Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005084.1 Hibiscus syriacus cultivar Beakdansim tig00011422_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: 52679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6304 original size:25 final size:25
Alignment explanation
Indices: 6270--6321 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
6260 ATATTGATCC
* *
6270 CCCGTCCCCGTCCCCGTTTAAAAAA
1 CCCGTACCCGTCCCCGCTTAAAAAA
6295 CCCGTACCCGTCCCCGCTTAAAAAA
1 CCCGTACCCGTCCCCGCTTAAAAAA
6320 CC
1 CC
6322 GCAAGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.46, G:0.12, T:0.17
Consensus pattern (25 bp):
CCCGTACCCGTCCCCGCTTAAAAAA
Found at i:6424 original size:12 final size:12
Alignment explanation
Indices: 6409--6439 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6399 GTTATTTAAA
*
6409 CGGGTATCGGGT
1 CGGGTATCGGGC
6421 CGGGTATCGGGC
1 CGGGTATCGGGC
6433 CGGGTAT
1 CGGGTAT
6440 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:6444 original size:2 final size:2
Alignment explanation
Indices: 6437--6505 Score: 88
Period size: 2 Copynumber: 35.5 Consensus size: 2
6427 TCGGGCCGGG
* *
6437 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
6479 T- TA AA TA TA TA AA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6506 TTTAATTTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6528 original size:32 final size:32
Alignment explanation
Indices: 6450--6512 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
6440 ATATATATAT
*
6450 ATATATATATATATATATATATATTTAAATTAA
1 ATATATAAATAT-TATATATATATTTAAATTAA
*
6483 ATATATAAATATTATATATATATTTTAATT
1 ATATATAAATATTATATATATATTTAAATT
6513 TAATTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATATAAATATTATATATATATTTAAATTAA
Found at i:6675 original size:29 final size:30
Alignment explanation
Indices: 6609--6678 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
6599 CCCGTCCCCA
* *
6609 TCCCCGTTTAGCATAAACGGTTTTTTTCCG
1 TCCCCGTTTAACATAAACGGTTTTTTCCCG
6639 TCCCCGTTTAACATAAACGG-TTTTTCCCG
1 TCCCCGTTTAACATAAACGGTTTTTTCCCG
**
6668 TCGTCGTTTAA
1 TCCCCGTTTAA
6679 TTCGATTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.39
Consensus pattern (30 bp):
TCCCCGTTTAACATAAACGGTTTTTTCCCG
Found at i:10963 original size:19 final size:19
Alignment explanation
Indices: 10935--10976 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
10925 TCATTTTATG
10935 AATT-TAAAAATACATAA-A
1 AATTATAAAAATA-ATAATA
10953 AATTATAAAAATAATAATA
1 AATTATAAAAATAATAATA
10972 AATTA
1 AATTA
10977 ATCACATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTATAAAAATAATAATA
Found at i:12783 original size:29 final size:29
Alignment explanation
Indices: 12741--12869 Score: 249
Period size: 29 Copynumber: 4.4 Consensus size: 29
12731 TACCGGGGGT
12741 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
12770 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
12799 AGGTCGCCATGCACGCCCGGCGCCCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
12828 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
12857 AGGTCGCCATGCA
1 AGGTCGCCATGCA
12870 GACCTACCCC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 98 1.00
ACGTcount: A:0.20, C:0.44, G:0.28, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:12914 original size:30 final size:30
Alignment explanation
Indices: 12880--12989 Score: 175
Period size: 30 Copynumber: 3.7 Consensus size: 30
12870 GACCTACCCC
12880 ACGACCTCCATGCACGCCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
* * *
12910 ACGACCTCCATGCATGCCCAGGCACGTCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
* *
12940 ACGACCTCCGTGCACGGCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
12970 ACGACCTCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCA
12990 GCTCGCCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.23, C:0.47, G:0.19, T:0.11
Consensus pattern (30 bp):
ACGACCTCCATGCACGCCCATGCACGCCCA
Found at i:13662 original size:21 final size:21
Alignment explanation
Indices: 13637--13680 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
13627 AATTTAGTTA
13637 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
13658 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
13679 AT
1 AT
13681 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:13694 original size:28 final size:28
