Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006946.1 Hibiscus syriacus cultivar Beakdansim tig00017851_pilon, 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: 83210
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1001 original size:28 final size:28
Alignment explanation
Indices: 961--1018 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
951 ATTTTCACCT
961 AACTAAATTGATGTAAGCAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
*
989 AACTAAATTGATGTAAGTAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
1017 AA
1 AA
1019 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (28 bp):
AACTAAATTGATGTAAGCAATGACATCA
Found at i:6490 original size:11 final size:11
Alignment explanation
Indices: 6474--6500 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6464 AAATTAAATG
6474 AATAAAATAAA
1 AATAAAATAAA
6485 AATAAAATAAA
1 AATAAAATAAA
6496 AATAA
1 AATAA
6501 TAAAAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:6716 original size:34 final size:34
Alignment explanation
Indices: 6609--6741 Score: 121
Period size: 34 Copynumber: 3.8 Consensus size: 34
6599 TATTATATAG
*
6609 TTTTCAAAATAATTTTAAAAATAT-TATATAAG--
1 TTTTCAAAA-AAATTTAAAAATATATATATAAGTT
** *
6641 TTTTCGAAAAATGTTTTTAAAACTATATATAT-AGTT
1 TTTTC-AAAAA--AATTTAAAAATATATATATAAGTT
*
6677 TTTTCAAAAAAATTTAAAATTATATATATAAGTT
1 TTTTCAAAAAAATTTAAAAATATATATATAAGTT
6711 TTTTCAAAAAAATATTTTAAAAACTATATAT
1 TTTTC-AAAAAA-A-TTTAAAAA-TATATAT
6742 TATATATATA
Statistics
Matches: 84, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
32 6 0.07
33 20 0.24
34 22 0.26
35 16 0.19
36 6 0.07
37 7 0.08
38 7 0.08
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (34 bp):
TTTTCAAAAAAATTTAAAAATATATATATAAGTT
Found at i:6790 original size:33 final size:35
Alignment explanation
Indices: 6742--6822 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 35
6732 AACTATATAT
6742 TATATA-TATAT-TTTCAAAATG-A-TTTC-AAAAC
1 TATATATTATATATTTCAAAA-GCATTTTCAAAAAC
6773 TATATATTATATATTTCAAAAGCATTTTCAAAAAC
1 TATATATTATATATTTCAAAAGCATTTTCAAAAAC
*
6808 TATACATTATATATT
1 TATATATTATATATT
6823 ATTATGTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
31 6 0.14
32 6 0.14
33 9 0.20
34 4 0.09
35 19 0.43
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (35 bp):
TATATATTATATATTTCAAAAGCATTTTCAAAAAC
Found at i:6844 original size:42 final size:40
Alignment explanation
Indices: 6773--6870 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 40
6763 ATTTCAAAAC
*
6773 TATATATTATATATTTCAAAAGCATTTTCAAAAACTATACAT-
1 TATATATTATATATTTCAAAA-CAATTTC-AAAACTATA-ATA
*
6815 TATATATTATTATGTTTTCAAAA-AATTTCAAAACTATAATA
1 TATATATTA-TAT-ATTTCAAAACAATTTCAAAACTATAATA
6856 TATATATATATATAT
1 TATATAT-TATATAT
6871 AATATATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
40 3 0.06
41 19 0.39
42 16 0.33
43 3 0.06
44 8 0.16
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (40 bp):
TATATATTATATATTTCAAAACAATTTCAAAACTATAATA
Found at i:6850 original size:76 final size:74
Alignment explanation
Indices: 6724--6864 Score: 198
Period size: 73 Copynumber: 1.9 Consensus size: 74
6714 TCAAAAAAAT
* *
6724 ATTTTAAAAACTATATATTATATATATATTTTCAAAATGATTTCAAAACTAT-ATAT-TATATAT
1 ATTTTAAAAACTATACATTATATATATATTTTCAAAATAATTTCAAAACTATAATATATATATAT
6787 TTCAAAAGC
66 TTCAAAAGC
6796 ATTTTCAAAAACTATACATTATATATTATTATGTTTTCAAAA-AATTTCAAAACTATAATATATA
1 ATTTT-AAAAACTATACATTATATA-TA-TA--TTTTCAAAATAATTTCAAAACTATAATATATA
6860 TATAT
61 TATAT
6865 ATATATAATA
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
72 5 0.08
73 18 0.30
74 2 0.03
75 2 0.03
76 13 0.22
77 13 0.22
78 7 0.12
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (74 bp):
ATTTTAAAAACTATACATTATATATATATTTTCAAAATAATTTCAAAACTATAATATATATATAT
TTCAAAAGC
Found at i:6858 original size:2 final size:2
Alignment explanation
Indices: 6849--6899 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
6839 ATTTCAAAAC
6849 TA TA -A TA TA TA TA TA TA TA TA TA -A 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
6889 TA TA TA TA TA T
1 TA TA TA TA TA T
6900 TCGAAATGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:7643 original size:84 final size:84
Alignment explanation
Indices: 7529--8324 Score: 920
Period size: 84 Copynumber: 9.5 Consensus size: 84
7519 GAACTCAAAA
* * * * * * *
7529 TTTTGTTGACATATAGCCCTTCTTGACTTGAGTTATGCTGTAAATTGACGTGCCTTTGAGCTGAG
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA-TGATGTGCCTTGGAGCTGAG
* *
7594 TGTAATCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* ** *
7614 -TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGCGCATGATATGCCTTGGAGCTGAGC
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
7678 GTAGTTGAACTCAAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * *
7697 TTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGTCTTGGAGCTGAGC
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
7762 GTAGTCGAACTAGAAGGTA
66 GTAGTCGAACTCGAAGGTC
* * * * * *
7781 TTTGGTTGGCAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATATGCCTTTGAGCTGAGC
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
7846 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * *
7865 TTTTGGTGGA-AGATAACCCTTCTAGCCTTGAGCTATGATGTAAATGATATGCCTTGAAGTTGAG
1 TTTT-GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAG
7929 CGTAGTCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * *
7949 TTTGGTT-AGCAGATAACCCTTCTATCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTAAG
1 TTTTGTTGA-CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAG
* * *
8013 CGTAGTAGAACTTGAAGATC
65 CGTAGTCGAACTCGAAGGTC
* * * * * *
8033 TTTTGGTGACAGATAGCCCTTCTAGCCTTAAGTTATACTACAAATG-TGTGCCTTGGAGCTGAGA
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
8097 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * * * * *
