Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006710.1 Hibiscus syriacus cultivar Beakdansim tig00016725_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: 2941931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:2079606 original size:24 final size:24
Alignment explanation
Indices: 2079539--2079608 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
2079529 GGTTTTTATT
*
2079539 TTATT-TTTTTATTTTATTTA-TTT
1 TTATTATTTTTATTTTA-TTACTTC
* *
2079562 TTATTTATTTTCAGTTT-TTACTTC
1 TTA-TTATTTTTATTTTATTACTTC
2079586 TTATTATTTTTATTTTATTACTT
1 TTATTATTTTTATTTTATTACTT
2079609 TATTTAACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 17 0.45
24 13 0.34
25 8 0.21
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (24 bp):
TTATTATTTTTATTTTATTACTTC
Found at i:2079633 original size:21 final size:20
Alignment explanation
Indices: 2079609--2079647 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2079599 TTTATTACTT
2079609 TATTTAACATTTTTCATTTAA
1 TATTTAACATTTTT-ATTTAA
*
2079630 TATTTAATATTTTTATTT
1 TATTTAACATTTTTATTT
2079648 TTATCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTAACATTTTTATTTAA
Found at i:2079675 original size:17 final size:17
Alignment explanation
Indices: 2079655--2079689 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2079645 TTTTTATCTT
2079655 TTTTTTCCTTTGATTTA
1 TTTTTTCCTTTGATTTA
*
2079672 TTTTTTCTTTTGATTTA
1 TTTTTTCCTTTGATTTA
2079689 T
1 T
2079690 ATAATATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.09, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTTTCCTTTGATTTA
Found at i:2084628 original size:36 final size:36
Alignment explanation
Indices: 2084555--2084670 Score: 117
Period size: 36 Copynumber: 3.1 Consensus size: 36
2084545 TTTCGTCCAT
*
2084555 TTTTTTTTATAGATCATTTTGAAAATTATATAATATATGG
1 TTTTTTTTA-A-AT-ATTTTGAAAA-TATATAATATATAG
2084595 TTTTTTTTAAATATTTTGAAAATATATAATATATAG
1 TTTTTTTTAAATATTTTGAAAATATATAATATATAG
** * * * *
2084631 -TTTTTGAAAACATTTTTGAAAATACATATTATATTG
1 TTTTTTTTAAATA-TTTTGAAAATATATAATATATAG
2084667 TTTT
1 TTTT
2084671 GAAAACTTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
35 9 0.13
36 33 0.49
37 13 0.19
38 2 0.03
39 1 0.01
40 9 0.13
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.53
Consensus pattern (36 bp):
TTTTTTTTAAATATTTTGAAAATATATAATATATAG
Found at i:2084629 original size:38 final size:40
Alignment explanation
Indices: 2084555--2084635 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 40
2084545 TTTCGTCCAT
2084555 TTTTTTTTATAGATCATTTTGAAAATTATATAATATATGG
1 TTTTTTTTATAGATCATTTTGAAAATTATATAATATATGG
*
2084595 TTTTTTTTA-A-AT-ATTTTGAAAA-TATATAATATATAG
1 TTTTTTTTATAGATCATTTTGAAAATTATATAATATATGG
2084631 TTTTT
1 TTTTT
2084636 GAAAACATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 18 0.45
37 10 0.25
38 2 0.05
39 1 0.03
40 9 0.22
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (40 bp):
TTTTTTTTATAGATCATTTTGAAAATTATATAATATATGG
Found at i:2084803 original size:73 final size:71
Alignment explanation
Indices: 2084614--2084899 Score: 278
Period size: 73 Copynumber: 4.0 Consensus size: 71
2084604 AATATTTTGA
* * * * *
2084614 AAATATATAATATATAGTTTTTGAAAACATTTTTGAAAATACATATTATATTGTTTTGAAAACTT
1 AAATATATATTATATAGATTTTGAAAACATTTTTAAAAATATATATTATATAGTTTTGAAAA-TT
2084679 --TTTTT
65 AGTTTTT
* * * *
2084684 AAATATATATAATATATAGCTTTTAAAAACATTTTGAAAAACATATATATTATATAATTTTGAAA
1 AAATATATAT--TATATAGATTTTGAAAACATTTT-TAAAA-ATATATATTATATAGTTTTGAAA
*
2084749 ATTAGTTTCT
62 ATTAGTTTTT
*
2084759 AAATATATATTATATA-ATTTTGAAAATTAGTTTTTAAAATATATATATTATATAGTTTTGAAAA
1 AAATATATATTATATAGATTTTGAAAA-CA-TTTTTAAAA-ATATATATTATATAGTTTTGAAAA
2084823 TTAGTTTTT
63 TTAGTTTTT
* ** ** * * *
2084832 AAAAATATATTATATA-ATTTTG--AATTTTTTTTTAAATATATGTTATGTGGTTTTGAAAATTA
1 AAATATATATTATATAGATTTTGAAAACATTTTTAAAAATATATATTATATAGTTTTGAAAATTA
*
2084894 TTTTTT
66 GTTTTT
2084900 TAAAAACATA
Statistics
Matches: 184, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
68 29 0.16
69 7 0.04
70 10 0.05
71 2 0.01
72 29 0.16
73 68 0.37
74 25 0.14
75 14 0.08
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (71 bp):
AAATATATATTATATAGATTTTGAAAACATTTTTAAAAATATATATTATATAGTTTTGAAAATTA
GTTTTT
Found at i:2084804 original size:38 final size:37
Alignment explanation
Indices: 2084608--2084937 Score: 242
Period size: 38 Copynumber: 9.2 Consensus size: 37
2084598 TTTTTAAATA
* * * *
2084608 TTTTGAAAATATATAATATATAGTTTTTGAAAA-CA-T
1 TTTTAAAAATATATATTATATA-ATTTTGAAAATTAGT
* * **
2084644 TTTTGAAAATACATATTATATTGTTTTGAAAACTT--T
1 TTTTAAAAATATATATTATATAATTTTGAAAA-TTAGT
* * * **
2084680 TTTTAAATATATATAATATATAGCTTTT-AAAAACA-T
1 TTTTAAAAATATATATTATATA-ATTTTGAAAATTAGT
*
2084716 TTTGAAAAACATATATATTATATAATTTTGAAAATTAGT
1 TTT-TAAAA-ATATATATTATATAATTTTGAAAATTAGT
*
2084755 TTCT--AAATATATATTATATAATTTTGAAAATTAGT
1 TTTTAAAAATATATATTATATAATTTTGAAAATTAGT
*
2084790 TTTTAAAATATATATATTATATAGTTTTGAAAATTAGT
1 TTTTAAAA-ATATATATTATATAATTTTGAAAATTAGT
2084828 TTTT-AAAA-ATATATTATATAATTTTG--AATT--T
1 TTTTAAAAATATATATTATATAATTTTGAAAATTAGT
** * * ** *
2084859 TTTTTTAAATATATGTTATGTGGTTTTGAAAATTATTT
1 TTTTAAAAATATATATTATATAATTTTGAAAATTA-GT
* * * *
2084897 TTTTAAAAACATATATTGTATAGTTTT-AAAAAT-GT
1 TTTTAAAAATATATATTATATAATTTTGAAAATTAGT
2084932 TTTTAA
1 TTTTAA
2084938 TTAATTTATT
Statistics
Matches: 238, Mismatches: 38, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
31 5 0.02
32 3 0.01
33 18 0.08
35 69 0.29
36 48 0.20
37 21 0.09
38 71 0.30
39 3 0.01
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (37 bp):
TTTTAAAAATATATATTATATAATTTTGAAAATTAGT
Found at i:2084847 original size:35 final size:36
Alignment explanation
Indices: 2084608--2084937 Score: 263
Period size: 35 Copynumber: 9.2 Consensus size: 36
2084598 TTTTTAAATA
* * *
2084608 TTTTGAAAATATATAATATATAGTTTTTGAAAA-CA-
1 TTTTTAAAATATATATTATATAG-TTTTGAAAATTAG
* *
2084643 TTTTTGAAAATACATATTATATTGTTTTGAAAACTT--
1 TTTTT-AAAATATATATTATATAGTTTTGAAAA-TTAG
* **
2084679 TTTTTAAATATATATAATATATAGCTTTT-AAAAACA-
1 TTTTTAAA-ATATATATTATATAG-TTTTGAAAATTAG
* *
2084715 TTTTGAAAAACATATATATTATATAATTTTGAAAATTAG
1 TTTT--TAAA-ATATATATTATATAGTTTTGAAAATTAG
* *
2084754 TTTCT-AAATATATATTATATAATTTTGAAAATTAG
1 TTTTTAAAATATATATTATATAGTTTTGAAAATTAG
2084789 TTTTTAAAATATATATATTATATAGTTTTGAAAATTAG
1 TTTTT-AAA-ATATATATTATATAGTTTTGAAAATTAG
* *
2084827 TTTTTAAAA-ATATATTATATAATTTTG--AATT-T
1 TTTTTAAAATATATATTATATAGTTTTGAAAATTAG
* * * * *
2084859 TTTTTTAAATATATGTTATGTGGTTTTGAAAATTATT
1 TTTTTAAAATATATATTATATAGTTTTGAAAATTA-G
* * *
2084896 TTTTTAAAAACATATATTGTATAGTTTT-AAAAAT-G
1 TTTTT-AAAATATATATTATATAGTTTTGAAAATTAG
2084931 TTTTTAA
1 TTTTTAA
2084938 TTAATTTATT
Statistics
Matches: 241, Mismatches: 35, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
32 8 0.03
33 18 0.07
34 2 0.01
35 74 0.31
36 43 0.18
37 24 0.10
38 69 0.29
39 3 0.01
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (36 bp):
TTTTTAAAATATATATTATATAGTTTTGAAAATTAG
Found at i:2084889 original size:106 final size:105
Alignment explanation
Indices: 2084650--2084937 Score: 278
Period size: 106 Copynumber: 2.7 Consensus size: 105
2084640 ACATTTTTGA
* ** * * * *
2084650 AAATACATATTATATTGTTTTGAAAACT-T-TTTTTAAATATATATAATATATAGCTTTTAAAAA
1 AAATATATATTATATAATTTTGAAAATTATGTTTTTAAAAACATATATTATATAG-TTTTAAAAA
** *
2084713 CATTTTGAAAAACATATATATTATATAATTTTGAAAATTAGTTTCT
65 TGTTTT--TAAA-A-ATATATTATATAATTTTG-AAATTAGTTTCT
*
2084759 AAATATATATTATATAATTTTGAAAATTA-GTTTTTAAAATATATATATTATATAGTTTTGAAAA
1 AAATATATATTATATAATTTTGAAAATTATGTTTTTAAAA-ACATATATTATATAGTTTT-AAAA
* ** *
2084823 TTAGTTTTTAAAAATATATTATATAATTTTG-AATTTTTTTTT
64 AT-GTTTTTAAAAATATATTATATAATTTTGAAATTAGTTTCT
* * ** * *
2084865 AAATATATGTTATGTGGTTTTGAAAATTATTTTTTTAAAAACATATATTGTATAGTTTTAAAAAT
1 AAATATATATTATATAATTTTGAAAATTATGTTTTTAAAAACATATATTATATAGTTTTAAAAAT
2084930 GTTTTTAA
66 GTTTTTAA
2084938 TTAATTTATT
Statistics
Matches: 152, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
104 8 0.05
105 5 0.03
106 50 0.33
107 9 0.06
108 18 0.12
109 25 0.16
110 15 0.10
111 18 0.12
112 4 0.03
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (105 bp):
AAATATATATTATATAATTTTGAAAATTATGTTTTTAAAAACATATATTATATAGTTTTAAAAAT
GTTTTTAAAAATATATTATATAATTTTGAAATTAGTTTCT
Found at i:2084965 original size:4 final size:4
Alignment explanation
Indices: 2084941--2084995 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
2084931 TTTTTAATTA
* * *
2084941 ATTT ATTA ATTT ATCT ATTT ATTT ATTT TTTT CATTT A-TT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT
2084989 ATTT ATT
1 ATTT ATT
2084996 ATTGTTTGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
3 3 0.07
4 37 0.86
5 3 0.07
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:2084968 original size:24 final size:23
Alignment explanation
Indices: 2084941--2084996 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
2084931 TTTTTAATTA
2084941 ATTTATTAATTTATCTATTTATTT
1 ATTTATTAATTTAT-TATTTATTT
* *
2084965 ATTTTTTTCATTTATTATTTATTT
1 A-TTTATTAATTTATTATTTATTT
2084989 ATTTATTA
1 ATTTATTA
2084997 TTGTTTGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.19
24 11 0.41
25 11 0.41
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTATTAATTTATTATTTATTT
Found at i:2085118 original size:30 final size:30
Alignment explanation
Indices: 2085084--2085143 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2085074 TTCTTGCTTA
2085084 GGGGACAACAGTAAACCCACAACGGATCGG
1 GGGGACAACAGTAAACCCACAACGGATCGG
*
2085114 GGGGACAACAGTAAACCCATAACGGATCGG
1 GGGGACAACAGTAAACCCACAACGGATCGG
2085144 CCGAGAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.30, T:0.08
Consensus pattern (30 bp):
GGGGACAACAGTAAACCCACAACGGATCGG
Found at i:2086203 original size:21 final size:20
Alignment explanation
Indices: 2086179--2086224 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2086169 TCTTTCATTT
2086179 TTATTATCTTTTTTATCTATC
1 TTATTATCTTTTTTAT-TATC
*
2086200 TTATT-TATTTTTTATTATC
1 TTATTATCTTTTTTATTATC
*
2086219 ATATTA
1 TTATTA
2086225 ACATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 8 0.36
20 9 0.41
21 5 0.23
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTATCTTTTTTATTATC
Found at i:2091368 original size:84 final size:84
Alignment explanation
Indices: 2091104--2091723 Score: 672
Period size: 84 Copynumber: 7.5 Consensus size: 84
2091094 TTTTTTAAAA
* * * * *
2091104 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTGACCAAAAGACCTTTGAGTTCG
2091169 ACTACGCTCAGCTCAACGG
66 ACTACGCTCAGCTCAACGG
* ***
2091188 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTGACCAAAAGACCTTTGAGTTCG
* * * * *
2091249 ATTGCACTCAGCTTCGAGGG
66 ACTACGCTCAGC-TCAACGG
* * * * *
2091269 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTGACCAAAAGACCTTTGAGTTCG
2091334 ACTACGCTCAGCTCAACGG
66 ACTACGCTCAGCTCAACGG
* ***
2091353 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTGACCAAAAGACCTTTGAGTTCG
* * * *
2091414 ATTACACTCAGCTTCGAGGG
66 ACTACGCTCAGC-TCAACGG
* * * * *
2091434 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTGACCAAAAGACCTTTGAGTTCG
2091499 ACTACGCTCAGCTCAACGG
66 ACTACGCTCAGCTCAACGG
* ***
2091518 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTGACCAAAAGACCTTTGAGTTCG
* *
2091579 ACTACGCTCAGCTCCAGGG
66 ACTACGCTCAGCTCAACGG
* * * * * * * ** *
2091598 CATATCATTTGCAACACAACTTAAGTCTAGAAAGGTTGTCTGCCATCAAAAGACCTTTGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTGACCAAAAGACCTTTGAGTTCG
2091663 ACTACGCTCAGCTCCAA-GG
66 ACTACGCTCAGCT-CAACGG
* *
