Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 39 of 125
Found at i:11754423 original size:12 final size:12
Alignment explanation
Indices: 11754406--11754430 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11754396 TGTCTCAGGT
11754406 AACTGTAAGGAA
1 AACTGTAAGGAA
11754418 AACTGTAAGGAA
1 AACTGTAAGGAA
11754430 A
1 A
11754431 TGAGCTAAAA
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:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (12 bp):
AACTGTAAGGAA
Found at i:11755444 original size:20 final size:20
Alignment explanation
Indices: 11755369--11755445 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 20
11755359 GGGTTTCTCA
* * *
11755369 AAAAAGTCAACGGTTAACCC
1 AAAAAGTCAACGATCAACCT
* * * *
11755389 AAGAAGACAATGGTCAACCT
1 AAAAAGTCAACGATCAACCT
* **
11755409 ATAAAGTCAATAATCAACCT
1 AAAAAGTCAACGATCAACCT
11755429 AAAAAGTCAACGATCAA
1 AAAAAGTCAACGATCAA
11755446 TGGTCAACGA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.17
Consensus pattern (20 bp):
AAAAAGTCAACGATCAACCT
Found at i:11768994 original size:43 final size:43
Alignment explanation
Indices: 11768941--11769277 Score: 397
Period size: 43 Copynumber: 7.8 Consensus size: 43
11768931 TGGTGATTAC
* * * *
11768941 TAAAAGGAAGACTCATGTCTTGGATAGAGCATGAGATTATTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTA
* * *
11768984 TAAATGGAAGACTTACGTCTTGGTTAGAGCATAAGATTATTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTA
11769027 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTA
* * *
11769070 TAAATGGAAGACTTATGTCTCGGTTGGAGCATAAGATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTA
* * * *
11769113 TAAAAGGAAGACTTGTGTCCCGTTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTA
* * * **
11769156 TAAAAAGAAGACTTATGTCTCGGTTGGAGAATAAGATTGGTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTA
* * * *
11769199 TAAAAGGAAGACTTATGTCTCAG-CAGGAGCATAAGGTTATTTG
1 TAAAAGGAAGACTTATGTCTCGGTTA-GAGCATAAGATTATTTA
* * * * *
11769242 GAAATAGAAAAACTTATGACTCGGTTGGAGCATAAG
1 TAAA-AGGAAGACTTATGTCTCGGTTAGAGCATAAG
11769278 GTTAATATAG
Statistics
Matches: 252, Mismatches: 39, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
43 228 0.90
44 24 0.10
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.31
Consensus pattern (43 bp):
TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTA
Found at i:11769963 original size:21 final size:21
Alignment explanation
Indices: 11769939--11769987 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
11769929 CGTTGTATTA
*
11769939 GTAGAACTGTATA-TTGTATCG
1 GTAGAACT-CATACTTGTATCG
11769960 GTAGTAA-TCATACTTGTATCG
1 GTAG-AACTCATACTTGTATCG
11769981 GTAGAAC
1 GTAGAAC
11769988 CTTCACAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 5 0.21
21 17 0.71
22 2 0.08
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (21 bp):
GTAGAACTCATACTTGTATCG
Found at i:11771732 original size:27 final size:27
Alignment explanation
Indices: 11771694--11771776 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
11771684 CTCATGGATT
11771694 TCCCGTGTTTACCT-TCCCGACGGACCA
1 TCCCGTGTTTA-CTATCCCGACGGACCA
* *
11771721 TCCCGTGTTTACTATCTCGATGGACCA
1 TCCCGTGTTTACTATCCCGACGGACCA
* * * *
11771748 TCCTGTGTTTAATGTCCCGACGAACCA
1 TCCCGTGTTTACTATCCCGACGGACCA
11771775 TC
1 TC
11771777 GAAGGATATC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.04
27 45 0.96
ACGTcount: A:0.18, C:0.34, G:0.18, T:0.30
Consensus pattern (27 bp):
TCCCGTGTTTACTATCCCGACGGACCA
Found at i:11773911 original size:10 final size:10
Alignment explanation
Indices: 11773858--11773915 Score: 73
Period size: 10 Copynumber: 5.8 Consensus size: 10
11773848 TGTCACGTGT
11773858 TAATCACATA
1 TAATCACATA
*
11773868 TAAGCACATA
1 TAATCACATA
11773878 TAATCACATA
1 TAATCACATA
*
11773888 TAGTTC-CATA
1 TA-ATCACATA
*
11773898 TAATCACATT
1 TAATCACATA
11773908 TAATCACA
1 TAATCACA
11773916 ATTTATGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
9 2 0.05
10 37 0.90
11 2 0.05
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (10 bp):
TAATCACATA
Found at i:11774385 original size:36 final size:36
Alignment explanation
Indices: 11774325--11774395 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
11774315 ACTATCACAC
* *
11774325 GGCATGAAAAACATACCCACATATTTACTGTCATAT
1 GGCATGAAAAACAAACCCACATATTCACTGTCATAT
* ** *
11774361 GGCATGAATAACAAACCCTTATATTCACTTTCATA
1 GGCATGAAAAACAAACCCACATATTCACTGTCATA
11774396 ACAGTCATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (36 bp):
GGCATGAAAAACAAACCCACATATTCACTGTCATAT
Found at i:11777895 original size:25 final size:25
Alignment explanation
Indices: 11777823--11777943 Score: 104
Period size: 26 Copynumber: 4.8 Consensus size: 25
11777813 CTTGAGCCAA
*
11777823 TGACTTTTAGCAGACTTCGAGCCGG
1 TGACTTTTAGCAGGCTTCGAGCCGG
* ** *
11777848 TGAATAAATAGCAGGCCTT-GAGCTGG
1 TGACT-TTTAGCAGG-CTTCGAGCCGG
*
11777874 TGACTTTTAACAGGCTTCGAGCCGG
1 TGACTTTTAGCAGGCTTCGAGCCGG
* *
11777899 TGA-TTAAATAGTAGGCCTT-GAGCCGG
1 TGACTT--TTAGCAGG-CTTCGAGCCGG
11777925 TGACTTTTAGCAGGCTTCG
1 TGACTTTTAGCAGGCTTCG
11777944 TCTCGGTGAA
Statistics
Matches: 73, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
24 8 0.11
25 26 0.36
26 31 0.42
27 8 0.11
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (25 bp):
TGACTTTTAGCAGGCTTCGAGCCGG
Found at i:11777952 original size:51 final size:51
Alignment explanation
Indices: 11777800--11777943 Score: 216
Period size: 51 Copynumber: 2.8 Consensus size: 51
11777790 AAAATAAGAG
* ** *
11777800 ATAAATAGTAAGCCTTGAGCCAATGACTTTTAGCAGACTTCGAGCCGGTGA
1 ATAAATAGTAGGCCTTGAGCCGGTGACTTTTAGCAGGCTTCGAGCCGGTGA
* * *
11777851 ATAAATAGCAGGCCTTGAGCTGGTGACTTTTAACAGGCTTCGAGCCGGTGA
1 ATAAATAGTAGGCCTTGAGCCGGTGACTTTTAGCAGGCTTCGAGCCGGTGA
*
11777902 TTAAATAGTAGGCCTTGAGCCGGTGACTTTTAGCAGGCTTCG
1 ATAAATAGTAGGCCTTGAGCCGGTGACTTTTAGCAGGCTTCG
11777944 TCTCGGTGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 82 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (51 bp):
ATAAATAGTAGGCCTTGAGCCGGTGACTTTTAGCAGGCTTCGAGCCGGTGA
Found at i:11787698 original size:18 final size:18
Alignment explanation
Indices: 11787667--11787718 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
11787657 ACATTTTAAA
**
11787667 CAGATGCAGGCACATAGC
1 CAGATGCAACCACATAGC
11787685 CAGATGCAACCACAATAGC
1 CAGATGCAACCAC-ATAGC
* *
11787704 CTG-TGCTACCACATA
1 CAGATGCAACCACATA
11787719 TGCAAGGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 3 0.10
18 19 0.66
19 7 0.24
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (18 bp):
CAGATGCAACCACATAGC
Found at i:11804190 original size:49 final size:49
Alignment explanation
Indices: 11804086--11804217 Score: 158
Period size: 49 Copynumber: 2.7 Consensus size: 49
11804076 CTGATGAAAC
* * * **
11804086 GATGAGATAACTCAAGCTACGGCTTAGCAGGCTTTTGAGCCAGTGTGGT
1 GATGAAATAACTCAAGCTATGGCTTAGCAGGCTTTAGAGCCAGTGAAGT
* * *
11804135 GATGAAATAACTCAAGCTATGACTTAGCAGGCTTTAGAGTCGGTGAAGT
1 GATGAAATAACTCAAGCTATGGCTTAGCAGGCTTTAGAGCCAGTGAAGT
* *
11804184 -AGTGAAATGACTCAAGCTTTGGCTTAGCAGGCTT
1 GA-TGAAATAACTCAAGCTATGGCTTAGCAGGCTT
11804218 GTAAACTGGT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 1 0.01
49 70 0.99
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (49 bp):
GATGAAATAACTCAAGCTATGGCTTAGCAGGCTTTAGAGCCAGTGAAGT
Found at i:11804229 original size:49 final size:49
Alignment explanation
Indices: 11804137--11804230 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
11804127 AGTGTGGTGA
* *
11804137 TGAAATAACTCAAGCTATGACTTAGCAGGCTTTAGAGTCGGTGAAGTAG
1 TGAAATAACTCAAGCTATGACTTAGCAGGCTTTAAACTCGGTGAAGTAG
* * *
11804186 TGAAATGACTCAAGCTTTGGCTTAGCAGGCTTGTAAACT-GGTGAA
1 TGAAATAACTCAAGCTATGACTTAGCAGGCTT-TAAACTCGGTGAA
11804231 ATAACTATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 35 0.90
50 4 0.10
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (49 bp):
TGAAATAACTCAAGCTATGACTTAGCAGGCTTTAAACTCGGTGAAGTAG
Found at i:11808743 original size:21 final size:20
Alignment explanation
Indices: 11808705--11808747 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
11808695 TTCTCTTCAT
* *
11808705 TCTTCTCTTTTTCTTTCTTC
1 TCTTCTCATTTTCCTTCTTC
11808725 TCTTCTTCATTTTCCTTCTTC
1 TCTTC-TCATTTTCCTTCTTC
11808746 TC
1 TC
11808748 CTTAGGTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (20 bp):
TCTTCTCATTTTCCTTCTTC
Found at i:11819987 original size:28 final size:28
Alignment explanation
Indices: 11819955--11820008 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
11819945 TGATGAAAAT
* *
11819955 AGCCACGAAGGTTTCCTTTAACAGAAGC
1 AGCCACAAAGGCTTCCTTTAACAGAAGC
11819983 AGCCACAAAGGCTTCCTTTAACAGAA
1 AGCCACAAAGGCTTCCTTTAACAGAA
11820009 TTAGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (28 bp):
AGCCACAAAGGCTTCCTTTAACAGAAGC
Found at i:11825127 original size:20 final size:21
Alignment explanation
Indices: 11825089--11825127 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11825079 GCCTGGATAT
11825089 TTCTACCGATACTTAAATTAG
1 TTCTACCGATACTTAAATTAG
*
11825110 TTCTACCGGTAC-TAAATT
1 TTCTACCGATACTTAAATT
11825128 TGACAGTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (21 bp):
TTCTACCGATACTTAAATTAG
Found at i:11825940 original size:16 final size:16
Alignment explanation
Indices: 11825916--11825979 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 16
11825906 AAAACATCGA
11825916 CACAAAGCCTACTAGG
1 CACAAAGCCTACTAGG
* *
11825932 CACATAGCCTGAATACACCGG
1 CACAAAGCCT-ACT--A--GG
11825953 CACAAAGCCTACTAGG
1 CACAAAGCCTACTAGG
*
11825969 CACATAGCCTA
1 CACAAAGCCTA
11825980 AATACACCAG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 21 0.55
17 2 0.05
18 1 0.03
19 1 0.03
20 2 0.05
21 11 0.29
ACGTcount: A:0.36, C:0.33, G:0.17, T:0.14
Consensus pattern (16 bp):
CACAAAGCCTACTAGG