8116 TCTTATTGGCAAATAGCCTTTCTCGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAACTGAGC
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* * *
8181 ATAGTCAAACTCTAAGGTC
66 GTAGTCGAACTCGAAGGTC
* *
8200 TTTTGGTGGA-AGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
1 TTTT-GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAG
* *
8264 CATAGTCTAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
*
8284 TTTTGTT-AGCAGATAACCCTTATAGCCTTGAGTTATGCTGC
1 TTTTGTTGA-CAGATAACCCTTCTAGCCTTGAGTTATGCTGC
8325 TAATAGTTTC
Statistics
Matches: 597, Mismatches: 105, Indels: 19
0.83 0.15 0.03
Matches are distributed among these distances:
82 2 0.00
83 103 0.17
84 486 0.81
85 6 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (84 bp):
TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTC
Found at i:8230 original size:335 final size:334
Alignment explanation
Indices: 7545--8324 Score: 1062
Period size: 335 Copynumber: 2.3 Consensus size: 334
7535 TGACATATAG
* * * * * *
7545 CCCTTCTTGACTTGAGTTATGCTGTAAATTGACGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
1 CCCTTCTAGCCTTGAGCTATGCTGTAAA-TGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCGAA
* **
7610 GGTCTTTGTT-GACAGATAACCCTTCTAGCCTTGAGTTATGTTGCGCATGATATGCCTTGGAGCT
64 GGTCTTTGTTAG-CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCT
* * * * * *
7674 GAGCGTAGTTGAACTCAAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGTTATACTGCA
128 AAGCGTAGTAGAACTCAAAGATCTTTTGGTGACAGATAGCCCTTCTAGCCTTAAGTTATACTACA
* * * *
7739 AATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTAGAAGGTATTTGGTTGGCAGATAACCCTTCT
193 AATGATGTGCCTTGGAGCTGAGAGTAGTCGAACTAGAAGGTATTTGATTGGCAAATAACCCTTCT
* * * * * * *
7804 ATCCTTGAGTTATGCTGTAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
258 AGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAACTGAGCATAGTCAAACTCGAAGGTCTTTT
7869 GGTGGAAGATAA
323 GGTGGAAGATAA
* * *
7881 CCCTTCTAGCCTTGAGCTATGATGTAAATGATATGCCTTGAAGTTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTG-AGCTGAGCGTAGTCGAACTCGAAG
* *
7946 GTCTTTGGTTAGCAGATAACCCTTCTATCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTA
65 GTCTTT-GTTAGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTA
**
8011 AGCGTAGTAGAACTTGAAGATCTTTTGGTGACAGATAGCCCTTCTAGCCTTAAGTTATACTACAA
129 AGCGTAGTAGAACTCAAAGATCTTTTGGTGACAGATAGCCCTTCTAGCCTTAAGTTATACTACAA
* * * *
8076 ATG-TGTGCCTTGGAGCTGAGAGTAGTCGAACTCGAAGGTCTCTT-ATTGGCAAATAGCCTTTCT
194 ATGATGTGCCTTGGAGCTGAGAGTAGTCGAACTAGAAGGTAT-TTGATTGGCAAATAACCCTTCT
* * * *
8139 CGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAACTGAGCATAGTCAAACTCTAAGGTCTTTT
258 AGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAACTGAGCATAGTCAAACTCGAAGGTCTTTT
8204 GGTGGAAGATAA
323 GGTGGAAGATAA
* * *
8216 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCTAACTCGAAG
1 CCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAG
*
8281 GTCTTTTGTTAGCAGATAACCCTTATAGCCTTGAGTTATGCTGC
65 GTC-TTTGTTAGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
8325 TAATAGTTTC
Statistics
Matches: 389, Mismatches: 49, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
334 3 0.01
335 244 0.63
336 141 0.36
337 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (334 bp):
CCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGG
TCTTTGTTAGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTAAG
CGTAGTAGAACTCAAAGATCTTTTGGTGACAGATAGCCCTTCTAGCCTTAAGTTATACTACAAAT
GATGTGCCTTGGAGCTGAGAGTAGTCGAACTAGAAGGTATTTGATTGGCAAATAACCCTTCTAGC
CTTGAGCTATGCTGCAAATGATATGCCTTGGAACTGAGCATAGTCAAACTCGAAGGTCTTTTGGT
GGAAGATAA
Found at i:9683 original size:95 final size:94
Alignment explanation
Indices: 9515--9700 Score: 266
Period size: 95 Copynumber: 2.0 Consensus size: 94
9505 CAATATATAA
* * * *
9515 ACCTTTATCAGGTTAGCTAAATCTTGTCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGGG
* *
9580 ACAGCTCAAGCTTTATTGTATAGTATAATT
66 ACAACTCAAACTTTATTGTAT-GTATAATT
* * *
9610 ACCTTTATCAGGCTAGCTGAATATTATCCATAAATCTAGGGCGTTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCT-TAGAGG
9674 GACAACTCAAACTTTATTGTATGTATA
65 GACAACTCAAACTTTATTGTATGTATA
9701 TATATATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
94 7 0.09
95 74 0.91
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (94 bp):
ACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAACTTTATTGTATGTATAATT
Found at i:13695 original size:35 final size:37
Alignment explanation
Indices: 13656--13747 Score: 84
Period size: 39 Copynumber: 2.5 Consensus size: 37
13646 TAAAAAGGAA
* *
13656 ATAGAAA-ATAATAAAATAAAAT-ATAAAAAAATAAT
1 ATAGAAAGATAATAAAATAAAATCATAAAAAAAAAAG
* *
13691 ATAGAGTATATATAATAAAA-ATAATCATAAAAAAAAAAG
1 ATAGA--A-AGATAATAAAATAAAATCATAAAAAAAAAAG
*
13730 AAAGAAAGA-AATAAAATA
1 ATAGAAAGATAATAAAATA
13748 TATATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
35 12 0.26
36 3 0.07
37 2 0.04
38 5 0.11
39 24 0.52
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.21
Consensus pattern (37 bp):
ATAGAAAGATAATAAAATAAAATCATAAAAAAAAAAG
Found at i:15042 original size:21 final size:21
Alignment explanation
Indices: 15018--15071 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
15008 TATTTCAAAA
*
15018 ATATTTTTTTAACTATATATT
1 ATATTTTTTAAACTATATATT
15039 ATATTTTTTAAACTATATATT
1 ATATTTTTTAAACTATATATT
15060 ATATTTTTTAAA
1 ATATTTTTTAAA
15072 AAAAGTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTTTAAACTATATATT
Found at i:15193 original size:40 final size:39
Alignment explanation
Indices: 15092--15391 Score: 168
Period size: 35 Copynumber: 7.9 Consensus size: 39
15082 AAAACTATAG
*
15092 TTTTCAAAAATGATTTT-AAA--A-ATATTATATAAGTT
1 TTTTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
*** *
15127 TTCAAAAAAATGTTTTTAAAACTATATATTATATAATTT
1 TTTTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
