Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016064.1 Corchorus olitorius cultivar O-4 contig16097, 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: 53225
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:151 original size:2 final size:2
Alignment explanation
Indices: 144--169 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
134 ATCCTCTTTG
144 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
170 TGAATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3643 original size:36 final size:36
Alignment explanation
Indices: 3410--3647 Score: 288
Period size: 36 Copynumber: 6.6 Consensus size: 36
3400 CATCCATGCA
*
3410 TAAAATTAGTCAAAGGACTTAATTCAGGGTAATTAAG
1 TAAAATCAGTCAAA-GACTTAATTCAGGGTAATTAAG
*
3447 TAAAATTAGTC-AAGAACTTAATTCAGGGTAATTAAG
1 TAAAATCAGTCAAAG-ACTTAATTCAGGGTAATTAAG
* * * *
3483 TAAAGTCAGTAATCTAACACTT-ATTCAGGGAAATTAAG
1 TAAAATCAG---TCAAAGACTTAATTCAGGGTAATTAAG
3521 TAAAATCAGT-AAAGGACTTAATTCAGGGTAATTAAG
1 TAAAATCAGTCAAA-GACTTAATTCAGGGTAATTAAG
* *
3557 TAAAATCAGT-ACATGACTTAATTTA-GGTAATTAAG
1 TAAAATCAGTCA-AAGACTTAATTCAGGGTAATTAAG
* *
3592 TAAAATCAGTAAAAGACTTAATTCTGGGTAATTAAG
1 TAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAG
3628 TAAAATCAGTCAAAGACTTA
1 TAAAATCAGTCAAAGACTTA
3648 GGGGTTGTTT
Statistics
Matches: 177, Mismatches: 14, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
34 2 0.01
35 36 0.20
36 96 0.54
37 12 0.07
38 23 0.13
39 6 0.03
40 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (36 bp):
TAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAG
Found at i:3646 original size:71 final size:72
Alignment explanation
Indices: 3410--3647 Score: 295
Period size: 71 Copynumber: 3.3 Consensus size: 72
3400 CATCCATGCA
* * *
3410 TAAAATTAGTCAAAGGACTTAATTCAGGGTAATTAAGTAAAATTAGT-CAAGAACTTAATTCAGG
1 TAAAATCAGTCAAA-GACTTAATTCAGGGTAATTAAGTAAAATCAGTAAAAG-ACTTAATTCAGG
3474 GTAATTAAG
64 GTAATTAAG
* * * * *
3483 TAAAGTCAGTAATCTAACACTT-ATTCAGGGAAATTAAGTAAAATCAGTAAAGGACTTAATTCAG
1 TAAAATCAG---TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTAAAAGACTTAATTCAG
3547 GGTAATTAAG
63 GGTAATTAAG
* * *
3557 TAAAATCAGT-ACATGACTTAATTTA-GGTAATTAAGTAAAATCAGTAAAAGACTTAATTCTGGG
1 TAAAATCAGTCA-AAGACTTAATTCAGGGTAATTAAGTAAAATCAGTAAAAGACTTAATTCAGGG
3620 TAATTAAG
65 TAATTAAG
3628 TAAAATCAGTCAAAGACTTA
1 TAAAATCAGTCAAAGACTTA
3648 GGGGTTGTTT
Statistics
Matches: 141, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
71 66 0.47
72 5 0.04
73 7 0.05
74 53 0.38
75 6 0.04
76 4 0.03
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (72 bp):
TAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTAAAAGACTTAATTCAGGGT
AATTAAG
Found at i:4083 original size:36 final size:36
Alignment explanation
Indices: 4043--4267 Score: 201
Period size: 36 Copynumber: 6.6 Consensus size: 36
4033 CAAACAGAAC
4043 CTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGGA
* * *
4079 CTTAATTCAAGGTAATTAAATAAAATCAGTAAAGAA
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGGA
*
4115 C--AATTCAGGG-AA-TCAG-----TC---AAAGG-
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGGA
* * *
4138 CTTAATTCAAGCTAATTAAGTAAAATTAGTCAAA-GA
1 CTTAATTCAGGGTAATTAAGTAAAATCAGT-AAAGGA
* * *
4174 CTTAATTTAGGGTAATTAAGTAAAATCGGCAAAGG-
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGGA
* * **
4209 CTTAATTTAGGGTAATTAAGTAAAATTAGTAAATAA
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGGA
*
4245 CTTGATTCAGGGTAATTAAGTAA
1 CTTAATTCAGGGTAATTAAGTAA
4268 GTAACTTAAT
Statistics
Matches: 149, Mismatches: 24, Indels: 32
0.73 0.12 0.16
Matches are distributed among these distances:
23 1 0.01
24 4 0.03
25 7 0.05
26 2 0.01
27 5 0.03
32 3 0.02
33 2 0.01
34 8 0.05
35 34 0.23
36 83 0.56
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29
Consensus pattern (36 bp):
CTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGGA
Found at i:4214 original size:35 final size:35
Alignment explanation
Indices: 4132--4234 Score: 143
Period size: 35 Copynumber: 2.9 Consensus size: 35
4122 GGGAATCAGT
* * * *
4132 CAAAGGCTTAATTCAAGCTAATTAAGTAAAATTAGT
1 CAAAGGCTTAATTTAGGGTAATTAAGTAAAA-TAGG
* *