Found at i:11825977 original size:37 final size:37
Alignment explanation
Indices: 11825839--11826055 Score: 215
Period size: 37 Copynumber: 5.9 Consensus size: 37
11825829 CTTGGATCAT
*
11825839 CGGCACAAAGCCTGCTAGGCACATAG-CTCGAAAAC-C
1 CGGCACAAAGCCTACTAGGCACATAGCCT-GAAAACAC
* * * *
11825875 CTGACACGAAGCCTACTAGGCACATAGCTTGAAAACAT
1 C-GGCACAAAGCCTACTAGGCACATAGCCTGAAAACAC
* *
11825913 CGACACAAAGCCTACTAGGCACATAGCCTGAATACAC
1 CGGCACAAAGCCTACTAGGCACATAGCCTGAAAACAC
11825950 CGGCACAAAGCCTACTAGGCACATAGCCT-AAATACAC
1 CGGCACAAAGCCTACTAGGCACATAGCCTGAAA-ACAC
* * ** * * * *
11825987 CAGCATAAAGCAGACTATGAACATAACCTAAAAACAC
1 CGGCACAAAGCCTACTAGGCACATAGCCTGAAAACAC
** * *
11826024 TAGCACAAAGCCTACTAGGCATATAACCTGAA
1 CGGCACAAAGCCTACTAGGCACATAGCCTGAA
11826056 TATTTAGATG
Statistics
Matches: 150, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
36 3 0.02
37 142 0.95
38 5 0.03
ACGTcount: A:0.40, C:0.29, G:0.17, T:0.15
Consensus pattern (37 bp):
CGGCACAAAGCCTACTAGGCACATAGCCTGAAAACAC
Found at i:11849736 original size:123 final size:123
Alignment explanation
Indices: 11849524--11849882 Score: 519
Period size: 123 Copynumber: 2.9 Consensus size: 123
11849514 GTTAAATATT
* * *
11849524 AAAACATGAATA-TTAATATCCTTTTTGGAAAGGATATAACGTTTTAAT-AACTTTCCATATGTT
1 AAAACATGAA-AGTTAATATCC-TTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATATATT
* *
11849587 TCTCTAAAGGAATAATTCCATTTTAATATGAGATATTTAATAAAAAGAAACTT-AATATAA
64 TCTCTAAAGGAATATTTCCATTTTAATATGAGATATTTAATAAAAGGAAA-TTGAATATAA
* *
11849647 AAAATATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATATATTTC
1 AAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATATATTTC
* *
11849712 TCTAAAGGAATATTTCCATTTTAATTTGAGATA-TTATATAAAAGGAAATTGAATATTA
66 TCTAAAGGAATATTTCCATTTTAATATGAGATATTTA-ATAAAAGGAAATTGAATATAA
* * *
11849770 AAAACATGAAAGTTAATATACTTTTGGAAATGATATAATGTTTTAATAAACCTTCTATATATTTC
1 AAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATATATTTC
* * *
11849835 TCTAAAAGAATATTTTCATTTTAATATGAGATATTAAATAAAAGGAAA
66 TCTAAAGGAATATTTCCATTTTAATATGAGATATTTAATAAAAGGAAA
11849883 GATAGCATAA
Statistics
Matches: 213, Mismatches: 18, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
122 31 0.15
123 180 0.85
124 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (123 bp):
AAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATATATTTC
TCTAAAGGAATATTTCCATTTTAATATGAGATATTTAATAAAAGGAAATTGAATATAA
Found at i:11854691 original size:17 final size:18
Alignment explanation
Indices: 11854653--11854693 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11854643 CTTTACTTTT
* *
11854653 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACACAGA
11854671 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
11854688 ATTTTA
1 ATTTTA
11854694 GTCACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:11854724 original size:41 final size:41
Alignment explanation
Indices: 11854678--11854772 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
11854668 TGAATTTTAT
*
11854678 TTTAACAAGAATTTTAGTCACCCAATTTTAACAATCTCCAC
1 TTTAACAAGAATTTTAGTCACCCAATTCTAACAATCTCCAC
11854719 TTTAACAAGAATTTTAGTCACCCAATTCTAACAATCTCCAC
1 TTTAACAAGAATTTTAGTCACCCAATTCTAACAATCTCCAC
* *
11854760 CTTGACAAGAATT
1 TTTAACAAGAATT
11854773 CTCTATGAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (41 bp):
TTTAACAAGAATTTTAGTCACCCAATTCTAACAATCTCCAC
Found at i:11866032 original size:26 final size:26
Alignment explanation
Indices: 11865996--11866056 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
11865986 TTTTGGGCGC
11865996 AATTCTGGACACGTTCATGCAGCGAT
1 AATTCTGGACACGTTCATGCAGCGAT
* *
11866022 AATTTTGGACATGTTCATGCAGCGAT
1 AATTCTGGACACGTTCATGCAGCGAT
*
11866048 AGTTCTGGA
1 AATTCTGGA
11866057 TGCAATTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (26 bp):
AATTCTGGACACGTTCATGCAGCGAT
Found at i:11866155 original size:37 final size:37
Alignment explanation
Indices: 11866114--11866190 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
11866104 GAAATATTCT
* * * * * *
11866114 TGCGGTGACAGTTTTGGGTGCAATTTGGAAGTGCTCA
1 TGCGGCGACAGTTATAGGCGCAATCTAGAAGTGCTCA
11866151 TGCGGCGACAGTTATAGGCGCAATCTAGAAGTGCTCA
1 TGCGGCGACAGTTATAGGCGCAATCTAGAAGTGCTCA
11866188 TGC
1 TGC
11866191 AACGACATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
TGCGGCGACAGTTATAGGCGCAATCTAGAAGTGCTCA
Found at i:11871533 original size:24 final size:24
Alignment explanation
Indices: 11871500--11871546 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
11871490 GTTAAGAGTA
11871500 AAAACTGTCA-ATGCAAATGTAATAT
1 AAAACTGTCATA-GCAAAT-TAATAT
11871525 AAAA-TGTCATAGCAAATTAATA
1 AAAACTGTCATAGCAAATTAATA
11871547 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (24 bp):
AAAACTGTCATAGCAAATTAATAT
Found at i:11874466 original size:12 final size:12
Alignment explanation
Indices: 11874431--11874471 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
11874421 TGTCGAGGCA
11874431 TCTTCCTTCTCT
1 TCTTCCTTCTCT
11874443 TCATTCTTCTTCTCT
1 TC-TTC--CTTCTCT
11874458 TCTTCCTTCTCT
1 TCTTCCTTCTCT
11874470 TC
1 TC
11874472 CTCATTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.42
13 3 0.12
14 3 0.12
15 9 0.35
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTTCCTTCTCT
Found at i:11874467 original size:18 final size:20
Alignment explanation
Indices: 11874440--11874487 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
11874430 ATCTTCCTTC
*
11874440 TCTTCATTCTTCTT-CTC-T
1 TCTTCCTTCTTCTTCCTCAT
11874458 TCTTCCTTC-TCTTCCTCAT
1 TCTTCCTTCTTCTTCCTCAT
11874477 T-TTCCTTCTTC
1 TCTTCCTTCTTC
11874488 AACTTAGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.04, C:0.38, G:0.00, T:0.58
Consensus pattern (20 bp):
TCTTCCTTCTTCTTCCTCAT
Found at i:11875863 original size:11 final size:12
Alignment explanation
Indices: 11875844--11875868 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11875834 GGTAAAGAAA
11875844 GCAAAAAAATTT
1 GCAAAAAAATTT
11875856 GCAAAAAAATTT
1 GCAAAAAAATTT
11875868 G
1 G
11875869 AAGACAATAG
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:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (12 bp):
GCAAAAAAATTT
Found at i:11903255 original size:28 final size:28
Alignment explanation
Indices: 11903201--11903255 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
11903191 AGCTCCAAAT
* *
11903201 TTTTTATTTTTGTGATACATGTGTTTTG
1 TTTTTATTTTTGTCATACATATGTTTTG
*
11903229 TTTTTGTTTTTGTCATAACATAT-TTTT
1 TTTTTATTTTTGTCAT-ACATATGTTTT
11903256 CTTTGCATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.16, C:0.05, G:0.13, T:0.65
Consensus pattern (28 bp):
TTTTTATTTTTGTCATACATATGTTTTG
Found at i:11912938 original size:18 final size:18
Alignment explanation
Indices: 11912903--11912964 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
11912893 AAACACAACT
* **
11912903 GAGAAGGAGGAACCTGAG
1 GAGAAGAAGGAAAATGAG
11912921 GAGAAGAAGGAAAATGAG
1 GAGAAGAAGGAAAATGAG
11912939 GAAGAA-AAGGAAGAA-GAG
1 G-AGAAGAAGGAA-AATGAG
*
11912957 AAGAAGAA
1 GAGAAGAA
11912965 TGAAGAGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
17 4 0.11
18 27 0.73
19 6 0.16
ACGTcount: A:0.55, C:0.03, G:0.39, T:0.03
Consensus pattern (18 bp):
GAGAAGAAGGAAAATGAG
Found at i:11913419 original size:17 final size:18
Alignment explanation
Indices: 11913380--11913433 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
11913370 ATGCATCTTA
*
11913380 TTTATTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
*
11913398 TTTATTTTTCACTGCA-T
1 TTTATTTGTCACTGCATT
* *
11913415 TTTATTTGTTAGTGCATT
1 TTTATTTGTCACTGCATT
11913433 T
1 T
11913434 GCATTGTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:11933985 original size:17 final size:17
Alignment explanation
Indices: 11933959--11933991 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
11933949 GTGTTCCTAA
11933959 AAAAATATTTTTCTTTTT
1 AAAAATA-TTTTCTTTTT
11933977 AAAAA-ATTTTCTTTT
1 AAAAATATTTTCTTTT
11933992 AACATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.60
17 1 0.07
18 5 0.33
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
AAAAATATTTTCTTTTT
Found at i:11943832 original size:12 final size:12
Alignment explanation
Indices: 11943817--11943845 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
11943807 TCAAGACGAG
11943817 GAAGAGAAAGAA
1 GAAGAGAAAGAA
11943829 GAAGAGAAAGAA
1 GAAGAGAAAGAA
11943841 GAAGA
1 GAAGA
11943846 AGAACCTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
GAAGAGAAAGAA
Found at i:11947738 original size:16 final size:15
Alignment explanation
Indices: 11947711--11947743 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
11947701 ATTAATGTAA
11947711 AATTAAATTAATTCT
1 AATTAAATTAATTCT
11947726 AATTAAATATAATTCT
1 AATTAAAT-TAATTCT
11947742 AA
1 AA
11947744 ATGTTCTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAAATTAATTCT
Found at i:11949124 original size:92 final size:92
Alignment explanation
Indices: 11949008--11949181 Score: 219
Period size: 92 Copynumber: 1.9 Consensus size: 92
11948998 AAATTCAGGG
* **
11949008 GCTTAATTGCTTTTTTTGAAAAAAA-TTAAGAGCCTTTTTGATGCATTTTGAAAGTTCACGTACC
1 GCTTAATT-CTTTTTTTGAAAAAAATTTAAGAGCCTTTTTGATGAATTTTG-AAGTTCAAATACC
11949072 TAATT-ATGTGCAAAAAAAAAAAAAGCAAGA
64 TAATTGA-GTG-AAAAAAAAAAAAAGCAAGA
* * * * *
11949102 GCTTAATT-TTTTTTTGGAAAAAATTTTAGGGTCTTTTTGATGAATTTTGAATTTCAAATACCTA
1 GCTTAATTCTTTTTTTGAAAAAAATTTAAGAGCCTTTTTGATGAATTTTGAAGTTCAAATACCTA
11949166 ATTGAGTGAAAAAAAA
66 ATTGAGTGAAAAAAAA
11949182 GCAGGAGCTT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
91 8 0.11
92 32 0.46
93 22 0.31
94 8 0.11
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (92 bp):
GCTTAATTCTTTTTTTGAAAAAAATTTAAGAGCCTTTTTGATGAATTTTGAAGTTCAAATACCTA
ATTGAGTGAAAAAAAAAAAAAGCAAGA
Found at i:11949138 original size:93 final size:91
