Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011876.1 Kokia drynarioides strain JFW-HI SEQ_126873, 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: 147952
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2027 original size:25 final size:25
Alignment explanation
Indices: 1926--2081 Score: 136
Period size: 25 Copynumber: 6.2 Consensus size: 25
1916 AATCTTCCAA
* * * *
1926 AATATAGCTCTAACGAGCCTAGAAAA
1 AATATCGCTCTTACGAGCC-AGATAG
* *
1952 AATAAT-GCTCTTATGAGCCAAATAG
1 AAT-ATCGCTCTTACGAGCCAGATAG
* * * * *
1977 ATTATCACTCTCAGGAG-CAGACAG
1 AATATCGCTCTTACGAGCCAGATAG
*
2001 AATATCGCTCTTACAAGCCAGATAG
1 AATATCGCTCTTACGAGCCAGATAG
* *
2026 AATATAGCTCTTACGAGCCAGATAA
1 AATATCGCTCTTACGAGCCAGATAG
* *
2051 AATATCGCTCTTATGAGCTAGATAG
1 AATATCGCTCTTACGAGCCAGATAG
2076 AATATC
1 AATATC
2082 TTCATCGTCT
Statistics
Matches: 103, Mismatches: 24, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
24 19 0.18
25 68 0.66
26 14 0.14
27 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (25 bp):
AATATCGCTCTTACGAGCCAGATAG
Found at i:2062 original size:50 final size:50
Alignment explanation
Indices: 1926--2080 Score: 163
Period size: 49 Copynumber: 3.1 Consensus size: 50
1916 AATCTTCCAA
*
1926 AATATAGCTCTAACGAGCCTAGAAAAAATAAT-GCTCTTATGAGCCAAATAG
1 AATATAGCTCTAACGAGCC-AGAAAAAAT-ATCGCTCTTATGAGCCAGATAG
* * * * * **
1977 ATTATCA-CTCTCAGGAG-CAGACAGAATATCGCTCTTACAAGCCAGATAG
1 AATAT-AGCTCTAACGAGCCAGAAAAAATATCGCTCTTATGAGCCAGATAG
* * *
2026 AATATAGCTCTTACGAGCCAGATAAAATATCGCTCTTATGAGCTAGATAG
1 AATATAGCTCTAACGAGCCAGAAAAAATATCGCTCTTATGAGCCAGATAG
2076 AATAT
1 AATAT
2081 CTTCATCGTC
Statistics
Matches: 84, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
48 3 0.04
49 35 0.42
50 33 0.39
51 12 0.14
52 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (50 bp):
AATATAGCTCTAACGAGCCAGAAAAAATATCGCTCTTATGAGCCAGATAG
Found at i:13820 original size:24 final size:24
Alignment explanation
Indices: 13788--13843 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
13778 AGACGTAAGC
13788 TCTTCCATTAAAGAAATCACCAAG
1 TCTTCCATTAAAGAAATCACCAAG
*
13812 TCTTCCATTAAAGATATCACCAAG
1 TCTTCCATTAAAGAAATCACCAAG
13836 TCTTCCAT
1 TCTTCCAT
13844 ATCATATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (24 bp):
TCTTCCATTAAAGAAATCACCAAG
Found at i:15016 original size:16 final size:16
Alignment explanation
Indices: 14969--15018 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
14959 TACATTTTTG
*
14969 TTTAATTATTTT-TTA
1 TTTAATTTTTTTATTA
* *
14984 TCTAA-TTTTTAACTTA
1 TTTAATTTTTTTA-TTA
15000 TTTAATTTTTTTATTA
1 TTTAATTTTTTTATTA
15016 TTT
1 TTT
15019 TAGGTGTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 4 0.15
15 4 0.15
16 13 0.48
17 6 0.22
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTAATTTTTTTATTA
Found at i:19714 original size:33 final size:33
Alignment explanation
Indices: 19670--19737 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
19660 TCTGATAGAC
*
19670 ACTACTGACAGCTTAAACCGTTGAGGGAATTTT
1 ACTACTAACAGCTTAAACCGTTGAGGGAATTTT
19703 ACTACTAACAGCTTAAACCGTTGAGGGAATTTT
1 ACTACTAACAGCTTAAACCGTTGAGGGAATTTT
19736 AC
1 AC
19738 ACCGAGTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (33 bp):
ACTACTAACAGCTTAAACCGTTGAGGGAATTTT
Found at i:21129 original size:13 final size:13
Alignment explanation
Indices: 21111--21135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21101 CTTAGATTAA
21111 TTTAGATTAATAC
1 TTTAGATTAATAC
21124 TTTAGATTAATA
1 TTTAGATTAATA
21136 TCATTCATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAGATTAATAC
Found at i:22598 original size:37 final size:37
Alignment explanation
Indices: 22532--22602 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
22522 TAATGTCGCT
* *
22532 GCATGAGCACTTCTAGATTGCGCCCAAAACTGTCGTC
1 GCATGAGCACTTCAAGATTGCACCCAAAACTGTCGTC
*
22569 GCATGAGCACTTCCAAG-TTGCACCTAAAACTGTC
1 GCATGAGCACTT-CAAGATTGCACCCAAAACTGTC
22603 ATCGTAGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 27 0.90
38 3 0.10
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.24
Consensus pattern (37 bp):
GCATGAGCACTTCAAGATTGCACCCAAAACTGTCGTC
Found at i:22721 original size:37 final size:38
Alignment explanation
Indices: 22645--22724 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
22635 CCGTCACTTT
* * *
22645 ATAAATATTCTTCAAATTGCATCCAGAACTATCGCTGC