4168 CAAAGACTTAATTTAGGGTAATTAAGTAAAATCGG
1 CAAAGGCTTAATTTAGGGTAATTAAGTAAAATAGG
4203 CAAAGGCTTAATTTAGGGTAATTAAGTAAAAT
1 CAAAGGCTTAATTTAGGGTAATTAAGTAAAAT
4235 TAGTAAATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 33 0.55
36 27 0.45
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (35 bp):
CAAAGGCTTAATTTAGGGTAATTAAGTAAAATAGG
Found at i:4257 original size:71 final size:71
Alignment explanation
Indices: 4132--4267 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 71
4122 GGGAATCAGT
* *
4132 CAAAGGCTTAATTCAAGCTAATTAAGTAAAATTAGTCAAAGACTTAATTTAGGGTAATTAAGTAA
1 CAAAGGCTTAATTCAAGCTAATTAAGTAAAATTAGTCAAAAACTTAATTCAGGGTAATTAAGTAA
4197 AATCGG
66 AATCGG
* * * *
4203 CAAAGGCTTAATTTAGGGTAATTAAGTAAAATTAGT-AAATAACTTGATTCAGGGTAATTAAGTA
1 CAAAGGCTTAATTCAAGCTAATTAAGTAAAATTAGTCAAA-AACTTAATTCAGGGTAATTAAGTA
4267 A
65 A
4268 GTAACTTAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 3 0.05
71 55 0.95
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (71 bp):
CAAAGGCTTAATTCAAGCTAATTAAGTAAAATTAGTCAAAAACTTAATTCAGGGTAATTAAGTAA
AATCGG
Found at i:4267 original size:27 final size:27
Alignment explanation
Indices: 4232--4290 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
4222 AATTAAGTAA
* *
4232 AATT-AGTAAATAACTTGATTCAGGGT
1 AATTAAGTAAATAACTTAATTCAAGGT
*
4258 AATTAAGTAAGTAACTTAATTCAAGGT
1 AATTAAGTAAATAACTTAATTCAAGGT
4285 AATTAA
1 AATTAA
4291 CTAATCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (27 bp):
AATTAAGTAAATAACTTAATTCAAGGT
Found at i:11254 original size:18 final size:19
Alignment explanation
Indices: 11213--11272 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
11203 TTTAGAAGAT
*
11213 ATTAAAAAAAGATATAATA
1 ATTAAAAAAAGAAATAATA
*
11232 A-TAAAAAAGGAAATAA-A
1 ATTAAAAAAAGAAATAATA
11249 ATTAAAATTAAA-AAATAA-A
1 ATTAAAA--AAAGAAATAATA
11268 ATTAA
1 ATTAA
11273 GCAAGATTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 18 0.51
19 13 0.37
20 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
ATTAAAAAAAGAAATAATA
Found at i:16063 original size:51 final size:51
Alignment explanation
Indices: 15970--16501 Score: 440
Period size: 51 Copynumber: 10.5 Consensus size: 51
15960 GTAACGGAAG
* * *
15970 GATT-AAATTTTTAAGTGATTTATGAATAAAGATAGAATTTTTAATTAAAA
1 GATTGAAACTTTTAAGTAATTTGTGAATAAAGATAGAATTTTTAATTAAAA
* *
16020 GATTGAAACTTTTGAGTAATTTATGAATAAAGATAGAATTTTTAATTAAAA
1 GATTGAAACTTTTAAGTAATTTGTGAATAAAGATAGAATTTTTAATTAAAA
* * *
16071 GATTGAAACTTTTGAGTAATTTATGAATAAAGATAGAAGTTTTAATTAAAA
1 GATTGAAACTTTTAAGTAATTTGTGAATAAAGATAGAATTTTTAATTAAAA
* *
16122 GATTGAAACTTTTGAGTAATTTATGAATAAAGATAGAATTTTTAATTAAAA
1 GATTGAAACTTTTAAGTAATTTGTGAATAAAGATAGAATTTTTAATTAAAA
* * * * * * * *
16173 GATTGAAACTTATGAGCAATTTGTAAATAAAGGTTGAAATTTTAATGAAAA
1 GATTGAAACTTTTAAGTAATTTGTGAATAAAGATAGAATTTTTAATTAAAA
* * * * * **
16224 G-TTGAAACCTTTAAGCAATTTGTAAATAAA-AGTGGAACCTTTTAAAAAAAAAA
1 GATTGAAACTTTTAAGTAATTTGTGAATAAAGA-TAGAA--TTTT-TAATTAAAA
* * * * *
16277 GATTG-AACTTTTAAGAAATTGGTGAATAAAGGTTAG-ACTTTCAATTAAAA
1 GATTGAAACTTTTAAGTAATTTGTGAATAAA-GATAGAATTTTTAATTAAAA
* * * * * *
16327 GGTTGAAACTTGTAAGTAGTTTGT-AAGTAAAGATTGGA-CTTTAGATTTAAAA
1 GATTGAAACTTTTAAGTAATTTGTGAA-TAAAGATAGAATTTTTA-A-TTAAAA
* * * * * ** *
16379 GA-TCAAACTTTTGAGCAATTTGTAAATAAAGGTTCAAATTTTAATTAAAA
1 GATTGAAACTTTTAAGTAATTTGTGAATAAAGATAGAATTTTTAATTAAAA
* * * *
16429 GATTG-AACTTTTAAGAAATTTGT-AAGTGAAAG-TTGAATTTTTAATGAGAA
1 GATTGAAACTTTTAAGTAATTTGTGAA-T-AAAGATAGAATTTTTAATTAAAA
*
16479 G-TTGAAACCTTTTAAGCAATTTG
1 GATTGAAA-CTTTTAAGTAATTTG
16502 CAAATAAAAA
Statistics
Matches: 403, Mismatches: 59, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
49 5 0.01
50 94 0.23
51 254 0.63
52 16 0.04
53 29 0.07
54 5 0.01
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.36
Consensus pattern (51 bp):
GATTGAAACTTTTAAGTAATTTGTGAATAAAGATAGAATTTTTAATTAAAA
Found at i:16103 original size:31 final size:31
Alignment explanation
Indices: 16068--16155 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 31
16058 TTTTTAATTA
16068 AAAGATTGAAACTTTTGAGTAATTTATGAAT
1 AAAGATTGAAACTTTTGAGTAATTTATGAAT
* *
16099 AAAGATAG-AA-GTTT---TAA--T-T--A-
1 AAAGATTGAAACTTTTGAGTAATTTATGAAT