Alignment explanation
Indices: 11949008--11949181 Score: 217
Period size: 93 Copynumber: 1.9 Consensus size: 91
11948998 AAATTCAGGG
* **
11949008 GCTTAATTGCTTTTTTTGAAAAAAATTAAGAGCCTTTTTGATGCATTTTGAAAGTTCACGTACCT
1 GCTTAATT-CTTTTTTTGAAAAAAATTAAGAGCCTTTTTGATGAATTTTG-AAGTTCAAATACCT
11949073 AATT-ATGTGCAAAAAAAAAAAAAGCAAGA
64 AATTGA-GTG-AAAAAAAAAAAAAGCAAGA
* * * * *
11949102 GCTTAATT-TTTTTTTGGAAAAAATTTTAGGGTCTTTTTGATGAATTTTGAATTTCAAATACCTA
1 GCTTAATTCTTTTTTT-GAAAAAAATTAAGAGCCTTTTTGATGAATTTTGAAGTTCAAATACCTA
11949166 ATTGAGTGAAAAAAAA
65 ATTGAGTGAAAAAAAA
11949182 GCAGGAGCTT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
91 8 0.11
92 25 0.36
93 29 0.41
94 8 0.11
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (91 bp):
GCTTAATTCTTTTTTTGAAAAAAATTAAGAGCCTTTTTGATGAATTTTGAAGTTCAAATACCTAA
TTGAGTGAAAAAAAAAAAAAGCAAGA
Found at i:11951870 original size:33 final size:33
Alignment explanation
Indices: 11951833--11951910 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
11951823 CTACCTCGAG
*
11951833 AGATGTTCTAATCAATGATGAAGCTGCCCTGAT
1 AGATGTTCCAATCAATGATGAAGCTGCCCTGAT
* *
11951866 AGATGTTCCAATCATTGATGAAGCTGCCTTGAT
1 AGATGTTCCAATCAATGATGAAGCTGCCCTGAT
* *
11951899 AGTTGCTCCAAT
1 AGATGTTCCAAT
11951911 GACTTATGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (33 bp):
AGATGTTCCAATCAATGATGAAGCTGCCCTGAT
Found at i:11952474 original size:41 final size:41
Alignment explanation
Indices: 11952417--11952553 Score: 256
Period size: 41 Copynumber: 3.3 Consensus size: 41
11952407 GAATTTTATT
*
11952417 TTAACAAGAATTCTAGTCACCTAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
11952458 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
11952499 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
11952540 TTGACAAGAATTCT
1 TTAACAAGAATTCT
11952554 CTACGAACAA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.28
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:11952565 original size:17 final size:17
Alignment explanation
Indices: 11952543--11952581 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
11952533 CTCCACCTTG
* *
11952543 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
11952560 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
11952577 ACAAG
1 ACAAG
11952582 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:11962072 original size:19 final size:19
Alignment explanation
Indices: 11962043--11962099 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
11962033 AATTACAAAA
*
11962043 AAAAGTTTAAAATAATTTTT
1 AAAAGTTTAAAAT-ATTTAT
11962063 AAAA-TTTAAAATATTTAT
1 AAAAGTTTAAAATATTTAT
**
11962081 AAAAAATTAAAAT-TTTAT
1 AAAAGTTTAAAATATTTAT
11962099 A
1 A
11962100 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 15 0.44
19 15 0.44
20 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAAAGTTTAAAATATTTAT
Found at i:11962094 original size:26 final size:24
Alignment explanation
Indices: 11962061--11962116 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
11962051 AAAATAATTT
11962061 TTAAAATTTAAAATATTTATAAAAAA
1 TTAAAATTT--AATATTTATAAAAAA
* *
11962087 TTAAAATTTTATATTTTTAAAAAA
1 TTAAAATTTAATATTTATAAAAAA
11962111 TTAAAA
1 TTAAAA
11962117 AATATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 19 0.68
26 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAAATTTAATATTTATAAAAAA
Found at i:11962147 original size:11 final size:11
Alignment explanation
Indices: 11962131--11962155 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11962121 TAAAAATTAA
11962131 AATTTTAAAAT
1 AATTTTAAAAT
11962142 AATTTTAAAAT
1 AATTTTAAAAT
11962153 AAT
1 AAT
11962156 AATTTTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTTAAAAT
Found at i:11966130 original size:41 final size:41
Alignment explanation
Indices: 11966071--11966434 Score: 453
Period size: 41 Copynumber: 8.9 Consensus size: 41
11966061 GCAAAAGATT
* *
11966071 GAGCAATAGCGGCGCTTATGGAGAAA-CACCGCTAAAGATCG
1 GAGCAATAGCGGCGCTTATGG-GAAAGCGCCGCTAAAGGTCG
* * ** *
11966112 GAGCAATAGTGGCACTTATAAGAATGCGCCGCTAAAGGTCG
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
11966153 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
* ** ** * *
11966194 GAGCAATAGCAGCGCTTATAAGAAATAGCAGCTAAAGGTCA
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
* * *
11966235 GAGCAATAGCGGCGCTTATGGGAAAGTGCCCCTAAAGGTCT
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
* **
11966276 GAGTAATAGCGGCGCTTATAAGAAAGCGCCG-TCAAAGGTCG
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT-AAAGGTCG
*
11966317 GAGCAATAGCGGCGCTTATGGGAAATCGCCGCTAAAGGTCG
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
* * * *
11966358 GAGAAATAGCGGCTCTTATGGGAAAGAGTCGCTAAAGGTCG
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
**
11966399 GATAAATAGCGGCGCTTATGGGAAAGCGCCGCTAAA
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAA
11966435 ATTTTTACAT
Statistics
Matches: 274, Mismatches: 46, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
40 4 0.01
41 269 0.98
42 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (41 bp):
GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
Found at i:11968131 original size:10 final size:10
Alignment explanation
Indices: 11968116--11968142 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
11968106 AGGAATCTTT
11968116 TAAATTCTAA
1 TAAATTCTAA
11968126 TAAATTCTAA
1 TAAATTCTAA
11968136 TAAATTC
1 TAAATTC
11968143 AAAATAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAATTCTAA
Found at i:11968218 original size:11 final size:11
Alignment explanation
Indices: 11968202--11968227 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11968192 GGCAGCTACT
11968202 ATTATTAAATA
1 ATTATTAAATA
11968213 ATTATTAAATA
1 ATTATTAAATA
11968224 ATTA
1 ATTA
11968228 AATAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTATTAAATA
Found at i:11969648 original size:18 final size:18
Alignment explanation
Indices: 11969602--11969750 Score: 75
Period size: 18 Copynumber: 7.6 Consensus size: 18
11969592 TAAAAGATTT
11969602 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
** **
11969620 AAGAAAATAATTATATTA
1 AATTATTTAATTATATTA
*
11969638 AATTATTTAATTATGTATTT
1 AATTATTTAATTA--TATTA
**
11969658 AATTATAAACAGTATCGATTAATTA
1 AATTATTTA-A-T-T--A-T-ATTA
*
11969683 AA-TATTTAAGTTAATAGATTT
1 AATTATTTAA-TT-AT--ATTA
11969704 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
11969722 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
11969740 AATTATTTAAT
1 AATTATTTAAT
11969751 CATGTTTAAT
Statistics
Matches: 96, Mismatches: 25, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
18 49 0.51
20 14 0.15
21 9 0.09
22 9 0.09
23 4 0.04
24 5 0.05
25 6 0.06
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (18 bp):
AATTATTTAATTATATTA
Found at i:11969712 original size:102 final size:102
Alignment explanation
Indices: 11969543--11969876 Score: 474
Period size: 102 Copynumber: 3.2 Consensus size: 102
11969533 AATAATTAAA
11969543 TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
*
11969608 TTAATTATATTAAAGAAAATAATTATATTAAATTATT
66 TTAATTATATTAAAGTAAATAATTATATTAAATTATT
* *
11969645 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAATAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
11969710 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTT
66 TTAATTATATTAAAGTAAATAATTATATT-AA--A--T--T-A--TT
* ** *
11969757 TAATTATGTATTTAATTACAAACAGTAATCCTTTAATTAAATATTTACGTTAAAAGATTTAATTA
1 TAATTATGTATTTAATTATAAACAGT-ATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTA
* *
11969822 TTTAATTGTATTAAAGTAAATAATTATATTTAATTATT
65 TTTAATTATATTAAAGTAAATAATTATATTAAATTATT
11969860 TAATTATG--TTTAATTAT
1 TAATTATGTATTTAATTAT
11969877 GTATTTAATT
Statistics
Matches: 210, Mismatches: 11, Indels: 23
0.86 0.05 0.09
Matches are distributed among these distances:
101 8 0.04
102 91 0.43
103 12 0.06
105 2 0.01
106 1 0.00
107 1 0.00
108 1 0.00
109 1 0.00
110 2 0.01
112 28 0.13
113 63 0.30
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (102 bp):
TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
TTAATTATATTAAAGTAAATAATTATATTAAATTATT
Found at i:11969824 original size:113 final size:112
Alignment explanation
Indices: 11969643--11969907 Score: 431
Period size: 113 Copynumber: 2.4 Consensus size: 112
11969633 TATTAAATTA
* *
11969643 TTTAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAATAGATTTAATT
1 TTTAATTATGTATTTAATTATAAACAGTATCCATTAATTAAATATTTAAGTTAAAAGATTTAATT
11969708 ATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATG
66 ATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATG
* * *
11969755 TTTAATTATGTATTTAATTACAAACAGTAATCCTTTAATTAAATATTTACGTTAAAAGATTTAAT
1 TTTAATTATGTATTTAATTATAAACAGT-ATCCATTAATTAAATATTTAAGTTAAAAGATTTAAT
* * *
11969820 TATTTAATTGTATTAAAGTAAATAATTATATTTAATTATTTAATTATG
65 TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATG
* *
11969868 TTTAATTATGTATTTAATTATAAACAATATCGATTAATTA
1 TTTAATTATGTATTTAATTATAAACAGTATCCATTAATTA
11969908 TTTAATTATA
Statistics
Matches: 140, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
112 37 0.26
113 103 0.74
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (112 bp):
TTTAATTATGTATTTAATTATAAACAGTATCCATTAATTAAATATTTAAGTTAAAAGATTTAATT
ATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATG
Found at i:11969863 original size:18 final size:18
Alignment explanation
Indices: 11969813--11970047 Score: 91
Period size: 18 Copynumber: 12.9 Consensus size: 18
11969803 ACGTTAAAAG
*
11969813 ATTTAATTATTTAATTGT
1 ATTTAATTATTTAATTAT
* * **
11969831 ATTAAAGTAAATAATTAT
1 ATTTAATTATTTAATTAT
11969849 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * *
11969867 GTTTAATTATGTATTTA-
1 ATTTAATTATTTAATTAT
*
