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 8 of 23
Found at i:1519408 original size:104 final size:103
Alignment explanation
Indices: 1519101--1519462 Score: 489
Period size: 104 Copynumber: 3.5 Consensus size: 103
1519091 CTTCAACAAT
* * *
1519101 CGGGTTCGTTCCCTCTTTCTCTAGGGATTATGGAACTCGAAT-ATCTTCTGCAAACGAGTTCGCT
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAATCATC-T-T-CAAACGGGTTCGCT
* *
1519165 -CTCTCTTTCTCTAGGGAGTATAGAACTCGAACAATTTTCAAA
63 CCT-TCTTTCTTTAGGGAGTATAGAACTCGAAC-ATCTTCAAA
* * *
1519207 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAA-CATCTTCAAACGGGTTCGATCCC
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAATCATCTTCAAACGGGTTCGCTCCT
* * *
1519271 TCTTTCTTTAGGGAGTATAGAACTCGGATATCTTCACA
66 TCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAA
1519309 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACATC-TCTTCAAACGGGTTCGCTC
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GA-ATCATCTTCAAACGGGTTCGCTC
* *
1519373 CTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCAAA
64 CTTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAA
* * *
1519413 CGGGTTCGCTCCCTCTCTCTCTAGGGAGTATGGAACTCAAATAATCTTCA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAATCATCTTCA
1519463 TTTGCTTCAC
Statistics
Matches: 228, Mismatches: 22, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
102 46 0.20
103 47 0.21
104 92 0.40
105 2 0.01
106 41 0.18
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (103 bp):
CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAATCATCTTCAAACGGGTTCGCTCCT
TCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAA
Found at i:1519705 original size:36 final size:36
Alignment explanation
Indices: 1519681--1519836 Score: 213
Period size: 36 Copynumber: 4.3 Consensus size: 36
1519671 ACTACTTTTT
* * *
1519681 GGTGAAGACTTAAGACGGTTTGCTTCACTACTCTCT
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
*
1519717 GGTGAAGACTTATGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
* * * *
1519753 GGTGAAGGCTTCAGATTGATTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
* *
1519789 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
*
1519825 GGTGAAGGCTTA
1 GGTGAAGACTTA
1519837 GGATTGACTT
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 108 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (36 bp):
GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
Found at i:1545040 original size:25 final size:23
Alignment explanation
Indices: 1544999--1545044 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1544989 CTTTATAAAT
*
1544999 AATATAATTTTAACCTTTAAATAA
1 AATATAATTTGAACC-TTAAATAA
*
1545023 AATATTAATTTGACCCTTAAAT
1 AATA-TAATTTGAACCTTAAAT
1545045 TTAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (23 bp):
AATATAATTTGAACCTTAAATAA
Found at i:1545171 original size:15 final size:17
Alignment explanation
Indices: 1545140--1545174 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
1545130 ATTATAAACC
1545140 AAACATAAAAATATTAT
1 AAACATAAAAATATTAT
1545157 AAACA-AAAAAT-TTAT
1 AAACATAAAAATATTAT
1545172 AAA
1 AAA
1545175 TTCGATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 6 0.33
17 5 0.28
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
AAACATAAAAATATTAT
Found at i:1545962 original size:8 final size:8
Alignment explanation
Indices: 1545949--1545975 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1545939 GTAGTCGTCC
1545949 TTTCAAAA
1 TTTCAAAA
1545957 TTTCAAAA
1 TTTCAAAA
1545965 TTTCAAAA
1 TTTCAAAA
1545973 TTT
1 TTT
1545976 TTAATTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (8 bp):
TTTCAAAA
Found at i:1546007 original size:26 final size:23
Alignment explanation
Indices: 1545984--1546034 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 23
1545974 TTTTAATTGA
1545984 TATTCTATTTTAAAATTTAAAATT
1 TATT-TATTTTAAAATTTAAAATT
1546008 TATTT-TTTTAAAATTTTATAAATT
1 TATTTATTTTAAAA-TTTA-AAATT
1546032 TAT
1 TAT
1546035 CCCTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.32
23 5 0.20
24 12 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTATTTTAAAATTTAAAATT
Found at i:1546011 original size:24 final size:24
Alignment explanation
Indices: 1545991--1546034 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
1545981 TGATATTCTA
1545991 TTTTAAAA-TTTA-AAATTTATTT
1 TTTTAAAATTTTATAAATTTATTT
1546013 TTTTAAAATTTTATAAATTTAT
1 TTTTAAAATTTTATAAATTTAT
1546035 CCCTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTAAAATTTTATAAATTTATTT
Found at i:1547736 original size:35 final size:35
Alignment explanation
Indices: 1547690--1547829 Score: 199
Period size: 36 Copynumber: 3.9 Consensus size: 35
1547680 AGATGAACAA
*
1547690 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCAT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAT
* *
1547725 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAT
* *
1547760 CTTGAATCGAAATTGCCGATGCTTCATTCCGTTCACT
1 -TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCA-T
* *
1547797 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
1547830 TTCTTATTCA
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 32 0.35
36 59 0.64
37 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAT
Found at i:1547824 original size:72 final size:71
Alignment explanation
Indices: 1547690--1547834 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 71
1547680 AGATGAACAA
* *
1547690 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCATTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCATTCCGTTCATTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1547755 TTCTTC
66 TTCTTC
* *
1547761 TTGAATCGAAATTGCCGATGCTTCATTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCATTCCGTTCA-TTTGAATCGAAAGTGCCGATGCTTCCTTTC
1547826 GTTCTTC
65 GTTCTTC
1547833 TT
1 TT
1547835 ATTCACCTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 31 0.45
72 38 0.55
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (71 bp):
TTGAATCGAAAGTGCCGATGCTTCATTCCGTTCATTTGAATCGAAAGTGCCGATGCTTCCTTTCG
TTCTTC
Found at i:1550654 original size:33 final size:31
Alignment explanation
Indices: 1550586--1550647 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
1550576 AAGAAAATTC
*
1550586 AATATATATATATATTTAATTAAAATTTTTA
1 AATATATATATATATTTAATTAAAATTTATA
* *
1550617 AATATATTTCATATATTTAATTTATAATTTA
1 AATATATAT-ATATATTTAA-TTAAAATTTA
1550648 ATAATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 8 0.31
32 10 0.38
33 8 0.31
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (31 bp):
AATATATATATATATTTAATTAAAATTTATA
Found at i:1551834 original size:14 final size:14
Alignment explanation
Indices: 1551815--1551848 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1551805 ATAATTCAAT
1551815 AATAAACAAATAAA
1 AATAAACAAATAAA
*
1551829 AATAAACAAATCAA
1 AATAAACAAATAAA
1551843 AATAAA
1 AATAAA
1551849 TACAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (14 bp):
AATAAACAAATAAA
Found at i:1551887 original size:12 final size:12
Alignment explanation
Indices: 1551872--1551946 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
1551862 AAAAAAGAGG
1551872 AAAATAATAAAT
1 AAAATAATAAAT
*
1551884 AAAAAAATAAAAT
1 AAAATAAT-AAAT
**
1551897 AAGCTTAA-AAAT
1 AA-AATAATAAAT
*
1551909 AAAATAAAAAAT
1 AAAATAATAAAT
1551921 -AAATAGA-AAA-
1 AAAATA-ATAAAT
*
1551931 AAAATGATAAAT
1 AAAATAATAAAT
1551943 AAAA
1 AAAA
1551947 ATTGGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
10 1 0.02
11 18 0.37
12 22 0.45
13 6 0.12
14 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:1551930 original size:18 final size:18
Alignment explanation
Indices: 1551872--1551948 Score: 59
Period size: 18 Copynumber: 4.0 Consensus size: 18
1551862 AAAAAAGAGG
1551872 AAAATAATAAATAAAAAAAT
1 AAAATAATAAAT--AAAAAT
*
1551892 AAAATAAGCTTAAAAATAAAAT
1 AAAATAA---TAAATA-AAAAT
1551914 AAAA-AATAAATAGAAAA-
1 AAAATAATAAATA-AAAAT
*
1551931 AAAATGATAAATAAAAAT
1 AAAATAATAAATAAAAAT
1551949 TGGATTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
17 8 0.17
18 16 0.34
20 7 0.15
21 3 0.06
22 9 0.19
23 4 0.09
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (18 bp):
AAAATAATAAATAAAAAT
Found at i:1553354 original size:35 final size:37
Alignment explanation
Indices: 1553278--1553377 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 37
1553268 CCAAAATGCT
* * * * * * *
1553278 TTTAAAAACTATATATTATACATGTTTTTAAAAACGT
1 TTTAAAAATTATATATAATATATATTTTCAGAAACGG
1553315 TTTAAAAATT-T-TATAATATATATTTTCAGAAACGG
1 TTTAAAAATTATATATAATATATATTTTCAGAAACGG
*
1553350 TTTAAAAATTATATATTATATATATTTT
1 TTTAAAAATTATATATAATATATATTTT
1553378 TAAAATGTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 28 0.53
36 2 0.04
37 23 0.43
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAAAAATTATATATAATATATATTTTCAGAAACGG
Found at i:1553402 original size:110 final size:110
Alignment explanation
Indices: 1553256--1553517 Score: 286
Period size: 110 Copynumber: 2.4 Consensus size: 110
1553246 AAAATATGTA
* * * * ** *
1553256 ATATATAAATTTCCAAAATGCTTTTAAAAACTATAT-AT-TATACATGTTTTTAAAAACGTTTTA
1 ATATAT-ATTTTCTAAAATGTTTTTAAAAACTATATAATATATAAATG-TTTTAAAAA-AATTCA
* * *
1553319 AAA-ATTTTATAATATATATTTTCAGAAACG-GTTTAAAAATTATATATT
63 AAACAATATATAATATAT-TTTTCA-AAACGAGTTTAAAAACTATATATT
* *
1553367 ATATATATTTT-TAAAATGTTTTTCAAAAATTATATAATATTTAAATGTTTTAAAAAAATTCAAA
1 ATATATATTTTCTAAAATGTTTTT-AAAAACTATATAATATATAAATGTTTTAAAAAAATTCAAA
* * *
