Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004197.1 Hibiscus syriacus cultivar Beakdansim tig00009179_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: 60214
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:874 original size:43 final size:42
Alignment explanation
Indices: 772--891 Score: 152
Period size: 43 Copynumber: 2.9 Consensus size: 42
762 TATAAAGTTA
*
772 CACGATATCCTTCATCGTGAAGTTAAAATCGTGGA-TGTGGG
1 CACGATATCCTTCATCGTGGAGTTAAAATCGTGGATTGTGGG
* * * * *
813 CACGATCTCCTTCGTCGTGGAGTTGAAATCATGGATTTTTGGG
1 CACGATATCCTTCATCGTGGAGTTAAAATCGTGGA-TTGTGGG
* *
856 TACGATATCCTTCATCGTGGACTTAAAATCGTGGAT
1 CACGATATCCTTCATCGTGGAGTTAAAATCGTGGAT
892 GGCTCATTCG
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 30 0.46
42 1 0.02
43 34 0.52
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (42 bp):
CACGATATCCTTCATCGTGGAGTTAAAATCGTGGATTGTGGG
Found at i:1811 original size:1 final size:1
Alignment explanation
Indices: 1801--1872 Score: 63
Period size: 1 Copynumber: 72.0 Consensus size: 1
1791 AATCACCTTA
* * * * * * * * *
1801 TTTTTCTTTTTTTCTTTTTTCTTTTTTTTCTTTTTGTTCTTTTTGTTCTTTTTTTTTTTTTTTTA
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1866 TTTTTTT
1 TTTTTTT
1873 CAATTTAAGG
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.01, C:0.08, G:0.03, T:0.88
Consensus pattern (1 bp):
T
Found at i:1814 original size:8 final size:8
Alignment explanation
Indices: 1801--1873 Score: 85
Period size: 8 Copynumber: 8.8 Consensus size: 8
1791 AATCACCTTA
1801 TTTTTCTT
1 TTTTTCTT
1809 TTTTTC-T
1 TTTTTCTT
1816 TTTTTCTTT
1 TTTTTC-TT
1825 TTTTTCTT
1 TTTTTCTT
1833 TTTGTTCTT
1 TTT-TTCTT
1842 TTTGTTCTTT
1 TTT-TTC-TT
*
1852 TTTTTTTT
1 TTTTTCTT
*
1860 TTTTTATT
1 TTTTTCTT
1868 TTTTTC
1 TTTTTC
1874 AATTTAAGGC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
7 7 0.12
8 25 0.43
9 21 0.36
10 5 0.09
ACGTcount: A:0.01, C:0.10, G:0.03, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1819 original size:9 final size:9
Alignment explanation
Indices: 1801--1872 Score: 89
Period size: 9 Copynumber: 8.4 Consensus size: 9
1791 AATCACCTTA
1801 TTTTTC-TT
1 TTTTTCTTT
1809 TTTTTC--T
1 TTTTTCTTT
1816 TTTTTCTTT
1 TTTTTCTTT
1825 TTTTTCTTT
1 TTTTTCTTT
*
1834 TTGTTCTTT
1 TTTTTCTTT
*
1843 TTGTTCTTT
1 TTTTTCTTT
1852 TTTTT-TTT
1 TTTTTCTTT
*
1860 TTTTTATTT
1 TTTTTCTTT
1869 TTTT
1 TTTT
1873 CAATTTAAGG
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
7 7 0.12
8 14 0.24
9 38 0.64
ACGTcount: A:0.01, C:0.08, G:0.03, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1821 original size:15 final size:15
Alignment explanation
Indices: 1801--1861 Score: 79
Period size: 17 Copynumber: 3.9 Consensus size: 15
1791 AATCACCTTA
1801 TTTTTCTTTTTTTCT
1 TTTTTCTTTTTTTCT
1816 TTTTTCTTTTTTTTCTT
1 TTTTTC-TTTTTTTC-T
1833 TTTGTTCTTTTTGTTCT
1 TTT-TTCTTTTT-TTCT
1850 TTTTT-TTTTTTT
1 TTTTTCTTTTTTT
1862 TTTATTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.05
15 11 0.26
16 10 0.24
17 13 0.31
18 6 0.14
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (15 bp):
TTTTTCTTTTTTTCT
Found at i:1927 original size:8 final size:8
Alignment explanation
Indices: 1910--1944 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
1900 ACCCTAAACA
1910 TTTTCTTT
1 TTTTCTTT
*
1918 TTTT-TCT
1 TTTTCTTT
1925 TTTTCTTT
1 TTTTCTTT
1933 TTTTCTTT
1 TTTTCTTT
1941 TTTT
1 TTTT
1945 GACTTAGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:1943 original size:15 final size:15
Alignment explanation
Indices: 1910--1942 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1900 ACCCTAAACA
1910 TTTTCTTTTTTTTCT
1 TTTTCTTTTTTTTCT
1925 TTTTC-TTTTTTTCT
1 TTTTCTTTTTTTTCT
1939 TTTT
1 TTTT
1943 TTGACTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTCTTTTTTTTCT
Found at i:13356 original size:19 final size:19
Alignment explanation
Indices: 13334--13370 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
13324 GAATAAAGCT
13334 AAAAAAA-TATAATAAAATG
1 AAAAAAAGTA-AATAAAATG
13353 AAAAAAAGTAAATAAAAT
1 AAAAAAAGTAAATAAAAT
13371 AAGCAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAAAAAGTAAATAAAATG
Found at i:13364 original size:28 final size:28
Alignment explanation
Indices: 13325--13456 Score: 98
Period size: 28 Copynumber: 4.7 Consensus size: 28
13315 TAAAAGAGTG
*
13325 AATAAAGCTAAAAAAATATAATAAAATGAA
1 AATAAAG-TAAAAAAATA-AACAAAATGAA
*
13355 AA-AAAGTAAATAAAATAAGCAAAATGAA
1 AATAAAGTAAA-AAAATAAACAAAATGAA
*
13383 AATAAAG--AAACAA-AAACAAAATAGAAA
1 AATAAAGTAAAAAAATAAACAAAAT-G-AA
* *
13410 AATAAAG-AAAATTAATAAACAAAGT-AA
1 AATAAAGTAAAA-AAATAAACAAAATGAA
13437 AATAAA-TAATAAAAAATAAA
1 AATAAAGT-A-AAAAAATAAA
13457 AATAAAGACA
Statistics