** *
15166 TTTTCAAAAATGTTTTTTTTAATTATATATTATATAAGTT
1 TTTTCAAAAATG-TTTTTAAAACTATATATTATATAAGTT
*
15206 TTTTCAAAAAAATGTTTTAAAAACTATACATATTATATATA-TAT
1 TTTTC--AAAAATGTTTTTAAAACTAT--ATATTATATA-AGT-T
* * *
15250 ATATTC-AAAATGATTTCAAAACTATATATTATAT-A---
1 -TTTTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
** *
15285 TTTTCAAAAGCAT-TTTCAAAAACTATATATTATAT-A-TG
1 TTTTCAAAA--ATGTTTTTAAAACTATATATTATATAAGTT
** * * *
15323 TTTTCAAAAA--AATTAAAAACTATATAATATAT-A-TA
1 TTTTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
* ** *
15358 TTTTC-GAAATGTTTTCGAAACTATATAGTATATA
1 TTTTCAAAAATGTTTTTAAAACTATATATTATATA
15392 TATTTTAGAA
Statistics
Matches: 211, Mismatches: 34, Indels: 38
0.75 0.12 0.13
Matches are distributed among these distances:
34 7 0.03
35 41 0.19
36 41 0.19
37 2 0.01
38 11 0.05
39 22 0.10
40 37 0.18
41 9 0.04
42 24 0.11
43 11 0.05
44 2 0.01
45 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (39 bp):
TTTTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
Found at i:15209 original size:42 final size:40
Alignment explanation
Indices: 15113--15335 Score: 162
Period size: 40 Copynumber: 5.6 Consensus size: 40
15103 GATTTTAAAA
*
15113 ATATTATATAAGTTTTCAAAAAAATG-TTTTTAAAACTAT
1 ATATTATATAATTTTTCAAAAAAATGTTTTTTAAAACTAT
*** ** *
15152 ATATTATATAATTTTTTTCAAAAATGTTTTTTTTAATTAT
1 ATATTATATAATTTTTCAAAAAAATGTTTTTTAAAACTAT
*
15192 ATATTATATAAGTTTTTTCAAAAAAATG-TTTTAAAAACTAT
1 ATATTATATAA--TTTTTCAAAAAAATGTTTTTTAAAACTAT
* *
15233 ACATATTATATATATATATATTC---AAAATG-ATTTCAAAACTAT
1 --ATATTATATA-AT-T-T-TTCAAAAAAATGTTTTTTAAAACTAT
** **
15275 ATATTATAT-A-TTTTCAAAAGCA--TTTTCAAAAACTAT
1 ATATTATATAATTTTTCAAAAAAATGTTTTTTAAAACTAT
15311 ATATTATAT-ATGTTTTCAAAAAAAT
1 ATATTATATAAT-TTTTCAAAAAAAT
15336 TAAAAACTAT
Statistics
Matches: 145, Mismatches: 23, Indels: 32
0.73 0.12 0.16
Matches are distributed among these distances:
34 3 0.02
35 1 0.01
36 21 0.14
37 2 0.01
38 11 0.08
39 22 0.15
40 30 0.21
41 9 0.06
42 30 0.21
43 11 0.08
44 2 0.01
45 3 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (40 bp):
ATATTATATAATTTTTCAAAAAAATGTTTTTTAAAACTAT
Found at i:15276 original size:81 final size:77
Alignment explanation
Indices: 15094--15321 Score: 220
Period size: 81 Copynumber: 2.9 Consensus size: 77
15084 AACTATAGTT
*
15094 TTCAAAAATGATTTTAAAA-ATATTATATAAG-TTTTCAAAAAAATGTTTTTAAAACTATATATT
1 TTCAAAAATGATTTTAAAATATATTATATAAGTTTTTCAAAAAAATGTTTTAAAAACTATATATT
* *
15157 ATATA-ATTTTT
66 ATATATATTATA
* *
15168 TTCAAAAATGTTTTTTTTAATTATATATTATATAAGTTTTTTCAAAAAAATGTTTTAAAAACTAT
1 TTCAAAAATG---ATTTTAA-AATATATTATATAAG-TTTTTCAAAAAAATGTTTTAAAAACTAT
15233 ACATATTATATATATATATA
61 --ATATTATATATAT-TATA
* ** *
15253 TTC-AAAATGATTTCAAAACTATA-TAT-TATA-TATTTTCAAAAGCAT-TTTCAAAAACTATAT
1 TTCAAAAATGATTTTAAAA-TATATTATATA-AGT-TTTTCAAAAAAATGTTTTAAAAACTATAT
15313 ATTATATAT
63 ATTATATAT
15322 GTTTTCAAAA
Statistics
Matches: 129, Mismatches: 11, Indels: 26
0.78 0.07 0.16
Matches are distributed among these distances:
74 10 0.08
76 11 0.09
77 6 0.05
78 14 0.11
79 25 0.19
80 5 0.04
81 35 0.27
83 10 0.08
84 8 0.06
85 5 0.04
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (77 bp):
TTCAAAAATGATTTTAAAATATATTATATAAGTTTTTCAAAAAAATGTTTTAAAAACTATATATT
ATATATATTATA
Found at i:15307 original size:36 final size:34
Alignment explanation
Indices: 15239--15397 Score: 146
Period size: 36 Copynumber: 4.5 Consensus size: 34
15229 CTATACATAT
*
15239 TATATA-TATATATATTCAAAATGA-TTTCAAAAC
1 TATATATTATATATTTTCAAAA-GATTTTCAAAAC
15272 TATATATTATATATTTTCAAAAGCATTTTCAAAAAC
1 TATATATTATATATTTTCAAAAG-ATTTTC-AAAAC
** *
15308 TATATATTATATATGTTTTCAAAA-AAATTAAAAAC
1 TATATATTATATA--TTTTCAAAAGATTTTCAAAAC
* *
15343 TATATAATATATATATTTTCGAAATG-TTTTCGAAAC
1 TATAT-AT-TATATATTTTC-AAAAGATTTTCAAAAC
15379 TATATAGTATATATATTTT
1 TATATA-T-TATATATTTT
15398 AGAAAACCGT
Statistics
Matches: 106, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
33 7 0.07
34 15 0.14
35 20 0.19
36 49 0.46
37 6 0.06
38 9 0.08
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (34 bp):
TATATATTATATATTTTCAAAAGATTTTCAAAAC
Found at i:20256 original size:3 final size:3
Alignment explanation
Indices: 20250--20312 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
20240 CGGGTCTTCT
* **
20250 TTA TTA TTA TTT TTA TCG TTA TT- TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
20295 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
20313 ATTTACAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20433 original size:25 final size:25
Alignment explanation
Indices: 20400--20470 Score: 133
Period size: 25 Copynumber: 2.8 Consensus size: 25
20390 AACCCATCAT
20400 ATTAGGGTTTCAAACCCTAAAACAG
1 ATTAGGGTTTCAAACCCTAAAACAG
*
20425 ATTATGGTTTCAAACCCTAAAACAG
1 ATTAGGGTTTCAAACCCTAAAACAG
20450 ATTAGGGTTTCAAACCCTAAA
1 ATTAGGGTTTCAAACCCTAAA
20471 TGTTCCAGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (25 bp):
ATTAGGGTTTCAAACCCTAAAACAG
Found at i:27749 original size:4 final size:4
Alignment explanation
Indices: 27740--27807 Score: 54
Period size: 4 Copynumber: 17.2 Consensus size: 4
27730 TCACAAATCA
* *
27740 ACAT ACAT ACAT -CAAT ACAA ACAT ATAT -CAAT ACAT ACAT ACAT -CAAT
1 ACAT ACAT ACAT AC-AT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT AC-AT
*
27788 ACAT ACAT ACCT A-AT ACAT A
1 ACAT ACAT ACAT ACAT ACAT A
27808 AAATTTGCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
3 4 0.08
4 44 0.86
5 3 0.06
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:27769 original size:16 final size:16
Alignment explanation
Indices: 27740--27807 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
27730 TCACAAATCA
27740 ACATACATACATCAAT
1 ACATACATACATCAAT
* *
27756 ACAAACATATATCAAT
1 ACATACATACATCAAT
27772 ACATACATACATCAAT
1 ACATACATACATCAAT
*
27788 ACATACATACCT-AAT