16119 AAAGATTGAAACTTTTGAGTAATTTATGAAT
1 AAAGATTGAAACTTTTGAGTAATTTATGAAT
16150 AAAGAT
1 AAAGAT
16156 AGAATTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 22
0.62 0.06 0.32
Matches are distributed among these distances:
20 7 0.17
21 3 0.07
22 3 0.07
23 1 0.02
24 1 0.02
25 3 0.07
26 3 0.07
27 1 0.02
28 1 0.02
29 3 0.07
30 3 0.07
31 13 0.31
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.36
Consensus pattern (31 bp):
AAAGATTGAAACTTTTGAGTAATTTATGAAT
Found at i:16163 original size:102 final size:101
Alignment explanation
Indices: 15970--16572 Score: 460
Period size: 102 Copynumber: 5.9 Consensus size: 101
15960 GTAACGGAAG
* ** * * *
15970 GATT-AAATTTTTAAGTGATTTATGAATAAAGATAGAATTTTTAATTAAAAGATTGAAACTTTTG
1 GATTGAAACTTTTAAGCAATTTGTGAATAAAGATAGAAATTTTAATTAAAAGATTGAAACTTTTA
*
16034 AGTAATTTATGAATAAAGATAGAATTTTTAATTAAAA
66 AGTAATTTGT-AATAAAGATAGAATTTTTAATTAAAA
* * * * *
16071 GATTGAAACTTTTGAGTAATTTATGAATAAAGATAGAAGTTTTAATTAAAAGATTGAAACTTTTG
1 GATTGAAACTTTTAAGCAATTTGTGAATAAAGATAGAAATTTTAATTAAAAGATTGAAACTTTTA
*
16136 AGTAATTTATGAATAAAGATAGAATTTTTAATTAAAA
66 AGTAATTTGT-AATAAAGATAGAATTTTTAATTAAAA
* * * * * * *
16173 GATTGAAACTTATGAGCAATTTGTAAATAAAGGTTGAAATTTTAATGAAAAG-TTGAAACCTTTA
1 GATTGAAACTTTTAAGCAATTTGTGAATAAAGATAGAAATTTTAATTAAAAGATTGAAACTTTTA
* * * **
16237 AGCAATTTGTAAATAAA-AGTGGAACCTTTTAAAAAAAAAA
66 AGTAATTTGT-AATAAAGA-TAGAA--TTTT-TAATTAAAA
* * * * * * *
16277 GATTG-AACTTTTAAGAAATTGGTGAATAAAGGTTAG-ACTTTCAATTAAAAGGTTGAAACTTGT
1 GATTGAAACTTTTAAGCAATTTGTGAATAAA-GATAGAAATTTTAATTAAAAGATTGAAACTTTT
* * * *
16340 AAGTAGTTTGTAAGTAAAGATTGGA-CTTTAGATTTAAAA
65 AAGTAATTTGTAA-TAAAGATAGAATTTTTA-A-TTAAAA
* * * * **
16379 GA-TCAAACTTTTGAGCAATTTGTAAATAAAGGTTCAAATTTTAATTAAAAGATTG-AACTTTTA
1 GATTGAAACTTTTAAGCAATTTGTGAATAAAGATAGAAATTTTAATTAAAAGATTGAAACTTTTA
* * * *
16442 AGAAATTTGTAAGTGAAAG-TTGAATTTTTAATGAGAA
66 AGTAATTTGTAA-T-AAAGATAGAATTTTTAATTAAAA
** * * *
16479 G-TTGAAACCTTTTAAGCAATTTGCAAATAAAAAT-GAAATCTTTAAATT-AAAGTAATG-AACC
1 GATTGAAA-CTTTTAAGCAATTTGTGAATAAAGATAGAAAT-TTT-AATTAAAAG-ATTGAAACT
* *
16540 TCTAACTAATTTGTAAATAAAGAT-GAAATTTTT
62 TTTAAGTAATTTGT-AATAAAGATAG-AATTTTT
16573 GATGGGCTTA
Statistics
Matches: 409, Mismatches: 70, Indels: 45
0.78 0.13 0.09
Matches are distributed among these distances:
100 15 0.04
101 96 0.23
102 218 0.53
103 40 0.10
104 39 0.10
105 1 0.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (101 bp):
GATTGAAACTTTTAAGCAATTTGTGAATAAAGATAGAAATTTTAATTAAAAGATTGAAACTTTTA
AGTAATTTGTAATAAAGATAGAATTTTTAATTAAAA
Found at i:16360 original size:205 final size:206
Alignment explanation
Indices: 16067--16453 Score: 498
Period size: 205 Copynumber: 1.9 Consensus size: 206
16057 ATTTTTAATT
* * * * *
16067 AAAAGATTGAAACTTTTGAGTAATTTATGAATAAAGATAGAAGTTTTAATTAAAAGATTGAAACT
1 AAAAGATTGAAACTTTTAAGAAATTGATGAATAAAGATAGAACTTTCAATTAAAAGATTGAAACT
* * * *
16132 TTTGAGTAATTTATGAATAAAGATAGAATTTTTA-A-TTAAAAGATTGAAACTTATGAGCAATTT
66 TGTAAGTAATTTATGAATAAAGATAGAA-CTTTAGATTTAAAAGA-TCAAACTTATGAGCAATTT
* *
16195 GTAAATAAAGGTTGAAATTTTAATGAAAAG-TTGAAACCTTTAAGCAATTTGTAAATAAAAGTGG
129 GTAAATAAAGGTTCAAATTTTAATGAAAAGATTG-AACCTTTAAGAAATTTGTAAATAAAAGTGG
16259 AACCTTTTAAAAAA
193 AACCTTTTAAAAAA
* * *
16273 AAAAGATTG-AACTTTTAAGAAATTGGTGAATAAAGGTTAG-ACTTTCAATTAAAAGGTTGAAAC
1 AAAAGATTGAAACTTTTAAGAAATTGATGAATAAA-GATAGAACTTTCAATTAAAAGATTGAAAC
* * * * *
16336 TTGTAAGTAGTTTGT-AAGTAAAGATTGGACTTTAGATTTAAAAGATCAAACTTTTGAGCAATTT
65 TTGTAAGTAATTTATGAA-TAAAGATAGAACTTTAGATTTAAAAGATCAAACTTATGAGCAATTT
* *
16400 GTAAATAAAGGTTCAAATTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAA
129 GTAAATAAAGGTTCAAATTTTAATGAAAAGATTGAACCTTTAAGAAATTTGTAA
16454 GTGAAAGTTG
Statistics
Matches: 155, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
204 6 0.04
205 125 0.81
206 24 0.15
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (206 bp):
AAAAGATTGAAACTTTTAAGAAATTGATGAATAAAGATAGAACTTTCAATTAAAAGATTGAAACT
TGTAAGTAATTTATGAATAAAGATAGAACTTTAGATTTAAAAGATCAAACTTATGAGCAATTTGT
AAATAAAGGTTCAAATTTTAATGAAAAGATTGAACCTTTAAGAAATTTGTAAATAAAAGTGGAAC
CTTTTAAAAAA
Found at i:16480 original size:19 final size:19
Alignment explanation
