Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004040.1 Hibiscus syriacus cultivar Beakdansim tig00008825_pilon, 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: 53414
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:533 original size:13 final size:14
Alignment explanation
Indices: 515--553 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
505 TAGATATAAT
515 CAATTGAAT-TTAA
1 CAATTGAATATTAA
528 CAATTGAATAAGTTAA
1 CAATTGAAT-A-TTAA
544 CAATTGAATA
1 CAATTGAATA
554 AGGTTGTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.39
15 1 0.04
16 13 0.57
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (14 bp):
CAATTGAATATTAA
Found at i:545 original size:16 final size:16
Alignment explanation
Indices: 524--555 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
514 TCAATTGAAT
524 TTAACAATTGAATAAG
1 TTAACAATTGAATAAG
540 TTAACAATTGAATAAG
1 TTAACAATTGAATAAG
556 GTTGTAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (16 bp):
TTAACAATTGAATAAG
Found at i:1239 original size:49 final size:49
Alignment explanation
Indices: 1167--1448 Score: 430
Period size: 49 Copynumber: 5.8 Consensus size: 49
1157 AAATACCATG
* * * * *
1167 AGTGACACCTTTTATGTCGAAATGCACCGTTCTGCGTTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
*
1216 AGTGGCACATTTTATGCCTAAATG--CCG-T-TGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
*
1261 AGTGGCACCTTTTATGCCGAAATGCACCG-TATTGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTA-TGCATTTAACTTTCATT
1310 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
*
1359 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGTATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
* *
1408 AGTGGCATCTTTTATGCCTAAATGCACTGTTATGCATTTAA
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAA
1449 TTTAGCACCT
Statistics
Matches: 216, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
45 38 0.18
46 1 0.00
47 7 0.03
49 168 0.78
50 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
Found at i:1380 original size:143 final size:146
Alignment explanation
Indices: 1167--1448 Score: 428
Period size: 143 Copynumber: 1.9 Consensus size: 146
1157 AAATACCATG
* * *
1167 AGTGACACCTTTTATGTCGAAATGCACCGTTCTGCGTTTAACTTTCATTAGTGGCACATTTTATG
1 AGTGACACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACATTTTATG
1232 CCTAAATG-CCG-T-TGCATTTAACTTTCATTAGTGGCACCTTTTATGCCGAAATGCACCG-TAT
66 CCTAAATGACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTA-
1293 TGCATTTAACTTTCATT
130 TGCATTTAACTTTCATT
* * *
1310 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATG
1 AGTGACACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACATTTTATG
* * * *
1375 CCTAAATGCACCGTTATGTATTTAACTTTCATTAGTGGCATCTTTTATGCCTAAATGCACTGTTA
66 CCTAAATG-ACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTA
1440 TGCATTTAA
130 TGCATTTAA
1449 TTTAGCACCT
Statistics
Matches: 124, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
143 67 0.54
145 3 0.02
146 1 0.01
147 51 0.41
148 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (146 bp):
AGTGACACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACATTTTATG
CCTAAATGACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTAT
GCATTTAACTTTCATT
Found at i:7353 original size:49 final size:48
Alignment explanation
Indices: 7291--7429 Score: 156
Period size: 49 Copynumber: 2.8 Consensus size: 48
7281 GAATACCATG
*
7291 AGTGGTACCTTTTATGCTGAAATGCATCGTTATGCATTTAACTTT-TATT
1 AGTGGAACCTTTTATGCT-AAATGCATCGTTATGCATTTAACTTTCT-TT
* * *
7340 AGTGGAACATTTTATTCCTAAATGCACCGTTATGCATTTAACTTTCTTT
1 AGTGGAACCTTTTA-TGCTAAATGCATCGTTATGCATTTAACTTTCTTT
* * *
7389 AGT-GACACCTTTTATGCCTAAATGTATTGTTATACATTTAA
1 AGTGGA-ACCTTTTATG-CTAAATGCATCGTTATGCATTTAA
7430 TTTAGCACCA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
48 3 0.04
49 69 0.91
50 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (48 bp):
AGTGGAACCTTTTATGCTAAATGCATCGTTATGCATTTAACTTTCTTT
Found at i:10203 original size:108 final size:108
Alignment explanation
Indices: 10010--10330 Score: 518
Period size: 108 Copynumber: 3.0 Consensus size: 108
10000 GGTTGGTGAC
* * * *
10010 ATTG-TTTCTTGAAAGTTTTGCCTTGGAATAAGATATTGAGATTTGGTCACAAAGGAAAGATTAG
1 ATTGTTTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAG
*
10074 TCTAAAATTTATTAGACCCTATGAGGTGTTAGAGCGTATAAAT
66 TCTAAAATTTATTGGACCCTATGAGGTGTTAGAGCGTATAAAT
* *
10117 ATTGTTTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAAATTTTGTCACAAAGGAAAGCTTAG
1 ATTGTTTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAG
* *
10182 TCTAAAATTTATTGGACCCTATGAGGTGTTATAGCGTATAGAT
66 TCTAAAATTTATTGGACCCTATGAGGTGTTAGAGCGTATAAAT
* * *
