Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 70 of 206
Found at i:19776655 original size:3 final size:3
Alignment explanation
Indices: 19776647--19776691 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
19776637 TAACTGAATA
19776647 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19776692 GTCAACTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19777821 original size:27 final size:28
Alignment explanation
Indices: 19777773--19777827 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
19777763 GTTTTGGGCC
*
19777773 TGTTGGGTATTTGGGCTTGGTT-TAATT
1 TGTTGGGTACTTGGGCTTGGTTGTAATT
*
19777800 TGTTGGGT-CTTGGGTTTGGGTTGTAATT
1 TGTTGGGTACTTGGGCTT-GGTTGTAATT
19777828 GGGTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.09, C:0.04, G:0.36, T:0.51
Consensus pattern (28 bp):
TGTTGGGTACTTGGGCTTGGTTGTAATT
Found at i:19780763 original size:43 final size:43
Alignment explanation
Indices: 19780701--19781009 Score: 302
Period size: 43 Copynumber: 7.2 Consensus size: 43
19780691 GCAAAGCTAT
* * *
19780701 TGACTTTTAGCGGCGCTTTTCCTATAAACGCCGCTATATAACA
1 TGACCTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAGAACA
* * *
19780744 TGACTTTTAGCGGCACTTTTCC-ACAAACGCCGCTATAAAACA
1 TGACCTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAGAACA
* * * ** *
19780786 AGACATTTAGCTGCG-TTTTTTTCACAAACGCCGCTATAAAACA
1 TGACCTTTAGCGGCGCTTTTCCT-ACAAACGCCGCTATAGAACA
** * * * *
19780829 AAACCTTTAGCGGCGCTTTTTCC-GCAAGCACCGCTACAGAACA
1 TGACCTTTAGCGGCGC-TTTTCCTACAAACGCCGCTATAGAACA
* * * *
19780872 TGACCTTTAGCAGCGCTTTT-CTCACAAATGCCACTAAAGAACA
1 TGACCTTTAGCGGCGCTTTTCCT-ACAAACGCCGCTATAGAACA
* * *
19780915 AGACCTTTACCGGCGCTTTTCCCACAAACGCCGCTATAGAACA
1 TGACCTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAGAACA
* * * *
19780958 TGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAAGAACA
1 TGACCTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAGAACA
19781001 TGACCTTTA
1 TGACCTTTA
19781010 AAAATATTTT
Statistics
Matches: 219, Mismatches: 40, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
41 5 0.02
42 33 0.15
43 176 0.80
44 1 0.00
45 4 0.02
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (43 bp):
TGACCTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAGAACA
Found at i:19780964 original size:129 final size:128
Alignment explanation
Indices: 19780706--19781009 Score: 349
Period size: 129 Copynumber: 2.4 Consensus size: 128
19780696 GCTATTGACT
* * * * * * *
19780706 TTTAGCGGCGCTTTTCCTATAAACGCCGCTATATAACATGACTTTTAGCGGCACTTTTCCACAAA
1 TTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGACCTTTAGCAGCACTTTTCCACAAA
* * * * **
19780771 CGCCGCTATAAAACAAGACATTTAGCTGCGTTTTTTTCACAAACGCCGCTATAAAACAAAACC
66 CGCCACTATAAAACAAGACATTTACCGGCGCTTTTCCCACAAACGCCGCTATAAAACAAAACC
* * * * *
19780834 TTTAGCGGCGCTTTTTCCGCAAGCACCGCTACAGAACATGACCTTTAGCAGCGCTTTTCTCACAA
1 TTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGACCTTTAGCAGCACTTTTC-CACAA
* * * **
19780899 ATGCCACTA-AAGAACAAGACCTTTACCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGACC
65 ACGCCACTATAA-AACAAGACATTTACCGGCGCTTTTCCCACAAACGCCGCTATAAAACAAAACC
* * *
19780963 TTTAGTGGCGCTTTTCCCACAAACGCCACTAAAGAACATGACCTTTA
1 TTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGACCTTTA
19781010 AAAATATTTT
Statistics
Matches: 145, Mismatches: 29, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
128 50 0.34
129 95 0.66
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (128 bp):
TTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGACCTTTAGCAGCACTTTTCCACAAA
CGCCACTATAAAACAAGACATTTACCGGCGCTTTTCCCACAAACGCCGCTATAAAACAAAACC
Found at i:19782715 original size:21 final size:21
Alignment explanation
Indices: 19782677--19782731 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
19782667 TCTAAACCCC
**
19782677 TAAACCCTAAATCATAAAATA
1 TAAACCCTAACCCATAAAATA
* * *
19782698 TAAACCCTAACCCCTAAATTT
1 TAAACCCTAACCCATAAAATA
*
19782719 TAAACCCCAACCC
1 TAAACCCTAACCC
19782732 TTCAACCATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCCTAACCCATAAAATA
Found at i:19782791 original size:29 final size:29
Alignment explanation
Indices: 19782758--19782842 Score: 69
Period size: 29 Copynumber: 3.2 Consensus size: 29
19782748 CTAAACCCTA
19782758 AACTCATAATCCATAAACCTTAAAATAGT
1 AACTCATAATCCATAAACCTTAAAATAGT
* **
19782787 AACTC----T---TAAATCTT-AAATCCT
1 AACTCATAATCCATAAACCTTAAAATAGT
*
19782808 AAACCCATAATCCATAAACCTTAAAATAGT
1 -AACTCATAATCCATAAACCTTAAAATAGT
19782838 AACTC
1 AACTC
19782843 TTAAATCTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 18
0.60 0.12 0.28
Matches are distributed among these distances:
21 5 0.13
22 11 0.28
25 1 0.03
26 1 0.03
29 16 0.41
30 5 0.13
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (29 bp):
AACTCATAATCCATAAACCTTAAAATAGT
Found at i:19782817 original size:51 final size:51
Alignment explanation
Indices: 19782749--19782863 Score: 212
Period size: 51 Copynumber: 2.3 Consensus size: 51
19782739 ATAAACCATC
* *
19782749 TAAACCCTAAACTCATAATCCATAAACCTTAAAATAGTAACTCTTAAATCT
1 TAAATCCTAAACCCATAATCCATAAACCTTAAAATAGTAACTCTTAAATCT
19782800 TAAATCCTAAACCCATAATCCATAAACCTTAAAATAGTAACTCTTAAATCT
1 TAAATCCTAAACCCATAATCCATAAACCTTAAAATAGTAACTCTTAAATCT
19782851 TAAATCCTAAACC
1 TAAATCCTAAACC
19782864 ATATACCCTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (51 bp):
TAAATCCTAAACCCATAATCCATAAACCTTAAAATAGTAACTCTTAAATCT
Found at i:19783343 original size:40 final size:40
Alignment explanation
Indices: 19783288--19783394 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 40
19783278 TAATTTTTTT
* * * *
19783288 GCGGCGTTTTCCAAAAAGTGCCGCTAATGGTCGACCTATA
1 GCGGCGTTTTTCAAAAAGAGCCACTAATGCTCGACCTATA
*
19783328 GCGGCGTTTTTCAAAAAGCAG-CACTAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAG-AGCCACTAATGCTCGACCTATA
* * *
19783368 GTGACGTTTTTCAAAAAGCGCCACTAA
1 GCGGCGTTTTTCAAAAAGAGCCACTAA
19783395 AGCTTAACGT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
39 1 0.02
40 55 0.96
41 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGAGCCACTAATGCTCGACCTATA
Found at i:19783497 original size:40 final size:40
Alignment explanation
Indices: 19783448--19783539 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 40
19783438 CCGCTAGTGG
* * * *
19783448 AGCGTCGTTTTTCAAAAAGCGCTACTAATGCTCAATTTAT
1 AGCGGCGTTTTTCAAAAAGCACCACTAATGCTCAATCTAT
* *
19783488 AGCGGCGTTTTTCAAAAGGCACCACTAATGCTCGATCTAT
1 AGCGGCGTTTTTCAAAAAGCACCACTAATGCTCAATCTAT
19783528 AGCGGCGTTTTT
1 AGCGGCGTTTTT
19783540 TATCCAACCG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
AGCGGCGTTTTTCAAAAAGCACCACTAATGCTCAATCTAT
Found at i:19787569 original size:21 final size:21
Alignment explanation
Indices: 19787543--19787613 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
19787533 AGGTGCAGGG
19787543 AAGACATGGTCATGTGGCTGA
1 AAGACATGGTCATGTGGCTGA
** * *
19787564 AAGACATTCTCGTGTGACTGA
1 AAGACATGGTCATGTGGCTGA
* * * *
19787585 TATACATGGCCATGTGGCTGG
1 AAGACATGGTCATGTGGCTGA
*
19787606 GAGACATG
1 AAGACATG
19787614 CTCGTCTGCG
Statistics
Matches: 36, Mismatches: 14, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (21 bp):
AAGACATGGTCATGTGGCTGA
Found at i:19790588 original size:29 final size:29
Alignment explanation
Indices: 19790546--19790736 Score: 100
Period size: 29 Copynumber: 6.5 Consensus size: 29
19790536 GATGGTCATC
* *
19790546 ACCATCTCGTTTCATAATCGATAGCCG-A
1 ACCATCCCTTTTCATAATCGATAGCCGTA
* * * * *
19790574 AGCTATCCCTTTTCATAATTCAATGGTCGTC
1 A-CCATCCCTTTTCATAA-TCGATAGCCGTA
* **
19790605 ACCATCCCGTTTCATAATCGATATTCG-A
1 ACCATCCCTTTTCATAATCGATAGCCGTA
* * * * *
19790633 AGCTATCCCTTTTCATAATTTGATGGTCGTC
1 A-CCATCCCTTTTCATAA-TCGATAGCCGTA
** * * * * *
19790664 ACCATTGCTTTTCATAGTTGATGGCTGTC
1 ACCATCCCTTTTCATAATCGATAGCCGTA
19790693 ACCATCCCTTTTCATAATCGATAGCCG-A
1 ACCATCCCTTTTCATAATCGATAGCCGTA
* *
19790721 AGCTATCACTTTTCAT
1 A-CCATCCCTTTTCAT
19790737 TGGTCGATGA
Statistics
Matches: 122, Mismatches: 34, Indels: 13
0.72 0.20 0.08
Matches are distributed among these distances:
28 3 0.02
29 77 0.63
30 40 0.33
31 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (29 bp):
ACCATCCCTTTTCATAATCGATAGCCGTA
Found at i:19790607 original size:59 final size:59
Alignment explanation
Indices: 19790537--19790668 Score: 210
Period size: 59 Copynumber: 2.2 Consensus size: 59
19790527 TGGAATCACG
* *
19790537 ATGGTCATCACCATCTCGTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATAATTCA
1 ATGGTCGTCACCATCCCGTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATAATTCA
** **
19790596 ATGGTCGTCACCATCCCGTTTCATAATCGATATTCGAAGCTATCCCTTTTCATAATTTG
1 ATGGTCGTCACCATCCCGTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATAATTCA
19790655 ATGGTCGTCACCAT
1 ATGGTCGTCACCAT
19790669 TGCTTTTCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 67 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.35
Consensus pattern (59 bp):
ATGGTCGTCACCATCCCGTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATAATTCA
Found at i:19790618 original size:30 final size:30
Alignment explanation
Indices: 19790535--19790714 Score: 131
Period size: 29 Copynumber: 6.1 Consensus size: 30
19790525 AGTGGAATCA
* * *
19790535 CGATGGTCATCACCATCTCGTTTCATAA-T
1 CGATGGTCGTCACCATCCCTTTTCATAATT
* * * *
19790564 CGATAGCCG-AAGCTATCCCTTTTCATAATT
1 CGATGGTCGTCA-CCATCCCTTTTCATAATT
* *
19790594 CAATGGTCGTCACCATCCCGTTTCATAA-T
1 CGATGGTCGTCACCATCCCTTTTCATAATT
** * *
19790623 CGATATTCG-AAGCTATCCCTTTTCATAATT
1 CGATGGTCGTCA-CCATCCCTTTTCATAATT
* ** *
19790653 TGATGGTCGTCACCATTGCTTTTCATAGTT
1 CGATGGTCGTCACCATCCCTTTTCATAATT
19790683 -GATGG-CTGTCACCATCCCTTTTCATAA-T
1 CGATGGTC-GTCACCATCCCTTTTCATAATT
19790711 CGAT
1 CGAT
19790715 AGCCGAAGCT
Statistics
Matches: 113, Mismatches: 30, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
28 4 0.04
29 65 0.58
30 42 0.37
31 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.36
Consensus pattern (30 bp):
CGATGGTCGTCACCATCCCTTTTCATAATT
Found at i:19798544 original size:10 final size:10
Alignment explanation
Indices: 19798522--19798568 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
19798512 AAATCTGTCG
*
19798522 AAAA-TAATA
1 AAAATTAATT
*
19798531 AAAATTAATC
1 AAAATTAATT
19798541 AAAATTAATTAT
1 AAAATTAA-T-T
19798553 AAAATTAATT
1 AAAATTAATT
19798563 AAAATT
1 AAAATT
19798569 CAACATGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 4 0.12
10 19 0.58
11 2 0.06
