Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017273.1 Corchorus olitorius cultivar O-4 contig17306, 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: 73441
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:6393 original size:14 final size:14
Alignment explanation
Indices: 6374--6401 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6364 AAATTTTTGA
6374 AAAAATTATGGCAT
1 AAAAATTATGGCAT
6388 AAAAATTATGGCAT
1 AAAAATTATGGCAT
6402 TAATTAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
AAAAATTATGGCAT
Found at i:7197 original size:21 final size:21
Alignment explanation
Indices: 7171--7217 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
7161 CAGGCTTGAT
7171 CGGGCAGGCGGCGCGGATGGC
1 CGGGCAGGCGGCGCGGATGGC
* * * *
7192 CGGGCATGTGGCTCGGGTGGC
1 CGGGCAGGCGGCGCGGATGGC
7213 CGGGC
1 CGGGC
7218 CATGGCCGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.06, C:0.28, G:0.55, T:0.11
Consensus pattern (21 bp):
CGGGCAGGCGGCGCGGATGGC
Found at i:10502 original size:15 final size:16
Alignment explanation
Indices: 10477--10506 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10467 TAGGGAATTG
10477 AGAATAACAATTAAAA
1 AGAATAACAATTAAAA
10493 AGAA-AACAATTAAA
1 AGAATAACAATTAAA
10507 CTAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (16 bp):
AGAATAACAATTAAAA
Found at i:12746 original size:35 final size:34
Alignment explanation
Indices: 12691--12788 Score: 105
Period size: 35 Copynumber: 3.0 Consensus size: 34
12681 ATGAAATAAG
* * * *
12691 ACAGTAATCAACTTAATTCAGGGTTATTAAGTAA
1 ACAGTAGTCAGCTTATTTCAGGGTAATTAAGTAA
*
12725 ACCAGTAGTCAGCTTATTTCAGGGTAATTAAGTCA
1 A-CAGTAGTCAGCTTATTTCAGGGTAATTAAGTAA
*
12760 AC---AGTCAGTTTATTTCA-GGTAATTAAGTA
1 ACAGTAGTCAGCTTATTTCAGGGTAATTAAGTA
12789 TACTTAATTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
30 11 0.20
31 14 0.25
34 2 0.04
35 29 0.52
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (34 bp):
ACAGTAGTCAGCTTATTTCAGGGTAATTAAGTAA
Found at i:12940 original size:59 final size:58
Alignment explanation
Indices: 12877--13018 Score: 151
Period size: 58 Copynumber: 2.4 Consensus size: 58
12867 TAATTTAGAG
* * * *
12877 TAATTAAGTTAGTTAAGAAGTAAAAAAGGGTAA-TCAGTAATAGTTGGCATAATTCAGGA
1 TAATTAAGTTAATTAAGAAGTAAAAAA-GGTAAGGCAGTAATA-ATAGCATAATTCAGGA
* ** * *
12936 TAATTAAGTTAACTAAGAAGTTGAAAAGGTAAGGCAGTAATAATAGCTTAATTCAGGG
1 TAATTAAGTTAATTAAGAAGTAAAAAAGGTAAGGCAGTAATAATAGCATAATTCAGGA
* * *
12994 TAATTGAGTTAATTGAGAAATAAAA
1 TAATTAAGTTAATTAAGAAGTAAAA
13019 GGCCTCACAA
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
58 36 0.54
59 31 0.46
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (58 bp):
TAATTAAGTTAATTAAGAAGTAAAAAAGGTAAGGCAGTAATAATAGCATAATTCAGGA
Found at i:12998 original size:58 final size:59
Alignment explanation
Indices: 12864--13005 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 59
12854 AAGGCAATTG
* * ** * * *
12864 GCTTAATTTAGAGTAATTAAGTTAGTTAAGAAGTAAAAAAGGGTAATCAGTAATAGTTG
1 GCTTAATTCAGGGTAATTAAGTTAACTAAGAAGTAAAAAAGGGTAAGCAGTAATAGATA
* * **
12923 GCATAATTCAGGATAATTAAGTTAACTAAGAAGTTGAAAA-GGTAAGGCAGTAATA-ATA
1 GCTTAATTCAGGGTAATTAAGTTAACTAAGAAGTAAAAAAGGGTAA-GCAGTAATAGATA
*
12981 GCTTAATTCAGGGTAATTGAGTTAA
1 GCTTAATTCAGGGTAATTAAGTTAA
13006 TTGAGAAATA
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
58 28 0.41
59 40 0.59
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (59 bp):
GCTTAATTCAGGGTAATTAAGTTAACTAAGAAGTAAAAAAGGGTAAGCAGTAATAGATA
Found at i:15732 original size:11 final size:11
Alignment explanation
Indices: 15703--15759 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
