Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005426.1 Kokia drynarioides strain JFW-HI SEQ_119452, 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: 40314
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Found at i:4196 original size:11 final size:11
Alignment explanation
Indices: 4180--4255 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
4170 TTTAATATTC
4180 TTAATATTAAA
1 TTAATATTAAA
4191 TTAATA--AAA
1 TTAATATTAAA
*
4200 -TACTATTAAA
1 TTAATATTAAA
*
4210 ATAAGTATTAAA
1 TTAA-TATTAAA
4222 TTAA-ATTTAATA
1 TTAATA-TTAA-A
4234 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
4247 ATAATATTA
1 TTAATATTA
4256 TTTTTGGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:4242 original size:37 final size:36
Alignment explanation
Indices: 4180--4255 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
4170 TTTAATATTC
4180 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
4217 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
4253 TTA
1 TTA
4256 TTTTTGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:5721 original size:20 final size:21
Alignment explanation
Indices: 5698--5745 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
5688 TCGAACATTT
5698 GTGCCCCTAT-TTGCACTTTG
1 GTGCCCCTATCTTGCACTTTG
*
5718 GTGCTCCTATCTTGCACTTATG
1 GTGCCCCTATCTTGCACTT-TG
*
5740 ATGCCC
1 GTGCCC
5746 TTGAAATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 9 0.39
21 8 0.35
22 6 0.26
ACGTcount: A:0.12, C:0.31, G:0.19, T:0.38
Consensus pattern (21 bp):
GTGCCCCTATCTTGCACTTTG
Found at i:7686 original size:25 final size:25
Alignment explanation
Indices: 7648--7813 Score: 172
Period size: 25 Copynumber: 6.6 Consensus size: 25
7638 TTATTCTAAT
* *
7648 TTTGGCTCGAAAGAGCGATATTATG
1 TTTGGCTCGTAAGAGCGATATTCTG
* *
7673 TTTGGCTCATAAGAGCGATATT-TT
1 TTTGGCTCGTAAGAGCGATATTCTG
* *
7697 TTCTGGCTTGTAAGAGTGATATTCTG
1 TT-TGGCTCGTAAGAGCGATATTCTG
* *
7723 ATTGGCTCGTAAGAGCGATATTCTA
1 TTTGGCTCGTAAGAGCGATATTCTG
* *
7748 TTTGGCTCGTAAGAGTGATATTATG
1 TTTGGCTCGTAAGAGCGATATTCTG
* * *
7773 TCTAGCTCGTACGAGCGATATTCTG
1 TTTGGCTCGTAAGAGCGATATTCTG
** *
7798 ACTGGCTCATAAGAGC
1 TTTGGCTCGTAAGAGC
7814 TAAACTCTGT
Statistics
Matches: 115, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
24 3 0.03
25 110 0.96
26 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
TTTGGCTCGTAAGAGCGATATTCTG
Found at i:7712 original size:50 final size:50
Alignment explanation
Indices: 7621--7796 Score: 194
Period size: 50 Copynumber: 3.5 Consensus size: 50
7611 GTAATTTGAT
* * * *
7621 TTTGGCTCG-AAGGAACGTTATTCTAATTTTGGCTCGAAAGAGCGATATTATG
1 TTTGGCTCGTAA-GAGCGATATTCT-A-TTTGGCTCGTAAGAGTGATATTATG
* * * *
7673 TTTGGCTCATAAGAGCGATATT-TTTTCTGGCTTGTAAGAGTGATATTCTG
1 TTTGGCTCGTAAGAGCGATATTCTATT-TGGCTCGTAAGAGTGATATTATG