1553431 ACAATATATTATATATTTTTCAAAATGATTTTAAAAACTATATATT
65 ACAATATATAATATATTTTTCAAAACGAGTTTAAAAACTATATATT
1553477 ATATATATTTTCTAAAATG-TTTT-AAAACTATATAATATATA
1 ATATATATTTTCTAAAATGTTTTTAAAAACTATATAATATATA
1553518 GTTTCAAAAA
Statistics
Matches: 128, Mismatches: 17, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
108 16 0.12
109 14 0.11
110 57 0.45
111 35 0.27
112 6 0.05
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (110 bp):
ATATATATTTTCTAAAATGTTTTTAAAAACTATATAATATATAAATGTTTTAAAAAAATTCAAAA
CAATATATAATATATTTTTCAAAACGAGTTTAAAAACTATATATT
Found at i:1553412 original size:29 final size:31
Alignment explanation
Indices: 1553364--1553426 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
1553354 AAAATTATAT
* **
1553364 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
1553395 ATTATATA-ATATTT-AAATGTTTTAAAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
1553424 ATT
1 ATT
1553427 CAAAACAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 16 0.55
30 5 0.17
31 8 0.28
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTATATATATATTTAAAATGTTTTAAAAAA
Found at i:1553468 original size:36 final size:35
Alignment explanation
Indices: 1553269--1553589 Score: 220
Period size: 36 Copynumber: 8.8 Consensus size: 35
1553259 TATAAATTTC
*
1553269 CAAAATGCTTTTAAAAACTATATATTATACATGTTTTT
1 CAAAATG-TTTTAAAAACTATATATTAT--ATATTTTT
* * * * *
1553307 AAAAACGTTTTAAAAATTTTATAATATATA-TTTT
1 CAAAATGTTTTAAAAACTATATATTATATATTTTT
* * *
1553341 CAGAAACGGTTTAAAAATTATATATTATATATATTTT
1 CA-AAATGTTTTAAAAACTATATATTATATAT-TTTT
* * * *
1553378 TAAAATGTTTTTCAAAAATTATATAATATTTAAATGTTTT
1 CAAAATG-TTTT-AAAAACTATAT-AT-TATATAT-TTTT
*** * *
1553418 -AAAA-AAATTCAAAACAATATATTATATATTTTT
1 CAAAATGTTTTAAAAACTATATATTATATATTTTT
1553451 CAAAATGATTTTAAAAACTATATATTATATATATTTT
1 CAAAATG-TTTTAAAAACTATATATTATATAT-TTTT
* *
1553488 CTAAAATGTTTT-AAAACTATATAATATATA-GTTT
1 C-AAAATGTTTTAAAAACTATATATTATATATTTTT
* * *
1553522 CAAAAAATATTTTTAAAACTATATATTATATACATTTT
1 C--AAAATGTTTTAAAAACTATATATTATATA-TTTTT
* *
1553560 CAAAATGTTTCAAAAATTATGTATATTATA
1 CAAAATGTTTTAAAAACTA--TATATTATA
1553590 AGTATTTTCA
Statistics
Matches: 226, Mismatches: 39, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
33 4 0.02
34 18 0.08
35 38 0.17
36 80 0.35
37 36 0.16
38 35 0.15
39 6 0.03
40 9 0.04
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (35 bp):
CAAAATGTTTTAAAAACTATATATTATATATTTTT
Found at i:1554375 original size:84 final size:83
Alignment explanation
Indices: 1554275--1554891 Score: 664
Period size: 84 Copynumber: 7.5 Consensus size: 83
1554265 CCAGGGGTCT
*
1554275 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGT
1554340 CGAACTCAAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* * * * * *
1554359 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCATAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGT
* *
1554424 CGAACTCGAAGG---TAT-
65 CGAACTCAAAGGTCTTTTG
* * * * *
1554439 TTGGCATATAGCCCTTCTCGACTTAAGCTATACTGGAAATGATGTGCCGTTGAGCTTAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGT
1554504 CGAACTCAAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* ** * * * * * * * * *
1554523 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAG
**
1554588 TCGAACTCGGAGGTC---T-
64 TCGAACTCAAAGGTCTTTTG
* *
1554604 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGT
1554669 CGAACTCAAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* * * * * **
1554688 GTGGCAGACAACCCTTCTGGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGT
*
1554753 CGAACTCAAAGGTCTTTGG
65 CGAACTCAAAGGTCTTTTG
* * *
1554772 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAG
***
1554837 TCGAACTCGGGGGTC---T-
64 TCGAACTCAAAGGTCTTTTG
*
1554853 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAA
1554892 GGATTGTAAA
Statistics
Matches: 437, Mismatches: 81, Indels: 33
0.79 0.15 0.06
Matches are distributed among these distances:
80 89 0.20
81 77 0.18
82 1 0.00
83 5 0.01
84 216 0.49
85 49 0.11
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (83 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTC
GAACTCAAAGGTCTTTTG
Found at i:1554455 original size:164 final size:164
Alignment explanation
Indices: 1554274--1554844 Score: 811
Period size: 164 Copynumber: 3.4 Consensus size: 164
1554264 CCCAGGGGTC
1554274 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
*
1554339 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
66 TCGAACTCAAAGGTCTTTTGGTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
*
1554404 GCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTA
131 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA
* * * *
1554438 TTTGGCATATAGCCCTTCTCGACTTAAGCTATACTGGAAATGATGTGCCGTTGAGCTTAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
** * * * * * *
1554503 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTAT
66 TCGAACTCAAAGGTCTTTTGGTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
* * * * *
1554568 GCCCTTGAAGCTGAGTGTAATCGAACTCGGAGGTC
131 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA
*
1554603 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC-TTGGAGCTGAGCGTA
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTA
* *
1554667 GTCGAACTCAAAGGTCTTTTGGTGGCAGACAACCCTTCTGGACTTAAGTTGTGCTGCAAATGACA
65 GTCGAACTCAAAGGTCTTTTGGTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATA
* *
1554732 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
130 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG--TA
* * * *
1554769 TGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
1 T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCG
*
1554834 TAATCGAACTC
63 TAGTCGAACTC
1554845 GGGGGTCTTT
Statistics
Matches: 355, Mismatches: 44, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
164 146 0.41
165 141 0.40
166 2 0.01
168 47 0.13
169 19 0.05
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (164 bp):
TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
TCGAACTCAAAGGTCTTTTGGTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA
Found at i:1554604 original size:249 final size:247
Alignment explanation
Indices: 1554279--1554891 Score: 777
Period size: 249 Copynumber: 2.5 Consensus size: 247
1554269 GGGTCTTTGG
* * * *
1554279 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCGA
** * * * * *
1554343 ACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCT
66 ACTCGGAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCT
* * * *
1554408 TGGAGCTGAGCATAGTCGAACTCGAAGG-TATT-TGGCATATAGCCCTTCTCGACTTAAGCTATA
127 TGGAGCTGAGCATAGTCGAACTCAAAGGCTATTGTGGCAGACAACCCTTCTCGACTTAAGCTATA
* ** *
1554471 CTGGAAATGATGTGCCGTT-GAGCTTAGCGTAGTCGAACTCAAAGGTCTTTTGG-TCA
192 CTGCAAATGACATGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTCA
* * * * * * *
1554527 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCGA
* *
1554592 ACTCGGAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGA
66 ACTCGGAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGA
* * * * * *
1554657 GCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTGGCAGACAACCCTTCTGGACTTAAGTTGTGCT
131 GCTGAGCATAGTCGAACTCAAAGG-CTATT-GTGGCAGACAACCCTTCTCGACTTAAGCTATACT
**
1554722 GCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGG
194 GCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCA
*
1554776 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCGA
*
1554841 ACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAA
66 ACTCGGAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAA
1554892 GGATTGTAAA
Statistics
Matches: 312, Mismatches: 46, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
245 68 0.22
246 1 0.00
247 3 0.01
248 46 0.15
249 194 0.62
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (247 bp):
CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCGA
ACTCGGAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGA
GCTGAGCATAGTCGAACTCAAAGGCTATTGTGGCAGACAACCCTTCTCGACTTAAGCTATACTGC
AAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCA
Found at i:1554650 original size:165 final size:164
Alignment explanation
Indices: 1554230--1554891 Score: 805
Period size: 165 Copynumber: 4.0 Consensus size: 164
1554220 GCTATGTTGT
** * * * *
1554230 AAATGATATGACCCCGAAGTTGAGTGTAATCGAAC-CCAGGGGTCTTTGGCAGATAGCCCTTCTC
1 AAATGATATG-CCTTGAAGCTGAGCGTAATCGAACTCGA-AGGTCTTTGGCAGATAGCCCTTCTC
1554294 GACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
64 GACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
* *
1554359 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
129 GTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGC
* * * * *
1554395 AAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTATTTGGCATATAGCCCTTCTCGA
1 AAATGATATGCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGA
* * *
1554460 CTTAAGCTATACTGGAAATGATGTGCCGTTGAGCTTAGCGTAGTCGAACTCAAAGGTCTTTTGGT
66 CTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGT
** * * * *
1554525 CACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
131 GGCAGACAACCCTTCTAGACTTAAGTTATGCTGC
* * *
1554559 AAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTCGGAGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATATG-CCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCG
*
1554624 ACTTAAGCTATTCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
65 ACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
* *