15693 TATAATATAT
15703 ACTATAAACGA
1 ACTATAAACGA
15714 AC-ATAAACGA
1 ACTATAAACGA
15724 ACTATAAACGA
1 ACTATAAACGA
**
15735 TTTATTAAACGA
1 ACTA-TAAACGA
15747 A-TAATAAACGA
1 ACT-ATAAACGA
15758 AC
1 AC
15760 ATTAATCGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 10 0.26
11 21 0.54
12 8 0.21
ACGTcount: A:0.54, C:0.16, G:0.09, T:0.21
Consensus pattern (11 bp):
ACTATAAACGA
Found at i:25569 original size:22 final size:23
Alignment explanation
Indices: 25530--25572 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
25520 AATCCTAATC
25530 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
25553 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
25573 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:30607 original size:22 final size:23
Alignment explanation
Indices: 30568--30610 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
30558 AATCCTAATC
30568 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
30591 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
30611 ACTCCTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:30621 original size:21 final size:22
Alignment explanation
Indices: 30572--30622 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
30562 CTAATCCTGG
* **
30572 TAGGAATAGTAAAACCTTTCTGG
1 TAGGAA-AGTAAAACCTTACTCC
30595 TAGGAAAGTAAAACC-TACTCC
1 TAGGAAAGTAAAACCTTACTCC
30616 TAGGAAA
1 TAGGAAA
30623 AACCATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 9 0.36
23 6 0.24
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (22 bp):
TAGGAAAGTAAAACCTTACTCC
Found at i:35897 original size:25 final size:25
Alignment explanation
Indices: 35863--35910 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
35853 AGATTATAGA
35863 AAGTTCTGTTGGCCTTTAGCGATAC
1 AAGTTCTGTTGGCCTTTAGCGATAC
35888 AAGTTCTGTTGGCCTTTAGCGAT
1 AAGTTCTGTTGGCCTTTAGCGAT
35911 CCATTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (25 bp):
AAGTTCTGTTGGCCTTTAGCGATAC
Found at i:38935 original size:10 final size:10
Alignment explanation
Indices: 38920--38945 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
38910 ATACCTCGAT
38920 ATATCCGTAA
1 ATATCCGTAA
38930 ATATCCGTAA
1 ATATCCGTAA
38940 ATATCC
1 ATATCC
38946 ATATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:39892 original size:12 final size:12
Alignment explanation
Indices: 39871--39916 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
39861 CATCGATACC
*
39871 TCGATCTATCCG
1 TCGATATATCCG
39883 TCGATATATCCG
1 TCGATATATCCG
* *
39895 TCAATATTTCCG
1 TCGATATATCCG
39907 TTCGATATAT
1 -TCGATATAT
39917 TTGTGGATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 21 0.75
13 7 0.25
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:40848 original size:41 final size:43
Alignment explanation
Indices: 40746--41079 Score: 441
Period size: 41 Copynumber: 7.9 Consensus size: 43
40736 CCAATAACCA
* *
40746 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
40789 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
40832 -AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
40874 GAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
40915 AAAGTCCCCAAACACATATATAACACAG-GGACAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGG-CATCTCTATTAC
*
40958 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
* *
40999 AAAGTCGCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
41042 AAAGTGCTCAAACACATATATAACACAGAGGCATCTCT
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCT
41080 CCTTATGGCA
Statistics