1 ACATACATACATCAAT
27803 ACATA
1 ACATA
27808 AAATTTGCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
15 8 0.17
16 39 0.83
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (16 bp):
ACATACATACATCAAT
Found at i:28133 original size:35 final size:35
Alignment explanation
Indices: 28094--28197 Score: 136
Period size: 35 Copynumber: 2.9 Consensus size: 35
28084 TGAGGGTGTT
* **
28094 TTTCTTGAAACAAATTTTGTCTCGCTTGAGACAGC
1 TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAAA
* *
28129 TTTCTAAAAACAAATTTTGTCTCGTTTGAGACAAA
1 TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAAA
* *
28164 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 TT-TCTTAAAACAAATTTTGTCTCGCTTGAGACA
28198 TTTTTCCTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 32 0.54
36 27 0.46
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (35 bp):
TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAAA
Found at i:28283 original size:105 final size:105
Alignment explanation
Indices: 28164--28360 Score: 290
Period size: 105 Copynumber: 1.9 Consensus size: 105
28154 TTGAGACAAA
* *
28164 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACC-AATTTTGAATTT
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGAT-CCAAATTTCGAATTT
28228 GATTCAC-TTAAAACAAAATTAATCTCACCTTAGATTGTTGT
65 GATTCACATT-AAACAAAATTAATCTCACCTTAGATTGTTGT
* * *
28269 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTG
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTG
* * *
28334 TTTCACATTAAACAAAGTTGATCTCAC
66 ATTCACATTAAACAAAATTAATCTCAC
28361 TTGAGATCGT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
104 2 0.02
105 78 0.95
106 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (105 bp):
TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTG
ATTCACATTAAACAAAATTAATCTCACCTTAGATTGTTGT
Found at i:28744 original size:28 final size:28
Alignment explanation
Indices: 28681--28782 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 28
28671 TCTGGAGACA
* * *
28681 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTCT
*
28709 GTTCCTTTTGAATAAAAATCTTTGAGT-T
1 GTTTCTTTTGAA-AAAAATCTTTGAGTCT
28737 GTTTCTTTTGAAACAAATATCTTTGAGTCT
1 GTTTCTTTTGAAA-AAA-ATCTTTGAGTCT
*
28767 ATTTCTTTTGAAAAAA
1 GTTTCTTTTGAAAAAA
28783 TTTATCTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
27 1 0.02
28 24 0.38
29 26 0.41
30 13 0.20
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTCT
Found at i:28837 original size:60 final size:63
Alignment explanation
Indices: 28738--28875 Score: 151
Period size: 62 Copynumber: 2.2 Consensus size: 63
28728 CTTTGAGTTG
*
28738 TTTCTTTTGAAACAAATATCTTTGAGTCTATTTCTTTTG-AA-AAAATTTATCTC-CTAAAGACA
1 TTTCTTTTG-AA-AAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTT-TCTCTCTAAAGACA
28800 A
63 A
* * **
28801 TTTCTTTTGAAAAA-ATCTTTGAGT-TGGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAA
1 TTTCTTTTGAAAAATATCTTTGAGTCT-ATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
*
28863 CTTCTTTTGAAAA
1 TTTCTTTTGAAAA
28876 TACCCACCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
59 1 0.02
60 18 0.28
61 8 0.12
62 29 0.45
63 9 0.14
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
TTTCTTTTGAAAAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
Found at i:29015 original size:15 final size:15
Alignment explanation
Indices: 28992--29035 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
28982 TTTTGAGTCG
*
28992 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
29007 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
29022 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
29036 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:29517 original size:40 final size:40
Alignment explanation
Indices: 29459--29823 Score: 211
Period size: 40 Copynumber: 8.7 Consensus size: 40
29449 CCAGTCGTCC
* * *
29459 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCT
* * * * *
29499 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * * *
29542 TCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
* *
29588 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * *
29628 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * *
29670 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
* *
29716 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * *
29756 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-AACTCT
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATCTCT
* * *
29798 TCATCACGTACGAGCAGTGTCGTCCC
1 TCATCACGTAGGAGCCGTGTCATCCC
29824 CAACAACCAA
Statistics
Matches: 250, Mismatches: 45, Indels: 58
0.71 0.13 0.16
Matches are distributed among these distances:
38 3 0.01
39 3 0.01
40 85 0.34
41 1 0.00
42 53 0.21
43 37 0.15
44 3 0.01
46 59 0.24
47 6 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
TCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCT
Found at i:29807 original size:128 final size:129
Alignment explanation
Indices: 29459--29791 Score: 589
Period size: 128 Copynumber: 2.6 Consensus size: 129
29449 CCAGTCGTCC
* * *
29459 TCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
*
29523 CATAGATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
29588 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
*
29652 CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
29716 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
29781 ATAGATAACCA
66 ATAGATAACCA
29792 AACTCTTCAT
Statistics
Matches: 195, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
128 125 0.64
129 65 0.33
130 5 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:29975 original size:3 final size:3
Alignment explanation
Indices: 29969--30027 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
29959 CGGGTCTTCT
* **
29969 TTA TTA TTA TTT TTA TCG TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30016 TTA TTA TTA TTA