1554688 GTGGCAGACAACCCTTCTGGACTTAAGTTGTGCTGC
129 GTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGC
* * * * *
1554724 AAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTC
1 AAATGATATGCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTC
* * * * ***
1554789 TCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--
62 TCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTT
* * * *
1554852 TT--TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
126 TTGGTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGC
1554889 AAA
1 AAA
1554892 GGATTGTAAA
Statistics
Matches: 427, Mismatches: 61, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
164 168 0.39
165 186 0.44
166 1 0.00
167 2 0.00
168 47 0.11
169 23 0.05
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (164 bp):
AAATGATATGCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGA
CTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGT
GGCAGACAACCCTTCTAGACTTAAGTTATGCTGC
Found at i:1558291 original size:18 final size:18
Alignment explanation
Indices: 1558268--1558311 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1558258 AGTTAATGTG
1558268 AATGCAAAGAAAA-AACAA
1 AATGCAAAGAAAATAA-AA
*
1558286 AATGCAAAGAAAATAAGA
1 AATGCAAAGAAAATAAAA
1558304 AATGCAAA
1 AATGCAAA
1558312 ATGTCTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.68, C:0.09, G:0.14, T:0.09
Consensus pattern (18 bp):
AATGCAAAGAAAATAAAA
Found at i:1560051 original size:14 final size:16
Alignment explanation
Indices: 1560026--1560068 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1560016 AAGATAATTC
1560026 AATAATAAACAAAT-AA
1 AATAA-AAACAAATCAA
1560042 AA-AAAAACAAATCAA
1 AATAAAAACAAATCAA
*
1560057 AATAAATACAAA
1 AATAAAAACAAA
1560069 AGAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
16 10 0.42
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (16 bp):
AATAAAAACAAATCAA
Found at i:1561575 original size:35 final size:37
Alignment explanation
Indices: 1561499--1561598 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 37
1561489 CCAAAATGCT
* * * * * * *
1561499 TTTAAAAACTATATATTATACATGTTTTTAAAAACGT
1 TTTAAAAATTATATATAATATATATTTTCAGAAACGG
1561536 TTTAAAAATT-T-TATAATATATATTTTCAGAAACGG
1 TTTAAAAATTATATATAATATATATTTTCAGAAACGG
*
1561571 TTTAAAAATTATATATTATATATATTTT
1 TTTAAAAATTATATATAATATATATTTT
1561599 TAAAATGTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 28 0.53
36 2 0.04
37 23 0.43
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAAAAATTATATATAATATATATTTTCAGAAACGG
Found at i:1561633 original size:29 final size:31
Alignment explanation
Indices: 1561585--1561647 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
1561575 AAAATTATAT
* **
1561585 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
1561616 ATTATATA-ATATTT-AAATGTTTTAAAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
1561645 ATT
1 ATT
1561648 CAAAACAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 16 0.55
30 5 0.17
31 8 0.28
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTATATATATATTTAAAATGTTTTAAAAAA
Found at i:1561732 original size:37 final size:37
Alignment explanation
Indices: 1561477--1561821 Score: 232
Period size: 38 Copynumber: 9.3 Consensus size: 37
1561467 AAAATATGTA
* *
1561477 ATATATAAATTTCCAAAATGCTTTTAAAAACTATATATT
1 ATATAT-ATTTTCTAAAATG-TTTTAAAAACTATATATT
* * * * *
1561516 ATACATGTTTT-TAAAAACGTTTTAAAAA-T-TTTATA
1 ATATATATTTTCT-AAAATGTTTTAAAAACTATATATT
* * *
1561551 ATATATATTTTC-AGAAACGGTTTAAAAATTATATATT
1 ATATATATTTTCTA-AAATGTTTTAAAAACTATATATT
* *
1561588 ATATATATTTT-TAAAATGTTTTTCAAAAATTATATAAT
1 ATATATATTTTCTAAAATG-TTTT-AAAAACTATATATT
* * *** * *
1561626 ATTTAAATGTTT-TAAAA-AAATTCAAAACAATATATT
1 ATATATAT-TTTCTAAAATGTTTTAAAAACTATATATT
*
1561662 ATATA-ATTTTTCAAAAATGATTTTAAAAACTATATATT
1 ATATATA-TTTTCTAAAATG-TTTTAAAAACTATATATT
1561700 ATATATATTTTCTAAAATGTTTTAAAAACTATATA--
1 ATATATATTTTCTAAAATGTTTTAAAAACTATATATT
* * * *
1561735 ATATATAGTTTCAAAAAATATTTTTAAAACTATATA-T
1 ATATATATTTTC-TAAAATGTTTTAAAAACTATATATT
* *
1561772 -TATACATTTTC-AAAATGTTTTCAAAAATTATGTATATT
1 ATATATATTTTCTAAAATGTTTT-AAAAACTA--TATATT
1561810 ATA-AGTATTTTC
1 ATATA-TATTTTC
1561822 AAAGACCGTT
Statistics
Matches: 242, Mismatches: 42, Indels: 44
0.74 0.13 0.13
Matches are distributed among these distances:
34 10 0.04
35 47 0.19
36 54 0.22
37 50 0.21
38 59 0.24
39 22 0.09
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATATTTTCTAAAATGTTTTAAAAACTATATATT
Found at i:1561758 original size:73 final size:72
Alignment explanation
Indices: 1561456--1561798 Score: 218
Period size: 74 Copynumber: 4.7 Consensus size: 72
1561446 ATATATATAT
* * * * * *
1561456 AAATATTTTCGAAAATATGTAATATATAAATTTCCAAAATGCTTTTAAAAACTATATATTATACA
1 AAATATTTT-AAAAATATATAATATATATATTTTCAAAATG-TTTTAAAAACTATATAATATATA
**
1561521 TGTTTTTAA
64 TGTTTCAAA
** * * * *
1561530 AAACGTTTTAAAAAT-T-TTATAATATATATTTTCAGAAACGGTTTAAAAATTATATATTATATA
1 AAATATTTTAAAAATATATAAT-ATATATATTTTCA-AAATGTTTTAAAAACTATATA--ATATA
*
1561593 TAT-TTTTAAA
62 TATGTTTCAAA
** * * * *** * * *
1561603 ATGT-TTTTCAAAAATTATATAATATTTAAATGTTTTAAAA-AAATTCAAAACAATATATTATAT
1 AAATATTTT-AAAAA-TATATAATATATATAT-TTTCAAAATGTTTTAAAAACTATATAATATAT
*
1561666 AATTTTTC-AA
63 -ATGTTTCAAA
*
1561676 AAATGATTTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTATATAATATAT
1 AAAT-ATTTTAAAAA-TATATAATATATATATTTTC-AAAATGTTTTAAAAACTATATAATATAT
1561741 A-GTTTCAAA
63 ATGTTTCAAA
* *
1561750 AAATATTTTTAAAACTATAT-AT-TATACATTTTCAAAATGTTTTCAAAAA
1 AAATA-TTTTAAAAATATATAATATATATATTTTCAAAATGTTTT-AAAAA
1561799 TTATGTATAT
Statistics
Matches: 207, Mismatches: 44, Indels: 39
0.71 0.15 0.13
Matches are distributed among these distances:
70 10 0.05
71 18 0.09
72 36 0.17
73 40 0.19
74 65 0.31
75 31 0.15
76 7 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (72 bp):
AAATATTTTAAAAATATATAATATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATG
TTTCAAA
Found at i:1561764 original size:36 final size:35
Alignment explanation
Indices: 1561456--1561786 Score: 184
Period size: 37 Copynumber: 9.1 Consensus size: 35
1561446 ATATATATAT
* * * *
1561456 AAATATTTTCGAAAA-TATGTAATATATAAATTTCCA
1 AAATATTTT-AAAAACTATATAATATAT-ATTTTCAA
* * * *
1561492 AAATGCTTTTAAAAACTATATATTATACATGTTTTTAA
1 AAAT-ATTTTAAAAACTATATA--ATATATATTTTCAA
** * * *
1561530 AAACGTTTTAAAAATTTTATAATATATATTTTCAG
1 AAATATTTTAAAAACTATATAATATATATTTTCAA
*** * *
1561565 AAACGGTTTAAAAATTATATATTATATATATTTT-TA
1 AAATATTTTAAAAACTATATA--ATATATATTTTCAA
* * * *
1561601 AAATGTTTTTCAAAAATTATATAATATTTAAATGTTTTAA
1 AAAT-ATTTT-AAAAACTATATAATA--TATAT-TTTCAA
* * * *
1561641 AAA-A-ATTCAAAACAATATATTATATAATTTTTCAA
1 AAATATTTTAAAAACTATATAATATAT-A-TTTTCAA
*
1561676 AAATGATTTTAAAAACTATATATTATATATATTTTCTA
1 AAAT-ATTTTAAAAACTATATA--ATATATATTTTCAA
* *
1561714 AAATGTTTTAAAAACTATATAATATATAGTTTCAAA
1 AAATATTTTAAAAACTATATAATATATATTTTC-AA
* * *
1561750 AAATATTTTTAAAACTATATATTATACATTTTCAA
1 AAATATTTTAAAAACTATATAATATATATTTTCAA
1561785 AA
1 AA
1561787 TGTTTTCAAA
Statistics
Matches: 229, Mismatches: 46, Indels: 41
0.72 0.15 0.13
Matches are distributed among these distances:
34 2 0.01
35 53 0.23
36 55 0.24
37 56 0.24
38 45 0.20
39 9 0.04
40 9 0.04
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (35 bp):
AAATATTTTAAAAACTATATAATATATATTTTCAA
Found at i:1564072 original size:6 final size:6
Alignment explanation
Indices: 1564061--1564087 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1564051 TTTGTGTGAA
1564061 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1564088 GCAGCAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1566036 original size:30 final size:30
Alignment explanation
Indices: 1566000--1566072 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
1565990 GTGCCCCAAT
* * * *
1566000 ATCACTTTGGATACGTGATAATGTCATGTG
1 ATCACTTTGGACACGTGACAATATCATGTC
*
1566030 ATCACTTTGAACACGTGACAATATCATGTC
1 ATCACTTTGGACACGTGACAATATCATGTC
1566060 ATCACTTTGGACA
1 ATCACTTTGGACA
1566073 TATATATGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (30 bp):
ATCACTTTGGACACGTGACAATATCATGTC
Found at i:1569323 original size:29 final size:30
Alignment explanation
Indices: 1569256--1569387 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 30
1569246 TAAATAAAAA
*
1569256 AACGATAAAAAATGA-TCGAAAATATTATT
1 AACGCTAAAAAATGACTCGAAAATATTATT
*
1569285 AGGCGCTAAAAAATGACT-GAAAATATTATT
1 A-ACGCTAAAAAATGACTCGAAAATATTATT
*
1569315 AACGTTAAAAAATGACT-GAAAATATTATT
1 AACGCTAAAAAATGACTCGAAAATATTATT
* *
1569344 AACGTTAAAAAATGA-TCAAAAATATTATT
1 AACGCTAAAAAATGACTCGAAAATATTATT
1569373 AACGCT-AAAAATGAC
1 AACGCTAAAAAATGAC
1569388 CAAAAATTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
28 9 0.10
29 58 0.62
30 25 0.27
31 1 0.01
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.27
Consensus pattern (30 bp):
AACGCTAAAAAATGACTCGAAAATATTATT
Found at i:1570434 original size:3 final size:3
Alignment explanation
Indices: 1570426--1570489 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
1570416 CTATCCACAC
1570426 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1570473 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
1570490 CTCAATGATA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1571072 original size:31 final size:32
Alignment explanation
Indices: 1571028--1571162 Score: 84
Period size: 31 Copynumber: 4.3 Consensus size: 32
1571018 TTAAAGACTA
* * *