1 ATAAATATTCTTCAAATTGCACCCACAAATATCGCTGC
* * *
22683 ATAAGTATTCTTC-AATTGCACCCACAAATGTCGTTGC
1 ATAAATATTCTTCAAATTGCACCCACAAATATCGCTGC
22720 ATAAA
1 ATAAA
22725 CATGTTCAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
37 23 0.66
38 12 0.34
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (38 bp):
ATAAATATTCTTCAAATTGCACCCACAAATATCGCTGC
Found at i:26718 original size:26 final size:26
Alignment explanation
Indices: 26689--26742 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
26679 CGCCCAGGAA
*
26689 TGTCACTGCATAAACATGTCCAGAAT
1 TGTCACTGCATAAACATGTCAAGAAT
* * *
26715 TGTCGCTGCATGAACGTGTCAAGAAT
1 TGTCACTGCATAAACATGTCAAGAAT
26741 TG
1 TG
26743 CGCTCAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (26 bp):
TGTCACTGCATAAACATGTCAAGAAT
Found at i:29593 original size:21 final size:21
Alignment explanation
Indices: 29547--29594 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
29537 CAATTATTTC
**
29547 TTTTTTCTTTTTTTTTTTCTT
1 TTTTTTCTCATTTTTTTTCTT
*
29568 CTTTTTCTCATTTTTTTT-TT
1 TTTTTTCTCATTTTTTTTCTT
*
29588 GTTTTTC
1 TTTTTTC
29595 AAGTGACTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (21 bp):
TTTTTTCTCATTTTTTTTCTT
Found at i:30651 original size:12 final size:12
Alignment explanation
Indices: 30634--30667 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30624 GGCAGGTTCT
*
30634 TCTTCTTCTTTC
1 TCTTCTTATTTC
30646 TCTTCTTATTTC
1 TCTTCTTATTTC
30658 TCTTCCTTAT
1 TCTT-CTTAT
30668 CTTGATCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (12 bp):
TCTTCTTATTTC
Found at i:45124 original size:9 final size:9
Alignment explanation
Indices: 45112--45148 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
45102 TTTTCTAATT
45112 TTTAATTTA
1 TTTAATTTA
45121 TTTAATTTA
1 TTTAATTTA
*
45130 -TTAACTT-
1 TTTAATTTA
45137 TTTAATTTA
1 TTTAATTTA
45146 TTT
1 TTT
45149 TAAATTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 12 0.50
9 12 0.50
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTAATTTA
Found at i:45128 original size:16 final size:15
Alignment explanation
Indices: 45094--45144 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
45084 GGTGGTAAGA
*
45094 AATTTTT-ATTTTCT
1 AATTTTTAATTTTTT
45108 AATTTTTAATTTATTT
1 AATTTTTAATTT-TTT
*
45124 AATTTATTAACTTTTT
1 AATTT-TTAATTTTTT
45140 AATTT
1 AATTT
45145 ATTTTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.22
15 4 0.12
16 15 0.47
17 6 0.19
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTTTTAATTTTTT
Found at i:45141 original size:8 final size:7
Alignment explanation
Indices: 45094--45144 Score: 50
Period size: 8 Copynumber: 6.7 Consensus size: 7
45084 GGTGGTAAGA
45094 AATTTTT
1 AATTTTT
45101 -ATTTTCT
1 AATTTT-T
45108 AATTTTT
1 AATTTTT
45115 AATTTATTT
1 AA-TT-TTT
45124 AATTTATT
1 AATTT-TT
45132 AACTTTTT
1 AA-TTTTT
45140 AATTT
1 AATTT
45145 ATTTTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
6 5 0.13
7 8 0.21
8 17 0.45
9 8 0.21
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (7 bp):
AATTTTT
Found at i:45159 original size:26 final size:25
Alignment explanation
Indices: 45110--45159 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
45100 TATTTTCTAA
*
45110 TTTTTAATTTATTTAATTTATTAAC
1 TTTTTAATTTATTTAAATTATTAAC
*
45135 TTTTTAATTTATTTTAAATTGTTAA
1 TTTTTAATTTA-TTTAAATTATTAA
45160 TATTTTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTTAATTTATTTAAATTATTAAC
Found at i:45165 original size:26 final size:24
Alignment explanation
Indices: 45107--45166 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
45097 TTTTATTTTC
*
45107 TAATTTTTAATTTATTTAATTTAT
1 TAATTTTTAATTTATTTAAATTAT
*
45131 TAACTTTTTAATTTATTTTAAATTGT
1 TAA-TTTTTAATTTA-TTTAAATTAT
45157 TAATATTTTA
1 TAAT-TTTTA
45167 TACTAATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 3 0.10
25 12 0.39
26 16 0.52
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TAATTTTTAATTTATTTAAATTAT
Found at i:50297 original size:28 final size:28
Alignment explanation
Indices: 50265--50320 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
50255 AAATGTATTG
50265 GACTAGAGTCAAATCTAATAGGGGAATT
1 GACTAGAGTCAAATCTAATAGGGGAATT
50293 GACTAGAGTCAAATCTAATAGGGGAATT
1 GACTAGAGTCAAATCTAATAGGGGAATT
50321 CATAGAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (28 bp):
GACTAGAGTCAAATCTAATAGGGGAATT
