Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016076.1 Corchorus olitorius cultivar O-4 contig16109, 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: 155689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2923 original size:11 final size:11
Alignment explanation
Indices: 2907--2932 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2897 ATGCCTAAAA
2907 AAAACTAGAAG
1 AAAACTAGAAG
2918 AAAACTAGAAG
1 AAAACTAGAAG
2929 AAAA
1 AAAA
2933 GAAATTATCT
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:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:18099 original size:15 final size:15
Alignment explanation
Indices: 18069--18110 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
18059 TTACTTTGTT
18069 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
18085 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
18100 TTGTTTTCTGT
1 TTGTTTTCTGT
18111 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:21080 original size:11 final size:11
Alignment explanation
Indices: 21060--21096 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
21050 CCACTACCAA
21060 GCCATT-ACCG
1 GCCATTCACCG
21070 GCCATTCACCG
1 GCCATTCACCG
21081 TGCCA-TCACCG
1 -GCCATTCACCG
21092 GCCAT
1 GCCAT
21097 GCCCGTGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.42
11 10 0.42
12 4 0.17
ACGTcount: A:0.19, C:0.43, G:0.19, T:0.19
Consensus pattern (11 bp):
GCCATTCACCG
Found at i:21085 original size:22 final size:21
Alignment explanation
Indices: 21060--21108 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
21050 CCACTACCAA
* *
21060 GCCATTACCGGCCATTCACCGT
1 GCCATCACCGGCCATGC-CCGT
21082 GCCATCACCGGCCATGCCCGT
1 GCCATCACCGGCCATGCCCGT
21103 GCCATC
1 GCCATC
21109 GCCATTCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.16, C:0.45, G:0.20, T:0.18
Consensus pattern (21 bp):
GCCATCACCGGCCATGCCCGT
Found at i:21106 original size:11 final size:11
Alignment explanation
Indices: 21060--21108 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
21050 CCACTACCAA
*
21060 GCCATTACCG-
1 GCCATCACCGT
21070 GCCATTCACCGT
1 GCCA-TCACCGT
21082 GCCATCACCG-
1 GCCATCACCGT
21092 GCCATGC-CCGT
1 GCCAT-CACCGT
21103 GCCATC
1 GCCATC
21109 GCCATTCCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 13 0.38
11 17 0.50
12 4 0.12
ACGTcount: A:0.16, C:0.45, G:0.20, T:0.18
Consensus pattern (11 bp):
GCCATCACCGT
Found at i:21483 original size:15 final size:14
Alignment explanation
Indices: 21463--21492 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
21453 ATCTTTTTAA
21463 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
21478 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
21492 T
1 T
21493 GCTTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:25543 original size:2 final size:2
Alignment explanation
Indices: 25536--25574 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25526 TTATTTAGAT
25536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25575 TTACAAGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25765 original size:11 final size:11
Alignment explanation
Indices: 25749--25780 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
25739 TTGCAATTTT
25749 AAGTAAAAAAA
1 AAGTAAAAAAA
25760 AAGT-AAAAAA
1 AAGTAAAAAAA
25770 AAG-AAAAAAA
1 AAGTAAAAAAA
25780 A
1 A
25781 GTCGGAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (11 bp):
AAGTAAAAAAA
Found at i:25769 original size:10 final size:10