1 TTA TTA TTA TTA
30028 ATTTACAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30144 original size:25 final size:25
Alignment explanation
Indices: 30115--30185 Score: 133
Period size: 25 Copynumber: 2.8 Consensus size: 25
30105 AACCCATCAT
30115 ATTAGGGTTTCAAACCCTAAAACAG
1 ATTAGGGTTTCAAACCCTAAAACAG
*
30140 ATTAGGGTTTCAAACCCTAAAATAG
1 ATTAGGGTTTCAAACCCTAAAACAG
30165 ATTAGGGTTTCAAACCCTAAA
1 ATTAGGGTTTCAAACCCTAAA
30186 TGTTCCAGCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (25 bp):
ATTAGGGTTTCAAACCCTAAAACAG
Found at i:33650 original size:231 final size:225
Alignment explanation
Indices: 33165--33668 Score: 651
Period size: 231 Copynumber: 2.2 Consensus size: 225
33155 AGAAAATAAT
** *
33165 AATAATGCTTAAGCTACATTCATCTCTCATTTCCAACCAATCATAATTCACCCCAACAGCATCTC
1 AATAATGCTTAAATTACATTCATCTTTCA-TTCCAACCAATCATAATTCACCCCAACAGCATCTC
*
33230 AATTTGGGCATTAGCTCTACAAAATCCAATACACGATAAGTTTAAAAGTAATACACTTGCAAAAA
65 AATGTGGGCATTAGCTCTACAAAATCCAATACACGATAAGTTTAAAAGTAATACACTTGCAAAAA
* * * *
33295 TAAATCAAACAAACCATCAACAACAGTACTAATGAGTACCAATTTATACAAAATGAAAAATAACA
130 TAAAGCAAACAAA-CATCAACAACAGTACTAATGAATACCAACTTACACAAAATGAAAAATAACA
* * *
33360 TATAGCACTGGTTTGAGGGGATATATAGCAAG
194 TATAGCACTAGTTTAAGGGGATATATAACAAG
* * * *
33392 AATAATGCTTAAATCACATTCATCTTTCCTTCCTGACCAATCATAATTCACCCTAACAGCATCTC
1 AATAATGCTTAAATTACATTCATCTTTCATTCC-AACCAATCATAATTCACCCCAACAGCATCTC
*
33457 AATGTGGGCATTAGCTCTACAAAATCCAATACATGATAAGGCAAGAGTTTAAAAGTAATACTACT
65 AATGTGGGCATTAGCTCTACAAAATCCAATACACGAT------A-AGTTTAAAAGTAATAC-ACT
*
33522 TGCAAAAATAAAGC-AAC-AA-AT-AATCAACAGTACTAATGAATATCAACTTACACAAAAAT-A
122 TGCAAAAATAAAGCAAACAAACATCAA-CAACAGTACTAATGAATACCAACTTACAC-AAAATGA
* *
33582 AAACTAACATATAGCACTAGTTTAAGGGGATATATAACAGG
185 AAAATAACATATAGCACTAGTTTAAGGGGATATATAACAAG
* *
33623 AATAATGCTTAAATTACATTAATCTTTCATTCCCAA-CAACCATAAT
1 AATAATGCTTAAATTACATTCATCTTTCATT-CCAACCAATCATAAT
33669 AACGGTTACA
Statistics
Matches: 241, Mismatches: 24, Indels: 21
0.84 0.08 0.07
Matches are distributed among these distances:
226 4 0.02
227 88 0.37
230 11 0.05
231 93 0.39
232 7 0.03
233 3 0.01
234 19 0.08
235 16 0.07
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (225 bp):
AATAATGCTTAAATTACATTCATCTTTCATTCCAACCAATCATAATTCACCCCAACAGCATCTCA
ATGTGGGCATTAGCTCTACAAAATCCAATACACGATAAGTTTAAAAGTAATACACTTGCAAAAAT
AAAGCAAACAAACATCAACAACAGTACTAATGAATACCAACTTACACAAAATGAAAAATAACATA
TAGCACTAGTTTAAGGGGATATATAACAAG
Found at i:36474 original size:36 final size:36
Alignment explanation
Indices: 36399--36473 Score: 143
Period size: 35 Copynumber: 2.1 Consensus size: 36
36389 ATTTTCGGGA
36399 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
36435 TTTTGCTA-TTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
36470 TTTT
1 TTTT
36474 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
35 31 0.79
36 8 0.21
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:41437 original size:36 final size:36
Alignment explanation
Indices: 41396--41471 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
41386 ATTTTCGGGA
41396 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
41432 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
41468 TTTT
1 TTTT
41472 TTTGCTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:45024 original size:70 final size:72
Alignment explanation
Indices: 44887--45058 Score: 179
Period size: 70 Copynumber: 2.3 Consensus size: 72
44877 AAAACATATA
* * * * * *
44887 TTTGAAAACGTATAATATATAGTTTTTTTTTTAAAATGATTTTGAAAATATATAATGTATAGTTT
1 TTTGAAAACGTAT-ATATATA--TTTTTTTTTAAAA-GATATTAAAAAAAGATAATATATAATTT
*
44952 TAAAAAACGATT
62 TAAAAAA-GAAT
44964 TTTGAAAACGTATA-ATATA-TTTTTTTTAAAA-ATATTAAAAAAAGATAATATATAATTTTAAA
1 TTTGAAAACGTATATATATATTTTTTTTTAAAAGATATTAAAAAAAGATAATATATAATTTTAAA
*
45026 AAATAAT
66 AAAGAAT
* *
45033 TTTGAAAACATATATAATATAGTTTT
1 TTTGAAAACGTATAT-ATATATTTTT
45059 CGAAAACATA
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
69 15 0.18
70 28 0.34
71 5 0.06
72 16 0.19
75 5 0.06
76 1 0.01
77 13 0.16
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (72 bp):
TTTGAAAACGTATATATATATTTTTTTTTAAAAGATATTAAAAAAAGATAATATATAATTTTAAA
AAAGAAT
Found at i:45051 original size:38 final size:38
Alignment explanation
Indices: 44919--45130 Score: 126
Period size: 37 Copynumber: 5.8 Consensus size: 38
44909 TTTTTTTTTT
* *
44919 AAAATGATTTTG-AAA-ATATATAATGTATAGTTTTAA
1 AAAATAATTTTGAAAACATATATAATATATAGTTTTAA
* * * ** *
44955 AAAACGATTTTTGAAAAC--GTATAATATATTTTTTTTA
1 AAAA-TAATTTTGAAAACATATATAATATATAGTTTTAA
* * *
44992 AAAAT-A--TT-AAAA-AAAGATAATATATAATTTTAA
1 AAAATAATTTTGAAAACATATATAATATATAGTTTTAA
45025 AAAATAATTTTGAAAACATATAT-A-ATATAGTTTTCGAA
1 AAAATAATTTTGAAAACATATATAATATATAGTTTT--AA
* *
45063 AACATACTTTTGAAAAC--ATATAATATATAGTTGTTAA
1 AAAATAATTTTGAAAACATATATAATATATAGTT-TTAA
* ** *
45100 AATGATTTTTTTTAAAAACATATATAATATA
1 AA--AATAATTTTGAAAACATATATAATATA
45131 GTTTTTGAAA
Statistics
Matches: 132, Mismatches: 25, Indels: 33
0.69 0.13 0.17
Matches are distributed among these distances:
32 4 0.03
33 21 0.16
34 1 0.01
36 19 0.14
37 33 0.25
38 32 0.24
39 12 0.09
41 10 0.08
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (38 bp):
AAAATAATTTTGAAAACATATATAATATATAGTTTTAA
Found at i:45053 original size:36 final size:36
Alignment explanation
Indices: 44926--45203 Score: 153
Period size: 38 Copynumber: 7.6 Consensus size: 36
44916 TTTAAAATGA
*
44926 TTTTG-AAA-ATATATAATGTATAGTTTTAAAAAACGAT
1 TTTTGAAAACATATATAA--TATAGTTTTAAAAAA-TAT
* ** *
44963 TTTTGAAAACGTATA-ATATATTTTTTTTAAAAATA-
1 TTTTGAAAACATATATA-ATATAGTTTTAAAAAATAT
*** * * *
44998 TTAAAAAAAGATA-AT-ATATAATTTTAAAAAATAA
1 TTTTGAAAACATATATAATATAGTTTTAAAAAATAT
* *
45032 TTTTGAAAACATATATAATATAGTTTTCGAAAACATAC
1 TTTTGAAAACATATATAATATAGTTTT--AAAAAATAT
