Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 23
Found at i:2911242 original size:29 final size:29
Alignment explanation
Indices: 2911186--2911242 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2911176 CAAAAATGTT
*
2911186 TTAAAACTATATTATATGTTTTAAAAAAA
1 TTAAAACTATATTATATATTTTAAAAAAA
* *
2911215 TTAAAATTATATTATATATATTTCAAAA
1 TTAAAACTATATTATATAT-TTTAAAAA
2911243 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (29 bp):
TTAAAACTATATTATATATTTTAAAAAAA
Found at i:2911260 original size:34 final size:33
Alignment explanation
Indices: 2911079--2911269 Score: 151
Period size: 35 Copynumber: 5.7 Consensus size: 33
2911069 AAAAAATTTG
2911079 TTTTAAAACTATATATAATATATATTTCAAAAATA
1 TTTTAAAACTATAT-T-ATATATATTTCAAAAATA
* * * *
2911114 TTTTCAAAACCACA-TACTATATAATTTAAAAAATG
1 TTTT-AAAACTATATTA-TATAT-ATTTCAAAAATA
* * *
2911149 TTTTCAAACCATATGT-TATATAATTTTCAAAAATG
1 TTTTAAAACTATAT-TATATAT-A-TTTCAAAAATA
*
2911184 TTTTAAAACTATATTATATGT-TTT-AAAAA-A
1 TTTTAAAACTATATTATATATATTTCAAAAATA
* * *
2911214 -ATTAAAATTATATTATATATATTTCAAAATTA
1 TTTTAAAACTATATTATATATATTTCAAAAATA
*
2911246 TTTTAAAAACTATATAATATATAT
1 TTTT-AAAACTATATTATATATAT
2911270 ATACATATGT
Statistics
Matches: 126, Mismatches: 18, Indels: 25
0.75 0.11 0.15
Matches are distributed among these distances:
29 17 0.13
30 3 0.02
31 9 0.07
32 4 0.03
33 3 0.02
34 38 0.30
35 44 0.35
36 8 0.06
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (33 bp):
TTTTAAAACTATATTATATATATTTCAAAAATA
Found at i:2912121 original size:84 final size:84
Alignment explanation
Indices: 2911898--2913025 Score: 1129
Period size: 84 Copynumber: 13.6 Consensus size: 84
2911888 ATCAGTCTCA
** * * * *
2911898 AAGGTCTTCAGTTGGCAGATAACCCTTATCGAATTAAGCTATGCTGCAAATGATGTGCCTTTGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
2911963 CTGAGCGTAGTCGAACTCG
66 CTGAGCGTAGTCGAACTCG
* *
2911982 AAGGTC--T--TTGGCAGATAGCCCTTTTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
2912043 CTGAGCGTAGTCGAACTCG
66 CTGAGCGTAGTCGAACTCG
* * *
2912062 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAGATGATATGCCTTAGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
* *
2912127 CTAAGCGTAGTCGAACTCA
66 CTGAGCGTAGTCGAACTCG
* * * * * *
2912146 AAGGTCTTTTGG-TGACAGATAACCCTTCTAG-CTTTGAGTTATGCTGTAAATGATATGCCCTCG
1 AAGGTC-TTTGGTTGGCAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGATGTG-CCTTG
* *
2912209 AAGCTGAGCGTAGTCAAACTCG
63 GAGCTGAGCGTAGTCGAACTCG
* * * * * * * *
2912231 -TGGGC-CT--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGTAAATGATGTGTCTTGGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
**
2912292 CTGAGCGTAAACGAACTCG
66 CTGAGCGTAGTCGAACTCG
* * *
2912311 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAGATGATATGCCTTAGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
2912376 CTGAGCGTAGTCGAACTCG
66 CTGAGCGTAGTCGAACTCG
* * * * * * * * *
2912395 AAGGTCTTTTGG-TGACAGATAACTCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGA
1 AAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGG
*
2912459 AGCTGAGCGTAGTCAAACTCG
64 AGCTGAGCGTAGTCGAACTCG
* * * *
2912480 AGGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATGTGCCTTGGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
*
2912541 CTGAGCATAGTCGAACTCG
66 CTGAGCGTAGTCGAACTCG
* * * ** * * *
2912560 AAGGTATTTGGTTGGCAGATAACACTTCTCGACTTAAGTTATGTTATAAATTATATGCCTTAGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
* *
2912625 CTGAGCGTAGTCAAACTTG
66 CTGAGCGTAGTCGAACTCG
* * * * * * * * * *
2912644 AAAGTCTTTTGG-TGACAGATAACCCTTATAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGA
1 AAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGG
* *
2912708 AGCTGAGCCTAGTCGAACTTG
64 AGCTGAGCGTAGTCGAACTCG
* * * *
2912729 AGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTTGGAA
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
*
2912790 CTGAGCGTAGTCGAACTCA
66 CTGAGCGTAGTCGAACTCG
* *
2912809 AAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGA
1 AAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
* *
2912874 ACTGAGAGTAGTCGAACTCG
65 GCTGAGCGTAGTCGAACTCG
* * * * * * * * * *
2912894 AAGGTCTTTTGG-TGACAGATAACCCTTCTAG-CAGTGAGTTATACTGTAAATGTTATCCCCTCG
1 AAGGTC-TTTGGTTGGCAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGATGT-GCCTTG
*
2912957 AAGCTGAGCGTAGTCGAACTCG
63 GAGCTGAGCGTAGTCGAACTCG
* * *
2912979 AGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
2913026 AGTTTGTTTA
Statistics
Matches: 855, Mismatches: 158, Indels: 65
0.79 0.15 0.06
Matches are distributed among these distances:
80 153 0.18
81 137 0.16
82 7 0.01
83 3 0.00
84 359 0.42
85 196 0.23
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (84 bp):
AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
CTGAGCGTAGTCGAACTCG
Found at i:2912280 original size:249 final size:249
Alignment explanation
Indices: 2911945--2913025 Score: 1698
Period size: 249 Copynumber: 4.3 Consensus size: 249
2911935 GCTATGCTGC
* * * *
2911945 AAATGATGTGCCTTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTTTCG
1 AAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCG
*
2912009 ACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
* *
2912074 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAGATGATATGCCTTAGAGCTAAGCGTAGTC
131 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTC
* *
2912139 GAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGCTTTGAGTTATGCTGT
196 GAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGT
* * * *
2912193 AAATGATATGCCCTCGAAGCTGAGCGTAGTCAAACTCGTGGGCCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCG
* * * **
2912258 ACTTAAGCTATGTTGTAAATGATGTGTCTTGGAGCTGAGCGTAAACGAACTCGAAGGTCTTTGGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
*
2912323 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAGATGATATGCCTTAGAGCTGAGCGTAGTC
131 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTC
* *
2912388 GAACTCGAAGGTCTTTTGGTGACAGATAACTCTTCTAGCCTTGAGTTATACTGT
196 GAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGT
* *
2912442 AAATGATGTGCCCTCGAAGCTGAGCGTAGTCAAACTCGAGGGTCTTTGGTAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCG
* * *
2912507 ACTTAAGCTATGATGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTATTTGGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
* * ** *
2912572 TGGCAGATAACACTTCTCGACTTAAGTTATGTTATAAATTATATGCCTTAGAGCTGAGCGTAGTC
131 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTC
* * *
2912637 AAACTTGAAA-GTCTTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATACTGT
196 GAAC-TCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGT
* *
2912691 AAATGATGTGCCCTCGAAGCTGAGCCTAGTCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCG
* * * *
2912756 ACTTAAGTTATGCTACAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
* *
2912821 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAACTGAGAGTAGT
130 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGT
* **
2912886 CGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCAGTGAGTTATACTGT
195 CGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGT
* * *
2912941 AAATGTTATCCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCG
2913006 ACTTAAGCTATGCTGCAAAT
66 ACTTAAGCTATGCTGCAAAT
2913026 AGTTTGTTTA
Statistics
Matches: 757, Mismatches: 72, Indels: 6
0.91 0.09 0.01
Matches are distributed among these distances:
248 13 0.02
249 555 0.73
250 189 0.25
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (249 bp):
AAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTC
GAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGT
Found at i:2912902 original size:165 final size:165
Alignment explanation
Indices: 2911909--2913025 Score: 1100
Period size: 165 Copynumber: 6.8 Consensus size: 165
2911899 AGGTCTTCAG
* * * * *
2911909 TTGGCAGATAACCCTTATCGAATTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGT
* * *
2911974 CGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTTTCGACTTAAGTTATGCTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
* *
2912035 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
131 CCTTAGAACTGAGCGTAGTCGAACTCGAAGGTC-TT
* * * *
2912071 GGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAGATGATATGCCTTAGAGCTAAGCGTA
1 --TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTA
* * * * *
2912136 GTCGAACTCAAAGGTCTTTTGG-TGACAGATAACCCTTCTAG-CTTTGAGTTATGCTGTAAATGA
64 GTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGA
* * * * * *
2912199 TATGCCCTCGAAGCTGAGCGTAGTCAAACTCG-TGGGCCT
127 TATGCCTTAGAA-CTGAGCGTAGTCGAACTCGAAGGTCTT
* * * * * **
2912238 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGTAAATGATGTGTCTTGGAGCTGAGCGTAAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGT
*
2912303 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAGATGATATG
66 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
*
2912368 CCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
131 CCTTAGAACTGAGCGTAGTCGAACTCGAAGGTCTT
* * * * * * *
2912403 TTGGTGACAGATAACTCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGCG
1 TT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAG-AGCTGAGCG
* * * * *
2912468 TAGTCAAACTCGAGGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGA
62 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * * * *
2912529 TGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTATTT
127 TATGCCTTAGAACTGAGCGTAGTCGAACTCGAAGGT-CTT
* * * * *
2912569 GGTTGGCAGATAACACTTCTCGACTTAAGTTATGTTATAAATTATATGCCTTAGAGCTGAGCGTA
1 --TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTA
* * * * * * * * * *
2912634 GTCAAACTTGAAAGTCTTTTGG-TGACAGATAACCCTTATAGCCTTGAGTTATACTGTAAATGAT
64 GTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * * * * *
2912698 GTGCCCTCGAAGCTGAGCCTAGTCGAACTTGAGGGTC-T
128 ATGCCTTAGAA-CTGAGCGTAGTCGAACTCGAAGGTCTT
* ** * *
2912736 TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTTGGAACTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGT
*
2912801 CGAACTCAAAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
66 CGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
*
2912866 GCCTTAGAACTGAGAGTAGTCGAACTCGAAGGTCTT
130 GCCTTAGAACTGAGCGTAGTCGAACTCGAAGGTCTT
* * * * * * * * *
2912902 TTGGTGACAGATAACCCTTCTAG-CAGTGAGTTATACTGTAAATGTTATCCCCTCGAAGCTGAGC
1 TT-G-G-CAGATAACCCTTCTCGAC-TTAAGTTATGCTGTAAATGATGTGCCTTAG-AGCTGAGC
* * *
2912966 GTAGTCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
61 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
2913026 AGTTTGTTTA
Statistics
Matches: 782, Mismatches: 142, Indels: 57
0.80 0.14 0.06
Matches are distributed among these distances:
164 118 0.15
165 357 0.46
166 51 0.07
167 8 0.01
168 123 0.16
169 101 0.13
170 24 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (165 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
CCTTAGAACTGAGCGTAGTCGAACTCGAAGGTCTT
Found at i:2917555 original size:14 final size:14
Alignment explanation
Indices: 2917536--2917581 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
2917526 ACCCCTAAAA
2917536 AGATAAAAAATATT
1 AGATAAAAAATATT
2917550 AGATAAAAAATA--
1 AGATAAAAAATATT
*
2917562 AGA-AATAAATATT
1 AGATAAAAAATATT
*
2917575 AAATAAA
1 AGATAAA
2917582 TCTAATCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
11 7 0.27
12 3 0.12
13 2 0.08
14 14 0.54
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (14 bp):
AGATAAAAAATATT
Found at i:2918035 original size:16 final size:16
Alignment explanation
Indices: 2918014--2918057 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
2918004 ATCAAGACGA
2918014 AGGAAACTACTTTTCG
1 AGGAAACTACTTTTCG
2918030 AGGAAACTACTTTTCG
1 AGGAAACTACTTTTCG
* *
2918046 AGTAAACGACTT
1 AGGAAACTACTT
2918058 GTTCTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (16 bp):
AGGAAACTACTTTTCG
Found at i:2918736 original size:23 final size:23
Alignment explanation