1571028 TTTTATAATAGTTAGATAGGTTTAATG-TCAT
1 TTTTATAACAGTTAGATAAGTTTAATGACCAT
* *
1571059 TTTTTTAACAGTTATATAAGTTTAATGACCAT
1 TTTTATAACAGTTAGATAAGTTTAATGACCAT
* * * * * *
1571091 TTTTGT-ACTATTTTGATAAAATTCAATGATC-T
1 TTTTATAAC-AGTTAGAT-AAGTTTAATGACCAT
*
1571123 TTTTATAACA-TATCA-ATAAGTTTAATGATCA-
1 TTTTATAACAGT-T-AGATAAGTTTAATGACCAT
1571154 TTTTATAAC
1 TTTTATAAC
1571163 TTTTAAAAGT
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
31 46 0.57
32 23 0.28
33 12 0.15
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (32 bp):
TTTTATAACAGTTAGATAAGTTTAATGACCAT
Found at i:1572242 original size:20 final size:21
Alignment explanation
Indices: 1572217--1572268 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
1572207 TTTTCCCAAT
1572217 TCGCAATGCGAATAAGT-AAA
1 TCGCAATGCGAATAAGTAAAA
* *
1572237 TCGCAACGCGAATTAGTAAAA
1 TCGCAATGCGAATAAGTAAAA
1572258 TCGCAATGCGA
1 TCGCAATGCGA
1572269 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATAAGTAAAA
Found at i:1572281 original size:41 final size:41
Alignment explanation
Indices: 1572236--1572391 Score: 156
Period size: 41 Copynumber: 3.8 Consensus size: 41
1572226 GAATAAGTAA
* * *
1572236 ATCGCAACGCGA-ATTAGTAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATA-CAAAATCGCAACGCGATACTGACT
1572277 ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
* * ** *
1572318 TTCGCAACGCGATACTGAC--TTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAAT-ACAAAATCGCAACGCGATACTGACT
* * * * *
1572358 TTCGCAACGAGATAATAGAGAATCGCAATGCGAT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGAT
1572392 TTTCAAAGTT
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 32 0.33
41 59 0.61
42 5 0.05
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
Found at i:1572282 original size:20 final size:20
Alignment explanation
Indices: 1572257--1572371 Score: 133
Period size: 20 Copynumber: 5.7 Consensus size: 20
1572247 AATTAGTAAA
*
1572257 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1572277 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1572298 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1572318 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1572338 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
1572358 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1572372 ATAGAGAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.77
21 15 0.18
22 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1572303 original size:21 final size:21
Alignment explanation
Indices: 1572234--1572311 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
1572224 GCGAATAAGT
* *
1572234 AAATCGCAACGCGA-ATTAGTA
1 AAATCGCAACGCGATAATA-CA
* *
1572255 AAATCGCAATGCGATACTGAC-
1 AAATCGCAACGCGATAAT-ACA
*
1572276 -TATCGCAACGCGATAATACA
1 AAATCGCAACGCGATAATACA
1572296 AAATCGCAACGCGATA
1 AAATCGCAACGCGATA
1572312 CTGACTTTCG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
19 2 0.04
20 14 0.30
21 27 0.59
22 2 0.04
23 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (21 bp):
AAATCGCAACGCGATAATACA
Found at i:1572767 original size:14 final size:14
Alignment explanation
Indices: 1572750--1572803 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1572740 GAAAATCGCA
1572750 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1572764 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
1572781 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
1572797 TTGCGAT
1 TTGCGAT
1572804 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1572949 original size:14 final size:14
Alignment explanation
Indices: 1572930--1572966 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1572920 CATCAATTAA
1572930 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1572944 ACAAATCATCTTTT
1 ACAAATCAACATTT
1572958 ACAAATCAA
1 ACAAATCAA
1572967 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1574837 original size:20 final size:20
Alignment explanation
Indices: 1574814--1574867 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1574804 GAAACTTAAA
1574814 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1574834 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
1574854 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1574868 TAAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1574876 original size:19 final size:19
Alignment explanation
Indices: 1574854--1574912 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1574844 GGAAATGGCT
1574854 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
*
1574873 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATAAAA
*
1574887 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATAAAA
1574906 ATCGCAA
1 ATCGCAA
1574913 CGACAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:1574889 original size:14 final size:14
Alignment explanation
Indices: 1574870--1574960 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
1574860 ATGCGAAATA
1574870 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1574884 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1574903 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1574917 AAAATTGCAATGCGAA
1 AAAATCGCAA--CGAC
1574933 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1574949 AAAATCGCAACG
1 AAAATCGCAACG
1574961 TGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 9 0.15
19 10 0.16
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1574896 original size:33 final size:33
Alignment explanation
Indices: 1574854--1574976 Score: 176
Period size: 33 Copynumber: 3.8 Consensus size: 33
1574844 GGAAATGGCT
1574854 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
*
1574887 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
* *
1574920 ATTGCAATGCGAAAT-GAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
* * * *
1574952 ATCGCAACGTGAAACACAAATCGCA
1 ATCGCAATGCGAAATAAAAATCGCA
1574977 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 27 0.33
33 54 0.67
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGACAAA
Found at i:1575013 original size:14 final size:14
Alignment explanation
Indices: 1574994--1575048 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1574984 TTTCATTTCG
1574994 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1575008 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
1575024 CGTATTGCAATTTTGT
1 CG--TTGCGATTTTGT
1575040 CGTTGCGAT
1 CGTTGCGAT
1575049 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.52
16 8 0.24
18 8 0.24
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1575024 original size:32 final size:32
Alignment explanation
Indices: 1574977--1575068 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
1574967 ACAAATCGCA
1574977 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
** *
1575010 TTGCGATTTCATTTCGTATTGCAATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
**
1575042 TTGCGATAGCCATTTCCGCGTTGCGAT
1 TTGCGAT-TTCATTT-CGCGTTGCGAT
1575069 AGTCATTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
32 30 0.61
33 11 0.22
34 8 0.16
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.45
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1575063 original size:20 final size:20
Alignment explanation
Indices: 1575040--1575087 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1575030 GCAATTTTGT
1575040 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATAGCCATTTCCG
* *
1575060 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGCCATTTCCG
*
1575080 TGTTGCGA
1 CGTTGCGA
1575088 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTCCG
Found at i:1575596 original size:18 final size:18
Alignment explanation
Indices: 1575570--1575615 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1575560 GTCGATCAGA
* *
1575570 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTAGGCGAGG
*
1575588 TGATAGCTCTAGGCGAGG
1 TGATGGCTCTAGGCGAGG
1575606 TGATGGCTCT
1 TGATGGCTCT
1575616 CAAAGTGGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.28
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:1576981 original size:20 final size:20
Alignment explanation
Indices: 1576933--1576991 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1576923 AATAGTTTCT
** *
1576933 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1576953 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1576973 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1576992 AGAGAATCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1577282 original size:22 final size:22
Alignment explanation
Indices: 1577254--1577297 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1577244 GACGGAGATA
*
1577254 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
1577276 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
1577298 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:1577528 original size:41 final size:41
Alignment explanation
Indices: 1577465--1577578 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
1577455 CGTTTAGAAA
* *
1577465 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
* * * *
1577506 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
*
1577547 ATCGCATTGCGA-TA-GTGAGTATCGCATTGCGA
1 ATCGCATTGCGATTATGT-ATTATCGCATTGCGA
1577579 TTTTCCCAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 2 0.03
40 15 0.24
41 45 0.73
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
Found at i:1577551 original size:20 final size:20
Alignment explanation