Alignment explanation
Indices: 25749--25782 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
25739 TTGCAATTTT
25749 AAGTAAAAAAA
1 AAGT-AAAAAA
25760 AAGTAAAAAA
1 AAGTAAAAAA
25770 AAG-AAAAAA
1 AAGTAAAAAA
25779 AAGT
1 AAGT
25783 CGGAACTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 9 0.41
11 4 0.18
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (10 bp):
AAGTAAAAAA
Found at i:29048 original size:106 final size:109
Alignment explanation
Indices: 28893--29359 Score: 538
Period size: 115 Copynumber: 4.2 Consensus size: 109
28883 ATGTTTGTTA
* * *
28893 TATGGAACGGCTTTTGGAACGGAGTTTTTAATGTTGGTTCTAAATTCCGTTCCATAGTGAAAAAT
1 TATGGAACGGATTTTGGAACGGA--TTTTAATGTTGGTTCCAAACTCCGTTCCATAGTGAAAAAT
*
28958 TTAGGTGGCAAT-AA-A-AAAA-TTGTTCAAATTTTTCTATTTTGG
64 TTAGGCGGCAATAAAGATAAAATTTGTTCAAATTTTTCTATTTTGG
* * * * * *
29000 TATGGAACGGATATGGGAACAGATCGTTAATGTTGGTACCAAATTCCGTTCCATAGTGAAAAATT
1 TATGGAACGGATTTTGGAACGGAT-TTTAATGTTGGTTCCAAACTCCGTTCCATAGTGAAAAATT
* *
29065 TAGGCGGC-----AGCTTAAAATTTGTTCAAATTTTTCTATTTGGG
65 TAGGCGGCAATAAAG-ATAAAATTTGTTCAAATTTTTCTATTTTGG
* * *
29106 TATTGAACGGATTTTTGGAATGGATTTCTAATGTTGGTTCCAAACTCTGTTCCATAGTGAAAAAT
1 TATGGAACGGA-TTTTGGAACGGATTT-TAATGTTGGTTCCAAACTCCGTTCCATAGTGAAAAAT
*
29171 TTAGGCGGCAATAAAACGAGCTTAAAATTTGTTCAATTTTTTCTATTTTGG
64 TTAGGCGGCAAT-AAA-GA---TAAAATTTGTTCAAATTTTTCTATTTTGG
* * *
29222 TTTGGAACGGCTTTTGGAACGGATTTTTAATGTTGGTTCCAAACTCCGTTCCATTGTGAAAAATT
1 TATGGAACGGATTTTGGAACGGA-TTTTAATGTTGGTTCCAAACTCCGTTCCATAGTGAAAAATT
29287 TAGGCGGCAATAAAATGAGCTTAAAATTTGTTCAAATTTTTCTATTTTGG
65 TAGGCGGCAAT-AAA-GA---TAAAATTTGTTCAAATTTTTCTATTTTGG
*
29337 TATGGAACGGCTTTTGGAACGGA
1 TATGGAACGGATTTTGGAACGGA
29360 AAACAATGCC
Statistics
Matches: 311, Mismatches: 31, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
102 1 0.00
105 5 0.02
106 77 0.25
107 71 0.23
113 1 0.00
114 1 0.00
115 117 0.38
116 38 0.12
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.37
Consensus pattern (109 bp):
TATGGAACGGATTTTGGAACGGATTTTAATGTTGGTTCCAAACTCCGTTCCATAGTGAAAAATTT
AGGCGGCAATAAAGATAAAATTTGTTCAAATTTTTCTATTTTGG
Found at i:29623 original size:118 final size:118
Alignment explanation
Indices: 29393--29631 Score: 347
Period size: 118 Copynumber: 2.0 Consensus size: 118
29383 AAACTTCACA
* * *
29393 TTTTCTAAGAACTCTCTCATTTTCTCTCTTCCTCTCTCCCATTTCCCTCTCAAGTCTCATCCTAT
1 TTTTCTAAGAACTCTCTCATTGTCACTCTTCCTCTCTCCCATTTCCCTCTCAAGGCTCATCCTAT
* **** * *
29458 CTCCCTTCCTACCATATTCTCCTACCAAATCTCCCCTTTTCTCTTTTTTTTTT
66 CTCCCTTCCTAACATATTCTCCTACCAAATCTCCCCCCCCCCCTTTTTTTTCT
*
29511 TTTTCTAAGAACTCTCTCATTGTCACTCTTCCTCTCTCCCATTTCCCTCTCAAGGCTCATCCTTT
1 TTTTCTAAGAACTCTCTCATTGTCACTCTTCCTCTCTCCCATTTCCCTCTCAAGGCTCATCCTAT
29576 CTCCCTTCAC-AACATATT-TCCTACCAAATCTCCCCCCCCCCCTTTTTTTTTCT
66 CTCCCTTC-CTAACATATTCTCCTACCAAATCTCCCCCCCCCCC-TTTTTTTTCT
29629 TTT
1 TTT
29632 CATCTTTCTT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
117 19 0.18
118 88 0.81
119 1 0.01
ACGTcount: A:0.15, C:0.38, G:0.03, T:0.44
Consensus pattern (118 bp):
TTTTCTAAGAACTCTCTCATTGTCACTCTTCCTCTCTCCCATTTCCCTCTCAAGGCTCATCCTAT
CTCCCTTCCTAACATATTCTCCTACCAAATCTCCCCCCCCCCCTTTTTTTTCT
Found at i:36115 original size:2 final size:2
Alignment explanation
Indices: 36110--36135 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36100 TATATAACGG
36110 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