12 8 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTAATT
Found at i:19799065 original size:21 final size:21
Alignment explanation
Indices: 19799027--19799066 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19799017 TTGTAAAATT
*
19799027 TTATAAAAATCATTAAAAAAA
1 TTATAAAAATCATCAAAAAAA
19799048 TTAT-AAAATACATCAAAAA
1 TTATAAAAAT-CATCAAAAA
19799067 GACTCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (21 bp):
TTATAAAAATCATCAAAAAAA
Found at i:19799674 original size:90 final size:88
Alignment explanation
Indices: 19799510--19799762 Score: 321
Period size: 90 Copynumber: 2.8 Consensus size: 88
19799500 TTTAGGGGTG
* *
19799510 GTTCAAATACCCAATTGAGTGCAAAAAAAAAAGTAGGGGCTTACTTGCTTTTTT-AAAAAGTTTA
1 GTTCAAGTACCCAATTGAGTGC--AAAAAAAAGTAGGGGCTTAATTGCTTTTTTGAAAAAGTTTA
* * *
19799574 AGAGTCTTTTTGATTCATTTTCAAA
64 AGGGTCTTTTTGATGCATTGTCAAA
* * * *
19799599 GTTCAAGTACTCAATTGAGTGCAAAAAAAGAGTAAGGGCTTAAATGCTCTTTTTGAAAAAGTTTG
1 GTTCAAGTACCCAATTGAGTGCAAAAAAA-AGTAGGGGCTTAATTGCT-TTTTTGAAAAAGTTTA
*
19799664 AGGGTCTTTTTGATGCATTGTGAAA
64 AGGGTCTTTTTGATGCATTGTCAAA
* * * *
19799689 GTTCAAGTACCCAAATGAGTACAAAAAAAAGTAGGGGCTTAATTTCTTTTTCTGAAAAATTTTAA
1 GTTCAAGTACCCAATTGAGTGCAAAAAAAAGTAGGGGCTTAATTGCTTTTT-TGAAAAAGTTTAA
19799754 GGG-CTTTTT
65 GGGTCTTTTT
19799763 ACACCCTTAA
Statistics
Matches: 142, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
87 7 0.05
88 25 0.18
89 54 0.38
90 56 0.39
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (88 bp):
GTTCAAGTACCCAATTGAGTGCAAAAAAAAGTAGGGGCTTAATTGCTTTTTTGAAAAAGTTTAAG
GGTCTTTTTGATGCATTGTCAAA
Found at i:19800066 original size:36 final size:36
Alignment explanation
Indices: 19799989--19800467 Score: 173
Period size: 36 Copynumber: 12.8 Consensus size: 36
19799979 GAAAAAATTT
* * ***
19799989 GTAAATCAGCAAACTGAAAAAATGACAGTTGTGATA
1 GTAAATCAGCGAACTGTAAAAATGACAGTCCAGATA
*
19800025 CTAAATCAGCGAACTGTAAAAATGACAGTCCAGATA
1 GTAAATCAGCGAACTGTAAAAATGACAGTCCAGATA
* * ** * *
19800061 GTAAATTAACGAACTGCTAGAAAACCAAAGGTCACA-CTA
1 GTAAATCAGCGAACTG-TA-AAAATGACA-GTC-CAGATA
* *
19800100 GTAAATCA-CCAGACCGTAAAAATGACAGT-CACGATA
1 GTAAATCAGCGA-ACTGTAAAAATGACAGTCCA-GATA
* * *
19800136 GTAAATCAGCGAACTAATAGAAACCTGA-AGGTCGC-GATC
1 GTAAATCAGCGAACT-GTA-AAA-ATGACA-GTC-CAGATA
* * * *
19800175 GAAAATTAACAGGTCATAAATTGTTAGAAAACTGA-AGGT-CGGATA
1 GTAAA-T--CA-G-C--GAACTG-TA-AAAA-TGACA-GTCCAGATA
** *
19800220 GTAAATCAGC-AGACCATAAAAATGACAGTGGC-GATA
1 GTAAATCAGCGA-ACTGTAAAAATGACAGT-CCAGATA
* * *
19800256 GTAAATCAACGAATTGT-AAAATGAAAGT-CATGATA
1 GTAAATCAGCGAACTGTAAAAATGACAGTCCA-GATA
* *
19800291 GTAAATTAGAGAACTGTAAAAATGACAGTCGCA-ATA
1 GTAAATCAGCGAACTGTAAAAATGACAGTC-CAGATA
*
19800327 GTAAATCAACGAACTGTTAGAAAACTGA-AGGTCGCA-ATA
1 GTAAATCAGCGAACTG-TA-AAAA-TGACA-GTC-CAGATA
* * * *
19800366 GTAAATCAGCGGACCGTAAAAATGACAATCGC-GAGA
1 GTAAATCAGCGAACTGTAAAAATGACAGTC-CAGATA
* * * *
19800402 GTAAATCAGAGAATTGTAAAAATGAAAAT-CACGATA
1 GTAAATCAGCGAACTGTAAAAATGACAGTCCA-GATA
* *
19800438 ATAAATTAGC-AATCTGTAAAAATGACAGTC
1 GTAAATCAGCGAA-CTGTAAAAATGACAGTC
19800468 GCAATAAGAA
Statistics
Matches: 334, Mismatches: 65, Indels: 87
0.69 0.13 0.18
Matches are distributed among these distances:
33 1 0.00
34 3 0.01
35 34 0.10
36 159 0.48
37 24 0.07
38 24 0.07
39 52 0.16
40 4 0.01
41 2 0.01
42 4 0.01
43 1 0.00
44 3 0.01
45 7 0.02
46 16 0.05
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.20
Consensus pattern (36 bp):
GTAAATCAGCGAACTGTAAAAATGACAGTCCAGATA
Found at i:19800291 original size:35 final size:36
Alignment explanation
Indices: 19800236--19800523 Score: 165
Period size: 36 Copynumber: 7.9 Consensus size: 36
19800226 CAGCAGACCA
* ** *
19800236 TAAAAATGACAGTGGCGATAGTAAATCAACGAATTG
1 TAAAAATGAAAGTCACGATAGTAAATCAACGAACTG
* *
19800272 T-AAAATGAAAGTCATGATAGTAAATTAGA-GAACTG
1 TAAAAATGAAAGTCACGATAGTAAATCA-ACGAACTG
* * *
19800307 TAAAAATGACAGTCGCAATAGTAAATCAACGAACTG
1 TAAAAATGAAAGTCACGATAGTAAATCAACGAACTG
* * * * * *
19800343 TTAGAAAACTGAAGGTCGCAATAGTAAATCAGCGGACCG
1 -TA-AAAA-TGAAAGTCACGATAGTAAATCAACGAACTG
* * *
19800382 TAAAAATGACAA-TCGCGAGAGTAAATCAGA-GAATTG
1 TAAAAATGA-AAGTCACGATAGTAAATCA-ACGAACTG
* * * *
19800418 TAAAAATGAAAATCACGATAATAAATTAGC-AATCTG
1 TAAAAATGAAAGTCACGATAGTAAATCAACGAA-CTG
* * * *
19800454 TAAAAATGACAGTCGCAATAAG-AAATCAATGAACTG
1 TAAAAATGAAAGTCACGAT-AGTAAATCAACGAACTG
* * * *
19800490 TTAGAAAATCAAAGATCGCAATAGGAAATCAACG
1 -TA-AAAATGAAAG-TCACGATAGTAAATCAACG
19800524 GACCATATGT
Statistics
Matches: 195, Mismatches: 40, Indels: 31
0.73 0.15 0.12
Matches are distributed among these distances:
35 32 0.16
36 95 0.49
37 12 0.06
38 16 0.08
39 40 0.21
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (36 bp):
TAAAAATGAAAGTCACGATAGTAAATCAACGAACTG
Found at i:19800390 original size:75 final size:74
Alignment explanation
Indices: 19800196--19800527 Score: 277
Period size: 75 Copynumber: 4.5 Consensus size: 74
19800186 GGTCATAAAT
* * * *
19800196 TGTTAGAAAACTGAAGGTCG-GATAGTAAATCAGCAGACCATAAAAATGACAGTGGCGATAGTAA
1 TGTTAGAAAA-TGAAGGTCGCGATAGTAAATCAGCGGACCGTAAAAATGACAGTCGCAATAGTAA
*
19800260 ATCAACGAAT
65 ATCAACGAAC
* ** * * * *
19800270 TG-T--AAAATGAAAGTCATGATAGTAAATTAGAGAACTGTAAAAATGACAGTCGCAATAGTAAA
1 TGTTAGAAAATGAAGGTCGCGATAGTAAATCAGCGGACCGTAAAAATGACAGTCGCAATAGTAAA
19800332 TCAACGAAC
66 TCAACGAAC
* * * *
19800341 TGTTAGAAAACTGAAGGTCGCAATAGTAAATCAGCGGACCGTAAAAATGACAATCGCGAGAGTAA
1 TGTTAGAAAA-TGAAGGTCGCGATAGTAAATCAGCGGACCGTAAAAATGACAGTCGCAATAGTAA
*
19800406 ATCAGA-GAAT
65 ATCA-ACGAAC
** * * * * *
19800416 TG-TA-AAAATGAAAATCACGATAATAAATTAGC-AATCTGTAAAAATGACAGTCGCAATAAG-A
1 TGTTAGAAAATGAAGGTCGCGATAGTAAATCAGCGGA-CCGTAAAAATGACAGTCGCAAT-AGTA
*
19800477 AATCAATGAAC
64 AATCAACGAAC
* * * * *
19800488 TGTTAGAAAATCAAAGATCGCAATAGGAAATCAACGGACC
1 TGTTAGAAAAT-GAAGGTCGCGATAGTAAATCAGCGGACC
19800528 ATATGTAATA
Statistics
Matches: 200, Mismatches: 45, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
70 7 0.04
71 53 0.26
72 48 0.24
73 9 0.05
74 13 0.06
75 68 0.34
76 2 0.01
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (74 bp):
TGTTAGAAAATGAAGGTCGCGATAGTAAATCAGCGGACCGTAAAAATGACAGTCGCAATAGTAAA
TCAACGAAC
Found at i:19800480 original size:147 final size:146
Alignment explanation
Indices: 19800196--19800530 Score: 455
Period size: 147 Copynumber: 2.3 Consensus size: 146
19800186 GGTCATAAAT
* * * * *
19800196 TGTTAGAAAACTGAAGGTCG-GATAGTAAATCAGCAGACCATAAAAATGACAGTGGCGATAGTAA
1 TGTTAGAAAACTGAAGGTCGCAATAGTAAATCAGCGGACCATAAAAATGACAATCGCGAGAGTAA
* * *
19800260 ATCAACGAATTGTAAAATGAAAGTCATGATAGTAAATTAGAGAACTGTAAAAATGACAGTCGCAA
66 ATCAACGAATTGTAAAATGAAAATCACGATAATAAATTAGAGAACTGTAAAAATGACAGTCGCAA
19800325 TAGTAAATCAACGAAC
131 TAGTAAATCAACGAAC
*
19800341 TGTTAGAAAACTGAAGGTCGCAATAGTAAATCAGCGGACCGTAAAAATGACAATCGCGAGAGTAA
1 TGTTAGAAAACTGAAGGTCGCAATAGTAAATCAGCGGACCATAAAAATGACAATCGCGAGAGTAA
*
19800406 ATCAGA-GAATTGTAAAAATGAAAATCACGATAATAAATTAGCA-ATCTGTAAAAATGACAGTCG
66 ATCA-ACGAATTGT-AAAATGAAAATCACGATAATAAATTAG-AGAACTGTAAAAATGACAGTCG
*
19800469 CAATAAG-AAATCAATGAAC
128 CAAT-AGTAAATCAACGAAC
* * * *
19800488 TGTTAGAAAA-TCAAAGATCGCAATAGGAAATCAACGGACCATA
1 TGTTAGAAAACT-GAAGGTCGCAATAGTAAATCAGCGGACCATA
19800531 TGTAATAGCT
Statistics
Matches: 168, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
145 20 0.12
146 50 0.30
147 95 0.57
148 3 0.02
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (146 bp):
TGTTAGAAAACTGAAGGTCGCAATAGTAAATCAGCGGACCATAAAAATGACAATCGCGAGAGTAA
ATCAACGAATTGTAAAATGAAAATCACGATAATAAATTAGAGAACTGTAAAAATGACAGTCGCAA
TAGTAAATCAACGAAC
Found at i:19801810 original size:25 final size:25
Alignment explanation
Indices: 19801775--19801837 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
19801765 TACACCACAA
* *
19801775 CTCTTACGAGCTTCCCATTATTTAG
1 CTCTTATGAGCTTCCCAATATTTAG
* * *
19801800 CTCTTATGAGCATCCTAATATTTGG
1 CTCTTATGAGCTTCCCAATATTTAG
19801825 CTCTCT-TGAGCTT
1 CTCT-TATGAGCTT
19801838 TCCGATAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.41
Consensus pattern (25 bp):
CTCTTATGAGCTTCCCAATATTTAG
Found at i:19803735 original size:29 final size:29
Alignment explanation
Indices: 19803693--19803750 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
19803683 AGAAGGATCA
19803693 AATAGCTATGGAATTCAAAATTTGAGGTC
1 AATAGCTATGGAATTCAAAATTTGAGGTC
19803722 AATAGCTATGGAATTCAAAATTTGAGGTC
1 AATAGCTATGGAATTCAAAATTTGAGGTC
19803751 CTTATATGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (29 bp):
AATAGCTATGGAATTCAAAATTTGAGGTC
Found at i:19805115 original size:50 final size:50
Alignment explanation
Indices: 19805057--19805162 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
19805047 TATTGAGGTT
* * *
19805057 ATGAGAGGT-CCCATGTAAGACCATGTCTCGG-ACATGGCGTTGGCACCGAG
1 ATGAGAGGTACCC-CGTAAGACCATGTCT-GGAACATGGCATGGGCACCGAG
* *
19805107 ATGAGAGGTACCCCGTAAGACCTTGTCTGGAACATGGCATGGGCACCGAT
1 ATGAGAGGTACCCCGTAAGACCATGTCTGGAACATGGCATGGGCACCGAG
19805157 ATGAGA
1 ATGAGA
19805163 ACTGTAATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 2 0.04
50 44 0.90
51 3 0.06
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTACCCCGTAAGACCATGTCTGGAACATGGCATGGGCACCGAG
Found at i:19805441 original size:5 final size:5
Alignment explanation
Indices: 19805413--19805488 Score: 97
Period size: 5 Copynumber: 15.6 Consensus size: 5
19805403 TTTTTATGTT
*
19805413 TTATA -TATA TTATT TTAT- TATATA TTATA TTATA TTATA TTATA TTA-A
1 TTATA TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA
19805461 TTATA TTATA TTATA TTAT- TATATA TTA
1 TTATA TTATA TTATA TTATA T-TATA TTA
19805489 AATAAACTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
4 10 0.16
5 52 0.81
6 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:19805465 original size:29 final size:30
Alignment explanation
Indices: 19805413--19805489 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 30
19805403 TTTTTATGTT
* *
19805413 TTATA-TATATTATTTTATTATATATTATA
1 TTATATTATATTATATTAATATATATTATA
19805442 TTATATTATATTATATTAAT-TATATTATA
1 TTATATTATATTATATTAATATATATTATA
19805471 TTATATTAT-TATATATTAA
1 TTATATTATAT-TATATTAA
19805490 ATAAACTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 1 0.02
29 31 0.70
30 12 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTATATTATATTATATTAATATATATTATA
Found at i:19806075 original size:22 final size:24
Alignment explanation
Indices: 19806047--19806090 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
