Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009687.1 Kokia drynarioides strain JFW-HI SEQ_124405, 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: 67151
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:490 original size:48 final size:48
Alignment explanation
Indices: 436--531 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
426 TATTGTCTTC
436 ACTTTATCATTTCAACTAAAACCGCACTTAATTTTTATATCTCTTTTT
1 ACTTTATCATTTCAACTAAAACCGCACTTAATTTTTATATCTCTTTTT
* *
484 ACTTTATTATTTCAACTAAACCCGCACTTAATTTTTATATCTCTTTTT
1 ACTTTATCATTTCAACTAAAACCGCACTTAATTTTTATATCTCTTTTT
532 TCTATAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.28, C:0.21, G:0.02, T:0.49
Consensus pattern (48 bp):
ACTTTATCATTTCAACTAAAACCGCACTTAATTTTTATATCTCTTTTT
Found at i:902 original size:6 final size:6
Alignment explanation
Indices: 891--917 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
881 AAATATAAAA
891 CCAAAG CCAAAG CCAAAG CCAAAG CCA
1 CCAAAG CCAAAG CCAAAG CCAAAG CCA
918 TAACTGTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.37, G:0.15, T:0.00
Consensus pattern (6 bp):
CCAAAG
Found at i:3790 original size:3 final size:3
Alignment explanation
Indices: 3782--3825 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3772 CCTGTAATCT
3782 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3826 TTGTTTCTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:6666 original size:12 final size:13
Alignment explanation
Indices: 6639--6671 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6629 TTTTTTTATT
*
6639 AATTTTATATTTA
1 AATTTTATATTAA
6652 AATTTTAT-TTAA
1 AATTTTATATTAA
6664 AATTTTAT
1 AATTTTAT
6672 CTATTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATTTTATATTAA
Found at i:6737 original size:19 final size:20
Alignment explanation
Indices: 6713--6760 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
6703 TTTAATATTT
6713 TATAAAAT-ATAAAAATACA
1 TATAAAATAATAAAAATACA
*
6732 TATAAACTTAATAAAAATACA
1 TATAAA-ATAATAAAAATACA
*
6753 TAAAAAAT
1 TATAAAAT
6761 GAATCTAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (20 bp):
TATAAAATAATAAAAATACA
Found at i:9316 original size:10 final size:11
Alignment explanation
Indices: 9303--9347 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
9293 TTTTAAATAA
*
9303 TTTTTATGATT
1 TTTTTATAATT
9314 TTTTTATAATT
1 TTTTTATAATT
*
9325 TTTATA-AATT
1 TTTTTATAATT
9335 TTTTTATATATT
1 TTTTTATA-ATT
9347 T
1 T
9348 ATCCAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.31
11 16 0.55
12 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:9322 original size:20 final size:21
Alignment explanation
Indices: 9299--9347 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
9289 TAAATTTTAA
*
9299 ATAATTTTTAT-GATTTTTTT
1 ATAATTTTTATAAATTTTTTT
9319 ATAATTTTTATAAATTTTTTT
1 ATAATTTTTATAAATTTTTTT
9340 ATATATTT
1 ATA-ATTT
9348 ATCCAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 11 0.42
21 11 0.42
22 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATAATTTTTATAAATTTTTTT
Found at i:9357 original size:22 final size:21
Alignment explanation
Indices: 9311--9349 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9301 AATTTTTATG
*
9311 ATTTTTTTATAATTTTTATAA
1 ATTTTTTTATAATATTTATAA
9332 ATTTTTTTAT-ATATTTAT
1 ATTTTTTTATAATATTTAT
9350 CCAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTTTTATAATATTTATAA
Found at i:12961 original size:12 final size:11
Alignment explanation