Matches: 255, Mismatches: 25, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
40 4 0.02
41 103 0.40
42 5 0.02
43 102 0.40
44 41 0.16
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:41104 original size:84 final size:84
Alignment explanation
Indices: 40746--41077 Score: 558
Period size: 84 Copynumber: 3.9 Consensus size: 84
40736 CCAATAACCA
* *
40746 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
*
40811 AACACAGAGGCACCTATATTC
65 AACACAGAGGCATCTATA-TC
*
40832 -AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACGAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
40896 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
40915 AAAGTCCCCAAACACATATATAACACAGGGACAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
40980 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
* * *
40999 AAAGTCGCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTGCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
41064 ACACAGAGGCATCT
66 ACACAGAGGCATCT
41078 CTCCTTATGG
Statistics
Matches: 233, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
83 2 0.01
84 191 0.82
85 40 0.17
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:47753 original size:36 final size:36
Alignment explanation
Indices: 47713--47808 Score: 115
Period size: 35 Copynumber: 2.7 Consensus size: 36
47703 GATTAAAGCT
* *
47713 CTTTCCTCATTCAACACTTGGGGGCTCCGGCAACCC
1 CTTTCATCATTCAACACTTGGGGGCTCCAGCAACCC
* **
47749 CTTTCATCATTCAACA-TTCGGGGCTCCAGCAATTC
1 CTTTCATCATTCAACACTTGGGGGCTCCAGCAACCC
**
47784 C-TTCATCATTCAATGCTTGGGGGCT
1 CTTTCATCATTCAACACTTGGGGGCT
47809 ATGTCATACT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 12 0.24
35 24 0.47
36 15 0.29
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (36 bp):
CTTTCATCATTCAACACTTGGGGGCTCCAGCAACCC
Found at i:48193 original size:72 final size:72
Alignment explanation
Indices: 48084--48564 Score: 742
Period size: 72 Copynumber: 6.8 Consensus size: 72
48074 CCTCTTCTTC
* * *
48084 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCATAATCCTTACGGGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
48149 CTTCCAT
66 CTTCCAT
* * *
48156 ATTACGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
*
48221 CTTCCGT
66 CTTCCAT
*
48228 ATTGCGGTTGTAGCCGAGGCAGTTCCAACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
48293 CTTCCAT
66 CTTCCAT
* *
48300 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
*
48365 CTTCCGT
66 CTTCCAT
* *
48372 ATTGCGGTTGTAGCCGAGGCAGTTCCAACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
48437 CTTCCAT
66 CTTCCAT
* * *
48444 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
*
48509 C-TCCCT
66 CTTCCAT
*
48515 CATTGC-G--G--GCCGAGGCAGTTCCCACA-TTGGCAGTCTTTCGCACAATCCTT
1 -ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
48565 GCTACTAATC
Statistics
Matches: 379, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
66 23 0.06
67 18 0.05
69 1 0.00
71 4 0.01
72 333 0.88
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (72 bp):
ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
CTTCCAT
Found at i:49226 original size:16 final size:16
Alignment explanation
Indices: 49201--49233 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
49191 CTGCAAAATC
49201 TTGCCACAACAGAATG
1 TTGCCACAACAGAATG
*
49217 TTGCCGCAACAGAATG
1 TTGCCACAACAGAATG
49233 T
1 T
49234 CCCCTGTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (16 bp):
TTGCCACAACAGAATG
Found at i:49906 original size:43 final size:43
Alignment explanation
Indices: 49772--50095 Score: 362
Period size: 43 Copynumber: 7.7 Consensus size: 43