Indices: 16445--16484 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
16435 ACTTTTAAGA
16445 AATTTGTAAGTGAAAGTTG
1 AATTTGTAAGTGAAAGTTG
*
16464 AATTTTTAA-TGAGAAGTTG
1 AATTTGTAAGTGA-AAGTTG
16483 AA
1 AA
16485 ACCTTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (19 bp):
AATTTGTAAGTGAAAGTTG
Found at i:17187 original size:48 final size:48
Alignment explanation
Indices: 17119--17410 Score: 424
Period size: 48 Copynumber: 6.1 Consensus size: 48
17109 AAAAGAATGG
* * *
17119 TGTTTTCAATGTTTTGTTCCTGTCTTGCCCTTCCCAGTCGGAAGGTGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
17167 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
*
17215 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
* * * * *
17263 TGTTTTTACACATTTTATTCTTGTTTTGCCCTTCCCAATCGGAACGTGT
1 TGTTTTCA-ATATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
* *
17312 TGTTTTCCACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
* * * * *
17360 TGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCTA-TCGGAAGGAGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
17407 TGTT
1 TGTT
17411 CCTATTCTCT
Statistics
Matches: 220, Mismatches: 23, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
47 13 0.06
48 166 0.75
49 41 0.19
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (48 bp):
TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
Found at i:17326 original size:97 final size:96
Alignment explanation
Indices: 17119--17410 Score: 415
Period size: 97 Copynumber: 3.0 Consensus size: 96
17109 AAAAGAATGG
** * *
17119 TGTTTTCAATGTTTTGTTCCTGTCTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTTTTCAACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATATTTTAT
*
17184 TCCTGTTTTGCCCTTCCCAGTCGGAAGGTGT
66 TCCTGTTTTGCCCTTCCCAATCGGAAGGTGT
* * * *
17215 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACACATTTTA
1 TGTTTTCAACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA-ATATTTTA
* *
17280 TTCTTGTTTTGCCCTTCCCAATCGGAACGTGT
65 TTCCTGTTTTGCCCTTCCCAATCGGAAGGTGT
* * *
17312 TGTTTTCCACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTCTTCAATGTTTTAT
1 TGTTTTCAACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATATTTTAT
* * *
17377 TCCCGTTTTGCCCTT-CCTATCGGAAGGAGT
66 TCCTGTTTTGCCCTTCCCAATCGGAAGGTGT
17407 TGTT
1 TGTT
17411 CCTATTCTCT
Statistics
Matches: 174, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
95 16 0.09
96 71 0.41
97 87 0.50
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (96 bp):
TGTTTTCAACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATATTTTAT
TCCTGTTTTGCCCTTCCCAATCGGAAGGTGT
Found at i:22947 original size:20 final size:21
Alignment explanation
Indices: 22905--22949 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
22895 ATGAATAATG
22905 AAGAAAAGAATTGAAAAAGAA
1 AAGAAAAGAATTGAAAAAGAA
*
22926 AAGAAAA-AGTTG-AAAAGCAA
1 AAGAAAAGAATTGAAAAAG-AA
22946 AAGA
1 AAGA
22950 CGAAGGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (21 bp):
AAGAAAAGAATTGAAAAAGAA
Found at i:24384 original size:54 final size:53
Alignment explanation
Indices: 24312--24605 Score: 351
Period size: 54 Copynumber: 5.5 Consensus size: 53
24302 CGATCTTTTA
* * *
24312 AAGTTTTCAGAGATTTAAGTTGATCTTCTA-ATAACCCTGTGCGGTCTTTCGTAG
1 AAGTTTTCAGAGATCTAAGTTGAT-TTC-AGATGACCCTGTGCGGTCTTTCATAG
* * * *
24366 AAGATTTT-AGAGATTTAAGTTGATTTTAAGATGACCTTGTGCGGTCTTTCGTAG
1 AAG-TTTTCAGAGATCTAAGTTGA-TTTCAGATGACCCTGTGCGGTCTTTCATAG
*
24420 AAGTTTTCAGAGATATAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGAT-TTCAGATGACCCTGTGCGGTCTTTCATAG
* *
24474 AAGTTTTCAGAAATCTAAGTTGAGTTTAAGATGACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGA-TTTCAGATGACCCTGTGCGGTCTTTCATAG
* * * **
24528 AAGCTTTCAGAGATCTAAGTTGATATTCAGATAACCCGGTGTTGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGAT-TTCAGATGACCCTGTGCGGTCTTTCATAG
*
24582 AAGTTTTTAGAGATC-AGAGTTGAT
1 AAGTTTTCAGAGATCTA-AGTTGAT
24606 CGACAAATGA
Statistics
Matches: 213, Mismatches: 19, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
53 8 0.04
54 199 0.93
55 6 0.03
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (53 bp):
AAGTTTTCAGAGATCTAAGTTGATTTCAGATGACCCTGTGCGGTCTTTCATAG
