATCGGTTTTGACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATTGTAACTCTGAGCTTGAG
1 ATCGGTTTCGACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAG
* * *
1781556 GACAAGCTCTTTCTCTAGCAAGGGAGTAAAATTATGCGCCAAATCTATAATAAGTTTGT-T-T-A
66 GACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTATAATAAGTTTGTGTGTCA
1781618 -A-
131 GAC
* * * * *
1781619 GTCGGTTTCAACTATTAGTAATGGAAGGGACCTTTTGCCAAAGTTTATCCTAGCTCCGAGCTTGA
1 ATCGGTTTCGACTATTAGTAATGAAAGGGACCTTTCGCC-AAGTTTATCCTAACTCCGAGCTTGA
*
1781684 GGACAAGCTCTTTCTCTAGTAAGGGAGTAATATTATGAGCCGAATCTATAATAAGTTTGTGTAGG
65 GGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTATAATAAGTTTGTGT--G
1781749 TCCATGACCCC
128 T-CA-GA---C
* * * * *
1781760 TATCGGTTTCGACTATTAGTAACGAAAGGGACCTTTCACCAAGTTCATCTTAACTCCAAGCTTGA
1 -ATCGGTTTCGACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGA
* * * *
1781825 GGACAATCTTTTTCTCTAGCAAGGTAGTAATATTATCAGCCGAATCTAT
65 GGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTAT
1781874 GTTAGGAAAG
Statistics
Matches: 213, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
128 34 0.16
129 77 0.36
130 1 0.00
133 1 0.00
135 1 0.00
137 1 0.00
141 65 0.31
142 33 0.15
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (133 bp):
ATCGGTTTCGACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAG
GACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTATAATAAGTTTGTGTGTCA
GAC
Found at i:1782321 original size:142 final size:141
Alignment explanation
Indices: 1782093--1782751 Score: 870
Period size: 142 Copynumber: 4.7 Consensus size: 141
1782083 AGTCTCGACG
1782093 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTC
1 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTC
** * * *
1782158 TCTAGCAAGGGAGTAATATTATGGGTTGAATCTATAATAAGCTTGTATGGGTCCACAACCCCTAT
66 TCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCCTAT
1782223 CGGTTTCAACT
131 CGGTTTCAACT
* * * * * * *
1782234 ATTAGCAATGGAAGGGACCTTTCACCATGTTTATCCTTAACTCTGAGCCTGAGGAAAAGCTCTTT
1 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCC-TAACTCCGAGCTTGAGGACAAGCTCTTT
* * *
1782299 CTCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAACAAGTTTGTGTAGGTCCACGACCCATA
65 CTCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCCTA
**
1782364 TCGGTTTTGAC-
130 TCGGTTTCAACT
* * *
1782375 --T--TAATG-AGGGGACCTTTCTCCAAGTTTATCCTAGCTCCGAGCTTGAGGACAAGCTCTTTC
1 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTC
* * *
1782435 TCTAGCAAGGGAGTGATATTATGGGCCGAATCTATAATAAGTTTGGGTAGGTCCACAACACCTAT
66 TCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCCTAT
1782500 CGGTTTCAACT
131 CGGTTTCAACT
1782511 ATTAGTAATGAAAAGGG-CCTTTCGCCAAGTTTATCCTAACTCCGAGAGCTTGAGGACAAGCTCT
1 ATTAGTAATG-AAAGGGACCTTTCGCCAAGTTTATCCTAACTCC--GAGCTTGAGGACAAGCTCT
* * **
1782575 TTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTATTATAAGTTTGTGTAGGTCCACAACCGT
63 TTCTCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCC
*
1782640 TATCGGTTTCGACT
128 TATCGGTTTCAACT
* * * * *
1782654 ATTAGTAA-CAAGGGGACCTTTCCCCAAGTTTATCCTAACTCC-ACGCTCGAGGACAAGTTCTTT
1 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGA-GCTTGAGGACAAGCTCTTT
* * * *
1782717 CTCTAGCAAGGAAGTGA-CTTATGGGCTGAATCTAT
65 CTCTAGCAAGGGAGTAATATTATGGGCCGAATCTAT
1782752 GTTAGGAAAG
Statistics
Matches: 452, Mismatches: 54, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
135 92 0.20
136 22 0.05
137 4 0.01
138 1 0.00
139 17 0.04
140 37 0.08
141 61 0.13
142 120 0.27
143 98 0.22
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (141 bp):
ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTC
TCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCCTAT
CGGTTTCAACT
Found at i:1803749 original size:18 final size:16
Alignment explanation
Indices: 1803728--1803762 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1803718 AAATATTATT
1803728 ATATTTAAATTAAATTAA
1 ATATTT-AATT-AATTAA
1803746 ATATTTAATTAATTAA
1 ATATTTAATTAATTAA
1803762 A
1 A
1803763 GTCAGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTTAATTAATTAA
Found at i:1811548 original size:2 final size:2
Alignment explanation
Indices: 1811501--1811533 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1811491 AAATTAGCAT