Found at i:56946 original size:13 final size:13
Alignment explanation
Indices: 56928--56952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56918 ATTAGATTAA
56928 TTTAGATTAATAC
1 TTTAGATTAATAC
56941 TTTAGATTAATA
1 TTTAGATTAATA
56953 TCATTCACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAGATTAATAC
Found at i:59075 original size:17 final size:19
Alignment explanation
Indices: 59044--59087 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
59034 GGTGGTAAGA
59044 AATTTATTTTCTAATTT-CT
1 AATTT-TTTTCTAATTTACT
*
59063 AATTTTTTT-TAATTTATT
1 AATTTTTTTCTAATTTACT
59081 AATTTTT
1 AATTTTT
59088 AATTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
AATTTTTTTCTAATTTACT
Found at i:59083 original size:25 final size:25
Alignment explanation
Indices: 59055--59108 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
59045 ATTTATTTTC
* *
59055 TAATTTCTAATTTTTTTTAATTTAT
1 TAATTTCTAATTTATTTTAAATTAT
* *
59080 TAATTTTTAATTTATTTTAAATTGT
1 TAATTTCTAATTTATTTTAAATTAT
59105 TAAT
1 TAAT
59109 ATTTTATACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
TAATTTCTAATTTATTTTAAATTAT
Found at i:60013 original size:21 final size:21
Alignment explanation
Indices: 59987--60029 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
59977 AACAGCAAGC
59987 TGAAGAAGAAGAAGAAGATCT
1 TGAAGAAGAAGAAGAAGATCT
*
60008 TGAAGAAGAAGAGGAAGATCT
1 TGAAGAAGAAGAAGAAGATCT
60029 T
1 T
60030 TAGGTGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.30, T:0.16
Consensus pattern (21 bp):
TGAAGAAGAAGAAGAAGATCT
Found at i:70869 original size:16 final size:16
Alignment explanation
Indices: 70834--70873 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
70824 GTATTTCACT
*
70834 AAAAAGAAGAAAAGAA
1 AAAAAGAAGAAAACAA
*
70850 AAAAAGAAGAAAACTGA
1 AAAAAGAAGAAAAC-AA
70867 AAAAAGA
1 AAAAAGA
70874 TAAAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAAGAAGAAAACAA
Found at i:72269 original size:26 final size:26
Alignment explanation
Indices: 72223--72294 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
72213 TTGGATATGC
* * *
72223 TCATGCAGCAACAACTT-TGGACATGT
1 TCATGCAACGACAA-TTCTGGACAAGT
*
72249 TCATGCAACGATAATTCTGGACAAGT
1 TCATGCAACGACAATTCTGGACAAGT
*
72275 TCATGCAGCGACAATTCTGG
1 TCATGCAACGACAATTCTGG
72295 GCGCAATTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 2 0.05
26 37 0.95
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (26 bp):
TCATGCAACGACAATTCTGGACAAGT
Found at i:73188 original size:101 final size:101
Alignment explanation
Indices: 73060--73330 Score: 328
Period size: 101 Copynumber: 2.7 Consensus size: 101
73050 GATCAAAAAT
* * * * *
73060 TACAATAGTAAATCTTTATCTCCCTGAAGATGCAATGGAACAAGATGAAGTTACGTCATCAAATC
1 TACAATAGCAAATCTTTATCTCCCTGAAGTTGCAATGGAGCAAGATGAAGCTACGACATCAAATC
* * * * * *
73125 CTATACCCCTGAAGTTGTAGTGGGTTGGATTGACAC
66 CTATACCCCTGAAGTTGCAATAGGTCGAATTGAAAC
* * * * * *
73161 TACAATGGGAAATCTTTATCTCTCTGAAGTTGCAATAGAGCAAGATGAAGCTACAACACCAAATC
1 TACAATAGCAAATCTTTATCTCCCTGAAGTTGCAATGGAGCAAGATGAAGCTACGACATCAAATC
* *
73226 TTATACCCTTGAAGTTGCAATAGGTCGAATTGAAAC
66 CTATACCCCTGAAGTTGCAATAGGTCGAATTGAAAC
* * *
73262 TATAGA-AGCAAATCTTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACGACATAAAAT
1 TACA-ATAGCAAATCTTTATCTCCCTGAAGTTGCAATGGAGCAAGATGAAGCTACGACATCAAAT
73326 CCTAT
65 CCTAT
73331 TTCTCTCTAA
Statistics
Matches: 141, Mismatches: 28, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
101 140 0.99
102 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (101 bp):
TACAATAGCAAATCTTTATCTCCCTGAAGTTGCAATGGAGCAAGATGAAGCTACGACATCAAATC
CTATACCCCTGAAGTTGCAATAGGTCGAATTGAAAC
Found at i:73247 original size:50 final size:50
Alignment explanation
Indices: 73185--73395 Score: 178
Period size: 52 Copynumber: 4.2 Consensus size: 50
73175 TTTATCTCTC
* *
73185 TGAAGTTGCAATAGAGCAAGATGAAGCTACAACACCAAATCTTATACCCT
1 TGAAGTTGCAATAGAGCAAGATGAAGCTACAACATCAAATCCTATACCCT
* * * * * *
73235 TGAAGTTGCAATAG-GTCGAA-TTGAAACTATAGA-AGCAAAT-CTTTATCTCCC
1 TGAAGTTGCAATAGAG-C-AAGATGAAGCTACA-ACATCAAATCCTATA-C-CCT
* * * * * *
73286 TGAAGTTGCAGTGGAGCAAGATGAAGCTACGACATAAAATCCTATTTCTCT
1 TGAAGTTGCAATAGAGCAAGATGAAGCTACAACATCAAATCCTA-TACCCT
* * *
73337 CTAAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATACCTT
1 -TGAAGTTGCAATAGAGCAAGATGAAGCTACAACATCAAATCCTATACCCT
73388 TGAAGTTG
1 TGAAGTTG
73396 TAGTGGGTCA