Indices: 12938--12972 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
12928 ATATTATATA
12938 ATTATTATTTT
1 ATTATTATTTT
*
12949 ATTGTTAATTTT
1 ATTATT-ATTTT
12961 ATTATTATTTT
1 ATTATTATTTT
12972 A
1 A
12973 AAGACATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:14224 original size:3 final size:3
Alignment explanation
Indices: 14218--14243 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
14208 ACTCTTTTTT
14218 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
14244 TAAGCATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:15150 original size:2 final size:2
Alignment explanation
Indices: 15143--15170 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15133 CGTATTCTTT
15143 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
15171 AATTATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15539 original size:29 final size:30
Alignment explanation
Indices: 15506--15569 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
15496 CGTACATTTG
**
15506 AAATTTAATAATTTTAC-TTTTATTTTTAA
1 AAATTTAATAATTTTACTTTTTAAATTTAA
**
15535 AAATTTAATTCTTTTACTTTTTAAATTTAA
1 AAATTTAATAATTTTACTTTTTAAATTTAA
15565 AAATT
1 AAATT
15570 ATAAGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (30 bp):
AAATTTAATAATTTTACTTTTTAAATTTAA
Found at i:15555 original size:23 final size:22
Alignment explanation
Indices: 15522--15564 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
15512 AATAATTTTA
*
15522 CTTTTATTTTTAAAAATTTAATT
1 CTTTTACTTTT-AAAATTTAATT
*
15545 CTTTTACTTTTTAAATTTAA
1 CTTTTACTTTTAAAATTTAA
15565 AAATTATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
CTTTTACTTTTAAAATTTAATT
Found at i:15563 original size:22 final size:22
Alignment explanation
Indices: 15522--15564 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
15512 AATAATTTTA
15522 CTTTTATTTTTAAAAATTTAATT
1 CTTTTATTTTT-AAAATTTAATT
15545 CTTTTACTTTTT-AAATTTAA
1 CTTTTA-TTTTTAAAATTTAA
15565 AAATTATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
CTTTTATTTTTAAAATTTAATT
Found at i:15578 original size:29 final size:27
Alignment explanation
Indices: 15513--15579 Score: 64
Period size: 30 Copynumber: 2.3 Consensus size: 27
15503 TTGAAATTTA
**
15513 ATAATTTTACTTTTATTTTTAAAAATT
1 ATAATTTTACTTTTAAATTTAAAAATT
15540 -TAATTCTTTTACTTTTTAAATTTAAAAATT
1 ATAA---TTTTAC-TTTTAAATTTAAAAATT
15570 ATAAGTTTTA
1 ATAA-TTTTA
15580 TTGTTAACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
26 3 0.09
29 11 0.34
30 15 0.47
31 3 0.09
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (27 bp):
ATAATTTTACTTTTAAATTTAAAAATT
Found at i:27093 original size:57 final size:56
Alignment explanation
Indices: 27002--27139 Score: 136
Period size: 57 Copynumber: 2.4 Consensus size: 56
26992 GTCATCATCC
* * ** * *
27002 AAAAAATATTTTTTTATCTGAGAAAGAGGATGATGATTATGGCTT-GACAAGCATAAA
1 AAAAAATATTTTTTTATTTGA-AAAGACGATGATGACCATGACTTAG-CAAGCACAAA
* * **
27059 AAAAAATATTTTTTTATTTGAAATAGGACG-TGATGGCCATGACTTAGCAAGCCCCCA
1 AAAAAATATTTTTTTATTTGAAA-A-GACGATGATGACCATGACTTAGCAAGCACAAA
27116 AAAAAATATTTTTTTATTTGAAAA
1 AAAAAATATTTTTTTATTTGAAAA
27140 ATGGGGATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
56 3 0.04
57 61 0.90
58 4 0.06
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (56 bp):
AAAAAATATTTTTTTATTTGAAAAGACGATGATGACCATGACTTAGCAAGCACAAA
Found at i:27836 original size:14 final size:14
Alignment explanation
Indices: 27799--27844 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