Indices: 2918690--2918739 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2918680 GTAAATAATA
* *
2918690 AATAAATAAGAATAATAAAGAAT
1 AATAAATAAGAATAAGAAAAAAT
2918713 AATAAATAA-AATAAGAATAAAAT
1 AATAAATAAGAATAAGAA-AAAAT
2918736 AATA
1 AATA
2918740 TATTATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (23 bp):
AATAAATAAGAATAAGAAAAAAT
Found at i:2918749 original size:10 final size:11
Alignment explanation
Indices: 2918734--2918766 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
2918724 TAAGAATAAA
2918734 ATAATATAT-T
1 ATAATATATAT
2918744 ATAATATATAT
1 ATAATATATAT
2918755 AT-ATATATAT
1 ATAATATATAT
2918765 AT
1 AT
2918767 TTTAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 19 0.86
11 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATAATATATAT
Found at i:2918801 original size:35 final size:35
Alignment explanation
Indices: 2918749--2918896 Score: 133
Period size: 35 Copynumber: 4.2 Consensus size: 35
2918739 ATATTATAAT
**
2918749 ATATATATATATATATATTTT-AAATTTGTTTTAAA
1 ATATATATA-ATATATATTTTAAAAAATGTTTTAAA
* *
2918784 ACTATATATAATATATATTTCAAAAATAT-TTTCAAA
1 A-TATATATAATATATATTTTAAAAA-ATGTTTTAAA
* *
2918820 ATCACATATAATATA-ATTTTAAAAAATGTTTTCAA
1 AT-ATATATAATATATATTTTAAAAAATGTTTTAAA
** *
2918855 AT-TATATGTTATATAGTTTTCAAAAATGTTTTAAA
1 ATATATATAATATATA-TTTTAAAAAATGTTTTAAA
2918890 ACTATAT
1 A-TATAT
2918897 TATATGTTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
33 8 0.09
34 3 0.03
35 46 0.51
36 30 0.33
37 4 0.04
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (35 bp):
ATATATATAATATATATTTTAAAAAATGTTTTAAA
Found at i:2918915 original size:35 final size:35
Alignment explanation
Indices: 2918775--2918913 Score: 105
Period size: 35 Copynumber: 4.0 Consensus size: 35
2918765 ATTTTAAATT
2918775 TGTTTTAAAACTATA-TATAATATA-TATTTCAAAAATA
1 TGTTTTAAAACTATAGT-T-ATATAGT-TTTCAAAAA-A
* * * *
2918812 T-TTTCAAAATCACATA-TAATATAATTTT-AAAAAA
1 TGTTTTAAAA-C-TATAGTTATATAGTTTTCAAAAAA
* *
2918846 TGTTTTCAAATTATATGTTATATAGTTTTC-AAAAA
1 TGTTTTAAAACTATA-GTTATATAGTTTTCAAAAAA
2918881 TGTTTTAAAACTATA-TTATAT-GTTTTCAAAAAA
1 TGTTTTAAAACTATAGTTATATAGTTTTCAAAAAA
2918914 AAAATTATAT
Statistics
Matches: 83, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
32 6 0.07
33 14 0.17
34 2 0.02
35 39 0.47
36 15 0.18
37 3 0.04
38 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (35 bp):
TGTTTTAAAACTATAGTTATATAGTTTTCAAAAAA
Found at i:2918939 original size:27 final size:27
Alignment explanation
Indices: 2918887--2918939 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2918877 AAAATGTTTT
*
2918887 AAAACTATATTATATGTTTTCAAAAAA
1 AAAACTATATTATATATTTTCAAAAAA
* *
2918914 AAAATTATATTATATATATTTTAAAA
1 AAAACTATATTATATAT-TTTCAAAA
2918940 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (27 bp):
AAAACTATATTATATATTTTCAAAAAA
Found at i:2920289 original size:56 final size:56
Alignment explanation
Indices: 2920222--2920418 Score: 295
Period size: 56 Copynumber: 3.5 Consensus size: 56
2920212 TATTTTCTAC
* *
2920222 ATATATTCGATTTCAGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAT
1 ATATACTCGATTTCAGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAG
* * * *
2920278 ATATACTCGATTTCGGGGCCTCTATTTTTATGTTTCTTAATGACAACAACTGATAG
1 ATATACTCGATTTCAGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAG
* * *
2920334 ATATACTCGATTTCAGGACCCCTATTTTTATTCTTATTAATGGCAACAACTGATAG
1 ATATACTCGATTTCAGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAG
* *
2920390 ATATACTCGATTTCGGGGCCCCTATTTTT
1 ATATACTCGATTTCAGGACCCCTATTTTT
2920419 TGAGGGCCCT
Statistics
Matches: 126, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 126 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (56 bp):
ATATACTCGATTTCAGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAG
Found at i:2924540 original size:32 final size:32
Alignment explanation
Indices: 2924415--2924544 Score: 152
Period size: 32 Copynumber: 4.1 Consensus size: 32
2924405 TAAGGTGACA
* * * * *
2924415 TTGGGTAGACTCTGAGGCCCCAAGGCATTTCC
1 TTGGGTAGGCTCTAAGGCCCCAAGGTACTCCC
2924447 TTGGGTAGGCTCTAAGGCCCCAAGGTACTCCC
1 TTGGGTAGGCTCTAAGGCCCCAAGGTACTCCC
* * * *
2924479 TTGCGTAGGCTCTTAGGCCCTAAGGTACTCTC
1 TTGGGTAGGCTCTAAGGCCCCAAGGTACTCCC
* **
2924511 TTGGGTAGGCTCTCAGGCCCCAATATACTCCC
1 TTGGGTAGGCTCTAAGGCCCCAAGGTACTCCC
2924543 TT
1 TT
2924545 AAGTTGGCTT
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 83 1.00
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (32 bp):
TTGGGTAGGCTCTAAGGCCCCAAGGTACTCCC
Found at i:2925762 original size:18 final size:17
Alignment explanation
Indices: 2925739--2925778 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
2925729 ATGTACATAT
2925739 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
2925756 AATGTCCCGAAGGACCAC
1 -ATGTCCCGAAGGACCAC
2925774 ATGTC
1 ATGTC
2925779 ATTCCTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.15
Consensus pattern (17 bp):
ATGTCCCGAAGGACCAC
Found at i:2925839 original size:111 final size:111
Alignment explanation
Indices: 2925645--2925964 Score: 487
Period size: 121 Copynumber: 2.8 Consensus size: 111
2925635 GCCATATAAT
** *
2925645 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
2925710 GTCTCACCAGACTTCACACATGTACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTACATATATGTCCCGAAGGACCAC
* * * *
2925756 AATGTCCCGAAGGACCACATGTCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
2925821 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACA---T-----G--TACATATATGTCCCGAAGGACCAC
2925877 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
2925942 GTCTCACCAGACTTCACACATGT
66 GTCTCACCAGACTTCACACATGT
2925965 TCCAAAGAAT
Statistics
Matches: 188, Mismatches: 11, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
111 79 0.42
113 1 0.01
114 1 0.01
118 1 0.01
119 1 0.01
121 105 0.56
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (111 bp):
AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTACATATATGTCCCGAAGGACCAC
Found at i:2925852 original size:62 final size:63
Alignment explanation
Indices: 2925786--2925981 Score: 164
Period size: 62 Copynumber: 3.2 Consensus size: 63
2925776 GTCATTCCTT
*
2925786 AAGAAT-CATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
* * * * * *
2925848 AAGAATACATAT--ATGTCCCGAAGGACCACA--A--TGTC-C-CGAAGGAC--CACATATCATT
1 AAGAATACATATACATATACC-AAGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTT
*
2925903 CCTT
61 CC-A
* *
2925907 AAGAAT-CATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
2925969 AAGAATACATATA
1 AAGAATACATATA
2925982 TGTCCCGAAG
Statistics
Matches: 100, Mismatches: 16, Indels: 35
0.66 0.11 0.23
Matches are distributed among these distances:
57 7 0.07
58 12 0.12
59 19 0.19
60 5 0.05
61 6 0.06
62 26 0.26
63 18 0.18
64 7 0.07
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (63 bp):
AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
Found at i:2925883 original size:18 final size:18
Alignment explanation
Indices: 2925860--2925895 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2925850 GAATACATAT
2925860 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
2925878 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
2925896 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:2925946 original size:121 final size:121
Alignment explanation
Indices: 2925732--2925998 Score: 498
Period size: 121 Copynumber: 2.2 Consensus size: 121
2925722 TTCACACATG
*
2925732 TACATATATGTCCCGAAGGACCACAATGTCCCGAAGGACCACATGTCATTCCTTAAGAATCATAT
1 TACATATATGTCCCGAAGGACCACAATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATAT
*
2925797 ACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAA
66 ACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAA
2925853 TACATATATGTCCCGAAGGACCACAATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATAT
1 TACATATATGTCCCGAAGGACCACAATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATAT
* *
2925918 ACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAA
66 ACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAA
2925974 TACATATATGTCCCGAAGGACCACA
1 TACATATATGTCCCGAAGGACCACA
2925999 TAGACCCTCG
Statistics
Matches: 142, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 142 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (121 bp):
TACATATATGTCCCGAAGGACCACAATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATAT
ACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAA
Found at i:2927294 original size:21 final size:21
Alignment explanation
Indices: 2927268--2927311 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2927258 ATTTTATTCG
* *
2927268 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
2927289 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
2927310 CT
1 CT
2927312 AGCCCGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:2930047 original size:23 final size:23
Alignment explanation
Indices: 2930021--2930074 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
2930011 ATGTGGATTG
2930021 TGTAACATCATCATTGATGTATA
1 TGTAACATCATCATTGATGTATA
2930044 TGTAACATCATCATTGATGTATA
1 TGTAACATCATCATTGATGTATA
*
2930067 TATAACAT
1 TGTAACAT
2930075 TTATCACGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (23 bp):
TGTAACATCATCATTGATGTATA
Found at i:2937315 original size:3 final size:3
Alignment explanation
Indices: 2937307--2937338 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2937297 TAACTTAAAC
2937307 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2937339 AGTATTCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2937666 original size:29 final size:30
Alignment explanation
Indices: 2937632--2937689 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
2937622 AGTTTATTTT
* * *
2937632 AATATA-AAAATCAAAATTTTATGTATAGA
1 AATATATAAAATAAAAATTATATATATAGA
2937661 AATATATTAAAATAAAAATTATATATATA
1 AATATA-TAAAATAAAAATTATATATATA
2937690 TATCGTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
31 18 0.75
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (30 bp):
AATATATAAAATAAAAATTATATATATAGA
Found at i:2943643 original size:10 final size:10
Alignment explanation
Indices: 2943628--2943652 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2943618 TAACAGCTAA
2943628 AGAAAATAAG
1 AGAAAATAAG
2943638 AGAAAATAAG
1 AGAAAATAAG
2943648 AGAAA
1 AGAAA
2943653 CCCATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (10 bp):
AGAAAATAAG
Found at i:2944094 original size:74 final size:72
Alignment explanation
Indices: 2943987--2944125 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 72
2943977 AGATCTCGAA
* *
2943987 CTTATTTTTGGACCCTTATTTTTTGGGACTTCTTAATGGCAATAACTGATAAATATACTTGATTT
1 CTTATTTTTGGACCCTTATTTTTTGGGACTTCTTAATGACAACAACTGATAAATATACTTGATTT
2944052 CGTGGCT
66 CGTGGCT
* *
2944059 CTTATTTTTTGGGA-CCTCTATTTTTTAGGG-TTTCTTAATGACAACAACTGATAGATATACTTG
1 CTTA-TTTTT-GGACCCT-TATTTTTT-GGGACTTCTTAATGACAACAACTGATAAATATACTTG
2944122 ATTT
62 ATTT
2944126 AGGAGCCCTA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
72 4 0.07
73 8 0.14
74 44 0.75
75 3 0.05
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.45
Consensus pattern (72 bp):
CTTATTTTTGGACCCTTATTTTTTGGGACTTCTTAATGACAACAACTGATAAATATACTTGATTT
CGTGGCT
Found at i:2944141 original size:74 final size:73
Alignment explanation
Indices: 2943987--2944141 Score: 185
Period size: 74 Copynumber: 2.1 Consensus size: 73
2943977 AGATCTCGAA
* *
2943987 CTTA-TTTTTGGACCCTTATTTTTTGGGACTTCTTAATGGCAATAACTGATAAATATACTTGATT
1 CTTATTTTTTGGACCCTTATTTTTTGGGACTTCTTAATGACAACAACTGATAAATATACTTGATT
* *
2944051 TCGTGGCT
66 TAGTGGCC
* *
2944059 CTTATTTTTTGGGA-CCTCTATTTTTTAGGG-TTTCTTAATGACAACAACTGATAGATATACTTG
1 CTTATTTTTT-GGACCCT-TATTTTTT-GGGACTTCTTAATGACAACAACTGATAAATATACTTG
2944122 ATTTAG-GAGCC
63 ATTTAGTG-GCC
2944133 C-TATTTTTT
1 CTTATTTTTT
2944142 AGAGTACTGC
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
72 4 0.06
73 17 0.24
74 48 0.67
75 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (73 bp):