Matches: 85, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
25 8 0.09
26 4 0.05
27 19 0.22
28 25 0.29
29 19 0.22
30 10 0.12
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (28 bp):
AATAAAGTAAAAAAATAAACAAAATGAA
Found at i:13420 original size:17 final size:16
Alignment explanation
Indices: 13400--13490 Score: 62
Period size: 17 Copynumber: 5.6 Consensus size: 16
13390 AAACAAAAAC
13400 AAAATAGAAAAATAAAG
1 AAAATA-AAAAATAAAG
* *
13417 AAAATTAATAAACAAAG
1 AAAA-TAAAAAATAAAG
*
13434 TAAAATAAATAAT-AA-
1 -AAAATAAAAAATAAAG
13449 AAAAT-AAAAATAAAG
1 AAAATAAAAAATAAAG
* *
13464 ACAAAAGAAAAAATGAAG
1 --AAAATAAAAAATAAAG
*
13482 TAAATAAAA
1 AAAATAAAA
13491 TATAGGCAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
13 5 0.09
14 7 0.12
16 9 0.16
17 21 0.37
18 15 0.26
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (16 bp):
AAAATAAAAAATAAAG
Found at i:13694 original size:4 final size:4
Alignment explanation
Indices: 13685--13732 Score: 57
Period size: 4 Copynumber: 12.5 Consensus size: 4
13675 ATATAGTACT
*
13685 TAAA TAAA TAAA TAAA TAAA TAAA T-AA TCAAA T-AA -AAA TAAT TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA
13731 TA
1 TA
13733 TATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 7 0.18
4 28 0.74
5 3 0.08
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:13817 original size:22 final size:22
Alignment explanation
Indices: 13792--13833 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13782 ATATGTATAT
13792 ATAAC-AAAATAAATAATATAAA
1 ATAACAAAAAT-AATAATATAAA
*
13814 ATAATAAAAATAATAATATA
1 ATAACAAAAATAATAATATA
13834 GGGATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAACAAAAATAATAATATAAA
Found at i:16149 original size:18 final size:18
Alignment explanation
Indices: 16122--16156 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16112 ACTGAATAAT
*
16122 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
16140 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
16157 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:16978 original size:19 final size:19
Alignment explanation
Indices: 16954--16999 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
16944 GGACGAAAAT
16954 CACTTCATTTCAGCTCAAA
1 CACTTCATTTCAGCTCAAA
*
16973 CACTTCATTTTAGCTCAAA
1 CACTTCATTTCAGCTCAAA
16992 CACTTCAT
1 CACTTCAT
17000 ATTTCATCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.35
Consensus pattern (19 bp):
CACTTCATTTCAGCTCAAA
Found at i:23039 original size:18 final size:18
Alignment explanation
Indices: 23016--23055 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
23006 ACTGAATAAT
23016 TGTCCCGAATG-ACCACTA
1 TGTCCCG-ATGTACCACTA
23034 TGTCCCGATGTACCACTA
1 TGTCCCGATGTACCACTA
23052 TGTC
1 TGTC
23056 TCAAAGGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.28
Consensus pattern (18 bp):
TGTCCCGATGTACCACTA
Found at i:23525 original size:23 final size:23
Alignment explanation
Indices: 23495--23546 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
23485 GGAACAGGAT
23495 TACATTTTATATCTACATAATCA
1 TACATTTTATATCTACATAATCA
23518 TACATTTTATATCTACATAATCA
1 TACATTTTATATCTACATAATCA
23541 TACATT
1 TACATT
23547 GATACATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.44
Consensus pattern (23 bp):
TACATTTTATATCTACATAATCA
Found at i:31560 original size:23 final size:23
Alignment explanation
Indices: 31534--31586 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
31524 CATATGAGGT
*
31534 AAAAAAAAT-ACTAATAATAATTA
1 AAAAAAAATGA-TAATAATAAATA
*
31557 AAAAAACATGATAATAATAAATA
1 AAAAAAAATGATAATAATAAATA
*
31580 AATAAAA
1 AAAAAAA
31587 TAAAATAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAAAAAATGATAATAATAAATA
Found at i:31561 original size:20 final size:20
Alignment explanation
Indices: 31536--31594 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
31526 TATGAGGTAA
31536 AAAAAATAC-TAATAATAATT
1 AAAAAATACATAATAATAA-T
*
31556 AAAAAA-ACATGATAATAAT
1 AAAAAATACATAATAATAAT
31575 AAATAAATA-A-AATAA-AAT
1 AAA-AAATACATAATAATAAT
31593 AA
1 AA
31595 GAATTTAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 18 0.53
21 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAAATACATAATAATAAT
Found at i:31802 original size:10 final size:10
Alignment explanation
Indices: 31784--31822 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
31774 GGCCTAAAAC
*
31784 CCCTAATTTT
1 CCCTCATTTT
31794 CCCTCATTTT
1 CCCTCATTTT
*
31804 CTCTCATTTT
1 CCCTCATTTT
*
31814 CACTCATTT
1 CCCTCATTT
31823 CTCTGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.51
Consensus pattern (10 bp):
CCCTCATTTT
Found at i:31832 original size:20 final size:20
Alignment explanation