36136 TCTATACGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36772 original size:2 final size:2
Alignment explanation
Indices: 36767--36801 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36757 TCCTTACTAC
36767 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36802 TAATCTACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40877 original size:14 final size:15
Alignment explanation
Indices: 40858--40887 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40848 TCTACATTGA
40858 CAAAA-TTTGAGCAG
1 CAAAATTTTGAGCAG
40872 CAAAATTTTGAGCAG
1 CAAAATTTTGAGCAG
40887 C
1 C
40888 TTATGTACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (15 bp):
CAAAATTTTGAGCAG
Found at i:40952 original size:2 final size:2
Alignment explanation
Indices: 40945--40981 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
40935 ACTATGCATA
*
40945 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40982 ATAAGTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:43616 original size:23 final size:23
Alignment explanation
Indices: 43583--43643 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
43573 GATAAAAAAA
*
43583 GCGCGGATCGCGACCTGGCCATG
1 GCGCGGGTCGCGACCTGGCCATG
43606 GCGCGGGTCGCGACCTGGCCATG
1 GCGCGGGTCGCGACCTGGCCATG
* *
43629 GCGTGGGTCGTGACC
1 GCGCGGGTCGCGACC
43644 GGCGCGCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.10, C:0.33, G:0.43, T:0.15
Consensus pattern (23 bp):
GCGCGGGTCGCGACCTGGCCATG
Found at i:43753 original size:23 final size:23
Alignment explanation
Indices: 43690--43745 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
43680 GACGCGGTTC
43690 GCGACCCGCGCCATGGCCAGATT
1 GCGACCCGCGCCATGGCCAGATT
43713 GCGACCCGCGCCATGGCCAGATT
1 GCGACCCGCGCCATGGCCAGATT
43736 GCGACCCGCG
1 GCGACCCGCG
43746 TCGCGGCCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.16, C:0.41, G:0.32, T:0.11
Consensus pattern (23 bp):
GCGACCCGCGCCATGGCCAGATT
Found at i:44095 original size:21 final size:22
Alignment explanation
Indices: 44069--44118 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
44059 ATTAGTATAA
*
44069 TATTTTTGG-GTGGCCATTGAT
1 TATTTTTGGAGGGGCCATTGAT
44090 TATTTTTGGAGGGGCCATTGAT
1 TATTTTTGGAGGGGCCATTGAT
44112 TGATTTT
1 T-ATTTT
44119 GGTGTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 9 0.35
22 12 0.46
23 5 0.19
ACGTcount: A:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (22 bp):
TATTTTTGGAGGGGCCATTGAT
Found at i:44686 original size:36 final size:36
Alignment explanation
Indices: 44646--44733 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
44636 TAGTATCCAC
44646 ATTAGTAATTAGGCATCATCATTCACATTAGTAATT
1 ATTAGTAATTAGGCATCATCATTCACATTAGTAATT
*
44682 ATTAGTAATTAGGCATCATCGTTCACATTAGTAATT
1 ATTAGTAATTAGGCATCATCATTCACATTAGTAATT
44718 ATTAGTAATTAGGCAT
1 ATTAGTAATTAGGCAT
44734 TGCATTCACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTAGTAATTAGGCATCATCATTCACATTAGTAATT
Found at i:55623 original size:2 final size:2
Alignment explanation
Indices: 55616--55658 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
55606 CATTTATTTT
* * *
55616 TA TA TA TA TT TA TT TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55658 T
1 T
55659 TTTGCATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:57747 original size:63 final size:63
Alignment explanation
Indices: 57648--57899 Score: 432
Period size: 63 Copynumber: 4.0 Consensus size: 63
57638 GGAGAGAGAT
*
57648 TTGCTGGTAAAACTTATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATA
1 TTGCTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATA
* *
57711 TTGCTGGTAAAACTCATGTACCTGGTATCAGTGGTGGCACTGTTTATGAACCAAAGCAAAATA
1 TTGCTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATA
* *
57774 TTGCTGGTAAAACTCATGTACCTGGTATTAGTGGTGGCACTATTTATGAACCAAAGCAAAATA
1 TTGCTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATA
* * *
57837 TTGCTGGTAATACTAATGTACCTGGTATTAGCGGTGGCACTGTTCATGAACCAAAGCAAAATA
1 TTGCTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATA
57900 AAGGTTCTTT
Statistics
Matches: 179, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 179 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (63 bp):
TTGCTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATA
Found at i:70728 original size:13 final size:13
Alignment explanation
Indices: 70710--70738 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
70700 AGATTTAGCC
70710 ATGTTAATATTGA
1 ATGTTAATATTGA
70723 ATGTTAATATTGA
1 ATGTTAATATTGA
70736 ATG
1 ATG
70739 CTTGGCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (13 bp):
ATGTTAATATTGA
Found at i:71023 original size:35 final size:35
Alignment explanation
Indices: 70977--71056 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
70967 TTATTTGATG
70977 GTTTGAGCATGTTTCTGATTTTGCTTTATGACTAT
1 GTTTGAGCATGTTTCTGATTTTGCTTTATGACTAT
*
71012 GTTTGAGCATGTTTCTGATTTTGCTTTGTGACTAT
1 GTTTGAGCATGTTTCTGATTTTGCTTTATGACTAT
71047 GTTTGAGCAT
1 GTTTGAGCAT
71057 ATCTAATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.16, C:0.11, G:0.23, T:0.50
Consensus pattern (35 bp):
GTTTGAGCATGTTTCTGATTTTGCTTTATGACTAT
Found at i:72228 original size:136 final size:136
Alignment explanation
Indices: 71984--72254 Score: 497
Period size: 136 Copynumber: 2.0 Consensus size: 136
71974 GGGGCTACTA
*
71984 GGAGGTGTAGTAGGTTACCATTATATGATAGGCATGCTGAAATTCCATACATTGAAAAGGAGATG
1 GGAGGCGTAGTAGGTTACCATTATATGATAGGCATGCTGAAATTCCATACATTGAAAAGGAGATG
* * *
72049 TTGTTTAGGAATGCTAATGAATTTAAGCATGTTGTTTTGTTACATGCCATTCGGACAAAAAGGCA
66 CTGTTTAGGAATGCTAATGAATTTAAGCATGTTATTCTGTTACATGCCATTCGGACAAAAAGGCA
72114 CATTAT
131 CATTAT
*
72120 GGAGGCGTAGTAGGTTCCCATTATATGATAGGCATGCTGAAATTCCATACATTGAAAAGGAGATG
1 GGAGGCGTAGTAGGTTACCATTATATGATAGGCATGCTGAAATTCCATACATTGAAAAGGAGATG
72185 CTGTTTAGGAATGCTAATGAATTTAAGCATGTTATTCTGTTACATGCCATTCGGACAAAAAGGCA
66 CTGTTTAGGAATGCTAATGAATTTAAGCATGTTATTCTGTTACATGCCATTCGGACAAAAAGGCA
72250 CATTA
131 CATTA
72255 AAGTCCAGAA
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 130 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.31
Consensus pattern (136 bp):
GGAGGCGTAGTAGGTTACCATTATATGATAGGCATGCTGAAATTCCATACATTGAAAAGGAGATG
CTGTTTAGGAATGCTAATGAATTTAAGCATGTTATTCTGTTACATGCCATTCGGACAAAAAGGCA
CATTAT
Found at i:73015 original size:25 final size:25
Alignment explanation
Indices: 72977--73091 Score: 128
Period size: 25 Copynumber: 4.7 Consensus size: 25
72967 CACAAGGTAC
72977 TCAAACTTTCTGTTTTTTATAAGCA
1 TCAAACTTTCTGTTTTTTATAAGCA
* *
73002 TCAAACTTTTTG-TTTTTATAAG-T
1 TCAAACTTTCTGTTTTTTATAAGCA
* *
73025 TTATAACTTTTTG-TTTTTATAAGCA
1 TCA-AACTTTCTGTTTTTTATAAGCA
* * *
73050 TCTAACTTTCTGTTTTTTACAAGTA
1 TCAAACTTTCTGTTTTTTATAAGCA
*
73075 TCTAACTTTCTGTTTTT
1 TCAAACTTTCTGTTTTT
73092 GGTCAATGGG
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 2 0.03
24 37 0.47
25 39 0.50
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.55
Consensus pattern (25 bp):