CTTATTTTTTGGACCCTTATTTTTTGGGACTTCTTAATGACAACAACTGATAAATATACTTGATT
TAGTGGCC
Found at i:2947066 original size:23 final size:23
Alignment explanation
Indices: 2947031--2947078 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2947021 ATCAAATACA
* *
2947031 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
2947054 ATAATGTAATAGGTAACGTTTAT
1 ATAATATAATAGGTAACGCTTAT
2947077 AT
1 AT
2947079 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:2947832 original size:182 final size:182
Alignment explanation
Indices: 2947518--2947893 Score: 535
Period size: 182 Copynumber: 2.1 Consensus size: 182
2947508 TTTCTATCGA
* * *
2947518 TTTTGTCATTTCGAGATTAATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTTGAGACTAATTTTGTCATATTTTTACCTGTTATATTGTTATGGACCGATACATT
* * * *
2947583 TTTATAAAATATCGACACTTTATTGACGCTATAGCATATTTTCTTTTAAATTTCAAAAGTATCGA
66 TTTATAAAATATCAACACTTTATTAACGCTATAACATATTCTCTTTTAAATTTCAAAAGTATCGA
* * * *
2947648 TACTTATAATAAAGTATCGACACTTTTAACATATCTAG-TAGCTCTTTA-CTGG
131 TACTTATAATAAAATATCGACACTATCAACATATC-AGATAGCGCTTTACCT-G
* *
2947700 TTTTGTCATTTTGAGACTGATTTTGTCATATTTTTACCTGTTATATTGTTATGGACCGATATATT
1 TTTTGTCATTTTGAGACTAATTTTGTCATATTTTTACCTGTTATATTGTTATGGACCGATACATT
* * * *
2947765 TTTATAAAATATCAATACTTTATTAACGCTATAACTTCTTCTCTTTTAAA-TTCTAATAA-TGTC
66 TTTATAAAATATCAACACTTTATTAACGCTATAACATATTCTCTTTTAAATTTC-AA-AAGTATC
2947828 GATACTTATAATAAAATATCGACACTATCAACATATCAGATAGCGCTTTACCTG
129 GATACTTATAATAAAATATCGACACTATCAACATATCAGATAGCGCTTTACCTG
2947882 TTTTGTCATTTT
1 TTTTGTCATTTT
2947894 TTTACCTGTT
Statistics
Matches: 173, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
181 5 0.03
182 164 0.95
183 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (182 bp):
TTTTGTCATTTTGAGACTAATTTTGTCATATTTTTACCTGTTATATTGTTATGGACCGATACATT
TTTATAAAATATCAACACTTTATTAACGCTATAACATATTCTCTTTTAAATTTCAAAAGTATCGA
TACTTATAATAAAATATCGACACTATCAACATATCAGATAGCGCTTTACCTG
Found at i:2948082 original size:112 final size:112
Alignment explanation
Indices: 2947881--2948389 Score: 731
Period size: 110 Copynumber: 4.6 Consensus size: 112
2947871 CGCTTTACCT
* *
2947881 GTTTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATATATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
2947946 TTCAATATATCTGATAACGCTTTACTTGTTTTGTCATTTATAAATCG
66 TTCAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAAATCG
* * * * ** *
2947993 GTTTTATCATTTTTTTACCTATTATATTATTATAGATAAATACATTTTTATAAAGTATCAACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
2948058 TTCAATATATCCGATAACGTTTTACCTGTTTTGTCATTTATAGATCG
66 TTCAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAAATCG
2948105 G--TTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * * *
2948168 TTTAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAGACCA
66 TTCAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAAATCG
* * *
2948215 ATTTTATCA-TTTTTTACCTGTTAT-TTGTTATGGATCGATACATTTTTATAAAATATCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * *
2948278 TTCAATATATCCGGTAACGTTTTACCTGTTTTATCATTTATAAA-CTG
66 TTCAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAAATC-G
* * *
2948325 ATTTTGTTATTTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACAC
1 GTTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
2948390 AAACCGACAA
Statistics
Matches: 356, Mismatches: 35, Indels: 11
0.89 0.09 0.03
Matches are distributed among these distances:
109 1 0.00
110 182 0.51
111 15 0.04
112 122 0.34
113 36 0.10
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.48
Consensus pattern (112 bp):
GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTCAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAAATCG
Found at i:2948339 original size:222 final size:223
Alignment explanation
Indices: 2947881--2948389 Score: 765
Period size: 222 Copynumber: 2.3 Consensus size: 223
2947871 CGCTTTACCT
* *
2947881 GTTTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATATATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * * **
2947946 TTCAATATATCTGATAACGCTTTACTTGTTTTGTCATTTATAAATCGGTTTTATCATTTTTTTAC
66 TTCAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAAACCAATTTTATCATTTTTTTAC
*
2948011 CTATTATATTATTATAGATAAATACATTTTTATAAAGTATCAACACTTTCAATATATCCGATAAC
131 CTATTATATTATTATAGATAAATACATTTTTATAAAATATCAACACTTTCAATATATCCGATAAC
* *
2948076 GTTTTACCTGTTTTGTCATTTATAGATC
196 GTTTTACCTGTTTTATCATTTATAAATC
*
2948104 G-GTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
2948168 TTTAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAGACCAATTTTATCA-TTTTTTAC
66 TTCAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAAACCAATTTTATCATTTTTTTAC
* * * ** * *
2948232 CTGTTAT-TTGTTATGGATCGATACATTTTTATAAAATATCGACACTTTCAATATATCCGGTAAC
131 CTATTATATTATTATAGATAAATACATTTTTATAAAATATCAACACTTTCAATATATCCGATAAC
2948296 GTTTTACCTGTTTTATCATTTATAAA-C
196 GTTTTACCTGTTTTATCATTTATAAATC
* *
2948323 TGATTTTGTTATTTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGAC
1 -G-TTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGAC
2948388 AC
63 AC
2948390 AAACCGACAA
Statistics
Matches: 259, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
219 1 0.00
220 75 0.29
221 14 0.05
222 114 0.44
223 55 0.21
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.48
Consensus pattern (223 bp):
GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTCAATATATCCGATAACGCTTTACCTGTTTTGTCATTTATAAACCAATTTTATCATTTTTTTAC
CTATTATATTATTATAGATAAATACATTTTTATAAAATATCAACACTTTCAATATATCCGATAAC
GTTTTACCTGTTTTATCATTTATAAATC
Found at i:2960291 original size:15 final size:15
Alignment explanation
Indices: 2960252--2960291 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2960242 TATTTTTTTA
*
2960252 ATTTTGAAATAATAT
1 ATTTTGAATTAATAT
* *
2960267 AATTTAAATTAATAT
1 ATTTTGAATTAATAT
2960282 ATTTTGAATT
1 ATTTTGAATT
2960292 TTTTTTTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (15 bp):
ATTTTGAATTAATAT
Found at i:2960714 original size:22 final size:22
Alignment explanation
Indices: 2960687--2960740 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2960677 ATTAAAAAAA
*
2960687 TCATTTATTTAATTT-TTCTTT
1 TCATTTATTTAATTTATTATTT
*
2960708 TCAATTT-TTTTATTTATTATTT
1 TC-ATTTATTTAATTTATTATTT
*
2960730 TCATATATTTA
1 TCATTTATTTA
2960741 TTATATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (22 bp):
TCATTTATTTAATTTATTATTT
Found at i:2960740 original size:17 final size:16
Alignment explanation
Indices: 2960717--2960763 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
2960707 TTCAATTTTT
2960717 TTATTTATTATTTTCA
1 TTATTTATTATTTTCA
2960733 TATATTTATTATATTT-A
1 T-TATTTATTAT-TTTCA
2960750 TTA-TT-TTATTTTCA
1 TTATTTATTATTTTCA
2960764 AGTATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 2 0.07
16 3 0.11
17 12 0.43
18 3 0.11
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTATTATTTTCA
Found at i:2960747 original size:9 final size:9
Alignment explanation
Indices: 2960718--2960759 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
2960708 TCAATTTTTT
2960718 TATTTATTA
1 TATTTATTA
2960727 T-TTTCA-TA
1 TATTT-ATTA
2960735 TATTTATTA
1 TATTTATTA
2960744 TATTTATTA
1 TATTTATTA
2960753 T-TTTATT
1 TATTTATT
2960760 TTCAAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 13 0.43
9 17 0.57
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
TATTTATTA
Found at i:2965365 original size:12 final size:11
Alignment explanation
Indices: 2965348--2965382 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
2965338 ACTCTCCAAC
2965348 AAAGAAGAAGAA
1 AAAGAAGAA-AA
2965360 AAAGAAGAAAA
1 AAAGAAGAAAA
2965371 AAAGAA-AAAA
1 AAAGAAGAAAA
2965381 AA
1 AA
2965383 GAAAAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.26
11 8 0.35
12 9 0.39
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAA
Found at i:2965366 original size:9 final size:9
Alignment explanation
Indices: 2965352--2965387 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2965342 TCCAACAAAG
2965352 AAGAAGAAA
1 AAGAAGAAA
2965361 AAGAAGAAA
1 AAGAAGAAA
2965370 AA-AAGAAA
1 AAGAAGAAA
*
2965378 AAAAAGAAA
1 AAGAAGAAA
2965387 A
1 A
2965388 GGAAAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:2965377 original size:17 final size:17
Alignment explanation
Indices: 2965355--2965387 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2965345 AACAAAGAAG
*
2965355 AAGAAAAAGAAGAAAAA
1 AAGAAAAAAAAGAAAAA
2965372 AAGAAAAAAAAGAAAA
1 AAGAAAAAAAAGAAAA
2965388 GGAAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAGAAAAA
Found at i:2967708 original size:81 final size:82
Alignment explanation
Indices: 2967571--2968044 Score: 843
Period size: 81 Copynumber: 5.8 Consensus size: 82
2967561 AGTCCAAACA
*
2967571 TGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TGAATTTAGAAGATGAA-GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
2967636 TTAGACAGAACCAATCAT
65 TTAGACAGAACCAATCAT
2967654 TGAATTTAGAAGATGAA-TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
1 TGAATTTAGAAGATGAAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
2967718 TAGACAGAACCAATCAT
66 TAGACAGAACCAATCAT
2967735 TGAATTTAGAAGATGAA-TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
1 TGAATTTAGAAGATGAAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
2967799 TAGACAGAACCAATCAT
66 TAGACAGAACCAATCAT
2967816 TGAATTTAGAAGATGAATGTGCT-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TGAATTTAGAAGATGAA-GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
2967880 TTATACAGAACCAATCAT
65 TTAGACAGAACCAATCAT
2967898 TGAATTTAGAAGATGAATGTGCTCATAGCA---TCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TGAATTTAGAAGATGAA-GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
2967960 TTATACAGAACCAATCAT
65 TTAGACAGAACCAATCAT
2967978 TGAATTTAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TGAATTTAGAAGATGAA-GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
2968043 TT
65 TT
2968045 TGATAGGAAC
Statistics
Matches: 383, Mismatches: 2, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
80 80 0.21
81 161 0.42
82 81 0.21
83 61 0.16
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (82 bp):
TGAATTTAGAAGATGAAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
TAGACAGAACCAATCAT
Found at i:2969279 original size:74 final size:75
Alignment explanation
Indices: 2969185--2969353 Score: 216
Period size: 74 Copynumber: 2.3 Consensus size: 75
2969175 AACAAGAAGT
* * * *
2969185 AAATATTGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAATA-
1 AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACAC
2969249 TT-TATCAGC
66 TTGTATCAGC
* * ** *
2969258 AAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACA
1 -AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACA
*
2969323 CTTGTATTAGC
65 CTTGTATCAGC
*
2969334 CAATGTTGGGGCATGCTGAA
1 AAATGTTGGGGCATGCTGAA
2969354 GGCCCACAAT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
74 55 0.67
75 21 0.26
76 6 0.07
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (75 bp):
AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACAC
TTGTATCAGC
Found at i:2970705 original size:22 final size:22
Alignment explanation
Indices: 2970676--2970752 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
2970666 ATCTACACTC
2970676 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2970698 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2970720 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2970742 TTCAAAGATGA
1 TTCAAAGATGA
2970753 AAGCTTTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2971600 original size:75 final size:76
Alignment explanation
Indices: 2971408--2972330 Score: 1597
Period size: 75 Copynumber: 12.4 Consensus size: 76
2971398 ACTATTTCCC
2971408 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCC-TC-GG-GCTTTTTGATG-TTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2971469 AA-CCTTCGGG
66 AAGCCTTCGGG
2971479 TCATCTGTAAGTCCTTCAGTGCATGATG-TTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2971543 AAGCCTTC-GG