19806037 TATGACAAGA
19806047 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
19806069 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
19806091 AGCTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:19814140 original size:231 final size:230
Alignment explanation
Indices: 19813726--19814171 Score: 585
Period size: 231 Copynumber: 1.9 Consensus size: 230
19813716 ATTTGGCTTC
* * * *
19813726 GGGAAGTTAGTTTTCTTGGGCATATAGTATCTGCTGAAGGCATCAGAGTGGACTTAAATAAAATT
1 GGGAAGTGAGTTTTCTTGGGCACATAGTATCGGCTGAAGGCATCAGAGTGGACTCAAATAAAATT
* *
19813791 TCAGCAATTGTTAACTAGAAACGACCAAAAATGTATCTGAAGTCAGAAGTTTTCTGGGATTAGCT
66 TCAGCAATTGTGAACTAGAAACCACCAAAAATGTATCTGAAGTCAGAAGTTTTCTGGGATTAGCT
* * * * * *
19813856 GGTTACTATCGGAGATTTGTAAAAGGATTTTCAATGATAGCCTCTCTGATGACACAATTGTTACA
131 GGTTACTATCGAAGATTAGTAAAAGGATTTTCAATGATAGCCTCACCGATGACACAACTATTACA
*
19813921 GAAAGATGTGAAGTTTGAATAGACTTATAAATTTT
196 GAAAGATGTGAAATTTGAATAGACTTATAAATTTT
* * *
19813956 GGGAAGTGAGTTTTC-TGGGACACATAGTATCGGCTGAAGGTATTAGAGTTGA-TCCAAATAAAA
1 GGGAAGTGAGTTTTCTTGGG-CACATAGTATCGGCTGAAGGCATCAGAGTGGACT-CAAATAAAA
* * * * *
19814019 TTTCAGCTATTGTGAACTGGAAACCAGCGAAAAGTGTATCTGAAGTTAGAAGTTTTC-GAGGATT
64 TTTCAGCAATTGTGAACTAGAAACCA-CCAAAAATGTATCTGAAGTCAGAAGTTTTCTG-GGATT
* * * * *
19814083 GGCTGGTTATTATCGAAGATTAGTAAAAGGGTTTTCGATGATAG-CTACACCGATGACACGACTA
127 AGCTGGTTACTATCGAAGATTAGTAAAAGGATTTTCAATGATAGCCT-CACCGATGACACAACTA
19814147 TTACAGAAAGATGTGAAATTTGAAT
191 TTACAGAAAGATGTGAAATTTGAAT
19814172 GGTTTGATAA
Statistics
Matches: 185, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
229 5 0.03
230 74 0.40
231 106 0.57
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (230 bp):
GGGAAGTGAGTTTTCTTGGGCACATAGTATCGGCTGAAGGCATCAGAGTGGACTCAAATAAAATT
TCAGCAATTGTGAACTAGAAACCACCAAAAATGTATCTGAAGTCAGAAGTTTTCTGGGATTAGCT
GGTTACTATCGAAGATTAGTAAAAGGATTTTCAATGATAGCCTCACCGATGACACAACTATTACA
GAAAGATGTGAAATTTGAATAGACTTATAAATTTT
Found at i:19818356 original size:56 final size:56
Alignment explanation
Indices: 19818265--19818370 Score: 158
Period size: 56 Copynumber: 1.9 Consensus size: 56
19818255 TTGAATTGCT
* * ** *
19818265 CACATGGCCTACCACACGGGCGTGTGGTTTGGCCGTGTGACCTAAGTCAGTATACC
1 CACACGGCCTACCACACGGGCGTATGACTTGGCCGTGTGACCCAAGTCAGTATACC
*
19818321 CACACGGCCTATCACACGGGCGTATGACTTGGCCGTGTGACCCAAGTCAG
1 CACACGGCCTACCACACGGGCGTATGACTTGGCCGTGTGACCCAAGTCAG
19818371 AGAGCTCATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21
Consensus pattern (56 bp):
CACACGGCCTACCACACGGGCGTATGACTTGGCCGTGTGACCCAAGTCAGTATACC
Found at i:19818853 original size:36 final size:35
Alignment explanation
Indices: 19818745--19818968 Score: 153
Period size: 36 Copynumber: 6.1 Consensus size: 35
19818735 GTGTTACACA
* * * *
19818745 GTAAAAATGACAGACGCAATAGTAAATCAGCGAACT
1 GTAAAAATGA-AGTCACGATAGTAAATTAGCGAACT
** ** *
19818781 GCTAGAAAATTGAACGTCGTGATAAAAAATTAGCGAATT
1 G-TA-AAAA-TGAA-GTCACGATAGTAAATTAGCGAACT
*
19818820 GTAAAAATGATAGTCACGATAGTAAATCAGCGAACT
1 GTAAAAATGA-AGTCACGATAGTAAATTAGCGAACT
* * * * *
19818856 GTTAGGAAATCGAAGGTCATGATCGAAAATTAGCGGACT
1 G-TA-AAAAT-GAA-GTCACGATAGTAAATTAGCGAACT
* * *
19818895 GTAAAAATGATAGTTAC-ACTAGTAAATAAGCAAACT
1 GTAAAAATGA-AGTCACGA-TAGTAAATTAGCGAACT
*
19818931 GTAAAAATGAAAGTCGCGATAGTAAATTAGCGAACT
1 GTAAAAATG-AAGTCACGATAGTAAATTAGCGAACT
19818967 GT
1 GT
19818969 TAGAAAATCA
Statistics
Matches: 144, Mismatches: 31, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
35 1 0.01
36 70 0.49
37 16 0.11
38 14 0.10
39 43 0.30
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (35 bp):
GTAAAAATGAAGTCACGATAGTAAATTAGCGAACT
Found at i:19818885 original size:75 final size:74
Alignment explanation
Indices: 19818745--19818968 Score: 220
Period size: 75 Copynumber: 3.0 Consensus size: 74
19818735 GTGTTACACA
* * * * * *
19818745 GTAAAAATGACAGACGCAATAGTAAATCAGCGAACTGCTAGAAAATTGAACGTCGTGATAAAAAA
1 GTAAAAATGATAGTCAC-ATAGTAAATCAGCGAACTGTTAGAAAATCGAACGTCATGATAAAAAA
*
19818810 TTAGCGAATT
65 TTAGCGAACT
* * **
19818820 GTAAAAATGATAGTCACGATAGTAAATCAGCGAACTGTTAGGAAATCGAAGGTCATGATCGAAAA
1 GTAAAAATGATAGTCAC-ATAGTAAATCAGCGAACTGTTAGAAAATCGAACGTCATGATAAAAAA
*
19818885 TTAGCGGACT
65 TTAGCGAACT
* * * * ** **
19818895 GTAAAAATGATAGTTACACTAGTAAATAAGCAAACTG-TA-AAAAT-GAAAGTCGCGATAGTAAA
1 GTAAAAATGATAGTCACA-TAGTAAATCAGCGAACTGTTAGAAAATCGAACGTCATGATAAAAAA
19818957 TTAGCGAACT
65 TTAGCGAACT
19818967 GT
1 GT
19818969 TAGAAAATCA
Statistics
Matches: 125, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
72 24 0.19
73 4 0.03
74 3 0.02
75 94 0.75
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (74 bp):
GTAAAAATGATAGTCACATAGTAAATCAGCGAACTGTTAGAAAATCGAACGTCATGATAAAAAAT
TAGCGAACT
Found at i:19819107 original size:75 final size:75
Alignment explanation
Indices: 19818931--19819269 Score: 294
Period size: 75 Copynumber: 4.5 Consensus size: 75
19818921 TAAGCAAACT
* * * * * * *
19818931 GTAAAAATGAAAGTCGCGATAGTAAATTAGCGAACTGTTAGAAAATCAAAGGTAAGGTGGCGATA
1 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACTATTAGAAAA--ATA---AAGGTCGCAATA
* * *
19818996 ATAAATCAATGGACC
61 GTAAATCAACGTACC
19819011 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACTATTAGAAAAATAAAGGTCGCAATAGTAAA
1 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACTATTAGAAAAATAAAGGTCGCAATAGTAAA
*
19819076 TCCACGTACC
66 TCAACGTACC
* * ** * *
19819086 GTAAAAATGAAAGTTGCAATAGTAAATCAG-TTA--ATT-GTAAAAATGACA-TTCGCAATAGTA
1 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACTATTAG-AAAAAT-AAAGGTCGCAATAGTA
*
19819146 AATCCACGTACC
64 AATCAACGTACC
* * * * * * * * *
19819158 ATAAAAATGACAGTCGAAATAATAAATCAGCAAACTGTTAGAAAACTGAAGGTCGCGATACTAAA
1 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACTATTAGAAAAATAAAGGTCGCAATAGTAAA
*
19819223 TCAATAG-ACC
66 TCAA-CGTACC
*
19819233 GTAAAAATGACAGTCTCGAATAGTAAATCAGCGAACT
1 GTAAAAATGACAGTCGC-AATAGTAAATCAGCGAACT
19819270 GTAAAAATGA
Statistics
Matches: 212, Mismatches: 38, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
71 1 0.00
72 57 0.27
73 3 0.01
74 2 0.01
75 87 0.41
76 19 0.09
78 2 0.01
80 41 0.19
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (75 bp):
GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACTATTAGAAAAATAAAGGTCGCAATAGTAAA
TCAACGTACC
Found at i:19819201 original size:147 final size:148
Alignment explanation
Indices: 19819012--19819296 Score: 396
Period size: 147 Copynumber: 1.9 Consensus size: 148
19819002 CAATGGACCG
* * * *
19819012 TAAAAATGACAGTCGCAATAGTAAATCAGCGAACTATTAGAAAAATAAAGGTCGCAATAGTAAAT
1 TAAAAATGACAGTCGAAATAATAAATCAGCAAACTATTAGAAAAATAAAGGTCGCAATACTAAAT
* * ** * *
19819077 CCA-CGTACCGTAAAAATGAAAGT-T-GCAATAGTAAATCAGTTAATTGTAAAAATGACATTCGC
66 CAATAG-ACCGTAAAAATGAAAGTCTCG-AATAGTAAATCAGCGAACTGTAAAAATGACAGTCGC
19819139 AATAGTAAATCCACGTACCA
129 AATAGTAAATCCACGTACCA
* * * *
19819159 TAAAAATGACAGTCGAAATAATAAATCAGCAAACTGTTAGAAAACTGAAGGTCGCGATACTAAAT
1 TAAAAATGACAGTCGAAATAATAAATCAGCAAACTATTAGAAAAATAAAGGTCGCAATACTAAAT
*
19819224 CAATAGACCGTAAAAATGACAGTCTCGAATAGTAAATCAGCGAACTGTAAAAATGACAGTCGCAA
66 CAATAGACCGTAAAAATGAAAGTCTCGAATAGTAAATCAGCGAACTGTAAAAATGACAGTCGCAA
19819289 TAGTAAAT
131 TAGTAAAT
19819297 TAGCAAACTG
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
147 75 0.62
148 44 0.37
149 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.22
Consensus pattern (148 bp):
TAAAAATGACAGTCGAAATAATAAATCAGCAAACTATTAGAAAAATAAAGGTCGCAATACTAAAT
CAATAGACCGTAAAAATGAAAGTCTCGAATAGTAAATCAGCGAACTGTAAAAATGACAGTCGCAA
TAGTAAATCCACGTACCA
Found at i:19819306 original size:36 final size:36
Alignment explanation
Indices: 19819011--19819307 Score: 235
Period size: 36 Copynumber: 8.1 Consensus size: 36
19819001 TCAATGGACC
19819011 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACT
1 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACT
* * * *
19819047 ATTAGAAAAAT-AAAGGTCGCAATAGTAAATCCA-CGTACC
1 -GT--AAAAATGACA-GTCGCAATAGTAAAT-CAGCGAACT
* * ** *
19819086 GTAAAAATGAAAGTTGCAATAGTAAATCAGTTAATT
1 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACT
* * *
19819122 GTAAAAATGACATTCGCAATAGTAAATCCA-CGTACC
1 GTAAAAATGACAGTCGCAATAGTAAAT-CAGCGAACT
* * * *
19819158 ATAAAAATGACAGTCGAAATAATAAATCAGCAAACT
1 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACT
* * ** *
19819194 GTTAGAAAACTGA-AGGTCGCGATACTAAATCA-ATAGACC
1 G-TA-AAAA-TGACA-GTCGCAATAGTAAATCAGCGA-ACT
*
19819233 GTAAAAATGACAGTCTCGAATAGTAAATCAGCGAACT
1 GTAAAAATGACAGTCGC-AATAGTAAATCAGCGAACT
* *
19819270 GTAAAAATGACAGTCGCAATAGTAAATTAGCAAACT
1 GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACT
19819306 GT
1 GT
19819308 TGGAAAACCG
Statistics
Matches: 202, Mismatches: 42, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
35 4 0.02
36 98 0.49
37 41 0.20
38 12 0.06
39 45 0.22
40 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.22
Consensus pattern (36 bp):
GTAAAAATGACAGTCGCAATAGTAAATCAGCGAACT
Found at i:19820188 original size:62 final size:59
Alignment explanation
Indices: 19820076--19820268 Score: 165
Period size: 62 Copynumber: 3.1 Consensus size: 59
19820066 ATCACTTTAA
* * *
19820076 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
19820135 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTTAATTTAATATTAAGATAATC
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAACATTAAATTAAATTTAATATT---A-AAT-
19820200 ACTTT
58 -C--T
* * ** *
19820205 AATATTAAATTAATAAAATAC-TATTAAGATAAGTATTAAATTTAATTTAATATTAAATC-
1 --TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
19820264 TATTA
1 TATTA
19820269 CAAAAATATT
Statistics
Matches: 111, Mismatches: 10, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
57 5 0.05
59 20 0.18
61 1 0.01
62 28 0.25
64 3 0.03
65 2 0.02
66 3 0.03
68 28 0.25
69 1 0.01
70 1 0.01
71 2 0.02
72 17 0.15
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:19820231 original size:25 final size:25
Alignment explanation
Indices: 19820177--19820231 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
19820167 AAACATTAAA
*
19820177 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
19820202 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
19820226 TATTAA
1 T-TTAA
19820232 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:19820277 original size:68 final size:71
Alignment explanation
Indices: 19820135--19820279 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 71
19820125 TATTAAATCT
* *