49762 CCAATAACCA
* *
49772 AAAGTCTCCAAACACATATATAACACAGGGGCATCTCTATTCCA-
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATT--AT
* *
49816 AAAGTCCTCAAACACATATATAACACAGAGGC-AC-CTA-TATT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTA-T
*
49857 CAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAT
* * **
49900 GAAGTCCTCAAACACATATATAACACAGATGC-A-TCTA-TATT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTA-T
*
49941 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAT
*** * * *
49984 AAAGTCGTGAAACACATATATAACACAGAGAC-A-TTTA-TAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAT
* *
50024 CAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 -AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAT
*
50068 AAAGTCCTCAAACACATATATAACACAG
1 AAAGTCCCCAAACACATATATAACACAG
50096 ATGCATCTCT
Statistics
Matches: 235, Mismatches: 32, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.00
40 4 0.02
41 93 0.40
42 8 0.03
43 94 0.40
44 35 0.15
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAT
Found at i:49946 original size:84 final size:84
Alignment explanation
Indices: 49772--50103 Score: 522
Period size: 84 Copynumber: 3.9 Consensus size: 84
49762 CCAATAACCA
* * *
49772 AAAGTCTCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
* *
49837 AACACAGAGGCACCTATATT
65 AACACAGATGCATCTATATT
* **
49857 CAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTATGAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
49922 ACACAGATGCATCTATATT
66 ACACAGATGCATCTATATT
* *
49941 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCGTGAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
* *
50006 ACACAGA-GACATTTATATC
66 ACACAGATG-CATCTATATT
*
50025 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
50090 ACACAGATGCATCT
66 ACACAGATGCATCT
50104 CTCCTTATGG
Statistics
Matches: 226, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
83 1 0.00
84 186 0.82
85 39 0.17
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGATGCATCTATATT
Found at i:50102 original size:43 final size:43
Alignment explanation
Indices: 49772--50105 Score: 405
Period size: 41 Copynumber: 7.9 Consensus size: 43
49762 CCAATAACCA
* *
49772 AAAGT-CTCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCT-CAAACACATATATAACACAGAGGCATCTCTATTAC
* *
49815 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 -AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
* * * *
49858 -AAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAT
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
49900 GAAGTCCTCAAACACATATATAACACAGATGCATCTATATT--
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
49941 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
49984 AAAGTCGTGAAACACATATATAACACAGAGACAT-T-TA-TATC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTA-C
* *
50025 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
*
50068 AAAGTCCTCAAACACATATATAACACAGATGCATCTCT
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCT
50106 CCTTATGGCA
Statistics
Matches: 248, Mismatches: 33, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
40 2 0.01
41 103 0.42
42 2 0.01
43 102 0.41
44 37 0.15
45 2 0.01
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (43 bp):
AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:52881 original size:105 final size:107
Alignment explanation
Indices: 52751--52961 Score: 365
Period size: 108 Copynumber: 2.0 Consensus size: 107
52741 TCAATTACAC
52751 TTTAATTTTAACTATTTTATCTATTTTAGCTTTTGATACTAGATGCC-A-A-GGTCTAAATTTTT