2091682 CACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG
2091724 CTAAAGACCT
Statistics
Matches: 432, Mismatches: 89, Indels: 30
0.78 0.16 0.05
Matches are distributed among these distances:
80 110 0.25
81 84 0.19
82 6 0.01
83 5 0.01
84 178 0.41
85 49 0.11
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (84 bp):
CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTGACCAAAAGACCTTTGAGTTCG
ACTACGCTCAGCTCAACGG
Found at i:2091708 original size:164 final size:165
Alignment explanation
Indices: 2091104--2091746 Score: 1092
Period size: 165 Copynumber: 3.9 Consensus size: 165
2091094 TTTTTTAAAA
2091104 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
2091169 ACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
66 ACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
*
2091234 AGACCCCCGAGTTCGATTGCACTCAGCTTCGAGGG
131 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
2091269 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
2091334 ACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
66 ACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
2091399 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
131 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
2091434 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
2091499 ACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
66 ACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
* * *
2091564 AGACCCCCGAGTTCGACTACGCTCAGC-TCCAGGG
131 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
* * * * * * * * ** *
2091598 CATATCATTTGCAACACAACTTAAGTCTAGAAAGGTTGTCTGCCATCAAAAGACCTTTGAGTTCG
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
* *
2091663 ACTACGCTCAGCTCCAA-GGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCTA
66 ACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
**
2091727 AAGACCTTCGAGTTCGATTA
130 AAGACCCCCGAGTTCGATTA
2091747 TATTCAACTT
Statistics
Matches: 457, Mismatches: 20, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
164 135 0.30
165 322 0.70
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (165 bp):
CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCG
ACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
Found at i:2092441 original size:36 final size:36
Alignment explanation
Indices: 2092375--2092666 Score: 160
Period size: 36 Copynumber: 8.0 Consensus size: 36
2092365 TTTTTTATAG
*
2092375 TTTG-AAATCATTTTGAAAATTATATAATATATGGTTT
1 TTTGAAAAT-ATTTTGAAAA-TATATAATATATAGTTT
**
2092412 TTTTTAAATATTTTGAAAATATATAATATATAG-TT
1 TTTGAAAATATTTTGAAAATATATAATATATAGTTT
* *
2092447 TTTGAAAACATTTTTGAAAATACAT-AT-TATA-TTGT
1 TTTGAAAATA-TTTTGAAAATATATAATATATAGTT-T
* * *
2092482 TTTGAAAACTTTTTTTAAATATATATAATATATAG-CT
1 TTTGAAAA-TATTTTGAAA-ATATATAATATATAGTTT
* * * *
2092519 TTTAAAAACATTTTGAAAA-ACATATATATTATA-TAAT
1 TTTGAAAATATTTTGAAAATATATA-ATA-TATAGT-TT
* ** * *
2092556 TTTGAAAATTAGTTTCTAAATATATATTATATA--AT
1 TTTGAAAA-TATTTTGAAAATATATAATATATAGTTT
*
2092591 TTTGAAAATTAGTTTTTAAAATATATATATTATATAG-TT
1 TTTGAAAA-TA-TTTTGAAAATATATA-A-TATATAGTTT
* * *
2092630 TTT-AAAATTAGTTTTTAAAA-ATATATTATATAATTT
1 TTTGAAAA-TA-TTTTGAAAATATATAATATATAGTTT
2092666 T
1 T
2092667 GAATTTTTTT
Statistics
Matches: 204, Mismatches: 31, Indels: 41
0.74 0.11 0.15
Matches are distributed among these distances:
34 9 0.04
35 50 0.25
36 57 0.28
37 40 0.20
38 40 0.20
39 8 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (36 bp):
TTTGAAAATATTTTGAAAATATATAATATATAGTTT
Found at i:2092459 original size:72 final size:71
Alignment explanation
Indices: 2092375--2092548 Score: 194
Period size: 72 Copynumber: 2.5 Consensus size: 71
2092365 TTTTTTATAG
* * * **
2092375 TTTGAAATCATTTTGAAAATTATATAATATATGGTTTTTTTTAAA-TATTTTGAAA-ATATATAA
1 TTTGAAAACATTTTGAAAA-TACATAATATAT--TGTTTTGAAAACTATTTTGAAATATATATAA
*
2092438 TATATAGTT
63 TATATAGCT
* * *
2092447 TTTGAAAACATTTTTGAAAATACATATTATATTGTTTTGAAAACTTTTTTTAAATATATATAATA
1 TTTGAAAACA-TTTTGAAAATACATAATATATTGTTTTGAAAACTATTTTGAAATATATATAATA
2092512 TATAGCT
65 TATAGCT
*
2092519 TTTAAAAACATTTTGAAAA-ACAT-ATATATT
1 TTTGAAAACATTTTGAAAATACATAATATATT
2092549 ATATAATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
69 6 0.07
70 12 0.14
71 17 0.19
72 44 0.50
73 9 0.10
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (71 bp):
TTTGAAAACATTTTGAAAATACATAATATATTGTTTTGAAAACTATTTTGAAATATATATAATAT
ATAGCT
Found at i:2092617 original size:73 final size:71
Alignment explanation
Indices: 2092428--2092713 Score: 269
Period size: 73 Copynumber: 4.0 Consensus size: 71
2092418 AATATTTTGA
* * * * *
2092428 AAATATATAATATATAGTTTTTGAAAACATTTTTGAAAATACATATTATATTGTTTTGAAAACTT
1 AAATATATATTATATAGATTTTGAAAACATTTTTAAAAATATATATTATATAGTTTTGAAAA-TT
2092493 --TTTTT
65 AGTTTTT
* * * *
2092498 AAATATATATAATATATAGCTTTTAAAAACATTTTGAAAAACATATATATTATATAATTTTGAAA
1 AAATATATAT--TATATAGATTTTGAAAACATTTT-TAAAA-ATATATATTATATAGTTTTGAAA
*
2092563 ATTAGTTTCT
62 ATTAGTTTTT
* *
2092573 AAATATATATTATATA-ATTTTGAAAATTAGTTTTTAAAATATATATATTATATAGTTTTTAAAA
1 AAATATATATTATATAGATTTTGAAAA-CA-TTTTTAAAA-ATATATATTATATAGTTTTGAAAA
2092637 TTAGTTTTT
63 TTAGTTTTT
* ** ** * * *
2092646 AAAAATATATTATATA-ATTTTG--AATTTTTTTTTAAATATATGTTATGTGGTTTTGAAAATTA
1 AAATATATATTATATAGATTTTGAAAACATTTTTAAAAATATATATTATATAGTTTTGAAAATTA
*
2092708 TTTTTT
66 GTTTTT
2092714 TAAAAACATA
Statistics
Matches: 182, Mismatches: 26, Indels: 18
0.81 0.12 0.08
Matches are distributed among these distances:
68 28 0.15
69 7 0.04
70 10 0.05
71 2 0.01
72 29 0.16
73 67 0.37
74 25 0.14
75 14 0.08
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (71 bp):
AAATATATATTATATAGATTTTGAAAACATTTTTAAAAATATATATTATATAGTTTTGAAAATTA
GTTTTT
Found at i:2092618 original size:38 final size:37
Alignment explanation
Indices: 2092422--2092751 Score: 233
Period size: 38 Copynumber: 9.2 Consensus size: 37
2092412 TTTTTAAATA
* * * *
2092422 TTTTGAAAATATATAATATATAGTTTTTGAAAA-CA-T
1 TTTTAAAAATATATATTATATA-ATTTTGAAAATTAGT
* * **
2092458 TTTTGAAAATACATATTATATTGTTTTGAAAACTT--T
1 TTTTAAAAATATATATTATATAATTTTGAAAA-TTAGT
* * * **
2092494 TTTTAAATATATATAATATATAGCTTTT-AAAAACA-T
1 TTTTAAAAATATATATTATATA-ATTTTGAAAATTAGT
*
2092530 TTTGAAAAACATATATATTATATAATTTTGAAAATTAGT
1 TTT-TAAAA-ATATATATTATATAATTTTGAAAATTAGT
*
2092569 TTCT--AAATATATATTATATAATTTTGAAAATTAGT
1 TTTTAAAAATATATATTATATAATTTTGAAAATTAGT
* *
2092604 TTTTAAAATATATATATTATATAGTTTTTAAAATTAGT
1 TTTTAAAA-ATATATATTATATAATTTTGAAAATTAGT
2092642 TTTT-AAAA-ATATATTATATAATTTTG--AATT--T
1 TTTTAAAAATATATATTATATAATTTTGAAAATTAGT
** * * ** *
2092673 TTTTTTAAATATATGTTATGTGGTTTTGAAAATTATTT
1 TTTTAAAAATATATATTATATAATTTTGAAAATTA-GT
* * * *
2092711 TTTTAAAAACATATATTGTATAGTTTT-AAAAAT-GT
1 TTTTAAAAATATATATTATATAATTTTGAAAATTAGT
2092746 TTTTAA
1 TTTTAA
2092752 TTAATTTATT
Statistics
Matches: 236, Mismatches: 40, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
31 5 0.02
32 3 0.01
33 18 0.08
35 68 0.29
36 48 0.20
37 21 0.09
38 70 0.30
39 3 0.01
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (37 bp):
TTTTAAAAATATATATTATATAATTTTGAAAATTAGT
Found at i:2092651 original size:14 final size:13
Alignment explanation
Indices: 2092590--2092649 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
2092580 TATTATATAA
*
2092590 TTTTGAAAATTAG
1 TTTTTAAAATTAG
2092603 TTTTTAAAATATA-
1 TTTTTAAAAT-TAG
* *
2092616 TATATT-ATA-TAG
1 T-TTTTAAAATTAG
2092628 TTTTTAAAATTAG
1 TTTTTAAAATTAG
2092641 TTTTTAAAA
1 TTTTTAAAA
2092650 ATATATTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
11 5 0.14
12 3 0.08
13 24 0.65
14 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
TTTTTAAAATTAG
Found at i:2092775 original size:25 final size:24
Alignment explanation
Indices: 2092747--2092811 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 24
2092737 TAAAAATGTT
2092747 TTTAATTAATTTATTAATTTATCTA
1 TTTAATTAATTTATTAATTTAT-TA
* * * *
2092772 TTTATTTATTTTTTTTCATTTATTA
1 TTTAATTA-ATTTATTAATTTATTA
*
2092797 TTT-ATTTATTTATTA
1 TTTAATTAATTTATTA
2092812 TTGTTTGTTT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
23 5 0.17
24 2 0.07
25 12 0.40
26 11 0.37
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTAATTAATTTATTAATTTATTA
Found at i:2092779 original size:4 final size:4
Alignment explanation
Indices: 2092755--2092810 Score: 64
Period size: 4 Copynumber: 14.8 Consensus size: 4
2092745 TTTTTAATTA
* * *
2092755 ATTT ATTA ATTT ATCT ATTT ATTT ATTT -TTT -TTC ATTT A-TT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2092800 ATTT ATTT ATT
1 ATTT ATTT ATT
2092811 ATTGTTTGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
3 8 0.18
4 36 0.82
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:2092784 original size:106 final size:106
Alignment explanation
Indices: 2092464--2092751 Score: 284
Period size: 106 Copynumber: 2.7 Consensus size: 106
2092454 ACATTTTTGA
* ** * * *
2092464 AAATACATATTATATTGTTTTGAAAACTT--TTTTT-AAATATATATAATATATAGCTTTTAAAA
1 AAATATATATTATATAATTTTGAAAA-TTAGTTTTTAAAATACATATATTATATAGTTTTTAAAA
* * * *
2092526 ACA-TTTTGAAAAACATATATATTATATAATTTTGAAAATTAGTTTCT
65 ATAGTTTT--TAAA-A-ATATATTATATAATTTTG-AATTTA-TTTTT
* *
2092573 AAATATATATTATATAATTTTGAAAATTAGTTTTTAAAATATATATATTATATAGTTTTTAAAAT
1 AAATATATATTATATAATTTTGAAAATTAGTTTTTAAAATACATATATTATATAGTTTTTAAAAA
*
2092638 TAGTTTTTAAAAATATATTATATAATTTTGAATTTTTTTTT
66 TAGTTTTTAAAAATATATTATATAATTTTGAATTTATTTTT
* * ** * *
2092679 AAATATATGTTATGTGGTTTTGAAAATTATTTTTTTAAAA-ACATATATTGTATAG-TTTTAAAA
1 AAATATATATTATATAATTTTGAAAATTA-GTTTTTAAAATACATATATTATATAGTTTTTAAAA
2092742 AT-GTTTTTAA
65 ATAGTTTTTAA
2092752 TTAATTTATT
Statistics
Matches: 155, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
104 8 0.05
105 9 0.06
106 42 0.27
107 13 0.08
108 20 0.13
109 24 0.15
110 8 0.05
111 27 0.17
112 4 0.03
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (106 bp):
AAATATATATTATATAATTTTGAAAATTAGTTTTTAAAATACATATATTATATAGTTTTTAAAAA
TAGTTTTTAAAAATATATTATATAATTTTGAATTTATTTTT
Found at i:2092933 original size:30 final size:30
Alignment explanation
Indices: 2092899--2092956 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
2092889 TTCTTGCTTA
2092899 GGGGACAACAGTAAACCCACAACGGATCAG
1 GGGGACAACAGTAAACCCACAACGGATCAG
2092929 GGGGACAACAGTAAACCCACAACGGATC
1 GGGGACAACAGTAAACCCACAACGGATC
2092957 GGCCGAGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.28, G:0.26, T:0.07
Consensus pattern (30 bp):
GGGGACAACAGTAAACCCACAACGGATCAG
Found at i:2100294 original size:55 final size:55
Alignment explanation
Indices: 2100210--2100793 Score: 845
Period size: 55 Copynumber: 10.7 Consensus size: 55
2100200 CTCCATAGTC
* *
2100210 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATTGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * ** * *
2100265 CTTCAGAGAGTATAAGACTCAAACAATCTTTAATGATCACGTCTGCCCCCCATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
*
2100320 CTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
2100373 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
2100428 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * * *
2100481 CTTCAGAGAGTATAAGACCCAAACAATCTTCAACAATCGTGTCCGCCCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
2100536 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
2100591 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
2100646 CCTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCT-CCCCTTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
2100700 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
2100755 CTTCAGAGAGTATGAGACTTGAACAATCTTCAACGATCG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
