Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011396.1 Kokia drynarioides strain JFW-HI SEQ_126378, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 196120
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Warning! 288 characters in sequence are not A, C, G, or T
Found at i:9646 original size:68 final size:69
Alignment explanation
Indices: 9565--9698 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 69
9555 AATATAATCA
*
9565 ATCACATGACATGAAGGACAT-ACATATTTTCTATCACATAGCATGAAGAACATACCCACATATT
1 ATCACATGACATGAAGAACATCACATATTTTCTATCACATAGCATGAAGAACATACCCACATATT
9629 TTCT
66 TTCT
* * *
9633 ATCACATGGCATGAAGAACATACCCACATATTTTCTGTCACATGGCATGAAGAACATACCCACAT
1 ATCACATGACATGAAGAACAT---CACATATTTTCTATCACATAGCATGAAGAACATACCCACAT
9698 A
63 A
9699 CTCACTTTCA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
68 19 0.33
72 39 0.67
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (69 bp):
ATCACATGACATGAAGAACATCACATATTTTCTATCACATAGCATGAAGAACATACCCACATATT
TTCT
Found at i:9710 original size:36 final size:36
Alignment explanation
Indices: 9586--9698 Score: 208
Period size: 36 Copynumber: 3.1 Consensus size: 36
9576 TGAAGGACAT
*
9586 ACATATTTTCTATCACATAGCATGAAGAACATACCC
1 ACATATTTTCTATCACATGGCATGAAGAACATACCC
9622 ACATATTTTCTATCACATGGCATGAAGAACATACCC
1 ACATATTTTCTATCACATGGCATGAAGAACATACCC
*
9658 ACATATTTTCTGTCACATGGCATGAAGAACATACCC
1 ACATATTTTCTATCACATGGCATGAAGAACATACCC
9694 ACATA
1 ACATA
9699 CTCACTTTCA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 75 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (36 bp):
ACATATTTTCTATCACATGGCATGAAGAACATACCC
Found at i:9817 original size:23 final size:23
Alignment explanation
Indices: 9780--10451 Score: 826
Period size: 23 Copynumber: 29.2 Consensus size: 23
9770 ATCTTAATTC
*
9780 TTTAAGCACAGATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
9803 TTTAATCATAAATCATATTCATA
1 TTTAAGCACAAATCACATTAATA
9826 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
9849 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
9872 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
9895 TTTAAGTACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
9918 TTTAAGTACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
9941 TTTGAGAACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
9964 TTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
9987 TTTGAG-ATCAAATCATATTAATA
1 TTTAAGCA-CAAATCACATTAATA
*
10010 TTTACGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
10033 TTTGAGAACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
10056 TTTACGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
10079 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
10102 TTTAAGCACAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
10125 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
10148 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
10171 TTTGAGCACAAATCATATTAACA
1 TTTAAGCACAAATCACATTAATA
*
10194 TTTAAGCATAAAT-ATCATTAATA
1 TTTAAGCACAAATCA-CATTAATA
* * * *
10217 CTTAAGCACAAACCGCATTACTA
1 TTTAAGCACAAATCACATTAATA
* * *
10240 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
10263 TTTAAGCATAAACCACATTAATC
1 TTTAAGCACAAATCACATTAATA
* *
10286 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
10309 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
10332 TTTAAGCATAAATCATATTAACA
1 TTTAAGCACAAATCACATTAATA
* *
10355 TTTAAGCATAAATCACAATAATA
1 TTTAAGCACAAATCACATTAATA
*
10378 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
10401 TTTAGGCATAAATCATATTAATT
1 TTTAAGCACAAATCACATTAATA
* *
10424 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
10447 TTTAA
1 TTTAA
10452 ACATAGATAT
Statistics
Matches: 557, Mismatches: 88, Indels: 8
0.85 0.13 0.01
Matches are distributed among these distances:
22 2 0.00
23 554 0.99
24 1 0.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:13212 original size:21 final size:21
Alignment explanation
Indices: 13180--13219 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13170 AACCGGAACC
*
13180 AGCCCCAGCTCC-AGACCCTG
1 AGCCCCACCTCCAAGACCCTG
13200 AGCCACCACCTCCAAGACCC
1 AGCC-CCACCTCCAAGACCC
13220 AGCCCTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.25, C:0.53, G:0.15, T:0.07
Consensus pattern (21 bp):
AGCCCCACCTCCAAGACCCTG
Found at i:16162 original size:24 final size:24
Alignment explanation
Indices: 16112--16162 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
16102 AACCCCCTGA
*
16112 TCCTGAACCGGAACCAGCCCCAGC
1 TCCTGAACCGGAACCAGCCCCACC
* *
16136 TCCTGATCCTGAACCA-CCACCACC
1 TCCTGAACCGGAACCAGCC-CCACC
16160 TCC
1 TCC
16163 CAAGCCAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.24, C:0.49, G:0.14, T:0.14
Consensus pattern (24 bp):
TCCTGAACCGGAACCAGCCCCACC
Found at i:22636 original size:30 final size:30
Alignment explanation
Indices: 22462--22772 Score: 234
Period size: 30 Copynumber: 10.3 Consensus size: 30
22452 TTTTTGGTAG
* ** *
22462 GTTTGAGGGTCAAAACATGATTTTGGAAAA
1 GTTTAAGGGTCAAAATGTAATTTTGGAAAA
** *
22492 GTTCGAGGGTCAAAATG-AAATTTGGAAAA
1 GTTTAAGGGTCAAAATGTAATTTTGGAAAA
* *
22521 GTTTAGGGGGTTAAAATGTAATTTTGGAAAA
1 GTTTA-AGGGTCAAAATGTAATTTTGGAAAA
* * * *
22552 GTTTGAGGATCAAAATGTGATTTTTAGG-AAG
1 GTTTAAGGGTCAAAATGT-AATTTT-GGAAAA
** *
22583 GTTTAAGGGTCAAAACATGATTTTGGAAAA
1 GTTTAAGGGTCAAAATGTAATTTTGGAAAA
* * *
22613 GTTCAAGGGTTAAAATGTAATTTTGGATAA
1 GTTTAAGGGTCAAAATGTAATTTTGGAAAA
* * * * *
22643 GCTTGAGGTTAAAAATGTAATTTT-AAAGAA
1 GTTTAAGGGTCAAAATGTAATTTTGGAA-AA
* * * *
22673 TTTTGAGGGTTAAAATGGAATTTTGGAAAA
1 GTTTAAGGGTCAAAATGTAATTTTGGAAAA
* * * *
22703 GTTT-AGCGATCAAGATATAATTTTTGAAAAA
1 GTTTAAG-GGTCAAAATGTAA-TTTTGGAAAA
* *
22734 GTTTAGGGGTCAAAATGTAATTTTGGATAA
1 GTTTAAGGGTCAAAATGTAATTTTGGAAAA
22764 GTTTAAGGG
1 GTTTAAGGG
22773 ACCTACTAGG
Statistics
Matches: 215, Mismatches: 56, Indels: 20
0.74 0.19 0.07
Matches are distributed among these distances:
29 18 0.08
30 133 0.62
31 61 0.28
32 3 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33
Consensus pattern (30 bp):
GTTTAAGGGTCAAAATGTAATTTTGGAAAA
Found at i:22688 original size:121 final size:119
Alignment explanation
Indices: 22405--22764 Score: 361
Period size: 121 Copynumber: 3.0 Consensus size: 119
22395 GGAGAATACA
* * * *
22405 AGGTCAAAATGTAATTTTAGAGAAGTTTGA-GGTCAAAATATGAATTTTTTTTGGTAGGTTTGAG
1 AGGTTAAAATGTAATTTTAAAGAAGTTTGAGGGTCAAAATGTG-A---TTTTTGGAAGGTTT-AG
* * * *
22469 GGTCAAAACATGATTTTGGAAAAGTTCGAGGGTCAAAATG-AAATTTGGAAAAGTTTAGG
61 GGTCAAAACATGATTTTGGAAAAGTTCAAGGGTCAAAATGTAATTTTGGATAAGCTTA-G
* * *
22528 GGGTTAAAATGTAATTTTGGAA-AAGTTTGAGGATCAAAATGTGATTTTTAGGAAGGTTTAAGGG
1 AGGTTAAAATGTAATTTT-AAAGAAGTTTGAGGGTCAAAATGTGATTTTT-GGAAGGTTT-AGGG
*
22592 TCAAAACATGATTTTGGAAAAGTTCAAGGGTTAAAATGTAATTTTGGATAAGCTT-G
63 TCAAAACATGATTTTGGAAAAGTTCAAGGGTCAAAATGTAATTTTGGATAAGCTTAG
* * * * *
22648 AGGTTAAAAATGTAATTTTAAAGAATTTTGAGGGTTAAAATG-GAATTTTGGAAAAGTTTAGCGA
1 AGGTT-AAAATGTAATTTTAAAGAAGTTTGAGGGTCAAAATGTGATTTTTGG-AAGGTTTAG-GG
* * * * * *
22712 TCAAGATATAATTTTTGAAAAAGTTTAGGGGTCAAAATGTAATTTTGGATAAG
63 TCAAAACATGA-TTTTGGAAAAGTTCAAGGGTCAAAATGTAATTTTGGATAAG
22765 TTTAAGGGAC
Statistics
Matches: 200, Mismatches: 28, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
119 4 0.02
120 33 0.17
121 114 0.57
122 13 0.06
123 25 0.12
124 11 0.05
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (119 bp):
AGGTTAAAATGTAATTTTAAAGAAGTTTGAGGGTCAAAATGTGATTTTTGGAAGGTTTAGGGTCA
AAACATGATTTTGGAAAAGTTCAAGGGTCAAAATGTAATTTTGGATAAGCTTAG
Found at i:23300 original size:27 final size:28
Alignment explanation
