Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold176
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: 960511
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:512510 original size:51 final size:48
Alignment explanation
Indices: 512420--512532 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 48
512410 TAAAGCCGGG
512420 GTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAATGAAATCGGA
1 GTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAATGAAATCGGA
*
512468 GTTGGAGTATCCCCGATTATAGAAAATT-AGTGTTTT-GAAAATGAAATCGGA
1 GTTGGAGTATCCCCGA-T-GA-AAAATTGA-TGTTTTAG-AAATGAAATCGGA
512519 GTTGG-GATATCCCC
1 GTTGGAG-TATCCCC
512533 AATTGCGGAG
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
48 16 0.28
49 1 0.02
50 4 0.07
51 37 0.64
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (48 bp):
GTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAATGAAATCGGA
Found at i:514920 original size:34 final size:33
Alignment explanation
Indices: 514875--514941 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
514865 AACTTCCTAG
*
514875 ATGTATCGATACAAAGAATAAATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCCATACA
* *
514909 ATGTATTGATACACAGAAAAATGTATCCATACA
1 ATGTATCGATACAAAGAAAAATGTATCCATACA
514942 TTCCCTTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCCATACA
Found at i:515001 original size:13 final size:13
Alignment explanation
Indices: 514983--515071 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
514973 ACAATACTTA
514983 TGTATCGATACAT
1 TGTATCGATACAT
514996 TGTATCGATACAATACT
1 TGTATCGATAC---A-T
515013 TAAGTATCGATACAT
1 T--GTATCGATACAT
515028 TGTATCGATACAACATTT
1 TGTATCGAT---ACA--T
515046 ATGTATCGATACAT
1 -TGTATCGATACAT
515060 TGTATCGATACA
1 TGTATCGATACA
515072 ACATTTATGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 31 0.48
14 1 0.02
15 2 0.03
16 8 0.12
17 2 0.03
18 1 0.02
19 19 0.30
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:515006 original size:32 final size:32
Alignment explanation
Indices: 514964--515090 Score: 200
Period size: 32 Copynumber: 4.0 Consensus size: 32
514954 TAGCTAATTA
* *
514964 TGTATTGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
* *
514996 TGTATCGATACAATACTTAAGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
*
515028 TGTATCGATACAACATTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
*
515060 TGTATCGATACAACATTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
515091 AATCGCTGAA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 90 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:515021 original size:19 final size:18
Alignment explanation
Indices: 514965--515091 Score: 68
Period size: 19 Copynumber: 7.7 Consensus size: 18
514955 AGCTAATTAT
*
514965 GTATTGATACAATACTTA
1 GTATCGATACAATACTTA
514983 TGTATCGATAC---A-TT-
1 -GTATCGATACAATACTTA
514997 GTATCGATACAATACTTAA
1 GTATCGATACAATACTT-A
515016 GTATCGATAC---A-TT-
1 GTATCGATACAATACTTA
* *
515029 GTATCGATACAACATTTA
1 GTATCGATACAATACTTA
515047 TGTATCGATAC---A-TT-
1 -GTATCGATACAATACTTA
* *
515061 GTATCGATACAACATTTA
1 GTATCGATACAATACTTA
515079 TGTATCGATACAA
1 -GTATCGATACAA
515092 ATCGCTGAAA
Statistics
Matches: 89, Mismatches: 1, Indels: 36
0.71 0.01 0.29
Matches are distributed among these distances:
13 30 0.34
15 6 0.07
16 6 0.07
17 6 0.07
19 41 0.46
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (18 bp):
GTATCGATACAATACTTA
Found at i:515154 original size:21 final size:21
Alignment explanation
Indices: 515128--515204 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
515118 GTTGGGACCC
* *
515128 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
* *
515149 TGTATCAATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
515170 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
515191 TGTATCGATACATT
1 TGTATCGATACATT
515205 TGGATAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:515922 original size:13 final size:13
Alignment explanation
Indices: 515904--515929 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
515894 ACAAAGATCC
515904 ATGTATCGATACA
1 ATGTATCGATACA
515917 ATGTATCGATACA
1 ATGTATCGATACA
515930 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:515941 original size:33 final size:33
Alignment explanation
Indices: 515884--515949 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
515874 AACTTCCTAG
*** *
515884 ATGTATCGATACAAAGATCCATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCCATACA
*
515917 ATGTATCGATACACAGAAAAATGTATCCATACA
1 ATGTATCGATACAAAGAAAAATGTATCCATACA
515950 TTTCCTTGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCCATACA
Found at i:516009 original size:13 final size:13
Alignment explanation
Indices: 515991--516015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
515981 ACAATACTTA
515991 TGTATCGATACAT
1 TGTATCGATACAT
516004 TGTATCGATACA
1 TGTATCGATACA
516016 AAACTTCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:516034 original size:32 final size:32
Alignment explanation
Indices: 515972--516034 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
515962 TAGCTAATTA
* * *
515972 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATATATCAATACAT
*
516004 TGTATCGATACAAAACTTCTATATCAATACA
1 TGTATCGATACAAAACTTATATATCAATACA
516035 AATTGTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATATATCAATACAT
Found at i:516098 original size:21 final size:22
Alignment explanation
Indices: 516072--516129 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
516062 GTTGGGATCC
* *
516072 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
516093 TGTATCGATACATTT-CACAAA
1 TGTATCGATACATTTGCACAAA
516114 TGTATCGATACATTTG
1 TGTATCGATACATTTG
516130 AAATTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:517062 original size:29 final size:28
Alignment explanation
Indices: 516917--517062 Score: 83
Period size: 28 Copynumber: 5.2 Consensus size: 28
516907 TTGAGGACTA
516917 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
516945 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
*
516973 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
* *
517000 GAAAGGTGTCCTA-C-TCTT-TG-GGGAC-TA
1 -AAAGGTG-CC-ACCAACTTGTGTGGG-CTTT
517027 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
517055 AAGAGGTG
1 AA-AGGTG
517063 TCCTGCTCTT
Statistics
Matches: 83, Mismatches: 20, Indels: 29
0.63 0.15 0.22
Matches are distributed among these distances:
24 1 0.01
25 6 0.07
26 15 0.18
27 14 0.17
28 22 0.27
29 18 0.22
30 6 0.07
31 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (28 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:517269 original size:59 final size:59
Alignment explanation
Indices: 516847--517725 Score: 992
Period size: 59 Copynumber: 15.2 Consensus size: 59
516837 AGTGTATCCT
* * * * * *
516847 GCTCATTGAGGACTAAAAAGTGCCACCAACTAGTGTGGGCTTT----G-AAAGGCATCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* * *
516902 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
** * *
516957 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* * * * *
517012 ACTCTTTGGGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* ** * *
517067 GCTCTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* ** * *
517122 ACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGAGTCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* * * * *
517177 GCTCTTTGGGGACTAAAAGGTGCCACCAACTTGTGT-GGCTTTGAAAAGAAAAAGCATCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCC
517237 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
*
517296 ACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* * *
517355 ACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCTC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
517414 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCTC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
*
517473 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
517532 GGTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
*
517591 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
** * * * * *
517650 GCTCTTTGAGGACTGGAAAATGTCACCAACTTATGGGGGCTTTTAAAAGGAAAAGGCATCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGC-TTTAAAA-GAAAAGGCGTCCC
517712 GCTCTTTGAGGACT
1 GCTCTTTGAGGACT
517726 AAAAAGTGGG
Statistics
Matches: 746, Mismatches: 60, Indels: 29
0.89 0.07 0.03
Matches are distributed among these distances:
53 2 0.00
54 6 0.01
55 268 0.36
57 2 0.00
59 390 0.52
60 46 0.06
61 7 0.01
62 25 0.03
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (59 bp):
GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
Found at i:517403 original size:177 final size:179
Alignment explanation
Indices: 516843--517729 Score: 1099
Period size: 177 Copynumber: 5.1 Consensus size: 179
516833 ATAAAGTGTA
* * *
516843 TCCTGCTCATTGAGGACTAAAAAGTGCCACCAACTAGTGTGGGCTTT----G-AAAGGCATCCTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCTG
* *
516903 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCTGCTCTT
66 CTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCCGCTCTT
*
516963 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
130 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * **
517008 TCCTACTCTTTGGGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCTG
* ** **
517068 CTCTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTACTCTT
66 CTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCCGCTCTT
*
517128 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGAG
130 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
517173 TCCTGCTCTTTGGGGACTAAAAGGTGCCACCAACTTGTGT-GGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCATCCT
* *
517237 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCACTCTT
65 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCCGCTCTT
**
517302 TGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
130 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * **
517351 TCCCACTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGT-CTC
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCT-
*
517414 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCTCGCTCTT
65 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCCGCTCTT
** *
517479 TGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAGGCG
130 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
517528 TCCCGGTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCTG
* *
517592 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGAAAAGGCGTCCCGCTCTTT
66 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCCGCTCTTT
* * * *
517657 GAGGACTGGAAAATGTCACCAACTTATGGGGGCTTTTAAAAGGAAAAGGCA
131 GAGGACTGGAAAATGCCACCAACTTGTGTGGGC-TTTAAAA-GAAAAGGCG
517708 TCCTGCTCTTTGAGGACTAAAA
1 TCCTGCTCTTTGAGGACTAAAA
517730 AGTGGGAGGA
Statistics
Matches: 640, Mismatches: 55, Indels: 38
0.87 0.08 0.05
Matches are distributed among these distances:
163 1 0.00
164 6 0.01
165 184 0.29
167 4 0.01
169 26 0.04
170 19 0.03
173 27 0.04
174 23 0.04
176 2 0.00
177 268 0.42
178 48 0.08
179 7 0.01
180 23 0.04
181 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (179 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCTG
CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCCGCTCTTT
GAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:518729 original size:15 final size:14
Alignment explanation
Indices: 518711--518754 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
518701 CTTTTCTCTC
518711 TTTTTCTTTGTTTTG
1 TTTTT-TTTGTTTTG