Found at i:24502 original size:108 final size:107
Alignment explanation
Indices: 24312--24588 Score: 394
Period size: 108 Copynumber: 2.6 Consensus size: 107
24302 CGATCTTTTA
* *
24312 AAGTTTTCAGAGATTTAAGTTGATCTTCTA-ATAACCCTGTGCGGTCTTTCGTAGAAGATTTTAG
1 AAGTTTTCAGAGATATAAGTTGATCTTC-AGATAACCCTGTGCGGTCTTTCATAGAAG-TTTTAG
* * * * *
24376 AGATTTAAGTTGATTTTAAGATGACCTTGTGCGGTCTTTCGTAG
64 AAATCTAAGTTGAGTTTAAGATGACCCTGTGCGGTCTTTCATAG
*
24420 AAGTTTTCAGAGATATAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
1 AAGTTTTCAGAGATATAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATAGAAGTTTT-AGA
24485 AATCTAAGTTGAGTTTAAGATGACCCTGTGCGGTCTTTCATAG
65 AATCTAAGTTGAGTTTAAGATGACCCTGTGCGGTCTTTCATAG
* * * * **
24528 AAGCTTTCAGAGATCTAAGTTGATATTCAGATAACCCGGTGTTGTCTTTCATAGAAGTTTT
1 AAGTTTTCAGAGATATAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATAGAAGTTTT
24589 TAGAGATCAG
Statistics
Matches: 152, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
107 5 0.03
108 147 0.97
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (107 bp):
AAGTTTTCAGAGATATAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATAGAAGTTTTAGAA
ATCTAAGTTGAGTTTAAGATGACCCTGTGCGGTCTTTCATAG
Found at i:24640 original size:162 final size:162
Alignment explanation
Indices: 24345--24642 Score: 368
Period size: 162 Copynumber: 1.8 Consensus size: 162
24335 TCTTCTAATA
* * * * * **
24345 ACCCTGTGCGGTCTTTCGTAGAAGATTTTAGAGATTTAAGTTGATTTTAAGATGACCTTGTGCGG
1 ACCCTGTGCGGTCTTTCATAGAAGATTTCAGAGATCTAAGTTGATATTAAGATAACCCGGTGCGG
* ** * * *
24410 TCTTTCGTAGAAGTTTTCAGAGATATAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGA
66 TCTTTCATAGAAGTTTTCAGAGATATAAGTTGATCGACAAATGACCCAGTGCGATCTTTCATAGA
24475 AGTTTTCAGAAATCTAAGTTGAGTTTAAGATG
131 AGTTTTCAGAAATCTAAGTTGAGTTTAAGATG
* * **
24507 ACCCTGTGCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATATTCAGATAACCCGGTGTTG
1 ACCCTGTGCGGTCTTTCATAGAAGATTTCAGAGATCTAAGTTGATATTAAGATAACCCGGTGCGG
* * *
24572 TCTTTCATAGAAGTTTTTAGAGATCA-GAGTTGATCGACAAATGATCCAGTGCGAT-TATTCCA-
66 TCTTTCATAGAAGTTTTCAGAGAT-ATAAGTTGATCGACAAATGACCCAGTGCGATCT-TT-CAT
24634 AGAAGTTTT
128 AGAAGTTTT
24643 GAATGATCAG
Statistics
Matches: 113, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
161 1 0.01
162 109 0.96
163 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (162 bp):
ACCCTGTGCGGTCTTTCATAGAAGATTTCAGAGATCTAAGTTGATATTAAGATAACCCGGTGCGG
TCTTTCATAGAAGTTTTCAGAGATATAAGTTGATCGACAAATGACCCAGTGCGATCTTTCATAGA
AGTTTTCAGAAATCTAAGTTGAGTTTAAGATG
Found at i:25263 original size:54 final size:54
Alignment explanation
Indices: 24580--25263 Score: 708
Period size: 54 Copynumber: 12.7 Consensus size: 54
24570 TGTCTTTCAT
* ** * * * *
24580 AGAAGTTTTTAGA-GATCAGAGTTGATCGACAAATGATCCAGTGCGATTATTCCA
1 AGAAGTTTTCA-ATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
* * * * *
24634 AGAAGTTTTGAATGATCAGAGTTGATCCCCAAATGATCTAATGCGATCATTTCA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
* * *
24688 AGAAGTTTTCAGTGATTAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
** *
24742 AGAAGTTTTCTTTGATCAGAGTTGAT-CCCAGATGA-CCAGTGCGGTCATTCCA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
* * * *
24794 AGAAGTTTT-AGA-GATCAGAGTTGATCCCTAGATGATCCAGTGTGGTCATTTCAA
1 AGAAGTTTTCA-ATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCA-TTCCA
* * *
24848 AGAAGTTTTCAGTGATCAGAGTTGATCCCCACATGATCCAGTGCGGTCATTCCA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
** * * *
24902 AGAAGTTTTCTTTGATTAGAGTTGAT-CCCAGATGACCTAGTGCGGTTATTCCA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
* * *
24955 AGAAATTTT-AGA-GATCAGAGTTGATCCCTAGATGATAC-AGTGCAGTCATTCCAA
1 AGAAGTTTTCA-ATGATCAGAGTTGATCCCCAGATGAT-CTAGTGCGGTCATTCC-A
** * *
25009 AGAAGTTTTCTTTGATCAGAGTTGAT--CCAGATGATCTAGTGCGATCATTTCA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
* * * *
25061 AGAAGTTTTCAGTGATCACAGAGTTGATCCCCAAATGATCTTGTGTGGTCATTCCA
1 AGAAGTTTTCAATGAT--CAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
** * * * *
25117 AGAAGTTTTCTTTGATCAGAGTTGAT-CCCATATGATCCAGTGTGATCATTCCAA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCC-A
* * *