Indices: 23270--23341 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 28
23260 TTTTCTCTTT
*
23270 TTTTTATTTTCTTT-GC-TTTCAAATCT-
1 TTTTTATTTT-TTTAACTTTTCAAATCTA
*
23296 GTTTTATTTTTTTAACTTTTCAAATCTA
1 TTTTTATTTTTTTAACTTTTCAAATCTA
23324 TTTTATTATTTCTTTTAA
1 -TTT-TTATTT-TTTTAA
23342 AACTAGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 3 0.08
26 10 0.27
27 10 0.27
29 2 0.05
30 6 0.16
31 6 0.16
ACGTcount: A:0.21, C:0.11, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTTATTTTTTTAACTTTTCAAATCTA
Found at i:24888 original size:85 final size:85
Alignment explanation
Indices: 24753--24912 Score: 241
Period size: 85 Copynumber: 1.9 Consensus size: 85
24743 TTTGGTTTAC
* * *
24753 TTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTGTGATCCACTTCTCTGTATCTCATTA
1 TTCTCTGTATCTCATCAGGAAGATGACCACTTCATTATTGTGATCCACTTCTCAGTATCTCATCA
24818 GGAAGATGGATTTGGTCCAT
66 GGAAGATGGATTTGGTCCAT
* * * *
24838 TTCTCTGTATCTCATCAGGAAGATGATCACTTTATTGTTTTGA-CCTACTTCTCAGTATCTCATC
1 TTCTCTGTATCTCATCAGGAAGATGACCACTTCATTATTGTGATCC-ACTTCTCAGTATCTCATC
24902 AGGAAGATGGA
65 AGGAAGATGGA
24913 GGTTCGAAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
84 2 0.03
85 65 0.97
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.38
Consensus pattern (85 bp):
TTCTCTGTATCTCATCAGGAAGATGACCACTTCATTATTGTGATCCACTTCTCAGTATCTCATCA
GGAAGATGGATTTGGTCCAT
Found at i:25034 original size:209 final size:207
Alignment explanation
Indices: 24674--25616 Score: 1223
Period size: 207 Copynumber: 4.5 Consensus size: 207
24664 CTCTTGGTCT
* * ** *
24674 ACTTCTCTGTATCTCATCAGGAAGATAGAGGTTTGGAA-TTTCACTTACATTGAA-CTTTGCTTC
1 ACTTCTCAGTATCTCATCAGGAAGAT-GAGGTTTCGAAGTTTCACTCGCATT-AAGCTTCGCTTC
* *
24737 ATTTGATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTGTGATCCACT
64 A-TCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCA--ATTGTGATCCACT
* * * * *
24802 TCTCTGTATCTCATTAGGAAGATGGATTTGGTCCATTTCTCTGTATCTCATCAGGAAGATGATCA
126 TCTCTATATCTCATCAAGAAGATGGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGATCA
*
24867 CTTTATTGTTTTGACCT
191 CTTTATTGTTTTGACCC
*
24884 ACTTCTCAGTATCTCATCAGGAAGATGGAGG-TTCGAAGTTTCGCTCGCATTAAGCTTCGCTTCA
1 ACTTCTCAGTATCTCATCAGGAAGAT-GAGGTTTCGAAGTTTCACTCGCATTAAGCTTCGCTTCA
* *
24948 TCGATTTGGTCTATTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTATGATCCACTTC
65 TCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCA--ATTGTGATCCACTTC
* * * *
25013 TCTATATCTCATCAAGAAGATGAATTTGGTCCACTTCTCTGAATCTCATCAAGAAGATGA-CTAC
128 TCTATATCTCATCAAGAAGATGGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGATC-AC
*
25077 TTTATTATTTTGACCC
192 TTTATTGTTTTGACCC
* * * ** *
25093 ACTTCTCAGTATCTCATCAAGAAGATAAGGATTCGAAGTTTTGCTCGCATTGAGCTT-GACTTCA
1 ACTTCTCAGTATCTCATCAGGAAGATGAGGTTTCGAAGTTTCACTCGCATTAAGCTTCG-CTTCA
* * * * *
25157 TCGATTTGGTCTACTTTTTTGTATCTCATCAGGAAGATGACTGCATCACTTGTGATCCACTTCTC
65 TCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCAATTGTGATCCACTTCTC
* * *
25222 TGTATCTCATCAAGAAGATGGATTTGATCCACTTCTCTATATCTCATCAGGAAGATGATCGCTTT
130 TATATCTCATCAAGAAGATGGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGATCACTTT
25287 ATTGTTTTGACCC
195 ATTGTTTTGACCC
* * *
25300 ACTTCTCAGTAACTCATCAGGAAGATGAGGGTTT-GAAGTTTCACTCGCATTGAGCTTCGTTTCA
1 ACTTCTCAGTATCTCATCAGGAAGATGA-GGTTTCGAAGTTTCACTCGCATTAAGCTTCGCTTCA
* * * *
25364 TCGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACTGCATCACTTGTGATCCACTTCTC
65 TCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCAATTGTGATCCACTTCTC
* * * * *
25429 TATATCTCATTAGGAAGATGGATTTGACCCATTTCTCTGTATCTCATCAGGAAGATGATTACTTT
130 TATATCTCATCAAGAAGATGGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGATCACTTT
*
25494 ATTGCTTTGACCC
195 ATTGTTTTGACCC
* * ** * *
25507 ACTTCTCAGTATCTCATCAGGAAGATTAGGTTTGGAAGTTTCACTTACATTAAGCTTCACTTCGT
1 ACTTCTCAGTATCTCATCAGGAAGATGAGGTTTCGAAGTTTCACTCGCATTAAGCTTCGCTTCAT
* * * *
25572 TGAATTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCTT
66 CGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTT
25617 AAAGTTTCAC
Statistics
Matches: 653, Mismatches: 71, Indels: 21
0.88 0.10 0.03
Matches are distributed among these distances:
206 5 0.01
207 355 0.54
208 11 0.02
209 234 0.36
210 48 0.07
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (207 bp):
ACTTCTCAGTATCTCATCAGGAAGATGAGGTTTCGAAGTTTCACTCGCATTAAGCTTCGCTTCAT
CGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCAATTGTGATCCACTTCTCT
ATATCTCATCAAGAAGATGGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGATCACTTTA
TTGTTTTGACCC
Found at i:25095 original size:85 final size:85
Alignment explanation
Indices: 24951--25118 Score: 239
Period size: 85 Copynumber: 2.0 Consensus size: 85
24941 CGCTTCATCG
* * * * * *
24951 ATTTGGTCTATTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTATGATCCACTTCTCT
1 ATTTGGTCCACTTCTCTGAATCTCATCAAGAAGATGACCACTTCATTATTATGACCCACTTCTC-
25016 A-TATCTCATCAAGAAGATGA
65 AGTATCTCATCAAGAAGATGA
* * *
25036 ATTTGGTCCACTTCTCTGAATCTCATCAAGAAGATGACTACTTTATTATTTTGACCCACTTCTCA
1 ATTTGGTCCACTTCTCTGAATCTCATCAAGAAGATGACCACTTCATTATTATGACCCACTTCTCA
25101 GTATCTCATCAAGAAGAT
66 GTATCTCATCAAGAAGAT
25119 AAGGATTCGA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 1 0.01
85 72 0.99
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (85 bp):
ATTTGGTCCACTTCTCTGAATCTCATCAAGAAGATGACCACTTCATTATTATGACCCACTTCTCA
GTATCTCATCAAGAAGATGA
Found at i:26641 original size:36 final size:36
Alignment explanation
Indices: 26591--26660 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
26581 GTTTCAAGAT
* * *
26591 GCCCTTTGCGGGTTTTCATCTTGATTTTTTTTAGAC
1 GCCCTTTACAGGTTTTCATCTCGATTTTTTTTAGAC
26627 GCCCTTTACAGGTTTTCATCTCGATTTTTTTTAG
1 GCCCTTTACAGGTTTTCATCTCGATTTTTTTTAG
26661 GCAAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (36 bp):
GCCCTTTACAGGTTTTCATCTCGATTTTTTTTAGAC
Found at i:33783 original size:24 final size:24
Alignment explanation
Indices: 33730--33776 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
33720 ACATCATTGT
*
33730 CATTTGTTCCTGTAACTATTTTTA
1 CATTTGTTCCTGCAACTATTTTTA
* *
33754 CATTTGTTCTTGCATCTATTTTT
1 CATTTGTTCCTGCAACTATTTTT
33777 GGATTTGCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (24 bp):
CATTTGTTCCTGCAACTATTTTTA
Found at i:37633 original size:28 final size:29
Alignment explanation
Indices: 37602--37662 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
37592 GAAAATGAAG
*
37602 TTTTAGAGAA-TATGGGGTCAAAATGTGA
1 TTTTAGAGAAGTATGGAGTCAAAATGTGA
* *
37630 TTTTGGAGAAGTTTGGAGTCAAAATGTGA
1 TTTTAGAGAAGTATGGAGTCAAAATGTGA
37659 TTTT
1 TTTT
37663 TGGGAAGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (29 bp):
TTTTAGAGAAGTATGGAGTCAAAATGTGA
Found at i:37694 original size:30 final size:29
Alignment explanation
Indices: 37660--37967 Score: 177
Period size: 30 Copynumber: 10.3 Consensus size: 29
37650 AAAATGTGAT
* *
37660 TTTTGGGAAGGTTTAAGGGTTAAAACATGA
1 TTTTGGGAA-GTTTAAGGGTTAAAATATAA
** *
37690 TTTTGGAGAAGTTCGAGGGTTAAAATGTAA
1 TTTTGG-GAAGTTTAAGGGTTAAAATATAA
* *
37720 TTTTGGAAAAGTTTAATGGTTAAAATATAA
1 TTTTGG-GAAGTTTAAGGGTTAAAATATAA
** * * * *
37750 TTTTAGAAAAGTTTAGGGGTCAAAATGTTAT
1 TTTT-GGGAAGTTTAAGGGTTAAAAT-ATAA
* * * * *
37781 TTTTGGGAAGATTTGAGGGTCAACATGTGAT
1 TTTTGGGAAG-TTTAAGGGTTAAAATAT-AA
* * ** * *
37812 TTTTGAGAAGTTCAAAAGTCAAAATGTAA
1 TTTTGGGAAGTTTAAGGGTTAAAATATAA
* * *
37841 TTTTGGAAAAGTTTAGGGGTTAAAATGTAA
1 TTTTGG-GAAGTTTAAGGGTTAAAATATAA
** * *
37871 TTTTTGAAAAGTTTGAGGGTTAAAATGTAA
1 -TTTTGGGAAGTTTAAGGGTTAAAATATAA
** * *
37901 TTTTGAAAATTTTAAGGGTTAAAATGTAA
1 TTTTGGGAAGTTTAAGGGTTAAAATATAA
* *
37930 TTTTGGAGAAGTTTAA-GGTCAAAATATGA
1 TTTTGG-GAAGTTTAAGGGTTAAAATATAA