2100794 TAGGGAACCT
Statistics
Matches: 478, Mismatches: 46, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
53 95 0.20
54 51 0.11
55 332 0.69
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
Found at i:2100401 original size:108 final size:109
Alignment explanation
Indices: 2100210--2100793 Score: 841
Period size: 108 Copynumber: 5.3 Consensus size: 109
2100200 CTCCATAGTC
* *
2100210 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATTGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * * * * *
2100275 TATAAGACTCAAACAATCTTTAATGATCACGTCTGCCCCCCATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* *
2100320 CTTCAGAGAGTATAAGACTC-ACAATCTTCATCAATCGCGTCTGCCCCCTATTTCGTCAGAGAGT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
*
2100384 ATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
66 ATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* *
2100428 CTTCAGAGAGTATAAGAC-CCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
* * * * *
2100492 ATAAGACCCAAACAATCTTCAACAATCGTGTCCGCCCTCTATTT
66 ATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* *
2100536 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCTCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * *
2100601 TATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* * *
2100646 CCTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCT-CCCCTTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
*
2100710 TATAAGACTTGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* * *
2100755 CTTCAGAGAGTATGAGACTTGAACAATCTTCAACGATCG
1 CTTCAGAGAGTATAAGAC-TCAACAATCTTCAACAATCG
2100794 TAGGGAACCT
Statistics
Matches: 436, Mismatches: 34, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
107 1 0.00
108 196 0.45
109 93 0.21
110 146 0.33
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (109 bp):
CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
ATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
Found at i:2100509 original size:163 final size:162
Alignment explanation
Indices: 2100210--2100772 Score: 826
Period size: 163 Copynumber: 3.5 Consensus size: 162
2100200 CTCCATAGTC
* * *
2100210 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATTGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * * * *
2100275 TATAAGACTCAAACAATCTTTAAT-GATCACGTCTGCCCCCCATTTCTTCAGAGAGTATAAGACT
66 TATAAGAC-C-CACAATC-TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACT
*
2100339 C-ACAATCTTCATCAATCGCGTCTGCCCCCTATTT
128 CAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
*
2100373 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
*
2100438 TATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCAA
66 TATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-A
* * *
2100503 ACAATCTTCAACAATCGTGTCCGCCCTCTATTT
130 ACAATCTTCAACAATCGCGTCTGCCCCCTATTT
*
2100536 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCTCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * * *
2100601 TATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCCTCAGAGAGTATAAGACTC
66 TATAAGACCC--ACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
* *
2100666 GAACAATCTTCAACTATCGCGTCT-CCCCTTATTT
129 -AACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
2100700 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCGTCCGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
*
2100765 TATGAGAC
66 TATAAGAC
2100773 TTGAACAATC
Statistics
Matches: 364, Mismatches: 31, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
160 4 0.01
161 43 0.12
162 1 0.00
163 171 0.47
164 77 0.21
165 68 0.19
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (162 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
TATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAA
CAATCTTCAACAATCGCGTCTGCCCCCTATTT
Found at i:2113087 original size:20 final size:20
Alignment explanation
Indices: 2113064--2113132 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
2113054 AACAACCTTC
2113064 AATTTAAAAAAATATATATA
1 AATTTAAAAAAATATATATA
* * *
2113084 AATTCATAAATATATATATA
1 AATTTAAAAAAATATATATA
* * *
2113104 TATTATAAAATACATATGTATA
1 AATT-TAAAA-AAATATATATA
2113126 TAATTTA
1 -AATTTA
2113133 CATAAAAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
20 20 0.54
21 3 0.08
22 11 0.30
23 3 0.08
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (20 bp):
AATTTAAAAAAATATATATA
Found at i:2113120 original size:18 final size:19
Alignment explanation
Indices: 2113072--2113120 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
2113062 TCAATTTAAA
2113072 AAAATATATATAAATTCAT
1 AAAATATATATAAATTCAT
*
2113091 AAATATATATATATATT-AT
1 AAA-ATATATATAAATTCAT
*
2113110 AAAATACATAT
1 AAAATATATAT
2113121 GTATATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 7 0.26
19 8 0.30
20 12 0.44
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATATATATAAATTCAT
Found at i:2113951 original size:3 final size:3
Alignment explanation
Indices: 2113943--2113988 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
2113933 GTTTCTAATA
* *
2113943 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2113989 TGTGGGTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2113961 original size:15 final size:15
Alignment explanation
Indices: 2113943--2113986 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
2113933 GTTTCTAATA
2113943 TATTATTATTATTAC
1 TATTATTATTATTAC
2113958 TATTATTATTATTAC
1 TATTATTATTATTAC
2113973 TATTATTATTATTA
1 TATTATTATTATTA
2113987 TTTGTGGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:2114973 original size:18 final size:19
Alignment explanation
Indices: 2114940--2114977 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2114930 GAATGAATCA
2114940 AAATTATAAAATATTAAAT
1 AAATTATAAAATATTAAAT
*
2114959 AAATTAT-ATATATTAAAT
1 AAATTATAAAATATTAAAT
2114977 A
1 A
2114978 CATATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTATAAAATATTAAAT
Found at i:2118441 original size:29 final size:29
Alignment explanation
Indices: 2118403--2118465 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
2118393 CGTTTTCCCT
* * * *
2118403 TTTATTTTTCAGTATTTCAATTTTAGTTC
1 TTTAATTTTCAGCATTTAAATTTTAGTCC
2118432 TTTAATTTTCAGCATTTAAATTTTAGTCC
1 TTTAATTTTCAGCATTTAAATTTTAGTCC
2118461 TTTAA
1 TTTAA
2118466 ATTCTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.57
Consensus pattern (29 bp):
TTTAATTTTCAGCATTTAAATTTTAGTCC
Found at i:2129331 original size:15 final size:16
Alignment explanation
Indices: 2129305--2129341 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2129295 TCCTAAATGC
*
2129305 ATGAAAACTAAATTAA
1 ATGAAAACTAAATGAA
2129321 ATGAAAA-TAAATGAA
1 ATGAAAACTAAATGAA
2129336 ATGAAA
1 ATGAAA
2129342 TGCAAGGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.22
Consensus pattern (16 bp):
ATGAAAACTAAATGAA
Found at i:2131229 original size:22 final size:21
Alignment explanation
Indices: 2131163--2131242 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 21
2131153 TTCTACGTGG
* *
2131163 TCCTTCGGGACATATATGT-A
1 TCCTTTGGAACATATATGTGA
* *
2131183 TCCTTTGGAACATATATGAGG
1 TCCTTTGGAACATATATGTGA
*
2131204 TCCTTCTTGG-ACATATATTTGA
1 TCC-T-TTGGAACATATATGTGA
2131226 TCCTTTGGAACATATAT
1 TCCTTTGGAACATATAT
2131243 ATGGTCCTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 20 0.41
21 12 0.24
22 13 0.27
23 4 0.08
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (21 bp):
TCCTTTGGAACATATATGTGA
Found at i:2131234 original size:43 final size:41
Alignment explanation
Indices: 2131160--2131258 Score: 137
Period size: 43 Copynumber: 2.4 Consensus size: 41
2131150 TAGTTCTACG
2131160 TGGTCCTTCGGGACATATATGTATCCTTTGGAACATATATGA
1 TGGTCCTTCGGGACATATATGTATCCTTTGGAACATATAT-A
* *
2131202 -GGTCCTTCTTGGACATATATTTGATCCTTTGGAACATATATA
1 TGGTCCTTC-GGGACATATATGT-ATCCTTTGGAACATATATA
*
2131244 TGGTCCTACGGGACA
1 TGGTCCTTCGGGACA
2131259 ATTCTATGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
41 8 0.16
42 17 0.34
43 25 0.50
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (41 bp):
TGGTCCTTCGGGACATATATGTATCCTTTGGAACATATATA
Found at i:2131250 original size:21 final size:21
Alignment explanation
Indices: 2131160--2131250 Score: 80
Period size: 20 Copynumber: 4.3 Consensus size: 21
2131150 TAGTTCTACG
* * *
2131160 TGGTCCTTCGGGACATATATG
1 TGGTCCTTTGGAACATATATA
*
2131181 T-ATCCTTTGGAACATATATGA
1 TGGTCCTTTGGAACATATAT-A
*
2131202 -GGTCCTTCTTGG-ACATATATT
1 TGGTCC-T-TTGGAACATATATA
*
2131223 TGATCCTTTGGAACATATATA
1 TGGTCCTTTGGAACATATATA
2131244 TGGTCCT
1 TGGTCCT
2131251 ACGGGACAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
20 19 0.35
21 19 0.35
22 13 0.24
23 4 0.07
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (21 bp):
TGGTCCTTTGGAACATATATA
Found at i:2131271 original size:23 final size:23
Alignment explanation
Indices: 2131244--2131302 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
2131234 AACATATATA
2131244 TGGTCCTACGGGACAATTCTATG
1 TGGTCCTACGGGACAATTCTATG
*
2131267 TGGTCCTACTGGACAATTCTATG
1 TGGTCCTACGGGACAATTCTATG
2131290 TGGTCCTACGGGA
1 TGGTCCTACGGGA
2131303 TATATATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (23 bp):
TGGTCCTACGGGACAATTCTATG
Found at i:2138293 original size:21 final size:21
Alignment explanation
Indices: 2138269--2138357 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 21
2138259 GACCTTCGGG
2138269 ACATATATGTGATCCTTTGGA
1 ACATATATGTGATCCTTTGGA
* *
2138290 ACATATATGAGGTCCTTCTTGG-
1 ACATATATGTGATCC-T-TTGGA
* *
2138312 ACATATATTTGATTCTTTGGA
1 ACATATATGTGATCCTTTGGA
* * * *
2138333 ATATATATGTGGTCATTTGGG
1 ACATATATGTGATCCTTTGGA
2138354 ACAT
1 ACAT
2138358 TTTATATGGC
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
20 4 0.08
21 32 0.62
22 12 0.23
23 4 0.08
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.40
Consensus pattern (21 bp):
ACATATATGTGATCCTTTGGA
Found at i:2138388 original size:23 final size:22
Alignment explanation
Indices: 2138355--2138408 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
2138345 TCATTTGGGA
*
2138355 CATTTTATATGGCACTTCGGTG
1 CATTTTATATGGCACTTAGGTG
*
2138377 CATTTCTATATGGTACTTAGGTG
1 CATTT-TATATGGCACTTAGGTG
2138400 CATTTTATA
1 CATTTTATA
2138409 CGAGCTGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (22 bp):
CATTTTATATGGCACTTAGGTG
Found at i:2142396 original size:20 final size:20
Alignment explanation
Indices: 2142335--2142404 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
2142325 CTTCTTCATG
* *
2142335 AGGTATCGATACTGAAAAGGT
1 AGGTATCGATAC-CATAAGGT
2142356 A-GTATCGATA-C-TAA-G-
1 AGGTATCGATACCATAAGGT
2142371 -GGTATCGATACCATAAGGT
1 AGGTATCGATACCATAAGGT
2142390 AGGTATCGATACCAT
1 AGGTATCGATACCAT
2142405 TTTGGAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
15 9 0.22
16 2 0.05
17 5 0.12
18 1 0.02
20 23 0.56
21 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (20 bp):
AGGTATCGATACCATAAGGT
Found at i:2143139 original size:43 final size:42
Alignment explanation
Indices: 2143072--2143170 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 42
2143062 GGTTCTACGT
*
2143072 GGTCCTTCGGGACATATATGTGATCCTTTGGAACATATATGA
1 GGTCCTTCGGGACATATATGTGATCATTTGGAACATATATGA
* * * *
2143114 GGTCCTTCTTGGATATATATTTGATCATTTGGAACATATATGT
1 GGTCCTTC-GGGACATATATGTGATCATTTGGAACATATATGA
2143157 GGTCCTAT-GGGACA
1 GGTCCT-TCGGGACA
2143171 ATTCTATATG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
42 12 0.25
43 35 0.73
44 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (42 bp):