Indices: 1577526--1577579 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1577516 GATTTTGTAT
1577526 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1577546 TATCGCATTGCGATAGTGAG
1 TATCGCATTGCGATAGTAAG
1577566 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1577580 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1577568 original size:61 final size:62
Alignment explanation
Indices: 1577465--1577582 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
1577455 CGTTTAGAAA
* * * *
1577465 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* *
1577527 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGATAGTGAGTATCGCATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1577583 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 2 0.04
61 35 0.71
62 12 0.24
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (62 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1580456 original size:8 final size:8
Alignment explanation
Indices: 1580443--1580473 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1580433 GTTTTCCTTT
1580443 TCCCACTC
1 TCCCACTC
1580451 TCCCACTC
1 TCCCACTC
1580459 TCCCACTC
1 TCCCACTC
*
1580467 TCACACT
1 TCCCACT
1580474 GTCACACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.16, C:0.58, G:0.00, T:0.26
Consensus pattern (8 bp):
TCCCACTC
Found at i:1583601 original size:20 final size:21
Alignment explanation
Indices: 1583563--1583604 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1583553 CGACTGATGC
1583563 AAATAAAAAAGAAGCAGAGAG
1 AAATAAAAAAGAAGCAGAGAG
1583584 AAATAAAAGAA-AAG-AGAGAG
1 AAATAAAA-AAGAAGCAGAGAG
1583604 A
1 A
1583605 GAGGCTCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 11 0.55
22 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.05
Consensus pattern (21 bp):
AAATAAAAAAGAAGCAGAGAG
Found at i:1587576 original size:17 final size:18
Alignment explanation
Indices: 1587542--1587576 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1587532 TCACGGATGT
1587542 AAGATTACCAGTGGAATA
1 AAGATTACCAGTGGAATA
*
1587560 AAGATTATCAG-GGAATA
1 AAGATTACCAGTGGAATA
1587577 GGATTACTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (18 bp):
AAGATTACCAGTGGAATA
Found at i:1588627 original size:36 final size:35
Alignment explanation
Indices: 1588573--1588646 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 35
1588563 TCATTGTCTG
1588573 ATATTCCACTTTCATCAGACGACCAACATATATAT
1 ATATTCCACTTTCATCAGACGACCAACATATATAT
*
1588608 ATATATCCACTTTCGTCAGACGACCAACATATATAT
1 ATAT-TCCACTTTCATCAGACGACCAACATATATAT
1588644 ATA
1 ATA
1588647 GTTTTGGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 4 0.11
36 33 0.89
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (35 bp):
ATATTCCACTTTCATCAGACGACCAACATATATAT
Found at i:1589694 original size:12 final size:12
Alignment explanation
Indices: 1589679--1589707 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1589669 AAAATTGATC
1589679 GATGAATTACAT
1 GATGAATTACAT
1589691 GATGAATTACAT
1 GATGAATTACAT
1589703 GATGA
1 GATGA
1589708 TTAGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (12 bp):
GATGAATTACAT
Found at i:1594871 original size:20 final size:20
Alignment explanation
Indices: 1594846--1594890 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1594836 TTTGGTTCAT
1594846 GGAATGTAGCATTACCTCCG
1 GGAATGTAGCATTACCTCCG
* *
1594866 GGAATGTAGCGTTACCTTCG
1 GGAATGTAGCATTACCTCCG
1594886 GGAAT
1 GGAAT
1594891 AGGATTACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (20 bp):
GGAATGTAGCATTACCTCCG
Found at i:1595295 original size:15 final size:15
Alignment explanation
Indices: 1595275--1595304 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1595265 ACCCTATGAA
*
1595275 TGGGTATCGATACCC
1 TGGGTACCGATACCC
1595290 TGGGTACCGATACCC
1 TGGGTACCGATACCC
1595305 CTATGACTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (15 bp):
TGGGTACCGATACCC
Found at i:1595554 original size:21 final size:21
Alignment explanation
Indices: 1595525--1595564 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1595515 TTTTTGCAGA
*
1595525 AAAATCATCCTCGAACGGCTCC
1 AAAATCATCC-CCAACGGCTCC
1595547 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1595565 AGATACAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1602741 original size:21 final size:23
Alignment explanation
Indices: 1602692--1602752 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
1602682 TTTAAATTTG
1602692 TGTTCATTAATATTTTTTTGATAAA
1 TGTTCATTAATA-TTTTTT-ATAAA
*
1602717 TGTTCATTAGTATTTTTT-T-AA
1 TGTTCATTAATATTTTTTATAAA
*
1602738 TGTTAATTAATATTT
1 TGTTCATTAATATTT
1602753 ATGTGTATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 15 0.45
22 1 0.03
24 6 0.18
25 11 0.33
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (23 bp):
TGTTCATTAATATTTTTTATAAA
Found at i:1608588 original size:14 final size:14
Alignment explanation
Indices: 1608569--1608596 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1608559 GCACTTTTTC
1608569 TTTTAAAATTATTT
1 TTTTAAAATTATTT
1608583 TTTTAAAATTATTT
1 TTTTAAAATTATTT
1608597 AAAATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAAATTATTT
Found at i:1614516 original size:14 final size:14
Alignment explanation
Indices: 1614497--1614529 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1614487 CGTTCGTGAA
1614497 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1614511 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
1614525 TGTTC
1 CGTTC
1614530 ATGTTCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.15, G:0.27, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1636191 original size:6 final size:6
Alignment explanation
Indices: 1636180--1636213 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
1636170 ACACCTATTT
1636180 AAAACA AAAACA AAAACA AAAA-A AAAACCA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAA-CA AAAA
1636214 TAATCTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.62
7 5 0.19
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:1637419 original size:18 final size:19
Alignment explanation
Indices: 1637384--1637420 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1637374 CACGGAATGT
1637384 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1637404 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1637421 GGATTACTGG
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:1641336 original size:21 final size:21
Alignment explanation
Indices: 1641312--1641356 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1641302 CCCTAACTTA
*
1641312 AAACCCTAAATTGATAACC-CT
1 AAACCCTAAACT-ATAACCTCT
1641333 AAACCCTAAACTATAACCTCT
1 AAACCCTAAACTATAACCTCT
1641354 AAA
1 AAA
1641357 TCTAAATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (21 bp):
AAACCCTAAACTATAACCTCT
Found at i:1642753 original size:349 final size:349
Alignment explanation
Indices: 1642114--1642810 Score: 1385
Period size: 349 Copynumber: 2.0 Consensus size: 349
1642104 GGTGGAGTGG
1642114 ATTTCGAATCCACTAAAGACCCCTAAAGATTGGGAATCAGTGATACAGAGGTTATCGTGTGCGTC
1 ATTTCGAATCCACTAAAGACCCCTAAAGATTGGGAATCAGTGATACAGAGGTTATCGTGTGCGTC
1642179 TTTGAGGGAGAATATTTTGGTTAAATCCATTCCGAGACGATGCAATGTAGAAGCTGATATGCTAG
66 TTTGAGGGAGAATATTTTGGTTAAATCCATTCCGAGACGATGCAATGTAGAAGCTGATATGCTAG
1642244 CAAAAAAGGCGATAGTGTAGAGGGCTTCTTGGTTGTTTTTGTGTGAGCCACTCGTCTAGCTTGGG
131 CAAAAAAGGCGATAGTGTAGAGGGCTTCTTGGTTGTTTTTGTGTGAGCCACTCGTCTAGCTTGGG
1642309 ATTGGGCTGCGCTGCTGTCAATGGAAGCTCAAGTTGCAGACCTCGTGGTTTGCTGCAGTTTTATT
196 ATTGGGCTGCGCTGCTGTCAATGGAAGCTCAAGTTGCAGACCTCGTGGTTTGCTGCAGTTTTATT
1642374 GGAGCACTGATGTTGTGAGGTAGCAGAGTATAATTGTTTTGTTGTTACTACGGTCTACGGTGGAC
261 GGAGCACTGATGTTGTGAGGTAGCAGAGTATAATTGTTTTGTTGTTACTACGGTCTACGGTGGAC
1642439 TAACTGCGTTTCTGCCCTGGTGCA
326 TAACTGCGTTTCTGCCCTGGTGCA
1642463 ATTTCGAATCCACTAAAGACCCCTAAAGATTGGGAATCAGTGATACAGAGGTTATCGTGTGCGTC
1 ATTTCGAATCCACTAAAGACCCCTAAAGATTGGGAATCAGTGATACAGAGGTTATCGTGTGCGTC
*
1642528 TTTGAGGGAGAATATTTTGGTTAAATCCATTCCGAGGCGATGCAATGTAGAAGCTGATATGCTAG
66 TTTGAGGGAGAATATTTTGGTTAAATCCATTCCGAGACGATGCAATGTAGAAGCTGATATGCTAG
1642593 CAAAAAAGGCGATAGTGTAGAGGGCTTCTTGGTTGTTTTTGTGTGAGCCACTCGTCTAGCTTGGG
131 CAAAAAAGGCGATAGTGTAGAGGGCTTCTTGGTTGTTTTTGTGTGAGCCACTCGTCTAGCTTGGG
1642658 ATTGGGCTGCGCTGCTGTCAATGGAAGCTCAAGTTGCAGACCTCGTGGTTTGCTGCAGTTTTATT
196 ATTGGGCTGCGCTGCTGTCAATGGAAGCTCAAGTTGCAGACCTCGTGGTTTGCTGCAGTTTTATT
1642723 GGAGCACTGATGTTGTGAGGTAGCAGAGTATAATTGTTTTGTTGTTACTACGGTCTACGGTGGAC
261 GGAGCACTGATGTTGTGAGGTAGCAGAGTATAATTGTTTTGTTGTTACTACGGTCTACGGTGGAC
1642788 TAACTGCGTTTCTGCCCTGGTGC
326 TAACTGCGTTTCTGCCCTGGTGC
1642811 GTATTCTTGG
Statistics
Matches: 347, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
349 347 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.32
Consensus pattern (349 bp):
ATTTCGAATCCACTAAAGACCCCTAAAGATTGGGAATCAGTGATACAGAGGTTATCGTGTGCGTC
TTTGAGGGAGAATATTTTGGTTAAATCCATTCCGAGACGATGCAATGTAGAAGCTGATATGCTAG
CAAAAAAGGCGATAGTGTAGAGGGCTTCTTGGTTGTTTTTGTGTGAGCCACTCGTCTAGCTTGGG
ATTGGGCTGCGCTGCTGTCAATGGAAGCTCAAGTTGCAGACCTCGTGGTTTGCTGCAGTTTTATT
GGAGCACTGATGTTGTGAGGTAGCAGAGTATAATTGTTTTGTTGTTACTACGGTCTACGGTGGAC
TAACTGCGTTTCTGCCCTGGTGCA
Found at i:1643508 original size:18 final size:19
Alignment explanation
Indices: 1643473--1643510 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1643463 CACGGAATGT
1643473 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
1643493 AAGATTACCA-GAGAATAA
1 AAGATTACCAGGAGAATAA
