Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014273.1 Kokia drynarioides strain JFW-HI SEQ_129306, 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: 147604
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:11058 original size:2 final size:2
Alignment explanation
Indices: 11051--11075 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11041 AGAAAAAGAA
11051 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
11076 ATAAATTCTA
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:18062 original size:19 final size:19
Alignment explanation
Indices: 18014--18055 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
18004 GAATGAGAAC
18014 ATGTTGAACATGTTAGTAA
1 ATGTTGAACATGTTAGTAA
18033 ATGTTGAACATGTTAGTAA
1 ATGTTGAACATGTTAGTAA
18052 ATGT
1 ATGT
18056 GAAACATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (19 bp):
ATGTTGAACATGTTAGTAA
Found at i:19377 original size:12 final size:12
Alignment explanation
Indices: 19360--19419 Score: 79
Period size: 12 Copynumber: 5.1 Consensus size: 12
19350 TTTAAAATTT
19360 AAAATTTATAAA
1 AAAATTTATAAA
19372 AAAA-TTATAAA
1 AAAATTTATAAA
19383 CAAAATTTA-AAA
1 -AAAATTTATAAA
*
19395 ATAATTTATAAA
1 AAAATTTATAAA
*
19407 ATAATTTATAAA
1 AAAATTTATAAA
19419 A
1 A
19420 GTATAAAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
11 14 0.32
12 27 0.61
13 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTTATAAA
Found at i:19379 original size:11 final size:11
Alignment explanation
Indices: 19360--19419 Score: 59
Period size: 11 Copynumber: 5.2 Consensus size: 11
19350 TTTAAAATTT
*
19360 AAAATTTATAA
1 AAAAATTATAA
19371 AAAAATTATAA
1 AAAAATTATAA
19382 ACAAAATT-TAA
1 A-AAAATTATAA
19393 AAATAATTTATAA
1 AAA-AA-TTATAA
*
19406 AATAATTTATAA
1 AA-AAATTATAA
19418 AA
1 AA
19420 GTATAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 2 0.05
11 17 0.40
12 16 0.38
13 6 0.14
14 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:27397 original size:24 final size:24
Alignment explanation
Indices: 27353--27398 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
27343 AATTTTTCAG
*
27353 TTAATTTTTGTCTTTTCTTTTACT
1 TTAATTTTTGTCTTTACTTTTACT
*
27377 TTAATTTGTT-TCTTTAGTTTTA
1 TTAATTT-TTGTCTTTACTTTTA
27399 GCAGGAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.15, C:0.09, G:0.07, T:0.70
Consensus pattern (24 bp):
TTAATTTTTGTCTTTACTTTTACT
Found at i:29183 original size:21 final size:21
Alignment explanation
Indices: 29146--29204 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
29136 GTATTGAAGC
29146 AAAAGAAGAAGAGAAGAGAAAAGA
1 AAAAGAAGAA-A-AAGAG-AAAGA
*
29170 AAAAGAA-AAAAAGAGAAGGA
1 AAAAGAAGAAAAAGAGAAAGA
*
29190 AAAATAAGAAAAAGA
1 AAAAGAAGAAAAAGA
29205 AGAAGACGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.31
21 12 0.38
22 1 0.03
23 2 0.06
24 7 0.22
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (21 bp):
AAAAGAAGAAAAAGAGAAAGA
Found at i:29200 original size:9 final size:9
Alignment explanation
Indices: 29141--29208 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
29131 TGAGGGTATT
*
29141 GAAGCAAAA
1 GAAGAAAAA
*
29150 GAAG-AAGA
1 GAAGAAAAA
*
29158 GAAG-AGAA
1 GAAGAAAAA
29166 -AAGAAAAA
1 GAAGAAAAA
*
29174 GAAAAAAAGA
1 GAAGAAAA-A
29184 GAAGGAAAAA
1 GAA-GAAAAA
*
29194 TAAGAAAAA
1 GAAGAAAAA
29203 GAAGAA
1 GAAGAA
29209 GACGTTACCC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
7 3 0.06
8 12 0.26