TCAAACTTTCTGTTTTTTATAAGCA
Found at i:73022 original size:24 final size:24
Alignment explanation
Indices: 72977--73091 Score: 124
Period size: 24 Copynumber: 4.7 Consensus size: 24
72967 CACAAGGTAC
72977 TCAAACTTTCTGTTTTTTATAAGCA
1 TCAAACTTTCTG-TTTTTATAAGCA
* *
73002 TCAAACTTTTTGTTTTTATAAG-T
1 TCAAACTTTCTGTTTTTATAAGCA
* *
73025 TTATAACTTTTTGTTTTTATAAGCA
1 TCA-AACTTTCTGTTTTTATAAGCA
* * *
73050 TCTAACTTTCTGTTTTTTACAAGTA
1 TCAAACTTTCTG-TTTTTATAAGCA
*
73075 TCTAACTTTCTGTTTTT
1 TCAAACTTTCTGTTTTT
73092 GGTCAATGGG
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.03
24 42 0.54
25 34 0.44
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.55
Consensus pattern (24 bp):
TCAAACTTTCTGTTTTTATAAGCA
Found at i:82525 original size:19 final size:18
Alignment explanation
Indices: 82492--82527 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
82482 TTTAAATAAT
82492 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
82510 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
82528 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:82535 original size:11 final size:10
Alignment explanation
Indices: 82492--82538 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
82482 TTTAAATAAT
82492 TCTTCAATGA
1 TCTTCAATGA
82502 TCTTCAA--A
1 TCTTCAATGA
*
82510 TCTTCAAATTA
1 TCTTC-AATGA
82521 TCTTCAATGA
1 TCTTCAATGA
82531 GTCTTCAA
1 -TCTTCAA
82539 ACACGAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:91608 original size:21 final size:21
Alignment explanation
Indices: 91582--91694 Score: 201
Period size: 21 Copynumber: 5.4 Consensus size: 21
91572 TGCTAGGAGA
91582 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
91603 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
91624 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
91645 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
91666 TCATTGGAGAAGGTTCCATGC
1 TCATTGGAGAAGGTTCCAAGC
91687 TCATTGGA
1 TCATTGGA
91695 ATTGCCTAAG
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
20 2 0.02
21 88 0.98
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:92600 original size:25 final size:24
Alignment explanation
Indices: 92564--92610 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
92554 TCCTTCTATT
92564 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
92587 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
92611 AATATTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:98030 original size:21 final size:21
Alignment explanation
Indices: 98004--98116 Score: 192
Period size: 21 Copynumber: 5.4 Consensus size: 21
97994 TGCTATGAGA
98004 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
98025 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
98046 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
98067 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
98088 TCACTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
98109 TCATTGGA
1 TCATTGGA
98117 ATTGCCTAAG
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
20 2 0.02
21 86 0.98
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:99818 original size:19 final size:18
Alignment explanation
Indices: 99785--99820 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
99775 TTGAAATAAT
99785 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
99803 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