Statistics
Matches: 123, Mismatches: 27, Indels: 22
0.72 0.16 0.13
Matches are distributed among these distances:
49 4 0.03
50 40 0.33
51 34 0.28
52 44 0.36
53 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (50 bp):
TGAAGTTGCAATAGAGCAAGATGAAGCTACAACATCAAATCCTATACCCT
Found at i:73366 original size:153 final size:150
Alignment explanation
Indices: 73179--73497 Score: 392
Period size: 153 Copynumber: 2.1 Consensus size: 150
73169 GAAATCTTTA
* * *
73179 TCTCTCTGAAGTTGCAATAGAGCAAGATGAAGCTACAACACCAAATCTTATACCCTTGAAGTTGC
1 TCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTACAACACCAAATCCTATACCCTTGAAGTTGC
* * * ***
73244 AATAGGTC-GAATTGAAACTATAGAAGCAAATCTTTATCTCCCTGAAGTTGCAGTGGAGCAAGAT
66 AATAGGTCAG-ATTGAAACTATAGAAGCAAAT-ATTATCTCCCTAAAGATGCAACAGAGCAAGAT
* *
73308 GAAGCTACGACATAAAATCCTATT
129 GAAG-T-CGACATAAAATCCCATG
* * *
73332 TCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATACCTTTGAAGTTGT
1 TCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTACAACACCAAATCCTATACCCTTGAAGTTGC
* * * ** *
73397 AGTGGGTCAGATTGGAGTTATAGAAGCAAATATTATCTCCTTAAAGATGCAACAGAGCAAGATGA
66 AATAGGTCAGATTGAAACTATAGAAGCAAATATTATCTCCCTAAAGATGCAACAGAGCAAGATGA
*
73462 AGTCGACATCAAATCCCATG
131 AGTCGACATAAAATCCCATG
73482 TC-C-CTAAAGTTGCAGT
1 TCTCTCTAAAGTTGCAGT
73498 GGACCAGATT
Statistics
Matches: 144, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
148 13 0.09
149 1 0.01
150 16 0.11
151 1 0.01
152 29 0.20
153 83 0.58
154 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (150 bp):
TCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTACAACACCAAATCCTATACCCTTGAAGTTGC
AATAGGTCAGATTGAAACTATAGAAGCAAATATTATCTCCCTAAAGATGCAACAGAGCAAGATGA
AGTCGACATAAAATCCCATG
Found at i:73540 original size:148 final size:152
Alignment explanation
Indices: 73179--73548 Score: 360
Period size: 153 Copynumber: 2.4 Consensus size: 152
73169 GAAATCTTTA
* * * ** * * *
73179 TCTCTCTGAAGTTGCAATAGAGCAAGATGAAGCTACAACACCAAATCTTATACCCTTGAAGTTGC
1 TCTCTCTAAAGTTGCAGTAGAGCAAGATAAAAATACAACATCAAATCCTATA-CTTTGAAGTTGC
* * * ** * * * ***
73244 AATAGGTC-GAATTGAAACTATAGAAGCAAATCTTTATCTCCCTGAAGTTGCAGTGGAGCAAGAT
65 AGTGGGTCAG-ATTGGAGTTATAGAAGCAAATCATTATCTCCCTAAAGATGCAACAGAGCAAGAT
* *
73308 GAAGCTACGACATAAAATCCTATT
129 GAAGCTACGACATAAAATCCCATG
* ** *
73332 TCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATACCTTTGAAGTTGT
1 TCTCTCTAAAGTTGCAGTAGAGCAAGATAAAAATACAACATCAAATCCTATA-CTTTGAAGTTGC
*
73397 AGTGGGTCAGATTGGAGTTATAGAAGCAAAT-ATTATCTCCTTAAAGATGCAACAGAGCAAGATG
65 AGTGGGTCAGATTGGAGTTATAGAAGCAAATCATTATCTCCCTAAAGATGCAACAGAGCAAGATG
*
73461 AAG-T-CGACATCAAATCCCATG
130 AAGCTACGACATAAAATCCCATG
* * *
73482 TC-C-CTAAAGTTGCAGTGGA-CCAGATTAAAAATACAATATCAAATCCTAT-CTTCCTGAAGTT
1 TCTCTCTAAAGTTGCAGTAGAGCAAGA-TAAAAATACAACATCAAATCCTATACTT--TGAAGTT
73543 GCAGTG
63 GCAGTG
73549 AAGCAGATAA
Statistics
Matches: 185, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
146 3 0.02
147 4 0.02
148 47 0.25
149 1 0.01
150 16 0.09
151 1 0.01
152 29 0.16
153 83 0.45
154 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (152 bp):
TCTCTCTAAAGTTGCAGTAGAGCAAGATAAAAATACAACATCAAATCCTATACTTTGAAGTTGCA
GTGGGTCAGATTGGAGTTATAGAAGCAAATCATTATCTCCCTAAAGATGCAACAGAGCAAGATGA
AGCTACGACATAAAATCCCATG
Found at i:73945 original size:18 final size:18
Alignment explanation
Indices: 73907--73955 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
73897 TCCATTAGTC
* **
73907 CAAATTACAAATGAATTA
1 CAAATTACAAATAAAAAA
73925 CAAATTACAAATAAAAAA
1 CAAATTACAAATAAAAAA
73943 C-AATTACAAATAA
1 CAAATTACAAATAA
73956 CCCAATACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.22
Consensus pattern (18 bp):
CAAATTACAAATAAAAAA
Found at i:76244 original size:17 final size:18
Alignment explanation
Indices: 76201--76253 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
76191 GTTTCGACAA
*
76201 AATATTTTTTATTTTTTC
1 AATAATTTTTATTTTTTC
* *
76219 AAGAGTTTTTATTTTTT-
1 AATAATTTTTATTTTTTC
76236 AATAATTTTTATATTTTT
1 AATAATTTTTAT-TTTTT
76254 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 10 0.33
18 20 0.67
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (18 bp):
AATAATTTTTATTTTTTC
Found at i:78188 original size:21 final size:19
Alignment explanation
Indices: 78164--78202 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
78154 TTTAAAACGA