19820135 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTTAATTTAATATTAAGATAATC
1 TATTAAATTAATAAAATATCTATCTA-AAGATAAACATTAAATTTAATTTAATATTAAGATAATC
***
19820200 ACTTTAA
65 ACAAAAA
** * *
19820207 TATTAAATTAATAAAATA-CTAT-T-AAGATAAGTATTAAATTTAATTTAATATTAA-ATCTATT
1 TATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTTAATTTAATATTAAGAT-AATC
19820268 ACAAAAA
65 ACAAAAA
19820275 TATTA
1 TATTA
19820280 TTTTTGGCAG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
67 2 0.03
68 40 0.63
70 1 0.02
71 3 0.05
72 17 0.27
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (71 bp):
TATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTTAATTTAATATTAAGATAATCA
CAAAAA
Found at i:19827460 original size:102 final size:102
Alignment explanation
Indices: 19827330--19827528 Score: 364
Period size: 102 Copynumber: 2.0 Consensus size: 102
19827320 GTCTCTTTAT
19827330 TTTTCTTGAAAATGTCCTCTTTTCGACATTCCACCCAAATCCAAGTAACATAAATACCAAGGATC
1 TTTTCTTGAAAATGTCCTCTTTTCGACATTCCACCCAAATCCAAGTAACATAAATACCAAGGATC
19827395 AGAGTA-CTTTTGGCCCTCAAATTGAGCAATAATAACA
66 AGAG-AGCTTTTGGCCCTCAAATTGAGCAATAATAACA
* *
19827432 TTTTCTTGAAAATGTCCTCTTTTTGACATTCCACCCAAATCCAAGTAACATAAATGCCAAGGATC
1 TTTTCTTGAAAATGTCCTCTTTTCGACATTCCACCCAAATCCAAGTAACATAAATACCAAGGATC
19827497 AGAGAGCTTTTGGCCCTCAAATTGAGCAATAA
66 AGAGAGCTTTTGGCCCTCAAATTGAGCAATAA
19827529 CAGCATCAAG
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
101 1 0.01
102 93 0.99
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (102 bp):
TTTTCTTGAAAATGTCCTCTTTTCGACATTCCACCCAAATCCAAGTAACATAAATACCAAGGATC
AGAGAGCTTTTGGCCCTCAAATTGAGCAATAATAACA
Found at i:19828256 original size:2 final size:2
Alignment explanation
Indices: 19828249--19828280 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19828239 TAGTTAGGAC
19828249 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
19828281 CTTCATTGAA
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:19829666 original size:17 final size:18
Alignment explanation
Indices: 19829641--19829674 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19829631 TTGGTTTTTG
19829641 TATAATTTTTTA-ATAAA
1 TATAATTTTTTACATAAA
*
19829658 TATATTTTTTTACATAA
1 TATAATTTTTTACATAA
19829675 TTTTTTGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATAATTTTTTACATAAA
Found at i:19829834 original size:26 final size:26
Alignment explanation
Indices: 19829774--19829837 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
19829764 TTTGGCAATA
*
19829774 CTTTTAAAAAGTGATTTTGAAAAGTG
1 CTTTTGAAAAGTGATTTTGAAAAGTG
** * *
19829800 CCGTGGAAAAGT-ACTTTTGAGAAGTG
1 CTTTTGAAAAGTGA-TTTTGAAAAGTG
19829826 CTTTTGAAAAGT
1 CTTTTGAAAAGT
19829838 TTAGTTTAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.34
Consensus pattern (26 bp):
CTTTTGAAAAGTGATTTTGAAAAGTG
Found at i:19830755 original size:16 final size:18
Alignment explanation
Indices: 19830722--19830760 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
19830712 TGTATTTAAA
19830722 TTAAAAATATATAAATTT
1 TTAAAAATATATAAATTT
19830740 TTAAAAA-ATA-AAATTT
1 TTAAAAATATATAAATTT
*
19830756 ATAAA
1 TTAAA
19830761 TTAATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 3 0.15
18 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAAAATATATAAATTT
Found at i:19830768 original size:24 final size:24
Alignment explanation
Indices: 19830725--19830770 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
19830715 ATTTAAATTA
**
19830725 AAAATATATAAATTTTTAAAAAAT
1 AAAATATATAAATTAATAAAAAAT
*
19830749 AAAATTTATAAATTAATAAAAA
1 AAAATATATAAATTAATAAAAA
19830771 GTATAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATATATAAATTAATAAAAAAT
Found at i:19830906 original size:15 final size:16
Alignment explanation
Indices: 19830881--19830920 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
19830871 TTGATAAACT
*
19830881 AAAAAATTAAGTGTTG
1 AAAAAATTAAGTGCTG
19830897 AAAAAA-TAAGTGCTG
1 AAAAAATTAAGTGCTG
19830912 -AAAAATTAA
1 AAAAAATTAA
19830921 TTATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 11 0.50
16 6 0.27
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (16 bp):
AAAAAATTAAGTGCTG
Found at i:19831396 original size:14 final size:15
Alignment explanation
Indices: 19831374--19831414 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
19831364 ATGCTTTTTG
*
19831374 TATATTTTTA-ATTA
1 TATAATTTTATATTA
*
19831388 TATAATTTTATATTT
1 TATAATTTTATATTA
19831403 TAT-ATTTTATAT
1 TATAATTTTATAT
19831415 ATCTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATAATTTTATATTA
Found at i:19832830 original size:14 final size:14
Alignment explanation
Indices: 19832765--19832832 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
19832755 TGCCCTGCCG
*
19832765 TTAGGGTTTTGGGT
1 TTAGGGTTTTAGGT
*
19832779 TTAAGGG--TTAGGG
1 TT-AGGGTTTTAGGT
*
19832792 TTAGGG-TTAAGGTT
1 TTAGGGTTTTAGG-T
*
19832806 TTGGGGTTTTTAGGT
1 TTAGGG-TTTTAGGT
19832821 TTAGGGTTTTAG
1 TTAGGGTTTTAG
19832833 AGAAATAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 4 0.10
13 10 0.24
14 13 0.31
15 10 0.24
16 5 0.12
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.46
Consensus pattern (14 bp):
TTAGGGTTTTAGGT
Found at i:19834649 original size:535 final size:535
Alignment explanation
Indices: 19833640--19834714 Score: 1900
Period size: 535 Copynumber: 2.0 Consensus size: 535
19833630 AATGGTGTAG
*
19833640 ACTCATCTCGCTAGTGGAGCACCCTATATTGAGTTATATGTACAATTTACATCGCCAAATGATGT
1 ACTCATCTCGCTAGTGGAGCACCCTATATTGAGTTATATGTACAATTTACATCGCCAAATAATGT
19833705 ACTTGCAACTGCGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTGATAAA
66 ACTTGCAACTGCGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTGATAAA
* *
19833770 ACACAGAACAGCCCATGTTTGGTAGTGGTATGGAATGCACATCCCCTGCAAGACACTCTGTCGGT
131 ACACAGAACAACCCATGTTTGGTAGCGGTATGGAATGCACATCCCCTGCAAGACACTCTGTCGGT
*
19833835 GGATGGGACATGTACCTCGATGGGTCGATGTTTGATGCTAGAAATACGTACTGGGGAACGGCATC
196 GGATGGGACATGTACCTCGATGGGTCGATGTTTGATGCTAGAAATACGTACTGGGGAACGACATC
19833900 AACTTCTAGTGGTTGGCAATCTACATTCAATTGAGGACGTTATAAAACGCCTAGAAGAAGGGATG
261 AACTTCTAGTGGTTGGCAATCTACATTCAATTGAGGACGTTATAAAACGCCTAGAAGAAGGGATG
*
19833965 ATGTACTCCCTACGACGTCCACCGGTGAGGGGACCTCGTATATTGCAGATGATGGTAGGTTAGAA
326 ATGTACTCCCTACGACGTCCACCGGTGAGGGGACCTCGTACATTGCAGATGATGGTAGGTTAGAA
19834030 GATGACTTCGATGTGGATCTACCTCGAGAGCCCAGGCCCGATGGTGCAGAAGTTGCATTATTTTC
391 GATGACTTCGATGTGGATCTACCTCGAGAGCCCAGGCCCGATGGTGCAGAAGTTGCATTATTTTC
* * *
19834095 TGAATCAAAGCCTATTCCAATCGAACCTGAAGATGTTGAAAAAGGTTTAGATAACAAAGAAAATC
456 TAAACCAAAGCCTATTCCAACCGAACCTGAAGATGTTGAAAAAGGTTTAGATAACAAAGAAAATC
*
19834160 CACGATTCAGGGCAT
521 CACAATTCAGGGCAT
* * *
19834175 ACTCATCTCGCTGGTGGAGCACCCTATATTGAGTTATATGTACAATTTATATCGCCAAATAATTT
1 ACTCATCTCGCTAGTGGAGCACCCTATATTGAGTTATATGTACAATTTACATCGCCAAATAATGT
* * * *
19834240 ACTTGCGATTGTGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTTATAAA
66 ACTTGCAACTGCGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTGATAAA
19834305 ACACAGAACAACCCATGTTTGGTAGCGGTATGGAATGCACATCCCCTGCAAGACACTCTGTCGGT
131 ACACAGAACAACCCATGTTTGGTAGCGGTATGGAATGCACATCCCCTGCAAGACACTCTGTCGGT
*
19834370 GGATGGGACATGTACCTCGGTGGGTCGATGTTTGATGCT-GAAAATACGTACTGGGGAACGACAT
196 GGATGGGACATGTACCTCGATGGGTCGATGTTTGATGCTAG-AAATACGTACTGGGGAACGACAT
* *
19834434 CAACTTCTAGTGGTTGGCAATCTACATTCAATTGGGGACGTTATAAAATGCCTAGAAGAAGGGAT
260 CAACTTCTAGTGGTTGGCAATCTACATTCAATTGAGGACGTTATAAAACGCCTAGAAGAAGGGAT
* *
19834499 GATGTACTCCCTACGACGTCCATCGGTGAGGGGATCTCGTACATTGCAGATGATGGTAGGTTAGA
325 GATGTACTCCCTACGACGTCCACCGGTGAGGGGACCTCGTACATTGCAGATGATGGTAGGTTAGA
*
19834564 AGATGACTTCGATGTGGATCTACCTCGAGAGCCCAGGCCCGATGGTGCAGAAGTTGTATTATTTT
390 AGATGACTTCGATGTGGATCTACCTCGAGAGCCCAGGCCCGATGGTGCAGAAGTTGCATTATTTT
* * * *
19834629 CTAAACCGAAGCCTATTCCAACCGAACCTGAAGATGTTGAAGAGGGTTTAGATGACAAAGAAAAT
455 CTAAACCAAAGCCTATTCCAACCGAACCTGAAGATGTTGAAAAAGGTTTAGATAACAAAGAAAAT
19834694 CCACAATTCAGGGCAT
520 CCACAATTCAGGGCAT
19834710 ACTCA
1 ACTCA
19834715 CCTCCAGCCC
Statistics
Matches: 513, Mismatches: 26, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
534 1 0.00
535 512 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (535 bp):
ACTCATCTCGCTAGTGGAGCACCCTATATTGAGTTATATGTACAATTTACATCGCCAAATAATGT
ACTTGCAACTGCGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTGATAAA
ACACAGAACAACCCATGTTTGGTAGCGGTATGGAATGCACATCCCCTGCAAGACACTCTGTCGGT
GGATGGGACATGTACCTCGATGGGTCGATGTTTGATGCTAGAAATACGTACTGGGGAACGACATC
AACTTCTAGTGGTTGGCAATCTACATTCAATTGAGGACGTTATAAAACGCCTAGAAGAAGGGATG
ATGTACTCCCTACGACGTCCACCGGTGAGGGGACCTCGTACATTGCAGATGATGGTAGGTTAGAA
GATGACTTCGATGTGGATCTACCTCGAGAGCCCAGGCCCGATGGTGCAGAAGTTGCATTATTTTC
TAAACCAAAGCCTATTCCAACCGAACCTGAAGATGTTGAAAAAGGTTTAGATAACAAAGAAAATC
CACAATTCAGGGCAT
Found at i:19837202 original size:21 final size:21
Alignment explanation
Indices: 19837176--19837239 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
19837166 TTTGTCCAAC
*
19837176 TTCCGGCGGGGGTTCTGGTTG
1 TTCCGGCGGGGATTCTGGTTG
* *
19837197 TTCCGGTGGGGATTCTGGTTC
1 TTCCGGCGGGGATTCTGGTTG
* ** *
19837218 CTCCGGTAGGGAATCTGGTTG
1 TTCCGGCGGGGATTCTGGTTG
19837239 T
1 T
19837240 CGGTGTTGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.06, C:0.19, G:0.41, T:0.34
Consensus pattern (21 bp):
TTCCGGCGGGGATTCTGGTTG
Found at i:19837642 original size:30 final size:30
Alignment explanation
Indices: 19837571--19837651 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
19837561 GTTGAACTGT
* * * * *
19837571 TGGGTCGGGTGACTGTGTCGGTGCTGTTGC
1 TGGGTCGGGTGAATGTATGGGTGCTGATGA
* * *
19837601 TGGGCCTGGTGATTGTATGGGTGCTGATGA
1 TGGGTCGGGTGAATGTATGGGTGCTGATGA
*
19837631 TGGGTCGGGTGAATGTCTGGG
1 TGGGTCGGGTGAATGTATGGG
19837652 CCTCGTTAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.09, C:0.12, G:0.47, T:0.32
Consensus pattern (30 bp):
TGGGTCGGGTGAATGTATGGGTGCTGATGA
Found at i:19839428 original size:10 final size:10
Alignment explanation
Indices: 19839379--19839432 Score: 63
Period size: 11 Copynumber: 5.0 Consensus size: 10
19839369 AAATAGGAAT
19839379 TTGAGAGGAAA
1 TTGAGA-GAAA
*
19839390 TTGAGACAAA
1 TTGAGAGAAA
19839400 TTTGAGAGAATA
1 -TTGAGAGAA-A
19839412 TTAGAGAGAAA
1 TT-GAGAGAAA
19839423 TTGAGAGAAA
1 TTGAGAGAAA
19839433 GGATTAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 11 0.29
11 19 0.50
12 8 0.21
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:19839430 original size:22 final size:21
Alignment explanation