27789 TTTATAATTA
*
27799 AAATATTATTAATTT
1 AAATATTATT-TTTT
27814 -AAT-TTATTTTTT
1 AAATATTATTTTTT
*
27826 AAATATTATTTTAT
1 AAATATTATTTTTT
27840 AAATA
1 AAATA
27845 ATGTCACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AAATATTATTTTTT
Found at i:29039 original size:25 final size:25
Alignment explanation
Indices: 28994--29041 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28984 TTGTATAATC
**
28994 ATTTTTAAAAACTTTAAATAAAAAT
1 ATTTTTAAAAAAATTAAATAAAAAT
*
29019 ATTTTTAAAAAAATTACATAAAA
1 ATTTTTAAAAAAATTAAATAAAA
29042 TTAAACAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTTTTAAAAAAATTAAATAAAAAT
Found at i:49170 original size:144 final size:145
Alignment explanation
Indices: 48899--49179 Score: 465
Period size: 145 Copynumber: 1.9 Consensus size: 145
48889 TGAAACGAGG
* * *
48899 CTCAAAGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGGCGAAGCAA
1 CTCAAAGCAAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAA
* *
48964 TAAAATGGTTAGTTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
66 TAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
49029 AAAGAAGTATACCAA
131 AAAGAAGTATACCAA
* * *
49044 CTCAATGCAAACAAATCTTCGACCCCCAGCTTTCTGATGAGATACTGAGAAGCAAGGCGAAGCAA
1 CTCAAAGCAAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAA
*
49109 TAAAA-GGTTAGCTTCCTGATGAGATACTAAGAAGTTGACCAAATTCGTCTTCCTGATGAGATAC
66 TAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
*
49173 AGAGAAG
131 AAAGAAG
49180 CGGATTGAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
144 62 0.49
145 64 0.51
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (145 bp):
CTCAAAGCAAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAA
TAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
AAAGAAGTATACCAA
Found at i:49276 original size:200 final size:199
Alignment explanation
Indices: 49044--50148 Score: 1354
Period size: 206 Copynumber: 5.5 Consensus size: 199
49034 AGTATACCAA
* * *
49044 CTCAATGCAAACAAATCTTCGACCCCCAGCTTTCTGATGAGATACTGAGAAGCAAGGCGAAGCAA
1 CTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAA
* *
49109 TAAAAGGTTAGCTTCCTGATGAGATACTAAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACA
66 TAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
* * *
49174 GAGAAGCGGATTGAAACTAGTAAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACTAACT
131 GAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACAAAC-
* *
49239 CGAGG
195 CCACG
* * * *
49244 CTCAATGCGAACAAGTCTTCGAACCTCAGCTTTCTGATGAGATACTGAGAAGCAGGGCGAAGCAA
1 CTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAA
* ** * *
49309 TAAAAGGTTAGCTTCTTGATGAGATTTTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGGTACA
66 TAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
* * * *
49374 GAGAAGCGGATTGAAACAAGTAAGGCGATCGTCTTCCTGATGAGATACAGAGAAGAATACCAACC
131 GAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACAAACC
49439 CACG
196 CACG
49443 CTCAATGC-AAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGC-AGGTCGAAGC
1 CTCAATGCGAA-CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGG-CGAAGC
* * *
49506 AATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGAACCGAATTCGTCTTCCTGATGAGAT
64 AATAAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* * * * * *
49571 ACGGAGAAGCAGATTGAAACAAGCGATGCAGTCACCTTCCTGATGAGATACTA-AGAAGAAGTCC
128 ACAGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATAC-AGAGAAGAA-T--
**
49635 AAATCAAACCCATA
189 --A-CAAACCCACG