Alignment explanation
Indices: 13657--13710 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
13647 TAGTATAAAT
*
13657 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
13685 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
13711 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:14192 original size:49 final size:49
Alignment explanation
Indices: 14086--14180 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 49
14076 AGTAATGATT
*
14086 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
14135 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTT
14181 TTGGTTCAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 24 0.55
49 20 0.45
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:14199 original size:7 final size:7
Alignment explanation
Indices: 14187--14220 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
14177 ATTTTTGGTT
14187 CAATGAA
1 CAATGAA
14194 CAATGAA
1 CAATGAA
14201 CAATGAA
1 CAATGAA
14208 CAATGAA
1 CAATGAA
14215 CAATGA
1 CAATGA
14221 TTTAGTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:14247 original size:26 final size:26
Alignment explanation
Indices: 14216--14353 Score: 96
Period size: 26 Copynumber: 5.5 Consensus size: 26
14206 AACAATGAAC
14216 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAGTAATAATCATTATAAA
*
14242 AATGA-TT--TAATAATGATT-T--A
1 AATGATTTAGTAATAATCATTATAAA
* * * * **
14262 AAT-ATTTAATGATTTGATGATT-TAGT
1 AATGATTTAGT-A-ATAATCATTATAAA
**
14288 AATGATTT-GATAATAATCATTATAGT
1 AATGATTTAG-TAATAATCATTATAAA
14314 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAGTAATAATCATTATAAA
*
14340 AATGATTTAATAAT
1 AATGATTTAGTAAT
14354 GATTTAAATA
Statistics
Matches: 90, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
19 1 0.01
20 6 0.07
22 2 0.02
23 11 0.12
24 8 0.09
25 8 0.09
26 48 0.53
27 6 0.07
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (26 bp):
AATGATTTAGTAATAATCATTATAAA
Found at i:14254 original size:98 final size:97
Alignment explanation
Indices: 14166--14434 Score: 289
Period size: 98 Copynumber: 2.8 Consensus size: 97
14156 ATTTATTATT
* *
14166 AATATTTAATGATTT-TTGGTTCAATGAA-CA-ATGAACAATGAA-CA-ATGAACAATGATTTAG
1 AATATTTAATGATTTGATGATTCAAT-AATCATATG-ACAAT-AATCATAT-AACAATGATTTAG
14226 TAATAATCATTATAAAAATGATTTAATAATGATTTA
62 TAATAATCATTATAAAAATGATTTAATAATGATTTA
* * * * * **
14262 AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTAGTAA
1 AATATTTAATGATTTGATGATTCAATAATCATATGACAATAATCA-TATAACAATGATTTAGTAA
14327 TAATCATTATAAAAATGATTTAATAATGATTTA
65 TAATCATTATAAAAATGATTTAATAATGATTTA
* * * * * *
14360 AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTA-TA
1 AATATTTAATGATTTGATGATTCAATAATCATATGACAATAATCA-TATAACAATGA-TTTAGTA
*
14424 ATAATTATTAT
64 ATAATCATTAT
14435 GTTATTATTT
Statistics
Matches: 155, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
96 19 0.12
97 13 0.08
98 117 0.75
99 6 0.04
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.42
Consensus pattern (97 bp):
AATATTTAATGATTTGATGATTCAATAATCATATGACAATAATCATATAACAATGATTTAGTAAT
AATCATTATAAAAATGATTTAATAATGATTTA
Found at i:14414 original size:26 final size:26
Alignment explanation
Indices: 14287--14434 Score: 121
Period size: 26 Copynumber: 5.9 Consensus size: 26
14277 GATGATTTAG
*
14287 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
14313 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
14339 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
14362 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
14385 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* *
14411 TAATGATTTTATAATAATTATTAT
1 TAATGATTTGATAATAATCATTAT
14435 GTTATTATTT
Statistics
Matches: 95, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.04
22 3 0.03
23 12 0.13
24 7 0.07
25 7 0.07
26 61 0.64
27 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:14595 original size:14 final size:13
Alignment explanation
Indices: 14576--14640 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
14566 TTTAAATATT
14576 TAATGATTTGATAC
1 TAATGATTT-ATAC
14590 TAATGA-TT-TAC
1 TAATGATTTATAC
*
14601 TAAT--TAT-TAC
1 TAATGATTTATAC
14611 TAATGATTTAATAC
1 TAATGATTT-ATAC
*
14625 TAATTATTTGATAC
1 TAATGATTT-ATAC
14639 TA
1 TA
14641 GTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 2 0.05
