Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014794.1 Kokia drynarioides strain JFW-HI SEQ_129836, 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: 232543
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 542 characters in sequence are not A, C, G, or T
Found at i:3199 original size:7 final size:7
Alignment explanation
Indices: 3187--3213 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3177 GATAATGATA
3187 ATTATTT
1 ATTATTT
3194 ATTATTT
1 ATTATTT
3201 ATTATTT
1 ATTATTT
3208 ATTATT
1 ATTATT
3214 ATAACTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTATTT
Found at i:6342 original size:22 final size:22
Alignment explanation
Indices: 6317--6359 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6307 TACGGAATGA
6317 TCTGTTAATTATTAAAATATAC
1 TCTGTTAATTATTAAAATATAC
* *
6339 TCTGTTGATTATTAAGATATA
1 TCTGTTAATTATTAAAATATA
6360 TTCAGGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (22 bp):
TCTGTTAATTATTAAAATATAC
Found at i:15701 original size:17 final size:18
Alignment explanation
Indices: 15679--15712 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
15669 TTGGTATGTG
15679 ATTTCAATGGGC-TTTTA
1 ATTTCAATGGGCGTTTTA
15696 ATTTCAATGGGCGTTTT
1 ATTTCAATGGGCGTTTT
15713 CGGAACAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (18 bp):
ATTTCAATGGGCGTTTTA
Found at i:37847 original size:24 final size:24
Alignment explanation
Indices: 37819--37869 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
37809 AGAAACAATC
* * *
37819 TTTCAGTTAAATTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
37843 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
37867 TTT
1 TTT
37870 GAATCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:38191 original size:8 final size:8
Alignment explanation
Indices: 38178--38202 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38168 ATTTGTGTGT
38178 TCAATTTC
1 TCAATTTC
38186 TCAATTTC
1 TCAATTTC
38194 TCAATTTC
1 TCAATTTC
38202 T
1 T
38203 TCCGTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAATTTC
Found at i:46126 original size:30 final size:31
Alignment explanation
Indices: 46092--46155 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
46082 ACATTCAATT
46092 ATTTAAATGAA-AATTTTTAAATAATTTAA-A
1 ATTTAAATGAATAATTTTTAAA-AATTTAATA
**
46122 ATTTAAATGAATTTTTTTTAAAAATTTAATA
1 ATTTAAATGAATAATTTTTAAAAATTTAATA
46153 ATT
1 ATT
46156 ATTTTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTTAAATGAATAATTTTTAAAAATTTAATA
Found at i:79419 original size:18 final size:20
Alignment explanation
Indices: 79396--79433 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
79386 TATTGCATAC
79396 ATAATA-AAT-TATATTTAT
1 ATAATATAATATATATTTAT
*
79414 ATAATATAATATTTATTTAT
1 ATAATATAATATATATTTAT
79434 TTATATGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAATATAATATATATTTAT
Found at i:94590 original size:22 final size:23
Alignment explanation
Indices: 94543--94590 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
94533 GTCCTTATAC
*
94543 TTTTATTTTTATAAATTTAATTA
1 TTTTATTTTTATAAATTTAATAA
*
94566 TTTTACTTTTTA-AATTTTAA-AA
1 TTTTA-TTTTTATAAATTTAATAA
94588 TTT
1 TTT
94591 AAGTCGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 12 0.55
24 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTATTTTTATAAATTTAATAA
Found at i:97616 original size:18 final size:18
Alignment explanation
Indices: 97582--97631 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
97572 CTTAAGATCC
97582 TTTCTTTCTTATC-TTTTCT
1 TTTCTTT-TT-TCTTTTTCT
97601 TTTCTTTTTTCTTTTTCT
1 TTTCTTTTTTCTTTTTCT
97619 TTT-TTTTTT-TTTT
1 TTTCTTTTTTCTTTT
97632 GTATTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.13
17 8 0.27
18 11 0.37
19 7 0.23
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTCTTTTTTCTTTTTCT
Found at i:97629 original size:13 final size:13
Alignment explanation
Indices: 97595--97629 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
97585 CTTTCTTATC
*
97595 TTTTCTTTTCTTT
1 TTTTTTTTTCTTT
*
97608 TTTCTTTTTCTTT
1 TTTTTTTTTCTTT
97621 TTTTTTTTT
1 TTTTTTTTT
97630 TTGTATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:97638 original size:23 final size:23
Alignment explanation
Indices: 97593--97638 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
97583 TTCTTTCTTA
*
97593 TCTTTTCTTTTCTTTTTTCTTTT
1 TCTTTTCTTTTCTTTTTTATTTT
*
97616 TCTTTT-TTTTTTTTTTGTATTTT
1 TCTTTTCTTTTCTTTTT-TATTTT
97639 ATACTTCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.85
Consensus pattern (23 bp):
TCTTTTCTTTTCTTTTTTATTTT
Found at i:103464 original size:24 final size:23
Alignment explanation
Indices: 103437--103482 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
103427 GAAGAAAAGA
*
103437 AACAGGTATGTTTTTGTTTTTTTT
1 AACA-GTAAGTTTTTGTTTTTTTT
*
103461 AACATTAAGTTTTTGTTTTTTT
1 AACAGTAAGTTTTTGTTTTTTT
103483 ATGTACTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.20, C:0.04, G:0.13, T:0.63
Consensus pattern (23 bp):
AACAGTAAGTTTTTGTTTTTTTT
Found at i:109276 original size:23 final size:22
Alignment explanation
Indices: 109250--109292 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
109240 TAAATCAAAA
109250 TATAATTTTATTATTTATTAATT
1 TATAATTTTA-TATTTATTAATT
*
109273 TATAATTTTATATTTTTTAA
1 TATAATTTTATATTTATTAA
109293 AAGGCTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATAATTTTATATTTATTAATT
Found at i:109880 original size:14 final size:14
Alignment explanation
Indices: 109861--109897 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
109851 AAAGGCAGAA
109861 CCCATTTCTGATTT
1 CCCATTTCTGATTT
109875 CCCATTTCTGATTT
1 CCCATTTCTGATTT
109889 CCCATTTCT
1 CCCATTTCT
109898 TCCCCTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.14, C:0.32, G:0.05, T:0.49
Consensus pattern (14 bp):
CCCATTTCTGATTT
Found at i:120526 original size:20 final size:20
Alignment explanation
Indices: 120513--120572 Score: 86
Period size: 21 Copynumber: 3.0 Consensus size: 20
120503 AAAATATTCT
120513 AAAAATAATTAAAATTATTAA
1 AAAAAT-ATTAAAATTATTAA
120534 AAAAATATTAGAAATTATTAA
1 AAAAATATTA-AAATTATTAA
*
120555 AAAAATACTAAAA-TATTA
1 AAAAATATTAAAATTATTA
120573 TTATTTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 5 0.14
20 7 0.19
21 25 0.68
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAATATTAAAATTATTAA
Found at i:121342 original size:11 final size:11
Alignment explanation
Indices: 121313--121343 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
121303 AAATGGGCAG
121313 AAGAAGAAAAA
1 AAGAAGAAAAA
121324 AAGAAAGAAAAA
1 AAG-AAGAAAAA
121336 AAGAAGAA
1 AAGAAGAA
121344 TGAGAGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAA
Found at i:121362 original size:24 final size:24
Alignment explanation
Indices: 121327--121373 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
121317 AGAAAAAAAG
121327 AAAGAAAAAAAGAAGAATGAGAGT
1 AAAGAAAAAAAGAAGAATGAGAGT
*
121351 AAAGAAAGAAAGAAGAATGAGAG
1 AAAGAAAAAAAGAAGAATGAGAG
121374 AAATGTACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAAAGAAGAATGAGAGT
Found at i:121491 original size:35 final size:35
Alignment explanation
Indices: 121399--121492 Score: 83
Period size: 35 Copynumber: 2.7 Consensus size: 35
121389 ATTTTTTAAA
*
121399 AATTTTAATTTG-TTAGTTA-GTTG--TTGTAATTTT
1 AATTTT-ATTTGTTTAG-TAGGTTGATTTGTAATTAT
* *
121432 AATTTTA-TTGTTTAATGT-GATTGATTTGTTATTAT
1 AATTTTATTTGTTT-A-GTAGGTTGATTTGTAATTAT
121467 AATTTTATTTGTTTAGTAGGTTGATT
1 AATTTTATTTGTTTAGTAGGTTGATT
121493 GATTAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
31 3 0.06
32 3 0.06
33 11 0.22
34 3 0.06
35 23 0.47
36 6 0.12
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (35 bp):
AATTTTATTTGTTTAGTAGGTTGATTTGTAATTAT
Found at i:122953 original size:30 final size:30
Alignment explanation
Indices: 122919--123040 Score: 106
Period size: 30 Copynumber: 4.1 Consensus size: 30
122909 GTTTAGTTCG
122919 TAAAATTGGATC-AAACTAAAATTTCATGTA
1 TAAAATTGGA-CAAAACTAAAATTTCATGTA
** *
122949 TAAAATTTTACAAAATTAAAATTTCATGTA
1 TAAAATTGGACAAAACTAAAATTTCATGTA
** * * *
122979 TAAAATTTTACAAAATTAAAA-CTCATGAA
1 TAAAATTGGACAAAACTAAAATTTCATGTA
* *
123008 TAAAATTGTACATTAAAC-AAAAGTTCATGTA
1 TAAAATTGGACA--AAACTAAAATTTCATGTA
123039 TA
1 TA
123041 CTTTTGAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
29 18 0.23
30 50 0.63
31 11 0.14
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (30 bp):
TAAAATTGGACAAAACTAAAATTTCATGTA
Found at i:122954 original size:14 final size:14
Alignment explanation
Indices: 122935--122986 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
122925 TGGATCAAAC
122935 TAAAATTTCATGTA
1 TAAAATTTCATGTA
**
122949 TAAAATTTTACA-AAA
1 TAAAA-TTT-CATGTA
122964 TTAAAATTTCATGTA
1 -TAAAATTTCATGTA
122979 TAAAATTT
1 TAAAATTT
122987 TACAAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 15 0.50
15 8 0.27
16 7 0.23
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (14 bp):
TAAAATTTCATGTA
Found at i:122970 original size:16 final size:16
Alignment explanation
Indices: 122949--122999 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
122939 ATTTCATGTA
122949 TAAAATTTTACAAAAT
1 TAAAATTTTACAAAAT
**
122965 TAAAA-TTT-C-ATGT
1 TAAAATTTTACAAAAT
122978 ATAAAATTTTACAAAAT
1 -TAAAATTTTACAAAAT
122995 TAAAA
1 TAAAA
123000 CTCATGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.07
14 6 0.22
15 6 0.22
16 11 0.41
17 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAATTTTACAAAAT
Found at i:123014 original size:29 final size:30
Alignment explanation
Indices: 122935--123019 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 30
122925 TGGATCAAAC
*
122935 TAAAATTTCATGTATAAAATTTTACAAAAT
1 TAAAATCTCATGTATAAAATTTTACAAAAT
*
122965 TAAAATTTCATGTATAAAATTTTACAAAAT
1 TAAAATCTCATGTATAAAATTTTACAAAAT
* *
122995 TAAAA-CTCATGAATAAAATTGTACA
1 TAAAATCTCATGTATAAAATTTTACA
123020 TTAAACAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 17 0.33
30 35 0.67