* * * * * *
49649 CTCAATACGAGCAAATCTTCGAACCCCAACCTCCTGATGAGATACTGAGAAGTAGGGCGAAGCAA
1 CTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAA
* * * *
49714 TAAAAGGGTTAGCTTCCTAATAAGATACTAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATAC
66 TAAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * *
49779 AGAGAAGCGAATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
130 AGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATAC--AG-AGAAGA--ATA
49844 TCAAACCCACG
190 -CAAACCCACG
* * *
49855 CTCAACGCGAGA-AAATCTTCGAACACCAGCTTCCTGATGAGATATTGAGAAG-AAGGGCGAAGC
1 CTCAATGCGA-ACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAA-GGCGAAGC
* *
49918 AATAAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCCTCTTGATGAGAT
64 AAT-AAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* * * * *
49983 ACAGAGATGCAGATTGAAACAAGTGAGGCGATCATCTTCCTAATGAGATACAGAGAAGTATATC-
128 ACAGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATA-CA
50047 -A---A--
192 AACCCACG
* *
50049 CTCAATGCGAACAAATCTTCG-ACCCCTAGCTTTCTGATGAGATACTGAGAAGCAGGGCGAAGCA
1 CTCAATGCGAACAAATCTTCGAACCCC-AGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCA
* *
50113 ATAAAAAGGTTAACTTCTTGATGAGATACTGAGAAG
65 AT-AAAAGGTTAGCTTCCTGATGAGATACTGAGAAG
50149 AAGGCCAAGT
Statistics
Matches: 789, Mismatches: 93, Indels: 52
0.84 0.10 0.06
Matches are distributed among these distances:
193 5 0.01
194 84 0.11
195 1 0.00
196 1 0.00
198 4 0.01
199 64 0.08
200 278 0.35
201 6 0.01
203 5 0.01
204 2 0.00
205 2 0.00
206 322 0.41
207 8 0.01
209 6 0.01
211 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (199 bp):
CTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAA
TAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
GAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACAAACC
CACG
Found at i:50544 original size:6 final size:6
Alignment explanation
Indices: 50522--50608 Score: 72
Period size: 6 Copynumber: 14.5 Consensus size: 6
50512 GTTTAAGTTC
* * *
50522 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTATCT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTA--A
* * *
50571 TTTTAA ATTTAA ATTTAA ATTT-G CTTTAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
50609 GATATTAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
4 2 0.03
5 5 0.08
6 50 0.79
7 2 0.03
8 4 0.06
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (6 bp):
ATTTAA
Found at i:50558 original size:17 final size:17
Alignment explanation
Indices: 50522--50587 Score: 87
Period size: 17 Copynumber: 3.6 Consensus size: 17
50512 GTTTAAGTTC
*
50522 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TCTTAA
50540 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
50557 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTATC---TTAA
50577 ATTTAAATTTA
1 ATTTAAATTTA
50588 AATTTGCTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
17 18 0.41
18 11 0.25
20 15 0.34
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:50604 original size:37 final size:35
Alignment explanation
Indices: 50522--50591 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 35
50512 GTTTAAGTTC
**
50522 ATTTAAATTTATTTTTAAATTTAAATTTATCTTAA
1 ATTTAAATTTATTTTTAAATTTAAATTTAAATTAA
50557 ATTTAAATTTATCTTTTTAAATTTAAATTTAAATT
1 ATTTAAATTTA--TTTTTAAATTTAAATTTAAATT
50592 TGCTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 11 0.35
37 20 0.65
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (35 bp):