13 2 0.05
14 23 0.55
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAC
Found at i:14612 original size:10 final size:11
Alignment explanation
Indices: 14587--14620 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
14577 AATGATTTGA
14587 TACTAATGATT
1 TACTAATGATT
*
14598 TACTAATTA-T
1 TACTAATGATT
14608 TACTAATGATT
1 TACTAATGATT
14619 TA
1 TA
14621 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:14630 original size:21 final size:21
Alignment explanation
Indices: 14587--14630 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
14577 AATGATTTGA
* *
14587 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
14608 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
14629 TA
1 TA
14631 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:14647 original size:17 final size:17
Alignment explanation
Indices: 14625--14657 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
14615 GATTTAATAC
14625 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
14642 TAATTATTTGATACTA
1 TAATTATTTGATACTA
14658 AACATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:16962 original size:32 final size:33
Alignment explanation
Indices: 16888--16968 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
16878 CCAAACCCTT
*
16888 AAAC-AACTAATAAAATATTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTATATAACTA
16920 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTT-A-TATAACTA
*
16953 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
16969 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 15 0.34
33 22 0.50
34 2 0.05
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.38
Consensus pattern (33 bp):
AAACTAACTAATAAACTATTTTTTATATAACTA
Found at i:17272 original size:4 final size:4
Alignment explanation
Indices: 17244--17300 Score: 54
Period size: 4 Copynumber: 15.5 Consensus size: 4
17234 CCTTATCTCC
*
17244 CTTT C-TT C-TT CTTA CTTT CCTTT CTTT C--T CTTT CTTT CTTT C-TT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT
17288 -TTT CTTT CTTT CT
1 CTTT CTTT CTTT CT
17301 CGGCTGAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
2 2 0.04
3 10 0.22
4 29 0.64
5 4 0.09
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:17278 original size:10 final size:10
Alignment explanation
Indices: 17244--17301 Score: 61
Period size: 10 Copynumber: 6.1 Consensus size: 10
17234 CCTTATCTCC
17244 CTTTC-TTCTT
1 CTTTCTTTC-T
*
17254 CTTACTTTC-
1 CTTTCTTTCT
17263 CTTTCTTTCT
1 CTTTCTTTCT
17273 CTTTC-TT-T
1 CTTTCTTTCT
*
17281 CTTTCTTTTT
1 CTTTCTTTCT
17291 CTTTCTTTCT
1 CTTTCTTTCT
17301 C
1 C
17302 GGCTGAATCT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 6 0.15
9 12 0.29
10 20 0.49
11 3 0.07
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (10 bp):
CTTTCTTTCT
Found at i:17280 original size:14 final size:14
Alignment explanation
Indices: 17258--17301 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
17248 CTTCTTCTTA
17258 CTTTCCTTTCTTTCT
1 CTTT-CTTTCTTTCT
17273 CTTTCTTTCTTTCT
1 CTTTCTTTCTTTCT
*
17287 TTTTCTTTCTTTCT
1 CTTTCTTTCTTTCT
17301 C
1 C
17302 GGCTGAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTCTTTCTTTCT
Found at i:17574 original size:50 final size:50
Alignment explanation
Indices: 17469--17564 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
17459 GCATGCTGTT
17469 GGCATGCAGCGGGGAGCAGGAGCACGTGAACTTATCTTGGCATGCATGCA
1 GGCATGCAGCGGGGAGCAGGAGCACGTGAACTTATCTTGGCATGCATGCA
*
17519 GGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTAT-TTGGC-TGCATG
1 GGCATGCAGCGGGGAGCAGGAGCACGTGAACTTATCTTGGCATGCATG
17565 TGCATGCATG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 6 0.13
49 5 0.11
50 34 0.76
ACGTcount: A:0.23, C:0.20, G:0.39, T:0.19
Consensus pattern (50 bp):
GGCATGCAGCGGGGAGCAGGAGCACGTGAACTTATCTTGGCATGCATGCA
Found at i:17599 original size:13 final size:13
Alignment explanation
Indices: 17581--17607 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17571 CATGGTCTCG
17581 GGAGGAAGTGGAC
1 GGAGGAAGTGGAC
17594 GGAGGAAGTGGAC
1 GGAGGAAGTGGAC
17607 G
1 G
17608 CTGGGGCGAC
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:0.07, G:0.56, T:0.07
Consensus pattern (13 bp):
GGAGGAAGTGGAC
Found at i:17645 original size:29 final size:29
Alignment explanation