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (30 bp):
TAAAATCTCATGTATAAAATTTTACAAAAT
Found at i:125792 original size:38 final size:38
Alignment explanation
Indices: 125741--125818 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
125731 CGATAACTCC
125741 ATTACAGGACCATGCAGATTTCAGATCAGCAAGCAGCA
1 ATTACAGGACCATGCAGATTTCAGATCAGCAAGCAGCA
125779 ATTACAGGACCATGCAGATTTCAGATCAGCAAGCAGCA
1 ATTACAGGACCATGCAGATTTCAGATCAGCAAGCAGCA
125817 AT
1 AT
125819 AGTGGAACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (38 bp):
ATTACAGGACCATGCAGATTTCAGATCAGCAAGCAGCA
Found at i:125814 original size:19 final size:19
Alignment explanation
Indices: 125754--125814 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
125744 ACAGGACCAT
125754 GCAGATTTCAGATCAGCAA
1 GCAGATTTCAGATCAGCAA
* *
125773 GCAGCAATTACAGGA-C--CAT
1 GCAG--ATTTCA-GATCAGCAA
125792 GCAGATTTCAGATCAGCAA
1 GCAGATTTCAGATCAGCAA
125811 GCAG
1 GCAG
125815 CAATAGTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 2 0.06
17 6 0.19
19 16 0.50
21 6 0.19
22 2 0.06
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (19 bp):
GCAGATTTCAGATCAGCAA
Found at i:128796 original size:32 final size:30
Alignment explanation
Indices: 128752--128811 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 30
128742 TTGAACTGCA
128752 CTTAGCCATCTCTATTTAGTATTTTGAATTGG
1 CTTAGCCATCTCTA-TTA-TATTTTGAATTGG
*
128784 CTTAGCTC-TCTCTATTATGTTTTGAATT
1 CTTAGC-CATCTCTATTATATTTTGAATT
128812 ACTCTTGGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 10 0.38
31 3 0.12
32 12 0.46
33 1 0.04
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (30 bp):
CTTAGCCATCTCTATTATATTTTGAATTGG
Found at i:134413 original size:11 final size:11
Alignment explanation
Indices: 134384--134427 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
134374 AATGAAAAAT
*
134384 AATAAATTAAA
1 AATATATTAAA
134395 AATA-ATTAAA
1 AATATATTAAA
*
134405 AATATATTACA
1 AATATATTAAA
134416 AATATATATAAA
1 AATATAT-TAAA
134428 TGGAAGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 10 0.34
11 16 0.55
12 3 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
AATATATTAAA
Found at i:135895 original size:15 final size:15
Alignment explanation
Indices: 135872--135915 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
135862 ATTTGAGTTC
*
135872 AAATTTATTTTTTTA
1 AAATATATTTTTTTA
135887 AAATATATTTAATTTTA
1 AAATATATTT--TTTTA
*
135904 AAATAAATTTTT
1 AAATATATTTTT
135916 ATGGCTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATATATTTTTTTA
Found at i:137257 original size:150 final size:150
Alignment explanation
Indices: 136986--137287 Score: 559
Period size: 150 Copynumber: 2.0 Consensus size: 150
136976 TAAATAAAAT
136986 GTTAATTTTGAGAAAAATTTCGATCAATTTAATAAAAGCTAAAACATAAATTACATTAAAAAAAA
1 GTTAATTTTGAGAAAAATTTCGATCAATTTAATAAAAGCTAAAACATAAATTACATTAAAAAAAA
*
137051 TCTATGTAGACAAAAAGGAGTCTGGCACGAATCGTTAAAGAGCTATTCATAAGGGATTAACATAT
66 TCTATGTAGACAAAAAAGAGTCTGGCACGAATCGTTAAAGAGCTATTCATAAGGGATTAACATAT
137116 GAATGTAATGTTTATTCCAC
131 GAATGTAATGTTTATTCCAC
*
137136 GTTAATTTTGAGAAAGATTTCGATCAATTTAATAAAAGCTAAAACATAAATTACATTAAAAAAAA
1 GTTAATTTTGAGAAAAATTTCGATCAATTTAATAAAAGCTAAAACATAAATTACATTAAAAAAAA
* * *
137201 TCTATGTAGACAAAAAAGAGTCTGGCACGAATCGTTAGAGAGCTGTTCATAAGGGATTGACATAT
66 TCTATGTAGACAAAAAAGAGTCTGGCACGAATCGTTAAAGAGCTATTCATAAGGGATTAACATAT