518726 TTTTTTTTGCTTTTG
1 TTTTTTTTG-TTTTG
*
518741 TTTTTTTTTTTTTG
1 TTTTTTTTGTTTTG
518755 AAGAGAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:518742 original size:20 final size:20
Alignment explanation
Indices: 518717--518754 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
518707 TCTCTTTTTC
518717 TTTGTTTTGTTTTTTTTGCT
1 TTTGTTTTGTTTTTTTTGCT
*
518737 TTTGTTTTTTTTTTTTTG
1 TTTGTTTTGTTTTTTTTG
518755 AAGAGAAGGT
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:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (20 bp):
TTTGTTTTGTTTTTTTTGCT
Found at i:520654 original size:21 final size:21
Alignment explanation
Indices: 520630--520685 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
520620 AAATATTTCA
520630 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
520651 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
520672 AATGTATCGATACA
1 AATGTATCGATACA
520686 GGGTTCCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTGG
Found at i:520759 original size:13 final size:13
Alignment explanation
Indices: 520741--520765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
520731 TAATAAGTTT
520741 TGTATCGATACAA
1 TGTATCGATACAA
520754 TGTATCGATACA
1 TGTATCGATACA
520766 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:520776 original size:32 final size:31
Alignment explanation
Indices: 520723--520784 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
520713 TTCAACAATT
*
520723 TGTATCGATAATAAGTTTTGTATCGATACAA
1 TGTATCGATAATAAGTATTGTATCGATACAA
520754 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATA-ATAAGTATTGTATCGATACA
520785 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (31 bp):
TGTATCGATAATAAGTATTGTATCGATACAA
Found at i:520778 original size:19 final size:19
Alignment explanation
Indices: 520722--520787 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
520712 ATTCAACAAT
*
520722 TTGTATCGATA-ATAAGTT
1 TTGTATCGATACATAAGTA
520740 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
520754 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
520772 TTGTATCGATACATAA
1 TTGTATCGATACATAA
520788 TTAGCTACTG
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.28
16 2 0.05
18 12 0.30
19 15 0.38
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:520845 original size:13 final size:13
Alignment explanation
Indices: 520827--520852 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
520817 CATTTTTCTG
520827 TGTATCGATACAT
1 TGTATCGATACAT
520840 TGTATCGATACAT
1 TGTATCGATACAT
520853 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:520849 original size:33 final size:33
Alignment explanation
Indices: 520807--520873 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
520797 GCCAAGGAAA
***
520807 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
520840 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
520873 T
1 T
520874 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:521043 original size:59 final size:59
Alignment explanation
Indices: 520971--521199 Score: 306
Period size: 59 Copynumber: 3.9 Consensus size: 59
520961 TTGGTGGCAC
* *
520971 TTTCTTTTAAAGCCCACCCAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCGGGACGCCT
1 TTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGCCT
* * * * **
521030 TTTCTTTTAAAGCCCACCCATGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGTTT
1 TTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGCCT
521089 TTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC-
1 TTTCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACGCCT
* *
521149 TTTC----AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 TTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGA
521200 TACACTTTAT
Statistics
Matches: 153, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
54 1 0.01
55 43 0.28
59 61 0.40
60 25 0.16
61 23 0.15
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (59 bp):
TTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGCCT
Found at i:521169 original size:55 final size:55
Alignment explanation
Indices: 520974--521199 Score: 249
Period size: 55 Copynumber: 3.9 Consensus size: 55
520964 GTGGCACTTT
* * *
520974 CTTTTAAAGCCCACCCAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCGGGACGC
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC
* * *
521028 CTTTTCTTTTAAAGCCCACCCATGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGATGTTTTTT
1 C-TTTC----AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG------
521092 C
55 C
*
521093 TTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC
* * *
521148 CTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
521200 TACACTTTAT
Statistics
Matches: 147, Mismatches: 12, Indels: 25
0.80 0.07 0.14
Matches are distributed among these distances:
54 1 0.01
55 52 0.35
59 43 0.29
60 24 0.16
61 22 0.15
64 4 0.03
65 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (55 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC
Found at i:522029 original size:19 final size:19
Alignment explanation
Indices: 522005--522072 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
521995 AATTCAACAA
522005 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
522024 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
522039 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
522056 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
522073 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:522044 original size:13 final size:13
Alignment explanation
Indices: 522026--522050 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
522016 ACATAAGTTT
522026 TGTATCGATACAA
1 TGTATCGATACAA
522039 TGTATCGATACA
1 TGTATCGATACA
522051 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:522048 original size:32 final size:32
Alignment explanation
Indices: 522007--522069 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
521997 TTCAACAATT
*
522007 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
522039 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
522070 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:522130 original size:13 final size:13
Alignment explanation
Indices: 522112--522137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
522102 CATTTTTCTG
522112 TGTATCGATACAT
1 TGTATCGATACAT
522125 TGTATCGATACAT
1 TGTATCGATACAT
522138 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:522134 original size:33 final size:33
Alignment explanation
Indices: 522092--522158 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
522082 GCCAAGGAAA
***
522092 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
522125 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
522158 T
1 T
522159 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:524677 original size:28 final size:27
Alignment explanation
Indices: 524607--524682 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
524597 TTTCTTCACA
* *
524607 ATCGGAGACACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
524634 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
524660 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
524683 ACTTTATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.09
27 21 0.49
28 18 0.42
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:524791 original size:52 final size:51
Alignment explanation
Indices: 524665--524834 Score: 214
Period size: 52 Copynumber: 3.3 Consensus size: 51
524655 TTATTTTCGA
* ***
524665 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * * *
524716 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTC-ATAATC
* *
524768 GGGGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAATACCAATTTTTCATAATC
*
524820 GAGGATACTCCAACC
1 GGGGATACTCCAACC
524835 TCGTTATTTC
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
51 37 0.37
52 48 0.48
53 14 0.14
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:524853 original size:28 final size:28
Alignment explanation
Indices: 524817--524898 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
524807 ATTTTTCACA
* *
524817 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
524845 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
524873 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCCGTTATT
524899 ATCTCCAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 42 0.89
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:524908 original size:211 final size:211
Alignment explanation
Indices: 524502--524923 Score: 593
Period size: 211 Copynumber: 2.0 Consensus size: 211
524492 AATTCTCCAC
* * *
524502 AATCGGGGATATTCCAACTCCGATTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCC
1 AATCGGGGATACTCCAACCCCGATTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCC
*
524567 AACTCCGATTTTATTTCTAAAAAACACCAATTTCTTCACAATCGGAGACACTCCAACCCCGTTAA
66 AACACCGATTTTATTTCTAAAAAACACCAATTTCTTCACAATCGGAGACACTCCAACCCCGTTAA
* * * * *
524632 TCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAA
131 TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATCTCCAAA
* *
524697 ATATT-GATTTTTCAT
196 ACATTAAATTTTTCAT
* *
524712 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCC-GATTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* * * *
524777 CCAACACCGATTTTATTTC-CAAAAATACCAATTT-TTCACAATC-GAGGATACTCCAACCTCGT
64 CCAACACCGATTTTATTTCTAAAAAACACCAATTTCTTCACAATCGGA-GACACTCCAACCCCGT
* *
524839 TATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG-TTATTATCT
128 TA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACT-TTATCT
524903 CCAAAACATTAAATTTTTCAT
191 CCAAAACATTAAATTTTTCAT
524924 CGGGAAATAT
Statistics
Matches: 187, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
209 2 0.01
210 45 0.24
211 97 0.52
212 43 0.23
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (211 bp):
AATCGGGGATACTCCAACCCCGATTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCC
AACACCGATTTTATTTCTAAAAAACACCAATTTCTTCACAATCGGAGACACTCCAACCCCGTTAA
TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATCTCCAAA
ACATTAAATTTTTCAT
Found at i:526582 original size:13 final size:13
Alignment explanation
Indices: 526564--526589 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
526554 TACACCAAGT
526564 ATGTATCGATACA
1 ATGTATCGATACA
526577 ATGTATCGATACA
1 ATGTATCGATACA
526590 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:526587 original size:32 final size:33
Alignment explanation
Indices: 526546--526609 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
526536 TAGCCAAACT
* **
526546 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
526578 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
526610 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:537873 original size:79 final size:77
Alignment explanation
Indices: 537759--537940 Score: 177
Period size: 79 Copynumber: 2.3 Consensus size: 77
537749 GTCCCCTTGA
* * ** *
537759 AAATGACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGAAAAAAACATCGGGATT
1 AAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCGAT-ATTTAGAAAAAAAC--CGGGATT
537823 GGAGTACCCCCTCGG
63 GGAGTACCCCCTCGG
* * * * * *
537838 AAATAACGGGGTTGGAGTATCCCTAATTATGAGAAATGGATATTTTTGGAATAAAGCCGGGGTTG
1 AAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCGATA--TTTAGAAAAAAACCGGGATTG
*
537903 GAGTATCCCCTCGG
64 GAGTACCCCCTCGG
** *
537917 AGGTAACAGGGTTGGAGTATCCCC
1 AAATAACGGGGTTGGAGTATCCCC
537941 GATGATTAAC
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
78 1 0.01
79 74 0.88
81 9 0.11