Indices: 17612--17706 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
17602 TGGACGCTGG
17612 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
17641 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
17670 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
17699 GGCGACCT
1 GGCGACCT
17707 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:17735 original size:32 final size:32
Alignment explanation
Indices: 17693--17764 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
17683 GTCGCCCAGA
*
17693 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
17725 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
17757 CTGCATGG
1 CTGCATGG
17765 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:17829 original size:24 final size:19
Alignment explanation
Indices: 17779--17816 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17769 TATATGGCTT
17779 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
17798 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
17817 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:18689 original size:20 final size:21
Alignment explanation
Indices: 18664--18756 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
18654 TTTTCCCAAT
*
18664 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
18684 TCGCAACGCTAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
18705 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
18725 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
18746 TCGCAATGCGA
1 TCGCAATGCGA
18757 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:18709 original size:41 final size:41
Alignment explanation
Indices: 18664--18756 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
18654 TTTTCCCAAT
*
18664 TCGCAATGCGAATAAGTAAATCGCAACGCTAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
18705 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
18746 TCGCAATGCGA
1 TCGCAATGCGA
18757 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:18769 original size:41 final size:41
Alignment explanation
Indices: 18683--18817 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
18673 GAATAAGTAA
* * *
18683 ATCGCAACGCTAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
18724 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
18765 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
18806 TTCGCAACGCGA
1 ATCGCAACGCGA
18818 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:18770 original size:20 final size:20
Alignment explanation
Indices: 18745--18859 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
18735 AATTGGGAAA
*
18745 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
18765 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
18786 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
18806 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
18826 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
18846 TTCGCAACGCGATA
1 ATCGCAACGCGATA
18860 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:18818 original size:41 final size:41
Alignment explanation
Indices: 18742--18879 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
18732 GCGAATTGGG
* * *
18742 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
18783 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
18825 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
18864 ATAATCACAATGCGAT
1 AAAATCGCAACGCGAT
18880 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.40
41 43 0.55
42 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:19077 original size:22 final size:22
Alignment explanation
Indices: 19049--19090 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19039 CTCTCTCACT
19049 CATCTCCGACGAAATCCGTCCC
1 CATCTCCGACGAAATCCGTCCC
*
19071 CATCTCCGGCGAAATCCGTC
1 CATCTCCGACGAAATCCGTC
19091 TATCTCCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.43, G:0.17, T:0.19
Consensus pattern (22 bp):
CATCTCCGACGAAATCCGTCCC
Found at i:19378 original size:20 final size:20
Alignment explanation
Indices: 19334--19397 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
19324 GCGATTTTAG
19334 TTTCGCGTTGCGATAGTCGA-
1 TTTCGCGTTGCGATAGTC-AT
*
19354 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
19374 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