11969884 ATTATAA--A--CAA-TAT
1 ATT-TAATTATTTAATTAT
11969898 CGA-TTAATTATTTAATTAT
1 --ATTTAATTATTTAATTAT
11969917 ATTTAATTAACTATTTAATTTAAAAT
1 ATTTAA-T---TATTTAA-TT---AT
*** **
11969943 ATTTTCGTAAATAATTAT
1 ATTTAATTATTTAATTAT
* * *
11969961 ATATAATTATCTAATTTT
1 ATTTAATTATTTAATTAT
11969979 ATTTAATTATTTAATTGAGAAT
1 ATTTAATTATTTAATT----AT
11970001 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
11970019 A-TTAA--A-TTAA--AT
1 ATTTAATTATTTAATTAT
11970031 ATTTAATTATTTAATTA
1 ATTTAATTATTTAATTA
11970048 ATAAAAACAG
Statistics
Matches: 158, Mismatches: 31, Indels: 56
0.64 0.13 0.23
Matches are distributed among these distances:
12 3 0.02
13 6 0.04
14 8 0.05
15 3 0.02
16 7 0.04
17 7 0.04
18 81 0.51
19 4 0.03
21 2 0.01
22 29 0.18
23 2 0.01
26 6 0.04
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.52
Consensus pattern (18 bp):
ATTTAATTATTTAATTAT
Found at i:11969988 original size:8 final size:8
Alignment explanation
Indices: 11969954--11970047 Score: 65
Period size: 8 Copynumber: 11.8 Consensus size: 8
11969944 TTTTCGTAAA
11969954 TAATTATAT
1 TAATTAT-T
*
11969963 ATAATTATC
1 -TAATTATT
11969972 TAATTTTATT
1 TAA--TTATT
11969982 TAATTATT
1 TAATTATT
11969990 TAATTGA--
1 TAATT-ATT
*
11969997 GAA-TATT
1 TAATTATT
11970004 TAATTATT
1 TAATTATT
11970012 TAATTATAT
1 TAATTAT-T
11970021 TAA--A-T
1 TAATTATT
*
11970026 TAAATATT
1 TAATTATT
11970034 TAATTATT
1 TAATTATT
11970042 TAATTA
1 TAATTA
11970048 ATAAAAACAG
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
5 5 0.07
6 1 0.01
7 6 0.09
8 38 0.55
9 5 0.07
10 14 0.20
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (8 bp):
TAATTATT
Found at i:11970013 original size:30 final size:30
Alignment explanation
Indices: 11969977--11970047 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
11969967 TTATCTAATT
11969977 TTATTTAATTAT-TT-AATTGAGAATATTTAA
1 TTATTTAATTATATTAAATT-A-AATATTTAA
11970007 TTATTTAATTATATTAAATTAAATATTTAA
1 TTATTTAATTATATTAAATTAAATATTTAA
11970037 TTATTTAATTA
1 TTATTTAATTA
11970048 ATAAAAACAG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
30 32 0.82
31 3 0.08
32 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
TTATTTAATTATATTAAATTAAATATTTAA
Found at i:11970028 original size:22 final size:21
Alignment explanation
Indices: 11969900--11970049 Score: 86
Period size: 22 Copynumber: 7.3 Consensus size: 21
11969890 AACAATATCG
11969900 ATTAATTATTTAATTATATTTA
1 ATTAATTATTTAATTATA-TTA
*
11969922 ATTAACTATTTAATT-TA--A
1 ATTAATTATTTAATTATATTA
* *
11969940 AAT-ATT-TTCGTAAATA-ATTA
1 ATTAATTATT--TAATTATATTA
*
11969960 TATATAATTATCTAA-T-T-TTA
1 -AT-TAATTATTTAATTATATTA
* * *
11969980 TTTAATTATTTAATTGAGAATA
1 ATTAATTATTTAATT-ATATTA
*
11970002 TTTAATTATTTAATTATATTAA
1 ATTAATTATTTAATTATATT-A
*
11970024 ATTAAATATTTAATTAT-TTA
1 ATTAATTATTTAATTATATTA
11970044 ATTAAT
1 ATTAAT
11970050 AAAAACAGTC
Statistics
Matches: 98, Mismatches: 15, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
16 2 0.02
17 2 0.02
18 18 0.18
19 2 0.02
20 10 0.10
21 9 0.09
22 51 0.52
23 3 0.03
24 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTAATTATTTAATTATATTA
Found at i:11970125 original size:31 final size:33
Alignment explanation
Indices: 11970069--11970135 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
11970059 CCAACTATTT
11970069 AAGTAAAATGTTGTCACTAATATATATATTTTA
1 AAGTAAAATGTTGTCACTAATATATATATTTTA
11970102 AAGTAAAATGTTGTCACTAATATATAT-TTTTA
1 AAGTAAAATGTTGTCACTAATATATATATTTTA
11970134 AA
1 AA
11970136 TTTAAATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (33 bp):
AAGTAAAATGTTGTCACTAATATATATATTTTA
Found at i:11973602 original size:66 final size:66
Alignment explanation
Indices: 11973496--11973649 Score: 227
Period size: 66 Copynumber: 2.3 Consensus size: 66
11973486 ATTGCTCAAT
* * *
11973496 TTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATCTAAAA
1 TTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATAAAGAACTCCACCTAAAA
11973561 C
66 C
* * *
11973562 TTAAAGAGGAGGCTGCAGTGAGAGAAGCAGAGTCTCAAAAAAAATATAAAGAACTCCACCTACAA
1 TTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATAAAGAACTCCACCTAAAA
11973627 C
66 C
* * *
11973628 TTAAAGTGGAGGCAGTAGCGAG
1 TTAAAGAGGAGGCTGCAGCGAG
11973650 GCAAGCGGAG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (66 bp):
TTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATAAAGAACTCCACCTAAAA
C
Found at i:11973661 original size:21 final size:21
Alignment explanation
Indices: 11973635--11973687 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
11973625 AACTTAAAGT
*
11973635 GGAGGCAGTAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
11973656 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
* *
11973677 GAAGGAAGCAG
1 GGAGGCAGCAG
11973688 AGGCTACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.47, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGGCAAGC
Found at i:11973908 original size:15 final size:15
Alignment explanation
Indices: 11973888--11973916 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11973878 ATTTGAAGTT
11973888 ATTGGTTGGATTTGC
1 ATTGGTTGGATTTGC
11973903 ATTGGTTGGATTTG
1 ATTGGTTGGATTTG
11973917 AATTTACAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.03, G:0.34, T:0.48
Consensus pattern (15 bp):
ATTGGTTGGATTTGC
Found at i:11974038 original size:43 final size:41
Alignment explanation
Indices: 11973985--11974098 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 41
11973975 ATCTGTTATA
* *
11973985 TTAGCGGCGCTTGTGGAAAAAGCACCGCTAAAGAACATGATCT
1 TTAGCGGCGCTTGTGG-AAAAGCGCCGCTAAA-AACATGACCT
* * * *
11974028 TTAGCAGCGCTTCTGGAAAAGCGCCGCTAAAAATATGGCCT
1 TTAGCGGCGCTTGTGGAAAAGCGCCGCTAAAAACATGACCT
* *
11974069 TTACCGGTGCTTGTGGTAAAAGCGCCGCTA
1 TTAGCGGCGCTTGTGG-AAAAGCGCCGCTA
11974099 TTTTTTGCGG
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 19 0.32
42 27 0.45
43 14 0.23
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (41 bp):
TTAGCGGCGCTTGTGGAAAAGCGCCGCTAAAAACATGACCT
Found at i:11976815 original size:35 final size:34
Alignment explanation
Indices: 11976747--11976816 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
11976737 TTAGTAAGCA
*
11976747 TTGTCATCGCATTCCCATTGTCAATACATTTTAG
1 TTGTCATCGCATTCCCATTGTCAATACAATTTAG
* * * *
11976781 TTGTCATTGCATTTCCATTTGTCATTATAATTTAG
1 TTGTCATCGCATTCCCA-TTGTCAATACAATTTAG
11976816 T
1 T
11976817 GTTAGTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 15 0.50
35 15 0.50
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (34 bp):
TTGTCATCGCATTCCCATTGTCAATACAATTTAG
Found at i:11978100 original size:52 final size:52
Alignment explanation
Indices: 11977884--11978124 Score: 265
Period size: 51 Copynumber: 4.6 Consensus size: 52
11977874 TTTCATTTAA
* ** * *
11977884 TACTCACGATGACA-TATAGTCATCGGACCCTTTTGTTCCGTATAAGAATTCATA
1 TACTCACGATAACACT-TAGTCATCGGACCC-TTTAATCCGTA-AAGGATTCATT
* * * *
11977938 TACTCACGATAACACTGAGTCATCGGA-CCTTTAATTCGTCATGGATTCATT
1 TACTCACGATAACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATT
* * * *
11977989 TACTCACGATGACACTTAATCATCGGA-CCTTTAATCCTTAAATGATTCATT
1 TACTCACGATAACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATT
*
11978040 TACTCACGATAACACTTAGTCATCGGACCCTTTAATCCATAAAGGATTCATT
1 TACTCACGATAACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATT
* * *
11978092 TA-TGCACGATGACACTTAGTCATCTGACTCTTT
1 TACT-CACGATAACACTTAGTCATCGGACCCTTT
11978125 CGTTTATATC
Statistics
Matches: 160, Mismatches: 24, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
51 77 0.48
52 57 0.36
53 2 0.01
54 23 0.14
55 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (52 bp):
TACTCACGATAACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATT
Found at i:11978115 original size:103 final size:103
Alignment explanation
Indices: 11977884--11978124 Score: 292
Period size: 103 Copynumber: 2.3 Consensus size: 103
11977874 TTTCATTTAA
**
11977884 TACTCACGATGACA-TATAGTCATCGGACCCTTTTGTTCCGTATAAGAATTCATATACTCACGAT
1 TACTCACGATGACACT-TAGTCATCGGA-CC-TTTAATCCGTATAAGAATTCATATACTCACGAT
* * * *
11977948 AACACTGAGTCATCGGACCTTTAATTCGTCATGGATTCATT
63 AACACTGAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * *
11977989 TACTCACGATGACACTTAATCATCGGACCTTTAATCCTTA-AATG-ATTCATTTACTCACGATAA
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATAA-GAATTCATATACTCACGATAA
*
11978052 CACTTAGTCATCGGACCCTTTAATCCATAAAGGATTCATT
65 CACTGAGTCATCGGA-CCTTTAATCCATAAAGGATTCATT
*
11978092 TA-TGCACGATGACACTTAGTCATCTGACTCTTT
1 TACT-CACGATGACACTTAGTCATCGGAC-CTTT
11978125 CGTTTATATC
Statistics
Matches: 119, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
102 35 0.29
103 53 0.45
104 6 0.05
105 24 0.20
106 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (103 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATAAGAATTCATATACTCACGATAAC
ACTGAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:11978898 original size:24 final size:25
Alignment explanation
Indices: 11978851--11978901 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
11978841 AAGATTGGAA
11978851 TTGAAAACCCTAGGTTTTTCCCCCT
1 TTGAAAACCCTAGGTTTTTCCCCCT
11978876 TTGAAAACCCTAGGTTTTTCCCCCT
1 TTGAAAACCCTAGGTTTTTCCCCCT
11978901 T
1 T
11978902 AGTGTCGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (25 bp):
TTGAAAACCCTAGGTTTTTCCCCCT
Found at i:11979033 original size:21 final size:20
Alignment explanation
Indices: 11979009--11979049 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
11978999 TTGAGACTTT
*
11979009 CATTATTAAGCTTTAATTAAA
1 CATTATTAACCTTT-ATTAAA
*
11979030 CATTTTTAACCTTTATTAAA
1 CATTATTAACCTTTATTAAA
11979050 TCTATTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.46
Consensus pattern (20 bp):
CATTATTAACCTTTATTAAA
Found at i:11980347 original size:26 final size:26