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (77 bp):
AAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCGATATTTAGAAAAAAACCGGGATTGGA
GTACCCCCTCGG
Found at i:537958 original size:27 final size:28
Alignment explanation
Indices: 537895--537972 Score: 104
Period size: 27 Copynumber: 2.8 Consensus size: 28
537885 GGAATAAAGC
***
537895 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAGGTAA
* *
537923 CAGGGTTGGAGTATCCCCGATGA-TTAA
1 CGGGGTTGGAGTATCCCCGATGAGGTAA
537950 CGGGGTTGGAGTATCCCCGATGA
1 CGGGGTTGGAGTATCCCCGATGA
537973 AAAATTGATG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAGGTAA
Found at i:540456 original size:21 final size:21
Alignment explanation
Indices: 540397--540457 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
540387 GTAAACTTCC
*
540397 TAGATGTATCGATACAAAGAA
1 TAGATGTATCGATACAATGAA
540418 TAGATGTATCGATACAATGAA
1 TAGATGTATCGATACAATGAA
540439 TAGATGTATCGATACAATG
1 TAGATGTATCGATACAATG
540458 TATCGATACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGATGTATCGATACAATGAA
Found at i:540460 original size:13 final size:13
Alignment explanation
Indices: 540442--540467 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
540432 CAATGAATAG
540442 ATGTATCGATACA
1 ATGTATCGATACA
540455 ATGTATCGATACA
1 ATGTATCGATACA
540468 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:540531 original size:19 final size:19
Alignment explanation
Indices: 540507--540572 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
540497 CAGTAGCTAA
540507 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
540526 TTATGTATCGATAC---A-
1 TTATGTATCGATACAATAC
*
540541 -T-TGTATCGATAAAATAC
1 TTATGTATCGATACAATAC
540558 TTATGTATCGATACA
1 TTATGTATCGATACA
540573 TTGTATTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
16 2 0.05
18 1 0.03
19 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (19 bp):
TTATGTATCGATACAATAC
Found at i:540549 original size:32 final size:32
Alignment explanation
Indices: 540510--540604 Score: 154
Period size: 32 Copynumber: 3.0 Consensus size: 32
540500 TAGCTAATTA
540510 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
*
540542 TGTATCGATAAAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
* * *
540574 TGTATTGATACAACATTTATGTATCGATACA
1 TGTATCGATACAATACTTATGTATCGATACA
540605 AATTGCTGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (32 bp):
TGTATCGATACAATACTTATGTATCGATACAT
Found at i:540602 original size:19 final size:18
Alignment explanation
Indices: 540506--540605 Score: 67
Period size: 19 Copynumber: 5.9 Consensus size: 18
540496 GCAGTAGCTA
*
540506 ATTATGTATCGATACAAT
1 ATTATGTATCGATACAAC
540524 ACTTATGTATCGAT---AC
1 A-TTATGTATCGATACAAC
* *
540540 A-T-TGTATCGATAAAAT
1 ATTATGTATCGATACAAC
540556 ACTTATGTATCGAT---AC
1 A-TTATGTATCGATACAAC
*
540572 A-T-TGTATTGATACAAC
1 ATTATGTATCGATACAAC
540588 ATTTATGTATCGATACAA
1 A-TTATGTATCGATACAA
540606 ATTGCTGAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 25
0.68 0.05 0.27
Matches are distributed among these distances:
13 17 0.27
14 2 0.03
16 9 0.14
18 3 0.05
19 33 0.52
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (18 bp):
ATTATGTATCGATACAAC
Found at i:540668 original size:21 final size:21
Alignment explanation
Indices: 540642--540718 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
540632 GTTGGGACCC
* *
540642 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
*
540663 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
*
540684 TGAATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
540705 TGTATCGATACATT
1 TGTATCGATACATT
540719 TGGATAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:541497 original size:42 final size:42
Alignment explanation
Indices: 541451--541896 Score: 170
Period size: 42 Copynumber: 11.2 Consensus size: 42
541441 ATGTAGTTCA
*
541451 TTTCCTTTTTTCCTTTGTCCTTAAAGAGCAGGACACACTTCT
1 TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGACACACTTCT
* * *
541493 TTTCC-----T--TTTGTCCTAAAGGAGTAGG----A-TGC-
1 TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGACACACTTCT
* * * *
541522 ATT-CTTTTTTCCTTTTTCCTTAAGGAGCAGGACCCATTTCTT
1 TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGACACACTTC-T
* * *
541564 TTTCCTTTTTCCCTTTGTCCTTAGGGAGCAGGACATAGACATT-T
1 TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGAC--ACAC-TTCT
* **
541608 TTT--TTGTTTTCCTTTTGTCCTTAAGGAACAGGATGCACTT-T
1 TTTCCTT-TTTTCC-TTTGTCCTTAAGGAGCAGGACACACTTCT
* * * * *
541649 ATTTCCTTTTTTCCTTTATCCTTAAAGAGTAAGACGCACTTCT
1 -TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGACACACTTCT
* * * ** *
541692 TTTCCTTTTGT-C--T-T-C--AAGGAACATGATGCA-TTCC
1 TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGACACACTTCT
* * * *
541726 TTT-C---TTT--TTTGTCCTCAAGGAGTAGGACCCATTTCTT
1 TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGACACACTTC-T
* * *
541763 TTTCCTTTTTCCCTTTGTCCTCAAGGAGCAGGGCACACTTCAT
1 TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGACACACTTC-T
* * *
541806 TTTCCTTTTTT-CTTTGTCCTCAAGGAGTAGGA-ACTATTTC-
1 TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGACAC-ACTTCT
* * * * * * *
541846 ATTCTCTTTTTTCCTTTATCCTCAAAGAGTAGGACATACTCCT
1 TTTC-CTTTTTTCCTTTGTCCTTAAGGAGCAGGACACACTTCT
541889 TTTCCTTT
1 TTTCCTTT
541897 GTCCTTAAAG
Statistics
Matches: 302, Mismatches: 59, Indels: 86
0.68 0.13 0.19
Matches are distributed among these distances:
28 1 0.00
29 2 0.01
30 4 0.01
31 2 0.01
32 1 0.00
33 3 0.01
34 6 0.02
35 52 0.17
36 3 0.01
37 5 0.02
38 2 0.01
39 2 0.01
40 5 0.02
41 15 0.05
42 94 0.31
43 78 0.26
44 24 0.08
45 1 0.00
46 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (42 bp):
TTTCCTTTTTTCCTTTGTCCTTAAGGAGCAGGACACACTTCT
Found at i:541566 original size:35 final size:34
Alignment explanation
Indices: 541457--541575 Score: 132
Period size: 35 Copynumber: 3.4 Consensus size: 34
541447 TTCATTTCCT
* *
541457 TTTTTCCTTTGTCCTTAAAGAGCAGGACACACTTC
1 TTTTTCCTTTTTCCTTAAGGAGCAGGACACA-TTC
* * **
541492 -TTTTCCTTTTGTCCTAAAGGAGTAGGATGCATTC
1 TTTTTCCTTTT-TCCTTAAGGAGCAGGACACATTC
*
541526 TTTTTTCCTTTTTCCTTAAGGAGCAGGACCCATTTC
1 -TTTTTCCTTTTTCCTTAAGGAGCAGGACACA-TTC
541562 TTTTTCCTTTTTCC
1 TTTTTCCTTTTTCC
541576 CTTTGTCCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
34 12 0.17
35 45 0.64
36 13 0.19
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.45
Consensus pattern (34 bp):
TTTTTCCTTTTTCCTTAAGGAGCAGGACACATTC
Found at i:541572 original size:43 final size:43
Alignment explanation
Indices: 541525--541700 Score: 148
Period size: 43 Copynumber: 4.1 Consensus size: 43
541515 AGGATGCATT
* *
541525 CTTTTTTCCTTTTTCCTTAAGGAGCAGGACCCATTTCTTTTTC
1 CTTTTTTCCTTTTTCCTTAAGGAGCAGGACGCACTTCTTTTTC
* * *
541568 CTTTTTCCCTTTGTCCTTAGGGAGCAGGACATAG-ACATT-TTTTT-
1 CTTTTTTCCTTTTTCCTTAAGGAGCAGGAC---GCAC-TTCTTTTTC
* * * *
541612 -TGTTTTCCTTTTGTCCTTAAGGAACAGGATGCACTT-TATTTC
1 CTTTTTTCCTTTT-TCCTTAAGGAGCAGGACGCACTTCTTTTTC
* * * *
541654 CTTTTTTCCTTTATCCTTAAAGAGTAAGACGCACTTC-TTTTC
1 CTTTTTTCCTTTTTCCTTAAGGAGCAGGACGCACTTCTTTTTC
541696 CTTTT
1 CTTTT
541701 GTCTTCAAGG
Statistics
Matches: 104, Mismatches: 20, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
41 7 0.07
42 29 0.28
43 46 0.44
44 14 0.13
45 6 0.06
46 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.47
Consensus pattern (43 bp):
CTTTTTTCCTTTTTCCTTAAGGAGCAGGACGCACTTCTTTTTC
Found at i:541665 original size:199 final size:199
Alignment explanation
Indices: 541403--541906 Score: 556
Period size: 199 Copynumber: 2.5 Consensus size: 199
541393 AAAGCAAGAT
** * * *
541403 ACATTTTTTTTGTTTTCCCTTTATCCTCAAGGAGTAGGATGTAGTTCATTTCCTTTTTTCCTTTG
1 ACATTTTTTTTGTTTTCCCTTTATCCTCAAGGAACAGGATGCACTTCATTTCCTTTTTTCCTTTA
* **
541468 TCCTTAAAGAGCAGGACACACTTCTTTTCCTTTTGTCCTAAAGGAGTAGGATGCATT-CTTT-TT
66 TCCTTAAAGAGCAAGACACACTTCTTTTCCTTTTGTCCTAAAGGAACAGGATGCATTCCTTTCTT
* * * *
541531 TCCTTTTTCCTTAAGGAGCAGGACCCATTTCTTTTTCCTTTTTCCCTTTGTCCTTAGGGAGCAGG
131 T--TTTGTCCTCAAGGAGCAGGACCCATTTCTTTTTCCTTTTTCCCTTTGTCCTCAAGGAGCAGG
541596 ACATAG
194 ACATAG
* * * *
541602 ACATTTTTTTTGTTTTCCTTTTGTCCTTAAGGAACAGGATGCACTTTATTTCCTTTTTTCCTTTA
1 ACATTTTTTTTGTTTTCCCTTTATCCTCAAGGAACAGGATGCACTTCATTTCCTTTTTTCCTTTA
* * * * *
541667 TCCTTAAAGAGTAAGACGCACTTCTTTTCCTTTTGTCTTCAAGGAACATGATGCATTCCTTTCTT
66 TCCTTAAAGAGCAAGACACACTTCTTTTCCTTTTGTCCTAAAGGAACAGGATGCATTCCTTTCTT
* *
541732 TTTTGTCCTCAAGGAGTAGGACCCATTTCTTTTTCCTTTTTCCCTTTGTCCTCAAGGAGCAGGGC
131 TTTTGTCCTCAAGGAGCAGGACCCATTTCTTTTTCCTTTTTCCCTTTGTCCTCAAGGAGCAGGAC
* *
541797 ACACT
196 ATA-G
* ** * ** * *
541802 TCATTTTCCTT-TTTT--CTTTGTCCTCAAGGAGTAGGA-ACTATTTCA-TTCTCTTTTTTCCTT
1 ACATTTTTTTTGTTTTCCCTTTATCCTCAAGGAACAGGATGC-ACTTCATTTC-CTTTTTTCCTT
* * * * *
541862 TATCCTCAAAGAGTAGGACATACTCCTTTTCC-TTTGTCCTTAAAG
64 TATCCTTAAAGAGCAAGACACACTTCTTTTCCTTTTGTCC-TAAAG
541907 AGCCACTCAA
Statistics
Matches: 257, Mismatches: 42, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
196 10 0.04
197 63 0.25
199 169 0.66
200 12 0.05
201 3 0.01
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (199 bp):
ACATTTTTTTTGTTTTCCCTTTATCCTCAAGGAACAGGATGCACTTCATTTCCTTTTTTCCTTTA
TCCTTAAAGAGCAAGACACACTTCTTTTCCTTTTGTCCTAAAGGAACAGGATGCATTCCTTTCTT
TTTTGTCCTCAAGGAGCAGGACCCATTTCTTTTTCCTTTTTCCCTTTGTCCTCAAGGAGCAGGAC
ATAG
Found at i:541782 original size:43 final size:42
Alignment explanation
Indices: 541733--541880 Score: 179
Period size: 42 Copynumber: 3.5 Consensus size: 42
541723 TCCTTTCTTT
*
541733 TTTGTCCTCAAGGAGTAGGACCCATTTCTTTTTCCTTTTTCCC
1 TTTGTCCTCAAGGAGTAGGACCCATTTCATTTTCCTTTTT-CC
* * * * *
541776 TTTGTCCTCAAGGAGCAGGGCACACTTCATTTTCCTTTTTTC
1 TTTGTCCTCAAGGAGTAGGACCCATTTCATTTTCCTTTTTCC
* * * *
541818 TTTGTCCTCAAGGAGTAGGAACTATTTCATTCTCTTTTTTCC
1 TTTGTCCTCAAGGAGTAGGACCCATTTCATTTTCCTTTTTCC
* *
541860 TTTATCCTCAAAGAGTAGGAC
1 TTTGTCCTCAAGGAGTAGGAC
541881 ATACTCCTTT
Statistics
Matches: 87, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 52 0.60
43 35 0.40
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (42 bp):
TTTGTCCTCAAGGAGTAGGACCCATTTCATTTTCCTTTTTCC
Found at i:542112 original size:31 final size:31
Alignment explanation
Indices: 542076--542566 Score: 277
Period size: 31 Copynumber: 15.1 Consensus size: 31
542066 ACACCTAAAT
*
542076 CTGAGTCAAAGCCCACACAAGTTGCCGGCAC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCAC
* * * * *
542107 TTGAGTCAAAGCCCACATACGCTGGTGGCAGCTAAGT
1 CTGAGTCAAAGCCCACACAAG-T--TGGCGGC--A-C
* * *
542144 TTGAGTCAAAGCCCACACAAGTTGGTGGTACC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCA-C
* * *** *
542176 CT-AGTCAAAGCCCGCATAAGCCAGCGTCAC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCAC
* * * * *
542206 CTGAGTCTAAGCTCACACGAGTTAGCGGTAC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCAC
* * ** *
542237 CTAAGTCATAGCCCACACAAGCTTTTGGCACCTAAGT
1 CTGAGTCAAAGCCCACACAAG---TTGGCGGC--A-C
* *
542274 CTGAGTCAAAGCCCACACGAGTTGGTGGCAC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCAC
* *
542305 CTAAGTTTGAGTCAAAGCCCGCACAAGCTGGCGGCAC
1 C------TGAGTCAAAGCCCACACAAGTTGGCGGCAC
* ** * * *
542342 CTGAGTCTAAGCCTGCACGAGTTGGTGACAC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCAC
* * * * *
542373 TTGAGTTAAAGCCCACACGAGTTAGTGGCACC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCA-C
*
542405 CT-AGTCAAAGCCCACACAAGTTGGTGGCAC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCAC
* * *
542435 CTGAGTCTAAGCCCACACGAGTTGGCAGCAC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCAC
*
542466 CTGAGTCAAAGCCCACACAAGTTGGTGGCAC
1 CTGAGTCAAAGCCCACACAAGTTGGCGGCAC