19394 TTTC
1 TTTC
19398 AGAAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:20735 original size:18 final size:18
Alignment explanation
Indices: 20714--20758 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
20704 TCCACTTCGG
*
20714 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
20732 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
20750 GAGCCATCA
1 GAGCCATCA
20759 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:21297 original size:19 final size:20
Alignment explanation
Indices: 21243--21309 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
21233 TAGTTTACTT
* *
21243 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
21263 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
21283 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
21302 TCGCAACG
1 TCGCAACG
21310 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:21317 original size:14 final size:14
Alignment explanation
Indices: 21298--21354 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21288 ATGCGAAATG
21298 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
21312 AAAATCGCAATTGCGAA
1 AAAATCGCAA---CGAC
21329 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
21345 AAAATCGCAA
1 AAAATCGCAA
21355 TGCTATTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 19 0.53
16 4 0.11
17 4 0.11
19 9 0.25
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:21336 original size:33 final size:34
Alignment explanation
Indices: 21282--21355 Score: 134
Period size: 33 Copynumber: 2.2 Consensus size: 34
21272 GGAAATGGCT
21282 ATCGCAA-TGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATTGCGAAATGAAAATCGCAACGACAAA
21315 ATCGCAATTGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATTGCGAAATGAAAATCGCAACGACAAA
21348 ATCGCAAT
1 ATCGCAAT
21356 GCTATTTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 31 0.77
34 9 0.22
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.15
Consensus pattern (34 bp):
ATCGCAATTGCGAAATGAAAATCGCAACGACAAA
Found at i:21337 original size:19 final size:18
Alignment explanation
Indices: 21282--21340 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
21272 GGAAATGGCT
21282 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
21301 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
21315 ATCGCAATTGCGAAATGAA
1 ATCGCAA-TGCGAAATGAA
21334 ATCGCAA
1 ATCGCAA
21341 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 9 0.27
17 8 0.24
19 16 0.48
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:21408 original size:18 final size:18
Alignment explanation
Indices: 21366--21431 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
21356 GCTATTTGTG
21366 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
21382 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
21398 TTTCGCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
21416 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
21432 TGTCATTGCG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
14 11 0.25
16 4 0.09
18 29 0.66
ACGTcount: A:0.09, C:0.20, G:0.24, T:0.47
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:23458 original size:19 final size:19
Alignment explanation
Indices: 23436--23503 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
23426 ATCGCAACGA
23436 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
23455 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
23474 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
23488 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
23504 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:23547 original size:20 final size:20
Alignment explanation
Indices: 23522--23559 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23512 TCGCATTGCG
*
23522 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
23542 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
23560 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:24622 original size:24 final size:24
Alignment explanation
Indices: 24595--24648 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
24585 GTATTCGAAA
* *
24595 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
24619 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
24643 TTTGAT
1 TTTGAT