Alignment explanation
Indices: 11980311--11980389 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
11980301 TTACTACTAA
* *
11980311 TGTCGCTGCATGAGCATGTCCAGAAT
1 TGTCACTGCATGAACATGTCCAGAAT
*
11980337 TGTCATTGCATGAACATGTCCAGAAT
1 TGTCACTGCATGAACATGTCCAGAAT
* * *
11980363 TGTCGCTGGATCAACATGTCCAGAAT
1 TGTCACTGCATGAACATGTCCAGAAT
11980389 T
1 T
11980390 ACGCCTAGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (26 bp):
TGTCACTGCATGAACATGTCCAGAAT
Found at i:11982273 original size:49 final size:49
Alignment explanation
Indices: 11982179--11982867 Score: 560
Period size: 49 Copynumber: 14.1 Consensus size: 49
11982169 TCTTCTTTAC
* * *
11982179 GGTATAAGATTTGCCATTGCGGC-TCAATCTTTCCCTCCAAATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
* *
11982227 GGTACAAGATTCGCCATTGCGGCTTCAATTTTTCCCTTCACATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
** * * * * *
11982276 GGTATAAGATTCATCATTGTGGCTTCAATCCTTCGCTTCATATCTCTAA
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
* *** * * * * *
11982325 GGTATAAGGTTCGTTGTTACAGCTTCAACCTTTTCCTTCACATCTCTAA
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
* * * * * ** *
11982374 CGTATAAGGTTTGCTATTACGATTTCAACCTTTCCC-TCTACATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTC-ACATCTCTAG
*** * * * *
11982423 GGTATAAGATTTATCGTTGCGGCTGCAATCTTTCCCATCACATCTCTAA
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
* * * * *
11982472 GGTATAAGGTTCACCATTACGGCTTCAACCTTTCCCTCCACATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
* * * * * *
11982521 GGTATAAGGTTCGCCACTGCGGCTTCAACCTTTCCCTCCATATCTTTA-
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
* * ** * * * *
11982569 GGTACAAGATTTGCCATTATGACTTCAATCTTT-CCTATCATATCTATAA
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCT-TCACATCTCTAG
* * * * *
11982618 GGTAAAAGATTCGTCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
* * * * *
11982667 GGTATAAGGTTCGCCGTTGTGGCTTTAACCTTTCCCTTCACATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
* * ** * * **
11982716 AGTATAAGATTTGCTGTTGTGGCTTTAATCTTTCCCACCACATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
* * * * * * *
11982765 GGTATAAGGTTCGCCTTTGTGGCTTCAACCTCTCCCTCCATATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
** * *
11982814 GGTATAAGATTCATCATCGCGGCTTCAATCTTTCCCATCACATCT-TCAG
1 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCT-AG
11982863 GGTAT
1 GGTAT
11982868 GGATTCAATG
Statistics
Matches: 516, Mismatches: 118, Indels: 13
0.80 0.18 0.02
Matches are distributed among these distances:
47 3 0.01
48 58 0.11
49 451 0.87
50 4 0.01
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (49 bp):
GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAG
Found at i:11982847 original size:147 final size:147
Alignment explanation
Indices: 11982179--11982867 Score: 674
Period size: 147 Copynumber: 4.7 Consensus size: 147
11982169 TCTTCTTTAC
* * * * * *
11982179 GGTATAAGATTTGCCATTGCGGC-TCAATCTTTCCCTCCAAATCTCTAGGGTACAAGATTCGCCA
1 GGTATAAGGTTCGCCATTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCA
** *
11982243 TTGCGGCTTCAATTTTTCCCTTCACATCTCTAGGGTATAAGA-TTCATCATTGTGGCTTCAATCC
66 TTGCGGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTTC-TCATTGTGGCTTCAATCT
* * *
11982307 TTCGCTTCATATCTCTAA
130 TTCCCATCACATCTCTAA
*** * * * * ** * *
11982325 GGTATAAGGTTCGTTGTTACAGCTTCAACCTTTTCCTTCACATCTCTAACGTATAAGGTTTGCTA
1 GGTATAAGGTTCGCCATTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCA
* ** * * * *
11982390 TTACGATTTCAACCTTTCCC-TCTACATCTCTAGGGTATAAGATTTATCGTTGCGGCTGCAATCT
66 TTGCGGCTTCAACCTTTCCCTTC-ACATCTCTAGGGTATAAGATTTCTCATTGTGGCTTCAATCT
11982454 TTCCCATCACATCTCTAA
130 TTCCCATCACATCTCTAA
* *
11982472 GGTATAAGGTTCACCATTACGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCA
1 GGTATAAGGTTCGCCATTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCA
* * * * * * *
11982537 CTGCGGCTTCAACCTTTCCCTCCATATCTTTA-GGTACAAGATTTGC-CATTATGACTTCAATCT
66 TTGCGGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTT-CTCATTGTGGCTTCAATCT
* * *
11982600 TTCCTATCATATCTATAA
130 TTCCCATCACATCTCTAA
* * * * * *
11982618 GGTAAAAGATTCGTCGTTGCGGCTTCAATCTTTCCCAT-CACATCTCTAAGGTATAAGGTTCGCC
1 GGTATAAGGTTCGCCATTGCGGCTTCAACCTTTCCC-TCCACATCTCTAGGGTATAAGGTTCGCC
* * * * * *
11982682 GTTGTGGCTTTAACCTTTCCCTTCACATCTCTAGAGTATAAGATTTGCT-GTTGTGGCTTTAATC
65 ATTGCGGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTT-CTCATTGTGGCTTCAATC
* *
11982746 TTTCCCACCACATCTCTAG
129 TTTCCCATCACATCTCTAA
* * * * * **
11982765 GGTATAAGGTTCGCCTTTGTGGCTTCAACCTCTCCCTCCATATCTCTAGGGTATAAGATTCATCA
1 GGTATAAGGTTCGCCATTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCA
* * *
11982830 TCGCGGCTTCAATCTTTCCCATCACATCT-TCAGGGTAT
66 TTGCGGCTTCAACCTTTCCCTTCACATCTCT-AGGGTAT
11982868 GGATTCAATG
Statistics
Matches: 430, Mismatches: 103, Indels: 19
0.78 0.19 0.03
Matches are distributed among these distances:
146 138 0.32
147 289 0.67
148 3 0.01
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (147 bp):
GGTATAAGGTTCGCCATTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCA
TTGCGGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTTCTCATTGTGGCTTCAATCTT
TCCCATCACATCTCTAA
Found at i:11982867 original size:98 final size:98
Alignment explanation
Indices: 11982179--11982858 Score: 634
Period size: 98 Copynumber: 7.0 Consensus size: 98
11982169 TCTTCTTTAC
* * * * * * * *
11982179 GGTATAAGATTTGCCATTGCGGC-TCAATCTTTCCCTCCAAATCTCTAGGGTACAAGATTCGCCA
1 GGTATAAGGTTCGCCATTGTGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGATTCGTCG
* * *
11982243 TTGCGGCTTCAATTTTTCCCTTCACATCTCTAG
66 TTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* ** * * * * * *
11982276 GGTATAAGATTCATCATTGTGGCTTCAATCC-TTCGCTTCATATCTCTAAGGTATAAGGTTCGTT
1 GGTATAAGGTTCGCCATTGTGGCTTCAA-CCTTTCCCTCCACATCTCTAGGGTATAAGATTCGTC
* * * * *
11982340 GTTACAGCTTCAACCTTTTCCTTCACATCTCTAA
65 GTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* * * ** ** * **
11982374 CGTATAAGGTTTGCTATTACGATTTCAACCTTTCCCTCTACATCTCTAGGGTATAAGATTTATCG
1 GGTATAAGGTTCGCCATTGTGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGATTCGTCG
*
11982439 TTGCGGCTGCAATCTTTCCCATCACATCTCTAA
66 TTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* ** * * *
11982472 GGTATAAGGTTCACCATTACGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCA
1 GGTATAAGGTTCGCCATTGTGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGATTCGTCG
* * * *
11982537 CTGCGGCTTCAACCTTTCCC-TC-CATATCTTTA
66 TTGCGGCTTCAATCTTTCCCATCACATCTC-TAA
* * * * * * * * * * *
11982569 GGTACAAGATTTGCCATTATGACTTCAATCTTT-CCTATCATATCTATAAGGTAAAAGATTCGTC
1 GGTATAAGGTTCGCCATTGTGGCTTCAACCTTTCCCT-CCACATCTCTAGGGTATAAGATTCGTC
11982633 GTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
65 GTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* * * * *
11982667 GGTATAAGGTTCGCCGTTGTGGCTTTAACCTTTCCCTTCACATCTCTAGAGTATAAGATTTG-CT
1 GGTATAAGGTTCGCCATTGTGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGATTCGTC-
* * * *
11982731 GTTGTGGCTTTAATCTTTCCCACCACATCTCTAG
65 GTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* * * * *
11982765 GGTATAAGGTTCGCCTTTGTGGCTTCAACCTCTCCCTCCATATCTCTAGGGTATAAGATTCATCA
1 GGTATAAGGTTCGCCATTGTGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGATTCGTCG
*
11982830 TCGCGGCTTCAATCTTTCCCATCACATCT
66 TTGCGGCTTCAATCTTTCCCATCACATCT
11982859 TCAGGGTATG
Statistics
Matches: 461, Mismatches: 112, Indels: 19
0.78 0.19 0.03
Matches are distributed among these distances:
96 8 0.02
97 90 0.20
98 353 0.77
99 10 0.02
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (98 bp):
GGTATAAGGTTCGCCATTGTGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGATTCGTCG
TTGCGGCTTCAATCTTTCCCATCACATCTCTAA
Found at i:11983828 original size:6 final size:6
Alignment explanation
Indices: 11983817--11983894 Score: 63
Period size: 6 Copynumber: 12.8 Consensus size: 6
11983807 TCGATAACTC
** * *
11983817 CTTTTT CTTTTTT CTTCTTT CTTTTT C-CCTT CTTTTC CTTCTTT -TCTTT
1 CTTTTT C-TTTTT CTT-TTT CTTTTT CTTTTT CTTTTT CTT-TTT CTTTTT
11983866 CTTTTTT CTTTTT CTTTTT CTTTTT -TTTT
1 C-TTTTT CTTTTT CTTTTT CTTTTT CTTTT
11983895 GGGTGAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
5 10 0.17
6 29 0.50
7 19 0.33
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:11983830 original size:7 final size:7
Alignment explanation
Indices: 11983818--11983891 Score: 64
Period size: 7 Copynumber: 10.7 Consensus size: 7
11983808 CGATAACTCC
11983818 TTTTTCT
1 TTTTTCT
11983825 TTTTTCT
1 TTTTTCT
*
11983832 TCTTTCT
1 TTTTTCT
*
11983839 TTTTCCCT
1 TTTT-TCT
*
11983847 TCTTTTCC
1 T-TTTTCT
*
11983855 TTCTT-T
1 TTTTTCT
*
11983861 TCTTTCT
1 TTTTTCT
11983868 TTTTTC-
1 TTTTTCT
11983874 TTTTTC-
1 TTTTTCT
11983880 TTTTTCT
1 TTTTTCT
11983887 TTTTT
1 TTTTT
11983892 TTTGGGTGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
6 15 0.28
7 30 0.57
8 5 0.09
9 3 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:11983849 original size:25 final size:23
Alignment explanation
Indices: 11983825--11983890 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 23
11983815 TCCTTTTTCT
11983825 TTTTTCTTCTTTCTTTTTCCCTTC
1 TTTTTCTTCTTTCTTTTT-CCTTC
* **
11983849 TTTTCCTTCTTTTCTTTCTTTTTTC
1 TTTTTCTTC-TTTCTTT-TTCCTTC
11983874 TTTTTCTT-TTTCTTTTT
1 TTTTTCTTCTTTCTTTTT
11983891 TTTTGGGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 2 0.06
23 7 0.19
24 8 0.22
25 17 0.47
26 2 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTCTTCTTTCTTTTTCCTTC
Found at i:11989811 original size:54 final size:54
Alignment explanation
Indices: 11989729--11989957 Score: 363
Period size: 54 Copynumber: 4.3 Consensus size: 54
11989719 ATAAATGCAA
11989729 AAAGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTATGGATT
1 AAAGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTATGGATT
*
11989783 AAAGGTCCGATGACTCTATGTCATCATGAGTTATATGATATCCTATTACT-GATT
1 AAAGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTA-TGGATT
* * * *
11989837 AAAGGTCCGATAACTCTGTGTCATCGTGAGTTATATGAAATCCTATTACGGATT
1 AAAGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTATGGATT
* * *
11989891 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATG-AATCCTATTATGGTTT
1 AAAGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTATGGATT
11989944 AAAGGTCCGATGAC
1 AAAGGTCCGATGAC
11989958 GAAGCTCCTA
Statistics
Matches: 164, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
53 28 0.17
54 135 0.82
55 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (54 bp):
AAAGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTATGGATT
Found at i:11990716 original size:21 final size:21
Alignment explanation
Indices: 11990655--11990706 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
11990645 GTTTTTAGTA
11990655 TCGGTAGAAGTATGACTTGTT
1 TCGGTAGAAGTATGACTTGTT
11990676 TCGGTAGAAGTATGACTTGTT
1 TCGGTAGAAGTATGACTTGTT
*
11990697 TCTGTAGAAG
1 TCGGTAGAAG
11990707 AGACACTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.29, T:0.37
Consensus pattern (21 bp):
TCGGTAGAAGTATGACTTGTT
Found at i:11992802 original size:25 final size:23
Alignment explanation
Indices: 11992774--11992831 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
11992764 AGAACAAAAT
11992774 AAAAGGATTAATTTAAAAAGGATAA
1 AAAAGGATTAA-TTAAAAA-GATAA
* *
11992799 AAAAGGATTTGATTAAAAAGATAC
1 AAAAGGA-TTAATTAAAAAGATAA
11992823 AAAAGGATT
1 AAAAGGATT
11992832 TAAATATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 2 0.07
24 11 0.37
25 14 0.47
26 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (23 bp):
AAAAGGATTAATTAAAAAGATAA
Found at i:11992842 original size:25 final size:25
Alignment explanation
Indices: 11992774--11992842 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
11992764 AGAACAAAAT
*
11992774 AAAAGGA-TTAATTTAAAAAGGATAA
1 AAAAGGATTTAA-ATAAAAAGGATAA
* * *
11992799 AAAAGGATTTGATTAAAAA-GATAC
1 AAAAGGATTTAAATAAAAAGGATAA
11992823 AAAAGGATTTAAATATAAAA
1 AAAAGGATTTAAATA-AAAA
11992843 AACAAGATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.45
25 18 0.47
26 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.14, T:0.25
Consensus pattern (25 bp):
AAAAGGATTTAAATAAAAAGGATAA
Found at i:11992907 original size:25 final size:25
Alignment explanation
Indices: 11992871--11992929 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
11992861 TTTTAAAAGG
*
11992871 AATAAAAATGAAAGGATTAATTTTTT
1 AATAAAAATGAAAGGATTAA-ATTTT
*
11992897 AA-AAAAATGAAAGGGTTAAATTTT
1 AATAAAAATGAAAGGATTAAATTTT
11992921 AATAAAAAT
1 AATAAAAAT
11992930 AAAATTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 6 0.20
25 22 0.73
26 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (25 bp):
AATAAAAATGAAAGGATTAAATTTT
Found at i:11996865 original size:29 final size:29
Alignment explanation
Indices: 11996823--11996879 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
11996813 TCCAGAAGCT
11996823 CCTCAATGATTGATATTGGAAATTTATCA
1 CCTCAATGATTGATATTGGAAATTTATCA
11996852 CCTCAATGATTGATATTGGAAATTTATC
1 CCTCAATGATTGATATTGGAAATTTATC
11996880 TCTTATAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (29 bp):
CCTCAATGATTGATATTGGAAATTTATCA
Found at i:11999471 original size:298 final size:298
Alignment explanation
Indices: 11998929--11999519 Score: 1058
Period size: 298 Copynumber: 2.0 Consensus size: 298
11998919 CGTCAGTGGC
11998929 CATAGAAACGTGCTTGCTCTGATACCATTGATGAGGGAAAGAACTTGAATGAGAAATAGAACCAG
1 CATAGAAACGTGCTTGCTCTGATACCATTGATGAGGGAAAGAACTTGAATGAGAAATAGAACCAG
* *
11998994 AAAAAAATGATCGGAGAAGAGTAGATGAATTTTCAGAGAGAAAGGAAAGAGAAAACCATGTCCAT
66 AAAAAAATGATCGAAGAAGAGTAGAAGAATTTTCAGAGAGAAAGGAAAGAGAAAACCATGTCCAT
*
11999059 TTTCATTTCTTAACTGTATTTCCCTTTTTGCAATAGGGTGAATATAAAAGAGTAACAACAAAAGA
131 TTTCATTTCATAACTGTATTTCCCTTTTTGCAATAGGGTGAATATAAAAGAGTAACAACAAAAGA
*
11999124 TTCCAATAGGCACCGTTTCCTACTATCTCCTATGCGAACCGTTTCATTAATAAAGCTAATTATCC
196 TGCCAATAGGCACCGTTTCCTACTATCTCCTATGCGAACCGTTTCATTAATAAAGCTAATTATCC
11999189 TTAAACAGAAGTTAACAAAATTACAAAATAGTAGTGAT
261 TTAAACAGAAGTTAACAAAATTACAAAATAGTAGTGAT
* ***
11999227 CATAGGAACGTGCTTGCTCTGATGTTATTGATGAGGGAAAGAACTTGAATGAGAAATAGAACCA-
1 CATAGAAACGTGCTTGCTCTGATACCATTGATGAGGGAAAGAACTTGAATGAGAAATAGAACCAG
*
11999291 AAAAGAAATGATCGAAGAAGAGTAGAAGAATTTTCAGAGAGAAAGGAACGAGAAAACCATGTCCA
66 AAAA-AAATGATCGAAGAAGAGTAGAAGAATTTTCAGAGAGAAAGGAAAGAGAAAACCATGTCCA
11999356 TTTTCATTTCATAACTGTATTTCCCTTTTTGCAATAGGGTGAATATAAAAGAGTAACAACAAAAG
130 TTTTCATTTCATAACTGTATTTCCCTTTTTGCAATAGGGTGAATATAAAAGAGTAACAACAAAAG
* * *
11999421 ATGCCAATAGGCACCGTTTCCTACTATCTCCTATGCGCACCGTTTCATTAATAGAGTTAATTATC
195 ATGCCAATAGGCACCGTTTCCTACTATCTCCTATGCGAACCGTTTCATTAATAAAGCTAATTATC
11999486 CTTAAACAGAAGTTAACAAAATTACAAAATAGTA
260 CTTAAACAGAAGTTAACAAAATTACAAAATAGTA
11999520 ATAGTTACCA
Statistics
Matches: 280, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
297 4 0.01
298 276 0.99
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (298 bp):
CATAGAAACGTGCTTGCTCTGATACCATTGATGAGGGAAAGAACTTGAATGAGAAATAGAACCAG
AAAAAAATGATCGAAGAAGAGTAGAAGAATTTTCAGAGAGAAAGGAAAGAGAAAACCATGTCCAT
TTTCATTTCATAACTGTATTTCCCTTTTTGCAATAGGGTGAATATAAAAGAGTAACAACAAAAGA
TGCCAATAGGCACCGTTTCCTACTATCTCCTATGCGAACCGTTTCATTAATAAAGCTAATTATCC
TTAAACAGAAGTTAACAAAATTACAAAATAGTAGTGAT
Found at i:12000570 original size:20 final size:20
Alignment explanation
Indices: 12000521--12000570 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
12000511 TGCTGTTTTA
12000521 TTTTT-ATTTAATTTAATCC
1 TTTTTAATTTAATTTAATCC
* * * *
12000540 TTTTTATTTTACTTTATTCT
1 TTTTTAATTTAATTTAATCC
12000560 TTTTTAATTTA
1 TTTTTAATTTA
12000571 TGCTTTAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTAATTTAATTTAATCC
Found at i:12000913 original size:3 final size:3
Alignment explanation
Indices: 12000905--12000942 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12000895 ACGTTTCCTT
12000905 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12000943 TATAACTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12001912 original size:22 final size:23
Alignment explanation
Indices: 12001873--12001917 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
12001863 TATCAAATAA
*
12001873 ATAGAAATTTATAAAAA-TATTG
1 ATAGAAATATATAAAAATTATTG
12001895 ATAGAAA-ATATAATAAATTATTG
1 ATAGAAATATATAA-AAATTATTG
12001918 TAAAATGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (23 bp):
ATAGAAATATATAAAAATTATTG
Found at i:12004946 original size:22 final size:20
Alignment explanation
Indices: 12004918--12004958 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
12004908 TATCAAATAA
12004918 ATAGAAATATATAAATATATTG
1 ATAGAAA-AT-TAAATATATTG
*
12004940 ATAGAAAATTTAATATATT
1 ATAGAAAATTAAATATATT
12004959 ATTAATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (20 bp):
ATAGAAAATTAAATATATTG
Found at i:12004961 original size:23 final size:22
Alignment explanation
Indices: 12004917--12004966 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
12004907 ATATCAAATA
12004917 AATAGAAATATATAAATATATT
1 AATAGAAATATATAAATATATT
* *
12004939 GATAGAAA-ATTTAATATATTATT
1 AATAGAAATATATAA-ATA-TATT
12004962 AATAG
1 AATAG
12004967 TTAGCTGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 5 0.22
22 10 0.43
23 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (22 bp):
AATAGAAATATATAAATATATT
Found at i:12008962 original size:23 final size:23
Alignment explanation
Indices: 12008921--12008969 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 23
12008911 TAATATTAAA
*
12008921 TTTAATCTTTAATCTTTATATATTT
1 TTTAATCTTAAATCTTTAT-T-TTT
12008946 TTTAAT-TTAAATC-TTATTTTT
1 TTTAATCTTAAATCTTTATTTTT
12008967 TTT
1 TTT
12008970 CTTTTGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 6 0.26
22 1 0.04
23 4 0.17
24 6 0.26
25 6 0.26
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAATCTTAAATCTTTATTTTT
Found at i:12027255 original size:2 final size:2
Alignment explanation
Indices: 12027248--12027278 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12027238 CAACTGATTC
12027248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12027279 AGGAAATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12027698 original size:1 final size:1
Alignment explanation
Indices: 12027692--12027721 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
12027682 TTAGGCTACC
*
12027692 TTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12027722 AGCATAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:12030173 original size:2 final size:2
Alignment explanation
Indices: 12030166--12030205 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
12030156 TGTGAACTCC
* *
12030166 CT CT CT CT CT CT CC CT CT CT CT CT CT CC CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12030206 GTTTGCTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:12030181 original size:14 final size:14
Alignment explanation
Indices: 12030162--12030205 Score: 88
Period size: 14 Copynumber: 3.1 Consensus size: 14
12030152 GGATTGTGAA
12030162 CTCCCTCTCTCTCT
1 CTCCCTCTCTCTCT
12030176 CTCCCTCTCTCTCT
1 CTCCCTCTCTCTCT
12030190 CTCCCTCTCTCTCT
1 CTCCCTCTCTCTCT
12030204 CT
1 CT
12030206 GTTTGCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (14 bp):
CTCCCTCTCTCTCT
Found at i:12030964 original size:18 final size:18
Alignment explanation
Indices: 12030938--12030972 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12030928 AAATTAAATT
12030938 AATTCGATTAATCGATCG
1 AATTCGATTAATCGATCG
*
12030956 AATTTGATTAATCGATC
1 AATTCGATTAATCGATC