9 21 0.45
10 7 0.15
11 4 0.09
ACGTcount: A:0.72, C:0.01, G:0.25, T:0.01
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:29208 original size:22 final size:20
Alignment explanation
Indices: 29168--29209 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29158 GAAGAGAAAA
29168 GAAAAAGAAAAAAAGAGAAG
1 GAAAAAGAAAAAAAGAGAAG
*
29188 GAAAAATAAGAAAAAGAAGAAG
1 GAAAAAGAA-AAAAAG-AGAAG
29210 ACGTTACCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
GAAAAAGAAAAAAAGAGAAG
Found at i:29251 original size:69 final size:68
Alignment explanation
Indices: 29173--29309 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 68
29163 GAAAAGAAAA
29173 AGAAAAAAAGAGAAGGAAAAATAAGAAAAAGAAGAAGACGTTACCCCGACAAATTTATCAGAGAA
1 AGAAAAAAAGAGAAGGAAAAATAAGAAAAAGAAGAAGACGTTACCCCGACAAATTTATCAGAGAA
29238 ATT
66 ATT
*
29241 NAGAAAAAAAGAGAAGGAAAAATAAGAAAAAGAAGAAGACGTTACCCCGACAAATTTATTAGAGA
1 -AGAAAAAAAGAGAAGGAAAAATAAGAAAAAGAAGAAGACGTTACCCCGACAAATTTATCAGAGA
29306 AATT
65 AATT
29310 TGTCGACTCA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.57, C:0.09, G:0.19, T:0.14
Consensus pattern (68 bp):
AGAAAAAAAGAGAAGGAAAAATAAGAAAAAGAAGAAGACGTTACCCCGACAAATTTATCAGAGAA
ATT
Found at i:33535 original size:8 final size:8
Alignment explanation
Indices: 33522--33568 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
33512 GATCATGAAA
33522 TTTAAATT
1 TTTAAATT
*
33530 TTTAAAAT
1 TTTAAATT
33538 TTTAAA-T
1 TTTAAATT
*
33545 TTCAAATT
1 TTTAAATT
33553 TTTAATTATT
1 TTTAA--ATT
33563 TTTAAA
1 TTTAAA
33569 GTACATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 6 0.18
8 19 0.58
10 8 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTAAATT
Found at i:34505 original size:38 final size:37
Alignment explanation
Indices: 34449--34522 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
34439 GTGATATTTG
* *
34449 ACCCATTTTTATTAGGGTGAATT-GTGGTTTTTGTTTCA
1 ACCCATTATCATTAGGGTGAATTAG-GG-TTTTGTTTCA
*
34487 ACCCATTATCATTGGGGTGAATTAGGGTTTTGTTTC
1 ACCCATTATCATTAGGGTGAATTAGGGTTTTGTTTC
34523 GATTAGGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 9 0.28
38 22 0.69
39 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (37 bp):
ACCCATTATCATTAGGGTGAATTAGGGTTTTGTTTCA
Found at i:35155 original size:28 final size:29
Alignment explanation
Indices: 35097--35155 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
35087 AAAATTATTA
**
35097 TTTCATAAAATTTTTAAGTTTTTAACTTT
1 TTTCATAAAATTTTTAAGTTTTTAAAATT
*
35126 TTTCAT-ATATTTTTATA-TTTTTAAAATT
1 TTTCATAAAATTTTTA-AGTTTTTAAAATT
35154 TT
1 TT
35156 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTCATAAAATTTTTAAGTTTTTAAAATT
Found at i:35176 original size:24 final size:24
Alignment explanation
Indices: 35149--35196 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35139 TATATTTTTA
* * *
35149 AAATTTTATATTTTTTTTAAATAC
1 AAATTTTAGAATTTTTATAAATAC
35173 AAATTTTAGAATTTTTATAAATAC
1 AAATTTTAGAATTTTTATAAATAC
35197 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATTTTAGAATTTTTATAAATAC
Found at i:35243 original size:19 final size:19
Alignment explanation
Indices: 35183--35245 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
35173 AAATTTTAGA
* *
35183 ATTTTTATAAA-TACTTTG
1 ATTTTTAAAAATTATTTTG
* *
35201 AATTTTAAAAATTATTTTCA
1 ATTTTTAAAAATTATTTT-G
*
35221 ATTTTTGAAAATTATTTTG
1 ATTTTTAAAAATTATTTTG
35240 ATTTTT
1 ATTTTT
35246 TTGTAATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 9 0.25