Indices: 19839376--19839432 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
19839366 TTTAAATAGG
19839376 AATTTGAGAGGAAATTGAGACA
1 AATTTGAGA-GAAATTGAGACA
*
19839398 AATTTGAGAGAATATTAGAGAGA
1 AATTTGAGAGAA-ATT-GAGACA
19839421 AA-TTGAGAGAAA
1 AATTTGAGAGAAA
19839433 GGATTAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 4 0.12
22 21 0.66
23 7 0.22
ACGTcount: A:0.49, C:0.02, G:0.26, T:0.23
Consensus pattern (21 bp):
AATTTGAGAGAAATTGAGACA
Found at i:19841600 original size:3 final size:3
Alignment explanation
Indices: 19841594--19841624 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
19841584 TTTGAGAAGA
19841594 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC A
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC A
19841625 TACTATGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:19850034 original size:44 final size:44
Alignment explanation
Indices: 19849971--19850055 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
19849961 TTTTTGAGTC
*
19849971 TACAAACTTTATCTTCCATACTAGGTGCCACAAATCCTGAAGGT
1 TACAAACTTTATCTTCCATACCAGGTGCCACAAATCCTGAAGGT
19850015 TACAAACTTTATCTTCCATACCAGGTGCCACAAATCCTGAA
1 TACAAACTTTATCTTCCATACCAGGTGCCACAAATCCTGAA
19850056 TGTTGCTCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (44 bp):
TACAAACTTTATCTTCCATACCAGGTGCCACAAATCCTGAAGGT
Found at i:19854288 original size:20 final size:19
Alignment explanation
Indices: 19854252--19854290 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
19854242 AATTTCAAAA
*
19854252 TTATAAAATTTGGAATTTT
1 TTATAAAATTTGAAATTTT
*
19854271 TTATAAATATTTTAAATTTT
1 TTATAAA-ATTTGAAATTTT
19854291 AAAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTATAAAATTTGAAATTTT
Found at i:19854330 original size:20 final size:20
Alignment explanation
Indices: 19854269--19854322 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
19854259 ATTTGGAATT
*
19854269 TTTTATAAA-TATTTT-AAA
1 TTTTAAAAATTATTTTAAAA
19854287 TTTTAAAAATTATTTTAAAA
1 TTTTAAAAATTATTTTAAAA
*
19854307 TTTTGAAAATTATTTT
1 TTTTAAAAATTATTTT
19854323 GTAATTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.25
19 6 0.19
20 18 0.56
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTAAAAATTATTTTAAAA
Found at i:19858468 original size:18 final size:18
Alignment explanation
Indices: 19858445--19858484 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
19858435 TATAGATACT
*
19858445 TTTGCTTTGT-ATTAATAA
1 TTTGCTTGGTGATTAA-AA
19858463 TTTGCTTGGTGATTAAAA
1 TTTGCTTGGTGATTAAAA
19858481 TTTG
1 TTTG
19858485 AGGAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.25, C:0.05, G:0.17, T:0.53
Consensus pattern (18 bp):
TTTGCTTGGTGATTAAAA
Found at i:19867324 original size:18 final size:18
Alignment explanation
Indices: 19867301--19867344 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
19867291 AGTTAATGAC
*
19867301 TTGAAATGGCAAATGATA
1 TTGAAATGACAAATGATA
* *
19867319 TTGAAATAACAAATGTTA
1 TTGAAATGACAAATGATA
19867337 -TGAAATGA
1 TTGAAATGA
19867345 AATTAAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.30
Consensus pattern (18 bp):
TTGAAATGACAAATGATA
Found at i:19876694 original size:9 final size:9
Alignment explanation
Indices: 19876680--19876705 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19876670 GGGGAGGCAA
19876680 GAAGAAAGG
1 GAAGAAAGG
19876689 GAAGAAAGG
1 GAAGAAAGG
19876698 GAAGAAAG
1 GAAGAAAG
19876706 TTAGTCCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (9 bp):
GAAGAAAGG
Found at i:19878347 original size:29 final size:29
Alignment explanation
Indices: 19878288--19878349 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
19878278 CATTACTTTA
* * *
19878288 AAATTATAAATTTCTAATTTTTATAATTC
1 AAATAATAAATTTCTAATTTTTACAACTC
*
19878317 AAATAATAATTTTCTAACTTTTT-CAACTC
1 AAATAATAAATTTCTAA-TTTTTACAACTC
19878346 AAAT
1 AAAT
19878350 CCCATTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATAATAAATTTCTAATTTTTACAACTC
Found at i:19885602 original size:21 final size:21
Alignment explanation
Indices: 19885578--19885630 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
19885568 CATTATTTCT
*
19885578 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
19885599 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
19885620 AATCTCACCGC
1 AATCTCACCGC
19885631 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.40, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:19885725 original size:28 final size:28
Alignment explanation
Indices: 19885685--19885752 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
19885675 CAAACTAGCC
*
19885685 CTAAGTGTGCGAGTTT-AATGGTAAAGCA
1 CTAAGTGTGCGAGTTTGAATAGTAAA-CA
* *
19885713 CTAAGTGTGCGAGTTTGATTATTAAACA
1 CTAAGTGTGCGAGTTTGAATAGTAAACA
19885741 CTAAGTGTGCGA
1 CTAAGTGTGCGA
19885753 ACTTATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 30 0.83
29 6 0.17
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGAATAGTAAACA
Found at i:19887773 original size:27 final size:27
Alignment explanation
Indices: 19887690--19887787 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
19887680 ATTCAGATGA
* *
19887690 TTGCCACAAAGGCTAATCTTTTTATTTT
1 TTGCCACAAAGGCT-TTCTTTTTATTGT
* *
19887718 TTGCCACAAAGGCTTTCTTTTCATGGT
1 TTGCCACAAAGGCTTTCTTTTTATTGT
*
19887745 TTGCCACCAAGGCTTTCTTTTTATTGT
1 TTGCCACAAAGGCTTTCTTTTTATTGT
* * *
19887772 TTACCCCAAAGACTTT
1 TTGCCACAAAGGCTTT
19887788 TTTACTGACG
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
27 45 0.76
28 14 0.24
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.43
Consensus pattern (27 bp):
TTGCCACAAAGGCTTTCTTTTTATTGT
Found at i:19890263 original size:25 final size:25
Alignment explanation
Indices: 19890235--19890307 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
19890225 ACAAATTTTC
*
19890235 TCAAAATTTTACTGGGGTAAAATCG
1 TCAAAATTTTACCGGGGTAAAATCG
* *
19890260 TCAAAATTTTACCGGGTTAAATTCG
1 TCAAAATTTTACCGGGGTAAAATCG
* *
19890285 TCAAAATTTTACCAGGTTAAAAT
1 TCAAAATTTTACCGGGGTAAAAT
19890308 TGGGGTGAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (25 bp):
TCAAAATTTTACCGGGGTAAAATCG
Found at i:19898270 original size:20 final size:20
Alignment explanation
Indices: 19898245--19898282 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19898235 TGCGTTAATG
19898245 ATTTAACATATATAATTATT
1 ATTTAACATATATAATTATT
*
19898265 ATTTAATATATATAATTA
1 ATTTAACATATATAATTA
19898283 ATATAATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTAACATATATAATTATT
Found at i:19898289 original size:18 final size:19
Alignment explanation
Indices: 19898252--19898289 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
19898242 ATGATTTAAC
*
19898252 ATATATAATTATTATTTAAT
1 ATATATAATTA-TATATAAT
19898272 ATATATAATTA-ATATAAT
1 ATATATAATTATATATAAT
19898290 TACTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATAATTATATATAAT
Found at i:19902007 original size:23 final size:24
Alignment explanation
Indices: 19901976--19902020 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
19901966 ATATCCCCAC
*
19901976 ATGGAGTGTAG-GGTTGGATGGAG
1 ATGGAGTGTAGAGGCTGGATGGAG
*
19901999 ATGGTGTGTAGAGGCTGGATGG
1 ATGGAGTGTAGAGGCTGGATGG
19902021 GTAGGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.02, G:0.51, T:0.27
Consensus pattern (24 bp):
ATGGAGTGTAGAGGCTGGATGGAG
Found at i:19903689 original size:21 final size:21
Alignment explanation
Indices: 19903665--19903705 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19903655 GAATTAAATG
*
19903665 AATATTCATTTGAAGAATTAT
1 AATATGCATTTGAAGAATTAT
* *
19903686 AATATGCCTTTGATGAATTA
1 AATATGCATTTGAAGAATTA
19903706 GGTGTAGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (21 bp):
AATATGCATTTGAAGAATTAT
Found at i:19905704 original size:27 final size:27
Alignment explanation
Indices: 19905674--19905971 Score: 361
Period size: 27 Copynumber: 11.1 Consensus size: 27
19905664 TCGATATCTG
*
19905674 GACCGTAATGCCCCTGTAGGATAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
*
19905701 GACCGTAATGCCCTTGTAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
** * * *
19905728 GGTCGTAATACCTCTGTAAGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
*
19905755 GACCGTAATACCCCTGTAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
* * *
19905782 GACCGCAATACCCGTGTAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
* *
19905809 AACCGTAATGCCCCTATAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
* *
19905836 GGCCGTAATACCCCTGTAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
**
19905863 GGTCGTAATGCCCCTGTAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
*
19905890 GACCGTACTGCCCCTGTAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
* *
19905917 AACCAG-AATACCCCTGTAGGGTAAAAT
1 GACC-GTAATGCCCCTGTAGGGTAAAAT
*
19905944 GACCATAATG-CCCTGGT-GGGT-AAAT
1 GACCGTAATGCCCCT-GTAGGGTAAAAT
19905969 GAC
1 GAC
19905972 TATTTTTTCC
Statistics
Matches: 234, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
25 7 0.03
26 8 0.03
27 218 0.93
28 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (27 bp):
GACCGTAATGCCCCTGTAGGGTAAAAT
Found at i:19906266 original size:32 final size:32
Alignment explanation
Indices: 19906225--19906436 Score: 209
Period size: 32 Copynumber: 6.6 Consensus size: 32
19906215 GAGATGCTAT
19906225 TGATGGCTTTGTGCCGATCATAGT-ACCGTTAC
1 TGATGGCTTTGTGCCGATCATA-TCACCGTTAC
* * *
19906257 TGATGGCTTTGTACTGATCATATTACCGTTA-
1 TGATGGCTTTGTGCCGATCATATCACCGTTAC
* *
19906288 TCGATGG-TTGTGTGCCGATCATTTCACTGTTAC
1 T-GATGGCTT-TGTGCCGATCATATCACCGTTAC
* * * *
19906321 TAATGG-TTGTGTGCCAATCATATCACTGCTAC
1 TGATGGCTT-TGTGCCGATCATATCACCGTTAC
* * *
19906353 TGATGGCTTTGTGTCGATCATGTTACCGTTAC
1 TGATGGCTTTGTGCCGATCATATCACCGTTAC
* *
19906385 TGATGG-TTGTGTGCCGATCATATCACTGCTAC
1 TGATGGCTT-TGTGCCGATCATATCACCGTTAC
*
19906417 TGATGGCTTTGTGCCAATCA
1 TGATGGCTTTGTGCCGATCA
19906437 CATTACTATA
Statistics
Matches: 149, Mismatches: 24, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
31 6 0.04
32 138 0.93
33 5 0.03
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATCACCGTTAC
Found at i:19906398 original size:96 final size:96
Alignment explanation
Indices: 19906227--19906436 Score: 284
Period size: 96 Copynumber: 2.2 Consensus size: 96
19906217 GATGCTATTG
* * *
19906227 ATGGCTTTGTGCCGATCATAGT-ACCGTTACTGATGGCTTTGTACTGATCATATTACCGTTATCG
1 ATGGCTTTGTGCCAATCATA-TCACTGCTACTGATGGCTTTGTACTGATCATATTACCGTTATCG
* *
19906291 ATGGTTGTGTGCCGATCATTTCACTGTTACTA