1 TTTAATTTTAACTATTTTATCTATTTTAGCTTTTGATACTAGATGCCAACATGGTCTAAATTTTT
*
52813 GTCTTATTAAATCTTTTTCCTGGTTACCTAATAAATGATAAT
66 GTCTTATTAAATCTCTTTCCTGGTTACCTAATAAATGATAAT
* *
52855 TTTAACTTTTCACTATTTTATCTATTTTAGCTTTTGATGCTAGATGCCAACATGGTCTAAATTTT
1 TTTAA-TTTTAACTATTTTATCTATTTTAGCTTTTGATACTAGATGCCAACATGGTCTAAATTTT
52920 TGTCTTATTAAATCTCTTTCCTGGTTACCTAATAAATGATAA
65 TGTCTTATTAAATCTCTTTCCTGGTTACCTAATAAATGATAA
52962 ATGGAATGCT
Statistics
Matches: 100, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
104 5 0.05
105 40 0.40
106 1 0.01
107 1 0.01
108 53 0.53
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (107 bp):
TTTAATTTTAACTATTTTATCTATTTTAGCTTTTGATACTAGATGCCAACATGGTCTAAATTTTT
GTCTTATTAAATCTCTTTCCTGGTTACCTAATAAATGATAAT
Found at i:55273 original size:23 final size:23
Alignment explanation
Indices: 55247--55300 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
55237 ACTTTGCCCT
55247 CATCCTCAATGCCATGCCACTTA
1 CATCCTCAATGCCATGCCACTTA
55270 CATCCTCAATGCCATGCCACTTA
1 CATCCTCAATGCCATGCCACTTA
55293 CATCCTCA
1 CATCCTCA
55301 CTTGGATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.41, G:0.07, T:0.26
Consensus pattern (23 bp):
CATCCTCAATGCCATGCCACTTA
Found at i:55469 original size:14 final size:14
Alignment explanation
Indices: 55450--55634 Score: 76
Period size: 14 Copynumber: 14.1 Consensus size: 14
55440 AACACAAAAA
55450 AAAACAGAAACTGC
1 AAAACAGAAACTGC
* **
55464 AAAACAGCAACTAA
1 AAAACAGAAACTGC
*
55478 AAAACAAAAACTGC
1 AAAACAGAAACTGC
* *
55492 ATAAA-AAAAACAG-
1 A-AAACAGAAACTGC
* *
55505 -AAACAGCAACAGC
1 AAAACAGAAACTGC
**
55518 --AACA-ACAACTAA
1 AAAACAGA-AACTGC
55530 AAAACAGAAACTGC
1 AAAACAGAAACTGC
* * *
55544 AAAAAAAAAACAG-
1 AAAACAGAAACTGC
* **
55557 -AAACAGCAACTAA
1 AAAACAGAAACTGC
*
55570 AAAACAGAAATTGC
1 AAAACAGAAACTGC
*
55584 ACAA-A-AAA----
1 AAAACAGAAACTGC
55592 A-AACAGAAACTGC
1 AAAACAGAAACTGC
55605 AAAACAGAAACTGC
1 AAAACAGAAACTGC
*
55619 AAAACAGAAACAGC
1 AAAACAGAAACTGC
55633 AA
1 AA
55635 CACAAAAACA
Statistics
Matches: 125, Mismatches: 30, Indels: 32
0.67 0.16 0.17
Matches are distributed among these distances:
7 2 0.02
8 2 0.02
9 3 0.02
11 3 0.02
12 23 0.18
13 2 0.02
14 86 0.69
15 4 0.03
ACGTcount: A:0.64, C:0.19, G:0.10, T:0.06
Consensus pattern (14 bp):
AAAACAGAAACTGC
Found at i:55532 original size:52 final size:50
Alignment explanation
Indices: 55445--55575 Score: 176
Period size: 52 Copynumber: 2.6 Consensus size: 50
55435 TTGCAAACAC
* *
55445 AAAAAAAAACAGAAACTGC-A-AAACAGCAACTAAAAAACAAAAACTGCA
1 AAAAAAAAACAGAAACAGCAACAAACAACAACTAAAAAACAAAAACTGCA
* *
55493 TAAAAAAAACAGAAACAGCAACAGCAACAACAACTAAAAAACAGAAACTGCA
1 AAAAAAAAACAGAAACAGCAACA--AACAACAACTAAAAAACAAAAACTGCA
*
55545 AAAAAAAAACAGAAACAGCAACTAAAAAACA
1 AAAAAAAAACAGAAACAGCAAC-AAACAACA
55576 GAAATTGCAC
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
48 17 0.24
49 1 0.01
50 1 0.01
51 6 0.08
52 46 0.64
53 1 0.01
ACGTcount: A:0.67, C:0.19, G:0.08, T:0.05
Consensus pattern (50 bp):
AAAAAAAAACAGAAACAGCAACAAACAACAACTAAAAAACAAAAACTGCA
Found at i:55551 original size:20 final size:20
Alignment explanation
Indices: 55528--55608 Score: 117
Period size: 20 Copynumber: 4.0 Consensus size: 20
55518 AACAACAACT
55528 AAAAAACAGAAACTGCAAAA
1 AAAAAACAGAAACTGCAAAA
* **
55548 AAAAAACAGAAACAGCAACT
1 AAAAAACAGAAACTGCAAAA
*
55568 AAAAAACAGAAATTGCACAAA
1 AAAAAACAGAAACTGCA-AAA
55589 AAAAAACAGAAACTGCAAAA
1 AAAAAACAGAAACTGCAAAA
55609 CAGAAACTGC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 35 0.67
21 17 0.33
ACGTcount: A:0.68, C:0.16, G:0.10, T:0.06
Consensus pattern (20 bp):