19 11 0.31
20 16 0.44
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTTTTAAAAATTATTTTG
Found at i:41219 original size:195 final size:195
Alignment explanation
Indices: 40879--41324 Score: 553
Period size: 195 Copynumber: 2.3 Consensus size: 195
40869 TTACCAGCCT
* * **
40879 GATGCTGCTCACACGAGCTGTTGAGGACTCGTAACATATGCGGTACC-CTAGTCATCGGTACGGT
1 GATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTC-AGCCATCAATACGGT
* * * * **
40943 GTCTTTCTATATAATTGTCTCCTAACGATGCTGCTCACACTAGTTATCGAGTGTATGCACTTATG
65 ATCGTGCTATATAATTGTCTCCTAACGATGCTGCTCACACTAGCTATCGAGAATATGCACTTATG
* * * * * ***
41008 CGTAAGTCCTAGCCATCGTAGGGCCTGTAATCCATTCTAGGATTC-ATATCTCTTTTTTTGACTC
130 CATAAATCCTAGCCATCATAGGGCATGTAATCCATTCTAGGATTCTATA-CTCATTTCCCGACTC
41072 AC
194 AC
* *
41074 GATGATGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAACCATCAATACGGTA
1 GATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCAATACGGTA
* *
41139 TCCGTGC-ATGTAACTAT-TC-CCTAACGATGCTGCTCACACTAGCTGTCGAGAATATGCACTTA
66 T-CGTGCTATATAA-T-TGTCTCCTAACGATGCTGCTCACACTAGCTATCGAGAATATGCACTTA
* *
41201 TGCATAAAT-CTCAGCCATCATAGGGCATGTAATCCATTCTTGGATTCTTTACTCATTTCCCGAC
128 TGCATAAATCCT-AGCCATCATAGGGCATGTAATCCATTCTAGGATTCTATACTCATTTCCCGAC
41265 TCAC
192 TCAC
* * *
41269 AATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTATCTCAGCCATC
1 GATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATC
41325 GCGTTGGTTT
Statistics
Matches: 216, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
194 2 0.01
195 204 0.94
196 9 0.04
197 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (195 bp):
GATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCAATACGGTA
TCGTGCTATATAATTGTCTCCTAACGATGCTGCTCACACTAGCTATCGAGAATATGCACTTATGC
ATAAATCCTAGCCATCATAGGGCATGTAATCCATTCTAGGATTCTATACTCATTTCCCGACTCAC
Found at i:49107 original size:21 final size:20
Alignment explanation
Indices: 49077--49133 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
49067 AGCATACTCG
* *
49077 ATGCATCCACAACAAATCCAC
1 ATGCAGCCACAACAAAT-CAA
* *
49098 ATGTAGCCACATCAGAATCAA
1 ATGCAGCCACAACA-AATCAA
49119 ATGCAGCCACAACAA
1 ATGCAGCCACAACAA
49134 TCTATAATGC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 25 0.86
22 3 0.10
ACGTcount: A:0.44, C:0.32, G:0.11, T:0.14
Consensus pattern (20 bp):
ATGCAGCCACAACAAATCAA
Found at i:54406 original size:17 final size:17
Alignment explanation
Indices: 54384--54416 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54374 TGTTAGTAAG
54384 CATTGTCATTGCATTTC
1 CATTGTCATTGCATTTC
54401 CATTGTCATTGCATTT
1 CATTGTCATTGCATTT
54417 TACTGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.48
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:55242 original size:134 final size:134
Alignment explanation
Indices: 55002--55270 Score: 520
Period size: 134 Copynumber: 2.0 Consensus size: 134
54992 AGAATATATA
55002 TATATATATATATATATTATTGTACAATAAATGATGTATTGGTAGATGAAATTTAGGATTTAAAG
1 TATATATATATATATATTATTGTACAATAAATGATGTATTGGTAGATGAAATTTAGGATTTAAAG
*
55067 CATGATGCTAGCTTTGATGAAGTTGCATGTCTTAGTTCTTCATACTTATGAGTTATCGACGCAAT
66 CATGATGCTAGCTTTGATGAAGTTGCATGTCTTAGTTCTTCATACTTATGAGATATCGACGCAAT
55132 ATTC
131 ATTC
*
55136 TATATATATGTATATATTATTGTACAATAAATGATGTATTGGTAGATGAAATTTAGGATTTAAAG
1 TATATATATATATATATTATTGTACAATAAATGATGTATTGGTAGATGAAATTTAGGATTTAAAG
55201 CATGATGCTAGCTTTGATGAAGTTGCATGTCTTAGTTCTTCATACTTATGAGATATCGACGCAAT