99821 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:99828 original size:11 final size:10
Alignment explanation
Indices: 99785--99831 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
99775 TTGAAATAAT
99785 TCTTCAATGA
1 TCTTCAATGA
99795 TCTTCAA--A
1 TCTTCAATGA
*
99803 TCTTCAAATTA
1 TCTTC-AATGA
99814 TCTTCAATGA
1 TCTTCAATGA
99824 GTCTTCAA
1 -TCTTCAA
99832 ACACGAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:100594 original size:17 final size:18
Alignment explanation
Indices: 100554--100597 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
100544 GTGCGTATTC
100554 ATAATAAATCATAATAGA
1 ATAATAAATCATAATAGA
* * *
100572 AAAATATAT-ATAATATA
1 ATAATAAATCATAATAGA
100589 ATAATAAAT
1 ATAATAAAT
100598 TTAAATAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAATAAATCATAATAGA
Found at i:100608 original size:22 final size:23
Alignment explanation
Indices: 100556--100610 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
100546 GCGTATTCAT
100556 AATAAATCATAATAGAAAAATATA
1 AATAAAT-ATAATAGAAAAATATA
* * *
100580 TAT-AATATAATA-ATAAATTTA
1 AATAAATATAATAGAAAAATATA
100601 AATAAATATA
1 AATAAATATA
100611 TCTATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.35
22 12 0.46
23 3 0.12
24 2 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAAATATAATAGAAAAATATA
Found at i:103328 original size:274 final size:273
Alignment explanation
Indices: 102833--103358 Score: 822
Period size: 274 Copynumber: 1.9 Consensus size: 273
102823 GAAATATAAT
* * *
102833 GATTAAATTGAAAGGTGATCAAAGGTTGAGGGGTATGTTAGCGATTACATCCAAAGCAAAAAAAG
1 GATTAAATTGAAAGGTGATCAAAGGTTAAGGGATATGTTAGCAATTACATCCAAAGCAAAAAAAG
* * *
102898 ACAAAAGAAAAATAGTGGGACGGCAACCCGCTAACTCGTCACCCTCTTTCCAAATTCTAACATTC
66 ACAAAAGAAAAATAGTGGGACAGCAACCCACTAACCCGTCACCCTCTTTCCAAATTCTAACATTC
* * * *
102963 CCTCATTCTCTTTTCTTTCACTTTCTCTCTCTATTCCTCCATTTTCAAGACAATCAAGCTTTTTC
131 CCTCATTCTCTGTTCTTTCACTTTCTCTCTCTATTCCTCCATTGTAAAGACAATCAAGCTTTCTC
* *
103028 TCTATAGTCTTTCTCCACCTAATAAATACTGAAGGAAAATGTAGACTATGAATTGTGAATGTGAT
196 TCTATAGCCTTTCTCCACCCAATAAATACTGAAGGAAAATGTAGACTATGAATTGTGAATGTGAT
103093 TAATCTGGTAGCG
261 TAATCTGGTAGCG
* * ** *
103106 GATTAAATTGAAAGGTGATCTAAGGTTAAGGGATATGTTAGTAATTACAATTTAAAGCAAAAAAG
1 GATTAAATTGAAAGGTGATCAAAGGTTAAGGGATATGTTAGCAATTAC-ATCCAAAGCAAAAAAA
**
103171 GAC-AAA-AAAAATAGTGGGACAGCAACCCACTAACCCGTCACCCTCTTTCCAAATTCTCTCATT
65 GACAAAAGAAAAATAGTGGGACAGCAACCCACTAACCCGTCACCCTCTTTCCAAATTCTAACATT
103234 CCCTCATTTTCTCTGTTCTTTCACTTTCTCTCTCTATTCCTCCATTGTAAAGACAATCAAGCTTT
130 CCCTCA--TTCTCTGTTCTTTCACTTTCTCTCTCTATTCCTCCATTGTAAAGACAATCAAGCTTT
* *
103299 CTCTCTATGGCCTTTTTCCACCCAATAAATACTGAAGGAAAATGTAGACTATGAATTGTG
193 CTCTCTATAGCCTTTCTCCACCCAATAAATACTGAAGGAAAATGTAGACTATGAATTGTG
103359 GATGGAATTA
Statistics
Matches: 229, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
272 58 0.25
273 46 0.20
274 125 0.55
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (273 bp):
GATTAAATTGAAAGGTGATCAAAGGTTAAGGGATATGTTAGCAATTACATCCAAAGCAAAAAAAG
ACAAAAGAAAAATAGTGGGACAGCAACCCACTAACCCGTCACCCTCTTTCCAAATTCTAACATTC
CCTCATTCTCTGTTCTTTCACTTTCTCTCTCTATTCCTCCATTGTAAAGACAATCAAGCTTTCTC
TCTATAGCCTTTCTCCACCCAATAAATACTGAAGGAAAATGTAGACTATGAATTGTGAATGTGAT
TAATCTGGTAGCG
Found at i:106438 original size:107 final size:106
Alignment explanation
Indices: 106252--106467 Score: 389
Period size: 107 Copynumber: 2.0 Consensus size: 106
106242 TCCCAAATAC
*
106252 CCCGATTTAGAGGGGAGGAAAATGGGGGGTTTGGAGGGGTGGGGTGGACCCCTTCTTACCCCTCA