12030973 AGTTAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (18 bp):
AATTCGATTAATCGATCG
Found at i:12040188 original size:16 final size:14
Alignment explanation
Indices: 12040157--12040190 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
12040147 TTATTTTATT
12040157 TTTTTATTATTTAC
1 TTTTTATTATTTAC
12040171 TTTTTAGTTATTTCAC
1 TTTTTA-TTATTT-AC
12040187 TTTT
1 TTTT
12040191 CGTCGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTTTATTATTTAC
Found at i:12040605 original size:11 final size:11
Alignment explanation
Indices: 12040578--12040607 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
12040568 AACTCGTGCA
12040578 TCCAAAAACAC
1 TCCAAAAACAC
12040589 TCCCAAAAACAC
1 T-CCAAAAACAC
12040601 TCCAAAA
1 TCCAAAA
12040608 CCTTCATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.37, G:0.00, T:0.10
Consensus pattern (11 bp):
TCCAAAAACAC
Found at i:12045480 original size:21 final size:21
Alignment explanation
Indices: 12045436--12045480 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12045426 TCAATTCCCT
*
12045436 TATAAAGTATCGATACCTTGG
1 TATAAAGTATCGATACCTTAG
* *
12045457 TATAATGTATCGATACTTTAG
1 TATAAAGTATCGATACCTTAG
12045478 TAT
1 TAT
12045481 GGTATTAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (21 bp):
TATAAAGTATCGATACCTTAG
Found at i:12048423 original size:21 final size:21
Alignment explanation
Indices: 12048397--12048437 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12048387 AGGCCCCTTC
12048397 TATACTAGCATTACTGAAAAG
1 TATACTAGCATTACTGAAAAG
* *
12048418 TATACTATCATTAGTGAAAA
1 TATACTAGCATTACTGAAAA
12048438 ATAGATGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (21 bp):
TATACTAGCATTACTGAAAAG
Found at i:12056539 original size:24 final size:24
Alignment explanation
Indices: 12056499--12056545 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12056489 ATTCATCTTT
**
12056499 TATTAATTTGCTTTGAC-ATTTTA
1 TATTAATTTGCACTGACAATTTTA
12056522 TATTACATTTGCACTGACAATTTT
1 TATTA-ATTTGCACTGACAATTTT
12056546 TACTCTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (24 bp):
TATTAATTTGCACTGACAATTTTA
Found at i:12057263 original size:21 final size:21
Alignment explanation
Indices: 12057239--12057285 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
12057229 TTTTCATCAT
12057239 ATTACTAA-ATTCACATTTAAA
1 ATTACTAATATTCA-ATTTAAA
* * *
12057260 ATTAATAATATTTAATTTAGA
1 ATTACTAATATTCAATTTAAA
12057281 ATTAC
1 ATTAC
12057286 ATGTTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTACTAATATTCAATTTAAA
Found at i:12060831 original size:22 final size:22
Alignment explanation
Indices: 12060803--12060846 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12060793 AATACATTAA
12060803 ACCCAAACCAATAAGCCCAAAT
1 ACCCAAACCAATAAGCCCAAAT
*
12060825 ACCCAAATCAATAAGCCCAAAT
1 ACCCAAACCAATAAGCCCAAAT
12060847 TAATTCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.34, G:0.05, T:0.11
Consensus pattern (22 bp):
ACCCAAACCAATAAGCCCAAAT
Found at i:12063165 original size:21 final size:21
Alignment explanation
Indices: 12063118--12063189 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
12063108 AATAGTAAAG
*
12063118 ACTTATACCGATACAAGTGAT
1 ACTTCTACCGATACAAGTGAT
* *
12063139 AGTTCTACCGATATAAGTGACT
1 ACTTCTACCGATACAAGTGA-T
** **
12063161 -CTTCTACTAATACAAGTCTT
1 ACTTCTACCGATACAAGTGAT
12063181 ACTTCTACC
1 ACTTCTACC
12063190 AGTACTAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAT
Found at i:12077053 original size:19 final size:19
Alignment explanation
Indices: 12077031--12077104 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 19
12077021 ACAAATTGTA
*
12077031 TATTTCTATACATATATAC
1 TATTTATATACATATATAC
* *
12077050 TA-TTATATATATATATATT
1 TATTTATATACATATATA-C
12077069 TATTTTATATACATATATA-
1 TA-TTTATATACATATATAC
12077088 T-TTT-T-TACATATATAC
1 TATTTATATACATATATAC
12077104 T
1 T
12077105 GTAATATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
15 10 0.21
16 2 0.04
17 3 0.06
18 13 0.28
19 5 0.11
21 14 0.30
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTATATACATATATAC
Found at i:12077058 original size:2 final size:2
Alignment explanation
Indices: 12077037--12077131 Score: 54
Period size: 2 Copynumber: 48.5 Consensus size: 2
12077027 TGTATATTTC
* * *
12077037 TA TA CA TA TA TA CTA T- TA TA TA TA TA TA TA TT TA T- TT TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
12077078 TA CA TA TA TA T- TT TT TA CA TA TA TA CTG TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* *
12077119 TA CA TA TA CA TA T
1 TA TA TA TA TA TA T
12077132 CTATTTTATA
Statistics
Matches: 71, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
1 4 0.06
2 64 0.90
3 3 0.04
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12077073 original size:56 final size:54
Alignment explanation
Indices: 12077013--12077120 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
12077003 TTTATATACA
* * *
12077013 TATTTTTTACAAATTGTATATTTCTATACATATATACTATTATATATATATATATT
1 TATTTTATACAAA-TATATATTT-TATACATATATACTATAATATATATATATATT
* * * *
12077069 TATTTTATATACATATATATTTTTTACATATATACTGTAATATATATATATA
1 TATTTTATACAAATATATATTTTATACATATATACTATAATATATATATATA
12077121 CATATACATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 27 0.60
55 8 0.18
56 10 0.22
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (54 bp):
TATTTTATACAAATATATATTTTATACATATATACTATAATATATATATATATT
Found at i:12077079 original size:17 final size:17
Alignment explanation
Indices: 12077029--12077143 Score: 76
Period size: 17 Copynumber: 6.8 Consensus size: 17
12077019 TTACAAATTG
*
12077029 TATATTTCTATACATATA
1 TATATTT-TATATATATA
12077047 TACTATTATATATATATATA
1 TA-TATT-T-TATATATATA
* *
12077067 TTTATTTTATATACATA
1 TATATTTTATATATATA
*
12077084 TATATTTT-T-TACATA
1 TATATTTTATATATATA
* *
12077099 TATACTGTA-ATATATA
1 TATATTTTATATATATA
** *
12077115 TATA-TACATATACATA
1 TATATTTTATATATATA
*
12077131 TCTATTTTATATA
1 TATATTTTATATA
12077144 AACTACTGTT
Statistics
Matches: 77, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
15 14 0.18
16 19 0.25
17 22 0.29
18 3 0.04
19 8 0.10
20 11 0.14
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (17 bp):
TATATTTTATATATATA
Found at i:12077096 original size:15 final size:17
Alignment explanation
Indices: 12077001--12077143 Score: 79
Period size: 15 Copynumber: 8.6 Consensus size: 17
12076991 TAGATTAGTA
12077001 ATTTTATATACATAT-T
1 ATTTTATATACATATAT
* *
12077017 -TTTTACA-A-AT-TGT
1 ATTTTATATACATATAT
*
12077030 ATATTTCTATACATATAT
1 AT-TTTATATACATATAT
*
12077048 ACTATTATATATATATATATTT
1 A-T-TT-TATATACATATA--T
12077070 ATTTTATATACATATAT
1 ATTTTATATACATATAT
12077087 ATTTT-T-TACATATAT
1 ATTTTATATACATATAT
* * *
12077102 ACTGTA-ATATATATAT
1 ATTTTATATACATATAT
** *
12077118 A-TACATATACATATCT
1 ATTTTATATACATATAT
12077134 ATTTTATATA
1 ATTTTATATA
12077144 AACTACTGTT
Statistics
Matches: 97, Mismatches: 16, Indels: 27
0.69 0.11 0.19
Matches are distributed among these distances:
12 1 0.01
13 3 0.03
14 2 0.02
15 24 0.25
16 20 0.21
17 14 0.14
18 3 0.03
19 15 0.15
20 12 0.12
21 1 0.01
22 2 0.02
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (17 bp):
ATTTTATATACATATAT
Found at i:12086096 original size:21 final size:22
Alignment explanation
Indices: 12086072--12086114 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12086062 TGCATAACTT
12086072 GTATCGGTAG-AACTTGCACAG
1 GTATCGGTAGAAACTTGCACAG
*
12086093 GTATCGGTAGAAATTTGCACAG
1 GTATCGGTAGAAACTTGCACAG
12086115 TTTCTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (22 bp):
GTATCGGTAGAAACTTGCACAG
Found at i:12090630 original size:21 final size:22
Alignment explanation
Indices: 12090562--12090632 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 22
12090552 TGACTTGAGT
*
12090562 TGTATCGGTAG-TTGGATTGCA
1 TGTATCGGTAGTTTGTATTGCA
*
12090583 AGTATCGGTAGTTATGTGTATTG-A
1 TGTATCGGTAG-T-T-TGTATTGCA
12090607 TGTATCGGTAGTTTGTA-TGCA
1 TGTATCGGTAGTTTGTATTGCA
12090628 TGTAT
1 TGTAT
12090633 TAATAGAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
20 2 0.05
21 20 0.48
22 1 0.02
23 1 0.02
24 12 0.29
25 6 0.14
ACGTcount: A:0.21, C:0.07, G:0.30, T:0.42
Consensus pattern (22 bp):
TGTATCGGTAGTTTGTATTGCA
Found at i:12094585 original size:20 final size:20
Alignment explanation
Indices: 12094557--12094595 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12094547 GCCCCACCCC
*
12094557 ACCCCATCCCCGCTCGCCCG
1 ACCCCATCCCCACTCGCCCG
*
12094577 ACCCTATCCCCACTCGCCC
1 ACCCCATCCCCACTCGCCC
12094596 CGCATCATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.64, G:0.10, T:0.13
Consensus pattern (20 bp):
ACCCCATCCCCACTCGCCCG
Found at i:12097949 original size:31 final size:31
Alignment explanation
Indices: 12097903--12097990 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
12097893 TAGTACTTAA
*
12097903 ATTTTTTGACTTAATTTAGTATCTGAACTTGAC
1 ATTTTTT--CTTAATTTAGTATCTAAACTTGAC
*
12097936 ACTTTTTT-TTAATTTGGTATCTAAACTTGAC
1 A-TTTTTTCTTAATTTAGTATCTAAACTTGAC
* *
12097967 ATTTTTTCTTAATTTGGTACCTAA
1 ATTTTTTCTTAATTTAGTATCTAA
12097991 GCTTTTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
30 6 0.12
31 37 0.74
33 1 0.02
34 6 0.12
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.51
Consensus pattern (31 bp):
ATTTTTTCTTAATTTAGTATCTAAACTTGAC
Found at i:12098227 original size:59 final size:59
Alignment explanation
Indices: 12098162--12098274 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 59
12098152 ATTAATATTA
*
12098162 AAAAAAGATTAGGTACCAA-ATTAGGAAAAAA-AGTCAAGTTCAGGTACCAAATTGAACCC
1 AAAAAAGATTAAGTACCAATATTA--AAAAAAGAGTCAAGTTCAGGTACCAAATTGAACCC
* * * *
12098221 AAAAAAGTTTAAGTACCAATTTTAAAAAAAGGTGTCAAGTTTAGGTACCAAATT
1 AAAAAAGATTAAGTACCAATATTAAAAAAA-GAGTCAAGTTCAGGTACCAAATT
12098275 AGGAAAATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 6 0.13