AAAAAACAGAAACTGCAAAA
Found at i:55556 original size:40 final size:40
Alignment explanation
Indices: 55512--55636 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
55502 CAGAAACAGC
55512 AACAGCAACAACAACTAAAAAACAGAAACTGCAAAAAAAA
1 AACAGCAACAACAACTAAAAAACAGAAACTGCAAAAAAAA
* * *
55552 AACAGAAACAGCAACTAAAAAACAGAAATTGCACAAAAAAA
1 AACAGCAACAACAACTAAAAAACAGAAACTGCA-AAAAAAA
** * *
55593 AACAG-----A-AACTGCAAAACAGAAACTGCAAAACAGA
1 AACAGCAACAACAACTAAAAAACAGAAACTGCAAAAAAAA
55627 AACAGCAACA
1 AACAGCAACA
55637 CAAAAACAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
34 10 0.14
35 18 0.26
40 30 0.43
41 12 0.17
ACGTcount: A:0.64, C:0.20, G:0.10, T:0.06
Consensus pattern (40 bp):
AACAGCAACAACAACTAAAAAACAGAAACTGCAAAAAAAA
Found at i:55590 original size:41 final size:40
Alignment explanation
Indices: 55512--55606 Score: 145
Period size: 40 Copynumber: 2.4 Consensus size: 40
55502 CAGAAACAGC
* *
55512 AACAGCAACAACAACTAAAAAACAGAAACTGCAAAAAAAA
1 AACAGAAACAGCAACTAAAAAACAGAAACTGCAAAAAAAA
*
55552 AACAGAAACAGCAACTAAAAAACAGAAATTGCACAAAAAAA
1 AACAGAAACAGCAACTAAAAAACAGAAACTGCA-AAAAAAA
*
55593 AACAGAAACTGCAA
1 AACAGAAACAGCAA
55607 AACAGAAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 30 0.60
41 20 0.40
ACGTcount: A:0.65, C:0.19, G:0.09, T:0.06
Consensus pattern (40 bp):
AACAGAAACAGCAACTAAAAAACAGAAACTGCAAAAAAAA
Found at i:55642 original size:20 final size:21
Alignment explanation
Indices: 55619--55668 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 21
55609 CAGAAACTGC
55619 AAAACAGAAA-CAGCAACACA
1 AAAACAGAAACCAGCAACACA
*
55639 AAAACAGAAACTGCAGCCACACA
1 AAAACAGAAAC--CAGCAACACA
55662 AAAACAG
1 AAAACAG
55669 GAACTAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.38
23 16 0.62
ACGTcount: A:0.60, C:0.26, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAACAGAAACCAGCAACACA
Found at i:55643 original size:14 final size:14
Alignment explanation
Indices: 55591--55645 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
55581 TGCACAAAAA
*
55591 AAAACAGAAACTGC
1 AAAACAGAAACAGC
*
55605 AAAACAGAAACTGC
1 AAAACAGAAACAGC
55619 AAAACAGAAACAGC
1 AAAACAGAAACAGC
* *
55633 AACACAAAAACAG
1 AAAACAGAAACAG
55646 AAACTGCAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.62, C:0.22, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAACAGAAACAGC
Found at i:55660 original size:23 final size:23
Alignment explanation
Indices: 55529--55673 Score: 80
Period size: 20 Copynumber: 6.6 Consensus size: 23
55519 ACAACAACTA
*
55529 AAAAACAGAAACTGCA--AA-AA
1 AAAAACAGAAACTGCAGCAACAC
55549 AAAAACAGAAA---CAGCAACTA-
1 AAAAACAGAAACTGCAGCAAC-AC
* *
55569 AAAAACAGAAATTGCA-CAA-AA
1 AAAAACAGAAACTGCAGCAACAC
55590 AAAAACAGAAACTGCA--AA-AC
1 AAAAACAGAAACTGCAGCAACAC
* * *
55610 AGAAACTGCAAAACAGAAACAGCAACAC
1 AAAAACAG--AAACTG---CAGCAACAC
*
55638 AAAAACAGAAACTGCAGCCACAC
1 AAAAACAGAAACTGCAGCAACAC
*
55661 AAAAACAGGAACT
1 AAAAACAGAAACT
55674 AAAACAGAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 29
0.72 0.07 0.21
Matches are distributed among these distances:
17 2 0.02
19 2 0.02
20 32 0.32
21 16 0.16
22 8 0.08
23 22 0.22
25 2 0.02
26 5 0.05
27 2 0.02
28 8 0.08
ACGTcount: A:0.62, C:0.21, G:0.12, T:0.06
Consensus pattern (23 bp):
AAAAACAGAAACTGCAGCAACAC
Found at i:55678 original size:69 final size:68
Alignment explanation
Indices: 55550--55682 Score: 180
Period size: 69 Copynumber: 1.9 Consensus size: 68
55540 CTGCAAAAAA
*
55550 AAAACAGAAACAGCAACTAAAAAACAGAAATTGCACAAAAAAAAACAGAAACTGCAAAACAGAAA
1 AAAACAGAAACAGCAACTAAAAAACAGAAACTGCACAAAAAAAAACAGAAACT-CAAAACAGAAA