1 CCCGATTTAGAGGGGAGGAAAATGGGGGGTTTGGAGGGGTGGGCTGGACCCCTTCTTACCCCTCA
106317 TCCTTCACAAACCCTCCAACCAAACAGACAACACCCCTCAAA
66 TCCTTCACAAACCCTCCAACCAAACAGACAACA-CCCTCAAA
*
106359 CCCGATTT-GAAGGGGTGGAAAATGGGGGGTTTGGAGGGGTGGGCTGGACCCCTTCTTACCCCTC
1 CCCGATTTAG-AGGGGAGGAAAATGGGGGGTTTGGAGGGGTGGGCTGGACCCCTTCTTACCCCTC
106423 ATCCTTCACAAACCCTCCAACCAAACAGACAACACCCTCAAA
65 ATCCTTCACAAACCCTCCAACCAAACAGACAACACCCTCAAA
106465 CCC
1 CCC
106468 CTCCTAACCC
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
106 12 0.11
107 94 0.89
ACGTcount: A:0.26, C:0.31, G:0.25, T:0.18
Consensus pattern (106 bp):
CCCGATTTAGAGGGGAGGAAAATGGGGGGTTTGGAGGGGTGGGCTGGACCCCTTCTTACCCCTCA
TCCTTCACAAACCCTCCAACCAAACAGACAACACCCTCAAA
Found at i:121402 original size:17 final size:17
Alignment explanation
Indices: 121382--121417 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
121372 GACCTTCACA
* *
121382 TCTCTTTCCCCTTTTCT
1 TCTCCTTCCCCATTTCT
121399 TCTCCTTCCCCATTTCT
1 TCTCCTTCCCCATTTCT
121416 TC
1 TC
121418 ACAATGGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.53
Consensus pattern (17 bp):
TCTCCTTCCCCATTTCT
Found at i:123368 original size:23 final size:22
Alignment explanation
Indices: 123342--123384 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
123332 TTGAGAACAG
123342 TTTTT-ATA-TTTATTATTATTTT
1 TTTTTCATAGTTT-TTA-TATTTT
123364 TTTTTCATAGTTTTTATATTT
1 TTTTTCATAGTTTTTATATTT
123385 ATTTGTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 6 0.32
24 3 0.16
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTCATAGTTTTTATATTTT
Found at i:124252 original size:56 final size:56
Alignment explanation
Indices: 124185--124301 Score: 216
Period size: 56 Copynumber: 2.1 Consensus size: 56
124175 GCATCCTAAG
* *
124185 ATAATACTATGTTTTTCAATACATTGTTAGTAAAAGTGTTTCTTTTTAATTTTTAT
1 ATAATACTATGTTTTTCAATACATTATAAGTAAAAGTGTTTCTTTTTAATTTTTAT
124241 ATAATACTATGTTTTTCAATACATTATAAGTAAAAGTGTTTCTTTTTAATTTTTAT
1 ATAATACTATGTTTTTCAATACATTATAAGTAAAAGTGTTTCTTTTTAATTTTTAT
124297 ATAAT
1 ATAAT
124302 TAAAGTAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (56 bp):
ATAATACTATGTTTTTCAATACATTATAAGTAAAAGTGTTTCTTTTTAATTTTTAT
Found at i:124300 original size:31 final size:31
Alignment explanation
Indices: 124213--124305 Score: 81
Period size: 26 Copynumber: 3.2 Consensus size: 31
124203 ATACATTGTT
124213 AGTAAAAGTGTTTCTTTTTAATTTTTATATA
1 AGTAAAAGTGTTTCTTTTTAATTTTTATATA
** * ***
124244 A-TACTA-TG--T-TTTTCAATACAT-TATA
1 AGTAAAAGTGTTTCTTTTTAATTTTTATATA
124269 AGTAAAAGTGTTTCTTTTTAATTTTTATATA
1 AGTAAAAGTGTTTCTTTTTAATTTTTATATA
*
124300 ATTAAA
1 AGTAAA
124306 GTAATTCACT
Statistics
Matches: 43, Mismatches: 13, Indels: 12
0.63 0.19 0.18
Matches are distributed among these distances:
25 5 0.12
26 11 0.26
27 3 0.07
29 3 0.07
30 11 0.26
31 10 0.23
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (31 bp):
AGTAAAAGTGTTTCTTTTTAATTTTTATATA
Found at i:139179 original size:82 final size:82
Alignment explanation
Indices: 139059--139225 Score: 253
Period size: 82 Copynumber: 2.0 Consensus size: 82
139049 ATTTTAATTT
* ** * *
139059 AAATATATTGGATCATATGCAACACACATGTAAGTGTGAAAGTGAAGACTAGTTATCTAAAAAAT
1 AAATATATTGGATCACATGCAACACACATAAAAATGTGAAAGTGAAGACTAATTATCTAAAAAAT
* *
139124 ACTTGTTGATTGTCGTC
66 ACTTGTTGATTATAGTC
* *
139141 AAATATATTGGGTCACATGCAACGCACATAAAAATGTGAAAGTGAAGACTAATTATCTAAAAAAT