*
7723 ATTGGCTCGTAAGAGCGATATTCTATTTGGCTCGTAAGAGTGATATTATG
1 TTTGGCTCGTAAGAGCGATATTCTATTTGGCTCGTAAGAGTGATATTATG
* * *
7773 TCTAGCTCGTACGAGCGATATTCT
1 TTTGGCTCGTAAGAGCGATATTCT
7797 GACTGGCTCA
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 2 0.02
50 80 0.77
51 4 0.04
52 16 0.15
53 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (50 bp):
TTTGGCTCGTAAGAGCGATATTCTATTTGGCTCGTAAGAGTGATATTATG
Found at i:7740 original size:75 final size:75
Alignment explanation
Indices: 7649--7813 Score: 213
Period size: 75 Copynumber: 2.2 Consensus size: 75
7639 TATTCTAATT
* * * * * * *
7649 TTGGCTCGAAAGAGCGATATTATGTTTGGCTCATAAGAGCGATATTTTTTCTGGCTTGTAAGAGT
1 TTGGCTCGTAAGAGCGATATTATATTTGGCTCATAAGAGCGATATTATGTCTAGCTCGTAAGAGC
7714 GATATTCTGA
66 GATATTCTGA
* * * *
7724 TTGGCTCGTAAGAGCGATATTCTATTTGGCTCGTAAGAGTGATATTATGTCTAGCTCGTACGAGC
1 TTGGCTCGTAAGAGCGATATTATATTTGGCTCATAAGAGCGATATTATGTCTAGCTCGTAAGAGC
7789 GATATTCTGA
66 GATATTCTGA
* *
7799 CTGGCTCATAAGAGC
1 TTGGCTCGTAAGAGC
7814 TAAACTCTGT
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (75 bp):
TTGGCTCGTAAGAGCGATATTATATTTGGCTCATAAGAGCGATATTATGTCTAGCTCGTAAGAGC
GATATTCTGA
Found at i:13877 original size:35 final size:36
Alignment explanation
Indices: 13764--13960 Score: 186
Period size: 35 Copynumber: 5.5 Consensus size: 36
13754 TTTATCTGAT
* * *
13764 TAGTGCTAGGCACACA-ACTTGTTGGTTTATCCAAC
1 TAGTGCTGGGCGCACATATTTGTTGGTTTATCCAAC
* *
13799 TAGTGCTGGGCACACA-ACTTGTTGGTTTATCCAAC
1 TAGTGCTGGGCGCACATATTTGTTGGTTTATCCAAC
* *
13834 TAGTGCTGGGCGCA-ATATTTGTTTGTATATCCAAC
1 TAGTGCTGGGCGCACATATTTGTTGGTTTATCCAAC
* * *
13869 TAGAGCTGGGCTCACATTTTATATTGTCGGTTTATCCAAC
1 TAGTGCTGGGCGCACA---TAT-TTGTTGGTTTATCCAAC
* * * *
13909 TAGTGTTGGACGCA-ATATTTGTTGATATATCCAAC
1 TAGTGCTGGGCGCACATATTTGTTGGTTTATCCAAC
* *
13944 TAGAGCTGGGCTCACAT
1 TAGTGCTGGGCGCACAT
13961 TTTATATCGT
Statistics
Matches: 134, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
34 1 0.01
35 99 0.74
36 6 0.04
39 4 0.03
40 24 0.18
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (36 bp):
TAGTGCTGGGCGCACATATTTGTTGGTTTATCCAAC
Found at i:13905 original size:40 final size:40
Alignment explanation
Indices: 13861--13994 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 40
13851 TTTGTTTGTA
*
13861 TATCCAACTAGAGCTGGGCTCACATTTTATATTGTCGGTT
1 TATCCAACTAGAGCTGGGCTCACATTTTATATTGTCGATT
* * * * * *
13901 TATCCAACTAGTGTTGGACGCA-A---TAT-TTGTTGATA
1 TATCCAACTAGAGCTGGGCTCACATTTTATATTGTCGATT
*
13936 TATCCAACTAGAGCTGGGCTCACATTTTATATCGTCGATT
1 TATCCAACTAGAGCTGGGCTCACATTTTATATTGTCGATT
*
13976 TATCCAACTAGCGCTGGGC
1 TATCCAACTAGAGCTGGGC
13995 ACAAACTCTT
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
35 24 0.32
36 4 0.05
39 4 0.05
40 42 0.57