Indices: 31786--31832 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31776 CCTAAAACCC
*
31786 CTAATTTTCCCTCATTTTCT
1 CTAATTTTCACTCATTTTCT
*
31806 CTCATTTTCACTCA-TTTCT
1 CTAATTTTCACTCATTTTCT
31825 CTGAATTT
1 CT-AATTT
31833 GAGAGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.17, C:0.28, G:0.02, T:0.53
Consensus pattern (20 bp):
CTAATTTTCACTCATTTTCT
Found at i:32695 original size:3 final size:3
Alignment explanation
Indices: 32687--32741 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
32677 ATAAATAGGA
*
32687 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
32733 AAT AAT AAT
1 AAT AAT AAT
32742 CTATATAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:32926 original size:70 final size:71
Alignment explanation
Indices: 32797--33074 Score: 248
Period size: 70 Copynumber: 3.8 Consensus size: 71
32787 ATGCTTTTTT
* ** * * *
32797 TTTTTAAAACTATATATTATACGTATTTTCAGAAACGTTTTTAAAAACATATACAATATATATAA
1 TTTTAAAAACTATATATTATATATATTTTCA-AAATG-TCTT-AAAAC-TATA-TATATATATAA
* *
32862 CTTCAAAAATATT
61 TTTC-AAAA-ATG
* * **
32875 TTTTAAAAACTATATATTATATATATTTTCAAAATGTCTT-ATA-TA-ATATATAAATGTTTTCA
1 TTTTAAAAACTATATATTATATATATTTTCAAAATGTCTTAAAACTATATATATATATAATTTCA
32937 AAAATG
66 AAAATG
* *
32943 TTTTCAAAACTATATA-T-TATA-ATTTTCAAAATGTTTTCAAAACTATATACTATATATAATTT
1 TTTTAAAAACTATATATTATATATATTTTCAAAATGTCTT-AAAACTATATA-TATATATAA-TT
33005 TC-AAAATG
63 TCAAAAATG
*
33013 TTTTAAAAACTATATATTATATATATTTTCAAAATGACTTTTAAAAACTATATA-ATATATAA
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG--TCTT-AAAACTATATATATATATAA
33075 ATGTTTTCGA
Statistics
Matches: 169, Mismatches: 20, Indels: 27
0.78 0.09 0.12
Matches are distributed among these distances:
65 15 0.09
66 4 0.02
67 3 0.02
68 19 0.11
69 7 0.04
70 37 0.22
71 6 0.04
72 6 0.04
73 20 0.12
74 2 0.01
75 15 0.09
76 3 0.02
77 4 0.02
78 28 0.17
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (71 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAATGTCTTAAAACTATATATATATATAATTTCA
AAAATG
Found at i:32943 original size:12 final size:12
Alignment explanation
Indices: 32926--32951 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
32916 TATAATATAT
32926 AAATGTTTTCAA
1 AAATGTTTTCAA
32938 AAATGTTTTCAA
1 AAATGTTTTCAA
32950 AA
1 AA
32952 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
AAATGTTTTCAA
Found at i:33010 original size:37 final size:37
Alignment explanation
Indices: 32914--33073 Score: 197
Period size: 37 Copynumber: 4.4 Consensus size: 37
32904 CAAAATGTCT
*
32914 TATATAATATATA-AATGTTTTCAAAAATGTTTTCAAAAC
1 TATATAATATATATAA--TTTTC-AAAATGTTTTAAAAAC
*
32953 --TAT-ATAT-TATAATTTTCAAAATGTTTTCAAAAC
1 TATATAATATATATAATTTTCAAAATGTTTTAAAAAC
*
32986 TATATACTATATATAATTTTCAAAATGTTTTAAAAAC
1 TATATAATATATATAATTTTCAAAATGTTTTAAAAAC
*
33023 TATATATTATATAT-ATTTTCAAAATGACTTTTAAAAAC
1 TATATAATATATATAATTTTCAAAATG--TTTTAAAAAC
33061 TATATAATATATA
1 TATATAATATATA
33074 AATGTTTTCG
Statistics
Matches: 110, Mismatches: 4, Indels: 15
0.85 0.03 0.12
Matches are distributed among these distances:
33 16 0.15
34 5 0.05
35 5 0.05
36 21 0.19
37 41 0.37
38 22 0.20
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
TATATAATATATATAATTTTCAAAATGTTTTAAAAAC
Found at i:33032 original size:138 final size:136
Alignment explanation
Indices: 32797--33135 Score: 359
Period size: 138 Copynumber: 2.4 Consensus size: 136
32787 ATGCTTTTTT
* * *
32797 TTTTTAAAACTATATATTATACGTATTTTCAGAAACGTTTTTAAAAAC-ATATACAATATATATA
1 TTTTCAAAACTATATATTATA---ATTTTCA-AAATG-TTTTCAAAACTATATAC--TATATATA
* * *
32861 ACTTCAAAAATATTTTTTAAAAACTATATATTATATATATTTTCAAAATGTCTTAT-ATAA-TAT
59 ACTTC-AAAATATGTTTTAAAAACTATATATTATATATATTTTCAAAATGACTTATAAAAACTAT
*
32924 ATAAATGTTTTCAAAAATG
123 AT-AA---TAT-AAAAATG
*
32943 TTTTCAAAACTATATATTATAATTTTCAAAATGTTTTCAAAACTATATACTATATATAATTTTC-
1 TTTTCAAAACTATATATTATAATTTTCAAAATGTTTTCAAAACTATATACTATATATAA-CTTCA
*
33007 AAA-ATGTTTTAAAAACTATATATTATATATATTTTCAAAATGACTTTTAAAAACTATATAATAT
65 AAATATGTTTTAAAAACTATATATTATATATATTTTCAAAATGACTTATAAAAACTATATAATAT
*
33071 ATAAATG
130 AAAAATG
* * *
33078 TTTTCGAAACTATATATTATATAATTTTTAAAAATGTTTTCAAAA-T-TATACAATATAT
1 TTTTCAAAACTATATA-T-TATAA-TTTTCAAAATGTTTTCAAAACTATATACTATATAT
33136 TTTTGAAAAA
Statistics
Matches: 173, Mismatches: 13, Indels: 24
0.82 0.06 0.11
Matches are distributed among these distances:
135 21 0.12
136 14 0.08
137 6 0.03
138 61 0.35
139 8 0.05
140 14 0.08
141 12 0.07
142 10 0.06
143 7 0.04
146 20 0.12
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (136 bp):
TTTTCAAAACTATATATTATAATTTTCAAAATGTTTTCAAAACTATATACTATATATAACTTCAA
AATATGTTTTAAAAACTATATATTATATATATTTTCAAAATGACTTATAAAAACTATATAATATA
AAAATG