66 AAGCCTTCGGG
2971553 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
2971618 AATCCTTCGGG
66 AAGCCTTCGGG
2971629 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 TCATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
2971693 AAAGCCTT-GGG
65 AAAGCCTTCGGG
2971704 TCATCTGTAAGTCCTTCAGTGCATGA-GTTTTCCAAAAAGCCTTC-GGAGCTTTTTGATGTTTTC
1 TCATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
2971767 AAATCCTTCGGG
65 AAAGCCTTCGGG
2971779 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2971843 AAGCCTTCGGG
66 AAGCCTTCGGG
2971854 TCATCTGTAAGTCCTTCA--GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATTGTTTTC
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA-TGTTTTC
*
2971917 AAATCCTT-GGG
65 AAAGCCTTCGGG
2971928 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTC-GGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
2971991 AAGCCTTAGGG
66 AAGCCTTCGGG
*
2972002 TCATCTGTAAGTCCTTCAGTGCATGATGTTT-CAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2972066 AAGCCTTCGGG
66 AAGCCTTCGGG
*
2972077 TCATCTGTAAGTCCTTCAGTGCATGA--TTTCC-AAAAGCCTTCGGAAGC-TTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2972138 AAGCCTTCGGG
66 AAGCCTTCGGG
2972149 TCATCTGTAAGTCC-TCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2972212 AAGCCTTCGGG
66 AAGCCTTCGGG
2972223 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2972288 AAGCCTTCGGG
66 AAGCCTTCGGG
2972299 TCATCTGTAAGTCCTTCAGTGCATGATGTTTC
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTC
2972331 ATATTTCAAT
Statistics
Matches: 817, Mismatches: 9, Indels: 47
0.94 0.01 0.05
Matches are distributed among these distances:
70 12 0.01
71 41 0.05
72 41 0.05
73 87 0.11
74 200 0.24
75 283 0.35
76 148 0.18
77 5 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTCGGG
Found at i:2974805 original size:2 final size:2
Alignment explanation
Indices: 2974798--2974883 Score: 151
Period size: 2 Copynumber: 44.5 Consensus size: 2
2974788 ACTCTGATCA
2974798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2974839 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2974879 AT AT A
1 AT AT A
2974884 ATCTTCTTTG
Statistics
Matches: 81, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 3 0.04
2 78 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2977565 original size:18 final size:18
Alignment explanation
Indices: 2977542--2977586 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2977532 AACATTCCTA
2977542 GTAATCTTATTCCCGA-TG
1 GTAATCTTATT-CCGACTG
* *
2977560 GTAATCCTATTCCTACTG
1 GTAATCTTATTCCGACTG
2977578 GTAATCTTA
1 GTAATCTTA
2977587 CATTCCGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCGACTG
Found at i:2979660 original size:13 final size:13
Alignment explanation
Indices: 2979642--2979667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2979632 CGGGTTCATG
2979642 GGTCTGGGTTGTA
1 GGTCTGGGTTGTA
2979655 GGTCTGGGTTGTA
1 GGTCTGGGTTGTA
2979668 CCCGAGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.46, T:0.38
Consensus pattern (13 bp):
GGTCTGGGTTGTA
Found at i:2979794 original size:3 final size:3
Alignment explanation
Indices: 2979775--2979810 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
2979765 CAAAATAGTG
*
2979775 TAA TAA TAC TAA TTAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
2979811 TAAACCCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2980147 original size:118 final size:110
Alignment explanation
Indices: 2979931--2980219 Score: 326
Period size: 118 Copynumber: 2.6 Consensus size: 110
2979921 CGTCGTTGGA
2979931 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCATGTGGATGAG--TTCTCATTATGAACTC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCAT-TGGATGAGTTTTCTCATTATGAACTC
* * *
2979994 TTCACTGAAAATGTTGAGTCACCTATTTCTGTGGTGGACTTGAAATCAAGG
65 TCCACTGAAAATGTTGAGTCACCTATTTCTCTGGTGAACTTG--A--AA-G
*
2980045 TTGAACAAGTTATTCTCATTATGAACTTCTTCTTACTCATTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-T-CTCATTGGATGAGTT-TTCTCATTATGAAC
* * *
2980110 TCTCCACTGGAAATGTTGA-TCCATCTCA-TTCTCTGGTGAATTTGAAAG
63 TCTCCACTGAAAATGTTGAGT-CACCT-ATTTCTCTGGTGAACTTGAAAG
*
2980158 --GAACAAGTTCTTCTCATTATGAAC-T-TTCTC-CTTTAGGATGAGTTATTCTCATTATGAACT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCATT-GGATGAGTT-TTCTCATTATGAACT
2980218 CT
64 CT
2980220 TTTGGAAATA
Statistics
Matches: 157, Mismatches: 10, Indels: 23
0.83 0.05 0.12
Matches are distributed among these distances:
106 3 0.02
107 27 0.17
108 1 0.01
109 3 0.02
110 1 0.01
111 23 0.15
113 1 0.01
114 33 0.21
115 9 0.06
116 6 0.04
117 1 0.01
118 48 0.31
119 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (110 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCATTGGATGAGTTTTCTCATTATGAACTCT
CCACTGAAAATGTTGAGTCACCTATTTCTCTGGTGAACTTGAAAG
Found at i:2980395 original size:136 final size:135
Alignment explanation
Indices: 2980158--2980499 Score: 457
Period size: 136 Copynumber: 2.6 Consensus size: 135
2980148 AATTTGAAAG
* *
2980158 GAACAAGTTCTTCTCATTATGAAC-T-TTCT-CCT-T-T-AGGATGAGTTATTCTCATTATGAA-
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCA-GATGAGTTCTTCTCATTATGAAT
** * * **
2980216 CTCTTTTGGAAATATTAATCCCTCAAGCGATGAGTCACTGATTCGAAATGTCGTGAATCAAGTGA
65 CTCAATTGGAAATATCAATCCCTCAAGCGAGGAGTCACTGATTCGAAATACCGTGAATCAAGTGA
2980281 TAGGTC
130 TAGGTC
*
2980287 GAACAAGCTCTTCTCATTATGGACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAATT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAA-T
* * * *
2980352 CTCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTCGAAATACCGTGAATCGAGTGA
65 CTCAATTGGAAATATCAATCCCTCAAGCGAGGAGTCACTGATTCGAAATACCGTGAATCAAGTGA
2980417 TAGGTC
130 TAGGTC
2980423 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTC-GAATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAG-ATGAGTTCTTCTCATTATGAA-
* *
2980487 TCTCCACTGGAAA
64 TCTCAATTGGAAA
2980500 CACTGATGTG
Statistics
Matches: 187, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
129 22 0.12
130 1 0.01
131 4 0.02
132 3 0.02
133 1 0.01
134 22 0.12
135 2 0.01
136 132 0.71
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.35
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAATC
TCAATTGGAAATATCAATCCCTCAAGCGAGGAGTCACTGATTCGAAATACCGTGAATCAAGTGAT
AGGTC
Found at i:2980619 original size:227 final size:227
Alignment explanation
Indices: 2980285--2980945 Score: 1006
Period size: 227 Copynumber: 2.9 Consensus size: 227
2980275 AAGTGATAGG
* * * **
2980285 TCGAACAAGCTCTTCTCATTATGGACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAA
1 TCGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTC-GTTGGATGAGTTCTTCTCATTATGAA
* * * ** * * * *
2980350 TTC-TCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTCGAAATACCGTGAATCGAG
65 CTCTTC-ACTGAAAATGTTGATTCCTCAAGCGAGGCGTCACTGATTCGAAATGCCGTGAATCGAG
2980414 TGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCA
129 TGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCA
2980479 TTATGAACTCTCCACTGGAAACACTGATGTGAGA
194 TTATGAACTCTCCACTGGAAACACTGATGTGAGA
* *
2980513 TCGAACAATTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTATTCTCATTATGAAC
1 TCGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
* * * *
2980578 TCTTCACTGAAAATGTTGATTCCTCAAGCGAGACATCACTGATTCAAAATGCCGTGAATCTAGTG
66 TCTTCACTGAAAATGTTGATTCCTCAAGCGAGGCGTCACTGATTCGAAATGCCGTGAATCGAGTG
*
2980643 ATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTC-AGATAAGTTCTTCTCAT
131 ATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGA-ATGAGTTCTTCTCAT
2980707 TATGAACTCTCCACTGGAAACACTGATGTGAGA
195 TATGAACTCTCCACTGGAAACACTGATGTGAGA
2980740 TCGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
1 TCGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
* *
2980805 TCTTCACTGAAAATGTTGATTCCTTAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTG
66 TCTTCACTGAAAATGTTGATTCCTCAAGCGAGGCGTCACTGATTCGAAATGCCGTGAATCGAGTG
* * * * *
2980870 ATAGGTCGAACAAGCTCTTTTCATTATGAACTTCTTATCTCT-TATTTG-ATGAGTTCTTCTCAT
131 ATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-GTCGAATGAGTTCTTCTCAT
2980933 TATGAACTCTCCA
195 TATGAACTCTCCA
2980946 TTGGGAATGT
Statistics
Matches: 394, Mismatches: 35, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
226 29 0.07
227 329 0.84
228 36 0.09
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (227 bp):
TCGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
TCTTCACTGAAAATGTTGATTCCTCAAGCGAGGCGTCACTGATTCGAAATGCCGTGAATCGAGTG
ATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATT
ATGAACTCTCCACTGGAAACACTGATGTGAGA
Found at i:2981331 original size:15 final size:15
Alignment explanation
Indices: 2981311--2981352 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
2981301 TCAAATGAAA
2981311 ACTGTCTCAAGCGAG
1 ACTGTCTCAAGCGAG
*
2981326 ACTGTCTCAAGTGAG
1 ACTGTCTCAAGCGAG
2981341 ACTGTCTCAAGC
1 ACTGTCTCAAGC
2981353 AAAAAGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (15 bp):
ACTGTCTCAAGCGAG
Found at i:2981423 original size:38 final size:37
Alignment explanation
Indices: 2981365--2982146 Score: 140
Period size: 40 Copynumber: 20.5 Consensus size: 37
2981355 AAAGAAGTAG
*
2981365 GTTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTT
1 GTTTCAAGAAAAACCATCTCAAGGGAGACAAAACTTT
* * *
2981402 GTTTCAAGAGAAAA-CAGTCTCAAGCGAGAC-GAA-GTT
1 GTTTCAAGA-AAAACCA-TCTCAAGGGAGACAAAACTTT
* * * *
2981438 GATTTTAAGAAAAACCATTTTAAGGGAGATAAAACTTT
1 G-TTTCAAGAAAAACCATCTCAAGGGAGACAAAACTTT
* ***
2981476 GTTTCAAGAGAAATTGTCTC-------A-AAAAC-TT
1 GTTTCAAGAAAAACCATCTCAAGGGAGACAAAACTTT
** *
2981504 GTTTCAA-AAGAAACTGTCTCAAGGGAGACAAAA-TTC
1 GTTTCAAGAA-AAACCATCTCAAGGGAGACAAAACTTT
** ** **
2981540 GTTTCAAGGGAAACGTTCTC-------A-AAATTTTGT
1 GTTTCAAGAAAAACCATCTCAAGGGAGACAAAACTT-T
* * *
2981570 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATCTTCT
1 GTTTCAAGAAAAACCATCTCAAGGGAGACAAAA-CTT-T
* ** * * *
2981609 GTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTT
1 GTTTCAAGAAAAACCATCTCAAGGGAGACAAAA-C-TTT
* ** * *
2981648 GTTTCAAGGAAAACCAATCTTGAGCGAGATAAAATCTTCT
1 GTTTCAAGAAAAACC-ATCTCAAGGGAGACAAAA-CTT-T
* * * *
2981688 GTTTCAAGGAAAAACAATCTTGAA-TGAGATAAAATCTTCT
1 GTTTCAA-GAAAAACCATC-TCAAGGGAGACAAAA-CTT-T
* ** * *
2981728 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTTT
1 GTTTCAA-GAAAAACCATCTCAAGGGAGACAAAA-C-TTT
* * * *
2981768 GTTTCAAGGAAAAACAATCTTGAA-TGAGATAAAATCTTCT
1 GTTTCAA-GAAAAACCATC-TCAAGGGAGACAAAA-CTT-T
* ** * *
2981808 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTTT
1 GTTTCAA-GAAAAACCATCTCAAGGGAGACAAAA-C-TTT
* * * * *
2981848 GTTTCAAGGAAAAACAATCTTGAA-TGAAATAAAATCTTCT
1 GTTTCAA-GAAAAACCATC-TCAAGGGAGACAAAA-CTT-T
* ** * *
2981888 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCT
1 GTTTCAA-GAAAAACCATCTCAAGGGAGACAAAA-CTT-T
* ** * *
2981928 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCT
1 GTTTCAA-GAAAAACCATCTCAAGGGAGACAAAA-CTT-T
* ** * *
2981968 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTTT
1 GTTTCAA-GAAAAACCATCTCAAGGGAGACAAAA-C-TTT
* * ** * *
2982008 GTTTCAAGGAAAACAATCTTGAGTGAGATAAAATCTTCT
1 GTTTCAAGAAAAACCATCTCAAGGGAGACAAAA-CTT-T
* ** * *
2982047 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCT
1 GTTTCAA-GAAAAACCATCTCAAGGGAGACAAAA-CTT-T
* * * *
2982087 GTTTCAAGGAAAAACAATCTTGAA-TGAGATAAAATCTTAT
1 GTTTCAA-GAAAAACCATC-TCAAGGGAGACAAAA-CTT-T
*
2982127 GTTTCAAGGAAAAACAATCT
1 GTTTCAA-GAAAAACCATCT
2982147 TGAGTGAGAT
Statistics
Matches: 635, Mismatches: 64, Indels: 90
0.80 0.08 0.11
Matches are distributed among these distances:
27 1 0.00
28 21 0.03
29 8 0.01
30 18 0.03
35 1 0.00
36 36 0.06
37 36 0.06
38 24 0.04
39 95 0.15
40 375 0.59
41 20 0.03
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (37 bp):
GTTTCAAGAAAAACCATCTCAAGGGAGACAAAACTTT
Found at i:2981508 original size:28 final size:29
Alignment explanation
Indices: 2981468--2981525 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
2981458 TAAGGGAGAT
* *