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (40 bp):
TATCCAACTAGAGCTGGGCTCACATTTTATATTGTCGATT
Found at i:13924 original size:75 final size:75
Alignment explanation
Indices: 13817--13992 Score: 282
Period size: 75 Copynumber: 2.3 Consensus size: 75
13807 GGCACACAAC
* *
13817 TTGTTGGTTTATCCAACTAGTGCTGGGCGCAATATTTGTTTG-TATATCCAACTAGAGCTGGGCT
1 TTGTCGGTTTATCCAACTAGTGCTGGACGCAATATTTG-TTGATATATCCAACTAGAGCTGGGCT
13881 CACATTTTATA
65 CACATTTTATA
*
13892 TTGTCGGTTTATCCAACTAGTGTTGGACGCAATATTTGTTGATATATCCAACTAGAGCTGGGCTC
1 TTGTCGGTTTATCCAACTAGTGCTGGACGCAATATTTGTTGATATATCCAACTAGAGCTGGGCTC
13957 ACATTTTATA
66 ACATTTTATA
* * *
13967 TCGTCGATTTATCCAACTAGCGCTGG
1 TTGTCGGTTTATCCAACTAGTGCTGG
13993 GCACAAACTC
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 3 0.03
75 90 0.97
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (75 bp):
TTGTCGGTTTATCCAACTAGTGCTGGACGCAATATTTGTTGATATATCCAACTAGAGCTGGGCTC
ACATTTTATA
Found at i:14795 original size:2 final size:2
Alignment explanation
Indices: 14788--14831 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
14778 CAAAGTATGA
14788 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
14830 AT
1 AT
14832 TAACCTTGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21560 original size:20 final size:20
Alignment explanation
Indices: 21535--21611 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
21525 GAAGTGCCCT
**
21535 TGTTTGCACTTTGGTGTTTC
1 TGTTTGCACTTTGGTGCATC
* *
21555 TGTTTGCACTTCGGTGCCTC
1 TGTTTGCACTTTGGTGCATC
*
21575 TATTTGCACAATTT-GTGCATC
1 TGTTTGCAC--TTTGGTGCATC
21596 TGTTTGCACTTTGGTG
1 TGTTTGCACTTTGGTG
21612 TCCTTGTCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.06
20 28 0.60
21 14 0.30
22 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.47
Consensus pattern (20 bp):
TGTTTGCACTTTGGTGCATC
Found at i:25151 original size:22 final size:22
Alignment explanation
Indices: 25109--25152 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
25099 GTAACAAAGA
**
25109 TTTTAATTTAACATGTTTAATT
1 TTTTAATTTAACATGAATAATT
25131 TTTTAATTTAAC-TCGAATAATT
1 TTTTAATTTAACAT-GAATAATT
25153 CCACTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTTAATTTAACATGAATAATT
Found at i:26804 original size:22 final size:22
Alignment explanation
Indices: 26779--26827 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
26769 TGATCTTTCT
26779 TTCAACAAAAAT-TATAAAAAAA
1 TTCAA-AAAAATCTATAAAAAAA
*
26801 TTCAAAAAAATCT-T-TAAAAA
1 TTCAAAAAAATCTATAAAAAAA
26821 TTCAAAA
1 TTCAAAA
26828 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 12 0.48
21 7 0.28
22 6 0.24
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (22 bp):
TTCAAAAAAATCTATAAAAAAA
Found at i:26819 original size:19 final size:20
Alignment explanation