Found at i:33076 original size:29 final size:27
Alignment explanation
Indices: 33051--33111 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
33041 TCAAAATGAC
33051 TTTTAAAAACTATATAATATATAAATG
1 TTTTAAAAACTATATAATATATAAATG
** *
33078 TTTTCGAAACTATATATTATAT-AAT-
1 TTTTAAAAACTATATAATATATAAATG
33103 TTTTAAAAA
1 TTTTAAAAA
33112 TGTTTTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 7 0.24
26 3 0.10
27 19 0.66
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (27 bp):
TTTTAAAAACTATATAATATATAAATG
Found at i:33090 original size:65 final size:63
Alignment explanation
Indices: 33008--33135 Score: 168
Period size: 65 Copynumber: 2.0 Consensus size: 63
32998 ATAATTTTCA
* *
33008 AAATGTTTTAAAAACTATATATTATAT-ATATTTTCAAAATGACTTTTAAAAACTATATAATATA
1 AAATGTTTTAAAAACTATATATTATATAAT-TTTTAAAAATG--TTTTAAAAACTATACAATATA
33072 T
63 T
** * *
33073 AAATGTTTTCGAAACTATATATTATATAATTTTTAAAAATGTTTTCAAAATTATACAATATAT
1 AAATGTTTTAAAAACTATATATTATATAATTTTTAAAAATGTTTTAAAAACTATACAATATAT
33136 TTTTGAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 19 0.34
65 35 0.62
66 2 0.04
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (63 bp):
AAATGTTTTAAAAACTATATATTATATAATTTTTAAAAATGTTTTAAAAACTATACAATATAT
Found at i:33116 original size:36 final size:36
Alignment explanation
Indices: 33073--33171 Score: 105
Period size: 34 Copynumber: 2.7 Consensus size: 36
33063 TATAATATAT
*
33073 AAATGTTTTCGAAACTATATATTATATAATTTTTAA
1 AAATGTTTTCAAAACTATATATTATATAATTTTTAA
**
33109 AAATGTTTTCAAAA-T-TATACAATAT-ATTTTTGAA
1 AAATGTTTTCAAAACTATATATTATATAATTTTT-AA
*
33143 AAACCGTTTTCTGAAAACTATATATTATA
1 AAA-TGTTTTC--AAAACTATATATTATA
33172 CTTTGTCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
33 6 0.12
34 13 0.25
35 7 0.14
36 13 0.25
37 4 0.08
38 1 0.02
39 7 0.14
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.43
Consensus pattern (36 bp):
AAATGTTTTCAAAACTATATATTATATAATTTTTAA
Found at i:33160 original size:138 final size:136
Alignment explanation
Indices: 32875--33171 Score: 347
Period size: 138 Copynumber: 2.2 Consensus size: 136
32865 CAAAAATATT
* * *
32875 TTTTAAAAACTATATATTATATATATTTTCAAAATGTCTTATATAATATATAAATGTTTTCAAAA
1 TTTTAAAAACTATATATTATATATATTTTCAAAATGACTTATAAAATATATAAA--TTATCAAAA
*
32940 ATGTTTTCAAAACTATATATTATAATTTTCAAAATGTTTTCAAAACTATATACTATATATAATTT
64 ATGTTTTCAAAACTATATATTATAATTTTAAAAATGTTTTCAAAACTATATACTATATATAATTT
* *
33005 TCAAAATG
129 TAAAAACG
* *
33013 TTTTAAAAACTATATATTATATATATTTTCAAAATGACTTTTAAAA-ACTATATAA-TAT-ATAA
1 TTTTAAAAACTATATATTATATATATTTTCAAAATGACTTATAAAATA-TATA-AATTATCAAAA
* *
33075 ATGTTTTCGAAACTATATATTATATAATTTTTAAAAATGTTTTCAAAA-T-TATAC-A-ATATAT
64 ATGTTTTCAAAACTATATA-T-TATAA-TTTTAAAAATGTTTTCAAAACTATATACTATATATAA
33136 TTTTGAAAAACCG
126 TTTT-AAAAA-CG
*
33149 TTTTCTGAAAACTATATATTATA
1 -TTT-TAAAAACTATATATTATA
33172 CTTTGTCAAA
Statistics
Matches: 139, Mismatches: 11, Indels: 18
0.83 0.07 0.11
Matches are distributed among these distances:
134 9 0.06
135 26 0.19
136 9 0.06
137 10 0.07
138 83 0.60
139 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (136 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAATGACTTATAAAATATATAAATTATCAAAAAT
GTTTTCAAAACTATATATTATAATTTTAAAAATGTTTTCAAAACTATATACTATATATAATTTTA
AAAACG
Found at i:33724 original size:84 final size:83
Alignment explanation
Indices: 33572--34545 Score: 1016
Period size: 84 Copynumber: 11.7 Consensus size: 83
33562 CTGAACGAAC
* * ** * *
33572 TCGAACTCGAAAGGTCTTT-GTTGACAGATAGCTTTTCTCGACTTAAGCTATACTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGGTTGGCAGATAACCCTTCTCGA-TTAAGTTATGCTGCAAATGATG
*
33636 TGCCTGGGAGCTGAGCGTAG
64 TGCCTTGGAGCTGAGCGTAG
* * * * * *
33656 TCGACCTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGATTCAAGTTGTGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATT-AAGTTATGCTGCAAATGATGT
33721 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* ** * * * *
33740 TCGAACTCGAAGATCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCG-ATTAAGTTATGCTGCAAATGATG
* * * *
33804 TGCCCTCGAAGCTGAGTGTAA
64 TG-CCTTGGAGCTGAGCGTAG
* * * * *
33825 TCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACCTAAGCTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA-TTAAGTTATGCTGCAAATGATGT
33886 GCCGTT-GAGCTGAGCGTAG
65 GCC-TTGGAGCTGAGCGTAG
* * * * * *
33905 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA-TTAAGTTATGCTGCAAATGATGT
33970 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
33989 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA-TTAAGTTATGCTGCAAATGATGT
34054 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * *
34073 TCGAACTCGAAGGTCTTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG-ATTAAGTTATGCTGCAAATGATGT