10225 CTTGTTTTCTTGAAAGTTACACCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAG
1 ATTGTTTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAG
10290 TCTAAAATTTTATTGGACCCTATGAGGTGTTAGAGCGTATA
66 TCTAAAA-TTTATTGGACCCTATGAGGTGTTAGAGCGTATA
10331 GATCCTATAG
Statistics
Matches: 197, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
107 4 0.02
108 161 0.82
109 32 0.16
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (108 bp):
ATTGTTTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAG
TCTAAAATTTATTGGACCCTATGAGGTGTTAGAGCGTATAAAT
Found at i:12159 original size:28 final size:28
Alignment explanation
Indices: 12099--12173 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
12089 CTTAGCTGGA
* * *
12099 TATGGATGAGTGGAACAACTTCGTTAAC
1 TATGGATGAGTGGAGCAACTACGCTAAC
* *
12127 CATGGATGAGTGGAGCAACTACGCTATC
1 TATGGATGAGTGGAGCAACTACGCTAAC
*
12155 TATGGAAGAGTGG-GCAACT
1 TATGGATGAGTGGAGCAACT
12174 TGTTGTCCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 6 0.15
28 34 0.85
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (28 bp):
TATGGATGAGTGGAGCAACTACGCTAAC
Found at i:14776 original size:39 final size:39
Alignment explanation
Indices: 14733--14811 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
14723 CGTAGGCTAC
14733 CATGCTTTGGTGGCCATTCAACACTCCAACCACCATCAA
1 CATGCTTTGGTGGCCATTCAACACTCCAACCACCATCAA
* *
14772 CATGCTTTGGTGGCTATTCAACACTCCGACCACCATCAA
1 CATGCTTTGGTGGCCATTCAACACTCCAACCACCATCAA
14811 C
1 C
14812 GGTGGTCGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (39 bp):
CATGCTTTGGTGGCCATTCAACACTCCAACCACCATCAA
Found at i:16276 original size:13 final size:13
Alignment explanation
Indices: 16258--16284 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16248 AAAGTGTTAA
16258 TGAATTTTAAGAT
1 TGAATTTTAAGAT
16271 TGAATTTTAAGAT
1 TGAATTTTAAGAT
16284 T
1 T
16285 TTATATTCGA
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:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TGAATTTTAAGAT
Found at i:19365 original size:3 final size:3
Alignment explanation
Indices: 19357--19382 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19347 GTTTGAAACA
19357 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
19383 AACCCAATTC
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:25222 original size:12 final size:12
Alignment explanation
Indices: 25205--25241 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
25195 TCTAGTCGAT
25205 CAAACCCACCTC
1 CAAACCCACCTC
*
25217 CAAACCCACCTT
1 CAAACCCACCTC
*
25229 CAAATCCACCTC
1 CAAACCCACCTC
25241 C
1 C
25242 TATTCCACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.54, G:0.00, T:0.14
Consensus pattern (12 bp):
CAAACCCACCTC
Found at i:25249 original size:24 final size:23
Alignment explanation
Indices: 25204--25255 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
25194 TTCTAGTCGA
25204 TCAAACCCACCTCCAAACCCACC
1 TCAAACCCACCTCCAAACCCACC
* * **
25227 TTCAAATCCACCTCCTATTCCACC
1 -TCAAACCCACCTCCAAACCCACC
25251 TCAAA
1 TCAAA
25256 ATCCTATCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.19
Consensus pattern (23 bp):
TCAAACCCACCTCCAAACCCACC
Found at i:26486 original size:14 final size:13
Alignment explanation
Indices: 26441--26486 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
26431 TTTGGATGGA
*
26441 TTTTGAATATTTG
1 TTTTGGATATTTG
*
26454 GTTTGGATATTTG
1 TTTTGGATATTTG
*
26467 TTTTGGATGTTTG
1 TTTTGGATATTTG
26480 ATTTTGG
1 -TTTTGG
26487 TCTGTTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (13 bp):
TTTTGGATATTTG
Found at i:32424 original size:3 final size:3
Alignment explanation
Indices: 32416--32447 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
32406 TACATTGGTT
32416 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
32448 CATACACGAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:34869 original size:22 final size:20
Alignment explanation
Indices: 34843--34884 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
34833 TGAACAGTAC
34843 CATGTATAAAACTTCAGTAAAA
1 CATGTATAAAAC-TCA-TAAAA
34865 CATGTATAAAACTCATAAAA
1 CATGTATAAAACTCATAAAA
34885 ATTCAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 3 0.15
22 12 0.60
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.26
Consensus pattern (20 bp):
CATGTATAAAACTCATAAAA
Found at i:35140 original size:21 final size:20
Alignment explanation
Indices: 35060--35141 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
35050 CGCAAATCAG
*
35060 TTTCCAGATTCGCAACGCGAT
1 TTTCCA-ATTCGCAATGCGAT
**
35081 TATGACAA-TCGCAATGCGAT
1 T-TTCCAATTCGCAATGCGAT
**
35101 TTTCCAATTTCGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