Indices: 26796--26845 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
26786 AAAATTATAA
26796 AAAAATTCAAAAAAATCTTT
1 AAAAATTCAAAAAAATCTTT
*
26816 AAAAATTCAAAATAAT-TTT
1 AAAAATTCAAAAAAATCTTT
*
26835 TAAAATTCAAA
1 AAAAATTCAAA
26846 TTATTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCAAAAAAATCTTT
Found at i:26858 original size:19 final size:18
Alignment explanation
Indices: 26813--26867 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
26803 CAAAAAAATC
*
26813 TTTAAAAATTCAAAATAAT
1 TTTAAAAATTC-AAATTAT
*
26832 TTTTAAAATTCAAATTAT
1 TTTAAAAATTCAAATTAT
26850 TTATAAAAATTACAAATT
1 TT-TAAAAATT-CAAATT
26868 TTATATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.26
19 17 0.55
20 6 0.19
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTAAAAATTCAAATTAT
Found at i:28715 original size:30 final size:31
Alignment explanation
Indices: 28681--28741 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
28671 TTGAATTTGA
*
28681 GAATATATTGGA-TTCTTTTTTTGTT-TTTTT
1 GAATAT-TTGGAGTTCTTTGTTTGTTATTTTT
*
28711 GAATATTTTGAGTTCTTTGTTTGTTATTTTT
1 GAATATTTGGAGTTCTTTGTTTGTTATTTTT
28742 TCTTTGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 4 0.15
30 18 0.67
31 5 0.19
ACGTcount: A:0.16, C:0.03, G:0.15, T:0.66
Consensus pattern (31 bp):
GAATATTTGGAGTTCTTTGTTTGTTATTTTT
Found at i:28749 original size:36 final size:35
Alignment explanation
Indices: 28704--28786 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 35
28694 TCTTTTTTTG
*
28704 TTTTTTTGAAT-ATTTTGAGTTCTTTGTTTGTTATT
1 TTTTTTTGAATGA-GTTGAGTTCTTTGTTTGTTATT
*
28739 TTTTCTTTGAATGAGTTGGGTTCTTTGTTTGTTATT
1 TTTT-TTTGAATGAGTTGAGTTCTTTGTTTGTTATT
28775 TGTTTTTT-AATG
1 T-TTTTTTGAATG
28787 GAGGCTGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 8 0.19
36 31 0.72
37 4 0.09
ACGTcount: A:0.13, C:0.04, G:0.18, T:0.65
Consensus pattern (35 bp):
TTTTTTTGAATGAGTTGAGTTCTTTGTTTGTTATT
Found at i:28888 original size:21 final size:21
Alignment explanation
Indices: 28863--28909 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
28853 CTAACTATCC
28863 AAAAACTGAA-A-AAAAAGAGAA
1 AAAAACTGAATACAAAAA-A-AA
*
28884 AAAAATTGAATACAAAAAAAA
1 AAAAACTGAATACAAAAAAAA
28905 AAAAA
1 AAAAA
28910 GATAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 16 0.70
22 2 0.09
23 5 0.22
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAAACTGAATACAAAAAAAA
Found at i:29875 original size:14 final size:14
Alignment explanation
Indices: 29856--29917 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
29846 TTTAAAATTA
29856 TTAAAATTATTTTT
1 TTAAAATTATTTTT
*
29870 TTAAAATATAAATTTT
1 TTAAAAT-T-ATTTTT
29886 TTAAAATTA---TT
1 TTAAAATTATTTTT
29897 TTAAAATTATTTTT
1 TTAAAATTATTTTT
*
29911 TAAAAAT
1 TTAAAAT
29918 ATAAAATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