1811501 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1811534 GATAAAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1812289 original size:151 final size:151
Alignment explanation
Indices: 1812078--1812377 Score: 345
Period size: 151 Copynumber: 2.0 Consensus size: 151
1812068 AATATACATG
* * ** * * *
1812078 CGAGGAATTATAAGTATCAAATTATTACATCATAGATTGTTCGAAGAATCACGAAATAGATCAAA
1 CGAGGAACTAAAAGTATCAAATTATTACAGAATAGATTGTCCAAAAAATCACGAAATAGATCAAA
* * ** * * *
1812143 CATTAAAGTATAA-TTGAAATAAG-AATAGGTACACTTTAGTCTAAGGCCAACAAACTAAATTAA
66 CATTAAAGCACAACCAG-AATAAGAAAT-GGTACACTTTAGACTAAAGCCAACAAACTAAACTAA
*
1812206 CTTGACTAAAACCCGCACATGTT
129 CTTGACTAAAACCCACACATGTT
* * *
1812229 CGAGGAACTAAAAGTATCGAATTATTATAGAATGGATTGTCCAAAAAATCAC-AAAGTAGATCAA
1 CGAGGAACTAAAAGTATCAAATTATTACAGAATAGATTGTCCAAAAAATCACGAAA-TAGATCAA
* * * * *
1812293 TCGTTAAAGCACAACCAGAATAAGAAATGGTACACTTTAGACTAAAGCCAATAAACTGAGCTAAC
65 ACATTAAAGCACAACCAGAATAAGAAATGGTACACTTTAGACTAAAGCCAACAAACTAAACTAAC
1812358 TTGACTAAAACCCACACATG
130 TTGACTAAAACCCACACATG
1812378 ACAATTGCAT
Statistics
Matches: 123, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
150 3 0.02
151 116 0.94
152 4 0.03
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (151 bp):
CGAGGAACTAAAAGTATCAAATTATTACAGAATAGATTGTCCAAAAAATCACGAAATAGATCAAA
CATTAAAGCACAACCAGAATAAGAAATGGTACACTTTAGACTAAAGCCAACAAACTAAACTAACT
TGACTAAAACCCACACATGTT
Found at i:1821381 original size:19 final size:20
Alignment explanation
Indices: 1821354--1821394 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1821344 CTTCATTCCA
* *
1821354 TTTATTTTATTAATA-ATTT
1 TTTAATTTAATAATATATTT
1821373 TTTAATTTAATAATATATTT
1 TTTAATTTAATAATATATTT
1821393 TT
1 TT
1821395 AAGTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTAATTTAATAATATATTT
Found at i:1822985 original size:14 final size:15
Alignment explanation
Indices: 1822958--1822986 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1822948 GCTGGGATGA
1822958 AAATAAATTTTAATT
1 AAATAAATTTTAATT
1822973 AAATAAA-TTTAATT
1 AAATAAATTTTAATT
1822987 TGAACTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATAAATTTTAATT
Found at i:1831635 original size:11 final size:11
Alignment explanation
Indices: 1831621--1831651 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
1831611 TTTTATAAAT
1831621 ATTTTTTAATA
1 ATTTTTTAATA
1831632 A-TTTTTAATA
1 ATTTTTTAATA
1831642 ATTTTTTAAT
1 ATTTTTTAAT
1831652 CGAATCAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:1836227 original size:11 final size:11
Alignment explanation
Indices: 1836211--1836255 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
1836201 TAGTTATTTA
1836211 TAATAAAATAT
1 TAATAAAATAT
1836222 TAATAAAATAT
1 TAATAAAATAT
*
1836233 CTCATTAAAATAT
1 -T-AATAAAATAT
1836246 TAATAAAATA
1 TAATAAAATA
1836256 ATATTTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 19 0.63
12 2 0.07
13 9 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:1838829 original size:19 final size:19
Alignment explanation
Indices: 1838793--1838860 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1838783 TCTCTCTCTA
*
1838793 CAAAA-ATTTAAAAAAATT
1 CAAAATATTTATAAAAATT
*
1838811 CAAAATAATTT-TTAAAATT
1 CAAAAT-ATTTATAAAAATT
*
1838830 TAAAATATTTATAAAAATT
1 CAAAATATTTATAAAAATT
*
1838849 CCAAA-ATTTATA
1 CAAAATATTTATA
1838861 TTTTTAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
18 16 0.39
19 21 0.51
20 4 0.10
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
CAAAATATTTATAAAAATT
Found at i:1838934 original size:9 final size:9
Alignment explanation
Indices: 1838794--1838935 Score: 56
Period size: 9 Copynumber: 14.7 Consensus size: 9
1838784 CTCTCTCTAC
1838794 AAAAATTTAA
1 AAAAATTT-A
*
1838804 AAAAATTCA
1 AAAAATTTA
*
1838813 AAATAATTTT
1 AAA-AATTTA
*
1838823 TAAAATTTA
1 AAAAATTTA
*
1838832 AAATATTTA
1 AAAAATTTA
*
1838841 TAAAAA-TTC
1 -AAAAATTTA
*
1838850 CAAAATTT-
1 AAAAATTTA
* **
1838858 ATATTTTTA
1 AAAAATTTA
1838867 AATAAA-TTA
1 AA-AAATTTA
1838876 TAAAAATTTCAAA
1 -AAAAATTT---A
1838889 AATAAATTCTA
1 AA-AAATT-TA
1838900 AAAAATATTA
1 AAAAAT-TTA
*
1838910 AAGAAAGTTAA
1 AA-AAA-TTTA
1838921 AAAAATTTA
1 AAAAATTTA
1838930 AAAAAT
1 AAAAAT
1838936 ATTCTAGAAT
Statistics
Matches: 98, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
8 8 0.08
9 36 0.37
10 33 0.34
11 11 0.11
12 3 0.03