34138 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * *
34157 TCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG-ATTAAGTTATGCTGCAAATGATGT
* * *
34221 GCCCTCGAAGCTGAACGTAG
65 G-CCTTGGAGCTGAGCGTAG
* * * *
34241 TCGAACTCGAGGGTC--T--TTGGC--ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA-TTAAGTTATGCTGCAAATGATGT
34300 GCCTT-GAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * *
34318 TCGAACTCAAAGGTCTTGGGTCGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA-TTAAGTTATGCTGCAAATGATGT
* * *
34383 GCCCTTGAAGCTGAGTGTAA
65 G-CCTTGGAGCTGAGCGTAG
** * * *
34403 TCGAACTCGGGGGTC-TT--TTGGCAGGTAGCCCTTCTCGACTTAA-TCTATACTGCAAATGATG
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA-TTAAGT-TATGCTGCAAATGATG
34464 TGCCTT-GAGCTGAGCGTAG
64 TGCCTTGGAGCTGAGCGTAG
* * *
34483 TCGAACTCAAAGGTTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCCGCAAATGAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA-TTAAGTTATGCTGCAAATGAT
34546 TTGTTTAAGA
Statistics
Matches: 746, Mismatches: 114, Indels: 61
0.81 0.12 0.07
Matches are distributed among these distances:
77 24 0.03
78 3 0.00
79 30 0.04
80 46 0.06
81 49 0.07
82 42 0.06
83 130 0.17
84 366 0.49
85 56 0.08
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTAAGTTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:37927 original size:18 final size:19
Alignment explanation
Indices: 37887--37931 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
37877 AGTTAATGTG
37887 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
37906 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAACAA
37924 AATGCAAA
1 AATGCAAA
37932 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:39796 original size:6 final size:5
Alignment explanation
Indices: 39772--39811 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
39762 TATACCAAAG
*
39772 AAATA AAATA CAATA AAATTA AAATTA AAATA AAATA AAA
1 AAATA AAATA AAATA AAA-TA AAA-TA AAATA AAATA AAA
39812 AAATAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 21 0.66
6 11 0.34
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:39902 original size:20 final size:20
Alignment explanation
Indices: 39877--39935 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
39867 ATATGAGGTA
39877 AAAAAATAC-TAATAATAATT
1 AAAAAATACATAATAATAA-T
*
39897 AAAAAA-ACATGATAATAAT
1 AAAAAATACATAATAATAAT
39916 AAATAAATA-A-AATAA-AAT
1 AAA-AAATACATAATAATAAT
39934 AA
1 AA
39936 GAATTTAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 18 0.53
21 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAAATACATAATAATAAT
Found at i:39902 original size:23 final size:23
Alignment explanation
Indices: 39876--39927 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
39866 CATATGAGGT
*
39876 AAAAAAAT-ACTAATAATAATTAA
1 AAAAAAATGA-TAATAATAAATAA
*
39899 AAAAACATGATAATAATAAATAA
1 AAAAAAATGATAATAATAAATAA
*
39922 ATAAAA
1 AAAAAA
39928 TAAAATAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAAAAATGATAATAATAAATAA
Found at i:41042 original size:3 final size:3
Alignment explanation
Indices: 41027--41071 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
41017 ATAAATAGGA
*
41027 AAT AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41072 CTATATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41268 original size:70 final size:73
Alignment explanation
Indices: 41130--41374 Score: 242
Period size: 70 Copynumber: 3.4 Consensus size: 73
41120 CTTTTTTTTT
** * * * *
41130 AAACTATATATTATACGTATTTTCAGAAACGTTTTTAAAAAC-ATATACAATATATATAA-CTTC
1 AAACTATATATTATATATATTTTCA-AAATG-TCTT-AAAACTATATAC--TATAAATAATTTTC
*
41193 AAAAATATTTTTTAA
61 -AAAA-ATGTTTTAA
*
41208 AAACTATATATTATATATATTTTCAAAATGTCTT-ATA-TA-ATA-TATAAAT-ATTTTCAAAAA
1 AAACTATATATTATATATATTTTCAAAATGTCTTAAAACTATATACTATAAATAATTTTCAAAAA
*
41268 TGTTTTCA
66 TGTTTTAA
* *
41276 AAACTATATA-T-TATA-ATTTTCAAAATGTTTTCAAAACTATATACTATATATAATTTTC-AAA
1 AAACTATATATTATATATATTTTCAAAATGTCTT-AAAACTATATACTATAAATAATTTTCAAAA
41337 ATGTTTTAA
65 ATGTTTTAA
41346 AAACTATATATTATATATATTTTCAAAAT
1 AAACTATATATTATATATATTTTCAAAAT
41375 AACTTTTAAA
Statistics
Matches: 143, Mismatches: 13, Indels: 27
0.78 0.07 0.15
Matches are distributed among these distances:
65 15 0.10
66 4 0.03
67 3 0.02
68 19 0.13
69 8 0.06
70 36 0.25
71 7 0.05
72 4 0.03
73 14 0.10
74 3 0.02
76 3 0.02
77 4 0.03
78 23 0.16
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (73 bp):
AAACTATATATTATATATATTTTCAAAATGTCTTAAAACTATATACTATAAATAATTTTCAAAAA
TGTTTTAA
Found at i:41337 original size:37 final size:36
Alignment explanation
Indices: 41078--41500 Score: 225