11 11 0.27
14 16 0.39
15 2 0.05
16 12 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAAATTATTTTT
Found at i:29893 original size:39 final size:40
Alignment explanation
Indices: 29845--29933 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 40
29835 TAGCAAATGA
* *
29845 TTTTAAAATTA-TTAAAATTATTTTTTTAAAATATAAATT
1 TTTTAAAATTATTTAAAATTATTTTTTAAAAATATAAAAT
29884 TTTTAAAATTATTTTAAAATTATTTTTTAAAAATATAAAAT
1 TTTTAAAATTA-TTTAAAATTATTTTTTAAAAATATAAAAT
*
29925 TATTAAAAT
1 TTTTAAAAT
29934 CATCATCTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 11 0.24
41 34 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
TTTTAAAATTATTTAAAATTATTTTTTAAAAATATAAAAT
Found at i:29900 original size:11 final size:11
Alignment explanation
Indices: 29879--29909 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
29869 TTTAAAATAT
29879 AAATT-TTTTA
1 AAATTATTTTA
29889 AAATTATTTTA
1 AAATTATTTTA
29900 AAATTATTTT
1 AAATTATTTT
29910 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:30968 original size:12 final size:12
Alignment explanation
Indices: 30951--30980 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30941 AAATTAAAAT
30951 GATGAAGAAGAA
1 GATGAAGAAGAA
*
30963 GATGAAGAAGAT
1 GATGAAGAAGAA
30975 GATGAA
1 GATGAA
30981 ATTGGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (12 bp):
GATGAAGAAGAA
Found at i:31044 original size:22 final size:22
Alignment explanation
Indices: 31001--31044 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
30991 AAAATTATTT
*
31001 AATAATTTTATTATTTCAAAAA
1 AATAATTTTATAATTTCAAAAA
*
31023 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATAATTTCAAAA
31045 TCATTTACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTATAATTTCAAAAA
Found at i:32959 original size:24 final size:24
Alignment explanation
Indices: 32910--32991 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 24
32900 ATAAGCTGAT
** * *
32910 GAGCATAAATATGTGCAAGTTGGC
1 GAGCATAAACGTGTGCAAGCTAGC
32934 GAGCATAAACGTGTGCAAGCTAGC
1 GAGCATAAACGTGTGCAAGCTAGC
*
32958 GAG-AGTAAACGTATGCAAGCTAGC
1 GAGCA-TAAACGTGTGCAAGCTAGC
32982 GAGCATAAAC
1 GAGCATAAAC
32992 ACATATATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
23 1 0.02
24 49 0.96
25 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (24 bp):
GAGCATAAACGTGTGCAAGCTAGC
Found at i:38470 original size:24 final size:24
Alignment explanation
Indices: 38443--38517 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
38433 ACACATATAT
*
38443 AAGTTGTCGAGCATAAACATGTGC
1 AAGTTGACGAGCATAAACATGTGC
* * * *
38467 AAGTGGAAGAGCGTAAA-ATAT--
1 AAGTTGACGAGCATAAACATGTGC
* *
38488 AAGCTGACGAGCATAAACGTGTGC
1 AAGTTGACGAGCATAAACATGTGC
38512 AAGTTG
1 AAGTTG
38518 GAGAGCGTAA
Statistics