*
37959 TTTTTGGAA
1 TTTTGGGAA
37968 AGTTCAGGGA
Statistics
Matches: 222, Mismatches: 48, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
28 3 0.01
29 53 0.24
30 128 0.58
31 38 0.17
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (29 bp):
TTTTGGGAAGTTTAAGGGTTAAAATATAA
Found at i:37699 original size:60 final size:59
Alignment explanation
Indices: 37616--37943 Score: 291
Period size: 60 Copynumber: 5.5 Consensus size: 59
37606 AGAGAATATG
* * * * *
37616 GGGTCAAAATGTGATTTTGGAGAAGTTTGGAGTCAAAATGTGATTTTTGGGAAGGTTTAA
1 GGGTTAAAATGTAATTTTGGAGAAGTTTGGAGTCAAAATGT-AATTTTGGAAAAGTTTAA
** * * * *
37676 GGGTTAAAACATGATTTTGGAGAAGTTCGAGGGTTAAAATGTAATTTTGGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAGAAGTTTG-GAGTCAAAATGTAATTTTGGAAAAGTTTAA
* * * * * * * *
37736 TGGTTAAAATATAATTTTAGAAAAGTTTAGGGGTCAAAATGTTATTTTTGG-GAAGATTTGA
1 GGGTTAAAATGTAATTTTGGAGAAGTTT-GGAGTCAAAATG-TAATTTTGGAAAAG-TTTAA
* * * * *** *
37797 GGGTCAACATGTGATTTTTGAGAAGTTCAAAAGTCAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATGTAATTTTGGAGAAGTT-TGGAGTCAAAATGTAATTTTGGAAAAGTTTAA
* * * * *
37857 GGGTTAAAATGTAATTTTTGAAAAGTTTGAGGGTTAAAATGTAATTTT-GAAAATTTTAA
1 GGGTTAAAATGTAATTTTGGAGAAGTTTG-GAGTCAAAATGTAATTTTGGAAAAGTTTAA
37916 GGGTTAAAATGTAATTTTGGAGAAGTTT
1 GGGTTAAAATGTAATTTTGGAGAAGTTT
37944 AAGGTCAAAA
Statistics
Matches: 214, Mismatches: 47, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
59 35 0.16
60 124 0.58
61 55 0.26
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (59 bp):
GGGTTAAAATGTAATTTTGGAGAAGTTTGGAGTCAAAATGTAATTTTGGAAAAGTTTAA
Found at i:37812 original size:121 final size:120
Alignment explanation
Indices: 37629--37968 Score: 373
Period size: 121 Copynumber: 2.8 Consensus size: 120
37619 TCAAAATGTG
* * * * * **
37629 ATTTTGGAGAAGTTTGGAGTCAAAATGTGATTTTTGGGAAGGTTTAAGGGTTAAAACATGATTTT
1 ATTTTAGAAAAGTTTGGGGTCAAAATGTTATTTTTGGGAAGATTTAAGGGTTAAAATGTGATTTT
* ** * *
37694 GGAGAAGTTCGAGGGTTAAAATGTAATTTTGGAAAAGTTTAATGGTTAAAATATA
66 GGAGAAGTTCAAAAGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATATA
* * *
37749 ATTTTAGAAAAGTTTAGGGGTCAAAATGTTATTTTTGGGAAGATTTGAGGGTCAACATGTGATTT
1 ATTTTAGAAAAGTTT-GGGGTCAAAATGTTATTTTTGGGAAGATTTAAGGGTTAAAATGTGATTT
* * *
37814 TTGAGAAGTTCAAAAGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTA
65 TGGAGAAGTTCAAAAGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATATA
* * * * *
37870 ATTTTTGAAAAGTTTGAGGGTTAAAATG-TAATTTT--GAAAATTTTAAGGGTTAAAATGTAATT
1 ATTTTAGAAAAGTTTG-GGGTCAAAATGTTATTTTTGGGAAGA-TTTAAGGGTTAAAATGTGATT
* * * *
37932 TTGGAGAAGTT-TAAGGTCAAAATATGATTTTTGGAAA
64 TTGGAGAAGTTCAAAAGTCAAAATGT-AATTTTGGAAA
37969 GTTCAGGGAC
Statistics
Matches: 185, Mismatches: 31, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
118 15 0.08
119 37 0.20
120 20 0.11
121 113 0.61
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (120 bp):
ATTTTAGAAAAGTTTGGGGTCAAAATGTTATTTTTGGGAAGATTTAAGGGTTAAAATGTGATTTT
GGAGAAGTTCAAAAGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATATA
Found at i:38640 original size:6 final size:6
Alignment explanation
Indices: 38629--38658 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
38619 TTAGATTTGA
38629 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
38659 CAAAACCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
GTTTTT
Found at i:43540 original size:21 final size:21
Alignment explanation
Indices: 43514--43561 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
43504 TTTTAAGGGA
43514 GAAAAAGCTAAAAATCAAGAG
1 GAAAAAGCTAAAAATCAAGAG
* * *
43535 GAAAAAGCTCAAAATTAAGTG
1 GAAAAAGCTAAAAATCAAGAG
43556 GAAAAA
1 GAAAAA
43562 TTTGATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.60, C:0.08, G:0.19, T:0.12
Consensus pattern (21 bp):
GAAAAAGCTAAAAATCAAGAG
Found at i:43877 original size:21 final size:20
Alignment explanation
Indices: 43846--43886 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
43836 TAAAATATTA
43846 TTAATATATTTTTATATAAAAT
1 TTAATATA-TTTTAT-TAAAAT
43868 TTAA-ATATTTTATTAAAAT
1 TTAATATATTTTATTAAAAT
43887 AATATCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 6 0.32
21 3 0.16
22 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATATATTTTATTAAAAT
Found at i:45433 original size:24 final size:23
Alignment explanation
Indices: 45379--45440 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
45369 TCATTAACAG
* *
45379 ATTATTATT-ACAAGTAAAAAAA
1 ATTATTATTAAAAATTAAAAAAA
*
45401 ATTAGTATTAAAAATTAAAATAAA
1 ATTATTATTAAAAATTAAAA-AAA
*
45425 ATTATTATTATAAATT
1 ATTATTATTAAAAATT
45441 CGGGCCAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 8 0.24
23 8 0.24
24 17 0.52
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (23 bp):
ATTATTATTAAAAATTAAAAAAA
Found at i:45897 original size:23 final size:24
Alignment explanation
Indices: 45844--45897 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
45834 AAAAAGGATC
* *
45844 AAAATT-AAATTATAATTTTTACG
1 AAAATTAAAAATATAATTTTTACA
*
45867 ATAA-TAAAAATATAATTTTTA-A
1 AAAATTAAAAATATAATTTTTACA
45889 AAAATTAAA
1 AAAATTAAA
45898 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
AAAATTAAAAATATAATTTTTACA
Found at i:46255 original size:15 final size:15
Alignment explanation
Indices: 46235--46285 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
46225 TTATTTTATA
46235 TTATGTTTTAGTCAC
1 TTATGTTTTAGTCAC
* *
46250 TTATGTTTGAAAT-A-
1 TTATGTTT-TAGTCAC
*
46264 TTACGTTTTAGTCAC
1 TTATGTTTTAGTCAC
46279 TTATGTT
1 TTATGTT
46286 ATCATTTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (15 bp):
TTATGTTTTAGTCAC
Found at i:46521 original size:18 final size:18
Alignment explanation
Indices: 46481--46523 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
46471 GTTCAAGGTG
46481 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
46499 CAATTAA-TTAAATTTCTT
1 TAATTAATTTAAAATT-TT
46517 TAATTAA
1 TAATTAA
46524 AAACCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:50404 original size:27 final size:27
Alignment explanation
Indices: 50344--50432 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
50334 ATGATTTTGT
* * **
50344 CACAAAGACAGTTCTATCAGAGTTTGC
1 CACAAAGGCATTTCTATCAGAGTTCAC
50371 CACAAAGGCATTTCTATCAGAGTTCAC
1 CACAAAGGCATTTCTATCAGAGTTCAC
* * * *
50398 CATAAAGGTATTTCT-TGTAGAGTTCGC
1 CACAAAGGCATTTCTAT-CAGAGTTCAC
50425 CACAAAGG
1 CACAAAGG
50433 TTGTTCATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 1 0.02
27 51 0.98
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (27 bp):
CACAAAGGCATTTCTATCAGAGTTCAC
Found at i:50433 original size:27 final size:27
Alignment explanation
Indices: 50355--50433 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
50345 ACAAAGACAG
* *
50355 TTCTATCAGAGTTTGCCACAAAGGCAT
1 TTCTATCAGAGTTCGCCACAAAGGTAT
* *
50382 TTCTATCAGAGTTCACCATAAAGGTAT
1 TTCTATCAGAGTTCGCCACAAAGGTAT
*
50409 TTCT-TGTAGAGTTCGCCACAAAGGT
1 TTCTAT-CAGAGTTCGCCACAAAGGT
50434 TGTTCATAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.02
27 43 0.98
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (27 bp):
TTCTATCAGAGTTCGCCACAAAGGTAT
Found at i:51388 original size:4 final size:4
Alignment explanation
Indices: 51379--51403 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
51369 AACCTCATAC
51379 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
51404 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:53047 original size:20 final size:20
Alignment explanation
Indices: 53015--53074 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
53005 ATTTAAAAGT
*
53015 GTTAAAATGATTTTGACTTG
1 GTTAAAATTATTTTGACTTG
* *
53035 GTTCAAATTATTTTGACATG