66 CATGATGCTAGCTTTGATGAAGTTGCATGTCTTAGTTCTTCATACTTATGAGATATCGACGCAAT
55266 ATTC
131 ATTC
55270 T
1 T
55271 GTCATCTGAA
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 133 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (134 bp):
TATATATATATATATATTATTGTACAATAAATGATGTATTGGTAGATGAAATTTAGGATTTAAAG
CATGATGCTAGCTTTGATGAAGTTGCATGTCTTAGTTCTTCATACTTATGAGATATCGACGCAAT
ATTC
Found at i:62890 original size:23 final size:22
Alignment explanation
Indices: 62842--62890 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
62832 ATAATTATTA
62842 AAATATATATTACTTATACTAAC
1 AAATATATATTACTTATACT-AC
*
62865 AAATATAATTTTACTTATTACT-C
1 AAATAT-ATATTACTTA-TACTAC
62888 AAA
1 AAA
62891 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 10 0.43
24 9 0.39
25 4 0.17
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATATATATTACTTATACTAC
Found at i:63812 original size:14 final size:14
Alignment explanation
Indices: 63788--63835 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
63778 AATTCTCTCA
63788 AAAAATAATTTATTT
1 AAAAAT-ATTTATTT
*
63803 AAAAATATTTATCTC
1 AAAAATATTTAT-TT
63818 AAAAATATTT-TTT
1 AAAAATATTTATTT
63831 AAAAA
1 AAAAA
63836 CAATACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.20
14 7 0.23
15 17 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAAATATTTATTT
Found at i:64405 original size:25 final size:27
Alignment explanation
Indices: 64366--64416 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
64356 CATTCATAAA
64366 ATATTAAATATTTTTA-A-AATATTAT
1 ATATTAAATATTTTTATATAATATTAT
64391 ATATT-AATATTTTTTATATAATATTA
1 ATATTAAATA-TTTTTATATAATATTA
64417 AAACAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 11 0.48
26 1 0.04
27 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATTAAATATTTTTATATAATATTAT
Found at i:74810 original size:14 final size:14
Alignment explanation
Indices: 74791--74826 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
74781 TCATTCTTTT
74791 TGTTCTTTATTCTC
1 TGTTCTTTATTCTC
74805 TGTTCTTTATTCTC
1 TGTTCTTTATTCTC
*
74819 CGTTCTTT
1 TGTTCTTT
74827 TATTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.22, G:0.08, T:0.64
Consensus pattern (14 bp):
TGTTCTTTATTCTC
Found at i:76334 original size:16 final size:16
Alignment explanation
Indices: 76302--76340 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
76292 AATAAATAAA
76302 AAATATATAAAATATT
1 AAATATATAAAATATT
76318 AAATAT-TAAAATAATT
1 AAATATATAAAAT-ATT
76334 AAATATA
1 AAATATA
76341 AATATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATATATAAAATATT
Found at i:76337 original size:23 final size:23
Alignment explanation
Indices: 76301--76359 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
76291 CAATAAATAA
*
76301 AAAATATATAAAATATTAAATA-TT
1 AAAATA-ATTAAATA-TAAATATTT
76325 AAAATAATTAAATATAAATATTT
1 AAAATAATTAAATATAAATATTT
*
76348 AAAAAAATTAAA
1 AAAATAATTAAA
76360 AAATAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 6 0.19
23 20 0.62
24 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATAATTAAATATAAATATTT
Found at i:76342 original size:15 final size:14
Alignment explanation
Indices: 76306--76346 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 14
76296 AATAAAAAAT
76306 ATATAAAATATTAA
1 ATATAAAATATTAA
76320 ATATTAAAATAATTAA
1 ATA-TAAAAT-ATTAA
76336 ATAT-AAATATT
1 ATATAAAATATT
76347 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 7 0.28