2981468 AAAACTTTGTTTCAAGAGAAATTGTCTCA
1 AAAACTTTGTTTCAAAAGAAACTGTCTCA
2981497 AAAAC-TTGTTTCAAAAGAAACTGTCTCA
1 AAAACTTTGTTTCAAAAGAAACTGTCTCA
2981525 A
1 A
2981526 GGGAGACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (29 bp):
AAAACTTTGTTTCAAAAGAAACTGTCTCA
Found at i:2981560 original size:64 final size:67
Alignment explanation
Indices: 2981459--2981630 Score: 190
Period size: 66 Copynumber: 2.6 Consensus size: 67
2981449 AAACCATTTT
* * * * * *
2981459 AAGGGAGATAAAACTTTGTTTCAAGAGAAATTGTCTCAAAA-ACT-TGTTTCAAAAGAAACTGTC
1 AAGGGAGACAAAACTTCGTTTCAAGGGAAACTATCTCAAAATACTGTGTTTCAAAAGAAACTATC
2981522 TC
66 TC
** *
2981524 AAGGGAGACAAAA-TTCGTTTCAAGGGAAACGT-TCTCAAAATTTTGTGTTTCAAGAGAAACTAT
1 AAGGGAGACAAAACTTCGTTTCAAGGGAAAC-TATCTCAAAATACTGTGTTTCAAAAGAAACTAT
2981587 CTC
65 CTC
* *
2981590 AAGAGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAA
1 AAGGGAGACAAAA-CTTC-GTTTCAAGGGAAACTATCTCAA
2981631 GCGAGATAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
64 22 0.24
65 14 0.16
66 31 0.34
68 4 0.04
69 19 0.21
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (67 bp):
AAGGGAGACAAAACTTCGTTTCAAGGGAAACTATCTCAAAATACTGTGTTTCAAAAGAAACTATC
TC
Found at i:2981683 original size:40 final size:40
Alignment explanation
Indices: 2981594--2982168 Score: 965
Period size: 40 Copynumber: 14.4 Consensus size: 40
2981584 TATCTCAAGA
* * * * ** *
2981594 GAGACAAAATCTTCTGTTTCGAGG-GAAACTATCTCAAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
2981633 GAGATAAAATCTTTTGTTTCAAGGAAAACCAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
2981673 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2981713 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
2981753 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2981793 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
2981833 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
2981873 GAAATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2981913 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2981953 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
2981993 GAGATAAAATCTTTTGTTTCAAGG-AAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2982032 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
2982072 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
2982112 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2982152 GAGATAAAATCTTCTGT
1 GAGATAAAATCTTCTGT
2982169 ATTAAATGAG
Statistics
Matches: 505, Mismatches: 29, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 59 0.12
40 446 0.88
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:2982065 original size:23 final size:23
Alignment explanation
Indices: 2982039--2982107 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
2982029 AGTGAGATAA
2982039 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
** * *
2982062 AATC-T-TGAGT-GA-G-ATAA-
1 AATCTTCTGTTTCAAGGAAAAAC
2982079 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
2982102 AATCTT
1 AATCTT
2982108 GAATGAGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 4 0.12
20 2 0.06
21 4 0.12
22 4 0.12
23 10 0.31
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:2987444 original size:19 final size:17
Alignment explanation
Indices: 2987399--2987445 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
2987389 AGGTATCGAT
2987399 TTCCAAAAGTAATCATTC
1 TTCCAAAAG-AATCATTC
*
2987417 TT-AAAAAGAATTTCATTC
1 TTCCAAAAGAA--TCATTC
2987435 TTCCAAAAGAA
1 TTCCAAAAGAA
2987446 CTTTTATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 5 0.21
18 10 0.42
19 7 0.29
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (17 bp):
TTCCAAAAGAATCATTC
Found at i:2991957 original size:2 final size:2
Alignment explanation
Indices: 2991950--2991996 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
2991940 TATATTATTT
*
2991950 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
*
2991991 TG TA TA
1 TA TA TA
2991997 GATGTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2991963 original size:21 final size:21
Alignment explanation
Indices: 2991939--2991979 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2991929 TTTATTTATA
* *
2991939 TTATATTATTTTATATATATC
1 TTATATCATTATATATATATC
2991960 TTATATCATTATATATATAT
1 TTATATCATTATATATATAT
2991980 ATATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATATCATTATATATATATC
Found at i:2992051 original size:18 final size:18
Alignment explanation
Indices: 2992028--2992089 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
2992018 TTACTATGCA
2992028 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
* *
2992046 TATATTTATACGTT--T-T
1 TATATTTTTTC-TTAATAT
2992062 TATATATTTTTCTTAATAT
1 TATAT-TTTTTCTTAATAT
*
2992081 TCTATTTTT
1 TATATTTTT
2992090 GTTTTTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
16 8 0.24
17 5 0.15
18 14 0.41
19 7 0.21
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:2992103 original size:33 final size:35
Alignment explanation
Indices: 2992027--2992103 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
2992017 TTTACTATGC
2992027 ATATATTTTTTCTTAATATTATATTTATACGTTTTT
1 ATATA-TTTTTCTTAATATTATATTTATACGTTTTT
* *
2992063 ATATATTTTTCTTAATATTCTATTT-T-TGTTTTT
1 ATATATTTTTCTTAATATTATATTTATACGTTTTT
*
2992096 ATTTATTT
1 ATATATTT
2992104 ATATATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 13 0.34
34 1 0.03
35 19 0.50
36 5 0.13
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (35 bp):
ATATATTTTTCTTAATATTATATTTATACGTTTTT
Found at i:2992286 original size:16 final size:16
Alignment explanation
Indices: 2992241--2992286 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
2992231 TATGTACACA
2992241 TTATTTTTATT-CCTTT
1 TTATTTTT-TTACCTTT
2992257 TTAATTTCTTTTACCTTT
1 TT-ATTT-TTTTACCTTT
2992275 TTATTTTTTTAC
1 TTATTTTTTTAC
2992287 TCAATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 8 0.30
17 10 0.37
18 9 0.33
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTTTTTTACCTTT
Found at i:2992360 original size:18 final size:18
Alignment explanation
Indices: 2992339--2992387 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2992329 ATTTTATTCA
*
2992339 TTTTGTTTATTTTTAT-TT
1 TTTTG-TTATTTTTATGTG
*
2992357 TTTTATTATTTTTTATGTG
1 TTTTGTTA-TTTTTATGTG
2992376 TTTTGTTATTTT
1 TTTTGTTATTTT
2992388 CCATTTCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 15 0.58
19 8 0.31
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (18 bp):
TTTTGTTATTTTTATGTG
Found at i:2992379 original size:19 final size:18
Alignment explanation
Indices: 2992348--2992387 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2992338 ATTTTGTTTA
*
2992348 TTTTTATTTTTTTATTAT
1 TTTTTATTGTTTTATTAT
*
2992366 TTTTTATGTGTTTTGTTAT
1 TTTTTAT-TGTTTTATTAT
2992385 TTT
1 TTT
2992388 CCATTTCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTTATTGTTTTATTAT
Found at i:2993957 original size:17 final size:17
Alignment explanation
Indices: 2993935--2993973 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2993925 GGTCAAAGGA
*
2993935 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGATCG
*
2993952 GGTCAACGGTCGGATCG
1 GGTCAACAGTCGGATCG
2993969 GGTCA
1 GGTCA
2993974 GATCGGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.23, G:0.41, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTCGGATCG
Found at i:2993993 original size:19 final size:19
Alignment explanation
Indices: 2993971--2994009 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2993961 TCGGATCGGG
*
2993971 TCAGATCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
2993990 TCAGACCGGTTAAACCGGT
1 TCAGACCGGTCAAACCGGT
2994009 T
1 T
2994010 TTCCAGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2995013 original size:42 final size:42
Alignment explanation
Indices: 2994949--2995045 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
2994939 TCAAATCTAC
*
2994949 TTGTATTGGGCCTTGGTAGGCTGTTGGGCTTCTGGATTATAT
1 TTGTTTTGGGCCTTGGTAGGCTGTTGGGCTTCTGGATTATAT
*
2994991 TTGTTTTGGGCCTTGGTAGGCTGTTGGGCTTCTGGATTGTAT
1 TTGTTTTGGGCCTTGGTAGGCTGTTGGGCTTCTGGATTATAT
2995033 TTGTTTTGGGCCT
1 TTGTTTTGGGCCT
2995046 GCAAAATAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.08, C:0.12, G:0.34, T:0.45
Consensus pattern (42 bp):
TTGTTTTGGGCCTTGGTAGGCTGTTGGGCTTCTGGATTATAT
Found at i:2995076 original size:3 final size:3
Alignment explanation
Indices: 2995057--2995116 Score: 102
Period size: 3 Copynumber: 19.7 Consensus size: 3
2995047 CAAAATAGTG
*
2995057 TAA TAA TAC TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2995103 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
2995117 TAAACTCAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2995796 original size:18 final size:19
Alignment explanation
Indices: 2995761--2995797 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2995751 CACGGAATGT
2995761 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2995781 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2995798 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2995977 original size:36 final size:37
Alignment explanation
Indices: 2995944--2996012 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 37
2995934 TACAAATTGT
2995944 AAAATATTTATAT-ATTTTCTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTTTCTTTACAAAATTAAATTC
* *
2995979 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTCTTTACAAAATTAAA
2996013 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 12 0.40
36 9 0.30
37 9 0.30
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATAATTTTCTTTACAAAATTAAATTC
Found at i:2998146 original size:31 final size:31
Alignment explanation
Indices: 2998108--2998167 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
2998098 CAACTGCGAC
*
2998108 GCTATTGCATAGCTTATAATTTGTGTTTCTG
1 GCTATTGCATAGCTTATAATTTGTATTTCTG
2998139 GCTATTGCATAGCTTATAATTTGTATTTC
1 GCTATTGCATAGCTTATAATTTGTATTTC
2998168 ATGTGGAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (31 bp):
GCTATTGCATAGCTTATAATTTGTATTTCTG
Found at i:3001684 original size:18 final size:18
Alignment explanation
Indices: 3001657--3001697 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3001647 GTCCCTAATA
3001657 ATAAATATAA-AAAAAAT
1 ATAAATATAAGAAAAAAT
*
3001674 ATAAATCATAAGAACAAAT
1 ATAAAT-ATAAGAAAAAAT
3001693 A-AAAT
1 ATAAAT
3001698 TAAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 8 0.38
19 7 0.33
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (18 bp):
ATAAATATAAGAAAAAAT
Found at i:3003803 original size:2 final size:2
Alignment explanation
Indices: 3003791--3003824 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
3003781 TGTATATCAC
3003791 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3003825 GAAACTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3006860 original size:11 final size:11
Alignment explanation
Indices: 3006821--3006867 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
3006811 CAATTTAACC
3006821 TTTTATTTATTA
1 TTTTATTT-TTA
*
3006833 TTTTA-TTTGA
1 TTTTATTTTTA
3006843 TTATTATTTTTA
1 TT-TTATTTTTA
*
3006855 TTTTATTTCTA
1 TTTTATTTTTA
3006866 TT
1 TT
3006868 ATACACGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 4 0.13
11 15 0.50
12 11 0.37
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:3008471 original size:12 final size:12
Alignment explanation
Indices: 3008454--3008478 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3008444 ATATATATAG
3008454 TTTTTGAAAACA
1 TTTTTGAAAACA
3008466 TTTTTGAAAACA
1 TTTTTGAAAACA
3008478 T
1 T
3008479 ATATATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:3008541 original size:74 final size:73
Alignment explanation
Indices: 3008364--3008604 Score: 274
Period size: 72 Copynumber: 3.3 Consensus size: 73
3008354 TTTTTAAAAC
* * * * * *
3008364 TATATAATATATAGTTTTAAAAAAACATTTTAGAAAATATATGTAGTATATAATCTTTTAAAATC
1 TATATATTATATAGTTTT-TAAAAACATTTTTGAAAACATATATA-T-TATAAT-TTTGAAAAT-
3008429 ATTTTGAAAAC-T
61 ATTTTGAAAACAT
* * *