GGTCCTTCGGGACATATATGTGATCATTTGGAACATATATGA
Found at i:2143214 original size:21 final size:20
Alignment explanation
Indices: 2143070--2143215 Score: 85
Period size: 21 Copynumber: 6.8 Consensus size: 20
2143060 AGGGTTCTAC
*
2143070 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTT-TGGACATATAT
*
2143091 GTGATCCTTTGGAACATATAT
1 GTGGTCCTTTGG-ACATATAT
* *
2143112 GAGGTCCTTCTTGGATATATAT
1 GTGGTCC-T-TTGGACATATAT
* * *
2143134 TTGATCATTTGGAACATATAT
1 GTGGTCCTTTGG-ACATATAT
* *
2143155 GTGGTCCTATGGGACAATTCTAT
1 GTGGTCCT-TTGGAC-A-TATAT
* * **
2143178 ATGGTCATACGAGACATATAT
1 GTGGTCCTTTG-GACATATAT
2143199 GTGGTCCTTTAGGACAT
1 GTGGTCCTTT-GGACAT
2143216 TTTATATGTC
Statistics
Matches: 92, Mismatches: 24, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
20 6 0.07
21 51 0.55
22 18 0.20
23 17 0.18
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (20 bp):
GTGGTCCTTTGGACATATAT
Found at i:2146669 original size:16 final size:16
Alignment explanation
Indices: 2146637--2146676 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2146627 GAAAATAATG
2146637 ATTGAAAGGAATGGAA
1 ATTGAAAGGAATGGAA
2146653 ATTGATAAGGAAT-GAA
1 ATTGA-AAGGAATGGAA
*
2146669 ATAGAAAG
1 ATTGAAAG
2146677 AATTGATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 12 0.55
17 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.20
Consensus pattern (16 bp):
ATTGAAAGGAATGGAA
Found at i:2148697 original size:14 final size:14
Alignment explanation
Indices: 2148678--2148705 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2148668 GATGATGGAG
2148678 GATGGTGATGGAAA
1 GATGGTGATGGAAA
2148692 GATGGTGATGGAAA
1 GATGGTGATGGAAA
2148706 TAGATAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:2149931 original size:20 final size:20
Alignment explanation
Indices: 2149906--2149993 Score: 58
Period size: 20 Copynumber: 4.4 Consensus size: 20
2149896 CTTTGCATGA
2149906 TATCGATATAGCCCTATAAG
1 TATCGATATAGCCCTATAAG
** *
2149926 TATCGATACTAGTTC-ATTAG
1 TATCGATA-TAGCCCTATAAG
* *
2149946 TATTG--ATA-CCCTATGCATG
1 TATCGATATAGCCCTAT--AAG
*
2149965 ATATCGATATAGCCCTAAAAG
1 -TATCGATATAGCCCTATAAG
2149986 TATCGATA
1 TATCGATA
2149994 CCCTATGTAG
Statistics
Matches: 49, Mismatches: 11, Indels: 16
0.64 0.14 0.21
Matches are distributed among these distances:
16 1 0.02
17 4 0.08
18 1 0.02
19 1 0.02
20 28 0.57
21 6 0.12
22 3 0.06
23 5 0.10
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (20 bp):
TATCGATATAGCCCTATAAG
Found at i:2163920 original size:500 final size:500
Alignment explanation
Indices: 2162976--2163950 Score: 1644
Period size: 500 Copynumber: 1.9 Consensus size: 500
2162966 TCAATCTAAC
*
2162976 TCTACGAGACAAATGGTGCAACTGTGGGTTTTTTTAAGCTCTGAAGTATCCATACTCTCATGTCA
1 TCTACGAGACAAATGGTGCAACTGTGGGTTTTTTCAAGCTCTGAAGTATCCATACTCTCATGTCA
* *
2163041 TAGCAACTTGCTCGCATACCCATCAAGACTATAATTGTTTCATGGATCTCGTATGATATGATCTC
66 TAGCAACTTGCTCACATACCCATCAAGACTATAACTGTTTCATGGATCTCGTATGATATGATCTC
*
2163106 GATTATGAGTTTCAAGTCATATATATGATTTCCCGATCATGATTCTAGTAAGAGATTGAATTGCT
131 GATTATGAGTTTCAAGTCATATATATGACTTCCCGATCATGATTCTAGTAAGAGATTGAATTGCT
* * *
2163171 TTCTTTGAACCTGAAAATCATGACTTGTAAGATGTTAATGAAAGATAGAGATGTAATGGAAATGA
196 TGCTTTGAACCTGAAAATCATGACTTATAAGATGTTAATGAAAAATAGAGATGTAATGGAAATGA
* * *
2163236 AGGATTTATATGGAAATGAATTTTAGGATTTGGTTAAGTACGGAAGATGATGGAAGTTTTAGTTT
261 AGGATTGATATGGAAATGAATTTTAGGATTTGGTTAAGTACGAAAGATGATGGAAGTTGTAGTTT
* *
2163301 GGATGGAATTGAAGTATGGAGAAAGTATGGGTTGGTAATGGCGTGGAACGTGTAAGATGGATTGA
326 GGATGGAATTGAAGTATGGAGAAAGTATGGGTTGGTAATGGCGTGGAACGTGTAAAATGGAATGA
* * * *
2163366 AAAGAAAACAGATTGTGACCCTCTAATTATATGGAGTTAGGAACCAACAATATAAAGAGATGGAA
391 AAAGAAAACAGATTGTCACCCTCTAACTATATGGAGTTAGGAACCAAAAATATAAAGAAATGGAA
*
2163431 TCGAAGTGGAACTAGATGGATTCAAGCTATCTCGTTCAGAGTTAA
456 TCAAAGTGGAACTAGATGGATTCAAGCTATCTCGTTCAGAGTTAA
* *
2163476 TCTACGAGACAGATGGTGTAACTGTGGGTTTTTTCAAGCTCTGAAGTATCCATACTCTCATGTCA
1 TCTACGAGACAAATGGTGCAACTGTGGGTTTTTTCAAGCTCTGAAGTATCCATACTCTCATGTCA
2163541 TAGCAACTTGCTCACATACCCATCAAGACTATAACTGTTTCATGGATCTCGTATGATATGATCTC
66 TAGCAACTTGCTCACATACCCATCAAGACTATAACTGTTTCATGGATCTCGTATGATATGATCTC
* * * *
2163606 GATTATGAGTTTCAAGTCATATATATGACTTCTCTATCATGATTCTAGTATGATATTGAATTGCT
131 GATTATGAGTTTCAAGTCATATATATGACTTCCCGATCATGATTCTAGTAAGAGATTGAATTGCT
2163671 TGCTTTGAACCTGAAAATCATGACTTATAAGATGTTAATGAAAAATAGAGATGTAATGGAAATGA
196 TGCTTTGAACCTGAAAATCATGACTTATAAGATGTTAATGAAAAATAGAGATGTAATGGAAATGA
* * * *
2163736 AGGATTGATATGGAAATTATTTTTAGGATTTGGTTAAGTACGAAAGATTATGGAAGTTGTATTTT
261 AGGATTGATATGGAAATGAATTTTAGGATTTGGTTAAGTACGAAAGATGATGGAAGTTGTAGTTT
* * * *
2163801 GGATGGAATTGAAGTATGTAGAAGGTATGGGTTGTTAATGGCGTGGAATGTGTAAAATGGAATGA
326 GGATGGAATTGAAGTATGGAGAAAGTATGGGTTGGTAATGGCGTGGAACGTGTAAAATGGAATGA
* *
2163866 AAAGAAAACAGATTGTCACCCTCTAACTATATTGAGTTAGGAACTAAAAATATAAAGAAATGGAA
391 AAAGAAAACAGATTGTCACCCTCTAACTATATGGAGTTAGGAACCAAAAATATAAAGAAATGGAA
*
2163931 TCAAAGTGGAAGTAGATGGA
456 TCAAAGTGGAACTAGATGGA
2163951 ACATGACCCA
Statistics
Matches: 441, Mismatches: 34, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
500 441 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (500 bp):
TCTACGAGACAAATGGTGCAACTGTGGGTTTTTTCAAGCTCTGAAGTATCCATACTCTCATGTCA
TAGCAACTTGCTCACATACCCATCAAGACTATAACTGTTTCATGGATCTCGTATGATATGATCTC
GATTATGAGTTTCAAGTCATATATATGACTTCCCGATCATGATTCTAGTAAGAGATTGAATTGCT
TGCTTTGAACCTGAAAATCATGACTTATAAGATGTTAATGAAAAATAGAGATGTAATGGAAATGA
AGGATTGATATGGAAATGAATTTTAGGATTTGGTTAAGTACGAAAGATGATGGAAGTTGTAGTTT
GGATGGAATTGAAGTATGGAGAAAGTATGGGTTGGTAATGGCGTGGAACGTGTAAAATGGAATGA
AAAGAAAACAGATTGTCACCCTCTAACTATATGGAGTTAGGAACCAAAAATATAAAGAAATGGAA
TCAAAGTGGAACTAGATGGATTCAAGCTATCTCGTTCAGAGTTAA
Found at i:2164857 original size:17 final size:17
Alignment explanation
Indices: 2164835--2164887 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
2164825 AATTAAGAGT
2164835 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
*
2164852 TAGTTTGATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
2164869 CAATTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
2164886 TA
1 TA
2164888 ACTTTCTTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2164982 original size:17 final size:17
Alignment explanation
Indices: 2164962--2165014 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
2164952 ACTACTTCCC
*
2164962 TAAATGAAATACATGCT
1 TAAATGAAATACATACT
* * *
2164979 TAAATGCAATGCATTCT
1 TAAATGAAATACATACT
* *
2164996 TTAATGAAAAACATACT
1 TAAATGAAATACATACT
2165013 TA
1 TA
2165015 TTAAATACAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (17 bp):
TAAATGAAATACATACT
Found at i:2175103 original size:27 final size:27
Alignment explanation
Indices: 2175052--2175103 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2175042 TATAACTATG
* *
2175052 TGGTGGTGGCAACATCTGGTGTGGAAA
1 TGGTGGTGGCAACATCTGATATGGAAA
*
2175079 TGGTGGTGGCGACATCTGATATGGA
1 TGGTGGTGGCAACATCTGATATGGA
2175104 TGCGGTGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.40, T:0.27
Consensus pattern (27 bp):
TGGTGGTGGCAACATCTGATATGGAAA
Found at i:2180771 original size:26 final size:26
Alignment explanation
Indices: 2180719--2180771 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2180709 GGGTAACTCG
*
2180719 TTTATGAGATTTACTGCAGTATAATT
1 TTTATGAGATTTACTGCACTATAATT
* *
2180745 TTTATGAGATTTACTGGACTATGATT
1 TTTATGAGATTTACTGCACTATAATT
2180771 T
1 T
2180772 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (26 bp):
TTTATGAGATTTACTGCACTATAATT
Found at i:2182792 original size:19 final size:19
Alignment explanation
Indices: 2182753--2182788 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2182743 ACCTTGTGCA
*
2182753 TTTGCATTTGCATTATTAT
1 TTTGCATTAGCATTATTAT
2182772 TTTGCATTAGC-TTATTA
1 TTTGCATTAGCATTATTA
2182789 ATTTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTGCATTAGCATTATTAT
Found at i:2188295 original size:37 final size:37
Alignment explanation
Indices: 2188249--2188434 Score: 293
Period size: 37 Copynumber: 5.0 Consensus size: 37
2188239 TGAGATTGGG
*
2188249 GCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAA
2188286 GCAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAA
*
2188323 GCAAATCAATCTTAAGCCTTTACGGAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAA
* ** *
2188360 GCAAATCAATCTTATGTTTTTCATGGAAGAGTAGTGAA
1 GCAAATCAATCTTAAG-CCTTCACGGAAGAGTAGTGAA
2188398 GCAAATCAATCTTAAGCCTTCACAGG-AGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCAC-GGAAGAGTAGTGAA
2188435 TCAAGCCATC
Statistics
Matches: 136, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
37 102 0.75
38 34 0.25
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAA
Found at i:2188416 original size:75 final size:74
Alignment explanation
Indices: 2188249--2188434 Score: 293
Period size: 75 Copynumber: 2.5 Consensus size: 74
2188239 TGAGATTGGG
*
2188249 GCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACGGAAG
1 GCAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACGGAAG
2188314 AGTAGTGAA
66 AGTAGTGAA
* * ** *
2188323 GCAAATCAATCTTAAGCCTTTACGGAAGAGTAGTGAAGCAAATCAATCTTATGTTTTTCATGGAA
1 GCAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCTTAAG-CCTTCACGGAA
2188388 GAGTAGTGAA
65 GAGTAGTGAA
2188398 GCAAATCAATCTTAAGCCTTCACAGG-AGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCAC-GGAAGAGTAGTGAA
2188435 TCAAGCCATC
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
74 50 0.49
75 51 0.50
76 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (74 bp):
GCAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACGGAAG
AGTAGTGAA
Found at i:2188631 original size:36 final size:36
Alignment explanation
Indices: 2188535--2188668 Score: 189
Period size: 36 Copynumber: 3.8 Consensus size: 36
2188525 ATTTTAATCT
*
2188535 TTCATGGAAGAGTAGTGAAACAAATCATCTTAAGCC
1 TTCACGGAAGAGTAGTGAAACAAATCATCTTAAGCC
* ** *
2188571 TTCATGG-AGAGTAGTGAAGGAAATCATCTTAATCC
1 TTCACGGAAGAGTAGTGAAACAAATCATCTTAAGCC
*
2188606 TTCACGGAAAAGTAGTGAAACAAATCATCTTAAGCC
1 TTCACGGAAGAGTAGTGAAACAAATCATCTTAAGCC
* *
2188642 TTCACAGAAGAGTAGTGAAGCAAATCA
1 TTCACGGAAGAGTAGTGAAACAAATCA
2188669 ATTTCGAGTT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
35 31 0.36
36 55 0.64
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (36 bp):
TTCACGGAAGAGTAGTGAAACAAATCATCTTAAGCC
Found at i:2188644 original size:71 final size:72
Alignment explanation
Indices: 2188528--2188668 Score: 221
Period size: 71 Copynumber: 2.0 Consensus size: 72
2188518 CCATGCCATT
* * * * * *
2188528 TTAATCTTTCATGGAAGAGTAGTGAAACAAATCATCTTAAGCCTTCA-TGGAGAGTAGTGAAGGA
1 TTAATCCTTCACGGAAAAGTAGTGAAACAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
2188592 AATCATC
66 AATCATC
2188599 TTAATCCTTCACGGAAAAGTAGTGAAACAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
1 TTAATCCTTCACGGAAAAGTAGTGAAACAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
2188664 AATCA
66 AATCA
2188669 ATTTCGAGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
71 44 0.70
72 19 0.30
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (72 bp):
TTAATCCTTCACGGAAAAGTAGTGAAACAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
AATCATC
Found at i:2189036 original size:110 final size:110
Alignment explanation
Indices: 2188734--2189066 Score: 429
Period size: 110 Copynumber: 3.0 Consensus size: 110
2188724 TTGTTCGAGT
*
2188734 TCTATACTCCCTGAAAGAATAGGGAGCGGACCCATTTTCAGAAAATTGTTCGAGTTCTATACTCC
1 TCTATACTCCCTGAAAGAATAGGGAGCGGACCCATTTTCAGAAGATTGTTCGAGTTCTATACTCC
* * * * * *
2188799 CTGAAAGAATAGGGAGCAAACCCATTTTCAAAAACGTGTTCGAGT-