15 7 0.28
16 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATAAAATATTAA
Found at i:80860 original size:22 final size:22
Alignment explanation
Indices: 80832--80879 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
80822 TCTACTCTAT
*
80832 AATTTCAAATGTAAGAAGACTG
1 AATTTCAAATGTAAGAAGACTA
*
80854 AATTTCAAATGTATGAAGACTA
1 AATTTCAAATGTAAGAAGACTA
80876 AATT
1 AATT
80880 ATTGAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (22 bp):
AATTTCAAATGTAAGAAGACTA
Found at i:94127 original size:19 final size:19
Alignment explanation
Indices: 94103--94148 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
94093 AATCCAGCTA
94103 TACATTCACGCAGATCTGG
1 TACATTCACGCAGATCTGG
*
94122 TACATTCACGTAGATCTGG
1 TACATTCACGCAGATCTGG
*
94141 TGCATTCA
1 TACATTCA
94149 ACAAGCAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (19 bp):
TACATTCACGCAGATCTGG
Found at i:97220 original size:9 final size:9
Alignment explanation
Indices: 97208--97250 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
97198 TTATATTTTT
97208 TAAAAAATA
1 TAAAAAATA
97217 TAAAAAATA
1 TAAAAAATA
97226 T--AAAATA
1 TAAAAAATA
97233 TAAAAGAATA
1 TAAAA-AATA
97243 TATAAAAA
1 TA-AAAAA
97251 AGTTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.23
9 12 0.40
10 8 0.27
11 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (9 bp):
TAAAAAATA
Found at i:97230 original size:16 final size:17
Alignment explanation
Indices: 97211--97244 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
97201 TATTTTTTAA
97211 AAAATATAAAA-AATAT
1 AAAATATAAAAGAATAT
97227 AAAATATAAAAGAATAT
1 AAAATATAAAAGAATAT
97244 A
1 A
97245 TAAAAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAATATAAAAGAATAT
Found at i:100904 original size:17 final size:17
Alignment explanation
Indices: 100882--100915 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
100872 CAATAACGAA
100882 CTCCCAACTCCCTAGGG
1 CTCCCAACTCCCTAGGG
100899 CTCCCAACTCCCTAGGG
1 CTCCCAACTCCCTAGGG
100916 ATAAGCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.18
Consensus pattern (17 bp):
CTCCCAACTCCCTAGGG
Found at i:102859 original size:21 final size:21
Alignment explanation
Indices: 102812--102864 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
102802 AATAGTGCAG
**
102812 ACTTCTACCGATACTTGAGAA
1 ACTTCTACCGATACAAGAGAA
* * *
102833 AGTTCTACCGATACAAGTGTA
1 ACTTCTACCGATACAAGAGAA
102854 ACTTCTACCGA
1 ACTTCTACCGA
102865 AACATGTCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (21 bp):
ACTTCTACCGATACAAGAGAA
Found at i:103625 original size:36 final size:36
Alignment explanation
Indices: 103555--103654 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 36
103545 CGTTATTCGC
* * * * **
103555 TTTACTCCTTGTTAACCCGAAGGTTATGGGGCTCAT
1 TTTAATCCCTGTTAACCCAAAGGTCATGATGCTCAT
* * *
103591 TTTACTCCCTGTTGACCCAATGGTCATGATGCTCAT
1 TTTAATCCCTGTTAACCCAAAGGTCATGATGCTCAT
*
103627 TTTAATCGCTGTTAACCCAAAGGTCATG
1 TTTAATCCCTGTTAACCCAAAGGTCATG
103655 CCTATTACCA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (36 bp):
TTTAATCCCTGTTAACCCAAAGGTCATGATGCTCAT
Found at i:105240 original size:22 final size:22
Alignment explanation
Indices: 105194--105258 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
105184 CTCTCCGTTA
*
105194 TTTAGCACGTATAGTGCTCTCCG
1 TTTAGCACGTTTA-TGCTCTCCG
*
105217 TTTAGCACGTTTATGCTCTTCG
1 TTTAGCACGTTTATGCTCTCCG
* * *