25171 AGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCTAGTGTGGTCATTCTA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
* * * * *
25225 AAAAGTTTGCAATGATCAGAGTTAATCTCTAGATGATCT
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCT
25264 GATTAGACCA
Statistics
Matches: 534, Mismatches: 76, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
51 13 0.02
52 62 0.12
53 113 0.21
54 243 0.46
55 68 0.13
56 35 0.07
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCA
Found at i:25748 original size:21 final size:21
Alignment explanation
Indices: 25698--25742 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25688 GTGACACCGC
*
25698 CCACCTGGGTCCTCAAGCAAA
1 CCACATGGGTCCTCAAGCAAA
* *
25719 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTCCTCAAGCAAA
25740 CCA
1 CCA
25743 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.13
Consensus pattern (21 bp):
CCACATGGGTCCTCAAGCAAA
Found at i:26531 original size:19 final size:18
Alignment explanation
Indices: 26507--26542 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
26497 TGAAGACTTA
26507 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
26526 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
26543 ATTATCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:30157 original size:54 final size:54
Alignment explanation
Indices: 30075--30232 Score: 271
Period size: 54 Copynumber: 2.9 Consensus size: 54
30065 CTTGGTCATT
*
30075 ATCCAATGCGGTCGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGATG
1 ATCCAGTGCGGTCGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGATG
* *
30129 ATCCAGTGCGGTCGTTTCAAAAAGTTTTCGAAGATCAGAGTTGATCTCTAGATG
1 ATCCAGTGCGGTCGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGATG
* *
30183 ATCCAGTGCGGTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCCA
1 ATCCAGTGCGGTCGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCA
30233 ATTGATACGG
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 97 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (54 bp):
ATCCAGTGCGGTCGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGATG
Found at i:32190 original size:75 final size:79
Alignment explanation
Indices: 32020--32191 Score: 190
Period size: 75 Copynumber: 2.2 Consensus size: 79
32010 AAATTTCAAG
* * *
32020 TAATCTTAACCCAAATAACTCAGAATCTTAAAGAACCCATAACCGATAAATTAAAGAACCCTTAT
1 TAATCTTAACCCAGATAACCCAGAATCTTAAAAAACCCATAA-C-ATAAATTAAAGAACCCTTAT
* ****
32085 AACCCTTAGCTGGTTA
64 AACCCTTAACTCAACA
* * * *
32101 TGATCTTAACCCAGATAACCCTGAATCTTAAAAAACCC-T-A-A-AATTTAATGAACCCTTATAA
1 TAATCTTAACCCAGATAACCCAGAATCTTAAAAAACCCATAACATAAATTAAAGAACCCTTATAA
32162 CCCTTAACTCAACA
66 CCCTTAACTCAACA
32176 TAATCTTAACCCAGAT
1 TAATCTTAACCCAGAT
32192 GACTAAAGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
75 42 0.54
76 1 0.01
79 1 0.01
80 1 0.01
81 33 0.42
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (79 bp):
TAATCTTAACCCAGATAACCCAGAATCTTAAAAAACCCATAACATAAATTAAAGAACCCTTATAA
CCCTTAACTCAACA
Found at i:32647 original size:13 final size:13
Alignment explanation
Indices: 32629--32655 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32619 TCAATCCATG
32629 ATTGCCCCACTTC
1 ATTGCCCCACTTC
32642 ATTGCCCCACTTC
1 ATTGCCCCACTTC
32655 A
1 A
32656 ATGAATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.44, G:0.07, T:0.30
Consensus pattern (13 bp):
ATTGCCCCACTTC
Found at i:33346 original size:46 final size:47
Alignment explanation
Indices: 33249--33351 Score: 190
Period size: 47 Copynumber: 2.2 Consensus size: 47
33239 ACCATCTTTT
*
33249 CTTTTTTTTTTTAGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAAC
1 CTTTTTTTTTGTAGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAAC
33296 CTTTTTTTTTGTAGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAA-
1 CTTTTTTTTTGTAGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAAC
33342 CTTTTTTTTT
1 CTTTTTTTTT
33352 CAAGTATAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 10 0.18
47 45 0.82
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (47 bp):
CTTTTTTTTTGTAGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAAC
Found at i:36780 original size:2 final size:2