Period size: 36 Copynumber: 11.8 Consensus size: 36
41068 TAATCTATAT
*
41078 AAAATTTTTTCAAAAAC-ATATA-ATATATAACTTTTC
1 AAAATGTTTTC-AAAACTATATATATATATAA-TTTTC
**
41114 AAAATGCTTTTTTTTTAAACTATATAT-TATACGT-ATTTTC
1 AAAATG----TTTTCAAAACTATATATATATA--TAATTTTC
* * * *
41154 AGAAACGTTTTTAAAAACATATACAATATATATAA-CTTC
1 A-AAATG-TTTTCAAAAC-TATA-TATATATATAATTTTC
* *
41193 AAAAATATTTTTTAAAAACTATATAT-TATATATATTTTC
1 --AAA-ATGTTTTCAAAACTATATATATATATA-ATTTTC
* * *
41232 AAAATGTCTT--ATA-TA-ATATATAAAT-ATTTTC
1 AAAATGTTTTCAAAACTATATATATATATAATTTTC
41263 AAAAATGTTTTCAAAAC--TATATAT-TATAATTTTC
1 -AAAATGTTTTCAAAACTATATATATATATAATTTTC
41297 AAAATGTTTTCAAAACTATATACTATATATAATTTTC
1 AAAATGTTTTCAAAACTATATA-TATATATAATTTTC
*
41334 AAAATGTTTTAAAAACTATATAT-TATATATATTTTC
1 AAAATGTTTTCAAAACTATATATATATATA-ATTTTC
* *
41370 AAAATAACTTTTAAAAAC--TATATA-ATAT-A---T-
1 AAAAT--GTTTTCAAAACTATATATATATATAATTTTC
* *
41400 -AAATGTTTTCGAAACTATATAT-TATATAATTTTTA
1 AAAATGTTTTCAAAACTATATATATATATAA-TTTTC
* * * *
41435 AAAATGTTTTCAAAATTATACA-ATATATATTTTTGA
1 AAAATGTTTTCAAAACTATATATATATATAATTTT-C
*
41471 AAAACCGTTTTCTGAAAACTATATAT-TATA
1 AAAA-TGTTTTC--AAAACTATATATATATA
41501 CTTTGTCAAA
Statistics
Matches: 307, Mismatches: 31, Indels: 95
0.71 0.07 0.22
Matches are distributed among these distances:
27 8 0.03
29 13 0.04
30 1 0.00
31 7 0.02
32 13 0.04
33 24 0.08
34 18 0.06
35 14 0.05
36 63 0.21
37 46 0.15
38 22 0.07
39 32 0.10
40 34 0.11
41 11 0.04
42 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (36 bp):
AAAATGTTTTCAAAACTATATATATATATAATTTTC
Found at i:41356 original size:138 final size:135
Alignment explanation
Indices: 41130--41500 Score: 358
Period size: 138 Copynumber: 2.6 Consensus size: 135
41120 CTTTTTTTTT
* * *
41130 AAACTATATATTATACGTATTTTCAGAAACGTTTTTAAAAAC-ATATACAATATATATAA-CTTC
1 AAACTATATATTATA---ATTTTCA-AAATG-TTTTCAAAACTATATAC--TATATATAATTTTC
* ** *
41193 AAAAATATTTTTTAAAAACTATATATTATATATATTTTCAAAATGTCTTAT-ATAA-TATATAAA
59 --AAA-ATGTTTTAAAAACTATATATTATATATATTTTCAAAATAACTTATAAAAACTATAT-AA
41256 TATTTTCAAAAATGTTTTCA
120 TA---T-AAAAATGTTTTCA
41276 AAACTATATATTATAATTTTCAAAATGTTTTCAAAACTATATACTATATATAATTTTCAAAATGT
1 AAACTATATATTATAATTTTCAAAATGTTTTCAAAACTATATACTATATATAATTTTCAAAATGT
* *
41341 TTTAAAAACTATATATTATATATATTTTCAAAATAACTTTTAAAAACTATATAATATATAAATGT
66 TTTAAAAACTATATATTATATATATTTTCAAAATAACTTATAAAAACTATATAATATAAAAATGT
*
41406 TTTCG
131 TTTCA
* * * *
41411 AAACTATATATTATATAATTTTTAAAAATGTTTTCAAAA-T-TATACAATATATATTTTTGAAAA
1 AAACTATATA-T-TATAA-TTTTCAAAATGTTTTCAAAACTATATACTATATATAATTTT-CAAA
* *
41474 ACCGTTTTCTGAAAACTATATATTATA
62 A-TG-TTT-TAAAAACTATATATTATA
41501 CTTTGTCAAA
Statistics
Matches: 198, Mismatches: 16, Indels: 28
0.82 0.07 0.12
Matches are distributed among these distances:
135 21 0.11
136 18 0.09
137 10 0.05
138 61 0.31
139 13 0.07
140 31 0.16
141 12 0.06
142 10 0.05
143 7 0.04
146 15 0.08
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (135 bp):
AAACTATATATTATAATTTTCAAAATGTTTTCAAAACTATATACTATATATAATTTTCAAAATGT
TTTAAAAACTATATATTATATATATTTTCAAAATAACTTATAAAAACTATATAATATAAAAATGT
TTTCA
Found at i:41408 original size:27 final size:25
Alignment explanation
Indices: 41373--41438 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 25
41363 TATTTTCAAA
*
41373 ATAACTTTTAAAAACTATATAATAT
1 ATAATTTTTAAAAACTATATAATAT
** *
41398 ATAAATGTTTTCGAAACTATATATTAT
1 AT-AAT-TTTTAAAAACTATATAATAT
41425 ATAATTTTTAAAAA
1 ATAATTTTTAAAAA
41439 TGTTTTCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 9 0.27
26 5 0.15
27 19 0.58
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (25 bp):
ATAATTTTTAAAAACTATATAATAT
Found at i:41417 original size:65 final size:63
Alignment explanation
Indices: 41335--41463 Score: 168
Period size: 65 Copynumber: 2.0 Consensus size: 63
41325 ATAATTTTCA
*
41335 AAATGTTTTAAAAACTATATATTATATATATTTTCAAAATAACTTTTAAAAACTATATAATATAT
1 AAATGTTTTAAAAACTATATATTATATA-ATTTTCAAAA-AACTTTTAAAAACTATACAATATAT
** * ** * *
41400 AAATGTTTTCGAAACTATATATTATATAATTTTTAAAAATGTTTTCAAAATTATACAATATAT
1 AAATGTTTTAAAAACTATATATTATATAATTTTCAAAAAACTTTTAAAAACTATACAATATAT
41463 A
1 A
41464 TTTTTGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 21 0.38
64 9 0.16
65 26 0.46
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (63 bp):
AAATGTTTTAAAAACTATATATTATATAATTTTCAAAAAACTTTTAAAAACTATACAATATAT
Found at i:41443 original size:36 final size:36
Alignment explanation
Indices: 41400--41517 Score: 114
Period size: 36 Copynumber: 3.2 Consensus size: 36
41390 TATAATATAT
41400 AAATGTTTTCGAAACTATATATTATATAATTTTT-AA
1 AAATGTTTTCGAAACTATATATTATAT-ATTTTTGAA
* * * *
41436 AAATGTTTTCAAAATTATACAATATATATTTTTGAA
1 AAATGTTTTCGAAACTATATATTATATATTTTTGAA