35122 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
35142 ATAAGTAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.08
20 12 0.25
21 25 0.52
22 7 0.15
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:35174 original size:21 final size:21
Alignment explanation
Indices: 35148--35201 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
35138 GCGAATAAGT
35148 AAATCGCAATGCAAATTTGGA
1 AAATCGCAATGCAAATTTGGA
35169 AAATCGCAATGCAAATTTGGA
1 AAATCGCAATGCAAATTTGGA
35190 AAATCGCAATGC
1 AAATCGCAATGC
35202 GATACTAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCAAATTTGGA
Found at i:35247 original size:21 final size:21
Alignment explanation
Indices: 35213--35279 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
35203 ATACTAACTA
* * *
35213 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
35234 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
35254 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
35275 TCGCA
1 TCGCA
35280 ACGCGATTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:35311 original size:21 final size:21
Alignment explanation
Indices: 35275--35369 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
35265 TTTTCATAAT
*
35275 TCGCAACGCG-ATTAAGTAAA
1 TCGCAATGCGAATTAAGTAAA
*
35295 TCGCAATGTGAATTAAGTAAA
1 TCGCAATGCGAATTAAGTAAA
* *
35316 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAAGTAAA
*
35337 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTAAGTAAA
*
35357 TCGCAATGTGAAT
1 TCGCAATGCGAAT
35370 CTTACTATCG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
20 25 0.38
21 40 0.62
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGTAAA
Found at i:35363 original size:41 final size:42
Alignment explanation
Indices: 35131--35369 Score: 125
Period size: 41 Copynumber: 5.8 Consensus size: 42
35121 TTTTCCCAAT
* **
35131 TCGCAATGCGAA-TAAGTAAATCGCAATGCAAATTTGGAAAA
1 TCGCAATGCGAATTAAGTAAATCGCAATGCGAATTAAGAAAA
* ** * * **
35172 TCGCAATGCAAATTTGGAAAATCGCAATGCGATACT-A-ACTA
1 TCGCAATGCGAATTAAGTAAATCGCAATGCGA-ATTAAGAAAA
*** * * * * * *
35213 TCGCAATGC-AATTTTCCTAATTCGCATTGCGATTTACG-TAT
1 TCGCAATGCGAA-TTAAGTAAATCGCAATGCGAATTAAGAAAA
** * * * * *
35254 TCGCGTTGCGATTTTCA-TAATTCGCAACGCG-ATTAAGTAAA
1 TCGCAATGCGA-ATTAAGTAAATCGCAATGCGAATTAAGAAAA
* *
35295 TCGCAATGTGAATTAAGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAAGTAAATCGCAATGCGAATTAAGAAAA
* *
35337 TCGCAATGCGAA-TACGTAAATCGCAATGTGAAT
1 TCGCAATGCGAATTAAGTAAATCGCAATGCGAAT
35370 CTTACTATCG
Statistics
Matches: 145, Mismatches: 43, Indels: 20
0.70 0.21 0.10
Matches are distributed among these distances:
40 10 0.07
41 96 0.66
42 37 0.26
43 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (42 bp):
TCGCAATGCGAATTAAGTAAATCGCAATGCGAATTAAGAAAA
Found at i:35965 original size:19 final size:19
Alignment explanation
Indices: 35901--35985 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
35891 TAGTTTCGAG
35901 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
35921 AAT-AACTATCGCAA--C--
1 AATGAA-AATCGCAACGCGA
*
35936 AA-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
35954 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
35973 AACCAAAATCGCA
1 AATGAAAATCGCA
35986 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
14 7 0.13
15 3 0.06
16 1 0.02
18 3 0.06
19 28 0.54
20 10 0.19
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:36026 original size:14 final size:14
Alignment explanation
Indices: 36003--36124 Score: 64
Period size: 14 Copynumber: 7.6 Consensus size: 14
35993 TTTCATTTCG
*
36003 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
36017 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
36036 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36050 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
36069 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
36083 CGTTGTGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
36102 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36116 CGTTGCGAT
1 CGTTGCGAT
36125 AGTCATTTCC
Statistics
Matches: 84, Mismatches: 9, Indels: 30
0.68 0.07 0.24
Matches are distributed among these distances:
14 38 0.45
16 8 0.10
17 8 0.10
19 30 0.36
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36028 original size:33 final size:33
Alignment explanation
Indices: 35986--36173 Score: 259
Period size: 33 Copynumber: 5.5 Consensus size: 33
35976 CAAAATCGCA
*
35986 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36019 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36052 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* **
36085 TTGTGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