78164 TTTTAAATTCTCTCTAAAGTG
1 TTTT-AATTCTC-CTAAAGTG
*
78185 TTTTAATTGTCCTAAAGT
1 TTTTAATTCTCCTAAAGT
78203 TAGATCACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (19 bp):
TTTTAATTCTCCTAAAGTG
Found at i:82072 original size:22 final size:22
Alignment explanation
Indices: 82040--82107 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
82030 TTTGACAAGC
*
82040 TTAATCATGTATACATAAGTCA
1 TTAATTATGTATACATAAGTCA
* *
82062 TTAATTGTGTAT-CACTAAGTTA
1 TTAATTATGTATACA-TAAGTCA
*
82084 TTTGATTATGTATACATAAGTCA
1 -TTAATTATGTATACATAAGTCA
82107 T
1 T
82108 CTCAATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.05
22 17 0.46
23 16 0.43
24 2 0.05
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (22 bp):
TTAATTATGTATACATAAGTCA
Found at i:82787 original size:198 final size:197
Alignment explanation
Indices: 82532--82907 Score: 594
Period size: 198 Copynumber: 1.9 Consensus size: 197
82522 GATTATAGTC
* *
82532 ATATAAAGCTCATTTCCTATTTTATCTTGTGCAATTTTTGGTGATTTTTCAAAGTCACTGCTAAA
1 ATATAAAGCTCACTTCCTATTTTATCTTGTGCAATTTTTCGTGATTTTTCAAAGTCACTGCTAAA
* * * *
82597 TCTGTTTTATAAGAATTCTGTTGCCAGATTTTTATGATCTTTTAACAATT-AAAAATTCATATAT
66 TATGTTTTATAAGAATTCTGCTGCCAGATTTTTATGACCTTTCAA-AATTCAAAAATTCATATAT
* * * *
82661 TTTAAACTACATATAGAAATCAATCTCCGTTTGTTCTAACTGAAACTAGAATTCAATAATGTTGT
130 TTTAAACTA-AAATAGAAACCAATCTCCATTTGTTCTAAATGAAACTAGAATTCAATAATGTTGT
82726 AGGG
194 AGGG
*
82730 ATAT-AAGACTCACTTCCTATTTTGTCTTGTGCAATTTTTCGTGATTTTTCAAAGTCACTGCTAA
1 ATATAAAG-CTCACTTCCTATTTTATCTTGTGCAATTTTTCGTGATTTTTCAAAGTCACTGCTAA
* *
82794 ATATGTTTTATAAGAATTCTGCTGCTAGATTTTTATGACCTTTCAATATTCAAAAATTCATATAT
65 ATATGTTTTATAAGAATTCTGCTGCCAGATTTTTATGACCTTTCAAAATTCAAAAATTCATATAT
82859 TTTAAACTAAAATAGAAACCAATCTCCATTTGTTCTAAATGAAACTAGA
130 TTTAAACTAAAATAGAAACCAATCTCCATTTGTTCTAAATGAAACTAGA
82908 CTGACTCATG
Statistics
Matches: 163, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
197 42 0.26
198 121 0.74
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (197 bp):
ATATAAAGCTCACTTCCTATTTTATCTTGTGCAATTTTTCGTGATTTTTCAAAGTCACTGCTAAA
TATGTTTTATAAGAATTCTGCTGCCAGATTTTTATGACCTTTCAAAATTCAAAAATTCATATATT
TTAAACTAAAATAGAAACCAATCTCCATTTGTTCTAAATGAAACTAGAATTCAATAATGTTGTAG
GG
Found at i:87871 original size:100 final size:101
Alignment explanation
Indices: 87736--88487 Score: 366
Period size: 102 Copynumber: 7.5 Consensus size: 101
87726 GACCCACTAT
* * * * *
87736 AACTTCAAGGGTATAGGATTTGGTATGGTAGCTTCA-TCT-TGCTCTACTACAACTACAGAGAGA
1 AACTTCAAGGATATAGGATTTGGT-TTGTAACTTCACTCTAT--TCCACTACAACTACAAAGAGA
*** * ** *
87799 TAAAGATTTGCTACTG-TAGCTTTATTTTGATCC-TTGC
63 TAAAGACCCGCTACTGTTAGCTTTAATAAGATCCACTGC
* * *
87836 AACTTCAAGGATATAGGATTTAGGTTTGTAACTTCACTCTATTCCACTGCAACTTCAAAGAGATT
1 AACTTCAAGGATATAGGATTT-GGTTTGTAACTTCACTCTATTCCACTACAACTACAAAGAGATA
*
87901 GAGACCCGCTACTGTTAGCTTTAATAAGATCCACTGC
65 AAGACCCGCTACTGTTAGCTTTAATAAGATCCACTGC
* * * * * ** *
87938 AATTTCAAGGATACAGGATTTGGGTTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATT
1 AACTTCAAGGATATAGGATTT-GGTTTGTAACTTCACTCTATTCCACTACAACTACAAAGAGATA
* * ** * * * * * *
88003 GAGATCTACTATTTTTAGTTTTAATCCA-ATCTACTGT
65 AAGACCCGCTACTGTTAGCTTTAAT-AAGATCCACTGC
* * ** ** * *
88040 AACTTCAGGGATATAAGATTTGGTGTTGTGGCTTCACTGC-ATTCCACTGTAACTTCAAGGAGAT
1 AACTTCAAGGATATAGGATTTGGT-TTGTAACTTCACT-CTATTCCACTACAACTACAAAGAGAT
** *** * * *
88104 TGAGATTTGCTACTGTTAGTTTTAATCTA-ATCCACTAC
64 AAAGACCCGCTACTGTTAGCTTTAAT-AAGATCCACTGC
* ** * * * * *
88142 AACTTCAGGGATATAGGATTTGGTGTTGTGGCTTCATTCCATTCCACTGCAGCTTCAGAA-AGAT
1 AACTTCAAGGATATAGGATTTGGT-TTGTAACTTCACTCTATTCCACTACAACTACA-AAGAGAT
** ** * * **
88206 TGAGATTCACTACTGTTAGTTTTAATCTGATCCACTGC
64 AAAGACCCGCTACTGTTAGCTTTAATAAGATCCACTGC
* * * * * * ** * *
88244 AACTTTAGGGATATAGGATTTGATGTTGTAACTTTACTCTACTCCACTGCAACTTTAAGGAGATT
1 AACTTCAAGGATATAGGATTTGGT-TTGTAACTTCACTCTATTCCACTACAACTACAAAGAGATA
* * * * * **
88309 GAGATCTGCTACTATTAGTTTTAATCTGATCCACTG-
65 AAGACCCGCTACTGTTAGCTTTAATAAGATCCACTGC
* * * * ** *
88345 ----T--A-GATATAGGATTTGGTGTTGTAACTTCACTCAATTACACTGCAACTTCAGGGAGATT
1 AACTTCAAGGATATAGGATTTGGT-TTGTAACTTCACTCTATTCCACTACAACTACAAAGAGATA
* * * * ** *
88403 GAGATCCGCTACTTTTAGTTTTAATCCGATCAACTGC
65 AAGACCCGCTACTGTTAGCTTTAATAAGATCCACTGC
* * *
88440 AACTTTAAGGATATAGAATTTGGTGTTGTAACTTCACTCCATTCCACT
1 AACTTCAAGGATATAGGATTTGGT-TTGTAACTTCACTCTATTCCACT