3008441 TATATA-TATATAGTTTTTGAAAACATTTTTGAAAACATATATATTGTAGTTTTGAAAATATTTT
1 TATATATTATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATAATTTTGAAAATATTTT
3008505 GAAAACATT
66 GAAAACA-T
* * * *
3008514 TATATATTATATAGTTTTTAAAAACATTTTTGAAAAC-T-TATATAATATTTTTGAAAACATGTT
1 TATATATTATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATAATTTTGAAAATATTTT
3008577 GAAAACAT
66 GAAAACAT
3008585 TAGTATATTATATAGTTTTT
1 TA-TATATTATATAGTTTTT
3008605 TTTAAAAAAA
Statistics
Matches: 146, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
71 14 0.10
72 52 0.36
73 12 0.08
74 30 0.21
75 21 0.14
76 11 0.08
77 6 0.04
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (73 bp):
TATATATTATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATAATTTTGAAAATATTTT
GAAAACAT
Found at i:3008571 original size:33 final size:34
Alignment explanation
Indices: 3008419--3008591 Score: 93
Period size: 34 Copynumber: 4.9 Consensus size: 34
3008409 GTATATAATC
* * *
3008419 TTTTAAAATCATTTTGAAAAC-TTATATATATATAGT
1 TTTTAAAAACATGTTGAAAACATTA-GTATA-ATA-T
* * ** *
3008455 TTTTGAAAACATTTTTGAAAACATATA-TATTGTAG
1 TTTTAAAAACA-TGTTGAAAACAT-TAGTATAATAT
* * * *
3008490 TTTTGAAAATATTTTGAAAACATTTATATATTATATAGT
1 TTTTAAAAACATGTTGAAAACA-TTA-GTA-TA-ATA-T
*
3008529 TTTTAAAAACATTTTTGAAAAC-TTA-TATAATAT
1 TTTTAAAAACA-TGTTGAAAACATTAGTATAATAT
*
3008562 TTTTGAAAACATGTTGAAAACATTAGTATA
1 TTTTAAAAACATGTTGAAAACATTAGTATA
3008592 TTATATAGTT
Statistics
Matches: 112, Mismatches: 13, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
32 9 0.08
33 14 0.12
34 20 0.18
35 13 0.12
36 15 0.13
37 14 0.12
38 6 0.05
39 11 0.10
40 10 0.09
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (34 bp):
TTTTAAAAACATGTTGAAAACATTAGTATAATAT
Found at i:3008724 original size:4 final size:5
Alignment explanation
Indices: 3008689--3008721 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
3008679 ATCTATTATT
3008689 ATTTA ATTTA ATTTA ATTTA A-TTA ATTT- ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
3008722 TTTTTTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTTA
Found at i:3009955 original size:4 final size:4
Alignment explanation
Indices: 3009946--3010029 Score: 59
Period size: 4 Copynumber: 21.0 Consensus size: 4
3009936 TTGAAATATT
* * *
3009946 TTTA TTTA TTTA TTTA TTTA TTT- TATA TTT- TATA TTTA TTT- TATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
3009991 TTTA TTT- TTCTT TTTA TTTC TTTGA TTTA CTTTGA TTTA
1 TTTA TTTA TT-TA TTTA TTTA TTT-A TTTA -TTT-A TTTA
3010030 CTTTTTTAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
3 8 0.13
4 43 0.68
5 11 0.17
6 1 0.02
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:3009973 original size:29 final size:29
Alignment explanation
Indices: 3009941--3010028 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
3009931 TACTTTTGAA
3009941 ATATTTTTATTTATTTATTTATTTATTTT
1 ATATTTTTATTTATTTATTTATTTATTTT
*
3009970 ATATTTTATATTTATTT-TATATTTATTTT
1 ATATTTT-TATTTATTTATTTATTTATTTT
* *
3009999 -TCTTTTTATTTCTTTGATTTACTTTGATTT
1 ATATTTTTATTTATTT-ATTTA-TTT-ATTT
3010029 ACTTTTTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
27 8 0.16
28 5 0.10
29 21 0.42
30 12 0.24
31 4 0.08
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (29 bp):
ATATTTTTATTTATTTATTTATTTATTTT
Found at i:3009985 original size:11 final size:11
Alignment explanation
Indices: 3009946--3009998 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
3009936 TTGAAATATT
*
3009946 TTTATTTATTTA
1 TTTATTT-TATA
*
3009958 TTTA-TTTATT
1 TTTATTTTATA
3009968 TTATATTTTATA
1 TT-TATTTTATA
3009980 TTTATTTTATA
1 TTTATTTTATA
3009991 TTTATTTT
1 TTTATTTT
3009999 TCTTTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.11
11 21 0.58
12 11 0.31
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTATTTTATA
Found at i:3010005 original size:18 final size:17
Alignment explanation
Indices: 3009952--3010007 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
3009942 TATTTTTATT
3009952 TATTTATTTATTTATTTTA
1 TATTTATTT-TTT-TTTTA
* *
3009971 TATTTTATATTTATTTTA
1 TA-TTTATTTTTTTTTTA
3009989 TATTTATTTTTCTTTTTA
1 TATTTATTTTT-TTTTTA
3010007 T
1 T
3010008 TTCTTTGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 8 0.26
18 13 0.42
19 4 0.13
20 6 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTTATTTTTTTTTTA
Found at i:3010115 original size:41 final size:41
Alignment explanation
Indices: 3010068--3010152 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 41
3010058 TTTTATTCAT
3010068 TTTTATGTTTTT-TATTACTAT-TATATATATATATATATATA
1 TTTTATGTTTTTCT-TTA-TATATATATATATATATATATATA
3010109 TTTTATGTTTTTGCCTTTATATATATATATATATATATATATA
1 TTTTATGTTTTT--CTTTATATATATATATATATATATATATA
3010152 T
1 T
3010153 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
41 12 0.30
42 3 0.08
43 24 0.60
44 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (41 bp):
TTTTATGTTTTTCTTTATATATATATATATATATATATATA
Found at i:3010133 original size:2 final size:2
Alignment explanation
Indices: 3010126--3010162 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3010116 TTTTTGCCTT
3010126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3010163 TCTATCTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3015411 original size:84 final size:83
Alignment explanation
Indices: 3015263--3015591 Score: 362
Period size: 84 Copynumber: 4.0 Consensus size: 83
3015253 CCATTTTTTT
* *
3015263 AAGACA-A-CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAG
1 AAGACATATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAG
* *
3015326 TTTGACTACACTCAGCTCC
65 TTCGACTACGCTCAGCTCC
* * * ** *
3015345 AAGACATATCATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
1 AAGACATATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAG
*
3015410 TTTGACTACGCTCAGCTCC
65 TTCGACTACGCTCAGCTCC
** * * * * * * *
3015429 AAGGTACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGT
1 AAGACATATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGT
*
3015491 TCGACTACGCTCAGCTTCG
66 TCGACTACGCTCAGC-TCC
* * * * *
3015510 AGGGCATATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAAGACCTTTGAGT
1 AAGACATATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGT
3015575 TCGACTACGCTCAGCTC
66 TCGACTACGCTCAGCTC
3015592 AACGGCACAT
Statistics
Matches: 211, Mismatches: 29, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
80 29 0.14
81 38 0.18
82 6 0.03
83 3 0.01
84 132 0.63
85 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (83 bp):
AAGACATATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGT
TCGACTACGCTCAGCTCC
Found at i:3015722 original size:120 final size:119
Alignment explanation
Indices: 3015486--3015722 Score: 332
Period size: 119 Copynumber: 2.0 Consensus size: 119
3015476 CAAAGACCCT
* * * *
3015486 CGAGTTCGACTACGCTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAAAAGGGTT
1 CGAGTTCGACTACACTAAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAAAAGGGTT
* *
3015551 ATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCCC
66 ATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCCC
* * * * * * *
3015605 CGAGTTCGATTACACTAAGTTTCGAGGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGGGTT
1 CGAGTTCGACTACACTAAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAAAAGGGTT
3015670 ATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAA-GGCACATC
66 ATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC-AACGGCACATC
3015723 ATTTGCAGCA
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
119 60 0.58
120 41 0.40
121 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (119 bp):
CGAGTTCGACTACACTAAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAAAAGGGTT
ATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCCC
Found at i:3015773 original size:84 final size:83
Alignment explanation
Indices: 3015631--3016095 Score: 560
Period size: 84 Copynumber: 5.6 Consensus size: 83
3015621 AAGTTTCGAG
* *
3015631 GGCACATTATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
3015696 CGACTACGCTCAGCTCTAA
66 CGACTACGCTCAGCTC-AA
* * * * *
3015715 GGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAATACCTTTGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
3015780 CGACTACGCTCAGCTCAA
66 CGACTACGCTCAGCTCAA
* * * **
3015798 CGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCCCGAGT
1 -GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGT
* * *
3015859 TCGATTACACTCAGCTTCGAG
65 TCGACTACGCTCAGC-TC-AA
** * * *
3015880 GGCACATCATTTATAGTATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
**
3015945 TTACTACGCTCAGCTCCAA
66 CGACTACGCTCAGCT-CAA
* * * * * * *
3015964 GGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGATTGTCTGCCAACAAAAGACCTTTGAGTC
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
3016029 CGACTACGCTCAGCTCAA
66 CGACTACGCTCAGCTCAA
* * *
3016047 CGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
1 -GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
3016096 AGACCTCCGA
Statistics
Matches: 316, Mismatches: 56, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
80 23 0.07
81 40 0.13
82 2 0.01
83 6 0.02
84 221 0.70
85 24 0.08
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
CGACTACGCTCAGCTCAA
Found at i:3015785 original size:204 final size:200
Alignment explanation
Indices: 3015434--3015802 Score: 542
Period size: 204 Copynumber: 1.8 Consensus size: 200
3015424 GCTCCAAGGT
*
3015434 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
* * * * *
3015499 GCTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAA
66 GCTCAGCTTCGAAGGCACATCATTTACAGCACAACTCAAGGCTAAAAGGGTTATCTGCCACAAAA
3015564 GACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCCCCGAGTTCGATTACACTAAGTTTCG
131 GACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCCCCGAGTTCGATTACACTAAGTTTCG
3015629 AGGGC
196 AGGGC
* * *
3015634 ACATTATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGA
* * * * * *
3015699 CTACGCTCAGC-TCTAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
62 CTACGCTCAGCTTCGAAGGCACATCATTTACAGCACAACTCAAGGCTAAAAGGGTTATCTGCC-A
*
3015763 CAAAATACCTTTGAGTTCGACTACGCTCAGCTCAACGGCA
126 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCA
3015803 TATCATTTGC
Statistics
Matches: 148, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
200 38 0.26
203 41 0.28
204 69 0.47
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (200 bp):
ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
GCTCAGCTTCGAAGGCACATCATTTACAGCACAACTCAAGGCTAAAAGGGTTATCTGCCACAAAA
GACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCCCCGAGTTCGATTACACTAAGTTTCG
AGGGC
Found at i:3015874 original size:284 final size:282
Alignment explanation
Indices: 3015355--3015874 Score: 729
Period size: 284 Copynumber: 1.8 Consensus size: 282
3015345 AAGACATATC
* *
3015355 ATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
3015420 CTCAGCTCCAAGGTACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
* * * *
3015485 TCGAGTTCGACTACGCTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAAAAGGGT
131 TCGAGTTCGACTACGCTCAGCTTCAACGGCATATCATTTACAGCATAACTCAAGGCGAAAAGGGC
*** *
3015550 TATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCCCCGAGTTCGAT
196 TATCTG--ACCAAAGACCCCCGAGTTCGACTACACTCAGCTCAACGGCACATCCCCGAGTTCGAT
3015615 TACACTAAGTTTCGAGGGCACATT
259 TACACTAAGTTTCGAGGGCACATT
*
3015639 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * * * *
3015704 CTCAGCTCTAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAT
66 CTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGGCTATCTG-C--C-AAAG
* * * * * * *
3015769 ACCTTTGAGTTCGACTACGCTCAGC-TCAACGGCATATCATTTGCAGCATAGCTTAAGTCGAGAA
127 ACCCTCGAGTTCGACTACGCTCAGCTTCAACGGCATATCATTTACAGCATAACTCAAGGCGAAAA
*
3015833 GGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACTCAGCT
192 GGGCTATCTGACCAAAGACCCCCGAGTTCGACTACACTCAGCT
3015875 TCGAGGGCAC
Statistics
Matches: 205, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