36118 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTATCTCG
1 TTGCGATTTTCATTT-CGCGTTGCGA--TTC----TCTCG
36158 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
36174 AACCAAAAGA
Statistics
Matches: 141, Mismatches: 7, Indels: 8
0.90 0.04 0.05
Matches are distributed among these distances:
33 109 0.77
34 10 0.07
36 3 0.02
39 1 0.01
40 18 0.13
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:36150 original size:20 final size:20
Alignment explanation
Indices: 36116--36173 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
36106 GCGATTCTCT
**
36116 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
36136 CGTTGCGATTTTCATTAT-CT
1 CGTTGCGATTTTCATT-TCCG
36156 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
36174 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:38327 original size:21 final size:21
Alignment explanation
Indices: 38303--38369 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
38293 TCATTCCTCG
38303 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
38324 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
38345 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
38366 AGAG
1 AGAG
38370 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:38327 original size:42 final size:42
Alignment explanation
Indices: 38281--38369 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
38271 CCTATCGTTG
*
38281 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
38323 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
38365 AAGAG
1 AAGAG
38370 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.10
42 35 0.85
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:39738 original size:14 final size:14
Alignment explanation
Indices: 39719--39754 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39709 ATTGTTTAAT
39719 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
39733 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
39747 TGATTTGT
1 TGATTTGT
39755 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:39883 original size:19 final size:19
Alignment explanation
Indices: 39861--39952 Score: 96
Period size: 19 Copynumber: 5.4 Consensus size: 19
39851 AAAAATTACT
39861 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39880 ATCGCAA--CG--AT-ATA
1 ATCGCAATGCGAAATGAAA
39894 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39913 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
39927 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39946 ATCGCAA
1 ATCGCAA
39953 CGACAAAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 19 0.32
15 3 0.05
16 4 0.07
17 4 0.07
18 3 0.05
19 26 0.44
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:39903 original size:33 final size:33
Alignment explanation
Indices: 39861--39986 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 33
39851 AAAAATTACT
* *
39861 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
39894 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
39927 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
39960 ATCGAAACGCGAAACT-AAAATCGCAAC
1 ATCGCAATGCGAAA-TGAAAATCGCAAC
39987 ATGAAACTAA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
33 85 0.99
34 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:39981 original size:19 final size:19
Alignment explanation
Indices: 39957--39997 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
39947 TCGCAACGAC
*
39957 AAAATCGAAACGCGAAACT
1 AAAATCGAAACACGAAACT
* *
39976 AAAATCGCAACATGAAACT
1 AAAATCGAAACACGAAACT
39995 AAA
1 AAA
39998 TTCGCATTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAATCGAAACACGAAACT
Found at i:40046 original size:33 final size:33
Alignment explanation
Indices: 40004--40095 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
39994 TAAATTCGCA
* *
40004 TTGCGATTTTTATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
* *
40037 TTGCGATTTTCATTTCACATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
40070 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
40096 AGTAATTTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
Found at i:40061 original size:19 final size:19
Alignment explanation
Indices: 40037--40095 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
40027 GATTCCCTCG
40037 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
* *
40056 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACA
*
40070 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCACA
40089 TTGCGAT
1 TTGCGAT
40096 AGTAATTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
16 3 0.10
17 3 0.10
19 16 0.52