137266 GAATGTAATGTTTATTCCAC
131 GAATGTAATGTTTATTCCAC
137286 GT
1 GT
137288 ACAACAAATA
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 147 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (150 bp):
GTTAATTTTGAGAAAAATTTCGATCAATTTAATAAAAGCTAAAACATAAATTACATTAAAAAAAA
TCTATGTAGACAAAAAAGAGTCTGGCACGAATCGTTAAAGAGCTATTCATAAGGGATTAACATAT
GAATGTAATGTTTATTCCAC
Found at i:137870 original size:22 final size:22
Alignment explanation
Indices: 137844--137885 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
137834 AATGAATTTT
*
137844 ATTTAAATTTATTCTAATTTAA
1 ATTTAAATATATTCTAATTTAA
*
137866 ATTTAAATATATTTTAATTT
1 ATTTAAATATATTCTAATTT
137886 CAATCTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTAAATATATTCTAATTTAA
Found at i:141384 original size:18 final size:20
Alignment explanation
Indices: 141351--141394 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
141341 CCTTTAAAAT
* *
141351 AATTTTTTTTTCATTT-T-A
1 AATTTTTTTATAATTTATAA
141369 AATTTTTTTATAATTTATAA
1 AATTTTTTTATAATTTATAA
141389 AATTTT
1 AATTTT
141395 AAATTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 1 0.05
20 7 0.32
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
AATTTTTTTATAATTTATAA
Found at i:143860 original size:3 final size:3
Alignment explanation
Indices: 143852--143952 Score: 168
Period size: 3 Copynumber: 34.0 Consensus size: 3
143842 GACCACAAGG
*
143852 AGA AGA AGA AGA AGA AGA AGT AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
143900 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA TGA AGA ATA A-A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
143947 AGA AGA
1 AGA AGA
143953 GTAGTTAAGA
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 2 0.02
3 90 0.98
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:145236 original size:17 final size:17
Alignment explanation
Indices: 145216--145248 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
145206 TTTAAGGACT
145216 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
145233 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
145249 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:145493 original size:50 final size:49
Alignment explanation
Indices: 145417--145561 Score: 127
Period size: 50 Copynumber: 2.9 Consensus size: 49
145407 CATTAACTCT
* * *
145417 CATGATTAGTTAAGTTTGCATCATAAATAATGA-CATTCATTAAGTAACTTA
1 CATG-TTAGTTAAATATGCATCATAAATAAT-ATCATGCATTAAGTAAC-TA
* ** * *
145468 CATGTTAGTTAAATATGCATTATAAATCCTATCATGCATTATGTAACTC
1 CATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAGTAACTA
* *
145517 CATGTTAGTT-AA-ATGCATCATTAAATCAA-GTCATGCATTTAGTAA
1 CATGTTAGTTAAATATGCATCA-TAAAT-AATATCATGCATTAAGTAA
145562 TCCATTAGTT
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
47 7 0.09
48 20 0.26
49 12 0.16
50 34 0.44
51 4 0.05
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (49 bp):
CATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAGTAACTA
Found at i:145780 original size:21 final size:21
Alignment explanation
Indices: 145754--145793 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
145744 TAACTTATTG
145754 GCATGTTTAA-ATTGTTTTAAT
1 GCATGTTTAATA-TGTTTTAAT
145775 GCATGTTTAATATGTTTTA
1 GCATGTTTAATATGTTTTA
145794 GAAATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.53