284 137 0.67
285 1 0.00
287 41 0.20
288 26 0.13
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (282 bp):
ATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
TCGAGTTCGACTACGCTCAGCTTCAACGGCATATCATTTACAGCATAACTCAAGGCGAAAAGGGC
TATCTGACCAAAGACCCCCGAGTTCGACTACACTCAGCTCAACGGCACATCCCCGAGTTCGATTA
CACTAAGTTTCGAGGGCACATT
Found at i:3016040 original size:249 final size:249
Alignment explanation
Indices: 3015602--3016148 Score: 905
Period size: 249 Copynumber: 2.2 Consensus size: 249
3015592 AACGGCACAT
* * * *
3015602 CCCCGAGTTCGATTACACTAAGTTTCGAGGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGG
1 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGG
*
3015667 GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGC
66 GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
* * *
3015732 ACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAATACCTTTGAGTTCGACTACGCTCAGCTCA
131 ACAACTTAAGTCTAGAAGGATTGTCTGCCAACAAAAGACCTTTGAGTCCGACTACGCTCAGCTCA
* *
3015797 ACGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
196 ACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * *
3015851 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGTATAACTTAAGTTGAGAAGG
1 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGG
** *
3015916 GTTATCTGCCAACCAAAGACCTTCGAGTTTTACTACGCTCAGCTCCAAGGCATATCATTTGCAGC
66 GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
3015981 ACAACTTAAGTCTAGAAGGATTGTCTGCCAACAAAAGACCTTTGAGTCCGACTACGCTCAGCTCA
131 ACAACTTAAGTCTAGAAGGATTGTCTGCCAACAAAAGACCTTTGAGTCCGACTACGCTCAGCTCA
3016046 ACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
196 ACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * * * *
3016100 CTCCGAGTTCGATTACACTCAACTTCGAGGTCATATCATTTACAACATA
1 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATA
3016149 GCTCAAGGCA
Statistics
Matches: 275, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
249 275 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (249 bp):
CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGG
GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
ACAACTTAAGTCTAGAAGGATTGTCTGCCAACAAAAGACCTTTGAGTCCGACTACGCTCAGCTCA
ACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
Found at i:3016137 original size:165 final size:163
Alignment explanation
Indices: 3015604--3016140 Score: 519
Period size: 165 Copynumber: 3.2 Consensus size: 163
3015594 CGGCACATCC
* * * * *
3015604 CCGAGTTCGATTACACT-AAGTTTCGAGGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGGG
1 CCGAGTTCGACTACACTCAA-CTTC-AAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
3015668 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCA
64 TTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTGCAGCA
* * * *
3015733 CAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAATACCT
127 TAACTTAAGTCGAGAAGGGTTATCTGCC--C-AAAGACCT
** * * * *
3015773 TTGAGTTCGACTACGCTCAGC-TCAACGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
1 CCGAGTTCGACTACACTCAACTTCAA-GGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
** * * * ** *
3015837 TATCTG-C--CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGTAT
65 TATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TC-AAGGCACATCATTTGCAGCAT
*
3015899 AACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCT
128 AACTTAAGTCGAGAAGGGTTATCTG-C--CCAAAGACCT
* ** * * * * * *
3015938 TCGAGTTTTACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGATT
1 CCGAGTTCGACTACACTCAACTTCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTT
* * * *
3016003 GTCTGCCAACAAAAGACCTTTGAGTCCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATA
66 ATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTGCAGCATA
* *
3016068 GCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCT
129 ACTTAAGTCGAGAAGGGTTATCTGCCCAAAGACCT
* *
3016102 CCGAGTTCGATTACACTCAACTTCGAGGTCATATCATTT
1 CCGAGTTCGACTACACTCAACTTCAAGG-CATATCATTT
3016141 ACAACATAGC
Statistics
Matches: 298, Mismatches: 57, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
164 56 0.19
165 113 0.38
166 6 0.02
167 3 0.01
168 83 0.28
169 36 0.12
170 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (163 bp):
CCGAGTTCGACTACACTCAACTTCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTT
ATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTGCAGCATAAC
TTAAGTCGAGAAGGGTTATCTGCCCAAAGACCT
Found at i:3016163 original size:81 final size:81
Alignment explanation
Indices: 3015604--3016167 Score: 436
Period size: 84 Copynumber: 6.8 Consensus size: 81
3015594 CGGCACATCC
* * * * * * * *
3015604 CCGAGTTCGATTACACTAAGTTTCGAGGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGGGT
1 CCGAGTTCGACTACACTCAGCTTC-AAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
3015669 TATCTGCCAACCAAAGACCT
65 TATCTG-C--CCAAAGACCT
* * * * * * *
3015689 TCGAGTTCGACTACGCTCAGC-TCTAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
1 CCGAGTTCGACTACACTCAGCTTC-AAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
* *
3015753 TGTCTGCCAACAAAATACCT
65 TATCTGCC--C-AAAGACCT
** *
3015773 TTGAGTTCGACTACGCTCAGC-TCAACGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
1 CCGAGTTCGACTACACTCAGCTTCAA-GGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
*
3015837 TATCTG-CCAAAGACCC
65 TATCTGCCCAAAGACCT
* * * ** * * * *
3015853 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGTATAACTTAAGTTGAGAAGGGT
1 CCGAGTTCGACTACACTCAGCTTC-AAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
3015918 TATCTGCCAACCAAAGACCT
65 TATCTG-C--CCAAAGACCT
* ** * * * * * **
3015938 TCGAGTTTTACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGATT
1 CCGAGTTCGACTACACTCAGCTTCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
*
3016003 GTCTGCCAACAAAAGACCT
66 ATCTGCC--C-AAAGACCT
** * * * *
3016022 TTGAGTCCGACTACGCTCAGC-TCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
1 CCGAGTTCGACTACACTCAGCTTCAA-GGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
3016086 TATCTG-CCAAAGACCT
65 TATCTGCCCAAAGACCT
* * * * * * * *
3016102 CCGAGTTCGATTACACTCAACTTCGAGGTCATATCATTTACAACATAGCTCAAGGCAAGAAGGGC
1 CCGAGTTCGACTACACTCAGCTTCAAGG-CATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
3016167 T
65 T
3016168 GTTTGTCAAT
Statistics
Matches: 386, Mismatches: 77, Indels: 36
0.77 0.15 0.07
Matches are distributed among these distances:
80 47 0.12
81 77 0.20
82 1 0.00
83 11 0.03
84 207 0.54
85 43 0.11
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (81 bp):
CCGAGTTCGACTACACTCAGCTTCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
ATCTGCCCAAAGACCT
Found at i:3016745 original size:2 final size:2
Alignment explanation
Indices: 3016738--3016773 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3016728 ATGTACATAC
*
3016738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3016774 TTTGAAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3017006 original size:74 final size:74
Alignment explanation
Indices: 3016820--3017070 Score: 245
Period size: 72 Copynumber: 3.3 Consensus size: 74
3016810 TTTTTAAAAC
* * * * * *
3016820 TATATAATATATAGTTTTTAAAAAAAACATTTTAGAAAATATATGTAGTATATTATCTTTTAAAA
1 TATATATTATATAGTTTTT---AAAAACATTTTTGAAAACATATATA-T-TATAAT-TTTGAAAA
3016885 TCATTTTGAAAACTTATAT
60 T-ATTTTGAAAAC--AT-T
* *
3016904 ATATATATATATATAGGTTTTGAAAACATTTTTGAAAACATATATATTATAATTTTGAAAATATT
1 -TATATAT-TATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATAATTTTGAAAATATT
*
3016969 TTGGAAACATT
64 TTGAAAACATT
* * * *
3016980 TATATATTATATAGTTTTTAAAAACATTTTTGAAAAC-T-TATATAATATTTTTGAAAACATGTT
1 TATATATTATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATAATTTTGAAAATATTTT
3017043 GAAAACATT
66 GAAAACATT
**
3017052 CGTATATTATATAGTTTTT
1 TATATATTATATAGTTTTT
3017071 TTAAAAAAGA
Statistics
Matches: 147, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
72 46 0.31
73 1 0.01
74 28 0.19
75 7 0.05
76 1 0.01
77 2 0.01
79 10 0.07
80 8 0.05
81 5 0.03
82 1 0.01
83 21 0.14
85 6 0.04
86 11 0.07
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (74 bp):
TATATATTATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATAATTTTGAAAATATTTT
GAAAACATT
Found at i:3018358 original size:5 final size:5
Alignment explanation
Indices: 3018330--3018385 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
3018320 TTTGAAATAT
*
3018330 TTTTA -TTTA -TTTA TTTTA TATTTA TTTTA TTTTTA TTTTA -TTT- TTTTC
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA -TTTTA TTTTA TTTTA TTTTA
3018378 TTTTA TTT
1 TTTTA TTT
3018386 CTTTGATTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
4 14 0.31
5 21 0.47
6 10 0.22
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:3018371 original size:11 final size:11
Alignment explanation
Indices: 3018327--3018374 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
3018317 ACTTTTGAAA
3018327 TATTTTTA-TT
1 TATTTTTATTT
3018337 TA--TTTATTT
1 TATTTTTATTT
*
3018346 TATATTTATTT
1 TATTTTTATTT
3018357 TATTTTTATTT
1 TATTTTTATTT
3018368 TATTTTT
1 TATTTTT
3018375 TTCTTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
8 4 0.12
9 4 0.12
10 2 0.06
11 24 0.71
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:3018461 original size:2 final size:2
Alignment explanation
Indices: 3018454--3018488 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3018444 TTATTACTAT
3018454 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3018489 CTATCTAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3019244 original size:56 final size:54
Alignment explanation
Indices: 3019139--3019244 Score: 158
Period size: 56 Copynumber: 1.9 Consensus size: 54
3019129 CCTTGTTACC
* *
3019139 TAAATCAATCATTTATGACAATTATAAATCGTAGGATTATGGTAGCAATACACT
1 TAAATCAATCATTCATGACAATTATAAATCGTAGGATTATGATAGCAATACACT
* *
3019193 TAAATCAATCATTCATGACAATTATATAAATTGTAGGCTTATGATAGCAATA
1 TAAATCAATCATTCATGACAA-T-TATAAATCGTAGGATTATGATAGCAATA
3019245 GAAAATTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 20 0.43
55 1 0.02
56 25 0.54
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (54 bp):
TAAATCAATCATTCATGACAATTATAAATCGTAGGATTATGATAGCAATACACT
Found at i:3019499 original size:2 final size:2
Alignment explanation
Indices: 3019482--3019542 Score: 104
Period size: 2 Copynumber: 30.0 Consensus size: 2
3019472 AGTGAGATTC
*
3019482 AT AT GAT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3019525 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
3019543 CGGAAAAACC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3023094 original size:29 final size:29
Alignment explanation
Indices: 3023052--3023107 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3023042 TTCAATCATT
3023052 TATGACAATTATAAACCGTAGGCTTATGG
1 TATGACAATTATAAACCGTAGGCTTATGG
**
3023081 TATGACAATTATAAATGGTAGGCTTAT
1 TATGACAATTATAAACCGTAGGCTTAT
3023108 TATAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (29 bp):
TATGACAATTATAAACCGTAGGCTTATGG
Found at i:3037244 original size:21 final size:21
Alignment explanation
Indices: 3037204--3037244 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3037194 GAAACATCCG
* *
3037204 AATATTATACTATTTTTTTAC
1 AATATTATACTAATTCTTTAC
3037225 AATATTATACTAATTCTTTA
1 AATATTATACTAATTCTTTA
3037245 AGTGACAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATTATACTAATTCTTTAC
Found at i:3039520 original size:23 final size:23
Alignment explanation
Indices: 3039471--3039533 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 23
3039461 AATATTTTAT
* * * *
3039471 TTTAATTAAATTACATTTAGATT
1 TTTAATTAATTTATAATTAGATA
*
3039494 TTTAATTAATTTATAATTATATA
1 TTTAATTAATTTATAATTAGATA
* *
3039517 TTT-AGTACTTTATAATT
1 TTTAATTAATTTATAATT
3039534 TAACATTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 12 0.36
23 21 0.64
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (23 bp):
TTTAATTAATTTATAATTAGATA
Found at i:3040992 original size:17 final size:17
Alignment explanation
Indices: 3040945--3040994 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