1 GTTAAAATTATTTTGACTTG
* *
53055 TTTAAAATTATTTTAACTTG
1 GTTAAAATTATTTTGACTTG
53075 AATTTTAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (20 bp):
GTTAAAATTATTTTGACTTG
Found at i:53168 original size:22 final size:24
Alignment explanation
Indices: 53143--53186 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
53133 AATTTTATTA
53143 ATTTTAACTTA-TAT-TCAAAAAT
1 ATTTTAACTTATTATATCAAAAAT
*
53165 ATTTTAATTTATTATATCAAAA
1 ATTTTAACTTATTATATCAAAA
53187 TACTTTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTTAACTTATTATATCAAAAAT
Found at i:53665 original size:9 final size:9
Alignment explanation
Indices: 53651--53685 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
53641 AATAGCCATT
53651 CTCTCCTCC
1 CTCTCCTCC
53660 CTCTCCT-C
1 CTCTCCTCC
53668 CTCTCCTCC
1 CTCTCCTCC
53677 CTCTCCTCC
1 CTCTCCTCC
53686 TCGTCTGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (9 bp):
CTCTCCTCC
Found at i:53696 original size:17 final size:17
Alignment explanation
Indices: 53651--53687 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
53641 AATAGCCATT
53651 CTCTCCTCCCTCTCCTC
1 CTCTCCTCCCTCTCCTC
53668 CTCTCCTCCCTCTCCTC
1 CTCTCCTCCCTCTCCTC
53685 CTC
1 CTC
53688 GTCTGCCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (17 bp):
CTCTCCTCCCTCTCCTC
Found at i:55967 original size:21 final size:20
Alignment explanation
Indices: 55921--55974 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
55911 TAGGGATTTG
*
55921 AGGTTTAGGGTTTGGGTTTA
1 AGGTTTAGGGTTTGGGGTTA
*
55941 AGGTTTAAGGGTTTGGGGTTC
1 AGGTTT-AGGGTTTGGGGTTA
* *
55962 ATGTTTTGGGTTT
1 AGGTTTAGGGTTT
55975 TACATTTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.13, C:0.02, G:0.39, T:0.46
Consensus pattern (20 bp):
AGGTTTAGGGTTTGGGGTTA
Found at i:58705 original size:3 final size:3
Alignment explanation
Indices: 58697--58743 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
58687 GTAGTAAAAT
58697 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
58744 AATTTCTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:60781 original size:52 final size:52
Alignment explanation
Indices: 60700--60993 Score: 471
Period size: 52 Copynumber: 5.7 Consensus size: 52
60690 ATTCCATTTA
* * * * * *
60700 ATACTCACGATGACACATAGTCATCGGACCTCTTAAACCGTGAAGGAATCAT
1 ATACTCACGATGACACATAGTCATTGGACCTTTTAATCCATAAAGGATTCAT
*
60752 ATACTCACGATGACACATAGTCCTTGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTTTTAATCCATAAAGGATTCAT
* *
60804 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCTATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTTTTAATCCATAAAGGATTCAT
*
60856 ATACTCACGATGACACATAGTCATTGAACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTTTTAATCCATAAAGGATTCAT
*
60908 ATACTCACAATGACACATAGTCATTGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTTTTAATCCATAAAGGATTCAT
* *
60960 ATACTCACGATGACACATAATCATCGGACCTTTT
1 ATACTCACGATGACACATAGTCATTGGACCTTTT
60994 CTTTATTTAC
Statistics
Matches: 224, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 224 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATTGGACCTTTTAATCCATAAAGGATTCAT
Found at i:64419 original size:21 final size:20
Alignment explanation
Indices: 64368--64419 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
64358 AAAATTCTAT
*
64368 AATAA-AATATTTAAATTAA
1 AATAATAATTTTTAAATTAA
* *
64387 ATTATTAATTTTTAAATTAA
1 AATAATAATTTTTAAATTAA
64407 AATAATAATTTTT
1 AATAATAATTTTT
64420 CTATTTAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATAATTTTTAAATTAA
Found at i:82958 original size:14 final size:15
Alignment explanation
Indices: 82934--82963 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
82924 TACTTTCTTT
82934 TTCTCTTTTCTTTAA
1 TTCTCTTTTCTTTAA
82949 TTCT-TTTTCTTTAA
1 TTCTCTTTTCTTTAA
82963 T
1 T
82964 AACAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TTCTCTTTTCTTTAA
Found at i:91853 original size:43 final size:43
Alignment explanation
Indices: 91388--91913 Score: 537
Period size: 43 Copynumber: 12.3 Consensus size: 43
91378 TTATGAGGAA
* * * * *
91388 AAACGCTGCTATAGAACATGGTCTTTAGCGACAC-TTTCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
91430 AAACGCCGCT--AGAACATGGTCTTTAGCGTCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * * *
91471 AAATGTCGTTAAAGAACATGGTCTTTAGCAGCTC-TTTCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * *
91513 AAATGCCGCTATAGAGCATGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * * *
91556 AAACGCCGCTAAAGAACATGGTTTTTAACAGCACTTTACCAAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * *
91599 AAACACCGCTAAAGAACATGGTCTTTAGCAGCACTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
91642 AAACACCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
91685 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGC-TTTCCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCC-CAC
*
91728 AAACGCCGCTAAAGAACATGGTCTTTAGTGGCGC-TTTCCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCC-CAC
* * * * *
91771 AAACGTCGCTAAAGAACATGATCTTTAGCAGCGCGTTTGCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * **
91814 AAACGCCGCTAAAGAACATGGTATTTAGTGGTGCTTTTGCTTAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTT-CCCAC
* * * * *
91858 AAACGTCGCTATAA-ATA-ATGTTCTTCAGTGGCGTTTTTCCCAC
1 AAACGCCGCTA-AAGA-ACATGGTCTTTAGCGGCGCTTTTCCCAC
*
91901 AAATGCCGCTAAA
1 AAACGCCGCTAAA
91914 ATTAACAGAT
Statistics
Matches: 407, Mismatches: 68, Indels: 18
0.83 0.14 0.04
Matches are distributed among these distances:
40 20 0.05
41 14 0.03
42 50 0.12
43 287 0.71
44 33 0.08
45 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:92231 original size:21 final size:21
Alignment explanation
Indices: 92216--92258 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
92206 CTGCTTCTTT
92216 CACTTCTCTCGCTGCTGCCTC
1 CACTTCTCTCGCTGCTGCCTC
*
92237 CACTTCTCTCGCTGTTGCCTC
1 CACTTCTCTCGCTGCTGCCTC
92258 C
1 C
92259 GCTTTAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.47, G:0.14, T:0.35
Consensus pattern (21 bp):
CACTTCTCTCGCTGCTGCCTC
Found at i:94452 original size:65 final size:65
Alignment explanation
Indices: 94348--94470 Score: 201
Period size: 65 Copynumber: 1.9 Consensus size: 65
94338 CATTTGCCAT
**
94348 AGTAATCCAACTCAACAATGTTTGTAAGAAGTCCGTAATACTCCACATTTCTCTCAATGGGATTA
1 AGTAATCCAACTCAACAATGTCCGTAAGAAGTCCGTAATACTCCACATTTCTCTCAATGGGATTA
* * *
94413 AGTAATCTAACTCAATAATGTCCGTAAGAAGTCCGTAATACTCTACATTTCTCTCAAT
1 AGTAATCCAACTCAACAATGTCCGTAAGAAGTCCGTAATACTCCACATTTCTCTCAAT
94471 AAGATTACTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (65 bp):
AGTAATCCAACTCAACAATGTCCGTAAGAAGTCCGTAATACTCCACATTTCTCTCAATGGGATTA
Found at i:98162 original size:70 final size:70
Alignment explanation
Indices: 98081--98213 Score: 214
Period size: 70 Copynumber: 1.9 Consensus size: 70
98071 AATAATTAAA
*
98081 TATTTTAAATTAAATA-TTAGGTTTTAGGGTTTAATAAATAACTAATTAAATGATTAAATATTTG
1 TATTTTAAATTAAATAGTTAGG-TTTAGGGTTTAATAAATAACTAATTAAATAATTAAATATTTG
98145 GGTTGT
65 GGTTGT
* * *
98151 TATTTTGAATTAAATAGTTCGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTT
1 TATTTTAAATTAAATAGTTAGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAAATATTT
98214 AAATAATTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 54 0.93
71 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (70 bp):
TATTTTAAATTAAATAGTTAGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAAATATTTGG
GTTGT
Found at i:98299 original size:122 final size:121
Alignment explanation
Indices: 98151--98564 Score: 607
Period size: 122 Copynumber: 3.4 Consensus size: 121
98141 TTTGGGTTGT
* *
98151 TATTTTGAATTAAATAGTTCGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTAA
1 TATTTTGAATTAAATA-TTTGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTA
* * *
98216 ATAATTTGGT-TGTTTTTAATAATGTAATATTTATTTAAATATAGTTAAATAATTTAA
65 AT-ATTTGTTCTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAA
* *
98273 TATTTTGAATTAAATATTTGGTTTTAGGATTTAATAAATAACTAATTAAATGATTAATTATTTTA
1 TATTTTGAATTAAATATTTGG-TTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTA
*
98338 ATATTTGTTCTGTTTTTAATAATTTAATATTTATTTAAATATAATTAGATAATTTAA
65 ATATTTGTTCTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAA
* *
98395 TATTTTGAATTAAATATTTTGATTTAGGGTTTAATGAATAACTAATTAAATAATTAATTATTTTA
1 TATTTTGAATTAAATA-TTTGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTA
* * * * *
98460 ATATTTGTTCTATTTTTAATAATTTAATATTTA-TTCAATAAAATTTAATATTTTAA
65 ATATTTGTTCTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAA
* *
98516 TATTTTGAATTAAATATTTCAGTTTAGAGTTTAATTAAATAACTAATTA
1 TATTTTGAATTAAATATTT-GGTTTAGGGTTTAA-TAAATAACTAATTA
98565 TTTTAATTGA
Statistics
Matches: 265, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
120 3 0.01
121 55 0.21
122 203 0.77
123 4 0.02
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (121 bp):
TATTTTGAATTAAATATTTGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTAA
TATTTGTTCTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAA
Found at i:98602 original size:109 final size:109
Alignment explanation
Indices: 98437--98682 Score: 354
Period size: 109 Copynumber: 2.3 Consensus size: 109
98427 AATGAATAAC
***
98437 TAATTAAATAATTAATTATTTTAATATTTGTTCTATTTTTAATAATTTAATATTTATTCAATAAA
1 TAATTAAATAATTAATTATTTTAAT-TGAATTCTATTTTTAATAATTTAATATTTATTCAAT-AA
* * *
98502 ATTT-AATATTTTAATATTTTGAATTAAATATTTCAGTTTAGAGTT
64 ATTTAAATAATTTAATATTTTGAATTAAATAGTTCAGTTTAGAGAT
* * *
98547 TAATTAAATAACTAATTATTTTAATTGAATTCTATTTTTAATAATTTAA-ATTTTATTTAATATA
1 TAATTAAATAATTAATTATTTTAATTGAATTCTATTTTTAATAATTTAATA-TTTATTCAATAAA
*
98611 TTTAAATAATTTAATATTTTGAATTAAATAGTTGAGTTTAGAGAT
65 TTTAAATAATTTAATATTTTGAATTAAATAGTTCAGTTTAGAGAT
98656 TAA-TAAATAATTAATTATTTTAATTGA
1 TAATTAAATAATTAATTATTTTAATTGA
98683 GTTTTATTGC
Statistics
Matches: 123, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
108 29 0.24
109 70 0.57
110 24 0.20
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (109 bp):
TAATTAAATAATTAATTATTTTAATTGAATTCTATTTTTAATAATTTAATATTTATTCAATAAAT
TTAAATAATTTAATATTTTGAATTAAATAGTTCAGTTTAGAGAT
Found at i:98614 original size:244 final size:242
Alignment explanation
Indices: 98151--98672 Score: 587
Period size: 244 Copynumber: 2.2 Consensus size: 242
98141 TTTGGGTTGT
*
98151 TATTTTGAATTAAATAGTTCGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTAA
1 TATTTTGAATTAAATAGTTCGATTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTAA
* * *
98216 ATAATTTGGTTGTTTTTAATAATGTAATATTTATTTAAATATAGTTAAATAATTTAATATTTTGA
66 ATAATTTGGTTATTTTTAATAATGTAATATTTATTTAAATAAAATTAAATAATTTAATATTTTGA
* * **
98281 ATTAAATATTTGGTTTTAGGATTTAATAAATAACTAATTAAATGATTAATTATTTTAATATTTGT
131 ATTAAATATTTAGTTTTAGGATTTAATAAATAACTAATTAAATAATTAATTATTTTAATATTTAA
*
98346 TCTGTTTTTAATAATTTAATATTTATTTAAATATAATTAGATAATTTAA
196 TCTGTTATT-ATAA-TTAATATTTATTTAAATATAATTAGATAATTTAA
* * * *
98395 TATTTTGAATTAAATATTTTGATTTAGGGTTTAATGAATAACTAATTAAATAATTAATTATTTTA
1 TATTTTGAATTAAATAGTTCGATTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTAA
* * * * *
98460 AT-ATTTGTTCTATTTTTAATAATTTAATATTTA-TTCAATAAAATTTAATATTTTAATATTTTG
66 ATAATTTGGT-TATTTTTAATAATGTAATATTTATTTAAATAAAATTAAATAATTTAATATTTTG
* *
98523 AATTAAATATTTCAG-TTTA-GAGTTTAATTAAATAACTAA-T---T-ATT--TTAATTGAAT-T
130 AATTAAATATTT-AGTTTTAGGA-TTTAA-TAAATAACTAATTAAATAATTAATTATTTTAATAT
* * * *
98578 CT-AT-T-TT-TAATAATTTAA-ATTTTATTT-AATATATTTAAATAATTTAA
192 TTAATCTGTTATTATAA-TTAATA-TTTATTTAAATATAATTAGATAATTTAA
* * *
98625 TATTTTGAATTAAATAGTT-GAGTTTAGAGATTAATAAATAATTAATTA
1 TATTTTGAATTAAATAGTTCGA-TTTAGGGTTTAATAAATAACTAATTA
98673 TTTTAATTGA
Statistics
Matches: 246, Mismatches: 26, Indels: 26
0.83 0.09 0.09
Matches are distributed among these distances:
229 2 0.01
230 59 0.24
231 16 0.07
232 1 0.00
233 2 0.01
234 1 0.00
235 1 0.00
236 2 0.01
237 8 0.03
239 3 0.01
240 1 0.00
242 2 0.01
243 53 0.22
244 95 0.39
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (242 bp):
TATTTTGAATTAAATAGTTCGATTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTAA
ATAATTTGGTTATTTTTAATAATGTAATATTTATTTAAATAAAATTAAATAATTTAATATTTTGA
ATTAAATATTTAGTTTTAGGATTTAATAAATAACTAATTAAATAATTAATTATTTTAATATTTAA
TCTGTTATTATAATTAATATTTATTTAAATATAATTAGATAATTTAA
Found at i:100548 original size:25 final size:25
Alignment explanation
Indices: 100495--100540 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
100485 GTTGGATCCC
100495 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
100520 AATTAAA-TCTAAACA-ATAATT
1 AATTAAATTCTAAAAAGATAATT
100541 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:100627 original size:13 final size:13
Alignment explanation
Indices: 100606--100639 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
100596 AAAATATAAT
100606 AATAATAATCCTA
1 AATAATAATCCTA
*
100619 AATATTAATCCTA
1 AATAATAATCCTA
*
100632 AAAAATAA
1 AATAATAA
100640 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:101189 original size:16 final size:16
Alignment explanation
Indices: 101168--101198 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
101158 ATTACTCCCC
101168 AACCATACTAGCAGAG
1 AACCATACTAGCAGAG
*
101184 AACCATACTTGCAGA
1 AACCATACTAGCAGA
101199 AATCACAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (16 bp):
AACCATACTAGCAGAG
Found at i:101552 original size:25 final size:25
Alignment explanation
Indices: 101518--101568 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
101508 GTAATTTAAT
*
101518 ATAATCTTTGAAAAGAGACAATCAA
1 ATAATATTTGAAAAGAGACAATCAA
101543 ATAATATTTGAAAAGAGACAATCAA
1 ATAATATTTGAAAAGAGACAATCAA
101568 A
1 A
101569 CATCAGCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (25 bp):
ATAATATTTGAAAAGAGACAATCAA
Found at i:105235 original size:41 final size:41
Alignment explanation
Indices: 105187--105544 Score: 356
Period size: 41 Copynumber: 8.7 Consensus size: 41
105177 ACATAAACGT
* * * *
105187 CGCTAATGCTCTGACCTTTAACGGTGTTTATGAGAAAGTGT
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
* * **
105228 CGTTAATGCTTTGATATTTAGCGGCGTTTTATGAGAAAGCGC
1 CGCTAATGCTCTGACCTTTAGCGGCG-TTTATGAGAAAGCGC
* * *** * * *
105270 CGCTAATGCTCTGACATTAAGCGATATATATGTGAAAGCGT
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
* * * *
105311 CGTTAATGCTCTGACCTTTAGCGGCATTTGTGAGAAAGCAC
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
* * * *
105352 CGCTAATGCTCTAACCTTTAGCAGCGTTTTTGAGAAAGCGT
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
* * *
105393 CGCTAATGATCTGACCTTTAGCGGCGTTTATGAAAAAGCGG
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
* * * * * * * *
105434 CACTAATGCCCAGACCTTTAACGGCTTTTAAGAGGAAGCAC
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
* *
105475 CGCTAATGCTCTGACCTTTAGCGGCATTTATGATAAAGCGC
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
* *
105516 CACTAATGCTCAGACCTTTAGCGGCGTTT
1 CGCTAATGCTCTGACCTTTAGCGGCGTTT
105545 TTTCTATAAA
Statistics
Matches: 252, Mismatches: 64, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
41 220 0.87
42 32 0.13
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (41 bp):
CGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
Found at i:107073 original size:17 final size:18
Alignment explanation
Indices: 107051--107092 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