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:40161 original size:20 final size:20
Alignment explanation
Indices: 40089--40161 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
40079 TCATTTCGCA
* *
40089 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* **
40109 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
40129 ATTGCGA-ATGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
40150 TTGCGATAGTCA
1 TTGCGATAGTCA
40162 AATGATTGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:43465 original size:20 final size:21
Alignment explanation
Indices: 43440--43488 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
43430 TCATAATTCA
*
43440 CAATGCGAA-TAAGTAAATCG
1 CAATGCGAATTAAGAAAATCG
* **
43460 CAATGCAAATTTGGAAAATCG
1 CAATGCGAATTAAGAAAATCG
43481 CAATGCGA
1 CAATGCGA
43489 TACTGACTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (21 bp):
CAATGCGAATTAAGAAAATCG
Found at i:43562 original size:20 final size:20
Alignment explanation
Indices: 43473--43564 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
43463 TGCAAATTTG
* *
43473 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
43493 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
43513 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
43534 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
43554 GAAAATCGCAA
1 GAAAATCGCAA
43565 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:43783 original size:14 final size:14
Alignment explanation
Indices: 43764--43793 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43754 TCATTTAACT
*
43764 ATCGCAACGGGGAA
1 ATCGCAACGCGGAA
43778 ATCGCAACGCGGAA
1 ATCGCAACGCGGAA
43792 AT
1 AT
43794 GGCTATCGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.23, G:0.30, T:0.10
Consensus pattern (14 bp):
ATCGCAACGCGGAA
Found at i:43803 original size:20 final size:20
Alignment explanation
Indices: 43778--43865 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
43768 CAACGGGGAA
*
43778 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
43798 ATCGCAACGCGAAAATTGCT
1 ATCGCAACGCGAAAATGGCT
* ***
43818 ATCGCAATGCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
* *
43838 ATCGCAAGGTGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
43858 ATCGCAAC
1 ATCGCAAC
43866 TAGAAAATCG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
19 4 0.08
20 44 0.83
21 5 0.09
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:43926 original size:19 final size:19
Alignment explanation
Indices: 43911--43959 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
43901 GATTTTCTCG
43911 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
43930 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
43949 TTGCGATTTTC
1 TTGCGATTTTC
43960 TCATTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:45983 original size:20 final size:20
Alignment explanation
Indices: 45908--46014 Score: 126
Period size: 20 Copynumber: 5.4 Consensus size: 20
45898 TAGTTTACTT
* * * *
45908 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
45928 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
45948 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
45968 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
45988 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
46007 TCGCAACG
1 TCGCAACG
46015 ACAAAATCGC
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 13 0.17
20 62 0.83
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:46022 original size:14 final size:14
Alignment explanation
Indices: 46003--46127 Score: 88
Period size: 14 Copynumber: 7.9 Consensus size: 14
45993 ATGCGAAATG
46003 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
46017 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
46036 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
46050 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
46069 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
46083 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
46102 AAAATCGCAACGAC
1 AAAATCGCAACGAC
46116 AAAATCGCAACG
1 AAAATCGCAACG
46128 CGAAACACAA
Statistics
Matches: 90, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
14 42 0.47
15 3 0.03
16 6 0.07
17 6 0.07
18 3 0.03
19 30 0.33
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:46143 original size:33 final size:33
Alignment explanation
Indices: 45987--46132 Score: 283
Period size: 33 Copynumber: 4.4 Consensus size: 33
45977 GAAAATGGCT
45987 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
46020 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
46053 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