* *
542497 CTAAGTTTGAGTCAAAGCCCACACAAGCTGGCAGCA-
1 C------TGAGTCAAAGCCCACACAAGTTGGCGGCAC
* *
542533 CTCGAGTCAAAGCCCACACAAGCTGGTGGCAC
1 CT-GAGTCAAAGCCCACACAAGTTGGCGGCAC
542565 CT
1 CT
542567 AAGTACGAGT
Statistics
Matches: 349, Mismatches: 82, Indels: 57
0.72 0.17 0.12
Matches are distributed among these distances:
30 7 0.02
31 222 0.64
32 8 0.02
34 18 0.05
36 4 0.01
37 90 0.26
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.18
Consensus pattern (31 bp):
CTGAGTCAAAGCCCACACAAGTTGGCGGCAC
Found at i:542131 original size:68 final size:67
Alignment explanation
Indices: 542012--542196 Score: 176
Period size: 68 Copynumber: 2.7 Consensus size: 67
542002 GTCTTAGAAT
**
542012 GTCAAAGCCCACACAAGTTGGTAGCACCCTAGTCAAAGCCTGCACAAGCTGGCAACACCTAAATC
1 GTCAAAGCCCACACAAGTTGCCAGCACCCTAGTCAAAGCC-GCACAAGCTGGCAACACCTAAATC
542077 TGA
65 TGA
* * *** * *
542080 GTCAAAGCCCACACAAGTTGCCGGCA-CTTGAGTCAAAGCC-CACATACGCTGGTGGCAGCTAAG
1 GTCAAAGCCCACACAAGTTGCCAGCACCCT-AGTCAAAGCCGCACA-A-GCTGGCAACACCTAAA
*
542143 TTTGA
63 TCTGA
*** * *
542148 GTCAAAGCCCACACAAGTTGGTGGTACCCTAGTCAAAGCCCGCATAAGC
1 GTCAAAGCCCACACAAGTTGCCAGCACCCTAGTCAAAG-CCGCACAAGC
542197 CAGCGTCACC
Statistics
Matches: 96, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
66 4 0.04
67 3 0.03
68 81 0.84
69 5 0.05
70 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.17
Consensus pattern (67 bp):
GTCAAAGCCCACACAAGTTGCCAGCACCCTAGTCAAAGCCGCACAAGCTGGCAACACCTAAATCT
GA
Found at i:542346 original size:68 final size:68
Alignment explanation
Indices: 542274--542579 Score: 316
Period size: 62 Copynumber: 4.7 Consensus size: 68
542264 GCACCTAAGT
* * *
542274 CTGAGTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTGAGTCAAAGCCCGCACAAGCTGGCGG
1 CTGAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTTGAGTCAAAGCCCACACAAGCTGGCAG
542339 CAC
66 CAC
* ** * * * * * * **
542342 CTGAGTCTAAGCCTGCACGAGTTGGT-G-A-C--A-CTTGAGTTAAAGCCCACACGAGTTAGTGG
1 CTGAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTTGAGTCAAAGCCCACACAAGCTGGCAG
542401 CACC
66 CA-C
* * *
542405 CT-AGTCAAAGCCCACACAAGTTGGTGGCACC------TGAGTCTAAGCCCACACGAGTTGGCAG
1 CTGAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTTGAGTCAAAGCCCACACAAGCTGGCAG
542463 CAC
66 CAC
542466 CTGAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTTGAGTCAAAGCCCACACAAGCTGGCAG
1 CTGAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTTGAGTCAAAGCCCACACAAGCTGGCAG
542531 CA-
66 CAC
* **
542533 CTCGAGTCAAAGCCCACACAAGCTGGTGGCACCTAAGTACGAGTCAA
1 CT-GAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTTGAGTCAA
542580 GTCCAAATTA
Statistics
Matches: 201, Mismatches: 25, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
61 3 0.01
62 96 0.48
63 5 0.02
64 1 0.00
65 2 0.01
66 1 0.00
67 3 0.01
68 90 0.45
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.17
Consensus pattern (68 bp):
CTGAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTTGAGTCAAAGCCCACACAAGCTGGCAG
CAC
Found at i:542392 original size:167 final size:167
Alignment explanation
Indices: 542108--542442 Score: 383
Period size: 167 Copynumber: 2.0 Consensus size: 167
542098 TGCCGGCACT
* * * * *
542108 TGAGTCAAAGCCCACATACGCTGGTGGCAGCTAAGTTTGAGTCAAAGCCCACACAAGTTGGTGGT
1 TGAGTCAAAGCCCACAGACGCTGGTGGCACCTAAGTTTGAGTCAAAGCCCACACAAGCTGGCGGC
* * * *
542173 ACCCTAGTCAAAGCCCGCATAAGCCAGCGTCACCTGAGTCTAAGCTCACACGAGTTAGCGGTA-C
66 ACCCTAGTCAAAGCCCGCACAAGCCAGCGACACCTGAGTCTAAGCCCACACGAGTTAGCGGCACC
* *
542237 CTAAGTCATAGCCCACACAAGCTT-TTGGCACCTAAGTC
131 CT-AGTCAAAGCCCACACAAG-TTGGTGGCACCTAAGTC
* *
542275 TGAGTCAAAGCCCACACGA-GTTGGTGGCACCTAAGTTTGAGTCAAAGCCCGCACAAGCTGGCGG
1 TGAGTCAAAGCCCACA-GACGCTGGTGGCACCTAAGTTTGAGTCAAAGCCCACACAAGCTGGCGG
* * * *** * * *
542339 CA-CCTGAGTCTAAGCCTGCACGAGTTGGTGACACTTGAGT-TAAAGCCCACACGAGTTAGTGGC
65 CACCCT-AGTCAAAGCCCGCACAAGCCAGCGACACCTGAGTCT-AAGCCCACACGAGTTAGCGGC
*
542402 ACCCTAGTCAAAGCCCACACAAGTTGGTGGCACCTGAGTC
128 ACCCTAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTC
542442 T
1 T
542443 AAGCCCACAC
Statistics
Matches: 140, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
166 6 0.04
167 130 0.93
168 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (167 bp):
TGAGTCAAAGCCCACAGACGCTGGTGGCACCTAAGTTTGAGTCAAAGCCCACACAAGCTGGCGGC
ACCCTAGTCAAAGCCCGCACAAGCCAGCGACACCTGAGTCTAAGCCCACACGAGTTAGCGGCACC
CTAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTC
Found at i:543179 original size:21 final size:22
Alignment explanation
Indices: 543155--543208 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
543145 TTCTACAATT
*
543155 TGTATCGATACAAT-TAGT-GAA
1 TGTATCGATACAATGT-CTCGAA
543176 TGTATCGATAC-ATGTCTCGAA
1 TGTATCGATACAATGTCTCGAA
543197 TGTATCGATACA
1 TGTATCGATACA
543209 GGACCATGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (22 bp):
TGTATCGATACAATGTCTCGAA
Found at i:551578 original size:195 final size:195
Alignment explanation
Indices: 551246--551642 Score: 785
Period size: 195 Copynumber: 2.0 Consensus size: 195
551236 CTTAGTGATA
551246 ATCATCACAGAGATAGGGATTAGGCTTCAACACGGAGGGGATGACATTCAGGCTTTGGTACAAGC
1 ATCATCACAGAGATAGGGATTAGGCTTCAACACGGAGGGGATGACATTCAGGCTTTGGTACAAGC
551311 CTATCATGACTTAGATGCAAAATGGGCCAACAAGTTATGGTAGGCTGAGGAGGATATCTTTAGGT
66 CTATCATGACTTAGATGCAAAATGGGCCAACAAGTTATGGTAGGCTGAGGAGGATATCTTTAGGT
*
551376 GGGCAGCCAACTCCTTCGGGCAACAAATGTATATCGATAATCTCATGGGGTAGATTCATTTGGCT
131 GGGCAGCCAACTCCTTCGGGCAACAAATGTATATCAATAATCTCATGGGGTAGATTCATTTGGCT
551441 ATCATCACAGAGATAGGGATTAGGCTTCAACACGGAGGGGATGACATTCAGGCTTTGGTACAAGC
1 ATCATCACAGAGATAGGGATTAGGCTTCAACACGGAGGGGATGACATTCAGGCTTTGGTACAAGC
551506 CTATCATGACTTAGATGCAAAATGGGCCAACAAGTTATGGTAGGCTGAGGAGGATATCTTTAGGT
66 CTATCATGACTTAGATGCAAAATGGGCCAACAAGTTATGGTAGGCTGAGGAGGATATCTTTAGGT
551571 GGGCAGCCAACTCCTTCGGGCAACAAATGTATATCAATAATCTCATGGGGTAGATTCATTTGGCT
131 GGGCAGCCAACTCCTTCGGGCAACAAATGTATATCAATAATCTCATGGGGTAGATTCATTTGGCT
551636 ATCATCA
1 ATCATCA
551643 AAGCAAGAGA
Statistics
Matches: 201, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
195 201 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (195 bp):
ATCATCACAGAGATAGGGATTAGGCTTCAACACGGAGGGGATGACATTCAGGCTTTGGTACAAGC
CTATCATGACTTAGATGCAAAATGGGCCAACAAGTTATGGTAGGCTGAGGAGGATATCTTTAGGT
GGGCAGCCAACTCCTTCGGGCAACAAATGTATATCAATAATCTCATGGGGTAGATTCATTTGGCT
Found at i:562534 original size:13 final size:13
Alignment explanation
Indices: 562516--562540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
562506 ACAAAAAATA
562516 TGTATCGATACAT
1 TGTATCGATACAT
562529 TGTATCGATACA
1 TGTATCGATACA
562541 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:562536 original size:32 final size:33
Alignment explanation
Indices: 562495--562560 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
562485 AGTAGCTTAA
562495 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
562527 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
562560 A
1 A
562561 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:562945 original size:43 final size:45
Alignment explanation
Indices: 562879--563096 Score: 250
Period size: 49 Copynumber: 4.8 Consensus size: 45
562869 CTATGGCATT
* * *
562879 CTGATTCAAGGCCAGCGATATTGGACTT-A-AAGGTGCCAATGTG
1 CTGATTCAAGGCCAGCTACATTGGACTTAAGAAGGTGCCAATATG
562922 CTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATG
1 CTGATTCAAGGCCAGCTACATTGGACTT----AAGAAGGTGCCAATATG
* * *
562971 CTGATTCAAGGCCAGCTATATTGAACTT-A-AAGGTGCCAATGTG
1 CTGATTCAAGGCCAGCTACATTGGACTTAAGAAGGTGCCAATATG
563014 CTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATG
1 CTGATTCAAGGCCAGCTACATTGGACTT----AAGAAGGTGCCAATATG
*
563063 CTGATTCAAGGCCAGCTATATTAGG-CTT-AGAAGG
1 CTGATTCAAGGCCAGCTACATT-GGACTTAAGAAGG
563097 GTTGCCACCG
Statistics
Matches: 152, Mismatches: 10, Indels: 25
0.81 0.05 0.13
Matches are distributed among these distances:
43 65 0.43
44 7 0.05
48 2 0.01
49 76 0.50
50 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (45 bp):
CTGATTCAAGGCCAGCTACATTGGACTTAAGAAGGTGCCAATATG
Found at i:562980 original size:49 final size:49
Alignment explanation
Indices: 562908--563080 Score: 268
Period size: 49 Copynumber: 3.7 Consensus size: 49
562898 ATTGGACTTA
*
562908 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
* *
562957 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTT-----A-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
*
563000 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
563049 AAGGTGCCAATATGCTGATTCAAGGCCAGCTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTA
563081 TATTAGGCTT
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
43 39 0.35
44 1 0.01
48 1 0.01
49 70 0.63
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (49 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
Found at i:563036 original size:92 final size:92
Alignment explanation
Indices: 562879--563084 Score: 394
Period size: 92 Copynumber: 2.2 Consensus size: 92
562869 CTATGGCATT
* *
562879 CTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
1 CTGATTCAAGGCCAGCTATATTGAACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
562944 GGACTTAAAGAAGAAGGTGCCAATATG
66 GGACTTAAAGAAGAAGGTGCCAATATG
562971 CTGATTCAAGGCCAGCTATATTGAACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
1 CTGATTCAAGGCCAGCTATATTGAACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
563036 GGACTTAAAGAAGAAGGTGCCAATATG
66 GGACTTAAAGAAGAAGGTGCCAATATG
563063 CTGATTCAAGGCCAGCTATATT
1 CTGATTCAAGGCCAGCTATATT
563085 AGGCTTAGAA
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 112 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (92 bp):
CTGATTCAAGGCCAGCTATATTGAACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
GGACTTAAAGAAGAAGGTGCCAATATG
Found at i:563130 original size:32 final size:32
Alignment explanation
Indices: 563089--563253 Score: 228
Period size: 32 Copynumber: 5.2 Consensus size: 32
563079 TATATTAGGC
563089 TTAGA-AGGGTTGCCACCGACTTGTGTGGGCT
1 TTAGAGAGGGTTGCCACCGACTTGTGTGGGCT
* *
563120 TTAGAGAGGGTTGCCACCAACTTGTTTGGGCT
1 TTAGAGAGGGTTGCCACCGACTTGTGTGGGCT
* * *
563152 TTAGAGAAGGTTGCCGCCGACTTGTGTGGGTT
1 TTAGAGAGGGTTGCCACCGACTTGTGTGGGCT
*
563184 TTAGA-AGGGTTACCACCGACTTGTGTGGGCT
1 TTAGAGAGGGTTGCCACCGACTTGTGTGGGCT
* *
563215 TTAGAAGAAGGTTGCCACTGACTTGTGTGGGCT
1 TTAG-AGAGGGTTGCCACCGACTTGTGTGGGCT
563248 TT-GAGA
1 TTAGAGA
563254 AGAAAAAGGT
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
31 34 0.29
32 58 0.50
33 25 0.21
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.30
Consensus pattern (32 bp):
TTAGAGAGGGTTGCCACCGACTTGTGTGGGCT
Found at i:563278 original size:37 final size:33
Alignment explanation
Indices: 563091--563285 Score: 161
Period size: 32 Copynumber: 5.9 Consensus size: 33
563081 TATTAGGCTT
* *
563091 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG-
1 AGAA-GGTTGCCACGGAATTGTGTGGGCTTTAGA
* * *
563124 AGAGGGTTGCCAC-CAACTTGTTTGGGCTTTAG-
1 AGAAGGTTGCCACGGAA-TTGTGTGGGCTTTAGA
* * * *
563156 AGAAGGTTGCCGCCGACTTGTGTGGGTTTTAGA
1 AGAAGGTTGCCACGGAATTGTGTGGGCTTTAGA
* * *
563189 AG--GGTTACCACCGACTTGTGTGGGCTTTAGA
1 AGAAGGTTGCCACGGAATTGTGTGGGCTTTAGA
* *
563220 AGAAGGTTGCCACTGACTTGTGTGGGCTTTGAGA
1 AGAAGGTTGCCACGGAATTGTGTGGGCTTT-AGA
563254 AGAAAAAGGTTGCCACGGAA-T-TGTGGGCTTTA
1 AG---AAGGTTGCCACGGAATTGTGTGGGCTTTA
563286 AAAGGGTGCC
Statistics
Matches: 136, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
31 29 0.21
32 47 0.35
33 30 0.22
34 6 0.04
35 10 0.07
36 1 0.01
37 13 0.10
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (33 bp):