1643511 TATTACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:1660699 original size:12 final size:12
Alignment explanation
Indices: 1660677--1660708 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1660667 AGGCCAACTC
1660677 CCACT-CTTTGA
1 CCACTACTTTGA
1660688 CCACTACTTTGA
1 CCACTACTTTGA
1660700 CCACTACTT
1 CCACTACTT
1660709 CCCTCATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.22, C:0.38, G:0.06, T:0.34
Consensus pattern (12 bp):
CCACTACTTTGA
Found at i:1660809 original size:31 final size:31
Alignment explanation
Indices: 1660764--1660876 Score: 172
Period size: 31 Copynumber: 3.6 Consensus size: 31
1660754 AGTGTTGAGC
1660764 TCGACTCGACTCGAAAACTCTGAAATAAAGT
1 TCGACTCGACTCGAAAACTCTGAAATAAAGT
* *
1660795 TTGACTTGACTCGAAAACTCTGAAATAAAGT
1 TCGACTCGACTCGAAAACTCTGAAATAAAGT
* * *
1660826 TCGACTTGACTCGAAAACTCTTAAATGAAGT
1 TCGACTCGACTCGAAAACTCTGAAATAAAGT
*
1660857 TCGACTCGGCTCGAAAACTC
1 TCGACTCGACTCGAAAACTC
1660877 GCGAGCTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (31 bp):
TCGACTCGACTCGAAAACTCTGAAATAAAGT
Found at i:1664995 original size:16 final size:16
Alignment explanation
Indices: 1664974--1665004 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1664964 ACTATTTACA
1664974 TGAATAGTGAATTTTG
1 TGAATAGTGAATTTTG
*
1664990 TGAATAGTGACTTTT
1 TGAATAGTGAATTTT
1665005 TGTCGGCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (16 bp):
TGAATAGTGAATTTTG
Found at i:1669096 original size:36 final size:35
Alignment explanation
Indices: 1669052--1669122 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
1669042 GGCAACCAAC
1669052 TTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTTA
1 TTTGAAAAATATTTTTCAAAGTTTGGTAAA-GTTTA
*
1669088 TTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTTA
1 TTTGAAAAATATTTTTCAAAGTTTGGTAAAGTTTA
1669123 GTAGATGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.46
Consensus pattern (35 bp):
TTTGAAAAATATTTTTCAAAGTTTGGTAAAGTTTA
Found at i:1672878 original size:24 final size:23
Alignment explanation
Indices: 1672851--1672895 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1672841 CATTTCATTT
1672851 AAAT-TAATCTTGATACTTTTATAC
1 AAATATAAT-TTGATA-TTTTATAC
*
1672875 AAATATGATTTGATATTTTAT
1 AAATATAATTTGATATTTTAT
1672896 TTAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 10 0.53
25 3 0.16
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (23 bp):
AAATATAATTTGATATTTTATAC
Found at i:1673166 original size:27 final size:27
Alignment explanation
Indices: 1673126--1673206 Score: 153
Period size: 27 Copynumber: 3.0 Consensus size: 27
1673116 GTTGTTATTT
*
1673126 TGTTTGAATTCAATGAAGCCATTAAGG
1 TGTTTGAATCCAATGAAGCCATTAAGG
1673153 TGTTTGAATCCAATGAAGCCATTAAGG
1 TGTTTGAATCCAATGAAGCCATTAAGG
1673180 TGTTTGAATCCAATGAAGCCATTAAGG
1 TGTTTGAATCCAATGAAGCCATTAAGG
1673207 CCAGAAAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (27 bp):
TGTTTGAATCCAATGAAGCCATTAAGG
Found at i:1678362 original size:17 final size:17
Alignment explanation
Indices: 1678338--1678370 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1678328 ATTTAACATC
1678338 TTTAATTATT-TAATTT
1 TTTAATTATTGTAATTT
1678354 TTTATATTATTGTAATT
1 TTTA-ATTATTGTAATT
1678371 ATTGAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTAATTATTGTAATTT
Found at i:1682739 original size:19 final size:19
Alignment explanation
Indices: 1682715--1682755 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1682705 ATTTTAAATT
*
1682715 AATTAAATATTATTATCTA
1 AATTAAATATAATTATCTA
*
1682734 AATTAAATATAATTATTTA
1 AATTAAATATAATTATCTA
1682753 AAT
1 AAT
1682756 AATTTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTAAATATAATTATCTA
Found at i:1687325 original size:32 final size:31
Alignment explanation
Indices: 1687289--1687376 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
1687279 TTTCAAAACG
*
1687289 TTATAAAATTATCACTAAACTTTATCAAACTA
1 TTATAAAATGATCACTAAAC-TTATCAAACTA
* ** *
1687321 TTATAAAATGGTCGTTAAACTTATCGAACTA
1 TTATAAAATGATCACTAAACTTATCAAACTA
* *
1687352 TTACAAAATGAAC-CTTAAACTTATC
1 TTATAAAATGATCAC-TAAACTTATC
1687377 GTATCACTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 30 0.65
32 16 0.35
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (31 bp):
TTATAAAATGATCACTAAACTTATCAAACTA
Found at i:1687351 original size:31 final size:31
Alignment explanation
Indices: 1687304--1687377 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
1687294 AAATTATCAC
* * ** *
1687304 TAAACTTTATCAAACTATTATAAAATGGTCGT
1 TAAAC-TTATCGAACTATTACAAAATGAACCT
1687336 TAAACTTATCGAACTATTACAAAATGAACCT
1 TAAACTTATCGAACTATTACAAAATGAACCT
1687367 TAAACTTATCG
1 TAAACTTATCG
1687378 TATCACTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (31 bp):
TAAACTTATCGAACTATTACAAAATGAACCT
Found at i:1693200 original size:51 final size:49
Alignment explanation
Indices: 1693124--1693232 Score: 155
Period size: 51 Copynumber: 2.2 Consensus size: 49
1693114 TAGAAGAAGG
* * *
1693124 ATCAATAAACGATTCATGTGTTCTTAGACATATATTTGACTGTTGCCACAA
1 ATCAATAAACGATTCATATATTCTTAGACATATATTTGACTATTG-CAC-A
*
1693175 ATCAATAAATGATTCATATATTCTTAGACATATATTTGACTATTGCACA
1 ATCAATAAACGATTCATATATTCTTAGACATATATTTGACTATTGCACA
1693224 ATGCAATAA
1 AT-CAATAA
1693233 TAACATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 3 0.06
50 9 0.17
51 41 0.77
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (49 bp):
ATCAATAAACGATTCATATATTCTTAGACATATATTTGACTATTGCACA
Found at i:1698430 original size:11 final size:10
Alignment explanation
Indices: 1698388--1698430 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1698378 TCTTTACACG
1698388 AAAAA-ATAA
1 AAAAATATAA
*
1698397 AAAAATATTA
1 AAAAATATAA
1698407 AAAAATCATAA
1 AAAAAT-ATAA
*
1698418 AATAATATAA
1 AAAAATATAA
1698428 AAA
1 AAA
1698431 CAAACAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 5 0.18
10 15 0.54
11 8 0.29
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAATATAA
Found at i:1700478 original size:7 final size:7
Alignment explanation
Indices: 1700462--1700512 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
1700452 AGCCTACTTC
*
1700462 TTCTTCT
1 TTCTTTT
1700469 TTCTTTT
1 TTCTTTT
1700476 TTCCTTTT
1 TT-CTTTT
1700484 TTCTTTT
1 TTCTTTT
1700491 TTCTTTT
1 TTCTTTT
*
1700498 TCCTTTT
1 TTCTTTT
1700505 TTCCTTTT
1 TT-CTTTT
1700513 GTCGTTTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
7 27 0.69
8 12 0.31
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (7 bp):
TTCTTTT
Found at i:1700484 original size:8 final size:8
Alignment explanation
Indices: 1700471--1700512 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
1700461 CTTCTTCTTT
1700471 CTTTTTTC
1 CTTTTTTC
1700479 CTTTTTT-
1 CTTTTTTC
1700486 CTTTTTT-
1 CTTTTTTC
1700493 C-TTTTTC
1 CTTTTTTC
1700500 CTTTTTTC
1 CTTTTTTC
1700508 CTTTT
1 CTTTT
1700513 GTCGTTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 5 0.16
7 9 0.28
8 18 0.56
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
CTTTTTTC
Found at i:1700488 original size:15 final size:15
Alignment explanation
Indices: 1700468--1700512 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
1700458 CTTCTTCTTC
1700468 TTTCTTTTTTCCTTT
1 TTTCTTTTTTCCTTT
1700483 TTTCTTTTTT-CTTT
1 TTTCTTTTTTCCTTT
*
1700497 TTCCTTTTTTCCTTT
1 TTTCTTTTTTCCTTT
1700512 T
1 T
1700513 GTCGTTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTTTCCTTT
Found at i:1700493 original size:22 final size:21
Alignment explanation
Indices: 1700462--1700512 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1700452 AGCCTACTTC
*
1700462 TTCTTCTTTCTTTTTTCCTTTT
1 TTCTTTTTTC-TTTTTCCTTTT
1700484 TTCTTTTTTCTTTTTCCTTTT
1 TTCTTTTTTCTTTTTCCTTTT
*
1700505 TTCCTTTT
1 TTCTTTTT
1700513 GTCGTTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTCTTTTTTCTTTTTCCTTTT
Found at i:1705465 original size:23 final size:22
Alignment explanation
Indices: 1705421--1705465 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1705411 AATGTCATGG
*
1705421 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
1705443 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1705466 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1706994 original size:103 final size:103
Alignment explanation
Indices: 1706563--1706986 Score: 803
Period size: 103 Copynumber: 4.1 Consensus size: 103
1706553 GTCGAGGGTC
1706563 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1706628 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
1706666 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1706731 TTGATCCCTAGTATATGTATATAATTATTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
1706769 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTTTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1706834 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
* *
1706872 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1706937 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
1706975 TATGTGGTCCTT
1 TATGTGGTCCTT
1706987 ATGGACATTA
Statistics
Matches: 312, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 312 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:1707052 original size:23 final size:23
Alignment explanation
Indices: 1706998--1707054 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
1706988 TGGACATTAT
1706998 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAACTC
*** * *
1707021 TACGCGGCACTATGGTGCAATTC
1 TATATGGCACTACGGTGCAACTC
1707044 TATATGGCACT
1 TATATGGCACT