* *
45070 TTTTGAAAACATATA-ATATATAGTTGTTAAAATGATTTT
1 TTTTGAAAACATATATA-ATATAGTT-TTAAAA--AATAT
*
45109 TTTTAAAAACATATATAATATAGTTTTTGAAAAACATATT
1 TTTTGAAAACATATATAATATAG-TTTT-AAAAA-ATA-T
* * * * **
45149 TTTTGAATATATATATAGT-T-TTTTTAAATGAT-T
1 TTTTGAAAACATATATAATATAGTTTTAAAAAATAT
*
45182 TTTTGAAAACGTATATAATATA
1 TTTTGAAAACATATATAATATA
45204 ATCTTTGAAA
Statistics
Matches: 183, Mismatches: 38, Indels: 42
0.70 0.14 0.16
Matches are distributed among these distances:
33 31 0.17
34 11 0.06
35 12 0.07
36 13 0.07
37 26 0.14
38 35 0.19
39 32 0.17
40 23 0.13
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTTGAAAACATATATAATATAGTTTTAAAAAATAT
Found at i:45132 original size:77 final size:73
Alignment explanation
Indices: 45032--45203 Score: 206
Period size: 77 Copynumber: 2.3 Consensus size: 73
45022 TAAAAAATAA
45032 TTTTGAAAACATATATAATATAGTTTTCG-AAAACATA-CTTTTGAAAACATATAATATATAG-T
1 TTTTGAAAACATATATAATATAGTTTTCGAAAAACATATCTTTTG---A-ATAT-ATATATAGTT
45094 TGTTAAAATGATTTT
61 TGTTAAAATGA--TT
* * * * *
45109 TTTTAAAAACATATATAATATAGTTTTTGAAAAACATATTTTTTGAATATATATATAGTTTTTTT
1 TTTTGAAAACATATATAATATAGTTTTCGAAAAACATATCTTTTGAATATATATATAGTTTGTTA
45174 AAATGATT
66 AAATGATT
*
45182 TTTTGAAAACGTATATAATATA
1 TTTTGAAAACATATATAATATA
45204 ATCTTTGAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
73 22 0.26
74 8 0.09
75 14 0.16
76 1 0.01
77 27 0.32
78 8 0.09
79 5 0.06
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (73 bp):
TTTTGAAAACATATATAATATAGTTTTCGAAAAACATATCTTTTGAATATATATATAGTTTGTTA
AAATGATT
Found at i:45223 original size:21 final size:21
Alignment explanation
Indices: 45193--45244 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
45183 TTTGAAAACG
*
45193 TATATAATATAATCTTTGAAA
1 TATATTATATAATCTTTGAAA
** *
45214 TATATTATATTTTTTTTGAAA
1 TATATTATATAATCTTTGAAA
45235 TATATTATAT
1 TATATTATAT
45245 TATATAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (21 bp):
TATATTATATAATCTTTGAAA
Found at i:45227 original size:75 final size:74
Alignment explanation
Indices: 45032--45213 Score: 185
Period size: 73 Copynumber: 2.4 Consensus size: 74
45022 TAAAAAATAA
* * *
45032 TTTTGAAAACATATATAATATAGT-TTTCG-AAAACATA-CTTTTGAAAACATATAATATATAGT
1 TTTTAAAAACATATATAATATAATCTTT-GAAAAACATATTTTTTG---A-ATATAATATATAGT
45094 TGTTAAAATGATTTT
61 TGTTAAAATGA-TTT
* * *
45109 TTTTAAAAACATATATAATATAGTTTTTGAAAAACATATTTTTTGAATAT-ATATATAGTTTTTT
1 TTTTAAAAACATATATAATATAATCTTTGAAAAACATATTTTTTGAATATAATATATAG-TTGTT
*
45173 TAAATGA-TT
65 AAAATGATTT
* *
45182 TTTTGAAAACGTATATAATATAATCTTTGAAA
1 TTTTAAAAACATATATAATATAATCTTTGAAA
45214 TATATTATAT
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
73 30 0.32
74 8 0.09
75 14 0.15
76 1 0.01
77 24 0.26
78 11 0.12
79 5 0.05
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (74 bp):
TTTTAAAAACATATATAATATAATCTTTGAAAAACATATTTTTTGAATATAATATATAGTTGTTA
AAATGATTT
Found at i:45293 original size:4 final size:4
Alignment explanation
Indices: 45278--45323 Score: 65
Period size: 4 Copynumber: 10.8 Consensus size: 4
45268 TATATTTTCT
45278 TTTA TCTTA TTTA TTTA TTTA TTTA TTTA TATGTA TTTA TTTA TTT
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTTA T-T-TA TTTA TTTA TTT
45324 TTATTTTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
4 30 0.77
5 6 0.15
6 3 0.08
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:47331 original size:28 final size:27
Alignment explanation
Indices: 47291--47344 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
47281 TAATTGTTTC
* *
47291 TTTCAAGCACTGGTTCGACGACATAATG
1 TTTCAAGAACTGGCTCGACG-CATAATG
*
47319 TTTCAAGAACTGGCTCGATGCATAAT
1 TTTCAAGAACTGGCTCGACGCATAAT
47345 ATAAACGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (27 bp):
TTTCAAGAACTGGCTCGACGCATAATG
Found at i:47999 original size:29 final size:29
Alignment explanation
Indices: 47967--48040 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
47957 GAGGTTAGAT
* *
47967 TAATATTTATCTAAAGTTTAGGATTAAAA
1 TAATATTTATCTAAAGTTTAAGATCAAAA
*
47996 TAATATTTTTCTAAAGTTTAAGATCAAAA
1 TAATATTTATCTAAAGTTTAAGATCAAAA
48025 TAATATTCTATCTAAA
1 TAATATT-TATCTAAA
48041 TTTCAAAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 33 0.82
30 7 0.17
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (29 bp):
TAATATTTATCTAAAGTTTAAGATCAAAA
Found at i:48160 original size:21 final size:21
Alignment explanation
Indices: 48119--48161 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
48109 TGGTTCAATG
* *
48119 ATAAAAATGTAACATTTAATA
1 ATAAAAATGTAACAATAAATA
48140 ATAAAAATGATAA-AATAAATA
1 ATAAAAATG-TAACAATAAATA
48161 A
1 A
48162 ATTAATAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (21 bp):
ATAAAAATGTAACAATAAATA
Found at i:50628 original size:18 final size:18
Alignment explanation
Indices: 50605--50671 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
50595 ACATGACCTC
50605 AAATTCAAATTGAA-ATTG
1 AAATTCAAATT-AACATTG
50623 AAATTCAAATTAACATTG
1 AAATTCAAATTAACATTG
* * *
50641 AAATTTACATT-ACATTA
1 AAATTCAAATTAACATTG
50658 AAATTCAAACTTAA
1 AAATTCAAA-TTAA
50672 ATTCCATTGC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 14 0.34
18 26 0.63
19 1 0.02
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.34
Consensus pattern (18 bp):
AAATTCAAATTAACATTG
Found at i:51590 original size:21 final size:21
Alignment explanation
Indices: 51564--51609 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
51554 GATTTCTGGG
* *
51564 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
51585 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
51606 CAAG
1 CAAG
51610 CGAATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:51679 original size:23 final size:22
Alignment explanation
Indices: 51635--51679 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
51625 AATGTCATGG
*