ATTTAAATTTATTTTTAAATTTAAATTTAAATTAA
Found at i:50616 original size:17 final size:17
Alignment explanation
Indices: 50577--50619 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
50567 ATCTTTTTAA
50577 ATTTAAATTTAAATTTG
1 ATTTAAATTTAAATTTG
*
50594 CTTTAAATTTAAA-TTG
1 ATTTAAATTTAAATTTG
50610 ATATTAAATT
1 AT-TTAAATT
50620 AAAAACCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTAAATTTG
Found at i:51350 original size:21 final size:22
Alignment explanation
Indices: 51302--51366 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 22
51292 TAAATGTCAT
* *
51302 TAATAATAATATTAATTATTATGG
1 TAATAATAATAATAA-TATTA-GC
51326 TAATAATAATAATAATATTA-C
1 TAATAATAATAATAATATTAGC
*
51347 TAAT-ATCATTAATAATATTA
1 TAATAAT-AATAATAATATTA
51367 ATGACGGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.05
21 16 0.43
23 5 0.14
24 14 0.38
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (22 bp):
TAATAATAATAATAATATTAGC
Found at i:52415 original size:28 final size:28
Alignment explanation
Indices: 52375--52475 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 28
52365 TTAAACTGTC
*
52375 CAAAAATTACATTTTTACCTCCGAACTT
1 CAAAAATTCCATTTTTACCTCCGAACTT
52403 CAAAAATTCCA-TTTTACC-CCTGAACTT
1 CAAAAATTCCATTTTTACCTCC-GAACTT
52430 CTAAAAATTCCATTTTTACCT-CGAAACTTT
1 C-AAAAATTCCATTTTTACCTCCG-AAC-TT
*
52460 AAAAAATTACCATTTT
1 CAAAAATT-CCATTTT
52476 GTCCCTGGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
26 2 0.03
27 14 0.22
28 21 0.33
29 18 0.28
30 9 0.14
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (28 bp):
CAAAAATTCCATTTTTACCTCCGAACTT
Found at i:52447 original size:29 final size:29
Alignment explanation
Indices: 52376--52562 Score: 119
Period size: 29 Copynumber: 6.5 Consensus size: 29
52366 TAAACTGTCC
*
52376 AAAAATTACATTTTTACCTCC-GAACTTC-
1 AAAAATTCCATTTTTACC-CCTGAACTTCT
52404 AAAAATTCCA-TTTTACCCCTGAACTTCT
1 AAAAATTCCATTTTTACCCCTGAACTTCT
*
52432 AAAAATTCCATTTTTACCTC-GAAACTT-T
1 AAAAATTCCATTTTTACCCCTG-AACTTCT
* *
52460 AAAAAATTACCATTTTGT--CCCTGGA-TGTCC
1 -AAAAATT-CCATTTT-TACCCCTGAACT-TCT
* *
52490 AAAAACTCCATTTTTGA-CCCTAAAAC-TCT
1 AAAAATTCCATTTTT-ACCCCT-GAACTTCT
* *
52519 CAAAATTACCA-TTTTACCCCTGAA-TGTCC
1 AAAAATT-CCATTTTTACCCCTGAACT-TCT
*
52548 AAAAATTCTATTTTT
1 AAAAATTCCATTTTT
52563 TATCCCAATT
Statistics
Matches: 125, Mismatches: 15, Indels: 37
0.71 0.08 0.21
Matches are distributed among these distances:
26 2 0.02
27 15 0.12
28 34 0.27
29 61 0.49
30 12 0.10
31 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCTGAACTTCT
Found at i:52500 original size:58 final size:57
Alignment explanation
Indices: 52371--52562 Score: 212
Period size: 58 Copynumber: 3.4 Consensus size: 57
52361 GTCCTTAAAC
* *
52371 TGTCCAAAAATTACATTTTTACCTCCG-AACTTCAAAAATT-CCATTTTACCCCTGAA
1 TGTCCAAAAATTCCATTTTTACCT-CGAAACTTTAAAAATTACCATTTTACCCCTGAA
* ** *
52427 CT-TCTAAAAATTCCATTTTTACCTCGAAACTTTAAAAAATTACCATTTTGTCCCTGGA
1 -TGTCCAAAAATTCCATTTTTACCTCGAAACTTT-AAAAATTACCATTTTACCCCTGAA
* * * *
52485 TGTCCAAAAACTCCATTTTTGACC-CTAAAACTCTCAAAATTACCATTTTACCCCTGAA
1 TGTCCAAAAATTCCATTTTT-ACCTC-GAAACTTTAAAAATTACCATTTTACCCCTGAA
*
52543 TGTCCAAAAATTCTATTTTT
1 TGTCCAAAAATTCCATTTTT
52563 TATCCCAATT
Statistics
Matches: 113, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
55 2 0.02
56 25 0.22
57 9 0.08
58 68 0.60
59 9 0.08
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (57 bp):
TGTCCAAAAATTCCATTTTTACCTCGAAACTTTAAAAATTACCATTTTACCCCTGAA