Alignment explanation
Indices: 36773--36800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36763 GGAGATCTGG
36773 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
36801 CTCTGTGTGT
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):
AT
Found at i:36809 original size:2 final size:2
Alignment explanation
Indices: 36804--36828 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36794 TATATATCTC
36804 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
36829 AAATAAAATG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:37065 original size:31 final size:31
Alignment explanation
Indices: 36973--37057 Score: 145
Period size: 30 Copynumber: 2.8 Consensus size: 31
36963 CTTTTAGAAA
* *
36973 TTAAAACAACCCAAGAAACAGTTCCATAAAT
1 TTAAAATAACCCAAGAAAAAGTTCCATAAAT
37004 TTAAAAT-ACCCAAGAAAAAGTTCCATAAAT
1 TTAAAATAACCCAAGAAAAAGTTCCATAAAT
37034 TTAAAATAACCCAAGAAAAAGTTC
1 TTAAAATAACCCAAGAAAAAGTTC
37058 AACAAATTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 29 0.57
31 22 0.43
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21
Consensus pattern (31 bp):
TTAAAATAACCCAAGAAAAAGTTCCATAAAT
Found at i:39537 original size:30 final size:30
Alignment explanation
Indices: 39503--39587 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
39493 TTCTGGCTTT
*
39503 GGTAAAGGTTTTGGTTTTGATAAGGATTCC
1 GGTAAAGGTTTTGGTTTGGATAAGGATTCC
* * *
39533 GGTAAAGGTTTTCGCTTGGATAAGGATTCT
1 GGTAAAGGTTTTGGTTTGGATAAGGATTCC
* *
39563 GATAAAGGTTTTGGTTTGGGTAAGG
1 GGTAAAGGTTTTGGTTTGGATAAGG
39588 GTTTTGATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.24, C:0.06, G:0.33, T:0.38
Consensus pattern (30 bp):
GGTAAAGGTTTTGGTTTGGATAAGGATTCC
Found at i:39596 original size:30 final size:30
Alignment explanation
Indices: 39505--39597 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
39495 CTGGCTTTGG
* * *
39505 TAAAGGTTTTGGTTTTGATAAGGATTCCGG
1 TAAAGGTTTTGGTTTGGATAAGGATTCTGA
* *
39535 TAAAGGTTTTCGCTTGGATAAGGATTCTGA
1 TAAAGGTTTTGGTTTGGATAAGGATTCTGA
* * *
39565 TAAAGGTTTTGGTTTGGGTAAGGGTTTTGA
1 TAAAGGTTTTGGTTTGGATAAGGATTCTGA
39595 TAA
1 TAA
39598 GCTAGATACG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.25, C:0.05, G:0.30, T:0.40
Consensus pattern (30 bp):
TAAAGGTTTTGGTTTGGATAAGGATTCTGA
Found at i:43726 original size:20 final size:20
Alignment explanation
Indices: 43698--43749 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
43688 TTTAGAAAAA
43698 TATTCTTTTA-AATTTATTAT
1 TATT-TTTTACAATTTATTAT
*
43718 TATTATTTTTATCAATTTTTTAT
1 TA-T-TTTTTA-CAATTTATTAT
43741 TATTTTTTA
1 TATTTTTTA
43750 TAAATGAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 2 0.07
21 12 0.44
22 2 0.07
23 11 0.41
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTTTACAATTTATTAT
Found at i:43797 original size:13 final size:13
Alignment explanation
Indices: 43781--43807 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43771 ACAATCTTGC
43781 TTAATTTTAATTT
1 TTAATTTTAATTT
43794 TTAATTTTAATTT
1 TTAATTTTAATTT
43807 T
1 T
43808 ATTTCCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTAATTTTAATTT
Found at i:43819 original size:18 final size:19
Alignment explanation
Indices: 43798--43840 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
43788 TAATTTTTAA
*
43798 TTTTAATT-TTATTTCCTT
1 TTTTAATTATTATATCCTT
*
43816 TTTT-ATTATTATATCTTT
1 TTTTAATTATTATATCCTT
43834 TTTTAAT
1 TTTTAAT
43841 ATCCTCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 16 0.76
19 2 0.10
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTAATTATTATATCCTT
Found at i:48529 original size:19 final size:18
Alignment explanation
Indices: 48505--48543 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
48495 GTTTTTAAGT
*
48505 AAAAAAATGTAATATATAA
1 AAAAAAATATAATAT-TAA
*
48524 AAAAAATTATAATATTAA
1 AAAAAAATATAATATTAA
48542 AA
1 AA
48544 TAATTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAAAATATAATATTAA
Found at i:48553 original size:18 final size:18
Alignment explanation
Indices: 48504--48553 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
48494 AGTTTTTAAG
48504 TAAAAAAATGTAAT-ATAT
1 TAAAAAAAT-TAATAATAT
*
48522 AAAAAAAATT-ATAATAT