51635 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
51657 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
51680 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:52837 original size:31 final size:31
Alignment explanation
Indices: 52801--52927 Score: 116
Period size: 31 Copynumber: 4.1 Consensus size: 31
52791 AGAGTCGAGG
52801 GTTTACCTA-GTTCTACGGAACATATGGACA
1 GTTTACCTAGGTTCTACGGAACATATGGACA
* * *
52831 GTTTTACCTATG-TCTTTC-GAGACATATGAACA
1 G-TTTACCTAGGTTC-TACGGA-ACATATGGACA
* * * *
52863 GTATACCTATGTTCTAAGGAATATATGGACA
1 GTTTACCTAGGTTCTACGGAACATATGGACA
* * *
52894 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTACGGAACATATGGACA
52925 GTT
1 GTT
52928 ACCGAGGATC
Statistics
Matches: 77, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
30 1 0.01
31 58 0.75
32 18 0.23
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTAGGTTCTACGGAACATATGGACA
Found at i:52926 original size:62 final size:61
Alignment explanation
Indices: 52803--52930 Score: 161
Period size: 62 Copynumber: 2.1 Consensus size: 61
52793 AGTCGAGGGT
* *
52803 TTACCTAGTTCTACGGAACATATGGACAGTTTTACCTATGTCTTTCGAGACATATGAACAG
1 TTACCTAGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTCGAGACATATGAACAG
* * * *
52864 TATACCTATGTTCTAAGGAATATATGGACAG-TTTACCTAGGT-TCTTCGGGACCTATGGACAG
1 T-TACCTA-GTTCTAAGGAACATATGGACAGTTTTACCTAGGTCT-TTCGAGACATATGAACAG
52926 TTACC
1 TTACC
52931 GAGGATCTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
61 6 0.10
62 32 0.55
63 20 0.34
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (61 bp):
TTACCTAGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTCGAGACATATGAACAG
Found at i:52947 original size:30 final size:30
Alignment explanation
Indices: 52886--52982 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
52876 CTAAGGAATA
* * ***
52886 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
52917 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
52947 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
52977 TCTGGA
1 TATGGA
52983 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:52983 original size:30 final size:30
Alignment explanation
Indices: 52913--52985 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
52903 GGTTCTTCGG
* *
52913 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
52943 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
52973 GACCTCTGGATAG
1 GACCTCTGGATAG
52986 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:56438 original size:21 final size:21
Alignment explanation
Indices: 56412--56457 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
56402 GATTTCTGGG
* *
56412 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
56433 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
56454 CAAG
1 CAAG
56458 CGAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:56528 original size:23 final size:22
Alignment explanation
Indices: 56484--56528 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
56474 AATGTCATGG
*
56484 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
56506 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
56529 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:57755 original size:31 final size:31
Alignment explanation
Indices: 57666--57793 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
57656 AGAGTCGAGG
57666 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* *
57697 GTTTTACCTATG-TCTTTC-GAGATATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
57729 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
57760 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
57791 GTT
1 GTT
57794 ACCGAGGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 53 0.66
32 27 0.34
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:57813 original size:30 final size:30
Alignment explanation
Indices: 57752--57848 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
57742 CTAAGGAACA
* * ***
57752 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
57783 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
57813 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
57843 TCTGGA
1 TATGGA
57849 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:57849 original size:30 final size:30
Alignment explanation
Indices: 57779--57851 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
57769 GGTTCTTCGG
* *
57779 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
57809 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
57839 GACCTCTGGATAG
1 GACCTCTGGATAG
57852 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:58868 original size:2 final size:2
Alignment explanation
Indices: 58861--58922 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
58851 CAAACACAAT
58861 TA TA TA TA TA TA TA TA TA TA 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
58903 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
58923 AACTCTTATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59209 original size:86 final size:86
Alignment explanation
Indices: 58990--59374 Score: 337
Period size: 85 Copynumber: 4.4 Consensus size: 86
58980 ATTTGATAAG
* * * * *
58990 TGACTGAAAATAAAAGGACTTGAATAGTTAAGATTCTCTGTCATTGAAAAGTATTGTTGTACAAT
1 TGACTGAAAAAAAAAGGACGTGAATAGTTAAGATTCTCTATGATTGAAAATTATTGTTGTAC---
* *
59055 TTCTCTATGAATAGTTAAGAAGTGACATA
63 CTAT-TATG-A-AGTT--GAAGTGACATA
* * * *
59084 TGACTGAGAAGATAAGGATGTGAATAGTTAAGATTCTCTATGATTGAAAATTATTGTTGTACCTA
1 TGACTGAAAAAAAAAGGACGTGAATAGTTAAGATTCTCTATGATTGAAAATTATTGTTGTACCTA
59149 TTATGAA-TTGAAGTGACATA
66 TTATGAAGTTGAAGTGACATA
* * * *
59169 TGACTGAAAAAAAACAGGACGTGAATAGTTAAGATTCTCTATGAATGGAAATTAGTGTTGTACCC
1 TGACTGAAAAAAAA-AGGACGTGAATAGTTAAGATTCTCTATGATTGAAAATTATTGTTGTACCT
* * * *
59234 GTTCTG-ATTTAAAGTGACATA
65 ATTATGAAGTTGAAGTGACATA
* * * * * * * *