AGAAGGTTGCCACGGAATTGTGTGGGCTTTAGA
Found at i:563297 original size:28 final size:27
Alignment explanation
Indices: 563257--563317 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
563247 TTTGAGAAGA
* *
563257 AAAAGGTTGCCACGGAA-TTGTGGGCTTT
1 AAAAGGGTGCCAC-GAAGTTGTGGAC-TT
563285 AAAAGGGTGCCACGAAGTTGTGGACTT
1 AAAAGGGTGCCACGAAGTTGTGGACTT
563312 AAAAGG
1 AAAAGG
563318 AACAAGGCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (27 bp):
AAAAGGGTGCCACGAAGTTGTGGACTT
Found at i:565041 original size:87 final size:86
Alignment explanation
Indices: 564845--565097 Score: 294
Period size: 87 Copynumber: 2.9 Consensus size: 86
564835 TTTATATTTA
* ** * * **
564845 ATTTGTCGTGATGGTTTTTGCCCTGATCAAACTCTTTTAATACCTTGTTTGACATGATGG-TCTT
1 ATTTGACGTGATGG-TTCAGCCCTGGTCAAACTC-TTT-ATATCTCATTTGACATGATGGTTC-T
* *
564909 CACCTTAGTCAAACAATTTTTTTTCTC
62 CGCCCTAGTCAAAC--TTTTTTTTCTC
* *
564936 ATTTGACATGATGGTTCAGCCCTGGTCAAACTCTTTATATCTCATTTGACGTGATGGTTCTCGCC
1 ATTTGACGTGATGGTTCAGCCCTGGTCAAACTCTTTATATCTCATTTGACATGATGGTTCTCGCC
565001 CTAGTCAAACTTTTTTTTCCTC
66 CTAGTCAAACTTTTTTTT-CTC
* * *
565023 ATTTGACGTGATGGTTCAGCCCTAGTTAAACTCTTTATATCTCATTTGACATGATGGTT-TAGCC
1 ATTTGACGTGATGGTTCAGCCCTGGTCAAACTCTTTATATCTCATTTGACATGATGGTTCTCGCC
*
565087 CTCGTCAAACT
66 CTAGTCAAACT
565098 CTTTATATTT
Statistics
Matches: 143, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
86 22 0.15
87 58 0.41
88 30 0.21
89 5 0.03
90 16 0.11
91 12 0.08
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (86 bp):
ATTTGACGTGATGGTTCAGCCCTGGTCAAACTCTTTATATCTCATTTGACATGATGGTTCTCGCC
CTAGTCAAACTTTTTTTTCTC
Found at i:565122 original size:43 final size:43
Alignment explanation
Indices: 564827--565105 Score: 251
Period size: 43 Copynumber: 6.3 Consensus size: 43
564817 TGGTTTAGGA
* * * * **
564827 TCAAACTCTTTATATTTAATTTGTCGTGATGGTTTTTGCCCT-G
1 TCAAACTCTTTATATCTCATTTGACATGATGG-TTCAGCCCTAG
* ** *
564870 ATCAAACTCTTTTAATACCTTGTTTGACATGATGGTCTTCA-CCTTAG
1 -TCAAACTC-TTT-ATATCTCATTTGACATGATGG--TTCAGCCCTAG
* * *
564917 TCAAACAAT-TTTTTTTCTCATTTGACATGATGGTTCAGCCCTGG
1 TCAAAC--TCTTTATATCTCATTTGACATGATGGTTCAGCCCTAG
* *
564961 TCAAACTCTTTATATCTCATTTGACGTGATGGTTCTCGCCCTAG
1 TCAAACTCTTTATATCTCATTTGACATGATGGTTC-AGCCCTAG
* * *
565005 TCAAACT-TTTTTTTCCTCATTTGACGTGATGGTTCAGCCCTAG
1 TCAAACTCTTTATAT-CTCATTTGACATGATGGTTCAGCCCTAG
* * *
565048 TTAAACTCTTTATATCTCATTTGACATGATGGTTTAGCCCTCG
1 TCAAACTCTTTATATCTCATTTGACATGATGGTTCAGCCCTAG
565091 TCAAACTCTTTATAT
1 TCAAACTCTTTATAT
565106 TTTGTTTTAC
Statistics
Matches: 192, Mismatches: 32, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
42 1 0.01
43 85 0.44
44 56 0.29
45 19 0.10
46 27 0.14
47 3 0.02
48 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.42
Consensus pattern (43 bp):
TCAAACTCTTTATATCTCATTTGACATGATGGTTCAGCCCTAG
Found at i:565141 original size:87 final size:86
Alignment explanation
Indices: 564865--565141 Score: 249
Period size: 87 Copynumber: 3.2 Consensus size: 86
564855 ATGGTTTTTG
* * ** *
564865 CCCTGATCAAACTCTTTTAATACCTTGTTTGACATGATGG-TCTTCA-CCTTAGTCAAACAATTT
1 CCCTGGTCAAACTC-TTT-ATATCTCATTTGACATGATGGTTC-T-AGCCCTAGTCAAAC--TTT
** *
564928 TTTTTCTCATTTGACATGATGGTTCAG
60 TTTTTCTCATTTGACATGATGGCCCAA
* *
564955 CCCTGGTCAAACTCTTTATATCTCATTTGACGTGATGGTTCTCGCCCTAGTCAAACTTTTTTTTC
1 CCCTGGTCAAACTCTTTATATCTCATTTGACATGATGGTTCTAGCCCTAGTCAAACTTTTTTTT-
* ** *
565020 CTCATTTGACGTGATGGTTCAG
65 CTCATTTGACATGATGGCCCAA
* * *
565042 CCCTAGTTAAACTCTTTATATCTCATTTGACATGATGGTT-TAGCCCTCGTCAAACTCTTTATAT
1 CCCTGGTCAAACTCTTTATATCTCATTTGACATGATGGTTCTAGCCCTAGTCAAACT-TTT-T-T
* *
565106 TT-T-GTTTTACATGATGGCCCCAA
63 TTCTCATTTGACATGATGG-CCCAA
565129 CCCTGGTCAAACT
1 CCCTGGTCAAACT
565142 TGTTACATCT
Statistics
Matches: 159, Mismatches: 21, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
86 33 0.21
87 75 0.47
88 30 0.19
89 8 0.05
90 13 0.08
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.40
Consensus pattern (86 bp):
CCCTGGTCAAACTCTTTATATCTCATTTGACATGATGGTTCTAGCCCTAGTCAAACTTTTTTTTC
TCATTTGACATGATGGCCCAA
Found at i:565353 original size:83 final size:84
Alignment explanation
Indices: 565182--565359 Score: 216
Period size: 83 Copynumber: 2.1 Consensus size: 84
565172 AAATCTTTTC
* * * * *
565182 TTGACTTGTCGGTTCAATCCCGGTTAACTTTTTATCCTTTGTTCACCTATCGGCTTAGTCTCAGG
1 TTGACTTGTCGATTCAATCCCGATCAACTTTTTATCCTTTATTCACCTATCGGCTTAATCTCAGG
** * *
565247 TAAATTTTTTTATCCTTTG
66 TAAATCCTTTCATCCTTTA
* * * *
565266 TTGACTTGTCGATTTAATCCCGATCAACTTTTTATCC-TTATTCACCTGTTGGCTTAATC-CTGG
1 TTGACTTGTCGATTCAATCCCGATCAACTTTTTATCCTTTATTCACCTATCGGCTTAATCTC-AG
565329 GTAAATCCTTTCATCCTTTA
65 GTAAATCCTTTCATCCTTTA
565349 TTGACTTGTCG
1 TTGACTTGTCG
565360 GTTTGTAGAC
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
82 1 0.01
83 46 0.57
84 33 0.41
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (84 bp):
TTGACTTGTCGATTCAATCCCGATCAACTTTTTATCCTTTATTCACCTATCGGCTTAATCTCAGG
TAAATCCTTTCATCCTTTA
Found at i:565686 original size:19 final size:18
Alignment explanation
Indices: 565646--565794 Score: 130
Period size: 19 Copynumber: 8.8 Consensus size: 18
565636 ATTTCAACGA
*
565646 TTTGTATCGATACAAAAAG
1 TTTGTATCGATAC-ATAAG
565665 TGTTGTATCGATACATAAG
1 T-TTGTATCGATACATAAG
565684 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
565700 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
565716 TTTTGTATCGATAC--AA-
1 -TTTGTATCGATACATAAG
565732 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
565748 TTTTGTATCGATAC--AA-
1 -TTTGTATCGATACATAAG
565764 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
565780 TTTTGTATCGATACA
1 -TTTGTATCGATACA
565795 ATATATCGCT
Statistics
Matches: 110, Mismatches: 1, Indels: 38
0.74 0.01 0.26
Matches are distributed among these distances:
13 33 0.30
15 6 0.05
17 6 0.05
19 53 0.48
20 12 0.11
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:565705 original size:13 final size:13
Alignment explanation
Indices: 565687--565775 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
565677 ACATAAGTGT
565687 TGTATCGATACAA
1 TGTATCGATACAA
565700 TGTATCGATACATAA
1 TGTATCGATAC--AA
565715 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
565732 TGTATCGATACATAA
1 TGTATCGATAC--AA
565747 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
565764 TGTATCGATACA
1 TGTATCGATACA
565776 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:565709 original size:32 final size:32
Alignment explanation
Indices: 565668--565807 Score: 253
Period size: 32 Copynumber: 4.4 Consensus size: 32
565658 CAAAAAGTGT
*
565668 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
565700 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
565732 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
565764 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
* *
565796 TATATCGCTACA
1 TGTATCGATACA
565808 AAGCTACTGC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 105 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:565851 original size:96 final size:96
Alignment explanation
Indices: 565668--565891 Score: 242
Period size: 96 Copynumber: 2.3 Consensus size: 96
565658 CAAAAAGTGT
* * ** * *
565668 TGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACATAAGTTTTGTATCGATACAAT
1 TGTATCGATACATAAGTTTTGTATCGATACAATATATCGATACATAAGTACTGCATAGATACAAT
* **
565733 GTATCGATACATAAGTTTTGTATCGATACAA
66 GTATCGATACATAACTAATGTATCGATACAA
*
565764 TGTATCGATACATAAGTTTTGTATCGATACAATATATCGCTACA-AAGCTACTGCCA-AGA-A-A
1 TGTATCGATACATAAGTTTTGTATCGATACAATATATCGATACATAAG-TACTG-CATAGATACA
* *
565825 ATGTATCGATACATTACTCAAATGTATCGATACAT
64 ATGTATCGATACATAACT--AATGTATCGATACAA
*
565860 TGTATCGATACACTGA-TCTTTGTATCGATACA
1 TGTATCGATACA-TAAGT-TTTGTATCGATACA
565892 TGCAGGCAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
94 17 0.16
95 4 0.04
96 71 0.65
97 17 0.16
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (96 bp):
TGTATCGATACATAAGTTTTGTATCGATACAATATATCGATACATAAGTACTGCATAGATACAAT
GTATCGATACATAACTAATGTATCGATACAA
Found at i:565865 original size:13 final size:13
Alignment explanation
Indices: 565847--565871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
565837 ATTACTCAAA
565847 TGTATCGATACAT
1 TGTATCGATACAT
565860 TGTATCGATACA
1 TGTATCGATACA
565872 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:569869 original size:165 final size:167
Alignment explanation
Indices: 569618--569951 Score: 383
Period size: 166 Copynumber: 2.0 Consensus size: 167
569608 TTCTTTTTAA
* * * *
569618 TTCATGAGTTTTTCAGTTTTTTCCTTGAAATCTCTTTATTTTCGAAATACGGAGTTTGCTCCTCC
1 TTCATGAGTTTTTCAGTTTTTTCCTTAAAATCTCTTTAGTTTCGAAAAACGGAGTTTGCTACTCC
* * * *
569683 ATAAATGTTTTTGGGGGATTTTTCTCAGTTCAAAA-TTTTAATATTCAT-TAAATATCATCATTT
66 ATAAATGTTTTTGGAGGATTTTTCTCAATTCAAAACTTTTAAAATTCATCT-AATATCATCATTA
* *
569746 AATTCATAGTAAATTAGTTTTAAAAAAATC-ATTTATT
130 AATTCACAGTAAATCAGTTTTAAAAAAATCAATTTATT
*** * *
569783 TTCATGAGTTTTTCA-TTTTTTCCTTAAAAT-TCTCTT-GTTTCGAAAAAATTTAGTTTTCTATT
1 TTCATGAGTTTTTCAGTTTTTTCCTTAAAATCTCT-TTAGTTTCG-AAAAACGGAGTTTGCTACT
* * **
569845 CCATAAATGTTTTTAGGAGGATTTTTCTCAATTTAAAACTTTTAAAATTTATCTAATATTGTCAT
64 CCATAAATGTTTTT-GGAGGATTTTTCTCAATTCAAAACTTTTAAAATTCATCTAATATCATCAT
* ** *
569910 TAAATTCACATTAAATCAGTTTTGTAAAATTCAATTTATT
128 TAAATTCACAGTAAATCAGTTTTAAAAAAATCAATTTATT
569950 TT
1 TT
569952 TTTTGTATAT
Statistics
Matches: 140, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
163 8 0.06
164 42 0.30
165 35 0.25
166 45 0.32
167 10 0.07
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (167 bp):
TTCATGAGTTTTTCAGTTTTTTCCTTAAAATCTCTTTAGTTTCGAAAAACGGAGTTTGCTACTCC
ATAAATGTTTTTGGAGGATTTTTCTCAATTCAAAACTTTTAAAATTCATCTAATATCATCATTAA
ATTCACAGTAAATCAGTTTTAAAAAAATCAATTTATT
Found at i:570454 original size:10 final size:10
Alignment explanation
Indices: 570439--570477 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
570429 AAAAAGAGAG
570439 AAGAAAAAAA
1 AAGAAAAAAA
**
570449 AAGAAAACGA
1 AAGAAAAAAA
*
570459 TAGAAAAAAA
1 AAGAAAAAAA
570469 AAGAAAAAA
1 AAGAAAAAA
570478 TTAAGCTAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:570961 original size:40 final size:40
Alignment explanation
Indices: 570914--571038 Score: 223
Period size: 40 Copynumber: 3.1 Consensus size: 40
570904 CATTTTGAGC
* *
570914 TGATTTGAGGGATTATTGGTGTGTTTTAATGACATTTCGG
1 TGATTTGAGGGATTATTAGTGTGTTTTAATGACATTTCGA
570954 TGATTTGAGGGATTATTAGTGTGTTTTAATGACATTTCGA
1 TGATTTGAGGGATTATTAGTGTGTTTTAATGACATTTCGA
*
570994 TGATTTGAGGGATTATTAGTGTGTTTTAATGACATTTTGA
1 TGATTTGAGGGATTATTAGTGTGTTTTAATGACATTTCGA
571034 TGATT
1 TGATT
571039 AGGGACTAAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.23, C:0.04, G:0.26, T:0.46
Consensus pattern (40 bp):
TGATTTGAGGGATTATTAGTGTGTTTTAATGACATTTCGA
Found at i:578592 original size:31 final size:31
Alignment explanation
Indices: 578557--578620 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
578547 TGAAATATGT
578557 AAATTTGCCTGCATGTATCGATACATTGAAG
1 AAATTTGCCTGCATGTATCGATACATTGAAG
578588 AAATTTGCCTGCATGTATCGATACATTGAAG
1 AAATTTGCCTGCATGTATCGATACATTGAAG
578619 AA
1 AA
578621 TGTATTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (31 bp):
AAATTTGCCTGCATGTATCGATACATTGAAG
Found at i:578721 original size:54 final size:51
Alignment explanation
Indices: 578600--578740 Score: 165
Period size: 54 Copynumber: 2.7 Consensus size: 51
578590 ATTTGCCTGC
* * *
578600 ATGTATCGATACATTGAAGAATGTATTGATACATTTAGGTCAAAACCTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAACCTAGA
* * * * *