Consensus pattern (21 bp):
GCATGTTTAATATGTTTTAAT
Found at i:165507 original size:14 final size:15
Alignment explanation
Indices: 165477--165505 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
165467 TAAAGGGTTA
165477 AAAATAATTTTTTTT
1 AAAATAATTTTTTTT
165492 AAAATAATTTTTTT
1 AAAATAATTTTTTT
165506 AATTTTTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAAATAATTTTTTTT
Found at i:166562 original size:79 final size:79
Alignment explanation
Indices: 166472--166631 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
166462 AATCTAGGTA
166472 AAATATAGGCAATTTAGACTTTACCTTTTTTGTCCTAATTCCAGCTTCAGTCCCTATATTTTTTA
1 AAATATAGGCAATTTAGACTTTACCTTTTTTGTCCTAATTCCAGCTTCAGTCCCTATATTTTTTA
166537 CATTATTAAATTTT
66 CATTATTAAATTTT
166551 AAATATAGGCAATTTAGACTTTACCTTTTTTGTCCTAATTCCAGCTTCAGTCCCTATATTTTTTA
1 AAATATAGGCAATTTAGACTTTACCTTTTTTGTCCTAATTCCAGCTTCAGTCCCTATATTTTTTA
166616 CATTATTAAATTTT
66 CATTATTAAATTTT
166630 AA
1 AA
166632 TCTTTCTACT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.46
Consensus pattern (79 bp):
AAATATAGGCAATTTAGACTTTACCTTTTTTGTCCTAATTCCAGCTTCAGTCCCTATATTTTTTA
CATTATTAAATTTT
Found at i:166845 original size:7 final size:8
Alignment explanation
Indices: 166818--166846 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
166808 AAATTTTCTT
166818 AATATTAA
1 AATATTAA
166826 AATATTAA
1 AATATTAA
166834 AATATT-A
1 AATATTAA
166841 AATATT
1 AATATT
166847 CAATCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AATATTAA
Found at i:167760 original size:29 final size:29
Alignment explanation
Indices: 167718--167777 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
167708 TCACTAATCG
*
167718 AACTTCGAAATAGACAAGATAAGAACCCT
1 AACTTCGAAATAGACAAGACAAGAACCCT
167747 AACTTCGAAATAGACAAGACAAGAACCCT
1 AACTTCGAAATAGACAAGACAAGAACCCT
167776 AA
1 AA
167778 TTATTATTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.50, C:0.22, G:0.13, T:0.15
Consensus pattern (29 bp):
AACTTCGAAATAGACAAGACAAGAACCCT
Found at i:172336 original size:42 final size:42
Alignment explanation
Indices: 172241--172344 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
172231 TTTGGATTCA
172241 AGGTTTAA-GATTTAGGTTTAAAGTTTAAGGGTTTGGGGTTAC
1 AGGTTTAATG-TTTAGGTTTAAAGTTTAAGGGTTTGGGGTTAC
* * * * *
172283 AAGCTTGATGTTTAGGGTTT-ATGTTTAAGGGTTTGGGGTTAT
1 AGGTTTAATGTTTA-GGTTTAAAGTTTAAGGGTTTGGGGTTAC
*
172325 AGGTTTAATGTTTTGGTTTA
1 AGGTTTAATGTTTAGGTTTA
172345 GGATTTTATA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
41 5 0.10
42 39 0.78
43 6 0.12
ACGTcount: A:0.22, C:0.02, G:0.31, T:0.45
Consensus pattern (42 bp):
AGGTTTAATGTTTAGGTTTAAAGTTTAAGGGTTTGGGGTTAC
Found at i:172337 original size:21 final size:21
Alignment explanation
Indices: 172261--172337 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
172251 TTTAGGTTTA
* *
172261 AAGTTTAAGGGTTTGGGGTTAC
1 AAGTTTAA-TGTTTGGGGTTAT
* * *
172283 AAGCTTGATGTTTAGGGTT-T
1 AAGTTTAATGTTTGGGGTTAT
* *
172303 ATGTTTAAGGGTTTGGGGTTAT
1 AAGTTTAA-TGTTTGGGGTTAT
*
172325 AGGTTTAATGTTT
1 AAGTTTAATGTTT
172338 TGGTTTAGGA
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
20 5 0.12
21 22 0.54
22 14 0.34
ACGTcount: A:0.21, C:0.03, G:0.32, T:0.44
Consensus pattern (21 bp):
AAGTTTAATGTTTGGGGTTAT
Found at i:178365 original size:13 final size:13