65 ATGGTTGTGTGCCGATCATATCACTGCTACTA
* *
19906323 ATGG-TTGTGTGCCAATCATATCACTGCTACTGATGGCTTTGT-GTCGATCATGTTACCGTTA-C
1 ATGGCTT-TGTGCCAATCATATCACTGCTACTGATGGCTTTGTACT-GATCATATTACCGTTATC
*
19906385 TGATGGTTGTGTGCCGATCATATCACTGCTACTG
64 -GATGGTTGTGTGCCGATCATATCACTGCTACTA
19906419 ATGGCTTTGTGCCAATCA
1 ATGGCTTTGTGCCAATCA
19906437 CATTACTATA
Statistics
Matches: 101, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
95 5 0.05
96 94 0.93
97 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (96 bp):
ATGGCTTTGTGCCAATCATATCACTGCTACTGATGGCTTTGTACTGATCATATTACCGTTATCGA
TGGTTGTGTGCCGATCATATCACTGCTACTA
Found at i:19906473 original size:22 final size:21
Alignment explanation
Indices: 19906448--19906512 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
19906438 ATTACTATAC
*
19906448 TTATGGCTTGTAGCCATTCTGT
1 TTATAGCTT-TAGCCATTCTGT
* *
19906470 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTT-TAGCCATTCTGT
*
19906492 TTACAGCTCTTAGCCATTCTG
1 TTATAGCT-TTAGCCATTCTG
19906513 CTACTGGCAG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (21 bp):
TTATAGCTTTAGCCATTCTGT
Found at i:19919457 original size:50 final size:50
Alignment explanation
Indices: 19919341--19919530 Score: 256
Period size: 50 Copynumber: 3.8 Consensus size: 50
19919331 GATAATAACA
* * ** * * *
19919341 TGCCAAAGCCATGTCCCATACATGGTCTTACATGGGATGTTTCATGT-AT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * * *
19919390 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
19919440 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
19919490 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
19919531 ATCCTCTTAA
Statistics
Matches: 123, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 39 0.32
50 84 0.68
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:19932605 original size:11 final size:11
Alignment explanation
Indices: 19932591--19932631 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
19932581 TTTATTTTTT
19932591 TATTTTTAAAA
1 TATTTTTAAAA
19932602 TATTTTTAAAA
1 TATTTTTAAAA
*
19932613 TACTTTTAAAA
1 TATTTTTAAAA
19932624 TACTTTTT
1 TA-TTTTT
19932632 TTATTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 23 0.85
12 4 0.15
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:19934152 original size:21 final size:19
Alignment explanation
Indices: 19934118--19934161 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
19934108 TATTACACAC
19934118 TTTTTTATTGTTT-AATTCA
1 TTTTTTATTGTTTAAATT-A
19934137 TTTTTTATTGAATTTAAATTA
1 TTTTTTATTG--TTTAAATTA
19934158 TTTT
1 TTTT
19934162 AGCACCACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTTATTGTTTAAATTA
Found at i:19937215 original size:22 final size:21
Alignment explanation
Indices: 19937190--19937234 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
19937180 AGGACATGAT
19937190 TTTAAAAAAAATTAAAAATTTA
1 TTTAAAAAAAATT-AAAATTTA
* *
19937212 TTTAGAAAATATTAAAATTTA
1 TTTAAAAAAAATTAAAATTTA
19937233 TT
1 TT
19937235 AGAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTAAAAAAAATTAAAATTTA
Found at i:19937622 original size:31 final size:31
Alignment explanation
Indices: 19937572--19937634 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
19937562 TTTTAAAAAT
*
19937572 AATAATTGCTTATAATTTTTAATAATT-TTTA
1 AATAATTGCCTATAATTTTT-ATAATTATTTA
* *
19937603 AATAATTTCCTATATTTTTTATAATTATTTA
1 AATAATTGCCTATAATTTTTATAATTATTTA
19937634 A
1 A
19937635 GAAACCACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (31 bp):
AATAATTGCCTATAATTTTTATAATTATTTA
Found at i:19939538 original size:21 final size:22
Alignment explanation
Indices: 19939499--19939539 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19939489 GCAAATCTGG
19939499 GATTAAAATTAACTTTTTAAGA
1 GATTAAAATTAACTTTTTAAGA
19939521 GATTAAAATTAA-TTTTTAA
1 GATTAAAATTAACTTTTTAA
19939540 TAAAAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
GATTAAAATTAACTTTTTAAGA
Found at i:19939680 original size:73 final size:70
Alignment explanation
Indices: 19939519--19939697 Score: 179
Period size: 71 Copynumber: 2.6 Consensus size: 70
19939509 AACTTTTTAA
* * **
19939519 GAGATTAAAATT--AATTTTTAATAAAAATAGTAAAGAAGTGAGTTATGGAAGTACTCTCTAGTC
1 GAGATTAAAATTAAAATTTTTAATTAAAATAGTGAAGAAGTGAACTATGGAAGTACTCTCTAGTC
19939582 AATGT
66 AATGT
* ** * *
19939587 -AGGATTTAAATTAATTTTTTTCAATTAAAATAGTGAAGAAGTGAACTA-GGAGAGTATTTTCTT
1 GA-GATTAAAATTAAAATTTTT-AATTAAAATAGTGAAGAAGTGAACTATGGA-AGTACTCTC-T
*
19939650 TGATCAATGT
62 AG-TCAATGT
*
19939660 GAGATTAAAATTAAAATTTTTAA-TGAAATAGTGAAGAA
1 GAGATTAAAATTAAAATTTTTAATTAAAATAGTGAAGAA
19939698 ATTGTCACTT
Statistics
Matches: 89, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
67 1 0.01
68 9 0.10
70 8 0.09
71 43 0.48
72 4 0.04
73 23 0.26
74 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.36
Consensus pattern (70 bp):
GAGATTAAAATTAAAATTTTTAATTAAAATAGTGAAGAAGTGAACTATGGAAGTACTCTCTAGTC
AATGT
Found at i:19939847 original size:87 final size:86
Alignment explanation
Indices: 19939676--19939848 Score: 224
Period size: 88 Copynumber: 2.0 Consensus size: 86
19939666 AAAATTAAAA
* * *
19939676 TTTTTAATGAAATAGTGAAGAAATTGTCACTTATTTATAAGGTTAGTGTGAGATATGATAGTGTT
1 TTTTTAATGAAATAGTGAAGAAATTGACACTTATTTATAAGGTAAGTGCGAGATATGA-AGTGTT
* **
19939741 CTCTAGTCAATGTGGGATTAAC
65 CTCTAGCCAATGTAAGATTAAC
* *
19939763 TTTTTAATGAAAATAGTGAAGAAATTGACACTTCTTTAT-AGAGTAAGTGCGAGCATGTG-AGTG
1 TTTTTAATG-AAATAGTGAAGAAATTGACACTTATTTATAAG-GTAAGTGCGAG-ATATGAAGTG
19939826 TTCTCTAGCCAATGTAAGATTAA
63 TTCTCTAGCCAATGTAAGATTAA
19939849 AATTAACCTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
87 35 0.47
88 36 0.48
89 4 0.05
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (86 bp):
TTTTTAATGAAATAGTGAAGAAATTGACACTTATTTATAAGGTAAGTGCGAGATATGAAGTGTTC
TCTAGCCAATGTAAGATTAAC
Found at i:19939869 original size:19 final size:20
Alignment explanation
Indices: 19939840--19939895 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
19939830 CTAGCCAATG
19939840 TAAGATTAAAATTAACCTTT
1 TAAGATTAAAATTAACCTTT
*
19939860 TAAG-TTAAAATTAACTTTT
1 TAAGATTAAAATTAACCTTT
19939879 TAAAGGATTAAAATTAA
1 T-AA-GATTAAAATTAA
19939896 TTTTTAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 15 0.47
20 6 0.19
21 1 0.03
22 10 0.31
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39
Consensus pattern (20 bp):
TAAGATTAAAATTAACCTTT
Found at i:19940306 original size:15 final size:15
Alignment explanation
Indices: 19940286--19940326 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
19940276 TATATAGGTG
19940286 AATTGAATTTTGAAT
1 AATTGAATTTTGAAT
19940301 AATTGAATTTTGAAT
1 AATTGAATTTTGAAT
*
19940316 AAGT-AATTTTG
1 AATTGAATTTTG
19940327 CCGAATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (15 bp):
AATTGAATTTTGAAT
Found at i:19946498 original size:43 final size:41
Alignment explanation
Indices: 19946438--19946594 Score: 192
Period size: 43 Copynumber: 3.7 Consensus size: 41
19946428 TATGTATTTT
*
19946438 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGTATA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCG-ATTGTG-ATA
* *
19946481 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATT-TGATT
1 CGTGTAAGACCACGTCTGGGACATTGGCATCG-ATTGTGATA
* *
19946522 TGTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TGTGA-TA
*
19946565 CATGTAAGACCACGTCTGGGACATTGGCAT
1 CGTGTAAGACCACGTCTGGGACATTGGCAT
19946595 TGTACGAGCC
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
40 2 0.02
41 31 0.32
42 5 0.05
43 59 0.60
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (41 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATTGTGATA
Found at i:19946540 original size:84 final size:84
Alignment explanation
Indices: 19946439--19946594 Score: 230
Period size: 84 Copynumber: 1.9 Consensus size: 84
19946429 ATGTATTTTC
* *
19946439 GTGTAAGACCACGTCTGGGAC-GTTGGCATCGA-ATTGTG-TATACGTGTAAGACCATGTCTGGG
1 GTGTAAGACCACGTCTGGGACAG-TGGCATCGATA-TGTGAT-TACATGTAAGACCACGTCTGGG
19946501 ACATTGGCATCGTATTTGATTT
63 ACATTGGCATCGTATTTGATTT
19946523 GTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGAC
1 GTGTAAGACCAC-GTCTGGGACAGTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGAC
19946587 ATTGGCAT
65 ATTGGCAT
19946595 TGTACGAGCC
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
83 1 0.02
84 62 0.94
85 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (84 bp):
GTGTAAGACCACGTCTGGGACAGTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:19949894 original size:67 final size:68
Alignment explanation
Indices: 19949815--19949991 Score: 191
Period size: 67 Copynumber: 2.6 Consensus size: 68
19949805 TTCTCTAGCT
* * *
19949815 AATGTGGGATTAAAAATAA-TTTTTAATGAAATAGTGAAGAAGTGA-ACTATGAGAGTATTCTCA
1 AATGTGAGATTAAAATTAACTTTTTAATGAAATAGTGAAGAAGTGAGA-TATGAGAGTATTATCA
19949878 AGTC
65 AGTC
* * *
19949882 AATGTGAGATTAAAATTAACTTTTCAATGAAAATAGTG-A-AAGTTAGATATGAGAGTATTATCT
1 AATGTGAGATTAAAATTAACTTTTTAATG-AAATAGTGAAGAAGTGAGATATGAGAGTATTATCA
19949945 AGTC
65 AGTC
** * * * *
19949949 GGTGTGTGACTAAAATTAACTGTTTAATAAAAATAGTGAAGAA
1 AATGTGAGATTAAAATTAACTTTTTAAT-GAAATAGTGAAGAA
19949992 ATTGTTACTT
Statistics
Matches: 91, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
67 70 0.77
68 11 0.12
69 10 0.11
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (68 bp):
AATGTGAGATTAAAATTAACTTTTTAATGAAATAGTGAAGAAGTGAGATATGAGAGTATTATCAA
GTC
Found at i:19951879 original size:17 final size:18
Alignment explanation
Indices: 19951855--19951898 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
19951845 TAAAAAAAAT
19951855 TAAT-TTAAAATTTTTAA
1 TAATATTAAAATTTTTAA
*
19951872 -AATATTAAGATTTTTAA
1 TAATATTAAAATTTTTAA
*
19951889 TATTATTAAA
1 TAATATTAAA
19951899 TATACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
18 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATATTAAAATTTTTAA
Found at i:19952131 original size:22 final size:24
Alignment explanation
Indices: 19952106--19952149 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
19952096 TTATTTAGTA
19952106 ATAAAT-TTTTA-TAATATAAAAT
1 ATAAATATTTTAGTAATATAAAAT
*
19952128 ATAAATATTTTAGTAGTATAAA
1 ATAAATATTTTAGTAATATAAA
19952150 TACGGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (24 bp):
ATAAATATTTTAGTAATATAAAAT
Found at i:19952549 original size:6 final size:7
Alignment explanation
Indices: 19952524--19952548 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19952514 AATGGATGCC
19952524 TTTTTCT
1 TTTTTCT