* * * *
41472 AAACCGTTTTCTGAAAACTATATATTATA-CTTTGTCAA
1 AAA-TGTTTTC-G-AAACTATATATTATATATTTTTGAA
41510 AAATGTTT
1 AAATGTTT
41518 GAGAAAAAAG
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
35 6 0.09
36 28 0.43
37 10 0.15
38 9 0.14
39 12 0.18
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (36 bp):
AAATGTTTTCGAAACTATATATTATATATTTTTGAA
Found at i:41535 original size:2 final size:2
Alignment explanation
Indices: 41530--41585 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
41520 GAAAAAAGAC
41530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41572 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
41586 AAAAGAAATC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49938 original size:31 final size:30
Alignment explanation
Indices: 49892--49969 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
49882 TTCGATAATA
*
49892 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
49923 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
49954 TAATAAGTATTTTATA
1 TAATAA-TATTTTATA
49970 CTTTTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.03
31 34 0.85
32 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:49977 original size:31 final size:29
Alignment explanation
Indices: 49892--49978 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 29
49882 TTCGATAATA
* *
49892 TAATAATTATTTTATAGTATTTAGATAAATT
1 TAATAA-TATTTTATATTTTTTA-ATAAATT
* *
49923 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTAT-ATTTTTTAATAAATT
49954 TAATAAGTATTTTATACTTTTTTAA
1 TAATAA-TATTTTATA-TTTTTTAA
49979 ACTTTATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
30 2 0.04
31 38 0.83
32 6 0.13
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (29 bp):
TAATAATATTTTATATTTTTTAATAAATT
Found at i:56013 original size:2 final size:2
Alignment explanation
Indices: 56006--56030 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55996 TTATGTTTTA
56006 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
56031 AAACGACTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59584 original size:51 final size:51
Alignment explanation
Indices: 59468--59724 Score: 170
Period size: 52 Copynumber: 4.9 Consensus size: 51
59458 AATGACGGGT
59468 CTGCTCCCTATTC-TTCAGGGAGTACAAGACTCGAACAATCTTCAACAAACGTA
1 CTGCTCCCTATTCATTCAGGGAGTA-AAGACTCGAACAA--TTCAACAAACGTA
* * * ** *
59521 TTGCTCCCTATTCATTCAGGGAGTAGAGACTCGAACAATTCAATAATGGGTC
1 CTGCTCCCTATTCATTCAGGGAGTAAAGACTCGAACAATTCAACAA-ACGTA
* * *
59573 CT-CTCCCTATTCATTCAGGGAGTATAGAACTCGAGCAATCTTCAACAAACG-G
1 CTGCTCCCTATTCATTCAGGGAGTAAAG-ACTCGAACAA--TTCAACAAACGTA
* * * *
59625 GT-CTCCCTATTTC-TTCAGAGAGTATAGGACTCGATC--TTCAACAAACGT-
1 CTGCTCCCTA-TTCATTCAGGGAGTA-AAGACTCGAACAATTCAACAAACGTA
* * * * * *
59673 GTGCTCTCTTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAAC
1 CTGCTC-CCTATTCATTCAGGGAGTA-AAGACTCGAACAA--TTCAACAAAC
59725 ATGTTCACTC
Statistics
Matches: 168, Mismatches: 21, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
48 13 0.08
49 6 0.04
50 24 0.14
51 31 0.18
52 37 0.22
53 29 0.17
54 28 0.17
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (51 bp):
CTGCTCCCTATTCATTCAGGGAGTAAAGACTCGAACAATTCAACAAACGTA
Found at i:59635 original size:52 final size:52
Alignment explanation
Indices: 59469--59862 Score: 241
Period size: 53 Copynumber: 7.6 Consensus size: 52
59459 ATGACGGGTC
* **
59469 TGCTCCCTATTCTTCAGGGAGTACA-AGACTCGAACAATCTTCAACAAACGTAT
1 TGCTCCCTATTCTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACG-GG
* * *
59522 TGCTCCCTATTCATTCAGGGAGTAGAG-ACTCGAACAA--TTCAA-TAATGGG
1 TGCTCCCTATTC-TTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGG
* *
59571 TCCTCTCCCTATTCATTCAGGGAGTATAGAACTCGAGCAATCTTCAACAAACGGG
1 T--GCTCCCTATTC-TTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGG
* * *
59626 T-CTCCCTATTTCTTCAGAGAGTATAGGACTCG----ATCTTCAACAAACGTG
1 TGCTCCCTA-TTCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGG
* * * * * *
59674 TGCTCTCTTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACATGT
1 TGCTC-CCTATT-CTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAAC-GGG
* * * * * * *
59729 TCACTCTCTATTCCTTTAGAGAGTATAGGACT----CTATCTTCAACAAACGTG
1 T-GCTCCCTATT-CTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGG
* * * * *
59779 TTCT-CCTATTCCTTCA--GAGTATGGGACTTGAACAATCTTCAACAAACGTG
1 TGCTCCCTATT-CTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGG
*
59829 TCCGCTCCCTATTCCTTCA--GAGTATAGGACTCGA
1 T--GCTCCCTATT-CTTCAGGGAGTATAGAACTCGA
59863 TCTCATAAAA
Statistics
Matches: 282, Mismatches: 34, Indels: 50
0.77 0.09 0.14
Matches are distributed among these distances:
46 11 0.04
48 26 0.09
49 8 0.03