Alignment explanation
Indices: 178347--178371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
178337 AACGCAATTC
178347 ATATTTTAAAGTG
1 ATATTTTAAAGTG
178360 ATATTTTAAAGT
1 ATATTTTAAAGT
178372 AATGTCGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
ATATTTTAAAGTG
Found at i:179061 original size:160 final size:160
Alignment explanation
Indices: 178884--179204 Score: 606
Period size: 160 Copynumber: 2.0 Consensus size: 160
178874 GATCTATACT
178884 TCGAAAAATATATAAAAGAATGAGATTTTGATAATCTTAATGATGCAGAATCAAATTTAAATGTT
1 TCGAAAAATATATAAAAGAATGAGATTTTGATAATCTTAATGATGCAGAATCAAATTTAAATGTT
178949 AATTAACTCATTTAAAAGACCAACAAATGATGATAATAAACATCTGTGTTAATTCTTACAATAAA
66 AATTAACTCATTTAAAAGACCAACAAATGATGATAATAAACATCTGTGTTAATTCTTACAATAAA
*** *
179014 TTGACACGCGACCAATATTATACTTTTTTC
131 TTGACACAAAAACAATATTATACTTTTTTC
179044 TCGAAAAATATATAAAAGAATGAGATTTTGATAATCTTAATGATGCAGAATCAAATTTAAATGTT
1 TCGAAAAATATATAAAAGAATGAGATTTTGATAATCTTAATGATGCAGAATCAAATTTAAATGTT
179109 AATTAACTCATTTAAAAGACCAACAAATGATGATAATAAACATCTGTGTTAATTCTTACAATAAA
66 AATTAACTCATTTAAAAGACCAACAAATGATGATAATAAACATCTGTGTTAATTCTTACAATAAA
179174 TTGACACAAAAACAATATTATACTTTTTTC
131 TTGACACAAAAACAATATTATACTTTTTTC
179204 T
1 T
179205 AAAGAATATT
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 157 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (160 bp):
TCGAAAAATATATAAAAGAATGAGATTTTGATAATCTTAATGATGCAGAATCAAATTTAAATGTT
AATTAACTCATTTAAAAGACCAACAAATGATGATAATAAACATCTGTGTTAATTCTTACAATAAA
TTGACACAAAAACAATATTATACTTTTTTC
Found at i:195864 original size:19 final size:18
Alignment explanation
Indices: 195842--195879 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
195832 AAAATACAAA
195842 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAA-ATTTAT
*
195861 AAAAATTCCAAAATTTAT
1 AAAAATTCAAAAATTTAT
195879 A
1 A
195880 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Found at i:196068 original size:16 final size:16
Alignment explanation
Indices: 196049--196079 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
196039 TTTGAAAAAT
196049 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
196065 TTTCAAATTTATATG
1 TTTCAAATATATATG
196080 CTATAACATA
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:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:198272 original size:15 final size:16
Alignment explanation
Indices: 198252--198281 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
198242 CTTCCCTATT
198252 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
198267 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
198282 TTGTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:198274 original size:22 final size:22
Alignment explanation
Indices: 198247--198304 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
198237 TCTGACTTCC
*
198247 CTATTTTCTATTTCTT-TTAATT
1 CTATTTTCT-TTTATTGTTAATT
198269 CTATTTTCTTTTATTGTTAATT
1 CTATTTTCTTTTATTGTTAATT
*
198291 CT-GTTTCTTTTATT
1 CTATTTTCTTTTATT
198305 TTTCCTCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.16, C:0.12, G:0.03, T:0.69
Consensus pattern (22 bp):
CTATTTTCTTTTATTGTTAATT
Found at i:198299 original size:21 final size:22
Alignment explanation
Indices: 198263--198304 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