88488 GTAACATTAG
Statistics
Matches: 545, Mismatches: 87, Indels: 38
0.81 0.13 0.06
Matches are distributed among these distances:
94 81 0.15
97 1 0.00
99 1 0.00
100 57 0.10
101 26 0.05
102 376 0.69
103 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (101 bp):
AACTTCAAGGATATAGGATTTGGTTTGTAACTTCACTCTATTCCACTACAACTACAAAGAGATAA
AGACCCGCTACTGTTAGCTTTAATAAGATCCACTGC
Found at i:87956 original size:102 final size:102
Alignment explanation
Indices: 87833--88520 Score: 729
Period size: 102 Copynumber: 6.8 Consensus size: 102
87823 TTTTGATCCT
* *
87833 TGCAACTTCAAGGATATAGGATTTAGGT-TTGTAACTTCACTCTATTCCACTGCAACTTCAAAGA
1 TGCAACTTCAAGGATATAGGATTT-GGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAAGGA
* * *
87897 GATTGAGACCCGCTACTGTTAGCTTTAATAAGATCCAC
65 GATTGAGATCCGCTACTGTTAGTTTTAATCAGATCCAC
* * *
87935 TGCAATTTCAAGGATACAGGATTTGG-GTTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGA
1 TGCAACTTCAAGGATATAGGATTTGGTG-TTGTAACTTCACTCCATTCCACTGCAACTTCAAGGA
** * * *
87999 GATTGAGATCTACTATTTTTAGTTTTAATCCA-ATCTAC
65 GATTGAGATCCGCTACTGTTAGTTTTAAT-CAGATCCAC
* * * ** * *
88037 TGTAACTTCAGGGATATAAGATTTGGTGTTGTGGCTTCACTGCATTCCACTGTAACTTCAAGGAG
1 TGCAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAAGGAG
**
88102 ATTGAGATTTGCTACTGTTAGTTTTAATCTA-ATCCAC
66 ATTGAGATCCGCTACTGTTAGTTTTAATC-AGATCCAC
* * ** * * *
88139 TACAACTTCAGGGATATAGGATTTGGTGTTGTGGCTTCATTCCATTCCACTGCAGCTTC-AGAAA
1 TGCAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAAG-GA
* * *
88203 GATTGAGATTCACTACTGTTAGTTTTAATCTGATCCAC
65 GATTGAGATCCGCTACTGTTAGTTTTAATCAGATCCAC
* * * * * * *
88241 TGCAACTTTAGGGATATAGGATTTGATGTTGTAACTTTACTCTACTCCACTGCAACTTTAAGGAG
1 TGCAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAAGGAG
* * *
88306 ATTGAGATCTGCTACTATTAGTTTTAATCTGATCCAC
66 ATTGAGATCCGCTACTGTTAGTTTTAATCAGATCCAC
* * *
88343 TG-----T--A-GATATAGGATTTGGTGTTGTAACTTCACTCAATTACACTGCAACTTCAGGGAG
1 TGCAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAAGGAG
* * *
88400 ATTGAGATCCGCTACTTTTAGTTTTAATCCGATCAAC
66 ATTGAGATCCGCTACTGTTAGTTTTAATCAGATCCAC
* * * *
88437 TGCAACTTTAAGGATATAGAATTTGGTGTTGTAACTTCACTCCATTCCACTGTAACATT-AGGGA
1 TGCAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAAC-TTCAAGGA
* * *
88501 GATTAAGATCAGCTATTGTT
65 GATTGAGATCCGCTACTGTT
88521 TTACTCCATT
Statistics
Matches: 494, Mismatches: 75, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
94 81 0.16
97 1 0.00
99 1 0.00
101 6 0.01
102 399 0.81
103 6 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (102 bp):
TGCAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAAGGAG
ATTGAGATCCGCTACTGTTAGTTTTAATCAGATCCAC
Found at i:88095 original size:50 final size:49
Alignment explanation
Indices: 88035--88199 Score: 134
Period size: 50 Copynumber: 3.3 Consensus size: 49
88025 AATCCAATCT
* *
88035 ACTGTAACTTCAGGGATATAAGATTTGGTGTTGTGGCTTCACTGCATTCC
1 ACTGCAACTTCAGGGATATAAGATTTGGTGTTGTGGCTTCAAT-CATTCC
* * * ** * * * *
88085 ACTGTAACTTCAAGGAGAT-TGAGATTTGCTACTGTTAGTTTTAATCTAATCC
1 ACTGCAACTTC-AGG-GATATAAGATTTGGTGTTG-TGGCTTCAATC-ATTCC
* * *
88137 ACTACAACTTCAGGGATATAGGATTTGGTGTTGTGGCTTCATTCCATTCC
1 ACTGCAACTTCAGGGATATAAGATTTGGTGTTGTGGCTTCAAT-CATTCC
*
88187 ACTGCAGCTTCAG
1 ACTGCAACTTCAG
88200 AAAGATTGAG
Statistics
Matches: 86, Mismatches: 23, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
50 35 0.41
51 29 0.34
52 22 0.26
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (49 bp):
ACTGCAACTTCAGGGATATAAGATTTGGTGTTGTGGCTTCAATCATTCC
Found at i:89134 original size:20 final size:20
Alignment explanation
Indices: 89108--89225 Score: 119
Period size: 20 Copynumber: 5.9 Consensus size: 20
89098 GAAAAGATTA
*
89108 AAAAAATAGCAAACATTGGT
1 AAAAAATGGCAAACATTGGT
* **
89128 CAAAAATTCCAAACATTGGT
1 AAAAAATGGCAAACATTGGT
* * * *
89148 CAATAATTGCAAATATTGGT
1 AAAAAATGGCAAACATTGGT
* *
89168 AAAAAATGGAAAACATTTGT
1 AAAAAATGGCAAACATTGGT
**
89188 AAAAAATGGCAAATGTTGGT
1 AAAAAATGGCAAACATTGGT
*
89208 AAGAAATGGCAAACATTG
1 AAAAAATGGCAAACATTG
89226 ATTAAGAATT
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (20 bp):
AAAAAATGGCAAACATTGGT
Found at i:95103 original size:21 final size:21
Alignment explanation
Indices: 95058--95103 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
95048 TTAAAAGAGC
*
95058 TTAATTAAATAAATAAAGGAC
1 TTAATTAAATAAATAAAGGAA