13 6 0.06
14 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTTA
Found at i:1843149 original size:24 final size:24
Alignment explanation
Indices: 1843112--1843158 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1843102 TATATATACC
1843112 AATTCAATCAATA-TAAATTCAATA
1 AATTCAATCAATATTAAA-TCAATA
1843136 AATTC-ATCACATATTAAATCAAT
1 AATTCAATCA-ATATTAAATCAAT
1843159 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCAATCAATATTAAATCAATA
Found at i:1843991 original size:19 final size:20
Alignment explanation
Indices: 1843967--1844005 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1843957 ATTAATAAGC
1843967 AATACATAT-TTTATTATTA
1 AATACATATGTTTATTATTA
1843986 AATACATATGTTTATTATTA
1 AATACATATGTTTATTATTA
1844006 CACATGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
AATACATATGTTTATTATTA
Found at i:1849594 original size:2 final size:2
Alignment explanation
Indices: 1849587--1849619 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1849577 ATGTAATAGA
1849587 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 A
1849620 ATAAAGGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1850288 original size:3 final size:3
Alignment explanation
Indices: 1850280--1850328 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1850270 ATTTTAATCC
1850280 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1850328 T
1 T
1850329 CCTTCTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1853632 original size:24 final size:22
Alignment explanation
Indices: 1853598--1853657 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
1853588 AAAATACACA
*
1853598 TTTTTTATATATACGTTTTCATT
1 TTTTTTATATATACATTTTCA-T
*
1853621 TTTTTTATTATAAACATTTTCAT
1 TTTTTTA-TATATACATTTTCAT
*
1853644 TATTTTATATATAC
1 TTTTTTATATATAC
1853658 TTCATTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 6 0.19
23 14 0.44
24 12 0.38
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTTATATATACATTTTCAT
Found at i:1853663 original size:19 final size:20
Alignment explanation
Indices: 1853639--1853676 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1853629 TATAAACATT
1853639 TTCATTATTT-TATATATAC
1 TTCATTATTTATATATATAC
1853658 TTCATTATTTATATATATA
1 TTCATTATTTATATATATA
1853677 TTGTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
TTCATTATTTATATATATAC
Found at i:1855957 original size:24 final size:24
Alignment explanation
Indices: 1855925--1855974 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1855915 GAAAAGAAAA
1855925 GGAACGGTATTCTTTGTGATTAGG
1 GGAACGGTATTCTTTGTGATTAGG
1855949 GGAACGGTATTCTTTGTGATTAGG
1 GGAACGGTATTCTTTGTGATTAGG
1855973 GG
1 GG
1855975 GCCTATCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.08, G:0.36, T:0.36
Consensus pattern (24 bp):
GGAACGGTATTCTTTGTGATTAGG
Found at i:1856150 original size:232 final size:232
Alignment explanation
Indices: 1855744--1856182 Score: 788
Period size: 232 Copynumber: 1.9 Consensus size: 232
1855734 GGGTTGGACC
* *
1855744 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAATATCTTGGGTCTTGAATA
1 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAACA
1855809 CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
66 CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
*
1855874 ATCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
131 ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
1855939 TGTGATTAGGGGAACGGTATTCTTTGTGATTAGGGGG
196 TGTGATTAGGGGAACGGTATTCTTTGTGATTAGGGGG
* *
1855976 CCTATCAGCCCCATTCCGTTGTCTTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAACA
1 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAACA
* * * *
1856041 TCCAAATTCGAGATTTACCGTACACAAACAAATGTTGGGATATCTGAATCTCTTTATAAATTGTT
66 CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
*
1856106 ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAATGGTATTCTT
131 ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
1856171 TGTGATTAGGGG
196 TGTGATTAGGGG
1856183 GCCTATAACT
Statistics
Matches: 197, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
232 197 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (232 bp):
CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAACA
CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
TGTGATTAGGGGAACGGTATTCTTTGTGATTAGGGGG
Done.