1707055 TCAGTGCATT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAACTC
Found at i:1710934 original size:23 final size:22
Alignment explanation
Indices: 1710890--1710934 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1710880 AATGTCATGG
*
1710890 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1710912 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1710935 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1712221 original size:103 final size:103
Alignment explanation
Indices: 1712042--1712464 Score: 839
Period size: 103 Copynumber: 4.1 Consensus size: 103
1712032 GTCGAGGGTC
1712042 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1712107 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
1712145 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1712210 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
1712248 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1712313 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
1712351 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAT-TGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1712415 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
1712453 TATGTGGTCCTT
1 TATGTGGTCCTT
1712465 ATGGACATTA
Statistics
Matches: 320, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
102 74 0.23
103 246 0.77
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:1712530 original size:23 final size:23
Alignment explanation
Indices: 1712476--1712548 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
1712466 TGGACATTAT
*
1712476 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
***
1712499 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
1712522 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
1712543 TATATG
1 TATATG
1712549 AGATGTGGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 33 0.79
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:1716362 original size:21 final size:20
Alignment explanation
Indices: 1716322--1716368 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1716312 CTAAATTGAG
*
1716322 GGTTTTAAGTTAGGGTTTAT
1 GGTTTAAAGTTAGGGTTTAT
1716342 GGTTTAAAGGTTATGGG-TTAT
1 GGTTTAAA-GTTA-GGGTTTAT
1716363 GGTTTA
1 GGTTTA
1716369 GGGTTATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 14 0.58
22 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (20 bp):
GGTTTAAAGTTAGGGTTTAT
Found at i:1720881 original size:2 final size:2
Alignment explanation
Indices: 1720874--1720921 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1720864 TATACGACTA
1720874 AT AT AT AT AT 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
1720916 AT AT AT
1 AT AT AT
1720922 TTCAAAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1729932 original size:20 final size:20
Alignment explanation
Indices: 1729908--1729947 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1729898 TTTTACCTTT
*
1729908 TTTTTTTATTAAAAACTTTAA
1 TTTTATTATTAAAAA-TTTAA
*
1729929 TTTTATTTTTAAAAATTTA
1 TTTTATTATTAAAAATTTA
1729948 TGACAGTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTATTAAAAATTTAA
Found at i:1737691 original size:3 final size:3
Alignment explanation
Indices: 1737678--1737707 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1737668 ATTATGTAAA
1737678 AAC ATAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC A-AC AAC AAC AAC AAC AAC AAC AAC AA
1737708 AACCCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.30, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:1739397 original size:28 final size:28
Alignment explanation
Indices: 1739359--1739415 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1739349 TCGTCGTTGT
*
1739359 TTTCAAGCACTGGCTCGACGATATAATG
1 TTTCAAGCACTGACTCGACGATATAATG
*
1739387 TTTCAAGCACTTACTCGACGATATAATG
1 TTTCAAGCACTGACTCGACGATATAATG
1739415 T
1 T
1739416 AAATGAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (28 bp):
TTTCAAGCACTGACTCGACGATATAATG
Found at i:1740427 original size:16 final size:16
Alignment explanation
Indices: 1740398--1740435 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1740388 ATAAATATTT
1740398 AATATTTTTATTTAAA
1 AATATTTTTATTTAAA
1740414 AATATATTTT-TTTAAA
1 AATAT-TTTTATTTAAA
1740430 AATATT
1 AATATT
1740436 AGGCCTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATTTTTATTTAAA
Found at i:1740990 original size:2 final size:2
Alignment explanation
Indices: 1740983--1741015 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1740973 TAAATAAAGA
1740983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1741016 ATCACTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1748352 original size:42 final size:42
Alignment explanation
Indices: 1748303--1748387 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
1748293 TTTGTTCTTC
* *
1748303 CTTTTCATCTTCATCTCCTATTTCCGACTGACTGTTCAATTT
1 CTTTTCATCTCCATCTCCTATGTCCGACTGACTGTTCAATTT
*
1748345 CTTTTCATCTCCATCTCCTATGTCCGGCTGACTGTTCAATTT
1 CTTTTCATCTCCATCTCCTATGTCCGACTGACTGTTCAATTT
1748387 C
1 C
1748388 CCTTCTCCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.15, C:0.31, G:0.09, T:0.45
Consensus pattern (42 bp):
CTTTTCATCTCCATCTCCTATGTCCGACTGACTGTTCAATTT
Found at i:1750292 original size:6 final size:6
Alignment explanation
Indices: 1750239--1750272 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1750229 TATACAACTC
1750239 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCT
1750273 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:1752370 original size:113 final size:109
Alignment explanation
Indices: 1752067--1752393 Score: 600
Period size: 109 Copynumber: 3.0 Consensus size: 109
1752057 CTTGATTGAT
*
1752067 GCCAAGGGGTTAGTGTCTCACACTTTTCTTCTCCTCCAAGGCTTGAATTCCTTGTAGCCCACCTC
1 GCCAAGGGGTTAGTGTCTCACACTTCTCTTCTCCTCCAAGGCTTGAATTCCTTGTAGCCCACCTC
1752132 AACTACGAGTTGGTTGGTTGGTTGAGCTCAGATTAGGTTAAAAATGAA
66 AACTACGA----GTTGGTTGGTTGAGCTCAGATTAGGTTAAAAATGAA
1752180 GCCAAGGGGTTAGTGTCTCACACTTCTCTTCTCCTCCAAGGCTTGAATTCCTTGTAGCCCACCTC
1 GCCAAGGGGTTAGTGTCTCACACTTCTCTTCTCCTCCAAGGCTTGAATTCCTTGTAGCCCACCTC
1752245 AACTACGAGTTGGTTGGTTGAGCTCAGATTAGGTTAAAAATGAA
66 AACTACGAGTTGGTTGGTTGAGCTCAGATTAGGTTAAAAATGAA
1752289 GCCAAGGGGTTAGTGTCTCACACTTCTCTTCTCCTCCAAGGCTTGAATTCCTTGTAGCCCACCTC
1 GCCAAGGGGTTAGTGTCTCACACTTCTCTTCTCCTCCAAGGCTTGAATTCCTTGTAGCCCACCTC
*
1752354 TACTACGAGTTGGTTGGTTGAGCTCAGATTAGGTTAAAAA
66 AACTACGAGTTGGTTGGTTGAGCTCAGATTAGGTTAAAAA
1752394 CTAGGTTTAC
Statistics
Matches: 212, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
109 140 0.66
113 72 0.34
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (109 bp):
GCCAAGGGGTTAGTGTCTCACACTTCTCTTCTCCTCCAAGGCTTGAATTCCTTGTAGCCCACCTC
AACTACGAGTTGGTTGGTTGAGCTCAGATTAGGTTAAAAATGAA
Found at i:1758658 original size:21 final size:21
Alignment explanation
Indices: 1758632--1758687 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1758622 TTCTGGGCAG
1758632 AGTGCATCGATGCACATTCAT
1 AGTGCATCGATGCACATTCAT
1758653 AGTGCATCGATGCACATTCAT
1 AGTGCATCGATGCACATTCAT
1758674 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1758688 TCAAGGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (21 bp):
AGTGCATCGATGCACATTCAT
Found at i:1758786 original size:64 final size:64
Alignment explanation
Indices: 1758718--1758942 Score: 206
Period size: 64 Copynumber: 3.5 Consensus size: 64
1758708 TTGTTTGAAT
* * * **
1758718 GTGCACCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATT
1758781 C
64 C
* * * *
1758782 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATTG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
** ** * ** *
1758846 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATATTACATCGAATACCTTTT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
* * *
1758910 ATGCACCGATACATCA-GTAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCAT
1758943 ACCTTCATTA
Statistics
Matches: 133, Mismatches: 24, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
63 1 0.01
64 125 0.94
65 7 0.05
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
Found at i:1759209 original size:26 final size:26
Alignment explanation
Indices: 1759180--1759244 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
1759170 TGTTGATTTT
1759180 TATA-ATACAATAGTTGTGA-ACATGCA
1 TATAGATA-AATA-TTGTGATACATGCA
*
1759206 TATATGATAATTATTGTGATACATGCA
1 TATA-GATAAATATTGTGATACATGCA
*
1759233 TA-AGATATATAT
1 TATAGATAAATAT
1759245 ATGTTCATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 7 0.21
26 11 0.33
27 12 0.36
28 3 0.09
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (26 bp):
TATAGATAAATATTGTGATACATGCA
Found at i:1759263 original size:24 final size:24
Alignment explanation
Indices: 1759236--1759297 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
1759226 ACATGCATAA
*
1759236 GATATAT-ATATGTTCATGTGATAT
1 GATATATGATATGAT-ATGTGATAT
1759260 GATATATGATATGATATGTGATAT
1 GATATATGATATGATATGTGATAT
* *
1759284 GACATGTGATATGA
1 GATATATGATATGA
1759298 GAACATGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.40
Consensus pattern (24 bp):
GATATATGATATGATATGTGATAT
Found at i:1759271 original size:12 final size:12
Alignment explanation
Indices: 1759222--1759297 Score: 64
Period size: 12 Copynumber: 6.2 Consensus size: 12
1759212 ATAATTATTG
*
1759222 TGATACATGCATA
1 TGATATATG-ATA
*
1759235 AGATATAT-ATA
1 TGATATATGATA
* *
1759246 TGTTCATGTGATA
1 TGAT-ATATGATA
1759259 TGATATATGATA
1 TGATATATGATA