66 CTGAAAGAATAAGGAGCGAACCCGTTTTCAAAAA-TTTTTCAAGTC
* *
2188844 TCTATACTCCCTGAAAGAATAGGGAGCGGACCCATTTTCAGAAGATTGTTTGAGATCTATACTCC
1 TCTATACTCCCTGAAAGAATAGGGAGCGGACCCATTTTCAGAAGATTGTTCGAGTTCTATACTCC
*
2188909 CT-AAGAGAATAAGGAGCGAACCCGTTTTCCAAATATTTTTCAAGTC
66 CTGAA-AGAATAAGGAGCGAACCCGTTTT-CAAAAATTTTTCAAGTC
* * * * * *
2188955 T-TATACTCCCTGAAAGAATAGGGAGTGAACCCGTTTTCATAAGATTATTCGGGTTCTATACTCC
1 TCTATACTCCCTGAAAGAATAGGGAGCGGACCCATTTTCAGAAGATTGTTCGAGTTCTATACTCC
* * * *
2189019 CTGAAAGAATAATGAGCGGACACGTTTTTCAAAGATTTTTCAAGTC
66 CTGAAAGAATAAGGAGCGAACCCG-TTTTCAAAAATTTTTCAAGTC
2189065 TC
1 TC
2189067 ACTTATTCTG
Statistics
Matches: 195, Mismatches: 22, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
109 2 0.01
110 181 0.93
111 12 0.06
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (110 bp):
TCTATACTCCCTGAAAGAATAGGGAGCGGACCCATTTTCAGAAGATTGTTCGAGTTCTATACTCC
CTGAAAGAATAAGGAGCGAACCCGTTTTCAAAAATTTTTCAAGTC
Found at i:2189055 original size:55 final size:55
Alignment explanation
Indices: 2188711--2189029 Score: 412
Period size: 55 Copynumber: 5.8 Consensus size: 55
2188701 GAAGCAGACT
*
2188711 CATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACC
1 CATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACC
* *
2188766 CATTTTCAGAAAATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAAACC
1 CATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACC
* * *
2188821 CATTTTCA-AAAACGTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACC
1 CATTTTCAGAAGA-TTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACC
* * *
2188876 CATTTTCAGAAGATTGTTTGAGATCTATACTCCCT-AAGAGAATAAGGAGCGAACC
1 CATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGAA-AGAATAGGGAGCGAACC
* * * * *
2188931 CGTTTTCCA-AATATTTTTCAAG-TCTTATACTCCCTGAAAGAATAGGGAGTGAACC
1 CATTTT-CAGAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAATAGGGAGCGAACC
* * * *
2188986 CGTTTTCATAAGATTATTCGGGTTCTATACTCCCTGAAAGAATA
1 CATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATA
2189030 ATGAGCGGAC
Statistics
Matches: 233, Mismatches: 23, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
54 10 0.04
55 214 0.92
56 9 0.04
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (55 bp):
CATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACC
Found at i:2193945 original size:12 final size:12
Alignment explanation
Indices: 2193910--2193948 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2193900 TCAATCTACA
*
2193910 ATATATAAATAA
1 ATATATAAATAT
*
2193922 ATAAATAAATAT
1 ATATATAAATAT
*
2193934 ATATATATATAT
1 ATATATAAATAT
2193946 ATA
1 ATA
2193949 ATTCACGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:2194066 original size:83 final size:84
Alignment explanation
Indices: 2193968--2194131 Score: 276
Period size: 83 Copynumber: 2.0 Consensus size: 84
2193958 ATACAATCAC
* *
2193968 GACACACGAATGTGTGTCATTTTCATTTATGACGGGGGCTTCAATGA-CACAACGTAAGTCATAA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACCACAACGTAAGTCATAA
2194032 ATGCGTGTCATAAATTTAT
66 ATGCGTGTCATAAATTTAT
* *
2194051 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGAC-CACAACGTAAGTCATA
2194116 AATGCGTGTCATAAAT
65 AATGCGTGTCATAAAT
2194132 GCACGTTATA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 45 0.60
85 30 0.40
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (84 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACCACAACGTAAGTCATAA
ATGCGTGTCATAAATTTAT
Found at i:2194126 original size:13 final size:13
Alignment explanation
Indices: 2194110--2194170 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
2194100 CGCAATGTAA
*
2194110 GTCATAAATGCGT
1 GTCATAAATGCGC
*
2194123 GTCATAAATGCAC
1 GTCATAAATGCGC
* *
2194136 GTTATAAATGCGT
1 GTCATAAATGCGC
2194149 GTCATAAATGCGC
1 GTCATAAATGCGC
2194162 GTCATAAAT
1 GTCATAAAT
2194171 TTATGACGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:2194132 original size:26 final size:26
Alignment explanation
Indices: 2194103--2194170 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
2194093 AATGACGCGC
*
2194103 AATGTAAGTCATAAATGCGTGTCATA
1 AATGCAAGTCATAAATGCGTGTCATA
* *
2194129 AATGCACGTTATAAATGCGTGTCATA
1 AATGCAAGTCATAAATGCGTGTCATA
**
2194155 AATGCGCGTCATAAAT
1 AATGCAAGTCATAAAT
2194171 TTATGACGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (26 bp):
AATGCAAGTCATAAATGCGTGTCATA
Found at i:2197451 original size:36 final size:37
Alignment explanation
Indices: 2197394--2197469 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
2197384 TTTCGTCCTA
*
2197394 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
1 CTAGGATTCAAACTCTCAAAAAAAGGATAGAATTATG
* *
2197431 CTAGGATTC-AACTC-CTAAAAAAATGATAGAATTTTG
1 CTAGGATTCAAACTCTC-AAAAAAAGGATAGAATTATG
2197467 CTA
1 CTA
2197470 TGTTTTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 1 0.03
36 25 0.71
37 9 0.26
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAAAAGGATAGAATTATG
Found at i:2198065 original size:51 final size:51
Alignment explanation
Indices: 2197999--2198109 Score: 222
Period size: 51 Copynumber: 2.2 Consensus size: 51
2197989 ACTATTATAT
2197999 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
1 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
2198050 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
1 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
2198101 TATTATTAT
1 TATTATTAT
2198110 CATTATATGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.56
Consensus pattern (51 bp):
TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
Found at i:2198258 original size:16 final size:16
Alignment explanation
Indices: 2198237--2198270 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2198227 CATGTATTTA
2198237 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
2198253 TATTATTTTACTTTAT
1 TATTATATTACATTAT
2198269 TA
1 TA
2198271 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:2198275 original size:21 final size:22
Alignment explanation
Indices: 2198251--2198301 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2198241 ATATTACATT
*
2198251 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
2198272 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
2198294 TTTATTAT
1 ATTATTAT
2198302 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:2201639 original size:12 final size:11
Alignment explanation
Indices: 2201621--2201690 Score: 61
Period size: 12 Copynumber: 6.1 Consensus size: 11
2201611 CAAAAAGGGC
2201621 AAAAAGAAAAA
1 AAAAAGAAAAA
2201632 AGAAAAGAAGAAA
1 A-AAAAGAA-AAA
*
2201645 AAAAGGAAAAA
1 AAAAAGAAAAA
* *
2201656 AACAAG-AACA
1 AAAAAGAAAAA
2201666 AAAAAGAAAGAA
1 AAAAAGAAA-AA
*
2201678 CAAAAATAAAAA
1 -AAAAAGAAAAA
2201690 A
1 A
2201691 GGGAACAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
10 8 0.17
11 11 0.23
12 16 0.34
13 12 0.26
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:2201654 original size:23 final size:23
Alignment explanation
Indices: 2201621--2201674 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2201611 CAAAAAGGGC
*
2201621 AAAAAGAAAAAAGAA-AAGAAGAA
1 AAAAAGAAAAAA-AACAAGAACAA
*
2201644 AAAAAGGAAAAAAACAAGAAC-A
1 AAAAAGAAAAAAAACAAGAACAA
2201666 AAAAAGAAA
1 AAAAAGAAA
2201675 GAACAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAAAACAAGAACAA
Found at i:2201657 original size:20 final size:20
Alignment explanation
Indices: 2201634--2201702 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
2201624 AAGAAAAAAG
2201634 AAAAGAAGAAAAAAAGGAAA
1 AAAAGAAGAAAAAAAGGAAA
* *
2201654 AAAACAAGAACAAAAAAGAAA
1 AAAAGAAGAA-AAAAAGGAAA
* * *
2201675 GAACAAAAATAAAAAAGGGAACA
1 -AA-AAGAAGAAAAAAAGGAA-A
2201698 AAAAG
1 AAAAG
2201703 CACATGCAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
20 9 0.24
21 11 0.29
22 11 0.29
23 7 0.18
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.01
Consensus pattern (20 bp):
AAAAGAAGAAAAAAAGGAAA
Found at i:2202328 original size:22 final size:22
Alignment explanation
Indices: 2202300--2202344 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2202290 CCCCATCAAT
2202300 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
2202322 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
2202344 C
1 C
2202345 ACAATGACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:2203284 original size:37 final size:37
Alignment explanation
Indices: 2203199--2203308 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
2203189 GTGCTCACTA
*
2203199 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACT
*
2203235 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACT
*
2203272 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAAC
2203309 ATTGAAAACA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 30 0.44
37 35 0.51
38 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACT
Found at i:2203393 original size:102 final size:102
Alignment explanation
Indices: 2203217--2203674 Score: 781
Period size: 102 Copynumber: 4.5 Consensus size: 102
2203207 CTTGAGACAG
** * * *
2203217 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
2203282 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * ** *
2203319 TTTCCCTTAAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
2203384 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
2203421 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
2203486 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
2203523 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
2203588 TGAGACAGTTTCTCTTGAAACATAAATATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
2203625 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
2203675 TAAACATTGA
Statistics
Matches: 334, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 334 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:2203488 original size:37 final size:37
Alignment explanation
Indices: 2203421--2203507 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
2203411 ATTGGAAACA
** * *
2203421 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
2203457 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
2203494 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2203508 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:2203580 original size:37 final size:38
Alignment explanation
Indices: 2203537--2203614 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
2203527 CCTTGAAATG
* *
2203537 AATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACA-A
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATA
* *
2203574 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATA
2203612 AAT
1 AAT
2203615 ATTGAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 32 0.89
38 4 0.11
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (38 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATA
Found at i:2203664 original size:65 final size:65
Alignment explanation
Indices: 2203574--2203743 Score: 288
Period size: 65 Copynumber: 2.6 Consensus size: 65
2203564 CTCGAAACAA
* * *
2203574 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAAAATTTCCCTTGAAATG
* *
2203639 AATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAAAATTTCCCTTGAAATG
2203704 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAAT
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAT
2203744 TTTGTCTCCC
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
64 3 0.03
65 95 0.97
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (65 bp):
AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAAAATTTCCCTTGAAATG
Found at i:2203675 original size:167 final size:169