1 AAATATATTGGATCACATGCAACACACATAAAAATGTGAAAGTGAAGACTAATTATCTAAAAAAT
139206 ACTTGTTGATTATAGTC
66 ACTTGTTGATTATAGTC
139223 AAA
1 AAA
139226 GTTTACTTGA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (82 bp):
AAATATATTGGATCACATGCAACACACATAAAAATGTGAAAGTGAAGACTAATTATCTAAAAAAT
ACTTGTTGATTATAGTC
Found at i:148408 original size:2 final size:2
Alignment explanation
Indices: 148401--148433 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
148391 TTTCTTGCAA
148401 AT 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 AT A
148434 CACACACTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:149473 original size:21 final size:20
Alignment explanation
Indices: 149428--149484 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
149418 TTAAAAAATT
*
149428 TTAAAAAATTTATAAAGTTA
1 TTAAAAAATCTATAAAGTTA
*
149448 CTAAAAAATCTACT-AAGCTTA
1 TTAAAAAATCTA-TAAAG-TTA
*
149469 TTAAAAGATCTTATAA
1 TTAAAAAATC-TATAA
149485 GATTATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 13 0.45
21 13 0.45
22 3 0.10
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (20 bp):
TTAAAAAATCTATAAAGTTA
Found at i:149485 original size:21 final size:20
Alignment explanation
Indices: 149428--149491 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
149418 TTAAAAAATT
149428 TTAAAAAAT-TTATAAAGTTA
1 TTAAAAAATCTTAT-AAGTTA
*
149448 CTAAAAAATC-TACTAAGCTTA
1 TTAAAAAATCTTA-TAAG-TTA
*
149469 TTAAAAGATCTTATAAGATTA
1 TTAAAAAATCTTATAAG-TTA
149490 TT
1 TT
149492 TTTAAAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 13 0.36
21 21 0.58
22 2 0.06
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (20 bp):
TTAAAAAATCTTATAAGTTA
Found at i:149543 original size:24 final size:24
Alignment explanation
Indices: 149516--149564 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
149506 AAAAGGTGTT
* *
149516 AAAAAATTTATAAGATTATTAAAA
1 AAAAAACTTATAAGATTACTAAAA
*
149540 AAAAAACTTATAAGGTTACTAAAA
1 AAAAAACTTATAAGATTACTAAAA
149564 A
1 A
149565 TGCTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (24 bp):
AAAAAACTTATAAGATTACTAAAA
Found at i:149988 original size:21 final size:21
Alignment explanation
Indices: 149955--149994 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
149945 ACTTTGTACT
*
149955 AAAAATACTTATATAGTTTATA
1 AAAAAAACTTATATA-TTTATA
149977 AAAAAAAC-TATATATTTA
1 AAAAAAACTTATATATTTA
149995 CAGACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAAAAACTTATATATTTATA
Found at i:151099 original size:28 final size:29
Alignment explanation
Indices: 151068--151141 Score: 98
Period size: 28 Copynumber: 2.5 Consensus size: 29
151058 CCAAATTGCC
*
151068 AGTTCAGGGGGCAAACGTCCAAAAT-TA-A
1 AGTTTAGGGGGCAAACGT-CAAAATCTAGA
151096 AGTTTAGGGGGCAACACGTCAAAATCGTAGA
1 AGTTTAGGGGGCAA-ACGTCAAAATC-TAGA
151127 AGTTTAGGGGGCAAA
1 AGTTTAGGGGGCAAA
151142 AAGAGCATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
28 19 0.46
29 4 0.10
30 3 0.07
31 15 0.37
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.19
Consensus pattern (29 bp):
AGTTTAGGGGGCAAACGTCAAAATCTAGA
Found at i:155342 original size:21 final size:20
Alignment explanation
Indices: 155294--155342 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
155284 AAAAAAGTGT
* *
155294 TAAAAATTTTATAAGATTAT
1 TAAAAATATTATAAGATTAG
*
155314 TAAAAAATAATTATAAGGTTAG
1 T-AAAAAT-ATTATAAGATTAG
155336 TAAAAAT
1 TAAAAAT
155343 GCTTAAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
TAAAAATATTATAAGATTAG
Done.