19952531 TTTTTCT
1 TTTTTCT
19952538 TTTTTCT
1 TTTTTCT
19952545 TTTT
1 TTTT
19952549 CCAACGTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:19964752 original size:4 final size:4
Alignment explanation
Indices: 19964743--19964773 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
19964733 AGTTGATCTT
*
19964743 TTTA TTTA TTTA TTTA TTTA TTTA TTCA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
19964774 GAATAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:19965328 original size:22 final size:22
Alignment explanation
Indices: 19965285--19965345 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
19965275 TTTAAAAAAT
19965285 AAATATAGAAATAAATATATAA
1 AAATATAGAAATAAATATATAA
* *
19965307 AAATTTAG-AATATATATAATAATA
1 AAATATAGAAATAAATAT-AT-A-A
*
19965331 AAATATAAAAATAAA
1 AAATATAGAAATAAA
19965346 AATTCATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 8 0.27
22 9 0.30
23 1 0.03
24 7 0.23
25 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (22 bp):
AAATATAGAAATAAATATATAA
Found at i:19965338 original size:13 final size:13
Alignment explanation
Indices: 19965279--19965346 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 13
19965269 TATCAATTTA
19965279 AAAAAT-AAATAT
1 AAAAATAAAATAT
*
19965291 AGAAATAAATATAT
1 AAAAATAAA-ATAT
19965305 AAAAATTTAGAATATAT
1 AAAAA--TA-AA-ATAT
19965322 ATAATAATAAAATAT
1 A-AA-AATAAAATAT
19965337 AAAAATAAAA
1 AAAAATAAAA
19965347 ATTCATTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
12 5 0.11
13 9 0.19
14 10 0.21
15 5 0.11
16 4 0.09
17 10 0.21
18 2 0.04
19 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAAATAAAATAT
Found at i:19965982 original size:22 final size:22
Alignment explanation
Indices: 19965954--19965997 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19965944 ATTTTCTAAC
19965954 AGATTTAATGAATAAATTCAAG
1 AGATTTAATGAATAAATTCAAG
19965976 AGATTTAATGAATAAATTCAAG
1 AGATTTAATGAATAAATTCAAG
19965998 GTTTCAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32
Consensus pattern (22 bp):
AGATTTAATGAATAAATTCAAG
Found at i:19966125 original size:24 final size:24
Alignment explanation
Indices: 19966072--19966125 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
19966062 TTCTACTGAG
* *
19966072 TTAATTTTTTTTAGATAATTATGT
1 TTAATTTTCTTTAAATAATTATGT
*
19966096 TT-ATTTTCTTTAAATTAATT-TTT
1 TTAATTTTCTTTAAA-TAATTATGT
19966119 TTAATTT
1 TTAATTT
19966126 AATGTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (24 bp):
TTAATTTTCTTTAAATAATTATGT
Found at i:19981227 original size:8 final size:8
Alignment explanation
Indices: 19981214--19981238 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19981204 AAATAGCGGA
19981214 AGAAATTG
1 AGAAATTG
19981222 AGAAATTG
1 AGAAATTG
19981230 AGAAATTG
1 AGAAATTG
19981238 A
1 A
19981239 ACACACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AGAAATTG
Found at i:19983778 original size:30 final size:29
Alignment explanation
Indices: 19983729--19983808 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 29
19983719 AGGTAATTTG
*
19983729 ATACATGAAA-TTTGATTTTGTGT-AAT-T
1 ATACATAAAACTTTGATTTTGT-TAAATGT
*
19983756 ATACATATTAAACTTTTATTTTGTTCAAATGT
1 ATACATA--AAACTTTGATTTTGTT-AAATGT
19983788 ATACATAAAACTTTGATTTTG
1 ATACATAAAACTTTGATTTTG
19983809 ATTCAGTTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 6 0.14
29 4 0.09
30 23 0.52
31 3 0.07
32 8 0.18
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (29 bp):
ATACATAAAACTTTGATTTTGTTAAATGT
Found at i:19983823 original size:31 final size:31
Alignment explanation
Indices: 19983739--19983829 Score: 91
Period size: 30 Copynumber: 3.0 Consensus size: 31
19983729 ATACATGAAA
19983739 TTTGATTTTGTGT--AAT-TATACATATTAAAC
1 TTTGATTTTGT-TCAAATGTATACATA-TAAAC
*
19983769 TTTTATTTTGTTCAAATGTATACATA-AAAC
1 TTTGATTTTGTTCAAATGTATACATATAAAC
** *
19983799 TTTGATTTTGATTCAGTTGTATACATTTAAA
1 TTTGATTTTG-TTCAAATGTATACATATAAA
19983830 TAAATGAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 23 0.45
31 16 0.31
32 11 0.22
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (31 bp):
TTTGATTTTGTTCAAATGTATACATATAAAC
Found at i:19984178 original size:25 final size:26
Alignment explanation
Indices: 19984130--19984178 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
19984120 GATTAAATCT
*
19984130 AAATATAAAATAAATAATTAAAATTC
1 AAATATAAAATAAATAACTAAAATTC
19984156 AAATA-AAAATAAAT-ACTAGAAAT
1 AAATATAAAATAAATAACTA-AAAT
19984179 AAATTGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (26 bp):
AAATATAAAATAAATAACTAAAATTC
Found at i:19989561 original size:102 final size:104
Alignment explanation
Indices: 19989383--19989586 Score: 304
Period size: 102 Copynumber: 2.0 Consensus size: 104
19989373 AGGCCATGTC
** *
19989383 ACACGGCCGTGTGCTACACACAACTGAGACACATGCCCGTGTCTCAGGCCGTGTAGCCTCAAAAT
1 ACACGGCCGTGTGCTACACACAACTGAGACACACACCCGTGTCTCAGACCGTGTAGCCTCAAAAT
* *
19989448 GAACCTTAAAACACAAGTTTACCATTTCAAATTGCTTCG
66 AAACCTTAAAACACAAGTTTACCATTCCAAATTGCTTCG
* ** * *
19989487 ACACGGTCGTGTGCTA-A-ACGGCTGAGACACACACTCGTGTCTCAGACCGTGTGGCCTCAAAAT
1 ACACGGCCGTGTGCTACACACAACTGAGACACACACCCGTGTCTCAGACCGTGTAGCCTCAAAAT
19989550 AAACCTTAAAACACAAGTTTACCATTCCAAATTGCTT
66 AAACCTTAAAACACAAGTTTACCATTCCAAATTGCTT
19989587 GGACCTTAAG
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 74 0.82
103 1 0.01
104 15 0.17
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (104 bp):
ACACGGCCGTGTGCTACACACAACTGAGACACACACCCGTGTCTCAGACCGTGTAGCCTCAAAAT
AAACCTTAAAACACAAGTTTACCATTCCAAATTGCTTCG
Found at i:19990392 original size:21 final size:21
Alignment explanation
Indices: 19990366--19990473 Score: 135
Period size: 21 Copynumber: 5.1 Consensus size: 21
19990356 GCTCGAAATT
*
19990366 TGAACAGAAGCTCACAAGAGC
1 TGAACAGAAGCTCATAAGAGC
*
19990387 TGAACAGAAACTCATAAGAGC
1 TGAACAGAAGCTCATAAGAGC
* *
19990408 TGAACAAAAACTCATAAGAGC
1 TGAACAGAAGCTCATAAGAGC
* * *
19990429 TTAATAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCATAAGAGC
* *
19990450 TGAACAGAAGCTCGTGAGAGC
1 TGAACAGAAGCTCATAAGAGC
19990471 TGA
1 TGA
19990474 TCCACCCAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (21 bp):
TGAACAGAAGCTCATAAGAGC
Found at i:19990989 original size:21 final size:18
Alignment explanation
Indices: 19990965--19991011 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
19990955 ATTTAATCCC
19990965 TTAAATAATTAATTCATCAAA
1 TTAAATAATT--TT-ATCAAA
*
19990986 TTAACTAATTTTATCAAA
1 TTAAATAATTTTATCAAA
19991004 -TAAATAAT
1 TTAAATAAT
19991012 CTATCCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 6 0.25
19 2 0.08
21 9 0.38
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAATAATTTTATCAAA
Found at i:19994442 original size:37 final size:37
Alignment explanation
Indices: 19994368--19994486 Score: 152
Period size: 37 Copynumber: 3.2 Consensus size: 37
19994358 ACTACGGAAA
* * * *
19994368 GAAGCTCAATCGAGCAAATCCTA-CGTTATGCTGAAT
1 GAAGCTCAATCAAGTAAATCCTATTGTTATACTGAAT
*
19994404 GAAGCTCAATCAAGTAAATCCTATTGTTATATTGAAT
1 GAAGCTCAATCAAGTAAATCCTATTGTTATACTGAAT
* *
19994441 GAAGCTCAATCAA-TCAAATCCTATTGTTATACAGAGT
1 GAAGCTCAATCAAGT-AAATCCTATTGTTATACTGAAT
19994478 GAAGCTCAA
1 GAAGCTCAA
19994487 ACGAGTAGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
36 22 0.30
37 51 0.70
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (37 bp):
GAAGCTCAATCAAGTAAATCCTATTGTTATACTGAAT
Found at i:19994517 original size:74 final size:73
Alignment explanation
Indices: 19994350--19994517 Score: 160
Period size: 74 Copynumber: 2.3 Consensus size: 73
19994340 AGAGCCATAT
* * * * * * *
19994350 CTACTAATACTACGGAAAGAAGCTCAATCGAGCAAATCCTACGTTATGCTGAATGAAGCTCAATC
1 CTACTGATA-TACTGAATGAAGCTCAATCAAGCAAATCCTACGTTATACAGAATGAAGCTCAAAC
19994415 AAGTAAATC
65 AAGTAAATC
* * * * * *
19994424 CTATTGTTATATTGAATGAAGCTCAATCAATCAAATCCTATTGTTATACAGAGTGAAGCTCAAAC
1 CTACTGATATACTGAATGAAGCTCAATCAAGCAAATCCTA-CGTTATACAGAATGAAGCTCAAAC
*
19994489 GAGTAGAAAT-
65 AAGT--AAATC
19994499 CTACTGATATACTG-ATGAA
1 CTACTGATATACTGAATGAA
19994518 AAGCTAAATC
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
73 26 0.35
74 33 0.45
75 11 0.15
76 4 0.05
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (73 bp):
CTACTGATATACTGAATGAAGCTCAATCAAGCAAATCCTACGTTATACAGAATGAAGCTCAAACA
AGTAAATC
Found at i:19997590 original size:46 final size:47
Alignment explanation
Indices: 19997506--19997872 Score: 388
Period size: 46 Copynumber: 7.6 Consensus size: 47
19997496 TTTGAGTACT
* *
19997506 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCT-TTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
* * * *
19997552 TCTGATCAAGTGACAAGTGGGAAGTGATAAGTAATAGCT-TCGGGTATACTTA
1 TCTGATCAAGTGAC-A-----AAGTGATAAGTGATAGCTATCAGCTACACTTA
* *
19997604 TCTGATCAAGTGACAAAGTGATAAGTGATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
*
19997650 TCTGATCAAGTGACAAAGTGATAAGTGATAGCT-TCAACTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
*
19997696 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCT-TCGGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTATCAGCTACACTTA
* *
19997748 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTATCAGCTACACTTA
* *
19997800 TCTGATCAAGAGACAAAGTGATAAGTGATAGCT-TTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
*
19997846 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
19997873 GCTACACTTA
Statistics
Matches: 290, Mismatches: 19, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
46 156 0.54
47 1 0.00
51 1 0.00
52 132 0.46
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (47 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
Found at i:19997626 original size:98 final size:96
Alignment explanation
Indices: 19997506--19997866 Score: 478
Period size: 98 Copynumber: 3.7 Consensus size: 96
19997496 TTTGAGTACT
* *
19997506 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
* *
19997571 GGAAGTGATAAGTAATAGCTTCGGGTATACTTA
65 -GAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
19997604 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-A---
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
** *
19997665 AAGTGATAAGTGATAGCTTCAACTACACTTA
66 AAGTGATAAGTGATAGCTTCGGCTATACTTA
*
19997696 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
19997761 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG--AAGTGATAAGTGATAGCTTCGGCTATACTTA
* * *
19997800 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