Alignment explanation
Indices: 2203457--2203774 Score: 532
Period size: 167 Copynumber: 1.9 Consensus size: 169
2203447 CTTGAGATAG
* *
2203457 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAA
* *
2203522 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
2203587 TTGAGACAG-TTTCTCTTGAAACATAAATATTGAAAACA
131 TTGAGACAGTTTTCTCTTGAAACATAAATATTGAAAACA
** * *
2203625 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAA
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAA
* *
2203689 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
2203754 TTGAGACAGTTTTCTCTTGAA
131 TTGAGACAGTTTTCTCTTGAA
2203775 GCATCATCTT
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
167 116 0.83
168 23 0.17
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAA
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
TTGAGACAGTTTTCTCTTGAAACATAAATATTGAAAACA
Found at i:2204731 original size:106 final size:107
Alignment explanation
Indices: 2204263--2204892 Score: 637
Period size: 109 Copynumber: 5.9 Consensus size: 107
2204253 TAGCTAGAGT
* * * *
2204263 CAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGCCAAC-AACAATTTCCCAATTTCGGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* *
2204327 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
66 ATTTCAACTCCACGACGGAGGATAT--TGCGACTCGAGACAACA
* * * *
2204371 CAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
*
2204436 ATTTCAACTCCACGACGGAGGATATCGTGCTAC-CTGAGACAACA
66 ATTTCAACTCCACGACGGAGGATAT--TGCGACTC-GAGACAACA
* * * **
2204480 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTT-TCAGTTTCA-TCCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCAATTTCAGAAC-
* *
2204543 CGATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACA
64 CAATTTCAACTCCACGACGGAGGATAT--TGCGACTCGAGACAACA
* * * * *
2204589 CAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* *
2204654 ATTTCAACTTCAC-AGCGAAGGATATTG-GACTCGAGACAACA
66 ATTTCAACTCCACGA-CGGAGGATATTGCGACTCGAGACAACA
* * * * **
2204695 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAA-TAA-GATTT--C--GTTCAGAGTCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* * *
2204754 ATTTCAACTTCAC-A-GTGAAGGATATT-AGACTCGAGACAGCA
66 ATTTCAACTCCACGACG-G-AGGATATTGCGACTCGAGACAACA
* * * ** ** *
2204795 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
*
2204860 ATTTCAACTTCAC-AGCGGAGGATATTG-GACTCG
66 ATTTCAACTCCACGA-CGGAGGATATTGCGACTCG
2204893 GAACAATATT
Statistics
Matches: 454, Mismatches: 48, Indels: 42
0.83 0.09 0.08
Matches are distributed among these distances:
98 1 0.00
100 79 0.17
101 2 0.00
102 4 0.01
104 4 0.01
105 2 0.00
106 85 0.19
107 3 0.01
108 44 0.10
109 226 0.50
110 4 0.01
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (107 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
ATTTCAACTCCACGACGGAGGATATTGCGACTCGAGACAACA
Found at i:2205410 original size:36 final size:37
Alignment explanation
Indices: 2205353--2205453 Score: 107
Period size: 36 Copynumber: 2.8 Consensus size: 37
2205343 TTTCGTCCTA
*
2205353 CTAGGATTCAAACTCTCAAAAATAGGATATAATTATG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
* *
2205390 CTAGGATTC-AACTC-CTAAAAATATGATAGAATTTTG
1 CTAGGATTCAAACTCTC-AAAAATAGGATAGAATTATG
* * * * *
2205426 CTATGTTTTAAACTCTTAAAGATAGGAT
1 CTAGGATTCAAACTCTCAAAAATAGGAT
2205454 CCACAATAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
35 1 0.02
36 28 0.54
37 23 0.44
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
Found at i:2205995 original size:26 final size:26
Alignment explanation
Indices: 2205966--2206048 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
2205956 TATTTATTAT
2205966 TATTTTACTATTAACGTATATAAATA
1 TATTTTACTATTAACGTATATAAATA
* * ** *
2205992 TATTTTTCTCTT-TTGCTACTAT-TAT-
1 TATTTTACTATTAACG-TA-TATAAATA
2206017 TATTTTACTATTAACGTATATAAATA
1 TATTTTACTATTAACGTATATAAATA
2206043 TATTTT
1 TATTTT
2206049 TCTCTTTTGC
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
24 3 0.07
25 15 0.36
26 21 0.50
27 3 0.07
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.54
Consensus pattern (26 bp):
TATTTTACTATTAACGTATATAAATA
Found at i:2206015 original size:51 final size:51
Alignment explanation
Indices: 2205960--2206070 Score: 222
Period size: 51 Copynumber: 2.2 Consensus size: 51
2205950 CTATTATATT
2205960 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
1 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
2206011 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
1 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
2206062 TATTATTAT
1 TATTATTAT
2206071 CATTATATGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.56
Consensus pattern (51 bp):
TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
Found at i:2206221 original size:16 final size:16
Alignment explanation
Indices: 2206200--2206233 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2206190 CATGTATTTA
2206200 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
2206216 TATTATTTTACTTTAT
1 TATTATATTACATTAT
2206232 TA
1 TA
2206234 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:2206238 original size:21 final size:22
Alignment explanation
Indices: 2206214--2206264 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2206204 ATATTACATT
*
2206214 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
2206235 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
2206257 TTTATTAT
1 ATTATTAT
2206265 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:2216394 original size:72 final size:75
Alignment explanation
Indices: 2216277--2216482 Score: 183
Period size: 72 Copynumber: 2.8 Consensus size: 75
2216267 TTTGTCCCTC
* * * * ** *
2216277 AAACGCCACAAAAAG-TATAGATACTTAACGGTGTTTTTTGGATACAAACGCCGCAAAATGT-C-
1 AAACGCCAC-AAAGGTTA-AGATATTTAGCGGCGTTTTTCAGATACAAACGCCGCAAAATATACG
2216339 AC-ATCTATG-A
64 ACGATCTATGAA
*
2216349 AAACGCCACAAATGGTTAAGATATTTAGCGGCGTTTTTCAGATACAAACGTCGCAAATATATAGC
1 AAACGCCACAAA-GGTTAAGATATTTAGCGGCGTTTTTCAGATACAAACGCCGCAAA-ATATA-C
* * *
2216414 GGCGTTTGTATGAA
63 GACG-ATCTATGAA
* * *
2216428 AAACGCCGCAAAGGTT--GGTATATAGCGGCGTTTTTCAGATACAAACGCCGCAAAA
1 AAACGCCACAAAGGTTAAGATATTTAGCGGCGTTTTTCAGATACAAACGCCGCAAAA
2216483 GGTCTGGTAT
Statistics
Matches: 110, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
71 3 0.03
72 43 0.39
73 5 0.05
75 2 0.02
76 36 0.33
78 9 0.08
79 12 0.11
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (75 bp):
AAACGCCACAAAGGTTAAGATATTTAGCGGCGTTTTTCAGATACAAACGCCGCAAAATATACGAC
GATCTATGAA
Found at i:2216475 original size:42 final size:42
Alignment explanation
Indices: 2216374--2216495 Score: 136
Period size: 40 Copynumber: 3.0 Consensus size: 42
2216364 TTAAGATATT
*
2216374 TAGCGGCGTTTTTCAGATACAAACGTCGCAAA------TATA
1 TAGCGGCGTTTTTCAGATACAAACGCCGCAAAGGTTGGTATA
*
2216410 TAGCGGCGTTTGT-ATGA-A-AAACGCCGCAAAGGTTGGTATA
1 TAGCGGCGTTTTTCA-GATACAAACGCCGCAAAGGTTGGTATA
2216450 TAGCGGCGTTTTTCAGATACAAACGCCGCAAAAGGTCTGGTATA
1 TAGCGGCGTTTTTCAGATACAAACGCCGC-AAAGGT-TGGTATA
2216494 TA
1 TA
2216496 AAGGCGTTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
34 11 0.15
35 2 0.03
36 14 0.20
40 18 0.25
41 2 0.03
42 9 0.13
43 6 0.08
44 9 0.13
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (42 bp):
TAGCGGCGTTTTTCAGATACAAACGCCGCAAAGGTTGGTATA
Found at i:2216514 original size:43 final size:42
Alignment explanation
Indices: 2216428--2216524 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 42
2216418 TTTGTATGAA
**
2216428 AAACGCCGC-AAAGGTTGGTATATAGCGGCGTTTTTCAGATAC
1 AAACGCCGCAAAAGGTTGGTATATAAAGGCGTTTTT-AGATAC
*
2216470 AAACGCCGCAAAAGGTCTGGTATATAAAGGCGTTATTT-GTTAC
1 AAACGCCGCAAAAGGT-TGGTATATAAAGGCGTT-TTTAGATAC
*
2216513 AAACACCG-AAAA
1 AAACGCCGCAAAA
2216525 TATCTAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
42 13 0.27
43 17 0.35
44 15 0.31
45 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTTGGTATATAAAGGCGTTTTTAGATAC
Found at i:2217626 original size:191 final size:193
Alignment explanation
Indices: 2217304--2217709 Score: 498
Period size: 191 Copynumber: 2.1 Consensus size: 193
2217294 TAAATGACGT
* *
2217304 TTATACATAATGTCACTTTATAATTGATACTCAATGACAACTAGTTACATCACTAAATTATATAA
1 TTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACATCACTAAATTATATAA
* * **
2217369 AATTTTGTTATTAATAATTTACACAGTCATGAATAATACATTAAAATCAATTTATATGTGACGAA
66 AATTTTGTTATTAATAATTTACACAGTCACGAATAATACAATAAAATCAACCTATATGTGACGAA
* *
2217434 AGAGATATTGTCACATTTTTAGTGACGTAATATAACGTTACCTAATAGTATTATGAATGA-CA
131 AGAGATATTGTCAAATTTTTAGTGACGTAATATAACGTTACCTAATAATATTATGAATGATCA
* * * **
2217496 CTTATGCATAACGTCATTTTATAATTTATATTGC-ATGACAGTTAGTTACGA-CACTAAATTATA
1 -TTATGCATAACGTCACTTTATAATTGATACT-CAATGACAACTAGTTAC-ATCACTAAATTATA
* * ** * *
2217559 TAATA-TTT-TTATTAATAATTTATATTGTCACGAATAATTCAATAAAATCAACCTATATGTTAC
63 TAAAATTTTGTTATTAATAATTTACACAGTCACGAATAATACAATAAAATCAACCTATATGTGAC
* * * ** * * *
2217622 GAAAGATATATTGTCAAATTTTTAGTGACGTGATATAATGTTATGTAATAATGTTTTGAATGATG
128 GAAAGAGATATTGTCAAATTTTTAGTGACGTAATATAACGTTACCTAATAATATTATGAATGATC
2217687 A
193 A
*
2217688 TTATGCATAACGTCACCTTATA
1 TTATGCATAACGTCACTTTATA
2217710 CAATTTTCTC
Statistics
Matches: 181, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
191 120 0.66
192 4 0.02
193 55 0.30
194 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (193 bp):
TTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACATCACTAAATTATATAA
AATTTTGTTATTAATAATTTACACAGTCACGAATAATACAATAAAATCAACCTATATGTGACGAA
AGAGATATTGTCAAATTTTTAGTGACGTAATATAACGTTACCTAATAATATTATGAATGATCA
Found at i:2225081 original size:22 final size:21
Alignment explanation
Indices: 2225045--2225085 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2225035 CATCTCCATT
2225045 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
*
2225066 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
2225086 TTCCGCAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:2225413 original size:18 final size:17
Alignment explanation
Indices: 2225385--2225470 Score: 111
Period size: 18 Copynumber: 4.8 Consensus size: 17
2225375 ATTGGAGTAC
2225385 AAAAAGAAAGAAAAGA-CAA
1 AAAAAG-AAGAAAA-ATC-A
2225404 AAAAAGAAGAAAAATTCA
1 AAAAAGAAGAAAAA-TCA
2225422 AAAAAGAAGAAAAATTCA
1 AAAAAGAAGAAAAA-TCA
2225440 AAAAAGAAGAAAAATTCA
1 AAAAAGAAGAAAAA-TCA
2225458 AAAAAGAAGAAAA
1 AAAAAGAAGAAAA
2225471 GAAAAAGAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
17 1 0.02
18 57 0.88
19 7 0.11
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.07
Consensus pattern (17 bp):
AAAAAGAAGAAAAATCA
Found at i:2225424 original size:36 final size:36
Alignment explanation
Indices: 2225385--2225476 Score: 136
Period size: 36 Copynumber: 2.6 Consensus size: 36
2225375 ATTGGAGTAC
2225385 AAAAAGAAAGAAAAGACAAAAAAAGAAGAAAAATTCA
1 AAAAAG-AAGAAAAGACAAAAAAAGAAGAAAAATTCA
2225422 AAAAAGAAGAAAA-ATTC-AAAAAAGAAGAAAAATTCA
1 AAAAAGAAGAAAAGA--CAAAAAAAGAAGAAAAATTCA
2225458 AAAAAGAAGAAAAGA-AAAA
1 AAAAAGAAGAAAAGACAAAA
2225477 GAATAATTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
35 4 0.08
36 39 0.76
37 8 0.16
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (36 bp):
AAAAAGAAGAAAAGACAAAAAAAGAAGAAAAATTCA
Found at i:2226572 original size:24 final size:25
Alignment explanation
Indices: 2226545--2226600 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
2226535 AAAATCATGG
* *
2226545 CTTTTGGAA-AACTAAAAGATGTGA
1 CTTTTGGAAGAACCAAAAGATATGA
* *
2226569 CTTTT-GAAGAACCAATAGTTATGA
1 CTTTTGGAAGAACCAAAAGATATGA
2226593 CTTTTGGA
1 CTTTTGGA