Matches: 36, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
21 13 0.36
22 2 0.06
23 3 0.08
24 18 0.50
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.21
Consensus pattern (24 bp):
AAGTTGACGAGCATAAACATGTGC
Found at i:38560 original size:50 final size:50
Alignment explanation
Indices: 38450--38733 Score: 237
Period size: 50 Copynumber: 5.7 Consensus size: 50
38440 TATAAGTTGT
* *
38450 CGAGCATAAACATGTGCAAG-TGGAAGAGCGTAAA--AT--ATAAGCTGA
1 CGAGCATAAACGTGTGCAAGCTGGAAGAGCGTAAACCATAAATAAGCTAA
*
38495 CGAGCATAAACGTGTGCAAGTTGG-AGAGCGTAAACGCATAAATAAGCTAA
1 CGAGCATAAACGTGTGCAAGCTGGAAGAGCGTAAAC-CATAAATAAGCTAA
* * * *
38545 CGAGCATAAATGTGTGCAAGCTGGTA-AGCGTAAACACATATATAAGCTGA
1 CGAGCATAAACGTGTGCAAGCTGGAAGAGCGTAAAC-CATAAATAAGCTAA
* * *
38595 CGAGCATAGACGTGTGGAAGCTGG-TGAGCGTAAACTCATATAGATAAGCTAA
1 CGAGCATAAACGTGTGCAAGCTGGAAGAGCGTAAAC-CATA-A-ATAAGCTAA
* * * * * *
38647 CGAGCATAAATGTGTGGAAGCTGGCA-AGTGTAAATGCATATATATATAAGCTGA
1 CGAGCATAAACGTGTGCAAGCTGGAAGAGCGTAAA--C-CATA-A-ATAAGCTAA
** *
38701 CGAGTGTAAACGTGTGCAAGCT-GACGAGCGTAA
1 CGAGCATAAACGTGTGCAAGCTGGAAGAGCGTAA
38734 GCGTATTAAA
Statistics
Matches: 196, Mismatches: 29, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
45 29 0.15
46 3 0.02
48 2 0.01
50 85 0.43
51 1 0.01
52 37 0.19
53 1 0.01
54 38 0.19
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (50 bp):
CGAGCATAAACGTGTGCAAGCTGGAAGAGCGTAAACCATAAATAAGCTAA
Found at i:38680 original size:102 final size:102
Alignment explanation
Indices: 38484--38733 Score: 335
Period size: 100 Copynumber: 2.4 Consensus size: 102
38474 AGAGCGTAAA
*
38484 ATATAAGCTGACGAGCATAAACGTGTGCAAGTTGGAGAGCGTAAACGCATAAATAAGCTAACGAG
1 ATATAAGCTGACGAGCATAAACGTGTGCAAGCTGGAGAGCGTAAACGCATAAATAAGCTAACGAG
*
38549 CATAAATGTGTGCAAGCTGGTAAGCGTAAA-C-ACAT
66 CATAAATGTGTGCAAGCTGGCAAGCGTAAAGCAACAT
* * * *
38584 ATATAAGCTGACGAGCATAGACGTGTGGAAGCTGGTGAGCGTAAACTCATATAGATAAGCTAACG
1 ATATAAGCTGACGAGCATAAACGTGTGCAAGCTGGAGAGCGTAAACGCATA-A-ATAAGCTAACG
* * *
38649 AGCATAAATGTGTGGAAGCTGGCAAGTGTAAATGCATATAT
64 AGCATAAATGTGTGCAAGCTGGCAAGCGTAAA-GCA-ACAT
**
38690 ATATAAGCTGACGAGTGTAAACGTGTGCAAGCT-GACGAGCGTAA
1 ATATAAGCTGACGAGCATAAACGTGTGCAAGCTGGA-GAGCGTAA
38734 GCGTATTAAA
Statistics
Matches: 129, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
100 46 0.36
101 1 0.01
102 40 0.31
104 1 0.01
105 1 0.01
106 40 0.31
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (102 bp):
ATATAAGCTGACGAGCATAAACGTGTGCAAGCTGGAGAGCGTAAACGCATAAATAAGCTAACGAG
CATAAATGTGTGCAAGCTGGCAAGCGTAAAGCAACAT
Found at i:38716 original size:54 final size:52
Alignment explanation
Indices: 38484--38733 Score: 242
Period size: 50 Copynumber: 4.8 Consensus size: 52
38474 AGAGCGTAAA
* * *
38484 ATATAAGCTGACGAGCATAAACGTGTGCAAGTTGG-AGAGCGTAAACGCATA-