50 45 0.16
51 43 0.15
52 36 0.13
53 50 0.18
54 30 0.11
55 30 0.11
56 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (52 bp):
TGCTCCCTATTCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGG
Found at i:59700 original size:50 final size:49
Alignment explanation
Indices: 59608--59865 Score: 258
Period size: 50 Copynumber: 5.1 Consensus size: 49
59598 AGAACTCGAG
* *
59608 CAATCTTCAACAAACGGGTCTC-CCTATTTCTTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACGTGTCTCTCCTATTCCTTCAGAGAGTATAGGACT
* *
59656 CGATCTTCAACAAACGTGTGCTCTCTTATTCCTTCAGAGAGTATAGGACTT
1 CAATCTTCAACAAACGTGT-CTCTCCTATTCCTTCAGAGAGTATAGGAC-T
* * *
59707 GAACAATCTTCAACAAACATGTTCACTCTCTATTCCTTTAGAGAGTATAGGACT
1 ---CAATCTTCAACAAACGTG-TCTCTC-CTATTCCTTCAGAGAGTATAGGACT
* *
59761 CTATCTTCAACAAACGTGT-TCTCCTATTCCTTC--AGAGTATGGGACTT
1 CAATCTTCAACAAACGTGTCTCTCCTATTCCTTCAGAGAGTATAGGAC-T
*
59808 GAACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTC--AGAGTATAGGACT
1 ---CAATCTTCAACAAACGTGT-CTCT-CCTATTCCTTCAGAGAGTATAGGACT
*
59860 CGATCT
1 CAATCT
59866 CATAAAATGA
Statistics
Matches: 177, Mismatches: 18, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
46 11 0.06
47 1 0.01
48 26 0.15
49 11 0.06
50 42 0.24
51 17 0.10
52 3 0.02
53 22 0.12
54 21 0.12
55 23 0.13
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (49 bp):
CAATCTTCAACAAACGTGTCTCTCCTATTCCTTCAGAGAGTATAGGACT
Found at i:59843 original size:101 final size:101
Alignment explanation
Indices: 59495--59865 Score: 360
Period size: 105 Copynumber: 3.6 Consensus size: 101
59485 GGGAGTACAA
* * * * * * * *
59495 GACTCGAACAATCTTCAACAAACGTATTGCTCCCTATTCATTCAGGGAGTAGA-GACTCGAACAA
1 GACTTGAACAATCTTCAACAAACGT-GTCCTCCCTATTCCTTTAGAGAGTATAGGACTCGATC--
* * * * *
59559 TTCAA-TAATGGGTCCTCTCCCTATTCATTCAGGGAGTATAG
63 TTCAACAAACGTGT-CTCT-CCTATTCCTTCA-AGAGTATAG
* * * * * *
59600 AACTCGAGCAATCTTCAACAAACGGGT-CTCCCTATTTCTTCAGAGAGTATAGGACTCGATCTTC
1 GACTTGAACAATCTTCAACAAACGTGTCCTCCCTATTCCTTTAGAGAGTATAGGACTCGATCTTC
*
59664 AACAAACGTGTGCTCTCTTATTCCTTCAGAGAGTATAG
66 AACAAACGTGT-CTCTCCTATTCCTTCA-AGAGTATAG
* * *
59702 GACTTGAACAATCTTCAACAAACATGTTCACTCTCTATTCCTTTAGAGAGTATAGGACTCTATCT
1 GACTTGAACAATCTTCAACAAACGTG-TC-CTCCCTATTCCTTTAGAGAGTATAGGACTCGATCT
*
59767 TCAACAAACGTGT-TCTCCTATTCCTTC-AGAGTATGG
64 TCAACAAACGTGTCTCTCCTATTCCTTCAAGAGTATAG
*
59803 GACTTGAACAATCTTCAACAAACGTGTCCGCTCCCTATTCC-TT-CAGAGTATAGGACTCGATCT
1 GACTTGAACAATCTTCAACAAACGTGT-C-CTCCCTATTCCTTTAGAGAGTATAGGACTCGATCT
59866 CATAAAATGA
Statistics
Matches: 228, Mismatches: 32, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
99 18 0.08
100 3 0.01
101 44 0.19
102 45 0.20
103 43 0.19
104 9 0.04
105 66 0.29
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (101 bp):
GACTTGAACAATCTTCAACAAACGTGTCCTCCCTATTCCTTTAGAGAGTATAGGACTCGATCTTC
AACAAACGTGTCTCTCCTATTCCTTCAAGAGTATAG
Found at i:59981 original size:71 final size:71
Alignment explanation
Indices: 59872--60052 Score: 253
Period size: 71 Copynumber: 2.5 Consensus size: 71
59862 ATCTCATAAA
*
59872 ATGAGTTTGCTTCACTGCTCTTTGTGAAGGCTTATAGATGATTTGCTTCACTACTC-TTGTG-AG
1 ATGA-TTTGCTTCACTGCTCTTCGTGAAGGCTTATAGATGATTTGCTTCACTACTCTTTGTGAAG
59935 GCTTATAG
65 GCTTA-AG
*
59943 ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTATAGATGATTTGCTTCACTACTCTTTGTGAAG
1 ATGATTTGCTTCACTGCTCTT-CGTGAAGGCTTATAGATGATTTGCTTCACTACTCTTTGTGAAG
60008 GCTTAAG
65 GCTTAAG
* *
60015 ATTGAATTGC-TCACTGCTCTTTCATGAAGGCTTA-AGAT
1 A-TGATTTGCTTCACTGCTC-TTCGTGAAGGCTTATAGAT
60053 TGACTTGTTT
Statistics
Matches: 100, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
70 16 0.16
71 41 0.41
72 27 0.27
73 16 0.16
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (71 bp):
ATGATTTGCTTCACTGCTCTTCGTGAAGGCTTATAGATGATTTGCTTCACTACTCTTTGTGAAGG
CTTAAG
Found at i:60055 original size:36 final size:36
Alignment explanation
Indices: 59872--60052 Score: 246
Period size: 36 Copynumber: 5.1 Consensus size: 36
59862 ATCTCATAAA
*
59872 ATGAGTTTGCTTCACTGCTCTTTGTGAAGGCTTATAG
1 ATGA-TTTGCTTCACTACTCTTTGTGAAGGCTTATAG
59909 ATGATTTGCTTCACTACTC-TTGTG-AGGCTTATAG
1 ATGATTTGCTTCACTACTCTTTGTGAAGGCTTATAG
*
59943 ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTATAG
1 ATGATTTGCTTCACTACTCTT-TGTGAAGGCTTATAG
59980 ATGATTTGCTTCACTACTCTTTGTGAAGGCTTA-AG
1 ATGATTTGCTTCACTACTCTTTGTGAAGGCTTATAG
* * *
60015 ATTGAATTGC-TCACTGCTCTTTCATGAAGGCTTA-AG
1 A-TGATTTGCTTCACTACTCTTT-GTGAAGGCTTATAG
60051 AT
1 AT
60053 TGACTTGTTT
Statistics
Matches: 133, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
34 29 0.22
35 21 0.16
36 48 0.36
37 35 0.26
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (36 bp):
ATGATTTGCTTCACTACTCTTTGTGAAGGCTTATAG
Done.