578651 ATGCATCGATACAATGAATATTGTATCGATACCTTTGGGTCAAAAACACCTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTC--AAA-ACCTAGA
* *
578705 ATGTATCGATAAAATGAAAAATGTACCGATACATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
578741 TCTTTCCAGA
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
51 34 0.46
53 3 0.04
54 37 0.50
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAACCTAGA
Found at i:578823 original size:20 final size:20
Alignment explanation
Indices: 578800--578838 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
578790 TTCAAACATA
*
578800 TATCAATACATTCACTTATG
1 TATCAAGACATTCACTTATG
578820 TATCAAGACATTCACTTAT
1 TATCAAGACATTCACTTAT
578839 TATATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (20 bp):
TATCAAGACATTCACTTATG
Found at i:579838 original size:52 final size:51
Alignment explanation
Indices: 579602--579838 Score: 172
Period size: 52 Copynumber: 4.5 Consensus size: 51
579592 TAAGGAAGAA
* * *
579602 AAGAGTGCCAATGTGCTAATTCAAGGCTAGTGACATT-GGACTTAAAGATGAG
1 AAGAGTGCCAATATGCTGATT-AAGGCCAGTGACATTAGG-CTTAAAGATGAG
*** * * * *
579654 AAGAACACCATTGTGCTGATTTAAGGCCAGTGACATTAGGCTTAAAAATGAT
1 AAGAGTGCCAATATGCTGA-TTAAGGCCAGTGACATTAGGCTTAAAGATGAG
* * * * * * ** *
579706 AAAAGTACCAATATACTGATTTAAGGCTAGTGATATCAAACTTAAAGATGAC
1 AAGAGTGCCAATATGCTGA-TTAAGGCCAGTGACATTAGGCTTAAAGATGAG
* * * * *
579758 AA-AGGTGCTAATTTGTTAATTCAAGGCCAGCGACATTAGGCTTAAAGATGAG
1 AAGA-GTGCCAATATGCTGATT-AAGGCCAGTGACATTAGGCTTAAAGATGAG
*
579810 AAGAGTGCCAATATTCTGATTAATGGCCA
1 AAGAGTGCCAATATGCTGATTAA-GGCCA
579839 ACGACGTTGG
Statistics
Matches: 140, Mismatches: 39, Indels: 12
0.73 0.20 0.06
Matches are distributed among these distances:
51 5 0.04
52 130 0.93
53 5 0.04
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (51 bp):
AAGAGTGCCAATATGCTGATTAAGGCCAGTGACATTAGGCTTAAAGATGAG
Found at i:580003 original size:33 final size:32
Alignment explanation
Indices: 579931--580045 Score: 113
Period size: 32 Copynumber: 3.6 Consensus size: 32
579921 TAACACCGAT
** * * * *
579931 TTGTGTGGGCTTTTGAAATGGTTGCCAATGAT
1 TTGTGTGGGCTTTAAAAAAGGTTGCCACTAAC
579963 TTGTGTGGGCTTTAGAAAAAGGTTGCCACTAAC
1 TTGTGTGGGCTTTA-AAAAAGGTTGCCACTAAC
* * * * *
579996 TTATGTGGGCTATAAAAAGGGTTGCTACCAAC
1 TTGTGTGGGCTTTAAAAAAGGTTGCCACTAAC
*
580028 TTGTATGGGCTTTAAAAA
1 TTGTGTGGGCTTTAAAAA
580046 GTGTTACCAC
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
32 43 0.63
33 25 0.37
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (32 bp):
TTGTGTGGGCTTTAAAAAAGGTTGCCACTAAC
Found at i:580029 original size:32 final size:32
Alignment explanation
Indices: 579966--580055 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
579956 CAATGATTTG
* *
579966 TGTGGGCTTTAGAAAAAGGTTGCCACTAACTTA
1 TGTGGGCTTTA-AAAAGGGTTGCCACCAACTTA
* * *
579999 TGTGGGCTATAAAAAGGGTTGCTACCAACTTG
1 TGTGGGCTTTAAAAAGGGTTGCCACCAACTTA
* * *
580031 TATGGGCTTTAAAAAGTGTTACCAC
1 TGTGGGCTTTAAAAAGGGTTGCCAC
580056 AGAGTTGTAG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 37 0.79
33 10 0.21
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (32 bp):
TGTGGGCTTTAAAAAGGGTTGCCACCAACTTA
Found at i:580073 original size:30 final size:30
Alignment explanation
Indices: 580037--580223 Score: 102
Period size: 30 Copynumber: 6.4 Consensus size: 30
580027 CTTGTATGGG
* *
580037 CTTTAAAAAGTGTTACCACAGAGTTGTAG-A
1 CTTTAAAAAGAGGTACCACAGAGTTGT-GCA
* *
580067 CTTTAAAAAAAGGTGCCACAGAGTTGTGCA
1 CTTTAAAAAGAGGTACCACAGAGTTGTGCA
* * * *
580097 CTTTAAAAAGGGGT---ATAGAGTTATGGA
1 CTTTAAAAAGAGGTACCACAGAGTTGTGCA
** * * *
580124 CTTTAAAAAG-GGTGTCATAAAGTTGTGGA
1 CTTTAAAAAGAGGTACCACAGAGTTGTGCA
* * * *
580153 CTTT-AAAA-AGCTACCACGGAGTTATGGA
1 CTTTAAAAAGAGGTACCACAGAGTTGTGCA
* * *
580181 CTTTTGAAAAAG-GGTGCCACAGAGTCGTGGA
1 C-TTT-AAAAAGAGGTACCACAGAGTTGTGCA
580212 CTTTGAAAAAGA
1 CTTT-AAAAAGA
580224 TTGCCATTGA
Statistics
Matches: 124, Mismatches: 23, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
26 3 0.02
27 20 0.16
28 17 0.14
29 19 0.15
30 46 0.37
31 19 0.15
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (30 bp):
CTTTAAAAAGAGGTACCACAGAGTTGTGCA
Found at i:580156 original size:56 final size:57
Alignment explanation
Indices: 580056--580162 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 57
580046 GTGTTACCAC
* *
580056 AGAGTTGTAGACTTTAAAAAAAGGTGCCACAGAGTTGTGCACTTTAAAAAGGGGTAT
1 AGAGTTATAGACTTTAAAAAAAGGTGCCACAAAGTTGTGCACTTTAAAAAGGGGTAT
* * * * *
580113 AGAGTTATGGACTTT-AAAAAGGGTGTCATAAAGTTGTGGACTTTAAAAAG
1 AGAGTTATAGACTTTAAAAAAAGGTGCCACAAAGTTGTGCACTTTAAAAAG
580163 CTACCACGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
56 30 0.70
57 13 0.30
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.28
Consensus pattern (57 bp):
AGAGTTATAGACTTTAAAAAAAGGTGCCACAAAGTTGTGCACTTTAAAAAGGGGTAT
Found at i:580157 original size:29 final size:29
Alignment explanation
Indices: 580037--580866 Score: 508
Period size: 29 Copynumber: 28.1 Consensus size: 29
580027 CTTGTATGGG
* * *
580037 CTTTAAAAAGTGTTACCACAGAGTTGTAGA
1 CTTTAAAAAG-GGTGCCACAGAGTTGTGGA
* *
580067 CTTTAAAAAAAGGTGCCACAGAGTTGTGCA
1 CTTT-AAAAAGGGTGCCACAGAGTTGTGGA
* * *
580097 CTTTAAAAAGGG-G-TATAGAGTTATGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
* * *
580124 CTTTAAAAAGGGTGTCATAAAGTTGTGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
* * * *
580153 CTTTAAAAA-GCTACCACGGAGTTATGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
*
580181 CTTTTGAAAAAGGGTGCCACAGAGTCGTGGA
1 C-TTT-AAAAAGGGTGCCACAGAGTTGTGGA
** ** *
580212 CTTTGAAAAAGATTGCCATTGAGTCGTGGA
1 CTTT-AAAAAGGGTGCCACAGAGTTGTGGA
* *** *
580242 CTTT-GAACTTGTGCCACTA-AGTCGTGGA
1 CTTTAAAAAGGGTGCCAC-AGAGTTGTGGA
*
580270 ATTT-AAAAGAGGTGCCAC-GAAGTTGTGGA
1 CTTTAAAAAG-GGTGCCACAG-AGTTGTGGA
* *
580299 CATTTAAAAAAAATGGTGCCACAGAGTTGTGAA
1 C-TTT---AAAAAGGGTGCCACAGAGTTGTGGA
* *
580332 CATTTAAAAAAAAAGGGTGCCACGGTGTTGTGGA
1 C-TTT----AAAAAGGGTGCCACAGAGTTGTGGA
* * * *
580366 CTTT-AAAAGAGTGCCACAAAGATATGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
** *
580394 CTTTAAAAA-GGTGCCATGGAGTTATGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
* **
580422 CTTTTAAAAAAAGGTGCCACTA-AGTCATGGA
1 C-TTT-AAAAAGGGTGCCAC-AGAGTTGTGGA
* * *
580453 CTTTGAAAAA-TGTGCCATTA-AGTCGTGGA
1 CTTT-AAAAAGGGTGCCA-CAGAGTTGTGGA
*
580482 CTTTAAAAAAGGGTGCCACGGAGTTGTGGA
1 CTTT-AAAAAGGGTGCCACAGAGTTGTGGA
* * * *
580512 CTTTAAAAAGGATGTCAC-GAATTTATGGA
1 CTTTAAAAAGGGTGCCACAG-AGTTGTGGA
* * *
580541 CTTTGAAAAGGGTGCCACGGAGTTATGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
* ** **
580570 CTTTTGAAAACGTATGCCACTA-AGTCATGGA
1 C-TTT-AAAAAGGGTGCCAC-AGAGTTGTGGA
* * *
580601 CTTTGAAAAA-TGTGCCATTA-AGTCGTGGA
1 CTTT-AAAAAGGGTGCCA-CAGAGTTGTGGA
*
580630 CTTTGAAAAAGGGTGCCACGGAGTTGTGGA
1 CTTT-AAAAAGGGTGCCACAGAGTTGTGGA
* * * *
580660 CTTTAAAAAAGATGCCATAGATTTGTGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
* *
580689 CTTTGAAAAGGGTGCTAC-GAAGTTGTGGA
1 CTTTAAAAAGGGTGCCACAG-AGTTGTGGA
* * *
580718 CTTTAAAAAGTGTGCCACGGATTTGTGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
* *
580747 CTTTGAGAAGGGTGCCACAGAGTTAG-GGA
1 CTTTAAAAAGGGTGCCACAGAGTT-GTGGA
* **
580776 CTTTAGAAAGGGTGTTACAGAGTTGTGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
* * *
580805 CTTTGAAAAGGGTGCTACGGAGTTGTGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
* * **
580834 CTTTGAAAAGGGTGCCACAAAGTCATGGA
1 CTTTAAAAAGGGTGCCACAGAGTTGTGGA
580863 CTTT
1 CTTT
580867 GAGAAGTTAC
Statistics
Matches: 635, Mismatches: 128, Indels: 75
0.76 0.15 0.09
Matches are distributed among these distances:
27 22 0.03
28 76 0.12
29 305 0.48
30 123 0.19
31 55 0.09
33 24 0.04
34 30 0.05
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.27
Consensus pattern (29 bp):
CTTTAAAAAGGGTGCCACAGAGTTGTGGA
Found at i:580351 original size:34 final size:33
Alignment explanation
Indices: 580274--580373 Score: 123
Period size: 34 Copynumber: 3.0 Consensus size: 33
580264 CGTGGAATTT
580274 AAAAGAGGTGCCACGAAGTTGTGGACATTT-AAAA
1 AAAAG-GGTGCCACG-AGTTGTGGACATTTAAAAA
* *
580308 AAAATGGTGCCACAGAGTTGTGAACATTTAAAAA
1 AAAAGGGTGCCAC-GAGTTGTGGACATTTAAAAA
*
580342 AAAAGGGTGCCACGGTGTTGTGGAC-TTTAAAA
1 AAAAGGGTGCCAC-GAGTTGTGGACATTTAAAA
580374 GAGTGCCACA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
33 28 0.48
34 30 0.52
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.23
Consensus pattern (33 bp):
AAAAGGGTGCCACGAGTTGTGGACATTTAAAAA
Found at i:580588 original size:148 final size:147
Alignment explanation
Indices: 580340--580866 Score: 577
Period size: 148 Copynumber: 3.6 Consensus size: 147
580330 AACATTTAAA
* * *
580340 AAAAAAGGGTGCCACGGTGTTGTGGACTTT-AAAA-GAGTGCCACAAAGATATGGACTTT-AAAA
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGGA-TGCCACGAAGTTATGGACTTTGAAAA
* * *
580402 AGGTGCCATGGAGTTATGGACTTTTAAAAAAAG-GTGCCACTAAGTCATGGACTTTGAAAAATGT
65 GGGTGCCACGAAGTTATGGACTTTT--AAAAAGTGTGCCACTAAGTCATGGACTTTGAAAAATGT
580466 GCCATTAAGTCGTGGACTTT
128 GCCATTAAGTCGTGGACTTT
* *
580486 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGGATGTCACGAATTTATGGACTTTGAAAAG
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGGATGCCACGAAGTTATGGACTTTGAAAAG
* * *
580551 GGTGCCACGGAGTTATGGACTTTTGAAAACGTATGCCACTAAGTCATGGACTTTGAAAAATGTGC
66 GGTGCCACGAAGTTATGGACTTTT-AAAAAGTGTGCCACTAAGTCATGGACTTTGAAAAATGTGC
580616 CATTAAGTCGTGGACTTT
130 CATTAAGTCGTGGACTTT
* * * * *
580634 GAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAAGATGCCA-TAGATTTGTGGACTTTGAAAA
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGGATGCCACGA-AGTTATGGACTTTGAAAA
* * ** * ** * **
580698 GGGTGCTACGAAGTTGTGGAC-TTTAAAAAGTGTGCCACGGATTTGTGGACTTTGAGAAGGGTGC
65 GGGTGCCACGAAGTTATGGACTTTTAAAAAGTGTGCCACTAAGTCATGGACTTTGAAAAATGTGC
* *
580762 CA-CAGAGTTAG-GGACTTT
130 CATTA-AG-TCGTGGACTTT
* ** * * * * * *
580780 -AGAAAGGGTGTTACAGAGTTGTGGACTTTGAAAAGGGTGCTACGGAGTTGTGGACTTTGAAAAG
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGGATGCCACGAAGTTATGGACTTTGAAAAG
* *
580844 GGTGCCACAAAGTCATGGACTTT
66 GGTGCCACGAAGTTATGGACTTT
580867 GAGAAGTTAC
Statistics
Matches: 327, Mismatches: 45, Indels: 18
0.84 0.12 0.05
Matches are distributed among these distances:
145 69 0.21
146 72 0.22
147 32 0.10
148 154 0.47
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (147 bp):
AAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGGATGCCACGAAGTTATGGACTTTGAAAAG
GGTGCCACGAAGTTATGGACTTTTAAAAAGTGTGCCACTAAGTCATGGACTTTGAAAAATGTGCC
ATTAAGTCGTGGACTTT
Found at i:588118 original size:19 final size:20
Alignment explanation
Indices: 588094--588145 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
588084 TAGCCAAACT
588094 TGTATCGATACAC-AAAATA
1 TGTATCGATACACAAAAATA
588113 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC-AAAAATA
588134 TGTATCGATACA
1 TGTATCGATACA
588146 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACAAAAATA
Found at i:592210 original size:15 final size:15
Alignment explanation
Indices: 592190--592220 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
592180 TAAAAATGTC
*
592190 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
592205 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
592220 C
1 C
592221 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:594091 original size:8 final size:8
Alignment explanation
Indices: 594078--594107 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
594068 TTGATTAAAC
594078 TTTGTGAT
1 TTTGTGAT
594086 TTTGTGAT
1 TTTGTGAT
594094 TTTGTGAT
1 TTTGTGAT
594102 TTTGTG
1 TTTGTG
594108 TTGAATGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (8 bp):
TTTGTGAT
Found at i:594328 original size:13 final size:13