2226601 GATTCACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 3 0.12
24 21 0.81
25 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (25 bp):
CTTTTGGAAGAACCAAAAGATATGA
Found at i:2228674 original size:22 final size:21
Alignment explanation
Indices: 2228638--2228678 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2228628 CATCTCCATT
2228638 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
*
2228659 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
2228679 TTCTACAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:2228740 original size:12 final size:12
Alignment explanation
Indices: 2228725--2228754 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2228715 CATTACTTAT
2228725 CTTATTATTCCA
1 CTTATTATTCCA
2228737 CTTATTATTCCA
1 CTTATTATTCCA
2228749 -TTATTA
1 CTTATTA
2228755 ACCATATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (12 bp):
CTTATTATTCCA
Found at i:2231279 original size:83 final size:82
Alignment explanation
Indices: 2231153--2231437 Score: 225
Period size: 83 Copynumber: 3.5 Consensus size: 82
2231143 AAAAGCGCCG
* * ** **
2231153 CTAAATTACTACTCTATAGCGGCGTTTATTAGACAAATGCCACTATAAACAACCCTATTGCGGTG
1 CTAAATTACTACTCTATAGCGGCGTTTGTTGGA-AAAAACCACTATAAACAACCCTATTGCGGCA
2231218 TTTATTTAATAAACGACA
65 TTTATTTAATAAACGACA
** * * * * *
2231236 CTAAATTACTACTCTATAGCATCATTTGTTGGAGAAACACCACTATAAATAACCCTGTTGTGGCA
1 CTAAATTACTACTCTATAGCGGCGTTTGTTGGA-AAAAACCACTATAAACAACCCTATTGCGGCA
* * * *
2231301 TTTATTTGATAGACGCCG
65 TTTATTTAATAAACGACA
* * * * * * *
2231319 CTATATTAATACTCTATTA-CGGCGTTTGTGGGAAAAAACCACTATAAACAACTCTATTCCGACG
1 CTAAATTACTACTCTA-TAGCGGCGTTTGTTGGAAAAAACCACTATAAACAACCCTATTGCGGCA
* * * *
2231383 TTTGTGCT-ATAAACGCCG
65 TTTAT-TTAATAAACGACA
* * *
2231401 CTGAATTACCACTCTATTA-CGGCTTTTGTTGGAAAAA
1 CTAAATTACTACTCTA-TAGCGGCGTTTGTTGGAAAAA
2231438 CATTGCTAAA
Statistics
Matches: 160, Mismatches: 40, Indels: 5
0.78 0.20 0.02
Matches are distributed among these distances:
82 67 0.42
83 91 0.57
84 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (82 bp):
CTAAATTACTACTCTATAGCGGCGTTTGTTGGAAAAAACCACTATAAACAACCCTATTGCGGCAT
TTATTTAATAAACGACA
Found at i:2235416 original size:16 final size:16
Alignment explanation
Indices: 2235395--2235425 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2235385 GAAATGTTGG
2235395 CTTTTTTGTTTTTTTC
1 CTTTTTTGTTTTTTTC
2235411 CTTTTTTGTTTTTTT
1 CTTTTTTGTTTTTTT
2235426 AAAAAAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (16 bp):
CTTTTTTGTTTTTTTC
Found at i:2239553 original size:90 final size:90
Alignment explanation
Indices: 2239400--2239577 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
2239390 CCTAACACAC
* * *
2239400 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGGTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
2239465 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* * *
2239490 CCTTTTATATCCAAGTTATCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTTAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
2239555 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
2239578 TTCAGGATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:2248018 original size:153 final size:153
Alignment explanation
Indices: 2247740--2248042 Score: 545
Period size: 153 Copynumber: 2.0 Consensus size: 153
2247730 GTTGACTCTT
**
2247740 AATGAGAAGGTAACCTGAGAATTTGTGCTTAAACCGATAAATTACTGATTTAATGGTTGAGATTT
1 AATGAGAAGGTAACCTGAGAATTTGTGCTTAAACCGATAAATTACTGATTTAATGGTTGAGATCC
*
2247805 TACTTTTGTATGGAAAATTCCTAATAATTCGTTAGTAATGTCTGAAAAGACTTTTAACCTAGAAA
66 TACTTTTGTATGGAAAATTCCTAATAATTCGTTAATAATGTCTGAAAAGACTTTTAACCTAGAAA
2247870 TC-TCTGAGCTATGAATAAATTTG
131 TCTTC-GAGCTATGAATAAATTTG
2247893 AATGAGAAGGTAACCTGAGAATTTGTGCTTAAACCGATAAATTACTGATTTAATGGTTGAGATCC
1 AATGAGAAGGTAACCTGAGAATTTGTGCTTAAACCGATAAATTACTGATTTAATGGTTGAGATCC
2247958 TACTTTTGTATGGAAAATTCCTAATAATTCGTTAATAATGTCTGAAAAGACTTTTAACCTAGAAA
66 TACTTTTGTATGGAAAATTCCTAATAATTCGTTAATAATGTCTGAAAAGACTTTTAACCTAGAAA
* *
2248023 TCTTCGAGTTATGAGTAAAT
131 TCTTCGAGCTATGAATAAAT
2248043 ACCTGAAGAA
Statistics
Matches: 144, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
153 142 0.99
154 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (153 bp):
AATGAGAAGGTAACCTGAGAATTTGTGCTTAAACCGATAAATTACTGATTTAATGGTTGAGATCC
TACTTTTGTATGGAAAATTCCTAATAATTCGTTAATAATGTCTGAAAAGACTTTTAACCTAGAAA
TCTTCGAGCTATGAATAAATTTG
Found at i:2258663 original size:41 final size:41
Alignment explanation
Indices: 2258604--2258838 Score: 159
Period size: 41 Copynumber: 5.7 Consensus size: 41
2258594 TTTCAAATTG
* * * * *
2258604 ATCATGGCAGTATGCAATATTTGATCATTCAACTTGATTCA
1 ATCATGGTAGCATACAATAATTCATCATTCAACTTGATTCA
* *
2258645 ATCATGGTAGCATACAATAATTCACCATTCAA-TTAAATTCA
1 ATCATGGTAGCATACAATAATTCATCATTCAACTT-GATTCA
* * * * * *
2258686 ATCATTGCT-GCATATAGTAGTTCATCAGTCAACTTGATTCC
1 ATCA-TGGTAGCATACAATAATTCATCATTCAACTTGATTCA
** * * * *
2258727 ATCATGGTAGCATACAATAACCCACCATTCGATTTAATTCA
1 ATCATGGTAGCATACAATAATTCATCATTCAACTTGATTCA
* * *** * ** **
2258768 GTCATGGTAACATACAACCGTTCATCATTAAACAAGATTTG
1 ATCATGGTAGCATACAATAATTCATCATTCAACTTGATTCA
* *
2258809 ATCATGGTAGCATGCAATAATTCACCATTC
1 ATCATGGTAGCATACAATAATTCATCATTC
2258839 GATTCAATTC
Statistics
Matches: 139, Mismatches: 51, Indels: 8
0.70 0.26 0.04
Matches are distributed among these distances:
40 5 0.04
41 129 0.93
42 5 0.04
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (41 bp):
ATCATGGTAGCATACAATAATTCATCATTCAACTTGATTCA
Found at i:2258719 original size:82 final size:82
Alignment explanation
Indices: 2258627--2258887 Score: 267
Period size: 82 Copynumber: 3.2 Consensus size: 82
2258617 GCAATATTTG
*
2258627 ATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCAATTAAATTCAATCATT
1 ATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCGATTAAATTCAATCA-T
* * **
2258692 GCT-GCATATAGTAGTTC
65 GCTAACATACAACAGTTC
* * ** * *
2258709 ATCAGTCAACTTGATTCCATCATGGTAGCATACAATAACCCACCATTCGATTTAATTCAGTCATG
1 ATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCGATTAAATTCAATCATG
* *
2258774 GTAACATACAACCGTTC
66 CTAACATACAACAGTTC
* ** ** * * * *
2258791 ATCATTAAACAAGATTTGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATTCAATAAAG
1 ATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCGATTAAATTCAATCATG
*
2258856 -TCAACATA-AATAGTTC
66 CT-AACATACAACAGTTC
*
2258872 ATTATTCAACTTGATT
1 ATCATTCAACTTGATT
2258888 TGACCATGAT
Statistics
Matches: 145, Mismatches: 32, Indels: 5
0.80 0.18 0.03
Matches are distributed among these distances:
81 22 0.15
82 123 0.85
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (82 bp):
ATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCGATTAAATTCAATCATG
CTAACATACAACAGTTC
Found at i:2267663 original size:30 final size:30
Alignment explanation
Indices: 2267629--2267691 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2267619 GTTTGGAAAC
2267629 GTTTAAAGACTAGAAA-TGCAATTTTCAAAA
1 GTTTAAAGACTA-AAAGTGCAATTTTCAAAA
** *
2267659 GTTTAGGGACTAAAAGTGTAATTTTCAAAA
1 GTTTAAAGACTAAAAGTGCAATTTTCAAAA
2267689 GTT
1 GTT
2267692 ATGTATCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.33
Consensus pattern (30 bp):
GTTTAAAGACTAAAAGTGCAATTTTCAAAA
Found at i:2269272 original size:81 final size:81
Alignment explanation
Indices: 2269178--2269752 Score: 731
Period size: 81 Copynumber: 7.1 Consensus size: 81
2269168 TGTTCTAAAA
* * * *
2269178 TAAAAGATTAATGGCCTAGTTTTGCATTTGGTAGAAATATGTTAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* *
2269243 GTTAAATACCTTTAAT
66 GTTAAATACCTTTGAG
* * * *
2269259 TAAAAGATTAATGGCTTAGCTATGCATTTGGAAAAAATGTGTCAATTATGCCAGTTAGATAAAAG
1 TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
2269324 GTTAAATACATTTGAG
66 GTTAAATACCTTTGAG
* * * * *
2269340 TCAAAGATTAATGGCATGGCTATCCATTTGGTAGAAATGTGTCAATTATGGCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
2269405 GTTAAATACCTTAT-AG
66 GTTAAATACCTT-TGAG
* * * * * * *
2269421 TAAATGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTTATTTATGCCAGTTAAATGAAAG
1 TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
2269486 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
2269502 TAAAAGATTAATGGCCTAGCCATGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAAATGAAAG
1 TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
2269567 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
2269583 TAAAATATTAATGGCCTAGCTGTGCATTTGGAAGAAAGGTATCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
2269648 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * ** * *
2269664 TAAAAGATTAATAGCCTAGCTGTGCATTTGGCA-AGAAGGTACCAATCATGCAAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGA-AATGTGTCAATTATGCCAGTTAGATGAAA
* ** *
2269728 GGCTAAAATATGTTTGGG
65 GG-TTAAATACCTTTGAG
2269746 TAAAAGA
1 TAAAAGA
2269753 GGAAATGCTT
Statistics
Matches: 434, Mismatches: 56, Indels: 7
0.87 0.11 0.01
Matches are distributed among these distances:
80 2 0.00
81 413 0.95
82 19 0.04
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:2283701 original size:2 final size:2
Alignment explanation
Indices: 2283694--2283718 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2283684 GAAAATTTGG
2283694 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 A
2283719 GTTTGTCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2285718 original size:55 final size:55
Alignment explanation
Indices: 2285607--2285761 Score: 163
Period size: 55 Copynumber: 2.8 Consensus size: 55
2285597 AACTAAGAAT
* ** * *
2285607 TTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAAATAATAAA
1 TTCATAATAAGTTTATGAATTTCTGTATTGGCACTGCGTGTACAAAAACAATAAA
* * **
2285662 TTCATAATAAGTTTATGAATTTCTGTATTGGTAGTGCGTGTACAACCCACAA-AAA
1 TTCATAATAAGTTTATGAATTTCTGTATTGGCACTGCGTGTACAA-AAACAATAAA
* * *
2285717 TT-ATAATAAGATTATGAATTAT-TGTATTGGCACTACGAGTACAAA
1 TTCATAATAAGTTTATGAATT-TCTGTATTGGCACTGCGTGTACAAA
2285762 CTATAGAATT
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
54 35 0.42
55 45 0.54
56 3 0.04
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (55 bp):
TTCATAATAAGTTTATGAATTTCTGTATTGGCACTGCGTGTACAAAAACAATAAA
Found at i:2285775 original size:54 final size:54
Alignment explanation
Indices: 2285596--2285777 Score: 163
Period size: 54 Copynumber: 3.4 Consensus size: 54
2285586 TATGTGTGCA
* ** *
2285596 AAACTA-AGAATTTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGC
1 AAACTATAGAATTT-ATAATAAGTTTATGAATTTCTGTATTGGCACTACGTGTAC
* * * * *
2285650 AAAAATAATA-AATTCATAATAAGTTTATGAATTTCTGTATTGGTAGTGCGTGTAC
1 -AAACT-ATAGAATTTATAATAAGTTTATGAATTTCTGTATTGGCACTACGTGTAC
* * * * * * *
2285705 AACCCACAAAAATTATAATAAGATTATGAATTAT-TGTATTGGCACTACGAGTAC
1 AAACTATAGAATTTATAATAAGTTTATGAATT-TCTGTATTGGCACTACGTGTAC
2285759 AAACTATAGAATTTATAAT
1 AAACTATAGAATTTATAAT
2285778 GAATTGAAGG
Statistics
Matches: 99, Mismatches: 24, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
53 2 0.02
54 52 0.53
55 39 0.39
56 5 0.05
57 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (54 bp):
AAACTATAGAATTTATAATAAGTTTATGAATTTCTGTATTGGCACTACGTGTAC
Found at i:2285941 original size:81 final size:81
Alignment explanation
Indices: 2285836--2286408 Score: 720
Period size: 81 Copynumber: 7.1 Consensus size: 81
2285826 TGTTCTAAAA
* * *
2285836 TAAAATATTAATGGCCTAGATGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGCAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2285901 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
** * *
2285917 TAAAAGATTAATGGATTAGTTGTGCATTTAGTAA-AAAAGTGTCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGTTGTGCATTT-GGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