107041 TCATTTAATA
107051 ATAAAACATA-ATT-TATT
1 ATAAAA-ATATATTATATT
107068 ATAAAAATATATTACTATT
1 ATAAAAATATATTA-TATT
107087 ATAAAA
1 ATAAAA
107093 TCTTTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
19 10 0.45
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAAATATATTATATT
Found at i:108003 original size:20 final size:22
Alignment explanation
Indices: 107962--108013 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
107952 ATTTTATTTG
107962 ATTTTTTATATTAAAAATATAT
1 ATTTTTTATATTAAAAATATAT
107984 ATTTTTTATATTAAAAATATAT
1 ATTTTTTATATTAAAAATATAT
108006 ATTTTTTA
1 ATTTTTTA
108014 AGATTTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTTTATATTAAAAATATAT
Found at i:114362 original size:15 final size:16
Alignment explanation
Indices: 114328--114362 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
114318 GCCATTATTC
*
114328 TTTTCTGTTCTTTTCT
1 TTTTCTGTTCTTTTAT
114344 TTTTCT-TTCTTTTAT
1 TTTTCTGTTCTTTTAT
114359 TTTT
1 TTTT
114363 GCAAGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTCTGTTCTTTTAT
Found at i:114711 original size:32 final size:33
Alignment explanation
Indices: 114660--114727 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
114650 TTTAAGGGCC
*
114660 AAAATTTTTTTTTACTAACTTTTAA-GAGATCTAA
1 AAAATTTTTTCTTA-TAACTTTTAAGGA-ATCTAA
114694 AAAATTTTTTCTT-TAACTTTTAAGGAATCTAA
1 AAAATTTTTTCTTATAACTTTTAAGGAATCTAA
114726 AA
1 AA
114728 TCTTATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 18 0.56
33 2 0.06
34 12 0.38
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (33 bp):
AAAATTTTTTCTTATAACTTTTAAGGAATCTAA
Found at i:118962 original size:18 final size:18
Alignment explanation
Indices: 118925--118963 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
118915 TCTATTTTTG
*
118925 AATTCTTTCATCTCCATC
1 AATTCTTTCATCTCAATC
118943 AATTCTTTC-TCTCAACTC
1 AATTCTTTCATCTCAA-TC
118961 AAT
1 AAT
118964 ACCTTGCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTCTTTCATCTCAATC
Found at i:123271 original size:30 final size:30
Alignment explanation
Indices: 123237--123438 Score: 133
Period size: 30 Copynumber: 6.9 Consensus size: 30
123227 GTAAAAGGAT
123237 AATTTTGAG-AGTTTCGAGGTAGAAAATGAA
1 AATTTTGAGAAGTTTCGAGGTA-AAAATGAA
* *
123267 AATTTTG-GAAGTTT-AAGGGTAAAAATG-G
1 AATTTTGAGAAGTTTCGA-GGTAAAAATGAA
*
123295 AATTTTTAGAAGTTTCGAGGTCAAAAATG-A
1 AATTTTGAGAAGTTTCGAGGT-AAAAATGAA
* * *
123325 GATTTTG-GAAG-TTCGTGGGT-AAAATGGA
1 AATTTTGAGAAGTTTCG-AGGTAAAAATGAA
* * * *
123353 ACTTTTG-GAAGTTTTGGGGTTAAAAATGGA
1 AATTTTGAGAAGTTTCGAGG-TAAAAATGAA
*
123383 ATTTTTG-GAAGTTTCGAGGTTAAAAATG-A
1 AATTTTGAGAAGTTTCGAGG-TAAAAATGAA
* *
123412 ATTTTTGA-AAG-TTCGGGGGTAAAAATG
1 AATTTTGAGAAGTTTC-GAGGTAAAAATG
123439 GGATTTTCAA
Statistics
Matches: 145, Mismatches: 15, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
27 6 0.04
28 34 0.23
29 43 0.30
30 62 0.43
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
AATTTTGAGAAGTTTCGAGGTAAAAATGAA
Found at i:123301 original size:29 final size:29
Alignment explanation
Indices: 123191--123445 Score: 181
Period size: 29 Copynumber: 8.8 Consensus size: 29
123181 TTTGGGAAAA
* * *
123191 TTTGAGGTTAAAAATAGAATTTTTAGACA-
1 TTTGAGGGTAAAAATGGAATTTTTGGA-AG
* *
123220 TTTGGGGGT-AAAA-GGATAATTTT-GAGAG
1 TTTGAGGGTAAAAATGGA-ATTTTTGGA-AG
* *
123248 TTTCGA-GGTAGAAAATGAAAATTTTGGAAG
1 TTT-GAGGGTA-AAAATGGAATTTTTGGAAG
* *
123278 TTTAAGGGTAAAAATGGAATTTTTAGAAG
1 TTTGAGGGTAAAAATGGAATTTTTGGAAG
123307 TTTCGA-GGTCAAAAAT-GAGA-TTTTGGAAG
1 TTT-GAGGGT-AAAAATGGA-ATTTTTGGAAG
* * *
123336 TTCGTGGGT-AAAATGGAACTTTTGGAAG
1 TTTGAGGGTAAAAATGGAATTTTTGGAAG
123364 TTTTG-GGGTTAAAAATGGAATTTTTGGAAG
1 -TTTGAGGG-TAAAAATGGAATTTTTGGAAG
* *
123394 TTTCGAGGTTAAAAAT-GAATTTTTGAAAG
1 TTT-GAGGGTAAAAATGGAATTTTTGGAAG
* * *
123423 TTCGGGGGTAAAAATGGGATTTT
1 TTTGAGGGTAAAAATGGAATTTT
123446 CAAATAGTTT
Statistics
Matches: 183, Mismatches: 23, Indels: 40
0.74 0.09 0.16
Matches are distributed among these distances:
27 11 0.06
28 40 0.22
29 73 0.40
30 53 0.29
31 6 0.03
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
TTTGAGGGTAAAAATGGAATTTTTGGAAG
Found at i:123377 original size:87 final size:86
Alignment explanation
Indices: 123164--123435 Score: 259
Period size: 87 Copynumber: 3.1 Consensus size: 86
123154 TCGGATATCA
* * * * * * *
123164 GGGGGTAAAATGATAATTTTGGGAAAATTTGAGGTTAAAAATAGAATTTTTAGACA-TTTGGGGG
1 GGGGGTAAAATGAAAATTTT-GG-AAGTTTAAGGGTAAAAATGGAATTTTTAGA-AGTTTCGAGG
*
123228 T-AAAAGGAT-AA-TTTTGAGAGTTTC
63 TCAAAA--ATGAATTTTTGAAAG-TTC
*
123252 -GAGGTAGAAAATGAAAATTTTGGAAGTTTAAGGGTAAAAATGGAATTTTTAGAAGTTTCGAGGT
1 GGGGGT--AAAATGAAAATTTTGGAAGTTTAAGGGTAAAAATGGAATTTTTAGAAGTTTCGAGGT
*
123316 CAAAAATGAGA-TTTTGGAAGTTC
64 CAAAAATGA-ATTTTTGAAAGTTC
* * * ** * *
123339 GTGGGTAAAATGGAACTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTTCGAGGTT
1 GGGGGTAAAATGAAAATTTTGGAAGTTTAAGGG-TAAAAATGGAATTTTTAGAAGTTTCGAGGTC
123404 AAAAATGAATTTTTGAAAGTTC
65 AAAAATGAATTTTTGAAAGTTC
123426 GGGGGTAAAA
1 GGGGGTAAAA
123436 ATGGGATTTT
Statistics
Matches: 155, Mismatches: 20, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
86 27 0.17
87 98 0.63
88 17 0.11
89 13 0.08
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (86 bp):
GGGGGTAAAATGAAAATTTTGGAAGTTTAAGGGTAAAAATGGAATTTTTAGAAGTTTCGAGGTCA
AAAATGAATTTTTGAAAGTTC
Found at i:124460 original size:12 final size:12
Alignment explanation
Indices: 124443--124467 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
124433 CTTTAAAATC
124443 TATTTTTATTGT
1 TATTTTTATTGT
124455 TATTTTTATTGT
1 TATTTTTATTGT
124467 T
1 T
124468 TGCAGATCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TATTTTTATTGT
Found at i:125119 original size:23 final size:23
Alignment explanation
Indices: 125093--125140 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
125083 AGTGGTTGAG
125093 GTGGACGGAAGCAGTGCAAATGA
1 GTGGACGGAAGCAGTGCAAATGA
125116 GTGGACGGAAGCAGTGCAAATGA
1 GTGGACGGAAGCAGTGCAAATGA
125139 GT
1 GT
125141 TTTTGTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.40, T:0.15
Consensus pattern (23 bp):
GTGGACGGAAGCAGTGCAAATGA
Found at i:125297 original size:24 final size:23
Alignment explanation
Indices: 125260--125306 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
125250 ATTGGACTTG
*
125260 ATTTAAATAGATTTAAACTTTAA
1 ATTTAAATAAATTTAAACTTTAA
*
125283 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAACTTTAA
125307 GTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATAAATTTAAACTTTAA
Found at i:125298 original size:17 final size:17
Alignment explanation
Indices: 125273--125357 Score: 100
Period size: 17 Copynumber: 4.9 Consensus size: 17
125263 TAAATAGATT
125273 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTATAA
125291 TAAATTTAAATTT-TAA
1 TAAATTTAAATTTATAA
* *
125307 GTAAATTTAAACTTAAAA
1 -TAAATTTAAATTTATAA
* *
125325 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTATAA
125342 TAAATTTAAATCTTAT
1 TAAATTTAAAT-TTAT
125358 TGGGCCCATA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.05
17 46 0.79
18 9 0.16
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:125300 original size:6 final size:6
Alignment explanation
Indices: 125270--125352 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
125260 ATTTAAATAG
* *
125270 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
125317 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
125353 CTTATTGGGC
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
4 2 0.03
5 13 0.22
6 36 0.61
7 8 0.14
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:127293 original size:59 final size:60