24649 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:24840 original size:12 final size:12
Alignment explanation
Indices: 24823--24847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24813 ATATAATCCT
24823 GAAGAAGAAAAA
1 GAAGAAGAAAAA
24835 GAAGAAGAAAAA
1 GAAGAAGAAAAA
24847 G
1 G
24848 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:25322 original size:20 final size:21
Alignment explanation
Indices: 25293--25345 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
25283 GCGCTATGTA
25293 AATC-GCGTTGCGAAAGTCAG
1 AATCTGCGTTGCGAAAGTCAG
25313 AAT-TGCGTTGCGAAAGTCAG
1 AATCTGCGTTGCGAAAGTCAG
*
25333 TATCT-CGTTGCGA
1 AATCTGCGTTGCGA
25346 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (21 bp):
AATCTGCGTTGCGAAAGTCAG
Found at i:25379 original size:20 final size:20
Alignment explanation
Indices: 25354--25407 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
25344 GATTTTGTAT
25354 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
25374 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
25394 TATCGCATTGCGAT
1 TATCGCATTGCGAT
25408 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:25426 original size:61 final size:61
Alignment explanation
Indices: 25294--25428 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
25284 CGCTATGTAA
* * * * * * ** *
25294 ATCGCGTTGCGAAAGTCAGAATTGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
25355 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
25417 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
25429 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:25518 original size:21 final size:21
Alignment explanation
Indices: 25478--25518 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25468 ACTGTATACC
**
25478 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
25499 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
25519 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:28569 original size:12 final size:13
Alignment explanation
Indices: 28540--28566 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28530 TCTTGATAGG
28540 AATCAAAAGGAAA
1 AATCAAAAGGAAA
28553 AATCAAAAGGAAA
1 AATCAAAAGGAAA
28566 A
1 A
28567 TCATTCAAAG
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:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (13 bp):
AATCAAAAGGAAA
Found at i:32919 original size:22 final size:22
Alignment explanation
Indices: 32891--32936 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
32881 TGGTTTCCCT
32891 TTCCTGGCTTAAGCCCCACATA
1 TTCCTGGCTTAAGCCCCACATA
*
32913 TTCCTGGCTTCAGCCCCACATA
1 TTCCTGGCTTAAGCCCCACATA
32935 TT
1 TT
32937 TGTTTGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (22 bp):
TTCCTGGCTTAAGCCCCACATA
Found at i:35168 original size:2 final size:2
Alignment explanation
Indices: 35163--35188 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35153 TTCATATTTG
35163 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
35189 CATGCAAAGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39801 original size:3 final size:3
Alignment explanation
Indices: 39795--39894 Score: 53
Period size: 3 Copynumber: 32.3 Consensus size: 3
39785 GGGGGGCACC
* * * *
39795 AAG AAG AAAG AAA AAG -AG GAG AAGG AAG AAAG AA- AGG AAA AAG AAAG
1 AAG AAG -AAG AAG AAG AAG AAG AA-G AAG -AAG AAG AAG AAG AAG -AAG
* * *
39842 AAG AAG AA- AAA AAG AAG AAG AAAG AAG AAGG AGG AAA AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG -AAG AAG AA-G AAG AAG AAG AAG AAG
*
39888 AAT AAG A
1 AAG AAG A
39895 GATGAAAATC
Statistics
Matches: 74, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
2 5 0.07
3 52 0.70
4 17 0.23
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:39828 original size:11 final size:11
Alignment explanation
Indices: 39814--39868 Score: 50
Period size: 10 Copynumber: 5.5 Consensus size: 11
39804 GAAAAAGAGG
39814 AGAAGGAAGAA
1 AGAAGGAAGAA
39825 AGAAAGGAA-AA
1 AG-AAGGAAGAA
*
39836 AGAAAGAAG-A
1 AGAAGGAAGAA
39846 AGAA--AA-AA
1 AGAAGGAAGAA
39854 AGAA-GAAGAA
1 AGAAGGAAGAA
39864 AGAAG
1 AGAAG
39869 AAGGAGGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
8 7 0.19
9 2 0.05
10 16 0.43
11 6 0.16
12 6 0.16
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AGAAGGAAGAA
Found at i:39832 original size:18 final size:18
Alignment explanation