3040935 GATATCACTC
*
3040945 ATTATTTTTAATACTAAA
1 ATTA-TTTTAATATTAAA
*
3040963 ATTGTTTTAATATTAAA
1 ATTATTTTAATATTAAA
3040980 ATTATTTTAATATTA
1 ATTATTTTAATATTA
3040995 CCACTAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 26 0.90
18 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTATTTTAATATTAAA
Found at i:3041845 original size:10 final size:10
Alignment explanation
Indices: 3041801--3041841 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
3041791 TTTCATCACA
3041801 TCAAATTCTC
1 TCAAATTCTC
3041811 TCAAATTCTC
1 TCAAATTCTC
*
3041821 TCAAATACTC
1 TCAAATTCTC
* *
3041831 TTATATTCTC
1 TCAAATTCTC
3041841 T
1 T
3041842 TATAACTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:3041922 original size:17 final size:18
Alignment explanation
Indices: 3041888--3041920 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3041878 TTTTGTTAGT
3041888 AATTTATTTAACTATTTA
1 AATTTATTTAACTATTTA
3041906 AATTT-TTTAA-TATTT
1 AATTTATTTAACTATTT
3041921 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTATTTAACTATTTA
Found at i:3043514 original size:25 final size:24
Alignment explanation
Indices: 3043464--3043532 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
3043454 GAAAAAAATG
* *
3043464 AATAAATGAAAAAATGAAGAA-TAAA
1 AATAAATAAAAAAAT-AA-AAGGAAA
*
3043489 AATAAGTAAAAAAAATAAAAGGAAA
1 AATAAAT-AAAAAAATAAAAGGAAA
*
3043514 AATAAATAAATAAATAAAA
1 AATAAATAAAAAAATAAAA
3043533 TAAATGAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 13 0.35
25 17 0.46
26 7 0.19
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (24 bp):
AATAAATAAAAAAATAAAAGGAAA
Found at i:3043520 original size:16 final size:16
Alignment explanation
Indices: 3043483--3043523 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3043473 AAAAATGAAG
*
3043483 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
3043499 AA-AAATAAAAGGAAA
1 AATAAATAAAAGGAAA
3043514 AATAAATAAA
1 AATAAATAAA
3043524 TAAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:3043632 original size:18 final size:19
Alignment explanation
Indices: 3043587--3043637 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
3043577 TAGAAAAATA
*
3043587 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
3043607 AGTAATATAAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
3043626 ATAATATAAAAA
1 ATAATATAAAAA
3043638 AAACCAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 11 0.38
19 6 0.21
20 8 0.28
21 4 0.14
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:3043852 original size:19 final size:19
Alignment explanation
Indices: 3043830--3043920 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
3043820 TAAAAAAAGT
3043830 ATATATATATAAATAATAA
1 ATATATATATAAATAATAA
* *
3043849 ATATAGTATTAAAAAATAACCAA
1 ATATA-TA-T-ATAAATAA-TAA
* *
3043872 ATGAATATAAATAAATAAAAA
1 AT--ATATATATAAATAATAA
* *
3043893 ATATATGTATATATAAT-A
1 ATATATATATAAATAATAA
3043911 ATA-ATATATA
1 ATATATATATA
3043921 GTGTAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
17 6 0.11
18 4 0.07
19 16 0.29
20 2 0.04
21 5 0.09
22 14 0.25
23 4 0.07
24 2 0.04
25 3 0.05
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (19 bp):
ATATATATATAAATAATAA
Found at i:3044485 original size:37 final size:37
Alignment explanation
Indices: 3044392--3044493 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
3044382 GTGCTTGTGG
* * * * * *
3044392 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
* *
3044429 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
3044466 ATCCTATTTTTAGGAGTTTGAATTCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
3044494 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:3044752 original size:22 final size:22
Alignment explanation
Indices: 3044726--3044776 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3044716 CAGCACGTGG
3044726 CTTCTCGTTACCCTTCGGTCTT
1 CTTCTCGTTACCCTTCGGTCTT
*
3044748 CTTCTCGTTGCCCTTCGGTCTT
1 CTTCTCGTTACCCTTCGGTCTT
3044770 CTTCTCG
1 CTTCTCG
3044777 GTTTAAAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.02, C:0.37, G:0.16, T:0.45
Consensus pattern (22 bp):
CTTCTCGTTACCCTTCGGTCTT
Found at i:3045452 original size:106 final size:106
Alignment explanation
Indices: 3045267--3046326 Score: 1548
Period size: 106 Copynumber: 10.0 Consensus size: 106
3045257 AGGATTGTTC
* * *
3045267 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * *
3045331 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
3045373 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** * *
3045438 ACCAGCGGTCCCTTCGTTTTGAAGTTGAACTTGCATCGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
3045479 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3045544 ACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
3045585 GGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
3045650 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
3045691 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * *
3045756 ACCATCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTATAT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
3045797 GGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
3045862 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
3045903 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
3045968 ACCAGCGGTCCCTTCGTCGTGAAGTTGGACTTACGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
3046009 GGAGTCCAATATCTTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
3046074 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
3046115 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** * * * * *
3046180 GTCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
* * * *
3046221 CAAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * *
3046286 ACCAACTGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
3046327 TGAGAGAAAC
Statistics
Matches: 863, Mismatches: 88, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
105 1 0.00
106 860 1.00
107 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:3046453 original size:37 final size:36
Alignment explanation
Indices: 3046331--3046468 Score: 138
Period size: 37 Copynumber: 3.8 Consensus size: 36
3046321 TTGTCTTGAG
* *
3046331 AGAA-ACTATCTCAAGGGAGACAAAATTT-TTTTCAA
1 AGAAGACTGTCTCAAGCGAGACAAAATTTGTTTT-AA
* * * *
3046366 GGAAGACTGTCTCAAGGGAGACGAAATTTGTTTCAA
1 AGAAGACTGTCTCAAGCGAGACAAAATTTGTTTTAA
* * *
3046402 AGAAAAACTATCTCAAGCGAGATAAAATCTTGTTTTAA
1 AG-AAGACTGTCTCAAGCGAGACAAAAT-TTGTTTTAA
3046440 ATG-AGACTGTCTCAAGCGAGACAAAATTT
1 A-GAAGACTGTCTCAAGCGAGACAAAATTT
3046469 ATATTGGAAA
Statistics
Matches: 84, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
35 3 0.04
36 27 0.32
37 44 0.52
38 9 0.11
39 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
AGAAGACTGTCTCAAGCGAGACAAAATTTGTTTTAA
Found at i:3047241 original size:22 final size:22
Alignment explanation
Indices: 3047215--3047291 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
3047205 TTGTGTTTGG
3047215 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* * *
3047237 TCAAATGTTTGGTATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
*
3047259 TCAAAGGTTTGTCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
3047281 TCAAAGGTTTG
1 TCAAAGGTTTG
3047292 ATGGGGTCGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3047949 original size:16 final size:15
Alignment explanation
Indices: 3047924--3047972 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
3047914 TTGTTCTTTC
3047924 TTTT-TTCTTTTGTT
1 TTTTCTTCTTTTGTT
3047938 TTCTTCTTC-TTTGCTT
1 TT-TTCTTCTTTTG-TT
3047954 CTTTTCTT-TTTTGTT
1 -TTTTCTTCTTTTGTT
3047969 TTTT
1 TTTT
3047973 TTTTCTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 6 0.20
15 8 0.27
16 14 0.47
17 2 0.07
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTCTTCTTTTGTT
Found at i:3047966 original size:31 final size:31
Alignment explanation
Indices: 3047921--3047980 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
3047911 TTTTTGTTCT
3047921 TTCTTTTTTCTTTTGTTTTCTTCTTCTTTGC
1 TTCTTTTTTCTTTTGTTTTCTTCTTCTTTGC
* *
3047952 TTCTTTTCTT-TTTTGTTTTTTTTTTCTTT
1 TTCTTTT-TTCTTTTGTTTTCTTCTTCTTT
3047981 TTGTTCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (31 bp):
TTCTTTTTTCTTTTGTTTTCTTCTTCTTTGC
Found at i:3047981 original size:11 final size:11
Alignment explanation
Indices: 3047911--3047982 Score: 63
Period size: 11 Copynumber: 6.3 Consensus size: 11
3047901 TTCTTTTTGA
*
3047911 TTTTTGTTCTT
1 TTTTTTTTCTT
*
3047922 TCTTTTTTCTT
1 TTTTTTTTCTT
3047933 TTGTTTTCTTCTT
1 TT-TTTT-TTCTT
* **
3047946 CTTTGCTTCTT
1 TTTTTTTTCTT
*
3047957 TTCTTTTTTGTT
1 TT-TTTTTTCTT
3047969 TTTTTTTTCTT
1 TTTTTTTTCTT
3047980 TTT
1 TTT
3047983 GTTCTGATTG
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
11 27 0.57
12 14 0.30
13 6 0.13
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:3052605 original size:18 final size:19
Alignment explanation
Indices: 3052560--3052610 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
3052550 TAGAAAAATA
*
3052560 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
3052580 ATTAATATAAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
3052599 ATAATATAAAAA
1 ATAATATAAAAA
3052611 AAACCAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 11 0.38
19 6 0.21
20 8 0.28
21 4 0.14
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:3052652 original size:27 final size:27
Alignment explanation
Indices: 3052590--3052652 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
3052580 ATTAATATAA
*
3052590 AAATAT-AATATAATATAAAAAAAACC
1 AAATATAAAAATAATATAAAAAAAACC
* * *
3052616 AAAAACAAAAATAA-ATAAATATAAACC
1 AAATATAAAAATAATATAAA-AAAAACC
3052643 AAATATAAAA
1 AAATATAAAA
3052653 GTATACATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (27 bp):
AAATATAAAAATAATATAAAAAAAACC
Found at i:3052741 original size:2 final size:2
Alignment explanation
Indices: 3052736--3052768 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3052726 AAACTAAATA
*
3052736 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3052769 ATAATACGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3053457 original size:37 final size:37
Alignment explanation
Indices: 3053364--3053465 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
3053354 GTGCTTGTGG
* * * * * *
3053364 ATCCTATATTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
3053401 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
3053438 ATCCTATTTTTAGGAGTTTGAATTCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
3053466 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:3058414 original size:175 final size:175
Alignment explanation
Indices: 3058123--3058474 Score: 686
Period size: 175 Copynumber: 2.0 Consensus size: 175
3058113 GAAAGGCGCG
3058123 TCTCGGAGATGTGCTTTACCCGTGTTTTCGCTGAGTTTGATGCCACGTATGGAAGGCGCATCCCC
1 TCTCGGAGATGTGCTTTACCCGTGTTTTCGCTGAGTTTGATGCCACGTATGGAAGGCGCATCCCC
3058188 GGGGACGCGCCTTCACTGACTCGACTGCCACGTGTGGAAAGCACATTCCCGGGAACGCGCCTTCC
66 GGGGACGCGCCTTCACTGACTCGACTGCCACGTGTGGAAAGCACATTCCCGGGAACGCGCCTTCC
3058253 ATTAAATGCCATAAATACCCCCATCCGTTTTCCCTAACTACCCCC
131 ATTAAATGCCATAAATACCCCCATCCGTTTTCCCTAACTACCCCC
* *
3058298 TCTCGGAGATGTGCTTTACCCGTGTTTTCGCTGAGTTTGATGCCACGTATGGAAGGCGTATCCCT
1 TCTCGGAGATGTGCTTTACCCGTGTTTTCGCTGAGTTTGATGCCACGTATGGAAGGCGCATCCCC
3058363 GGGGACGCGCCTTCACTGACTCGACTGCCACGTGTGGAAAGCACATTCCCGGGAACGCGCCTTCC
66 GGGGACGCGCCTTCACTGACTCGACTGCCACGTGTGGAAAGCACATTCCCGGGAACGCGCCTTCC
3058428 ATTAAATGCCATAAATACCCCCATCCGTTTTCCCTAACTACCCCC
131 ATTAAATGCCATAAATACCCCCATCCGTTTTCCCTAACTACCCCC
3058473 TC
1 TC
3058475 CTCCCCTATA
Statistics
Matches: 175, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 175 1.00
ACGTcount: A:0.20, C:0.33, G:0.22, T:0.25
Consensus pattern (175 bp):
TCTCGGAGATGTGCTTTACCCGTGTTTTCGCTGAGTTTGATGCCACGTATGGAAGGCGCATCCCC
GGGGACGCGCCTTCACTGACTCGACTGCCACGTGTGGAAAGCACATTCCCGGGAACGCGCCTTCC
ATTAAATGCCATAAATACCCCCATCCGTTTTCCCTAACTACCCCC
Done.