95079 TTAATTAAAACTAAA-AAA-GAA
1 TTAATT-AAA-TAAATAAAGGAA
95100 TTAA
1 TTAA
95104 AGGTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 12 0.55
22 6 0.27
23 4 0.18
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (21 bp):
TTAATTAAATAAATAAAGGAA
Found at i:95135 original size:25 final size:25
Alignment explanation
Indices: 95081--95136 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
95071 TAAAGGACTT
95081 AATTAAAACTAAAAAAGAATTAAAG
1 AATTAAAACTAAAAAAGAATTAAAG
* *
95106 -GTTAAAATTAGAAAAAGAA-TAAAG
1 AATTAAAACTA-AAAAAGAATTAAAG
95130 AATTAAA
1 AATTAAA
95137 TTAATCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.21
Consensus pattern (25 bp):
AATTAAAACTAAAAAAGAATTAAAG
Found at i:96245 original size:23 final size:24
Alignment explanation
Indices: 96214--96258 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
96204 GGCCTTTAGA
96214 TTGGGTTA-GGTAATTGGGTTATT
1 TTGGGTTAGGGTAATTGGGTTATT
*
96237 TTGGTTTAGGGTAATTGGGTTA
1 TTGGGTTAGGGTAATTGGGTTA
96259 ATTGTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.47
Consensus pattern (24 bp):
TTGGGTTAGGGTAATTGGGTTATT
Found at i:98699 original size:20 final size:20
Alignment explanation
Indices: 98654--98702 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
98644 TAATAGAAAA
98654 TATAAAAAAATATTAATAAT
1 TATAAAAAAATATTAATAAT
*
98674 TGTAAAAAAAT-TATAA-AAT
1 TATAAAAAAATAT-TAATAAT
98693 GTATAAAAAA
1 -TATAAAAAA
98703 GATCCTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
TATAAAAAAATATTAATAAT
Found at i:101101 original size:20 final size:19
Alignment explanation
Indices: 101063--101105 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
101053 ACTAGGAACT
101063 AATTTGAAAACAATTAGAA
1 AATTTGAAAACAATTAGAA
101082 AATTTGAGAAA-AAGTTAGAA
1 AATTTGA-AAACAA-TTAGAA
101102 AATT
1 AATT
101106 ATATGTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (19 bp):
AATTTGAAAACAATTAGAA
Found at i:103670 original size:22 final size:21
Alignment explanation
Indices: 103645--103696 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
103635 TTTTCACACA
103645 AATTTCT-TCTAATTTCTTCTAT
1 AATTTCTCTCTAA-TT-TTCTAT
*
103667 AATTTTCTCTTTAATTTTCTAT
1 AA-TTTCTCTCTAATTTTCTAT
103689 AATTTCTC
1 AATTTCTC
103697 ACTTAATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.22
22 10 0.37
23 7 0.26
24 4 0.15
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTCTCTCTAATTTTCTAT
Found at i:103702 original size:22 final size:22
Alignment explanation
Indices: 103661--103704 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
103651 TTCTAATTTC
*
103661 TTCTATAATTTTCTCTTTAATT
1 TTCTATAATTTTCTCCTTAATT
103683 TTCTATAA-TTTCTCACTTAATT
1 TTCTATAATTTTCTC-CTTAATT
103705 CTCAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (22 bp):
TTCTATAATTTTCTCCTTAATT
Found at i:103938 original size:32 final size:32
Alignment explanation
Indices: 103876--103941 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
103866 GTAAGAATTA
* *
103876 ATTTCATTTTTTTAATATTTTTAAATATTTTT
1 ATTTCATTTTTATAATATTATTAAATATTTTT
103908 ATTTCATTTTTATAAT-TTAATT-AATAATTTTT
1 ATTTCATTTTTATAATATT-ATTAAAT-ATTTTT
103940 AT
1 AT
103942 AATTTGTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 25 0.83
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (32 bp):
ATTTCATTTTTATAATATTATTAAATATTTTT
Found at i:114184 original size:12 final size:12
Alignment explanation
Indices: 114169--114207 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
114159 ACAATTCATA
114169 TCACTTTCAATT
1 TCACTTTCAATT
*
114181 TCACTTTCACTT
1 TCACTTTCAATT
114193 TCACTTTCAATT
1 TCACTTTCAATT
114205 TCA
1 TCA
114208 ATTTTTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:114188 original size:6 final size:6
Alignment explanation
Indices: 114169--114207 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
114159 ACAATTCATA
* *
114169 TCACTT TCAATT TCACTT TCACTT TCACTT TCAATT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
114208 ATTTTTATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:114208 original size:6 final size:6
Alignment explanation
Indices: 114150--114211 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
114140 TAATAGGGAT
* * * * *
114150 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAC TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
114197 TTTCAA TTTCAA TTT