Found at i:52657 original size:59 final size:60
Alignment explanation
Indices: 52520--52659 Score: 146
Period size: 59 Copynumber: 2.4 Consensus size: 60
52510 TAAAACTCTC
* * * * *
52520 AAAATTACCATTTTACCCCT-GAATGTCCAAAAATTCTATTTTTTATCCCAATTTTTCTA
1 AAAATTACCATTTTACCCCTCGAATGTCCAAAAATTCCATATTTAAACCCAATTTTCCTA
** * *
52579 AAAATTGTCGTTTTA-CCCTCGAATGT-CTAAAATTCCA-ATTTAAACCCTAAATTTTCCT-
1 AAAATTACCATTTTACCCCTCGAATGTCCAAAAATTCCATATTTAAACCC--AATTTTCCTA
52637 AAAATTACCATTTTACCCCTCGA
1 AAAATTACCATTTTACCCCTCGA
52660 GAATCCTAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
57 7 0.11
58 25 0.38
59 33 0.51
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
AAAATTACCATTTTACCCCTCGAATGTCCAAAAATTCCATATTTAAACCCAATTTTCCTA
Found at i:52671 original size:29 final size:29
Alignment explanation
Indices: 52633--52698 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
52623 CCCTAAATTT
52633 TCCTAAAATTACCATTTTACCCCTCGAGAA
1 TCCTAAAATTACCATTTTACCCC-CGAGAA
*
52663 TCCT-AAATTACCATTTTACCCCCGAGTA
1 TCCTAAAATTACCATTTTACCCCCGAGAA
*
52691 TCCAAAAA
1 TCCTAAAA
52699 GTCTCATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 8 0.24
29 21 0.64
30 4 0.12
ACGTcount: A:0.35, C:0.30, G:0.06, T:0.29
Consensus pattern (29 bp):
TCCTAAAATTACCATTTTACCCCCGAGAA
Found at i:60433 original size:68 final size:68
Alignment explanation
Indices: 60324--60458 Score: 243
Period size: 68 Copynumber: 2.0 Consensus size: 68
60314 ACTCTATTGG
*
60324 AATTAATTGATCCCAAATAGTACCCTTCGCTACAGGACAGTCCCTAATGACATGCAACACATCCT
1 AATTAATTGATCCCAAATAGTACCCTTCGCTACAGAACAGTCCCTAATGACATGCAACACATCCT
60389 CAT
66 CAT
* *
60392 AATTAATTGATCCCAAATAGTACCCTTCGCTACAGAACAGTCCCTAATGGCGTGCAACACATCCT
1 AATTAATTGATCCCAAATAGTACCCTTCGCTACAGAACAGTCCCTAATGACATGCAACACATCCT
60457 CA
66 CA
60459 GAAGCATGTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (68 bp):
AATTAATTGATCCCAAATAGTACCCTTCGCTACAGAACAGTCCCTAATGACATGCAACACATCCT
CAT
Found at i:62719 original size:18 final size:19
Alignment explanation
Indices: 62686--62721 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
62676 TTTTACATTA
*
62686 ATTATATAATTAAAAAATT
1 ATTATATAAATAAAAAATT
62705 ATTAT-TAAATAAAAAAT
1 ATTATATAAATAAAAAAT
62722 AAATAGGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTATATAAATAAAAAATT
Found at i:63621 original size:21 final size:22
Alignment explanation
Indices: 63597--63643 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
63587 ATGTAAATAT
*
63597 AATAATATAATT-AACAACATA
1 AATAACATAATTCAACAACATA
* *
63618 AATAACATAATTCAATACCATA
1 AATAACATAATTCAACAACATA
63640 AATA
1 AATA
63644 TCACAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAACATAATTCAACAACATA
Found at i:66434 original size:73 final size:73
Alignment explanation
Indices: 66355--66514 Score: 248
Period size: 73 Copynumber: 2.2 Consensus size: 73
66345 ATATTTTATT
*** * *
66355 ATATATATCAACAAGTGTTGTGGATTGAATCTTAAATCGATCTATATCAATATCGTTTTAAACAT
1 ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGATCGATATCAATATCGTTTTAAACAT
66420 TGTATCAA
66 TGTATCAA
* *
66428 ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGGTCGATATCAATATCGTTTTAGACAT
1 ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGATCGATATCAATATCGTTTTAAACAT
66493 TGTATCAA
66 TGTATCAA
*
66501 ATATATGTCAACAA
1 ATATATATCAACAA
66515 ATGATAAATT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (73 bp):
ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGATCGATATCAATATCGTTTTAAACAT
TGTATCAA
Done.