Alignment explanation
Indices: 594310--594347 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
594300 CATTTTTCTT
594310 TGTATCGATACAA
1 TGTATCGATACAA
*
594323 TGTATCGATACAC
1 TGTATCGATACAA
594336 TGTATCGATACA
1 TGTATCGATACA
594348 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:594502 original size:20 final size:20
Alignment explanation
Indices: 594459--594504 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
594449 AAATCTTTTG
594459 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
594480 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
594500 CAAAA
1 CAAAA
594505 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:596900 original size:19 final size:20
Alignment explanation
Indices: 596876--596927 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
596866 TAGCCAAACT
596876 TGTATCGATACAC-AAAATA
1 TGTATCGATACACAAAAATA
596895 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC-AAAAATA
596916 TGTATCGATACA
1 TGTATCGATACA
596928 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACAAAAATA
Found at i:599467 original size:29 final size:29
Alignment explanation
Indices: 599419--600031 Score: 410
Period size: 29 Copynumber: 20.6 Consensus size: 29
599409 TGGCAATATG
*
599419 CTTTAAAAAAGGTTGCCACGGAGTTGTGGA
1 CTTTGAAAAAGG-TGCCACGGAGTTGTGGA
* *
599449 CTTTGTAAAAGGTGCCACGGAGTTGTGGG
1 CTTTGAAAAAGGTGCCACGGAGTTGTGGA
* * * *
599478 CTTTAAAAAAGGTGCCATGAAGTTGTGAA
1 CTTTGAAAAAGGTGCCACGGAGTTGTGGA
* *
599507 CTTTTGAAAAATGGTGCCACAGAGTTGTGAA
1 C-TTTGAAAAA-GGTGCCACGGAGTTGTGGA
** *
599538 CTTTGAAAAAGGTTGCCACTAAGTCGTGGA
1 CTTTGAAAAAGG-TGCCACGGAGTTGTGGA
*** ** *
599568 CTTTGAACTTGGTGCCACTAAGTGGTGGA
1 CTTTGAAAAAGGTGCCACGGAGTTGTGGA
* * * *
599597 CTTTCAAAAGGGTGTCACGAAGTTGTGGA
1 CTTTGAAAAAGGTGCCACGGAGTTGTGGA
* *
599626 CATTTAGAAAAAATGTGCCATGGAGTTGTGGA
1 C-TTT-G-AAAAAGGTGCCACGGAGTTGTGGA
* * * *
599658 CTTT-AAAAAGAGTGTCACAGAATTGTAGA
1 CTTTGAAAAAG-GTGCCACGGAGTTGTGGA
* *
599687 CTTT-AAAAAGGATGCCACGAAGTTATGGA
1 CTTTGAAAAAGG-TGCCACGGAGTTGTGGA
* ** *
599716 CTTTTGAAAAATGGCGCCACTAAGTCGTGGA
1 C-TTTGAAAAA-GGTGCCACGGAGTTGTGGA
* * * ** **
599747 CTTTGGAAAATGTGCTATTGAGTCATGGA
1 CTTTGAAAAAGGTGCCACGGAGTTGTGGA
* ***
599776 CTTTGAAAAATGGTACCTTAGAGTTGTGGA
1 CTTTGAAAAA-GGTGCCACGGAGTTGTGGA
* ** *
599806 CTTT-AAAAATGATGCCATAGAGTTGTAGA
1 CTTTGAAAAA-GGTGCCACGGAGTTGTGGA
* * *
599835 CTTTGAGAAGGGTGCCACGAAGTTGTGGA
1 CTTTGAAAAAGGTGCCACGGAGTTGTGGA
*
599864 CTTTAGAAAAGGGTGCCACGGAGTTGTGGA
1 CTTT-GAAAAAGGTGCCACGGAGTTGTGGA
* *
599894 CTTTG-AGAAGAGTTCCACGGAGTTGTGGA
1 CTTTGAAAAAG-GTGCCACGGAGTTGTGGA
*
599923 CTTT-AGAAAAGGATGCCACAGAGTTGTGGA
1 CTTTGA-AAAAGG-TGCCACGGAGTTGTGGA
* * ***
599953 C-TTCAAAAAGGGGTGCCACGTAGTTGCAAA
1 CTTTGAAAAA--GGTGCCACGGAGTTGTGGA
* * *
599983 CTTTAGAAAAGGGTACCACGAAGTTGTGGA
1 CTTT-GAAAAAGGTGCCACGGAGTTGTGGA
*
600013 CTTTGAAAAGGGGTGCCAC
1 CTTTGAAAA-AGGTGCCAC
600032 AGAGCCACGG
Statistics
Matches: 462, Mismatches: 97, Indels: 48
0.76 0.16 0.08
Matches are distributed among these distances:
28 9 0.02
29 215 0.47
30 169 0.37
31 43 0.09
32 26 0.06
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (29 bp):
CTTTGAAAAAGGTGCCACGGAGTTGTGGA
Found at i:599645 original size:90 final size:90
Alignment explanation
Indices: 599419--599756 Score: 209
Period size: 90 Copynumber: 3.8 Consensus size: 90
599409 TGGCAATATG
* * * * ** * *
599419 CTTTAAAAAAGGTTGCCACGGAGTTGTGGACTTT-GTAAAA-GGTGCCACGGAGTTGTGGGCTTT
1 CTTT-AAAAAGGATGCCACGAAGTTATGGACTTTAGAAAAATGGTGCCACTAAGTCGTGGACTTT
* * *
599482 AAAAAAG-GTGCCA-TGAAGTTGT-GAA
65 GAAAAAGAGTGCCACAGAA-TGGTAG-A
* *
599507 CTTTTGAAAAATGG-TGCCAC-AGAGTTGTGAACTTT-GAAAAA-GGTTGCCACTAAGTCGTGGA
1 C-TTT-AAAAA-GGATGCCACGA-AGTTATGGACTTTAGAAAAATGG-TGCCACTAAGTCGTGGA
*** * *
599568 CTTTGAACTTG-GTGCCACTA-AGTGGTGGA
61 CTTTGAAAAAGAGTGCCAC-AGAATGGTAGA
* * * * * *
599597 CTTTCAAAAGGGTGTCACGAAGTTGTGGACATTTAGAAAAAAT-GTGCCA-TGGAGTTGTGGACT
1 CTTTAAAAAGGATGCCACGAAGTTATGGAC-TTTAG-AAAAATGGTGCCACT-AAGTCGTGGACT
* *
599660 TT-AAAAAGAGTGTCACAGAATTGTAGA
63 TTGAAAAAGAGTGCCACAGAATGGTAGA
* *
599687 CTTTAAAAAGGATGCCACGAAGTTATGGACTTTTGAAAAATGGCGCCACTAAGTCGTGGACTTTG
1 CTTTAAAAAGGATGCCACGAAGTTATGGACTTTAGAAAAATGGTGCCACTAAGTCGTGGACTTTG
*
599752 GAAAA
66 AAAAA
599757 TGTGCTATTG
Statistics
Matches: 195, Mismatches: 36, Indels: 36
0.73 0.13 0.13
Matches are distributed among these distances:
87 2 0.01
88 25 0.13
89 66 0.34
90 94 0.48
91 8 0.04
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (90 bp):
CTTTAAAAAGGATGCCACGAAGTTATGGACTTTAGAAAAATGGTGCCACTAAGTCGTGGACTTTG
AAAAAGAGTGCCACAGAATGGTAGA
Found at i:599666 original size:119 final size:119
Alignment explanation
Indices: 599419--600031 Score: 303
Period size: 119 Copynumber: 5.2 Consensus size: 119
599409 TGGCAATATG
* * * * *
599419 CTTTAAAAAAGGTTGCCACGGAGTTGTGGACTTTGTAAAAGGTGCCACGGAGTTGTGGGCTTTAA
1 CTTTAAAAAAGGTTGCCACGAAGTCGTGGACTTTGTAAAAGGTGCCACGAAGTGGTGGACTTTAA
* *
599484 AAAAGGTGCCATGAAGTTGTGAACTTTTGAAAAATGGTGCCACAGAGTTGTGAA
66 AAAAGGTGCCACGAAGTTGTGAACTTTAGAAAAATGGTGCCACAGAGTTGTGAA
* * ** * *
599538 CTTTGAAAAAGGTTGCCACTAAGTCGTGGACTTTG-AACTTGGTGCCACTAAGTGGTGGACTTTC
1 CTTTAAAAAAGGTTGCCACGAAGTCGTGGACTTTGTAA-AAGGTGCCACGAAGTGGTGGACTTTA
* * * ** *
599602 AAAAGGGTGTCACGAAGTTGTGGACATTTAGAAAAAAT-GTGCCATGGAGTTGTGGA
65 AAAAAGGTGCCACGAAGTTGTGAAC-TTTAG-AAAAATGGTGCCACAGAGTTGTGAA
* * * * **
599658 CTTT-AAAAAGAG-TGTCACAGAA-TTGTAGACTTT-AAAAAGGATGCCACGAAGTTATGGACTT
1 CTTTAAAAAAG-GTTGCCAC-GAAGTCGTGGACTTTGTAAAAGG-TGCCACGAAGTGGTGGAC-T
* * * * * * * ** ** *
599719 TTGAAAAATGGCGCCACTAAGTCGTGGACTTT-GGAAAAT-GTGCTATTGAGTCATGGA
62 TT-AAAAAAGGTGCCACGAAGTTGTGAACTTTAGAAAAATGGTGCCACAGAGTTGTGAA
* * * * * * * *
599776 CTTTGAAAAATGG-TACCTTA-G-AGTTGTGGACTTT-AAAAATGATGCCA-TAGAGTTGTAGAC
1 CTTT-AAAAAAGGTTGCC--ACGAAGTCGTGGACTTTGTAAAA-GGTGCCACGA-AGTGGTGGAC
* * * * * * *
599836 TTTGAGAAGGGTGCCACGAAGTTGTGGACTTTAG-AAAAGGGTGCCACGGAGTTGTGGA
61 TTTAAAAAAGGTGCCACGAAGTTGTGAACTTTAGAAAAATGGTGCCACAGAGTTGTGAA
* * * * *
599894 CTTT-GAGAAGAGTT-CCACGGAGTTGTGGACTTTAG-AAAAGGATGCCAC-AGAGTTGTGGACT
1 CTTTAAAAAAG-GTTGCCACGAAGTCGTGGACTTT-GTAAAAGG-TGCCACGA-AGTGGTGGACT
* * * ** * * *
599955 TCAAAAAGGGGTGCCACGTAGTTGCAAACTTTAG-AAAAGGGTACCAC-GAAGTTGTGGA
62 TTAAAAA-AGGTGCCACGAAGTTGTGAACTTTAGAAAAATGGTGCCACAG-AGTTGTGAA
* * *
600013 CTTTGAAAAGGGGTGCCAC
1 CTTTAAAAAAGGTTGCCAC
600032 AGAGCCACGG
Statistics
Matches: 388, Mismatches: 76, Indels: 59
0.74 0.15 0.11
Matches are distributed among these distances:
115 1 0.00
116 4 0.01
117 44 0.11
118 77 0.20
119 190 0.49
120 45 0.12
121 27 0.07
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (119 bp):
CTTTAAAAAAGGTTGCCACGAAGTCGTGGACTTTGTAAAAGGTGCCACGAAGTGGTGGACTTTAA
AAAAGGTGCCACGAAGTTGTGAACTTTAGAAAAATGGTGCCACAGAGTTGTGAA
Found at i:599703 original size:148 final size:146
Alignment explanation
Indices: 599444--600031 Score: 514
Period size: 148 Copynumber: 4.0 Consensus size: 146
599434 CCACGGAGTT
* * * * *
599444 GTGGACTTTGTAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAAGGTGCCAT-GAAGTTGTGAAC
1 GTGGACTTTGGAAAAGGTGTCACGGAGTTGTGGACTTTGAAAAAGGTGCCATAG-AGTTGTGGAC
* * *
599508 TTTTGAAAAATG-GTGCCACAGAGTTGT-GAACTTTGAAAAAGGTTGCCACTAAGTCGTGGACTT
65 -TTT-AAAAATGAGTGCCACAGAGTTGTAG-ACTTT-AAAAAGGATGCCACGAAGTTGTGGACTT
** *
599571 TGAACTTGGTGCCACTAAGTG
126 TGAAAATGGTGCCACTAAGTC
* * * *
599592 GTGGACTTT-CAAAAGGGTGTCACGAAGTTGTGGACATTTAGAAAAAATGTGCCATGGAGTTGTG
1 GTGGACTTTGGAAAA-GGTGTCACGGAGTTGTGGAC-TTT-G-AAAAAGGTGCCATAGAGTTGTG
* * *
599656 GACTTTAAAAA-GAGTGTCACAGAATTGTAGACTTTAAAAAGGATGCCACGAAGTTATGGACTTT
62 GACTTTAAAAATGAGTGCCACAGAGTTGTAGACTTTAAAAAGGATGCCACGAAGTTGTGGAC-TT
*
599720 TGAAAAATGGCGCCACTAAGTC
126 TG-AAAATGGTGCCACTAAGTC
* ** ** * *
599742 GTGGACTTTGGAAAATGTG-CTATTGAGTCATGGACTTTGAAAAATGGTACCTTAGAGTTGTGGA
1 GTGGACTTTGGAAAAGGTGTC-ACGGAGTTGTGGACTTTGAAAAA-GGTGCCATAGAGTTGTGGA
* * * *
599806 CTTTAAAAATGA-TGCCATAGAGTTGTAGACTTTGAGAAGGGTGCCACGAAGTTGTGGACTTTAG
64 CTTTAAAAATGAGTGCCACAGAGTTGTAGACTTTAAAAAGGATGCCACGAAGTTGTGGACTTT-G
* ** *
599870 AAAAGGGTGCCACGGAGTT
128 AAAATGGTGCCACTAAGTC
* *
599889 GTGGACTTT-GAGAAGAGT-TCCACGGAGTTGTGGACTTT-AGAAAAGGATGCCACAGAGTTGTG
1 GTGGACTTTGGAAAAG-GTGT-CACGGAGTTGTGGACTTTGA-AAAAGG-TGCCATAGAGTTGTG
* * * * * * *
599951 GACTTCAAAAAGGGGTGCCAC-GTAGTTGCAAACTTTAGAAAAGGGTACCACGAAGTTGTGGACT
62 GACTTTAAAAATGAGTGCCACAG-AGTTGTAGACTTTA-AAAAGGATGCCACGAAGTTGTGGACT
*
600015 TTGAAAAGGGGTGCCAC
125 TTGAAAA-TGGTGCCAC
600032 AGAGCCACGG
Statistics
Matches: 359, Mismatches: 58, Indels: 45
0.78 0.13 0.10
Matches are distributed among these distances:
146 7 0.02
147 78 0.22
148 137 0.38
149 71 0.20
150 40 0.11
151 25 0.07
152 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (146 bp):
GTGGACTTTGGAAAAGGTGTCACGGAGTTGTGGACTTTGAAAAAGGTGCCATAGAGTTGTGGACT
TTAAAAATGAGTGCCACAGAGTTGTAGACTTTAAAAAGGATGCCACGAAGTTGTGGACTTTGAAA
ATGGTGCCACTAAGTC
Found at i:599837 original size:59 final size:56
Alignment explanation
Indices: 599772--599955 Score: 199
Period size: 59 Copynumber: 3.1 Consensus size: 56
599762 TATTGAGTCA
* * *
599772 TGGACTTTGAAAAATGGTACCTTAGAGTTGTGGACTTTA-AAAATGATGCCATAGAGTTG
1 TGGACTTTG-AGAA-GGTACC--AGAGTTGTGGACTTTAGAAAAGGATGCCACAGAGTTG
* * * *
599831 TAGACTTTGAGAAGGGTGCCACGAAGTTGTGGACTTTAGAAAAGGGTGCCACGGAGTTG
1 TGGACTTTGAGAA-GGTACCA-G-AGTTGTGGACTTTAGAAAAGGATGCCACAGAGTTG
*
599890 TGGACTTTGAGAAGAGTTCCACGGAGTTGTGGACTTTAGAAAAGGATGCCACAGAGTTG
1 TGGACTTTGAGAAG-GTACCA--GAGTTGTGGACTTTAGAAAAGGATGCCACAGAGTTG
599949 TGGACTT
1 TGGACTT
599956 CAAAAAGGGG
Statistics
Matches: 107, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
56 1 0.01
57 1 0.01
58 23 0.21
59 81 0.76
60 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (56 bp):
TGGACTTTGAGAAGGTACCAGAGTTGTGGACTTTAGAAAAGGATGCCACAGAGTTG
Found at i:600340 original size:11 final size:11
Alignment explanation
Indices: 600324--600352 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
600314 TGATGTTATA
600324 ATGGCATGATC
1 ATGGCATGATC
600335 ATGGCATGATC
1 ATGGCATGATC
600346 ATGGCAT
1 ATGGCAT
600353 AAAAGTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (11 bp):
ATGGCATGATC
Found at i:607539 original size:19 final size:19
Alignment explanation
Indices: 607511--607551 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
607501 TGACTATAGA
607511 ATGGACATGT-CAAAATGC
1 ATGGACATGTACAAAATGC
607529 ATGGAACATGTCACAAAATGC
1 ATGG-ACATGT-ACAAAATGC
607550 AT
1 AT
607552 AAATATGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
21 10 0.50
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (19 bp):
ATGGACATGTACAAAATGC
Found at i:608473 original size:51 final size:53
Alignment explanation
Indices: 608418--608556 Score: 158
Period size: 53 Copynumber: 2.7 Consensus size: 53
608408 TTTTTCTGCT
* * * *
608418 TGTATAGATACATTGAAGAATGTATCGATACATTT-GGATC-AAAATCTAAAA
1 TGTATAGATACAATGAAAAATGTATCGATACATTTGGGATCAAAAACCCAAAA
* * * * *
608469 TGTATTGATACAATGAATAATGTATTGATACATTTGGGGTCAAAAACCCAGAA
1 TGTATAGATACAATGAAAAATGTATCGATACATTTGGGATCAAAAACCCAAAA
*
608522 TGTATCA-ATACAATAAAAAATGTATCGATACATTT
1 TGTAT-AGATACAATGAAAAATGTATCGATACATTT
608557 TCTTTTCAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
51 31 0.42
52 4 0.05
53 38 0.52
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (53 bp):
TGTATAGATACAATGAAAAATGTATCGATACATTTGGGATCAAAAACCCAAAA
Found at i:618059 original size:63 final size:63
Alignment explanation
Indices: 617992--618119 Score: 202
Period size: 63 Copynumber: 2.0 Consensus size: 63
617982 TGATGATTTT
* * *