1 ATATAAGCTGACGAGCATAAACGTGTGGAAGCTGGCA-AGCGTAAACTCATAT
* * * * *
38535 A-ATAAGCTAACGAGCATAAATGTGTGCAAGCTGGTAAGCGTAAA--CACAT
1 ATATAAGCTGACGAGCATAAACGTGTGGAAGCTGGCAAGCGTAAACTCATAT
* **
38584 ATATAAGCTGACGAGCATAGACGTGTGGAAGCTGGTGAGCGTAAACTCATAT
1 ATATAAGCTGACGAGCATAAACGTGTGGAAGCTGGCAAGCGTAAACTCATAT
* * * *
38636 AGATAAGCTAACGAGCATAAATGTGTGGAAGCTGGCAAGTGTAAA-TGCATATAT
1 ATATAAGCTGACGAGCATAAACGTGTGGAAGCTGGCAAGCGTAAACT-C--ATAT
** * * *
38690 ATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGACGAGCGTAA
1 ATATAAGCTGACGAGCATAAACGTGTGGAAGCTGGCAAGCGTAA
38734 GCGTATTAAA
Statistics
Matches: 165, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
48 3 0.02
49 1 0.01
50 76 0.46
51 3 0.02
52 43 0.26
54 39 0.24
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (52 bp):
ATATAAGCTGACGAGCATAAACGTGTGGAAGCTGGCAAGCGTAAACTCATAT
Found at i:38745 original size:24 final size:24
Alignment explanation
Indices: 38694--38746 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
38684 ATATATATAT
* * *
38694 AAGCTGACGAGTGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATGA
* *
38718 AAGCTGACGAGCGTAAGCGTATTA
1 AAGCTGACGAGCGTAAACGTATGA
38742 AAGCT
1 AAGCT
38747 AGTGAGTGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTATGA
Found at i:38746 original size:102 final size:99
Alignment explanation
Indices: 38484--38747 Score: 300
Period size: 102 Copynumber: 2.6 Consensus size: 99
38474 AGAGCGTAAA
* * *
38484 ATATAAGCTGACGAGCATAAACGTGTGCAAGTTGGAGAGCGTAAACGCATAAATAAGCTAACGAG
1 ATATAAGCTGACGAGCATAAACGTGTGCAAGCT-GAGAGCGTAAACGTATATATAAGCTAACGAG
*
38549 CATAAATGTGTGCAAGCTGGTAAGCGTAAACACAT
65 CATAAATGTGTGCAAGCTGGCAAGCGTAAACACAT
* * *
38584 ATATAAGCTGACGAGCATAGACGTGTGGAAGCTGGTGAGCGTAAAC-TCATATAGATAAGCTAAC
1 ATATAAGCTGACGAGCATAAACGTGTGCAAGCT-GAGAGCGTAAACGT-ATAT--ATAAGCTAAC
* * *
38648 GAGCATAAATGTGTGGAAGCTGGCAAGTGTAAATGCATATAT
62 GAGCATAAATGTGTGCAAGCTGGCAAGCGTAAA--C--ACAT
** *
38690 ATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGACGAGCGTAAGCGTAT-TA-AAGCTA
1 ATATAAGCTGACGAGCATAAACGTGTGCAAGCTGA-GAGCGTAAACGTATATATAAGCTA
38748 GTGAGTGTAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
100 45 0.32
102 46 0.33
103 1 0.01
104 1 0.01
105 2 0.01
106 43 0.31
107 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (99 bp):
ATATAAGCTGACGAGCATAAACGTGTGCAAGCTGAGAGCGTAAACGTATATATAAGCTAACGAGC
ATAAATGTGTGCAAGCTGGCAAGCGTAAACACAT
Found at i:39979 original size:19 final size:19
Alignment explanation
Indices: 39955--39991 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39945 TGTGCCCTTG
*
39955 TTTTCTCAAACTTTTCAAC
1 TTTTCTCAAAATTTTCAAC
*
39974 TTTTCTTAAAATTTTCAA
1 TTTTCTCAAAATTTTCAA
39992 TTTGATTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTCTCAAAATTTTCAAC
Done.