46086 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
46119 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
46133 CACAAATCGC
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 112 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:46161 original size:19 final size:19
Alignment explanation
Indices: 46139--46221 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
46129 GAAACACAAA
*
46139 TCGCATTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
46158 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
46177 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
46193 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
46210 TCGCATTGCGAT
1 TCGCATTGCGAT
46222 AGACATTTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 3 0.06
19 34 0.63
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:46823 original size:18 final size:18
Alignment explanation
Indices: 46800--46847 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
46790 CGGGTTGATT
46800 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
46818 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
46836 AGGTGATGGCTC
1 AGGTGATGGCTC
46848 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:48215 original size:20 final size:20
Alignment explanation
Indices: 48167--48225 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
48157 AATAGTTTCT
* *
48167 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
48187 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
48207 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
48226 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:48501 original size:22 final size:22
Alignment explanation
Indices: 48474--48517 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
48464 GATGGAGATA
48474 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
48496 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
48518 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:48736 original size:20 final size:21
Alignment explanation
Indices: 48711--48773 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
48701 TATTATCTCA
*
48711 TTGCGAAAGTCAA-TATTGAG
1 TTGCGAAAGTCAAGTATCGAG
*
48731 TTGCGAAA-TTAAGTATCGAG
1 TTGCGAAAGTCAAGTATCGAG
*
48751 TTGCGAAAGTC-AGTATCGCG
1 TTGCGAAAGTCAAGTATCGAG
48771 TTG
1 TTG
48774 AGATTTTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 33 0.89
21 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (21 bp):
TTGCGAAAGTCAAGTATCGAG
Found at i:48803 original size:41 final size:41
Alignment explanation
Indices: 48744--48821 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
48734 CGAAATTAAG
48744 TATCGAGTTGCGAAAGTCAGTATCGCGTTGAGATTTTGTAT
1 TATCGAGTTGCGAAAGTCAGTATCGCGTTGAGATTTTGTAT
* * * *
48785 TATCGCGTTGTGATAGTCAGTATCGCGTTGCGATTTT
1 TATCGAGTTGCGAAAGTCAGTATCGCGTTGAGATTTT
48822 CCAAATTCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (41 bp):
TATCGAGTTGCGAAAGTCAGTATCGCGTTGAGATTTTGTAT
Found at i:48810 original size:20 final size:20
Alignment explanation
Indices: 48742--48814 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
48732 TGCGAAATTA
* * *
48742 AGTATCGAGTTGCGAAAGTC
1 AGTATCGCGTTGAGATAGTC
*
48762 AGTATCGCGTTGAGATTTTGT-
1 AGTATCGCGTTGAGA--TAGTC
* *
48783 ATTATCGCGTTGTGATAGTC
1 AGTATCGCGTTGAGATAGTC
48803 AGTATCGCGTTG
1 AGTATCGCGTTG
48815 CGATTTTCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.07
20 24 0.57
21 13 0.31
22 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.36
Consensus pattern (20 bp):
AGTATCGCGTTGAGATAGTC
Found at i:48854 original size:20 final size:20
Alignment explanation
Indices: 48826--48878 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
48816 GATTTTCCAA
*
48826 ATTCACATTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
*
48846 ATTCGCATTGCAATTTACTT
1 ATTCGCATTGCGATTTACTT
48866 ATTCGCATTGCGA
1 ATTCGCATTGCGA
48879 ATTGGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:48892 original size:21 final size:20
Alignment explanation
Indices: 48868--48920 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
48858 ATTTACTTAT
48868 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
48889 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
48910 TCGCATTGCGA
1 TCGCATTGCGA
48921 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:49631 original size:23 final size:22
Alignment explanation
Indices: 49605--49647 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
49595 ATTAGGGGTA
*
49605 TATGAAATTTTTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
49628 TATGTATTTGTCCCGAAGGA
1 TATGAATTTGTCCCGAAGGA
49648 TCGGGTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Done.