55615 CTGC
65 CTGC
* * *
55619 AAAACAGAAACAGCAAC-ACAAAAACAGAAACTGCAGCCACACAAAAACAGGAACT-AAAACAGA
1 AAAACAGAAACAGCAACTA-AAAAACAGAAACTGCA--CAAAAAAAAACAGAAACTCAAAACAGA
55682 A
63 A
55683 TCAAGTAGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
68 1 0.02
69 41 0.72
71 15 0.26
ACGTcount: A:0.62, C:0.21, G:0.12, T:0.05
Consensus pattern (68 bp):
AAAACAGAAACAGCAACTAAAAAACAGAAACTGCACAAAAAAAAACAGAAACTCAAAACAGAAAC
TGC
Found at i:60721 original size:2 final size:2
Alignment explanation
Indices: 60714--60797 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
60704 TCAAACAAAT
60714 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
60756 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
60798 TATATATATA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:61742 original size:15 final size:17
Alignment explanation
Indices: 61710--61747 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
61700 ATAACCAAAA
*
61710 TTATATTATTTCTCATT
1 TTATTTTATTTCTCATT
61727 TTATTTTATTT-T-ATT
1 TTATTTTATTTCTCATT
61742 TTATTT
1 TTATTT
61748 GCAATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 1 0.05
17 10 0.50
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTTTATTTCTCATT
Found at i:62808 original size:60 final size:61
Alignment explanation
Indices: 62673--62836 Score: 208
Period size: 60 Copynumber: 2.7 Consensus size: 61
62663 GCTAATTGCT
* ** * *
62673 CAAATAAGGGCCTAACAATTGTCAAAAAATTCAAATAAGGG-CTTGATCTTTTAGTTTGGC
1 CAAATAAGGGCCTAACATTTGTCAAAATGTTCAAATAAGGGTCTCGATCTTTTAATTTGGC
* *
62733 TAAATAAGGACCTAACATTTGTCAAAATGTTCAAATAAGGGTC-CGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACATTTGTCAAAATGTTCAAATAAGGGTCTCGATCTTTTAATTTGGC
* * *
62793 CAAATAAGGGTCTAAC-TTTATCGAAAATGCTCAAATAAGGGTCT
1 CAAATAAGGGCCTAACATTTGTC-AAAATGTTCAAATAAGGGTCT
62837 GGAGTCGAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 5 0.06
60 83 0.93
61 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (61 bp):
CAAATAAGGGCCTAACATTTGTCAAAATGTTCAAATAAGGGTCTCGATCTTTTAATTTGGC
Found at i:65119 original size:23 final size:24
Alignment explanation
Indices: 65093--65139 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
65083 AATGAAACTA
65093 TTATATATA-TTAT-TCTAAATTTC
1 TTATATATATTTATCTC-AAATTTC
*
65116 TTATATTTATTTATCTCAAATTTC
1 TTATATATATTTATCTCAAATTTC
65140 AACGAGTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 11 0.52
25 2 0.10
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATATATATTTATCTCAAATTTC
Found at i:65136 original size:24 final size:23
Alignment explanation
Indices: 65093--65139 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
65083 AATGAAACTA
65093 TTATATATATTATTCTAAATTTC
1 TTATATATATTATTCTAAATTTC
*
65116 TTATATTTATT-TATCTCAAATTTC
1 TTATATATATTAT-TCT-AAATTTC
65140 AACGAGTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 13 0.62
24 7 0.33
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATATATATTATTCTAAATTTC
Found at i:65191 original size:14 final size:14
Alignment explanation
Indices: 65172--65199 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
65162 CCCAATATGA
65172 ACAAAGTTTGACGT
1 ACAAAGTTTGACGT
65186 ACAAAGTTTGACGT
1 ACAAAGTTTGACGT
65200 GGGTTGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
ACAAAGTTTGACGT
Found at i:65872 original size:44 final size:39
Alignment explanation
Indices: 65740--65909 Score: 126
Period size: 39 Copynumber: 4.2 Consensus size: 39
65730 ACGACTCAAT
** * *
65740 TTTAAAAACTTTGATGGGATCCTTCCCCT-TATTGAAAAC
1 TTTAAAAAAATTGATGGGAT-CTTTCCCTAAATTGAAAAC
* * * * * *