198253 TCTATTTCTT
*
198263 TTAATTCTATTTTCTTTTATTG
1 TTAATTCTAGTTTCTTTTATTG
198285 TTAATTCT-GTTTCTTTTATT
1 TTAATTCTAGTTTCTTTTATT
198305 TTTCCTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (22 bp):
TTAATTCTAGTTTCTTTTATTG
Found at i:202784 original size:15 final size:16
Alignment explanation
Indices: 202764--202793 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
202754 CTTCCCTATT
202764 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
202779 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
202794 TTGTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:202786 original size:22 final size:22
Alignment explanation
Indices: 202759--202816 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
202749 TTCGACTTCC
*
202759 CTATTTTCTATTTCTT-TTAATT
1 CTATTTTCT-TTTATTGTTAATT
202781 CTATTTTCTTTTATTGTTAATT
1 CTATTTTCTTTTATTGTTAATT
*
202803 CT-GTTTCTTTTATT
1 CTATTTTCTTTTATT
202817 TTTCCTCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.16, C:0.12, G:0.03, T:0.69
Consensus pattern (22 bp):
CTATTTTCTTTTATTGTTAATT
Found at i:202811 original size:21 final size:22
Alignment explanation
Indices: 202775--202816 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
202765 TCTATTTCTT
*
202775 TTAATTCTATTTTCTTTTATTG
1 TTAATTCTAGTTTCTTTTATTG
202797 TTAATTCT-GTTTCTTTTATT
1 TTAATTCTAGTTTCTTTTATT
202817 TTTCCTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (22 bp):
TTAATTCTAGTTTCTTTTATTG
Found at i:203599 original size:16 final size:16
Alignment explanation
Indices: 203578--203608 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
203568 TCTACAATTA
*
203578 AATTATTTAAAATATT
1 AATTATATAAAATATT
203594 AATTATATAAAATAT
1 AATTATATAAAATAT
203609 CGGTGTAAAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTATATAAAATATT
Found at i:207286 original size:31 final size:30
Alignment explanation
Indices: 207225--207289 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 30
207215 ACTTAAATCC
207225 CAATAACTTAAATAAAAATTTTAAATAATT
1 CAATAACTTAAATAAAAATTTTAAATAATT
*
207255 CAATAATTTAAATAAAAA-TTTACGAATAATT
1 CAATAACTTAAATAAAAATTTTA--AATAATT
207286 CAAT
1 CAAT
207290 GATCAAATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 4 0.12
30 17 0.53
31 11 0.34
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (30 bp):
CAATAACTTAAATAAAAATTTTAAATAATT
Found at i:215302 original size:27 final size:27
Alignment explanation
Indices: 215271--215328 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
215261 TAGGTTGTGT
*
215271 TTTTAAAAATTTAAGA-AAATAAATTGA
1 TTTTAAAAA-TTAAGATAAATAAATCGA
*
215298 TTTTAAAAATTCAGATAAATAAATCGA
1 TTTTAAAAATTAAGATAAATAAATCGA
215325 TTTT
1 TTTT
215329 GAAGAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (27 bp):
TTTTAAAAATTAAGATAAATAAATCGA
Found at i:224403 original size:49 final size:49
Alignment explanation
Indices: 224331--224424 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
224321 AATTAAAATA
224331 TTTAAGTACAGCTTGAAAAAAAAAACACAGCATAAACCTTTTTTTTTTT
1 TTTAAGTACAGCTTGAAAAAAAAAACACAGCATAAACCTTTTTTTTTTT
* *
224380 TTTAAGTACAGCTTGAAAGAAAAAACACAGCCTAAACCTTTTTTT
1 TTTAAGTACAGCTTGAAAAAAAAAACACAGCATAAACCTTTTTTT
224425 AACCGCCAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (49 bp):
TTTAAGTACAGCTTGAAAAAAAAAACACAGCATAAACCTTTTTTTTTTT
Done.