1 TAAAAAAATTAATAATAT
*
48539 TAAAATAATTAATAA
1 TAAAAAAATTAATAA
48554 ATAACCGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 2 0.07
17 13 0.48
18 12 0.44
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
TAAAAAAATTAATAATAT
Found at i:49156 original size:16 final size:16
Alignment explanation
Indices: 49135--49168 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
49125 TTATTAATCA
49135 TAAAATTAAAGCCAAT
1 TAAAATTAAAGCCAAT
*
49151 TAAAATTGAAGCCAAT
1 TAAAATTAAAGCCAAT
49167 TA
1 TA
49169 CTCATCATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (16 bp):
TAAAATTAAAGCCAAT
Found at i:50798 original size:28 final size:28
Alignment explanation
Indices: 50766--50822 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
50756 ATAGATTATT
*
50766 ATCCGTAAATTGACAATTGATTTAAGCA
1 ATCCGTAAATTGACAAATGATTTAAGCA
50794 ATCCGTAAATTGACAAATGATTTAAGCA
1 ATCCGTAAATTGACAAATGATTTAAGCA
50822 A
1 A
50823 GCATGACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (28 bp):
ATCCGTAAATTGACAAATGATTTAAGCA
Found at i:51862 original size:347 final size:350
Alignment explanation
Indices: 51217--51912 Score: 1060
Period size: 347 Copynumber: 2.0 Consensus size: 350
51207 ATTGCCAAGG
* * *
51217 CAGATGTCTTGAAATCTAAATCTGATATTCTTAGACCCAATTCGTTACTATGGAAGCCCAAAGAA
1 CAGATGTCTTGAAATCTAAATCTGATATTCTTAAACCCAATTCATTAATATGGAAGCCCAAAGAA
* * *
51282 GGAGTTCAAGTCCAATCAGTACTTATGATGCAGTAATGATTCAGCTCTGATGCAGCATTGTTAAA
66 GGAGTTCAAGTCCAATCAGTAATTATAATGCAGTAATGATTCAGCCCTGATGCAGCATTGTTAAA
* * * *
51347 TCATATTCGAAGGAGGACTTCACAGGAGCAGTTTTTGAAGAAAATTCATAATTTTTGATCCGAAA
131 TCATATTCGAA-GAGGACTTCACAAGAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCAGAAA
*
51412 CTTAGAAAAATGAAAATGAGGTACTGTTGGAAAGAAGATTCCAAGATCTACAACTTTTATGTTTA
195 CTTAGAAAAATGAAAATGAGGTACCGTTGGAAAGAAGATTCCAAGATCTACAACTTTTATGTTTA
* * * * * * *
51477 CATCGAGACCTAATTCTGCAGTTTAGGTGGATGATTTTGCCCTTGAAATTTCTGGATATAATTGA
260 CATCAAGACCTAATTCTACAGTTAAGGTAGACGATTTTGCCCTTGAAATTTCTGGACAGAATTGA
* *
51542 TCTTCTTCTAAACCGGCTTGGGGAGC
325 TCTTCTCCTAAACCGACTTGGGGAGC
* *
51568 CAGATGTCTTGAAGTCTAAATCTGATTTTCTTAAACCCAATTCATTAATATGGAAGCCCAAAGAA
1 CAGATGTCTTGAAATCTAAATCTGATATTCTTAAACCCAATTCATTAATATGGAAGCCCAAAGAA
51633 GGAG-TCTAAGTCCAATCAGTAATTATAATGCAGTAATG-TTCAGCCCTGATGCAGCATTGTTAA
66 GGAGTTC-AAGTCCAATCAGTAATTATAATGCAGTAATGATTCAGCCCTGATGCAGCATTGTTAA
* * *
51696 ATCCTATT-TAA-AGGACTTCACAAGAGCAGTTTTGGAAGAAAATTCATAACTTTTGTTCTAG-A
130 ATCATATTCGAAGAGGACTTCACAAGAGCAGTTTTGGAAGAAAATTCATAACTTTTGATC-AGAA
* * *
51758 GCTTAGAAAAATGCAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTT
194 ACTTAGAAAAATGAAAATGAGGTACCGTTGGAAAGAAGATTCCAAGATCTACAACTTTTATGTTT
* *
51823 ACCTCAAGACCTAATTCTACCGTTAAGGTAGACGATTTTGCCCTTGAAATTTCTGGACAGAATTG
259 ACATCAAGACCTAATTCTACAGTTAAGGTAGACGATTTTGCCCTTGAAATTTCTGGACAGAATTG
51888 ATCTTCTCCTAAACCGACTTGGGGA
324 ATCTTCTCCTAAACCGACTTGGGGA
51913 ATGTTTTGGA
Statistics
Matches: 313, Mismatches: 30, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
347 184 0.59
348 1 0.00
349 2 0.01
350 33 0.11
351 93 0.30
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (350 bp):
CAGATGTCTTGAAATCTAAATCTGATATTCTTAAACCCAATTCATTAATATGGAAGCCCAAAGAA
GGAGTTCAAGTCCAATCAGTAATTATAATGCAGTAATGATTCAGCCCTGATGCAGCATTGTTAAA
TCATATTCGAAGAGGACTTCACAAGAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCAGAAAC
TTAGAAAAATGAAAATGAGGTACCGTTGGAAAGAAGATTCCAAGATCTACAACTTTTATGTTTAC
ATCAAGACCTAATTCTACAGTTAAGGTAGACGATTTTGCCCTTGAAATTTCTGGACAGAATTGAT
CTTCTCCTAAACCGACTTGGGGAGC
Found at i:52276 original size:45 final size:45
Alignment explanation
Indices: 52201--52297 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
52191 AGTGCATTAC
* **
52201 CTAA-ATTCTAGTACTCCATCTATAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTACTCCATCTATACATAATTCATCAAAATAAAG
* * *
52245 CTAATATTCTACTCCTCCATCTCTACATAATTCATTAAAATAAAG
1 CTAATATTCTACTACTCCATCTATACATAATTCATCAAAATAAAG
*
52290 TTAATATT
1 CTAATATT
52298 AATTGTTTCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 4 0.09
45 41 0.91
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (45 bp):
CTAATATTCTACTACTCCATCTATACATAATTCATCAAAATAAAG
Done.