Alignment explanation
Indices: 127206--127342 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 60
127196 GGAAAACAGC
* * * * * *
127206 CAAGTTCAGGTATCAAATTAGGT-CAAAAAAGATTTAGGTATCAAACTAG-GAAAAAGTGT
1 CAAGTTCAGGTACCAAATTAGGTAAAAAAAAG-TTTAAGTACCAAACTAGAAAAAAAATGT
* *
127265 CAAGTTCAGGTACCAAATT-GAGTAAAAAAAAGTTTAAGTACCGAATTAGAAAAAAAATGT
1 CAAGTTCAGGTACCAAATTAG-GTAAAAAAAAGTTTAAGTACCAAACTAGAAAAAAAATGT
*
127325 CAAGTTCAAGTACCAAAT
1 CAAGTTCAGGTACCAAAT
127343 GTTATATTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
58 1 0.02
59 33 0.50
60 32 0.48
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (60 bp):
CAAGTTCAGGTACCAAATTAGGTAAAAAAAAGTTTAAGTACCAAACTAGAAAAAAAATGT
Found at i:127329 original size:26 final size:28
Alignment explanation
Indices: 127266--127329 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
127256 AAAAAGTGTC
*
127266 AAGTTCAGGTACCAAATTGAGTAAAAAA
1 AAGTTCAAGTACCAAATTGAGTAAAAAA
* *
127294 AAGTTTAAGTACCGAATT-AG-AAAAAA
1 AAGTTCAAGTACCAAATTGAGTAAAAAA
127320 AA-TGTCAAGT
1 AAGT-TCAAGT
127330 TCAAGTACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 13 0.42
27 2 0.06
28 15 0.48
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.23
Consensus pattern (28 bp):
AAGTTCAAGTACCAAATTGAGTAAAAAA
Found at i:127683 original size:69 final size:68
Alignment explanation
Indices: 127605--127796 Score: 226
Period size: 69 Copynumber: 2.8 Consensus size: 68
127595 GATCTTAAAA
* *
127605 CATGAAATGGATACAATTAATGTCATTTTGGATAGCAATTCACATTCATATTTGGACAAGATTCT
1 CATGAAATGGATACAATTAATG-CATTTTGGACAGCAATTCACATTCAAATTTGGACAAG-TTCT
127670 -GAAG
64 CGAAG
* * * ** * *
127674 CATGTAATGGATATATTTAATAGCATTGCGGACAACAATTCACATTCAAATTTGGACAAGTTTTC
1 CATGAAATGGATACAATTAAT-GCATTTTGGACAGCAATTCACATTCAAATTTGGACAAGTTCTC
127739 GAAG
65 GAAG
* *
127743 CATGCAATGGATAC-ATCTAATACCATTTTGGACAGCAATTCACATTCAAATTTG
1 CATGAAATGGATACAAT-TAAT-GCATTTTGGACAGCAATTCACATTCAAATTTG
127797 ATACTCCAAC
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
68 4 0.04
69 99 0.95
70 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (68 bp):
CATGAAATGGATACAATTAATGCATTTTGGACAGCAATTCACATTCAAATTTGGACAAGTTCTCG
AAG
Found at i:128320 original size:24 final size:24
Alignment explanation
Indices: 128293--128354 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
128283 TTTTTAGAAG
* *
128293 ATTTAGTATTTATTAGCATAATAT
1 ATTTAGTATTTATTAACATAAAAT
128317 ATTTTA-TATTTATTAACATAAAAT
1 A-TTTAGTATTTATTAACATAAAAT
*
128341 CTTT-GTTATTTATT
1 ATTTAG-TATTTATT
128355 TCAATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 3 0.09
24 25 0.78
25 4 0.12
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (24 bp):
ATTTAGTATTTATTAACATAAAAT
Found at i:129473 original size:27 final size:27
Alignment explanation
Indices: 129443--129496 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
129433 GAAGGAGAAA
129443 TGGTCATTTTGGAATAAAAGAGTATTT
1 TGGTCATTTTGGAATAAAAGAGTATTT
129470 TGGTCATTTTGGAATAAAAGAGTATTT
1 TGGTCATTTTGGAATAAAAGAGTATTT
129497 ATGATAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (27 bp):
TGGTCATTTTGGAATAAAAGAGTATTT
Found at i:131173 original size:35 final size:36
Alignment explanation
Indices: 131134--131222 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 36
131124 TTTGGTGCAT
* *
131134 TTTGGTTGTGTAGGGATTG-ATGCACTTTTGTACAA
1 TTTGGTTGTGTAGGGATAGAATGCACTTGTGTACAA
*
131169 TTTGGTTGTGTAGGGA-AGAATGCACTTGTGTGCAA
1 TTTGGTTGTGTAGGGATAGAATGCACTTGTGTACAA
* *
131204 TTTTGTTGGGT-GGGATAGA
1 TTTGGTTGTGTAGGGATAGA
131223 TCCTAAGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 5 0.11
35 42 0.89
ACGTcount: A:0.20, C:0.07, G:0.34, T:0.39
Consensus pattern (36 bp):
TTTGGTTGTGTAGGGATAGAATGCACTTGTGTACAA
Found at i:132038 original size:25 final size:25
Alignment explanation
Indices: 132010--132063 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
132000 CGTATATCCT
132010 TACTCATT-GCGTATTATAACCCTCG
1 TACTC-TTCGCGTATTATAACCCTCG
132035 TACTCTTCGCGTATTATAACCCTCG
1 TACTCTTCGCGTATTATAACCCTCG
132060 TACT
1 TACT
132064 TGTTGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.37
Consensus pattern (25 bp):
TACTCTTCGCGTATTATAACCCTCG
Found at i:132656 original size:68 final size:68
Alignment explanation
Indices: 132547--132683 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
132537 AAAATGCCAA
132547 AGAGTAACTCGGACTTTCAGAGGACATTGCACTAACCAAATTTTCTTAAAGATCTTCCAATCAAT
1 AGAGTAACTCGGACTTTCAGAGGACATTGCACTAACCAAATTTTCTTAAAGATCTTCCAATCAAT
132612 AGG
66 AGG
132615 AGAGTAACTCGGACTTTCAGAGGACATTGCACTAACCAAATTTTCTTAAAGATCTTCCAATCAAT
1 AGAGTAACTCGGACTTTCAGAGGACATTGCACTAACCAAATTTTCTTAAAGATCTTCCAATCAAT
132680 AGG
66 AGG
132683 A
1 A
132684 CACAGTTTGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (68 bp):
AGAGTAACTCGGACTTTCAGAGGACATTGCACTAACCAAATTTTCTTAAAGATCTTCCAATCAAT
AGG
Found at i:134796 original size:50 final size:52
Alignment explanation
Indices: 134736--134889 Score: 127
Period size: 54 Copynumber: 3.0 Consensus size: 52
134726 AAGGAATAAT
* *
134736 GCTCTCATGAGCCATACAAAATTATAC-CT-TTACGAACCAG-A-CAGAATTAC
1 GCTCTTATGAGCCAGACAAAA-T-TACGCTCTTACGAACCAGAATCAGAATTAC
* * * *
134786 GCTCTTATGAGCTAGATAAAATTACGCTCTTATGAGCCAGAATCAGAATTAC
1 GCTCTTATGAGCCAGACAAAATTACGCTCTTACGAACCAGAATCAGAATTAC
* * ** * * *
134838 GCTCTTACGAGCCAGAATCAGAATTACATTCTTATGAGCCAAAATCAGAATT
1 GCTCTTATGAGCCAG-A-CAAAATTACGCTCTTACGAACCAGAATCAGAATT
134890 TCTTCATCAT
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
48 3 0.04
49 3 0.04
50 26 0.31
51 1 0.01
52 22 0.26
53 1 0.01
54 29 0.34
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (52 bp):
GCTCTTATGAGCCAGACAAAATTACGCTCTTACGAACCAGAATCAGAATTAC
Found at i:134843 original size:27 final size:27
Alignment explanation
Indices: 134777--134889 Score: 158
Period size: 27 Copynumber: 4.3 Consensus size: 27
134767 ACGAACCAGA
*
134777 CAGAATTACGCTCTTATGAGCTAG-AT
1 CAGAATTACGCTCTTATGAGCCAGAAT
*
134803 -AAAATTACGCTCTTATGAGCCAGAAT
1 CAGAATTACGCTCTTATGAGCCAGAAT
*
134829 CAGAATTACGCTCTTACGAGCCAGAAT
1 CAGAATTACGCTCTTATGAGCCAGAAT
** *
134856 CAGAATTACATTCTTATGAGCCAAAAT
1 CAGAATTACGCTCTTATGAGCCAGAAT
134883 CAGAATT
1 CAGAATT
134890 TCTTCATCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
25 21 0.27
26 2 0.03
27 54 0.70
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (27 bp):
CAGAATTACGCTCTTATGAGCCAGAAT
Found at i:144310 original size:25 final size:25
Alignment explanation
Indices: 144275--144434 Score: 113
Period size: 27 Copynumber: 6.2 Consensus size: 25
144265 TACAGAATAT
* * * *
144275 CGCTCTCACGAGCTAGATAGAATTA
1 CGCTCTTACGAGCCAGACAAAATTA
*
144300 CGCCCTTACGAGCCAGACAAAATTA
1 CGCTCTTACGAGCCAGACAAAATTA
* *
144325 TGCTCTAACGAGCCAGACAAAATTA
1 CGCTCTTACGAGCCAGACAAAATTA
* * * *
144350 CGCACTTATGAGCCAAAATCAGAATTA
1 CGCTCTTACGAGCC-AGA-CAAAATTA
* * *
144377 CGCTCTTACAAGCCAAAATCAGAATTA
1 CGCTCTTACGAGCC-AGA-CAAAATTA
* * *
144404 CTCTCTTACAAGCTAGAATCAAAATTA
1 CGCTCTTACGAGCCAG-A-CAAAATTA
144431 CGCT
1 CGCT
144435 TTTATGAGTC
Statistics
Matches: 110, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
25 52 0.47
26 3 0.03
27 55 0.50
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.23
Consensus pattern (25 bp):
CGCTCTTACGAGCCAGACAAAATTA
Found at i:144377 original size:27 final size:27
Alignment explanation
Indices: 144345--144456 Score: 125
Period size: 27 Copynumber: 4.1 Consensus size: 27
144335 AGCCAGACAA
* **
144345 AATTACGCACTTATGAGCCAAAATCAG
1 AATTACGCTCTTACAAGCCAAAATCAG
144372 AATTACGCTCTTACAAGCCAAAATCAG
1 AATTACGCTCTTACAAGCCAAAATCAG
* * * *
144399 AATTACTCTCTTACAAGCTAGAATCAA
1 AATTACGCTCTTACAAGCCAAAATCAG