617992 ATTTTGCAACACTTTCACTTTTGATATTTCCTCTTCATTGCTTTGGTTGTTGTTGACGATCTC
1 ATTTTGCAACACTTTCACTTTTGATATTTCCTCTTCAGTCCTTTGGTTGTTGTTAACGATCTC
* * *
618055 ATTTTGGAACACTTTCACTTTTGATGTTTCCTCTTCAGTCCTTTGGTTGTTGTTAATGATCTC
1 ATTTTGCAACACTTTCACTTTTGATATTTCCTCTTCAGTCCTTTGGTTGTTGTTAACGATCTC
618118 AT
1 AT
618120 CTTCATCGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (63 bp):
ATTTTGCAACACTTTCACTTTTGATATTTCCTCTTCAGTCCTTTGGTTGTTGTTAACGATCTC
Found at i:619145 original size:13 final size:13
Alignment explanation
Indices: 619127--619154 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
619117 TGAAACAAAC
619127 AATATATATTTGT
1 AATATATATTTGT
619140 AATATATATTTGT
1 AATATATATTTGT
619153 AA
1 AA
619155 AAACTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
AATATATATTTGT
Found at i:619405 original size:5 final size:5
Alignment explanation
Indices: 619397--619430 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
619387 AAAAAAATAA
619397 AAAAT AAAAT AATAAT AACAAT AAAAT AAAAT AA
1 AAAAT AAAAT AA-AAT AA-AAT AAAAT AAAAT AA
619431 GAGGTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 17 0.63
6 10 0.37
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:620285 original size:28 final size:27
Alignment explanation
Indices: 620232--620286 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
620222 GTAAATTTAA
* **
620232 AATTAATTTTTATGATTTTATTAATTT
1 AATTAATTTTTATGAATTTAAAAATTT
*
620259 AATTAATATTTTATTAATTTAAAAATTT
1 AATTAAT-TTTTATGAATTTAAAAATTT
620287 TATGATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
AATTAATTTTTATGAATTTAAAAATTT
Found at i:627031 original size:48 final size:46
Alignment explanation
Indices: 626905--627033 Score: 143
Period size: 48 Copynumber: 2.7 Consensus size: 46
626895 TAAGTCATAG
* * *
626905 AAAATGACTTAAATACCTTTAAATTGCATAAAAGTCCTAGATCATGA
1 AAAATGACCTAAATACC-TTAAATTACATAAAAGTCCCAGATCATGA
** *
626952 AAAATGACCTCAACATATATAAAATTACATAAAAGTCCCCAGATCATGA
1 AAAATGACCT-AA-ATACCTTAAATTACATAAAAGT-CCCAGATCATGA
627001 AAAATGACCTAAATGACCTTAACATT-CATAAAA
1 AAAATGACCTAAAT-ACCTTAA-ATTACATAAAA
627034 TTACATTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
47 11 0.16
48 30 0.44
49 27 0.40
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.26
Consensus pattern (46 bp):
AAAATGACCTAAATACCTTAAATTACATAAAAGTCCCAGATCATGA
Found at i:627121 original size:59 final size:58
Alignment explanation
Indices: 626953--627158 Score: 254
Period size: 58 Copynumber: 3.5 Consensus size: 58
626943 AGATCATGAA
* *
626953 AAATGACCTCAACATAT-ATAAAATTACAT-AAAAGTCCCCAGATCATGAAAAATGACCT
1 AAATGACCCCAACAT-TCATAAAATTACATCAAAA-TCCCTAGATCATGAAAAATGACCT
** * *
627011 AAATGACCTTAACATTCATAAAATTACATTAAAATCCCTAGATCATGAAAAATAACCT
1 AAATGACCCCAACATTCATAAAATTACATCAAAATCCCTAGATCATGAAAAATGACCT
* * * * * *
627069 AAATAACCCCAACATTCATTAAAATTGCATCCAAGTTCGTAGATCATGAAAAATGACCT
1 AAATGACCCCAACATTCA-TAAAATTACATCAAAATCCCTAGATCATGAAAAATGACCT
627128 AAATGACCCCTAACATTCATAAAATTACATC
1 AAATGACCCC-AACATTCATAAAATTACATC
627159 TAATTTCCTA
Statistics
Matches: 129, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
57 1 0.01
58 63 0.49
59 57 0.44
60 8 0.06
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.25
Consensus pattern (58 bp):
AAATGACCCCAACATTCATAAAATTACATCAAAATCCCTAGATCATGAAAAATGACCT
Found at i:627184 original size:59 final size:59
Alignment explanation
Indices: 626953--627171 Score: 243
Period size: 59 Copynumber: 3.7 Consensus size: 59
626943 AGATCATGAA
* * * *
626953 AAATGACCTC-AACATAT-ATAAAATTACAT-AAAAGTCCCCAGATCATGAAAAATGACCT
1 AAATGACCCCTAACAT-TCATAAAATTACATCTAAA-TTCCTAGATCATGAAAAATGACCT
* * *
627011 AAATGA-CCTTAACATTCATAAAATTACAT-TAAAATCCCTAGATCATGAAAAATAACCT
1 AAATGACCCCTAACATTCATAAAATTACATCT-AAATTCCTAGATCATGAAAAATGACCT
* * * * *
627069 AAATAACCCC-AACATTCATTAAAATTGCATCCAAGTTCGTAGATCATGAAAAATGACCT
1 AAATGACCCCTAACATTCA-TAAAATTACATCTAAATTCCTAGATCATGAAAAATGACCT
*
627128 AAATGACCCCTAACATTCATAAAATTACATCTAATTTCCTAGAT
1 AAATGACCCCTAACATTCATAAAATTACATCTAAATTCCTAGAT
627172 TACAAAAAAT
Statistics
Matches: 136, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
57 2 0.01
58 58 0.43
59 68 0.50
60 8 0.06
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.26
Consensus pattern (59 bp):
AAATGACCCCTAACATTCATAAAATTACATCTAAATTCCTAGATCATGAAAAATGACCT
Found at i:628034 original size:11 final size:11
Alignment explanation
Indices: 628018--628050 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
628008 AAGCTATCAC
628018 TCTTATTTTTT
1 TCTTATTTTTT
*
628029 TCTTATTTTTC
1 TCTTATTTTTT
628040 TC-TATTTTTT
1 TCTTATTTTTT
628050 T
1 T
628051 TGCTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTATTTTTT
Found at i:628996 original size:17 final size:17
Alignment explanation
Indices: 628971--629003 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
628961 TTGGTATGAT
*
628971 TTTTTATTATTATTTTA
1 TTTTCATTATTATTTTA
628988 TTTTCATTATTATTTT
1 TTTTCATTATTATTTT
629004 TTTGTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCATTATTATTTTA
Found at i:630503 original size:32 final size:31
Alignment explanation
Indices: 630345--630504 Score: 113
Period size: 32 Copynumber: 5.0 Consensus size: 31
630335 TCCATCATCG
*
630345 AGAAAGATATAGGTTTGGCTTTTGACTTATTT
1 AGAAAGATATAGGTTTGACTTTTGACTTA-TT
* * * *
630377 AAAAAAAGATACAAGTTTAACTTTTGACTTATT
1 --AGAAAGATATAGGTTTGACTTTTGACTTATT
* * ** * *
630410 CAAAAAGATATTGGTTCAAATTTTAACTTATT
1 -AGAAAGATATAGGTTTGACTTTTGACTTATT
* * ** *
630442 AGAAAAGATACAAGTTTGACTCCTAACTTATAT
1 AG-AAAGATATAGGTTTGACTTTTGACTTAT-T
*
630475 AGAAAGATATAGGTTTGGCTTTTGACTTAT
1 AGAAAGATATAGGTTTGACTTTTGACTTAT
630505 GTGGGAAAAT
Statistics
Matches: 97, Mismatches: 27, Indels: 6
0.75 0.21 0.05
Matches are distributed among these distances:
31 1 0.01
32 67 0.69
33 5 0.05
34 24 0.25
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (31 bp):
AGAAAGATATAGGTTTGACTTTTGACTTATT
Found at i:630517 original size:64 final size:64
Alignment explanation
Indices: 630345--630545 Score: 181
Period size: 64 Copynumber: 3.1 Consensus size: 64
630335 TCCATCATCG
* ** *
630345 AGAAAGATATAGGTTTGGCTTTTGACTTATTTAAAAAAAGATACAAGTTTAACTTTTGACTTATT
1 AGAAAGATATAGGTTTGGCTTTTGACTTA-TT-AGAAAAGATACAAGTTTAACTCCTAACTTATT
630410 C
64 C
* * **** * *
630411 AAAAAGATATTGGTTCAAATTTTAACTTATTAGAAAAGATACAAGTTTGACTCCTAACTTATAT-
1 AGAAAGATATAGGTTTGGCTTTTGACTTATTAGAAAAGATACAAGTTTAACTCCTAACTTAT-TC
* * * * *
630475 AGAAAGATATAGGTTTGGCTTTTGACTTATGTGGGAAA-ATACAAGGTTAATCTCTTAACCTATT
1 AGAAAGATATAGGTTTGGCTTTTGACTTAT-TAGAAAAGATACAAGTTTAA-CTCCTAACTTATT
*
630539 T
64 C
630540 AGAAAG
1 AGAAAG
630546 GCACAGGTTT
Statistics
Matches: 106, Mismatches: 25, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
64 60 0.57
65 24 0.23
66 22 0.21
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (64 bp):
AGAAAGATATAGGTTTGGCTTTTGACTTATTAGAAAAGATACAAGTTTAACTCCTAACTTATTC
Found at i:644114 original size:18 final size:19
Alignment explanation
Indices: 644088--644124 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
644078 ATCTTTCACT
644088 CAATA-TTTTAAAAATATG
1 CAATATTTTTAAAAATATG
*
644106 CAATGTTTTTAAAAATATG
1 CAATATTTTTAAAAATATG
644125 TATGATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
CAATATTTTTAAAAATATG
Found at i:646461 original size:20 final size:20
Alignment explanation
Indices: 646438--646478 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
646428 TTTAAACAAG
*
646438 ATTATTTAAAT-ATTAAATTA
1 ATTATATAAATAATT-AATTA
646458 ATTATATAAATAATTAATTA
1 ATTATATAAATAATTAATTA
646478 A
1 A
646479 CCTATATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTATATAAATAATTAATTA
Found at i:652189 original size:53 final size:54
Alignment explanation
Indices: 652094--652214 Score: 149
Period size: 53 Copynumber: 2.3 Consensus size: 54
652084 TACGGGTTCG
*
652094 AGTCATT-TCAGATTCGGGTCAATCGGATTTAACACTTAAGTT-AATCAGGTTCA
1 AGTCATTCT-AGATTCGGGTCAATCGGATTTAACACTTAAGTTAAATCAGATTCA
* * * *
652147 GGTTATTCTAGATTCGGGTCAATTGGATTTAACA-TTCGAGTTAAATCAGATTCA
1 AGTCATTCTAGATTCGGGTCAATCGGATTTAACACTT-AAGTTAAATCAGATTCA
*
652201 AGTCATTTTAGATT
1 AGTCATTCTAGATT
652215 TTTTATATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
52 2 0.04
53 33 0.58
54 22 0.39
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (54 bp):
AGTCATTCTAGATTCGGGTCAATCGGATTTAACACTTAAGTTAAATCAGATTCA
Found at i:652898 original size:16 final size:15
Alignment explanation
Indices: 652877--652928 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
652867 TATTCAGGTT
652877 ATTTCGAGTTTGGATC
1 ATTTCGAGTTTGG-TC
*
652893 ATTTCGAGTTCAGGTC
1 ATTTCGAGTT-TGGTC
652909 ATTTC-AGATTTGGGTC
1 ATTTCGAG-TTT-GGTC
652925 ATTT
1 ATTT
652929 TAAGTTCGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 27 0.87
17 2 0.06
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.44
Consensus pattern (15 bp):
ATTTCGAGTTTGGTC
Found at i:652913 original size:32 final size:32
Alignment explanation
Indices: 652869--652944 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
652859 AGGTTAATTA
* *
652869 TTCAGGTTATTTC-GAGTTTGGATCATTTCGAG
1 TTCAGGTCATTTCAGA-TTTGGATCATTTCAAG
* *
652901 TTCAGGTCATTTCAGATTTGGGTCATTTTAAG
1 TTCAGGTCATTTCAGATTTGGATCATTTCAAG
*
652933 TTCGGGTCATTT
1 TTCAGGTCATTT
652945 TTGAGTTCGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.18, C:0.13, G:0.24, T:0.45
Consensus pattern (32 bp):
TTCAGGTCATTTCAGATTTGGATCATTTCAAG
Found at i:652951 original size:17 final size:17
Alignment explanation
Indices: 652898--652954 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 17
652888 GGATCATTTC
* **
652898 GAGTTCAGGTCATTTCA
1 GAGTTCGGGTCATTTTT
*
652915 GA-TTTGGGTCA-TTTT
1 GAGTTCGGGTCATTTTT
*
652930 AAGTTCGGGTCATTTTT
1 GAGTTCGGGTCATTTTT
652947 GAGTTCGG
1 GAGTTCGG
652955 ATCGATCGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 3 0.10
16 15 0.48
17 13 0.42
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.42
Consensus pattern (17 bp):
GAGTTCGGGTCATTTTT
Found at i:663521 original size:13 final size:13
Alignment explanation
Indices: 663503--663527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
663493 ATTCATCATG
663503 TATCGATACAATT
1 TATCGATACAATT
663516 TATCGATACAAT
1 TATCGATACAAT
663528 GTACCATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TATCGATACAATT
Found at i:663525 original size:33 final size:33
Alignment explanation
Indices: 663478--663546 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
663468 CTGTTAGAAG
*
663478 CAATGTATCGATACAAT-TCATCATGTATCGATA
1 CAATGTATCGATACAATGT-ACCATGTATCGATA
*
663511 CAATTTATCGATACAATGTACCATGTATCGATA
1 CAATGTATCGATACAATGTACCATGTATCGATA
663544 CAA
1 CAA
663547 ATAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCGATA
Found at i:663600 original size:20 final size:19
Alignment explanation
Indices: 663575--663630 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
663565 CTGCCTGTTT
**
663575 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
663595 CATGTATCGATATACAATGAA
1 CATGTATCG--ATACAATGAA
663616 CATGTATCGATACAA
1 CATGTATCGATACAA
663631 GGCATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 9 0.28
21 11 0.34
22 6 0.19
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:672328 original size:13 final size:13
Alignment explanation
Indices: 672310--672340 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
672300 AGAATTCATC
672310 ATGTATCGATACA
1 ATGTATCGATACA
*
672323 ATGTATCGCTACA
1 ATGTATCGATACA
672336 ATGTA
1 ATGTA
672341 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Done.