Indices: 39796--39870 Score: 60
Period size: 15 Copynumber: 4.6 Consensus size: 18
39786 GGGGGCACCA
39796 AGAAGAAAGAAA-AAGAGG
1 AGAAG-AAGAAAGAAGAGG
39814 AGAAGGAAGAAAGAA-AGG
1 AGAA-GAAGAAAGAAGAGG
39832 A-AA-AAGAAAGAAGA--
1 AGAAGAAGAAAGAAGAGG
*
39846 AGAA-AA-AAAGAAGAAG
1 AGAAGAAGAAAGAAGAGG
39862 A-AAGAAGAA
1 AGAAGAAGAA
39871 GGAGGAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
14 9 0.18
15 15 0.31
16 4 0.08
17 4 0.08
18 14 0.29
19 3 0.06
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAAAGAAGAGG
Found at i:39867 original size:43 final size:42
Alignment explanation
Indices: 39795--39889 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 42
39785 GGGGGGCACC
* * *
39795 AAGAAGAAAGAAAAAGAGGAGAAGGAAGAAAGAA-AGGAAAAAG
1 AAGAAG-AAGAAAAAAAGAAGAAGAAAG-AAGAAGAGGAAAAAG
39838 AAAGAAGAAGAAAAAAAGAAGAAGAAAGAAGAAGGAGGAAAAAG
1 -AAGAAGAAGAAAAAAAGAAGAAGAAAGAAGAA-GAGGAAAAAG
39882 AAGAAGAA
1 AAGAAGAA
39890 TAAGAGATGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
42 5 0.11
43 26 0.57
44 15 0.33
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (42 bp):
AAGAAGAAGAAAAAAAGAAGAAGAAAGAAGAAGAGGAAAAAG
Found at i:40993 original size:24 final size:24
Alignment explanation
Indices: 40966--41049 Score: 168
Period size: 24 Copynumber: 3.5 Consensus size: 24
40956 GCATGAGTAG
40966 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
40990 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
41014 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
41038 TGCATCGATGCA
1 TGCATCGATGCA
41050 TGGTATAATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAGGGA
Found at i:42279 original size:17 final size:17
Alignment explanation
Indices: 42253--42292 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
42243 GTTTGAGCAT
*
42253 TTCAAGCCTATTTTTCA
1 TTCAATCCTATTTTTCA
42270 TTCAATCCTATTTTTCA
1 TTCAATCCTATTTTTCA
42287 TTCAAT
1 TTCAAT
42293 ATTCATTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.25, C:0.23, G:0.03, T:0.50
Consensus pattern (17 bp):
TTCAATCCTATTTTTCA
Found at i:46839 original size:49 final size:49
Alignment explanation
Indices: 46780--46939 Score: 284
Period size: 49 Copynumber: 3.3 Consensus size: 49
46770 TCTGTAACGC
*
46780 CAGACGTGCTAAATCATCATCAATCGCAGCACCACCGTCACAAAGATGT
1 CAGACGTGCTAAATCATCATCAATCGTAGCACCACCGTCACAAAGATGT
* *
46829 CAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAGACGT
1 CAGACGTGCTAAATCATCATCAATCGTAGCACCACCGTCACAAAGATGT
*
46878 CAGACGTGCTAAATCATCATCAATCGTAGCACCACAGTCACAAAGATGT
1 CAGACGTGCTAAATCATCATCAATCGTAGCACCACCGTCACAAAGATGT
46927 CAGACGTGCTAAA
1 CAGACGTGCTAAA
46940 AGCTCCACCT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 105 1.00
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.19
Consensus pattern (49 bp):
CAGACGTGCTAAATCATCATCAATCGTAGCACCACCGTCACAAAGATGT
Found at i:47075 original size:52 final size:52
Alignment explanation
Indices: 47003--47107 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
46993 TAAATCATTT
* * * *
47003 ATCATTCACCTATCAGAATCTTTTCAAATATCATCAAAATCAAGTATCATAC
1 ATCATTCACCTATCAAAATCTTTTCAAACATCAACAAAATCAAGTATAATAC
* *
47055 ATCATTCA-CTCATCAAAATCTTTTTAAACATTAACAAAATCAAGTATAATAC
1 ATCATTCACCT-ATCAAAATCTTTTCAAACATCAACAAAATCAAGTATAATAC
47107 A
1 A
47108 ATATAAATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
51 2 0.04
52 44 0.96
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (52 bp):
ATCATTCACCTATCAAAATCTTTTCAAACATCAACAAAATCAAGTATAATAC
Found at i:49179 original size:29 final size:30
Alignment explanation
Indices: 49132--49192 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
49122 TTTTGGTCCT
**
49132 TAAACTTTTCAAAGTTTATACTTTAGCCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
*
49162 TAAAC-TTTCAAAACTTATACTTTAGTCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
49191 TA
1 TA
49193 GACAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATACTTTAGCCAC
Found at i:49743 original size:21 final size:21
Alignment explanation
Indices: 49718--49760 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
49708 TTTTAAATCA
49718 GCATAAGATTTCTGTCTATCT
1 GCATAAGATTTCTGTCTATCT
49739 GCATAAGATTTCTGTCTATCT
1 GCATAAGATTTCTGTCTATCT
49760 G
1 G
49761 AAGCTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (21 bp):
GCATAAGATTTCTGTCTATCT
Done.