59 17 0.37
60 23 0.50
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (59 bp):
AAAAAAGATTAAGTACCAATATTAAAAAAAGAGTCAAGTTCAGGTACCAAATTGAACCC
Found at i:12098263 original size:32 final size:31
Alignment explanation
Indices: 12098225--12098305 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
12098215 GAACCCAAAA
* *
12098225 AAGTTTAAGTACCAATTTTAAAAAAAGGTGTC
1 AAGTTTAAGTACCAA-ATTAAAAAAAGGTCTC
* ** *
12098257 AAGTTTAGGTACCAAATTAGGAAAATGTCTC
1 AAGTTTAAGTACCAAATTAAAAAAAGGTCTC
*
12098288 AAGTTTGAGTACCAAATT
1 AAGTTTAAGTACCAAATT
12098306 GGACAAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 27 0.66
32 14 0.34
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAGGTCTC
Found at i:12098329 original size:91 final size:90
Alignment explanation
Indices: 12098170--12098363 Score: 223
Period size: 91 Copynumber: 2.1 Consensus size: 90
12098160 TAAAAAAAGA
* ** *
12098170 TTAGGTACCAAATTAGGAAAAAAAGTCAAGTTCAGGTACCAAATTGAACCCAAAAAAGTTTAAGT
1 TTAGGTACCAAATTAGGAAAAAAACTCAAGTTCAGGTACCAAATTGAACAAAAAAAAATTTAAGT
* * *
12098235 ACCAATTTTAA-AAAAAGGTGTCAAGT
66 ACCAA-ATTAAGAAAAA-GTATCAAAT
*** * *
12098261 TTAGGTACCAAATTAGGAAAATGTCTCAAGTT-TGAGTACCAAATTGGACAAAAAAAAATTT-AG
1 TTAGGTACCAAATTAGGAAAAAAACTCAAGTTCAG-GTACCAAATTGAACAAAAAAAAATTTAAG
12098324 ATACCAAATTAAGAAAAAGTATCAAAT
65 -TACCAAATTAAGAAAAAGTATCAAAT
12098351 TTAGGTACCAAAT
1 TTAGGTACCAAAT
12098364 GTTATATTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
90 27 0.31
91 61 0.69
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (90 bp):
TTAGGTACCAAATTAGGAAAAAAACTCAAGTTCAGGTACCAAATTGAACAAAAAAAAATTTAAGT
ACCAAATTAAGAAAAAGTATCAAAT
Found at i:12099966 original size:30 final size:30
Alignment explanation
Indices: 12099933--12099990 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
12099923 ATTAATACAT
12099933 AAAATAATTACATA-ATATATAACTATTACTA
1 AAAAT-ATTA-ATACATATATAACTATTACTA
*
12099964 AAAATATTAATACATGTATAACTATTA
1 AAAATATTAATACATATATAACTATTA
12099991 TTATAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 3 0.12
30 17 0.68
31 5 0.20
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATATTAATACATATATAACTATTACTA
Found at i:12100078 original size:17 final size:18
Alignment explanation
Indices: 12100056--12100116 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
12100046 TCACTGATAC
12100056 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
* *
12100073 ATATATTATATACTATATT
1 ATATA-TATAAACTATATA
*
12100092 ATATGATATAACATTATATA
1 ATAT-ATATAA-ACTATATA
12100112 ATATA
1 ATATA
12100117 GTAGGAGGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.14
18 9 0.26
19 10 0.29
20 11 0.31
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:12111829 original size:45 final size:45
Alignment explanation
Indices: 12111779--12111880 Score: 177
Period size: 45 Copynumber: 2.3 Consensus size: 45
12111769 CCCTAGCAGG
**
12111779 ATCTTCTGATTTTCTACTAACATAACAATTCAAGAAGAACTACTT
1 ATCTTCTGACCTTCTACTAACATAACAATTCAAGAAGAACTACTT
*
12111824 ATCTTCTGACCTTCTACTAACATAACGATTCAAGAAGAACTACTT
1 ATCTTCTGACCTTCTACTAACATAACAATTCAAGAAGAACTACTT
12111869 ATCTTCTGACCT
1 ATCTTCTGACCT
12111881 CACAATTCAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (45 bp):
ATCTTCTGACCTTCTACTAACATAACAATTCAAGAAGAACTACTT
Found at i:12119549 original size:17 final size:17
Alignment explanation
Indices: 12119527--12119566 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12119517 AACTAAGAGG
12119527 AATGCAGTG-ATAACAAA
1 AATGCAG-GCATAACAAA
*
12119544 AATGCAGGCATAAGAAA
1 AATGCAGGCATAACAAA
12119561 AATGCA
1 AATGCA
12119567 TGAAAACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.15
Consensus pattern (17 bp):
AATGCAGGCATAACAAA
Found at i:12122988 original size:21 final size:21
Alignment explanation
Indices: 12122945--12122988 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12122935 TGCCACCAAA
* * *
12122945 ATGGCCTCCATAAGGGGCGTC
1 ATGGCCTCCATAAAGGACATC
12122966 ATGGCCTCCATAAAGGACATC
1 ATGGCCTCCATAAAGGACATC
12122987 AT
1 AT
12122989 TTCTTCTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (21 bp):
ATGGCCTCCATAAAGGACATC
Found at i:12135596 original size:21 final size:20
Alignment explanation
Indices: 12135552--12135596 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
12135542 TACAACTCAA
12135552 TTTTATTTTATTTTATTACCT
1 TTTTATTTTATTTTATTA-CT
12135573 TTTTATTTGTATTTTTATTA-T
1 TTTTATTT-TA-TTTTATTACT
12135594 TTT
1 TTT
12135597 ATGCTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.55
22 2 0.09
23 8 0.36
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTATTTTATTTTATTACT
Found at i:12144081 original size:23 final size:23
Alignment explanation
Indices: 12144055--12144099 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12144045 AAAATATTTC
* *
12144055 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTTAAATTA
*
12144078 ATTAATTAAATTGGGTTAAATT
1 ATTAAATAAATTGGGTTAAATT
12144100 TATTCTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (23 bp):
ATTAAATAAATTGGGTTAAATTA
Found at i:12151931 original size:26 final size:26
Alignment explanation
Indices: 12151902--12151997 Score: 77
Period size: 26 Copynumber: 3.7 Consensus size: 26
12151892 CTAATGTTGT
* *
12151902 TGCATGAGCATGTCCAGAATTGTCAC
1 TGCATGAACATGTCCAGAATTGTCGC
* * *
12151928 TGCA-GAAACTTGTCCAAAATTATCGC
1 TGCATG-AACATGTCCAGAATTGTCGC
* * * *
12151954 TGTATGAATATGTCCAGAGTTGTCGT
1 TGCATGAACATGTCCAGAATTGTCGC
* *
12151980 TGTATGAGCATGTCCAGA
1 TGCATGAACATGTCCAGA
12151998 GTTGCACCCA
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
25 1 0.02
26 52 0.96
27 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (26 bp):
TGCATGAACATGTCCAGAATTGTCGC
Found at i:12154486 original size:18 final size:18
Alignment explanation
Indices: 12154465--12154523 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
12154455 TTCCACAGGA
12154465 TCTTCCTCAGGATCTTCT
1 TCTTCCTCAGGATCTTCT
* *
12154483 TCTTCTTCAAGATCTTCT
1 TCTTCCTCAGGATCTTCT
12154501 TCTTCCTCAGGATCTTCT
1 TCTTCCTCAGGATCTTCT
12154519 TCTTC
1 TCTTC
12154524 AGCTTGCTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.12, C:0.32, G:0.08, T:0.47
Consensus pattern (18 bp):
TCTTCCTCAGGATCTTCT
Found at i:12164102 original size:60 final size:60
Alignment explanation
Indices: 12164009--12164146 Score: 240
Period size: 60 Copynumber: 2.3 Consensus size: 60
12163999 GACTGATAGT
* * *
12164009 AGTATGCAGCACCTTAACTCTACTAATGGTAAGTATTTCTCCCAACTACCCTCGAACTCA
1 AGTATACAGCACCGTAACTCTACTAAAGGTAAGTATTTCTCCCAACTACCCTCGAACTCA
12164069 AGTATACAGCACCGTAACTCTACTAAAGGTAAGTATTTCTCCCAACTACCCTCGAACTCA
1 AGTATACAGCACCGTAACTCTACTAAAGGTAAGTATTTCTCCCAACTACCCTCGAACTCA
*
12164129 AGTATATAGCACCGTAAC
1 AGTATACAGCACCGTAAC
12164147 ATATCTTCCA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 74 1.00
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (60 bp):
AGTATACAGCACCGTAACTCTACTAAAGGTAAGTATTTCTCCCAACTACCCTCGAACTCA
Found at i:12169476 original size:129 final size:129
Alignment explanation
Indices: 12169248--12169485 Score: 329
Period size: 129 Copynumber: 1.8 Consensus size: 129
12169238 TATATCACTT
* *
12169248 TATCACATGTTCATATGGAATGTACTTCTAAATGATTAAACACAGTCAATACAGTCCAAGAAACA
1 TATCACATGTTCATATGAAATGTACTTCTAAATCATTAAACACAGTCAATACAGTCCAAGAAACA
* * * *
12169313 GTAAAATGTAAGCTTTAATACCACAAAATATAACACCCAAAACCCTAAACATGTGATATCATAC
66 CTAAAATATAAACTCTAATACCACAAAATATAACACCCAAAACCCTAAACATGTGATATCATAC
* *
12169377 TATCACATGTTCATATGAAATGTACTTCTAAATCATTAAACATAGTCAA-ACAGTCCAAGAAATG
1 TATCACATGTTCATATGAAATGTACTTCTAAATCATTAAACACAGTCAATACAGTCCAAGAAA-C
* * *
12169441 ACTAAACA-ATAAACTCTGATACC-CTTAAATGTAACACCCAAAACC
65 ACTAAA-ATATAAACTCTAATACCAC-AAAATATAACACCCAAAACC
12169486 AAAAATAGTC
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
128 14 0.15
129 80 0.84
130 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (129 bp):
TATCACATGTTCATATGAAATGTACTTCTAAATCATTAAACACAGTCAATACAGTCCAAGAAACA
CTAAAATATAAACTCTAATACCACAAAATATAACACCCAAAACCCTAAACATGTGATATCATAC
Found at i:12169781 original size:21 final size:20
Alignment explanation
Indices: 12169757--12169809 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
12169747 CTTGTGATAG
12169757 TTCTACCGATACAAGTGTA-GC
1 TTCTACCGATAC-AGT-TATGC
* *
12169778 TTCTACTGAAACAGTTATGC
1 TTCTACCGATACAGTTATGC
*
12169798 TTCTACCAATAC
1 TTCTACCGATAC
12169810 GAAAAACTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 10 0.38
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (20 bp):
TTCTACCGATACAGTTATGC
Found at i:12180643 original size:24 final size:24
Alignment explanation
Indices: 12180610--12180658 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
12180600 TGATTTCCTA
12180610 AAAATGGAGAAATAAGGAAGGAGAG
1 AAAATGGAGAAATAA-GAAGGAGAG
* *
12180635 AAAA-GGAGAAGTAAGAAGGTGAG
1 AAAATGGAGAAATAAGAAGGAGAG
12180658 A
1 A
12180659 TCAAGTGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 9 0.41
25 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.37, T:0.08
Consensus pattern (24 bp):
AAAATGGAGAAATAAGAAGGAGAG
Found at i:12187624 original size:8 final size:7
Alignment explanation
Indices: 12187597--12187621 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12187587 CATGACAATT
12187597 AAAACTG
1 AAAACTG
12187604 AAAACTG
1 AAAACTG
12187611 AAAACTG
1 AAAACTG
12187618 AAAA
1 AAAA
12187622 ACTCACTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAACTG
Found at i:12192781 original size:13 final size:13
Alignment explanation
Indices: 12192763--12192787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12192753 TAAGTTAAAA
12192763 ATGCTAAAAATGC
1 ATGCTAAAAATGC
12192776 ATGCTAAAAATG
1 ATGCTAAAAATG
12192788 ATAAAATGGG
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Done.