65779 TTTGAAGAAGACTGGATGGGATCTTTCCCCAAATTGAACAT
1 TTT-AA-AAAAATTGATGGGATCTTTCCCTAAATTGAAAAC
65820 TTTAAAAAAAAAAATTAGATGGGATCTTTCCCTAAATTGAAAAC
1 TTT----AAAAAAATT-GATGGGATCTTTCCCTAAATTGAAAAC
* * * *
65864 TTTGAAAAACTTGATGGGATCTCTCCCTATATTGAAAAC
1 TTTAAAAAAATTGATGGGATCTTTCCCTAAATTGAAAAC
65903 TCTTAAA
1 T-TTAAA
65910 TTGAATATTA
Statistics
Matches: 102, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
39 29 0.28
40 19 0.19
41 21 0.21
43 4 0.04
44 29 0.28
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (39 bp):
TTTAAAAAAATTGATGGGATCTTTCCCTAAATTGAAAAC
Found at i:65883 original size:39 final size:39
Alignment explanation
Indices: 65743--65903 Score: 144
Period size: 44 Copynumber: 3.9 Consensus size: 39
65733 ACTCAATTTT
* *
65743 AAAAACTTTGATGGGATCCTTCCCCT-TATTGAAAACTTTG
1 AAAAAC-TTGATGGGAT-CTTTCCCTAAATTGAAAACTTTG
* * * * *
65783 AAGAAGACTGGATGGGATCTTTCCCCAAATTGAACATTTTAAAAA
1 AA-AA-ACTTGATGGGATCTTTCCCTAAATTGAAAACTTT----G
*
65828 AAAAAATTAGATGGGATCTTTCCCTAAATTGAAAACTTTG
1 AAAAACTT-GATGGGATCTTTCCCTAAATTGAAAACTTTG
* *
65868 AAAAACTTGATGGGATCTCTCCCTATATTGAAAACT
1 AAAAACTTGATGGGATCTTTCCCTAAATTGAAAACT
65904 CTTAAATTGA
Statistics
Matches: 97, Mismatches: 16, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
39 26 0.27
40 15 0.15
41 21 0.22
42 2 0.02
43 2 0.02
44 29 0.30
45 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (39 bp):
AAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
Found at i:65966 original size:52 final size:52
Alignment explanation
Indices: 65850--66020 Score: 209
Period size: 52 Copynumber: 3.2 Consensus size: 52
65840 GGGATCTTTC
* * * *
65850 CCTAAATTGAAAACTTTGAAAAACTTGATGGGATCTCTCCCTATATTGAAAACT
1 CCTAAATTGAATACTTTG-AAAACTTGATGGGATCTTTCCC-ATTTTGAAAAAT
* * *
65904 CTTAAATTGAATA-TTATGAAAACTAGATGGGATCTTTCCCATTTTGAAAAGT
1 CCTAAATTGAATACTT-TGAAAACTTGATGGGATCTTTCCCATTTTGAAAAAT
* * *
65956 CCTAAATTGAATACTTTGAAAATTTGATGGGATCTTTCCCAATTTGAAAAAA
1 CCTAAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCATTTTGAAAAAT
*
66008 CTTAAATTGAATA
1 CCTAAATTGAATA
66021 AATTCTTTTT
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
52 65 0.64
53 24 0.24
54 13 0.13
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (52 bp):
CCTAAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCATTTTGAAAAAT
Found at i:66055 original size:17 final size:18
Alignment explanation
Indices: 66033--66066 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
66023 TTCTTTTTTA
66033 TTTTT-GAGTTTTGAAAT
1 TTTTTGGAGTTTTGAAAT
*
66050 TTTTTGGATTTTTGAAA
1 TTTTTGGAGTTTTGAAA
66067 ATCTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (18 bp):
TTTTTGGAGTTTTGAAAT
Found at i:69455 original size:31 final size:31
Alignment explanation
Indices: 69420--69481 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
69410 CTAAGCCCAA
69420 TGTCCAAATGCAAGCCCAAAAGTCCAAGATC
1 TGTCCAAATGCAAGCCCAAAAGTCCAAGATC
*
69451 TGTCCAAATGCAAGCCCCAAAGTCCAAGATC
1 TGTCCAAATGCAAGCCCAAAAGTCCAAGATC
69482 CCAAAATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.31, G:0.16, T:0.16
Consensus pattern (31 bp):
TGTCCAAATGCAAGCCCAAAAGTCCAAGATC
Found at i:71554 original size:37 final size:37
Alignment explanation
Indices: 71504--71574 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
71494 TCACACTCAC
*
71504 AAACCTTGGTAGAAGGCCACCACATTGACATTGGACT
1 AAACCTTGGTAGAAGCCCACCACATTGACATTGGACT
*
71541 AAACCTTGGTAGAATCCCACCACATTGACATTGG
1 AAACCTTGGTAGAAGCCCACCACATTGACATTGG
71575 GCCATTAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (37 bp):
AAACCTTGGTAGAAGCCCACCACATTGACATTGGACT
Done.