19997865 GA
65 GA
19997867 TAAGTGGCTA
Statistics
Matches: 233, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
92 40 0.17
97 2 0.01
98 144 0.62
99 6 0.03
104 41 0.18
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (96 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:19997854 original size:196 final size:196
Alignment explanation
Indices: 19997520--19997872 Score: 598
Period size: 196 Copynumber: 1.8 Consensus size: 196
19997510 ATCAAGTGAC
* * **
19997520 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGGAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
19997585 ATAGCTTCGGGTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
19997650 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAACTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAACTACACTTATCTGATCAAGTGACAAGTG
19997715 G
196 G
* *
19997716 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
19997781 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
19997846 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTG
19997873 GCTACACTTA
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 145 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAACTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:19997880 original size:37 final size:37
Alignment explanation
Indices: 19997836--19997981 Score: 251
Period size: 37 Copynumber: 4.0 Consensus size: 37
19997826 GATAGCTTTA
*
19997836 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19997873 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19997910 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
19997947 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19997982 ATCATACGTA
Statistics
Matches: 106, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
35 12 0.11
36 4 0.04
37 90 0.85
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:19997909 original size:150 final size:149
Alignment explanation
Indices: 19997506--19997861 Score: 440
Period size: 150 Copynumber: 2.4 Consensus size: 149
19997496 TTTGAGTACT
* * * * *
19997506 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAACTACACTTATCTGATCAAGAGACAAGTG
* * ** * *
19997571 GGAAGTGATAAGTAATAGCTTC-G---GGTATACTTATC---TGATCAAGTGACAAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGCAAACTAAACTGATCAAGTGA-CAAGTGACAAAGTGATAAG
19997629 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
* *
19997650 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAACTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAACTACACTTATCTGATCAAGAGACAAGTG
* * * * *
19997715 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA-AAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAACTGATCAAGTGACAAGTGACAAAGTGATAAG
19997779 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
* *
19997800 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAACTACACTTATCTGATCAAGAGACAA
19997862 AGTGATAAGT
Statistics
Matches: 189, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
144 82 0.43
145 1 0.01
149 6 0.03
150 90 0.48
151 7 0.04
152 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (149 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAACTACACTTATCTGATCAAGAGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAACTGATCAAGTGACAAGTGACAAAGTGATAAGTG
ATAGCTTCGGCTATACTTA
Found at i:20003289 original size:18 final size:18
Alignment explanation
Indices: 20003269--20003310 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20003259 AATTTGTTTT
**
20003269 AAAATATATAAATTATTTA
1 AAAATAT-TAAAAAATTTA
20003288 AAAATATTAAAAAATTTA
1 AAAATATTAAAAAATTTA
20003306 AAAAT
1 AAAAT
20003311 TCTTTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATTAAAAAATTTA
Found at i:20003422 original size:19 final size:19
Alignment explanation
Indices: 20003394--20003435 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20003384 AAATATTGTG
20003394 AAAATCATTAAAAAATT-TA
1 AAAATCATT-AAAAATTATA
*
20003413 AAAATGATTAAAAATTATA
1 AAAATCATTAAAAATTATA
20003432 AAAA
1 AAAA
20003436 ATAATAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATCATTAAAAATTATA
Found at i:20003426 original size:29 final size:28
Alignment explanation
Indices: 20003353--20003437 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
20003343 TGTAATTCTT
* * *
20003353 TTTAAAATG-TAAAAAAGCATTAAATAA
1 TTTAAAATGATTAAAAATCATTAAAAAA
*
20003380 TTTAAAAT-ATTGTGAAAATCATTAAAAAA
1 TTTAAAATGA-T-TAAAAATCATTAAAAAA
*
20003409 TTTAAAAATGATTAAAAATTA-TAAAAAA
1 TTT-AAAATGATTAAAAATCATTAAAAAA
20003437 T
1 T
20003438 AATAAGATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
27 8 0.17
28 9 0.19
29 23 0.49
30 6 0.13
31 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (28 bp):
TTTAAAATGATTAAAAATCATTAAAAAA
Found at i:20003774 original size:19 final size:18
Alignment explanation
Indices: 20003752--20003798 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
20003742 AATGATTGCA
20003752 ATTTTTAAAATTTTTAATG
1 ATTTTTAAAATTTTT-ATG
* *
20003771 ATTTTCACAAATTTTTGTG
1 ATTTTTA-AAATTTTTATG
20003790 -TTTTTAAAA
1 ATTTTTAAAA
20003799 AAATTGCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.12
18 5 0.21
19 8 0.33
20 8 0.33
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (18 bp):
ATTTTTAAAATTTTTATG
Found at i:20004598 original size:20 final size:19
Alignment explanation
Indices: 20004569--20004646 Score: 68
Period size: 19 Copynumber: 4.0 Consensus size: 19
20004559 TTGGAGCATA
20004569 AATAATTTTATATATTTTTT
1 AATAATTTTATA-ATTTTTT
* * * *
20004589 AATAAATTTAAAATTTCTA
1 AATAATTTTATAATTTTTT
20004608 AATAATTATTATAATTTTTT
1 AATAATT-TTATAATTTTTT
* *
20004628 -ATATTTTTACAAATTTTTT
1 AATAATTTTA-TAATTTTTT
20004647 TTCACTTCTA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
18 3 0.07
19 24 0.52
20 19 0.41
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
AATAATTTTATAATTTTTT
Found at i:20008538 original size:19 final size:19
Alignment explanation
Indices: 20008516--20008579 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
20008506 TTTTTATTAT
*
20008516 AAATTATTAATAATTTTTA
1 AAATTATTAATATTTTTTA
20008535 AAATTATTACATATTTATTTA
1 AAATTATTA-ATATTT-TTTA
*
20008556 TAA-TATCTAATATTTTTTA
1 AAATTAT-TAATATTTTTTA
*
20008575 TAATT
1 AAATT
20008580 TAAAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 16 0.41
20 15 0.38
21 8 0.21
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATTATTAATATTTTTTA
Found at i:20009448 original size:29 final size:30
Alignment explanation
Indices: 20009407--20009479 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
20009397 ATTTAATTAT
* * *
20009407 AAATTTAATTATACATGAAAT-GTTTTTAA
1 AAATTTAAATATACATGAAATAATATTTAA
*
20009436 AAATTTAAATATAATATGAAATAATATTTAA
1 AAATTTAAATAT-ACATGAAATAATATTTAA
20009467 ATAATTT-AATATA
1 A-AATTTAAATATA
20009480 ATTATACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 11 0.30
30 9 0.24
31 12 0.32
32 5 0.14
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (30 bp):
AAATTTAAATATACATGAAATAATATTTAA
Found at i:20026061 original size:21 final size:22
Alignment explanation
Indices: 20026037--20026082 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
20026027 GTTTATACAC
20026037 TTGTAATTTTTTTT-GAATAGA
1 TTGTAATTTTTTTTCGAATAGA
20026058 TTGTAATTTTTTTTCGAATAGA
1 TTGTAATTTTTTTTCGAATAGA
20026080 TTG
1 TTG
20026083 GTTAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (22 bp):
TTGTAATTTTTTTTCGAATAGA
Found at i:20026071 original size:22 final size:21
Alignment explanation
Indices: 20026037--20026082 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
20026027 GTTTATACAC
*
20026037 TTGTAATTTTTTTTGAATAGA
1 TTGTAATTTTTTTCGAATAGA
20026058 TTGTAATTTTTTTTCGAATAGA
1 TTGTAA-TTTTTTTCGAATAGA
20026080 TTG
1 TTG
20026083 GTTAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTAATTTTTTTCGAATAGA
Found at i:20033436 original size:14 final size:15
Alignment explanation
Indices: 20033417--20033445 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20033407 CCTTAGTTGC
20033417 TGAAAAAT-AAAAGA
1 TGAAAAATGAAAAGA
20033431 TGAAAAATGAAAAGA
1 TGAAAAATGAAAAGA
20033446 ATGGGGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (15 bp):
TGAAAAATGAAAAGA
Found at i:20048888 original size:2 final size:2
Alignment explanation
Indices: 20048881--20048939 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
20048871 ATTGGCCAAC
20048881 TA TA TA TA TA TA 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 TA TA TA TA TA TA
20048923 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
20048940 TAAAACGCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20049895 original size:20 final size:21
Alignment explanation
Indices: 20049858--20049896 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
20049848 TTTTAGAATT
20049858 TTTTTCATATTCTTAAAATCA
1 TTTTTCATATTCTTAAAATCA
20049879 TTTTT-ATATT-TTGAAAAT
1 TTTTTCATATTCTT-AAAAT
20049897 TATAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 10 0.59
21 5 0.29
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTTTCATATTCTTAAAATCA
Found at i:20061611 original size:52 final size:52
Alignment explanation
Indices: 20061528--20061634 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
20061518 GTAGGTAAAA
* *
20061528 CTTACTTTTTGGCTATAGATTCTACAACATAAACTTCGCCGTTGGAATCGGC
1 CTTACTTTTTGGCTATAGATTCTACAACATAAACTTCGCCATTGGAATCAGC
* *
20061580 CTTACTTTTTGGCTATAGATTCTATAGCATAAACTTCGCCATTGGAATCAGC
1 CTTACTTTTTGGCTATAGATTCTACAACATAAACTTCGCCATTGGAATCAGC
20061632 CTT
1 CTT
20061635 TAGCTGTGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (52 bp):
CTTACTTTTTGGCTATAGATTCTACAACATAAACTTCGCCATTGGAATCAGC
Found at i:20063961 original size:8 final size:9
Alignment explanation
Indices: 20063938--20063964 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
20063928 GAAAATCAAA
20063938 ATAAAAATT
1 ATAAAAATT
20063947 ATAAAAATT
1 ATAAAAATT
20063956 ATAAAAATT
1 ATAAAAATT
20063965 GGTTCAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:20064155 original size:20 final size:21
Alignment explanation
Indices: 20064118--20064156 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
20064108 TTTTGGAATT
20064118 TTTTTCATATTCTTAAAATCA
1 TTTTTCATATTCTTAAAATCA
20064139 TTTTT-ATATT-TTGAAAAT
1 TTTTTCATATTCTT-AAAAT
20064157 TATAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 10 0.59
21 5 0.29
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTTTCATATTCTTAAAATCA
Done.