* ** *
144426 AATTACGCTTTTATGAGTCAAAATCAG
1 AATTACGCTCTTACAAGCCAAAATCAG
144453 AATT
1 AATT
144457 TGTTCGTCAT
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (27 bp):
AATTACGCTCTTACAAGCCAAAATCAG
Found at i:165300 original size:22 final size:22
Alignment explanation
Indices: 165248--165302 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
165238 TTAGCACTTT
*
165248 AGTGCTCTCTGTTCAACACTTC
1 AGTGCTCTCTGTTCAACACTAC
* *
165270 AGTGTTCTCTGTTTAGA-ACTAC
1 AGTGCTCTCTGTTCA-ACACTAC
*
165292 GGTGCTCTCTG
1 AGTGCTCTCTG
165303 GTGTTGTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.38
Consensus pattern (22 bp):
AGTGCTCTCTGTTCAACACTAC
Found at i:171391 original size:2 final size:2
Alignment explanation
Indices: 171384--171424 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
171374 AGTTGTGTAC
* *
171384 AT AT AT AT AT AT AT AT AT AT AT AG AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
171425 CATGTGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:172741 original size:17 final size:17
Alignment explanation
Indices: 172708--172757 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
172698 TGATTTGATC
*
172708 ATGA-AATGAAATTAAA
1 ATGAGAATGAAATGAAA
*
172724 ATGAGAATGATATGAAA
1 ATGAGAATGAAATGAAA
*
172741 AT-AGAATTGAGATGAAA
1 ATGAGAA-TGAAATGAAA
172758 CGAATTATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (17 bp):
ATGAGAATGAAATGAAA
Found at i:172746 original size:16 final size:18
Alignment explanation
Indices: 172721--172757 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
172711 AAATGAAATT
*
172721 AAAATGAGAA-TGATATG
1 AAAATGAGAATTGAGATG
172738 AAAAT-AGAATTGAGATG
1 AAAATGAGAATTGAGATG
172755 AAA
1 AAA
172758 CGAATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22
Consensus pattern (18 bp):
AAAATGAGAATTGAGATG
Found at i:172755 original size:22 final size:22
Alignment explanation
Indices: 172708--172757 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
172698 TGATTTGATC
*
172708 ATGAAATGAAATTAAAATGAGA
1 ATGAAATGAAAATAAAATGAGA
* *
172730 ATGATATGAAAATAGAATTGAG-
1 ATGAAATGAAAATA-AAATGAGA
172752 ATGAAA
1 ATGAAA
172758 CGAATTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (22 bp):
ATGAAATGAAAATAAAATGAGA
Found at i:186636 original size:26 final size:26
Alignment explanation
Indices: 186600--186653 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
186590 TAAATTTTCC
186600 CCTTAGTCTCTGTAATTACGAATATA
1 CCTTAGTCTCTGTAATTACGAATATA
186626 CCTTAGTCTCTGTAATTACGAATATA
1 CCTTAGTCTCTGTAATTACGAATATA
186652 CC
1 CC
186654 ACGTTGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (26 bp):
CCTTAGTCTCTGTAATTACGAATATA
Found at i:189765 original size:24 final size:25
Alignment explanation
Indices: 189738--189790 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
189728 ATAATTAATT
* * *
189738 TTTATTTTTATTTTTAAATTTTA-A
1 TTTATCTTTATTTTGAAATATTATA
*
189762 TTTATCTTTCTTTTGAAATATTATA
1 TTTATCTTTATTTTGAAATATTATA
189787 TTTA
1 TTTA
189791 ATTAATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTATCTTTATTTTGAAATATTATA
Found at i:192742 original size:13 final size:14
Alignment explanation
Indices: 192721--192755 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
192711 TTCGGCTCAA
*
192721 ATTTTTTTTATTTT
1 ATTTATTTTATTTT
192735 A-TTATTTTATTTT
1 ATTTATTTTATTTT
192748 ATTTATTT
1 ATTTATTT
192756 AACAAACGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:195791 original size:168 final size:168
Alignment explanation
Indices: 195506--195837 Score: 565
Period size: 168 Copynumber: 2.0 Consensus size: 168
195496 ACTGAAACAG
* *
195506 TAACAATGAAAATGATGCCCTCTTTAGTGAGATTATTTGAACAAATGCCCGAACCTAAATATGGT
1 TAACAATGAAAATGATACCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTAAATATGGT
** *
195571 ATTGCTATGGGGGCGTGTACAATTACAGGAGGGATGTTCAGTACTGATTCTTATAGTACTGTTCG
66 ATTGCTATGGACGCGTGTACAATTACAGGAGGGATGTTCAGTACTAATTCTTATAGTACTGTTCG
* * * *
195636 AGGGGTTGATAAGCTAATTCCTGTGGATGTCTATACAA
131 AGGGATGGATAAACTAATTCCCGTGGATGTCTATACAA
* *
195674 TAACAATGAAAATGGTACCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTAAATATGTT
1 TAACAATGAAAATGATACCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTAAATATGGT
195739 ATTGCTATGGACGCGTGTACAATTACAGGAGGGATGTTCAGTACTAATTCTTATAGTACTGTTCG
66 ATTGCTATGGACGCGTGTACAATTACAGGAGGGATGTTCAGTACTAATTCTTATAGTACTGTTCG
195804 AGGGATGGATAAACTAATTCCCGTGGATGTCTAT
131 AGGGATGGATAAACTAATTCCCGTGGATGTCTAT
195838 TTGTCGGGTT
Statistics
Matches: 153, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
168 153 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (168 bp):
TAACAATGAAAATGATACCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTAAATATGGT
ATTGCTATGGACGCGTGTACAATTACAGGAGGGATGTTCAGTACTAATTCTTATAGTACTGTTCG
AGGGATGGATAAACTAATTCCCGTGGATGTCTATACAA
Found at i:195923 original size:11 final size:12
Alignment explanation
Indices: 195898--195927 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
195888 AGACTAAATA
195898 TAAATAATAATT
1 TAAATAATAATT
195910 TAAATAAT-ATT
1 TAAATAATAATT
195921 TAAATAA
1 TAAATAA
195928 AATAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAATAATAATT
Found at i:195924 original size:29 final size:29
Alignment explanation
Indices: 195892--195947 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
195882 CTAAATAGAC
*
195892 TAAATATAAATAATAATTTA-AATAATATT
1 TAAATA-AAATAATAATATATAATAATATT
195921 TAAATAAAATAATAATATATAATAATA
1 TAAATAAAATAATAATATATAATAATA
195948 GATAGAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAATAAAATAATAATATATAATAATATT
Found at i:195943 original size:38 final size:39
Alignment explanation
Indices: 195867--195947 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 39
195857 AACCCTAGGC
* *
195867 AATTATAAATAAATTCTAAATAGACTAAATATAAATAAT
1 AATTATAAATAAATTCTAAATAAAATAAATATAAATAAT
195906 AATT-TAAATAATATT-TAAATAAAATAATAATATATAATAAT
1 AATTATAAATAA-ATTCTAAATAAAAT-A-AATATA-AATAAT
195947 A
1 A
195948 GATAGAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
38 15 0.42
39 8 0.22
40 6 0.17
41 7 0.19
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (39 bp):
AATTATAAATAAATTCTAAATAAAATAAATATAAATAAT
Found at i:196054 original size:40 final size:40
Alignment explanation
Indices: 196003--196080 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
195993 CGAAATATAT
*
196003 TAATATAAATATAAAAATATATTAATTA-TTAATGTAAATA
1 TAATATAAATATAAAAAT-TATTAATTACTTAATATAAATA
* *
196043 TAATATTAATATAAATATTATTAATTACTTAATATAAA
1 TAATATAAATATAAAAATTATTAATTACTTAATATAAA
196081 GATTATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 9 0.26
40 25 0.74
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (40 bp):
TAATATAAATATAAAAATTATTAATTACTTAATATAAATA
Found at i:196061 original size:29 final size:29
Alignment explanation
Indices: 195999--196062 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
195989 AAATCGAAAT
195999 ATATTAATATAAATATAAAAATATATTAA
1 ATATTAATATAAATATAAAAATATATTAA
* * * *
196028 TTATTAATGTAAATATAATATTA-ATATAA
1 ATATTAATATAAATATAAAAATATAT-TAA
196057 ATATTA
1 ATATTA
196063 TTAATTACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
ATATTAATATAAATATAAAAATATATTAA
Found at i:196076 original size:23 final size:23
Alignment explanation
Indices: 196048--196105 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
196038 AAATATAATA
196048 TTAATATAAATATTATTAATTAC
1 TTAATATAAATATTATTAATTAC
*
196071 TTAATATAAAGATTATTAATTAC
1 TTAATATAAATATTATTAATTAC
*
196094 TTAATATTAATA
1 TTAATATAAATA
196106 ACAAATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAATATAAATATTATTAATTAC
Done.