2285981 TGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * * * * * * *
2285998 TAAAAGATTAATGGCCTAGTTGTACATTTGGTAGAAATGTGTCAACTATGTCAATTGGATTAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2286063 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
2286079 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAATTAGATGAAGG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2286144 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * ** * *
2286160 TAAAAGATTAATGTCATAACTGTGCATTT-GATAGAAAGGTGTTAATTAGGCCA-TTAGATGAAA
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGA-AGAAAGGTGTCAATTATGCCAGTTAGATGAAA
2286223 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * * * * * *
2286240 CAGAATATTAATGGCCTAGTTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTCATATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2286305 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
2286321 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGGAAGGTGTCAATCATGCAAGCTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
2286386 GCTAAAATGCCTTTGGG
66 G-TTAAATACCTTTGAG
2286403 TAAAAG
1 TAAAAG
2286409 GCTAAAATGC
Statistics
Matches: 424, Mismatches: 62, Indels: 11
0.85 0.12 0.02
Matches are distributed among these distances:
80 69 0.16
81 334 0.79
82 21 0.05
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:2286328 original size:242 final size:244
Alignment explanation
Indices: 2285836--2286408 Score: 753
Period size: 242 Copynumber: 2.4 Consensus size: 244
2285826 TGTTCTAAAA
* * * *
2285836 TAAAATATTAATGGCCTAGATGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGCAA-
1 TAAAAGATTAATGGCCTAGATGTGCATTTGGCAGAAAGGTGTCAATTATGCCAATTAGATGAAAG
* **
2285900 GGTTAAATACCTTTGAGTAAAAGATTAATGGATTAGTTGTGCATTTAGTAAAAAAGTGTCAATTA
66 GGTTAAATACCTTTGAGTAAAAGATTAATGCATTAACTGTGCATTTAGTAAAAAAGTGTCAATTA
* * * *
2285965 TGCCAGTTAGATGAAATGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTACATTTGGT
131 GGCCAGTTAGATGAAAGGTTAAATACCTTTGAGCAAAAGATTAATGGCCTAGTTGTACATTTGGC
* * ** *
2286030 AGAAATGTGTCAACTATGTCAATTGGATTAAAGGTTAAATACCTTTGAG
196 AGAAAGGTGTCAACTATGCCAATCAGATGAAAGGTTAAATACCTTTGAG
* *
2286079 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAATTAGATG-AAG
1 TAAAAGATTAATGGCCTAGATGTGCATTTGGCAGAAAGGTGTCAATTATGCCAATTAGATGAAAG
* * *
2286143 GGTTAAATACCTTTGAGTAAAAGATTAATGTCA-TAACTGTGCATTT-GATAGAAAGGTGTTAAT
66 GGTTAAATACCTTTGAGTAAAAGATTAATG-CATTAACTGTGCATTTAG-TAAAAAAGTGTCAAT
* * *
2286206 TAGGCCA-TTAGATGAAAGGTTAAATACCTTTGAGCAGAATATTAATGGCCTAGTTGTGCATTTG
129 TAGGCCAGTTAGATGAAAGGTTAAATACCTTTGAGCAAAAGATTAATGGCCTAGTTGTACATTTG
* * * *
2286270 GCATAAAGGTGTCAATTATGCCAGTCATATGAAAGGTTAAATACCTTTGAG
194 GCAGAAAGGTGTCAACTATGCCAATCAGATGAAAGGTTAAATACCTTTGAG
* * * *
2286321 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGGAAGGTGTCAATCATG-CAAGCTAGATGAAA
1 TAAAAGATTAATGGCCTAGATGTGCATTTGGCAGAAAGGTGTCAATTATGCCAA-TTAGATGAAA
* * * *
2286385 GGCTAAAATGCCTTTGGGTAAAAG
65 GGGTTAAATACCTTTGAGTAAAAG
2286409 GCTAAAATGC
Statistics
Matches: 289, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
241 3 0.01
242 148 0.51
243 137 0.47
244 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.32
Consensus pattern (244 bp):
TAAAAGATTAATGGCCTAGATGTGCATTTGGCAGAAAGGTGTCAATTATGCCAATTAGATGAAAG
GGTTAAATACCTTTGAGTAAAAGATTAATGCATTAACTGTGCATTTAGTAAAAAAGTGTCAATTA
GGCCAGTTAGATGAAAGGTTAAATACCTTTGAGCAAAAGATTAATGGCCTAGTTGTACATTTGGC
AGAAAGGTGTCAACTATGCCAATCAGATGAAAGGTTAAATACCTTTGAG
Found at i:2286408 original size:23 final size:23
Alignment explanation
Indices: 2286382--2286431 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
2286372 AAGCTAGATG
2286382 AAAGGCTAAAATGCCTTTGGGTA
1 AAAGGCTAAAATGCCTTTGGGTA
2286405 AAAGGCTAAAATGCCTTTGGGTA
1 AAAGGCTAAAATGCCTTTGGGTA
2286428 AAAG
1 AAAG
2286432 AAAAAATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (23 bp):
AAAGGCTAAAATGCCTTTGGGTA
Found at i:2288629 original size:26 final size:26
Alignment explanation
Indices: 2288600--2288668 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 26
2288590 AAACGAGACC
* *
2288600 TTCAAGTGCAATTGATAAATTACACT
1 TTCAAGTGCAATTGATAAATGACAAT
* *
2288626 TTCAAGTGCAAGTG--AAATGGCAAT
1 TTCAAGTGCAATTGATAAATGACAAT
*
2288650 TTCGAGTGCAATTGATAAA
1 TTCAAGTGCAATTGATAAA
2288669 GGGCGTTATG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 19 0.54
26 16 0.46
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (26 bp):
TTCAAGTGCAATTGATAAATGACAAT
Found at i:2289437 original size:2 final size:2
Alignment explanation
Indices: 2289430--2289458 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2289420 ATAGTAGAAG
2289430 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 T
2289459 GAAACCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2291345 original size:170 final size:163
Alignment explanation
Indices: 2291089--2291518 Score: 402
Period size: 170 Copynumber: 2.6 Consensus size: 163
2291079 CAAATTTATT
* * * *
2291089 TTTGATGGGAT-ACTACACTATGACATGGCAGAGATTCCCTGAGCAATGGAAAAACGCTTCCCTA
1 TTTGATGGGATGA-AACACTATGACATGGCAGAGATTCCTTGAGAAAAGG-AAAACGCTTCCCTA
* * * * * *
2291153 -GAATGAGTCTTTCCTCTTTGTCAAATTTTATCCGCATACCTCACTAAATTATGTTGAATTTATG
64 GGAACGAGCCTTTACTTTTTGTCAAATTTTATCCGCACACCTCACTAAATTATGTTGAAGTTATG
* * * *
2291217 ATGTAT-GAAGTCGGGGAACTACTT-TTGTCAATCAGATTAA
129 ATGT-TGGAAGTCAGAGAACTA-TTCTCGTCAA-C----CAA
* **
2291257 TGTTTGATGGGATGAAACACTATGACATGGTAGAGATTCCTTGAGAAAAGGAAAGGGCTTCCCTA
1 --TTTGATGGGATGAAACACTATGACATGGCAGAGATTCCTTGAGAAAAGGAAAACGCTTCCCTA
* * * * * *
2291322 GGAACAAGCCTTTTCTTTTTGTCATAA-TTTATCTGCACGCCTCACTAATTTATGTTTAAGTTAT
64 GGAACGAGCCTTTACTTTTTGTCA-AATTTTATCCGCACACCTCACTAAATTATGTTGAAGTTAT
* *
2291386 TATGTTGGGAGTCAGAGAACTATTCTCGTCAACCAA
128 GATGTTGGAAGTCAGAGAACTATTCTCGTCAACCAA
* * * * * * * *
2291422 TTTGATGGGATGAGACACTATGACATGACAAAGATTCTTTAAGAAAAGAAAAATGCTTCCCTTGG
1 TTTGATGGGATGAAACACTATGACATGGCAGAGATTCCTTGAGAAAAGGAAAACGCTTCCCTAGG
*
2291487 AACGAGCCTTTACTTTTTTGTCATATTTTATC
66 AACGAGCCTTTAC-TTTTTGTCAAATTTTATC
2291519 TATATGCCAG
Statistics
Matches: 216, Mismatches: 37, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
163 67 0.31
164 15 0.07
165 2 0.01
169 16 0.07
170 113 0.52
171 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (163 bp):
TTTGATGGGATGAAACACTATGACATGGCAGAGATTCCTTGAGAAAAGGAAAACGCTTCCCTAGG
AACGAGCCTTTACTTTTTGTCAAATTTTATCCGCACACCTCACTAAATTATGTTGAAGTTATGAT
GTTGGAAGTCAGAGAACTATTCTCGTCAACCAA
Found at i:2298146 original size:31 final size:30
Alignment explanation
Indices: 2298108--2298171 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
2298098 TATATTGAGG
*
2298108 CCTCAGCTACCATCTAGCTACTGTTCAGCTA
1 CCTCAGCTACCATCCAGCTACTG-TCAGCTA
* *
2298139 CCTCAGCTACCTTCCAGCTAGTGTCAGCTA
1 CCTCAGCTACCATCCAGCTACTGTCAGCTA
2298169 CCT
1 CCT
2298172 TCTTGGTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.20, C:0.38, G:0.14, T:0.28
Consensus pattern (30 bp):
CCTCAGCTACCATCCAGCTACTGTCAGCTA
Found at i:2300061 original size:17 final size:17
Alignment explanation
Indices: 2300039--2300110 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
2300029 AATTAAGAGA
2300039 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
2300056 TAGTTTGATGAATGAAA
1 TAGTTTAATAAATGAAC
* *
2300073 TAGTTTAATTAATAAAC
1 TAGTTTAATAAATGAAC
* * *
2300090 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
2300108 TAG
1 TAG
2300111 ATGCATGAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
17 29 0.69
18 13 0.31
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2306350 original size:18 final size:18
Alignment explanation
Indices: 2306327--2306382 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
2306317 TTTCAACTTA
2306327 TTTTTCTTTGCAATTTTC
1 TTTTTCTTTGCAATTTTC
* *
2306345 TTTTTCTTTTC-TTTTTC
1 TTTTTCTTTGCAATTTTC
2306362 -TTTTCTTCTTGCAA-TTTC
1 TTTTTC-T-TTGCAATTTTC
2306380 TTT
1 TTT
2306383 ACTGATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 5 0.17
17 6 0.20
18 17 0.57
19 2 0.07
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
TTTTTCTTTGCAATTTTC
Found at i:2306356 original size:11 final size:11
Alignment explanation
Indices: 2306340--2306368 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2306330 TTCTTTGCAA
2306340 TTTTCTTTTTC
1 TTTTCTTTTTC
2306351 TTTTCTTTTTC
1 TTTTCTTTTTC
2306362 TTTTCTT
1 TTTTCTT
2306369 CTTGCAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:2310298 original size:15 final size:14
Alignment explanation
Indices: 2310278--2310316 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2310268 TGTTGTTTTG
2310278 TTTTCAAGAGTTATC
1 TTTTCAAGAGTTA-C
*
2310293 TTTTCAATAGTTAC
1 TTTTCAAGAGTTAC
2310307 TTGTTCAAGA
1 TT-TTCAAGA
2310317 CATTTCTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (14 bp):
TTTTCAAGAGTTAC
Found at i:2312414 original size:24 final size:24
Alignment explanation
Indices: 2312387--2312432 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2312377 TCTTTTGCCA
2312387 CTCCAAAAGACATGTTCTTTGATT
1 CTCCAAAAGACATGTTCTTTGATT
* *
2312411 CTCCAAAGGTCATGTTCTTTGA
1 CTCCAAAAGACATGTTCTTTGA
2312433 ATCATGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (24 bp):
CTCCAAAAGACATGTTCTTTGATT
Found at i:2326226 original size:17 final size:17
Alignment explanation
Indices: 2326204--2326237 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2326194 TTAGAGTTAA
2326204 TTTAATAAACGAACTAG
1 TTTAATAAACGAACTAG
* *
2326221 TTTAATTAATGAACTAG
1 TTTAATAAACGAACTAG
2326238 ATGATTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (17 bp):
TTTAATAAACGAACTAG
Found at i:2332345 original size:12 final size:12
Alignment explanation
Indices: 2332328--2332378 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
2332318 GGACTGTTCG
2332328 AAAGAAAAATAA
1 AAAGAAAAATAA
2332340 AAAGAAAAATAA
1 AAAGAAAAATAA
*
2332352 AAA-AAGACATGAA
1 AAAGAA-AAAT-AA
*
2332365 AAAGAAAAAGAA
1 AAAGAAAAATAA
2332377 AA
1 AA
2332379 CAAAACAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.06
12 22 0.67
13 7 0.21
14 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (12 bp):
AAAGAAAAATAA
Found at i:2332347 original size:6 final size:6
Alignment explanation
Indices: 2332328--2332378 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
2332318 GGACTGTTCG
* * *
2332328 AAAGAA AAATAA AAAGAA AAATAA AAA-AA GACATGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -A-AAGAA AAAGAA AAAGAA
2332377 AA
1 AA
2332379 CAAAACAACA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
5 2 0.05
6 31 0.84
7 2 0.05
8 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:2338519 original size:23 final size:24
Alignment explanation
Indices: 2338493--2338554 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
2338483 AAATCCAGCA
2338493 AAGAAAATCAAAGAACTC-AAAAG
1 AAGAAAATCAAAGAACTCAAAAAG
* *
2338516 AAGAAAATTC-CAGCACTCAAAAAG
1 AAGAAAA-TCAAAGAACTCAAAAAG
*
2338540 AAGAAAAGCAAAGAA
1 AAGAAAATCAAAGAA
2338555 AAGAAAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.63, C:0.15, G:0.15, T:0.08
Consensus pattern (24 bp):
AAGAAAATCAAAGAACTCAAAAAG
Found at i:2338551 original size:15 final size:15
Alignment explanation
Indices: 2338540--2338569 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2338530 ACTCAAAAAG
2338540 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
2338555 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
2338569 A
1 A
2338570 GTTGAAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Done.