59255 TGACTGAAAAGAACATGACGTGAATAGTTAAGATTATCTTTCGA-TGGAAATTATTGTTGTATCA
1 TGACTGAAAAAAAAAGGACGTGAATAGTTAAGATTCTCTAT-GATTGAAAATTATTGTTGTACCT
* *
59319 ATTCT-AATTTGAAGTGACATA
65 ATTATGAAGTTGAAGTGACATA
* * ** **
59340 TGTCTGAGAAAATTATAACGTGAATAGTTAAGATT
1 TGACTGAAAAAAAAAGGACGTGAATAGTTAAGATT
59375 ATGTGTCAAC
Statistics
Matches: 250, Mismatches: 37, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
85 111 0.44
86 75 0.30
87 2 0.01
88 1 0.00
89 1 0.00
90 4 0.02
91 2 0.01
94 54 0.22
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (86 bp):
TGACTGAAAAAAAAAGGACGTGAATAGTTAAGATTCTCTATGATTGAAAATTATTGTTGTACCTA
TTATGAAGTTGAAGTGACATA
Found at i:59313 original size:85 final size:84
Alignment explanation
Indices: 59073--59376 Score: 342
Period size: 85 Copynumber: 3.6 Consensus size: 84
59063 GAATAGTTAA
* * * *
59073 GAAGTGACATATGACTGAGAAGATA-AGGATGTGAATAGTTAAGATTCTCTATGATTGAAAATTA
1 GAAGTGACATATGACTGAAAAGA-ACAGGACGTGAATAGTTAAGATTATCTATGA-TGGAAATTA
* * *
59137 TTGTTGTACCTATTATGAATT
64 TTGTTGTACCAATTCTGATTT
* *
59158 GAAGTGACATATGACTGAAAAAAAACAGGACGTGAATAGTTAAGATTCTCTATGAATGGAAATTA
1 GAAGTGACATATGACTG-AAAAGAACAGGACGTGAATAGTTAAGATTATCTATG-ATGGAAATTA
* **
59223 GTGTTGTACCCGTTCTGATTT
64 TTGTTGTACCAATTCTGATTT
* * *
59244 AAAGTGACATATGACTGAAAAGAACATGACGTGAATAGTTAAGATTATCTTTCGATGGAAATTAT
1 GAAGTGACATATGACTGAAAAGAACAGGACGTGAATAGTTAAGATTATCTAT-GATGGAAATTAT
* *
59309 TGTTGTATCAATTCTAATTT
65 TGTTGTACCAATTCTGATTT
* ** **
59329 GAAGTGACATATGTCTGAGAAA-ATTATAACGTGAATAGTTAAGATTAT
1 GAAGTGACATATGACTGA-AAAGAACAGGACGTGAATAGTTAAGATTAT
59377 GTGTCAACGT
Statistics
Matches: 190, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
85 114 0.60
86 75 0.39
87 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (84 bp):
GAAGTGACATATGACTGAAAAGAACAGGACGTGAATAGTTAAGATTATCTATGATGGAAATTATT
GTTGTACCAATTCTGATTT
Found at i:59577 original size:85 final size:85
Alignment explanation
Indices: 59388--59716 Score: 370
Period size: 77 Copynumber: 3.9 Consensus size: 85
59378 TGTCAACGTA
* * * * ** *
59388 AATTATTTTAATTTATCTGATTTGATGTGATATGTCAATGAAAAGAAAATGATGTGAATACATCA
1 AATTATTTCAATTTATCTGATTTGAGGTGATATGTCAATGAAAAGCAAAGGACATGAATA-AT-T
* *
59453 TAGATTCTTTGATTCT-TAGTCAAT
64 TAGATTCTCTAATTCTCTA---AAT
* *
59477 GGAAATTATTTCAATTTATCTAATTTGTGGTGATATGTCAATGAAAAGCAAAGGACATGAATAAT
1 ---AATTATTTCAATTTATCTGATTTGAGGTGATATGTCAATGAAAAGCAAAGGACATGAATAAT
59542 TTAGATTCTCTAATTCTCTAAAT
63 TTAGATTCTCTAATTCTCTAAAT
* * *
59565 AATTATTTCAATTTATCTGATTTGAGGTGATATGTCAATGAAAAGCAAAGAACGTGAATAGTTTA
1 AATTATTTCAATTTATCTGATTTGAGGTGATATGTCAATGAAAAGCAAAGGACATGAATAATTTA
59630 G--------ATTCTCTAAAT
66 GATTCTCTAATTCTCTAAAT
** *
59642 AATTATTTCAGCTTATCTGATTTGAGGTGATATGTCAATGAAAAACAAAGGACATGAATAATTTA
1 AATTATTTCAATTTATCTGATTTGAGGTGATATGTCAATGAAAAGCAAAGGACATGAATAATTTA
59707 GATTCTCTAA
66 GATTCTCTAA
59717 AATGTTTAAA
Statistics
Matches: 206, Mismatches: 22, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
77 71 0.34
85 62 0.30
88 3 0.01
90 14 0.07
91 4 0.02
92 52 0.25
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (85 bp):
AATTATTTCAATTTATCTGATTTGAGGTGATATGTCAATGAAAAGCAAAGGACATGAATAATTTA
GATTCTCTAATTCTCTAAAT
Found at i:63006 original size:14 final size:14
Alignment explanation
Indices: 62987--63027 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
62977 CCTTTGCCCA
62987 TTAAAAAATATTTT
1 TTAAAAAATATTTT
63001 TTAAAAAATA--TT
1 TTAAAAAATATTTT
63013 TT-AAAAATATTTT
1 TTAAAAAATATTTT
63026 TT
1 TT
63028 TATATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.28
12 4 0.16
13 4 0.16
14 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAAAAATATTTT
Found at i:63020 original size:11 final size:12
Alignment explanation
Indices: 62987--63025 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
62977 CCTTTGCCCA
62987 TTAAAAAATATTTT
1 TTAAAAAATA--TT
63001 TTAAAAAATATT
1 TTAAAAAATATT
63013 TT-AAAAATATT
1 TTAAAAAATATT
63024 TT
1 TT
63026 TTTATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.44
12 4 0.16
14 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:63029 original size:14 final size:13
Alignment explanation
Indices: 62990--63027 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
62980 TTGCCCATTA
62990 AAAAATATTTTTT
1 AAAAATATTTTTT
*
63003 AAAAA-ATATTTT
1 AAAAATATTTTTT
63015 AAAAATATTTTTT
1 AAAAATATTTTTT
63028 TATATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:70436 original size:31 final size:30
Alignment explanation
Indices: 70377--70436 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
70367 TCATATTCTA
*
70377 TTTGATTTTATTATAAAAAAAGTTAATAAT
1 TTTGATTTTATTATAAAAAAAGTAAATAAT
70407 TTTGATGTTTAATTA-AAAAATAA-TAAATAA
1 TTTGAT-TTT-ATTATAAAAA-AAGTAAATAA
70437 ATAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
30 6 0.23
31 14 0.54
32 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTGATTTTATTATAAAAAAAGTAAATAAT
Found at i:77036 original size:29 final size:29
Alignment explanation
Indices: 76990--77046 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
76980 TACCGAAAAT
* *
76990 ATTTTTATAAATATGTAAAGATATTATTA
1 ATTTTTATAAATAGGTAAAAATATTATTA
77019 ATTTTT-TAAATAGGGTAAAAATATTATT
1 ATTTTTATAAATA-GGTAAAAATATTATT
77047 TTAACAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (29 bp):
ATTTTTATAAATAGGTAAAAATATTATTA
Found at i:81707 original size:35 final size:33
Alignment explanation
Indices: 81668--81751 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
81658 GTATTTCAGT
81668 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
81703 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
*
81738 TAA-TTTGTTGTATT
1 TAATTTTGTTATATT
81752 TAAATTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
32 2 0.05
33 1 0.02
34 6 0.14
35 18 0.42
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Done.