1 TTTCAA TTTCAA TTT
114212 TTATCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 40 0.85
7 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:117630 original size:12 final size:12
Alignment explanation
Indices: 117615--117653 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
117605 ACAATTCATA
117615 TCACTTTCAATT
1 TCACTTTCAATT
*
117627 TCACTTTCACTT
1 TCACTTTCAATT
117639 TCACTTTCAATT
1 TCACTTTCAATT
117651 TCA
1 TCA
117654 ATTTTTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:117634 original size:6 final size:6
Alignment explanation
Indices: 117615--117653 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
117605 ACAATTCATA
* *
117615 TCACTT TCAATT TCACTT TCACTT TCACTT TCAATT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
117654 ATTTTTATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:117654 original size:6 final size:6
Alignment explanation
Indices: 117596--117657 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
117586 TAATAGGGAT
* * * * *
117596 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAC TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
117643 TTTCAA TTTCAA TTT
1 TTTCAA TTTCAA TTT
117658 TTATCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 40 0.85
7 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:121353 original size:12 final size:12
Alignment explanation
Indices: 121336--121364 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
121326 AACTCTTTAC
121336 TTAATCCCGACT
1 TTAATCCCGACT
121348 TTAATCCCGACT
1 TTAATCCCGACT
121360 TTAAT
1 TTAAT
121365 ATCCACAATC
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:0.28, C:0.28, G:0.07, T:0.38
Consensus pattern (12 bp):
TTAATCCCGACT
Found at i:145174 original size:27 final size:28
Alignment explanation
Indices: 145144--145250 Score: 119
Period size: 28 Copynumber: 3.8 Consensus size: 28
145134 AAACAAAATT
145144 CATCTCATCAAAATT-TTTTTT-AGAAC
1 CATCTCATCAAAATTATTTTTTCAGAAC
* *
145170 ACATCACATCAAATTTATTTTTTCAGAAC
1 -CATCTCATCAAAATTATTTTTTCAGAAC
*
145199 CCTCTCATCAAAATTATTTTTTCAGAATC
1 CATCTCATCAAAATTATTTTTTCAGAA-C
* ** *
145228 CATTTTGTTAAAATTATTTTTTC
1 CATCTCATCAAAATTATTTTTTC
145251 CCAAAACAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
27 13 0.19
28 30 0.45
29 24 0.36
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.45
Consensus pattern (28 bp):
CATCTCATCAAAATTATTTTTTCAGAAC
Found at i:146601 original size:31 final size:30
Alignment explanation
Indices: 146559--146632 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
146549 CTTAACAAGC
*
146559 TAGTGACTAAATAAAAACTTTTAAATAATT
1 TAGTGACTAAATAAAAACTTTCAAATAATT
* * * *
146589 TAGTGACTTAAATGAAAAGTTTCGAATAGTT
1 TAGTGAC-TAAATAAAAACTTTCAAATAATT
*
146620 TAGTGACCAAATA
1 TAGTGACTAAATA
146633 GTAATTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 11 0.31
31 25 0.69
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.34
Consensus pattern (30 bp):
TAGTGACTAAATAAAAACTTTCAAATAATT
Found at i:147180 original size:88 final size:88
Alignment explanation
Indices: 147073--147278 Score: 270
Period size: 89 Copynumber: 2.3 Consensus size: 88
147063 TTAAGGGTGT
* * * *
147073 AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAACTCATGCAATTTTTT-CACTCAATTGGG
1 AAAAAGCCCTCAAACTTTTTCAAAAAAAACAATTAAACCCATACAATTTTTTGCACTCAATTGGA
*
147137 TACTTGAACTACCAAAATGCATA
66 TACTTGAAATACCAAAATGCATA
* * *
147160 AAAAAGACCTTCAAACTTTTTCAAAAAAAACAATTAAACCCCTACATTTTTTTGCACTCAATTGG
1 AAAAAG-CCCTCAAACTTTTTCAAAAAAAACAATTAAACCCATACAATTTTTTGCACTCAATTGG
**
147225 ATACTTGAAATTTCAAAATGCATCA
65 ATACTTGAAATACCAAAATGCAT-A
* * *
147250 AAAAGGCCCTCAAACTTATTAAAAAAAAA
1 AAAAAGCCCTCAAACTTTTTCAAAAAAAA
147279 AAAAAGCAAT
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
87 6 0.06
88 40 0.39
89 50 0.49
90 6 0.06
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (88 bp):
AAAAAGCCCTCAAACTTTTTCAAAAAAAACAATTAAACCCATACAATTTTTTGCACTCAATTGGA
TACTTGAAATACCAAAATGCATA
Found at i:147470 original size:13 final size:14
Alignment explanation
Indices: 147454--147485 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
147444 CTTAAAATTT
147454 AAAATTAAAAG-CC
1 AAAATTAAAAGTCC
147467 AAAATTAAAAGTCC
1 AAAATTAAAAGTCC
147481 AAAAT
1 AAAAT
147486 AATTACAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAATTAAAAGTCC
Done.