105239 TTTAACACCTTTGTGCTCTC
1 TTTAGCACGTTTATGCTCTC
105259 TGTTCATTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 24 0.67
23 12 0.33
ACGTcount: A:0.15, C:0.26, G:0.17, T:0.42
Consensus pattern (22 bp):
TTTAGCACGTTTATGCTCTCCG
Found at i:109639 original size:16 final size:16
Alignment explanation
Indices: 109603--109633 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
109593 TAGTTCATAA
109603 AAATTTAAACTCAAAT
1 AAATTTAAACTCAAAT
109619 AAATTTAAACTCAAA
1 AAATTTAAACTCAAA
109634 ATAATTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATTTAAACTCAAAT
Found at i:114581 original size:15 final size:15
Alignment explanation
Indices: 114561--114592 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
114551 GTGCTTGATA
114561 TGGCAGTGTTGGTTT
1 TGGCAGTGTTGGTTT
114576 TGGCAGTGTTGGTTT
1 TGGCAGTGTTGGTTT
114591 TG
1 TG
114593 TAAGAAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.41, T:0.47
Consensus pattern (15 bp):
TGGCAGTGTTGGTTT
Found at i:117607 original size:26 final size:26
Alignment explanation
Indices: 117578--117638 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
117568 CAACAGTCAC
117578 CACCATCTCCCAAACCCAACCACCTT
1 CACCATCTCCCAAACCCAACCACCTT
117604 CACCATCTCCCAAACCCAACCACCTT
1 CACCATCTCCCAAACCCAACCACCTT
117630 CACCATCTC
1 CACCATCTC
117639 AGTAGTCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.54, G:0.00, T:0.16
Consensus pattern (26 bp):
CACCATCTCCCAAACCCAACCACCTT
Found at i:117911 original size:2 final size:2
Alignment explanation
Indices: 117904--117942 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
117894 GCAATCCACG
*
117904 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
117943 GGGGCTTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:135038 original size:3 final size:3
Alignment explanation
Indices: 135030--135061 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
135020 TGGGTTTATA
135030 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
135062 CTACCAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:135381 original size:20 final size:20
Alignment explanation
Indices: 135345--135383 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
135335 GAAGATGCGT
*
135345 AACAGAGGCACTAAAGTGAA
1 AACAGAGGCACCAAAGTGAA
*
135365 AACAGAGGCACCGAAGTGA
1 AACAGAGGCACCAAAGTGA
135384 GAGCCAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.18, G:0.28, T:0.08
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGAA
Found at i:140103 original size:11 final size:11
Alignment explanation
Indices: 140087--140162 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
140077 GAAAATCACT
140087 TTAATATTAAA
1 TTAATATTAAA
140098 TTAATA--AAA
1 TTAATATTAAA
*
140107 -TATTATTAAA
1 TTAATATTAAA
*
140117 ATAAGTATTAAA
1 TTAA-TATTAAA
140129 TTAA-ATTTAATA
1 TTAATA-TTAA-A
140141 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
140154 ATAATATTA
1 TTAATATTA
140163 TTTTGGAATA
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:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:140452 original size:19 final size:19
Alignment explanation
Indices: 140414--140453 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
140404 ATAATATCAT
* *
140414 ATTAATTTTATTTAATTTG
1 ATTAATTTAATTTAACTTG
*
140433 ATTAATTTAATTTTACTTG
1 ATTAATTTAATTTAACTTG
140452 AT
1 AT
140454 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTAATTTAACTTG
Done.