*
1759271 TGATATGTGATA
1 TGATATATGATA
* *
1759283 TGACATGTGATA
1 TGATATATGATA
1759295 TGA
1 TGA
1759298 GAACATGATA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
11 5 0.10
12 35 0.67
13 12 0.23
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (12 bp):
TGATATATGATA
Found at i:1759310 original size:25 final size:24
Alignment explanation
Indices: 1759278--1759330 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1759268 ATATGATATG
1759278 TGATATGACATGTGATATGAGA-ACA
1 TGATATGA-A-GTGATATGAGATACA
*
1759303 TGATATGAAGTGTTATGAGATACA
1 TGATATGAAGTGATATGAGATACA
1759327 TGAT
1 TGAT
1759331 CACAAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 8 0.31
25 8 0.31
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (24 bp):
TGATATGAAGTGATATGAGATACA
Found at i:1762408 original size:19 final size:19
Alignment explanation
Indices: 1762371--1762408 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1762361 CATTATATGA
1762371 TATGACTATGTGGGAAAAGT
1 TATGACTATGT-GGAAAAGT
1762391 TATGAGCTATGT-GAAAAG
1 TATGA-CTATGTGGAAAAG
1762409 GTAAGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (19 bp):
TATGACTATGTGGAAAAGT
Found at i:1762701 original size:149 final size:150
Alignment explanation
Indices: 1762512--1762827 Score: 555
Period size: 150 Copynumber: 2.1 Consensus size: 150
1762502 GGGTAGAGGG
* * *
1762512 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAGGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
1762576 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1762641 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
1762661 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1762726 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1762791 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
1762811 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1762828 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 51 0.32
150 108 0.68
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:1762839 original size:23 final size:23
Alignment explanation
Indices: 1762795--1762839 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1762785 ATCATTATAT
*
1762795 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1762818 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1762840 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1769448 original size:19 final size:19
Alignment explanation
Indices: 1769411--1769448 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1769401 CATTATATGA
1769411 TATGACTATGTGGGAAAAGT
1 TATGACTATGT-GGAAAAGT
1769431 TATGAGCTATGT-GAAAAG
1 TATGA-CTATGTGGAAAAG
1769449 GTAAGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (19 bp):
TATGACTATGTGGAAAAGT
Found at i:1769822 original size:150 final size:149
Alignment explanation
Indices: 1769552--1769867 Score: 535
Period size: 150 Copynumber: 2.1 Consensus size: 149
1769542 GGGTAGAGGG
* * * * *
1769552 TCTACGCGGTCCTTCAGGATATCTGTATATTCTTTGGAACATGTATGAGGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTATGAAGTCTTGAAAGACACAT
* *
1769617 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
1769682 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
1769701 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTATGAAGTCTT-GAAAGACACA
1769766 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1769831 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
1769851 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1769868 TGCATTTATA
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 49 0.31
150 108 0.69
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTATGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1769879 original size:23 final size:23
Alignment explanation
Indices: 1769835--1769879 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1769825 ATCATTATAT
*
1769835 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1769858 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1769880 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1774425 original size:64 final size:64
Alignment explanation
Indices: 1774357--1774581 Score: 175
Period size: 64 Copynumber: 3.5 Consensus size: 64
1774347 TTGTTTGAAT
* ** * **
1774357 GTGCACCGATGCATTGGTAATGCATCGGTGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAAGTAATGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATT
1774420 C
64 C
* * * * *
1774421 GTGCATCGATGTATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATTG
1 GTGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
* * * ** ** * * ** *
1774485 GTGCATCGATGCATAAGGAGTGCATCGATGTATCCCAGCAATAATACTACATAGAATACCTTTT
1 GTGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
* * * *
1774549 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAATGCATCGATGCAT
1774582 ACCTTCATTA
Statistics
Matches: 129, Mismatches: 30, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
64 124 0.96
65 5 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
Found at i:1774902 original size:24 final size:24
Alignment explanation
Indices: 1774875--1774923 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1774865 ACATGCATAA
*
1774875 GATATAT-ATATGTTCATGTGATAT
1 GATATATGATATGAT-ATGTGATAT
*
1774899 GATATGTGATATGATATGTGATAT
1 GATATATGATATGATATGTGATAT
1774923 G
1 G
1774924 GCCTGTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (24 bp):
GATATATGATATGATATGTGATAT
Found at i:1774907 original size:12 final size:12
Alignment explanation
Indices: 1774890--1774923 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1774880 ATATATGTTC
1774890 ATGTGATATGAT
1 ATGTGATATGAT
1774902 ATGTGATATGAT
1 ATGTGATATGAT
1774914 ATGTGATATG
1 ATGTGATATG
1774924 GCCTGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:1780912 original size:16 final size:17
Alignment explanation
Indices: 1780877--1780913 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1780867 TTATATCATA
*
1780877 TATTAATATTTTTTTGG
1 TATTAATAATTTTTTGG
1780894 TATTAATAATTTTTT-G
1 TATTAATAATTTTTTGG
1780910 TATT
1 TATT
1780914 TTTTATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (17 bp):
TATTAATAATTTTTTGG
Found at i:1784314 original size:21 final size:20
Alignment explanation
Indices: 1784299--1784516 Score: 237
Period size: 21 Copynumber: 10.6 Consensus size: 20
1784289 TTCGCATTGT
1784299 GATAG-TCCAAGTTCGCGTTGC
1 GATAGCTCCAAGTT--CGTTGC
**
1784320 GAT-TTTCCAAGTTCGTTGC
1 GATAGCTCCAAGTTCGTTGC
1784339 GATAGTCTCCAAGTTCGTTGC
1 GATAG-CTCCAAGTTCGTTGC
1784360 GATAGTCTCCAAGTTCGTTGC
1 GATAG-CTCCAAGTTCGTTGC
*
1784381 GATAGTCTCCAAATTCGTTGC
1 GATAG-CTCCAAGTTCGTTGC
**
1784402 GATAGTCTCCAAGTTCGTTAT
1 GATAG-CTCCAAGTTCGTTGC
1784423 GATAGTCTCCAAGTGT-GTTGC
1 GATAG-CTCCAAGT-TCGTTGC
*
1784444 GATAGTCTCCAAGTGCGTTGC
1 GATAG-CTCCAAGTTCGTTGC
*
1784465 GATAGTCTCCAAATTCGTTGC
1 GATAG-CTCCAAGTTCGTTGC
*
1784486 GATAGTCTCCAAATTCGTTGC
1 GATAG-CTCCAAGTTCGTTGC
1784507 GATAG-TCCAA
1 GATAGCTCCAA
1784517 AATCGCAACG
Statistics
Matches: 180, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
19 14 0.08
21 165 0.92
22 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (20 bp):
GATAGCTCCAAGTTCGTTGC
Found at i:1784371 original size:42 final size:42
Alignment explanation
Indices: 1784304--1784513 Score: 309
Period size: 42 Copynumber: 5.0 Consensus size: 42
1784294 ATTGTGATAG
*
1784304 TCCAAGTTCGCGTTGCGAT--TTTCCAAGTTCGTTGCGATAGTC
1 TCCAAGTT--CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
1784346 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
* **
1784388 TCCAAATTCGTTGCGATAGTCTCCAAGTTCGTTATGATAGTC
1 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
*
1784430 TCCAAGTGT-GTTGCGATAGTCTCCAAGTGCGTTGCGATAGTC
1 TCCAAGT-TCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
* *
1784472 TCCAAATTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
1784514 CAAAATCGCA
Statistics
Matches: 153, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
40 9 0.06
41 1 0.01
42 142 0.93
43 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
Found at i:1784511 original size:63 final size:63
Alignment explanation
Indices: 1784304--1784513 Score: 309
Period size: 63 Copynumber: 3.3 Consensus size: 63
1784294 ATTGTGATAG
*
1784304 TCCAAGTTCGCGTTGCGAT--TTTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
1 TCCAAGTT--CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
* **
1784367 TCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTTCGTTATGATAGTC
1 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
* *
1784430 TCCAAGTGT-GTTGCGATAGTCTCCAAGTGCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
1 TCCAAGT-TCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
*
1784493 TCCAAATTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
1784514 CAAAATCGCA
Statistics
Matches: 133, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
61 9 0.07
62 1 0.01
63 122 0.92
64 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (63 bp):
TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
Found at i:1784617 original size:6 final size:6
Alignment explanation
Indices: 1784606--1784642 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1784596 GACACGTATT
* *
1784606 ACCACG ACCACG ACCACG ACCACG AGCACG AGCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1784643 GCGCGAGACG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.35, C:0.43, G:0.22, T:0.00
Consensus pattern (6 bp):
ACCACG
Done.