Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001870.1 Hibiscus syriacus cultivar Beakdansim tig00003790_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: 83928
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:814 original size:17 final size:17
Alignment explanation
Indices: 792--831 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
782 ATGCTGTTGT
792 TATGCACGATATAATTA
1 TATGCACGATATAATTA
809 TATGCACGATATAATTA
1 TATGCACGATATAATTA
826 TATGCA
1 TATGCA
832 GGGTAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TATGCACGATATAATTA
Found at i:4151 original size:15 final size:16
Alignment explanation
Indices: 4131--4170 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
4121 GATAGGTGCA
*
4131 TGCATGGGG-GATCGG
1 TGCATGGGGAGATCAG
4146 TGCATGGGGAGATCAG
1 TGCATGGGGAGATCAG
4162 TGCATGGGG
1 TGCATGGGG
4171 CATGCACGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.17, C:0.12, G:0.50, T:0.20
Consensus pattern (16 bp):
TGCATGGGGAGATCAG
Found at i:4356 original size:65 final size:65
Alignment explanation
Indices: 4247--4386 Score: 226
Period size: 65 Copynumber: 2.2 Consensus size: 65
4237 GACCAAGCTG
* * * *
4247 TGGGAGATTCCTTCACCGCGACCAAGCTTTAACCCTATCCCTCATGCATGTGTTGCATCCATAGC
1 TGGGAGATTCATGCACCGCGACCAAGCTTTAACCCTATCACTCATGCATGCGTTGCATCCATAGC
* *
4312 TGGGAGATTCATGCATCGCGACCAAGCTTTAACCCTATCACTCATGCATGCGTTGCATCCATAGT
1 TGGGAGATTCATGCACCGCGACCAAGCTTTAACCCTATCACTCATGCATGCGTTGCATCCATAGC
4377 TGGGAGATTC
1 TGGGAGATTC
4387 CTACATCCGT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (65 bp):
TGGGAGATTCATGCACCGCGACCAAGCTTTAACCCTATCACTCATGCATGCGTTGCATCCATAGC
Found at i:4824 original size:21 final size:21
Alignment explanation
Indices: 4799--4842 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4789 AATCTAGTTA
4799 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
4820 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
4841 AT
1 AT
4843 ATATTATATT
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:5409 original size:23 final size:24
Alignment explanation
Indices: 5365--5409 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5355 TATTGTGTTT
*
5365 AAAAATATTTAGTGTTATTTTAAA
1 AAAAATATTTAGTGTTAATTTAAA
*
5389 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
5410 TATTGTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (24 bp):
AAAAATATTTAGTGTTAATTTAAA
Found at i:8692 original size:49 final size:49
Alignment explanation
Indices: 8639--8975 Score: 559
Period size: 49 Copynumber: 6.9 Consensus size: 49
8629 GGCACCCATC
* *
8639 TATTATTAATATTTAATGATTTGATAATAATGATTAGTAATAATAAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
8688 TATTATTAATTTTTAATGATTTGATAGTAATGAATAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
8737 TATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
8786 TATCATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
8835 TATTATTAAT-TTTTATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
8883 TATCATTAATATTTAATGATTTGATAGTAATGATTAATAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
8932 TATCATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAAT
8976 AATGGAGGGA
Statistics
Matches: 271, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
48 46 0.17
49 225 0.83
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.45
Consensus pattern (49 bp):
TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
Found at i:8899 original size:22 final size:22
Alignment explanation
Indices: 8874--8950 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
8864 TGATTAGTAA
8874 TAATGAAATTATCATTAATATT
1 TAATGAAATTATCATTAATATT
* * *
8896 TAATGATTTGATAGTAATGATTAATA-A
1 TAATGA----A-A-TTATCATTAATATT
*
8923 TAATGAAATTATCATTAATTTT
1 TAATGAAATTATCATTAATATT
8945 TAATGA
1 TAATGA
8951 TTTGATAGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
21 9 0.22
22 13 0.32
23 1 0.02
26 1 0.02
27 7 0.17
28 10 0.24
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (22 bp):
TAATGAAATTATCATTAATATT
Found at i:8909 original size:146 final size:147
Alignment explanation
Indices: 8643--8977 Score: 609
Period size: 146 Copynumber: 2.3 Consensus size: 147
8633 CCCATCTATT
*
8643 ATTAATATTTAATGATTTGATAATAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGAT
1 ATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGAT
* *
8708 TTGATAGTAATGAATAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
66 TTGATAGTAATGAATAGTAATAATGAAATTATCATTAATATTTAATGATTTGATAGTAATGATTA
8773 ATAATAATGAAATTATC
131 ATAATAATGAAATTATC
*
8790 ATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-ATGAT
1 ATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGAT
*
8854 TTGATAGTAATGATTAGTAATAATGAAATTATCATTAATATTTAATGATTTGATAGTAATGATTA
66 TTGATAGTAATGAATAGTAATAATGAAATTATCATTAATATTTAATGATTTGATAGTAATGATTA
8919 ATAATAATGAAATTATC
131 ATAATAATGAAATTATC
*
8936 ATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATAA
1 ATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAA
8978 TGGAGGGACC
Statistics
Matches: 181, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
146 124 0.69
147 57 0.31
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.45
Consensus pattern (147 bp):
ATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGAT
TTGATAGTAATGAATAGTAATAATGAAATTATCATTAATATTTAATGATTTGATAGTAATGATTA
ATAATAATGAAATTATC
Found at i:9085 original size:12 final size:11
Alignment explanation
Indices: 9064--9106 Score: 68
Period size: 12 Copynumber: 3.7 Consensus size: 11
9054 CATAAAAATG
9064 ATTTAATAATA
1 ATTTAATAATA
9075 ATTTAAATAATA
1 ATTT-AATAATA
9087 ATTTAATAATAA
1 ATTTAATAAT-A
9099 ATTTAATA
1 ATTTAATA
9107 TTTAATGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:9153 original size:14 final size:13
Alignment explanation
Indices: 9136--9330 Score: 129
Period size: 14 Copynumber: 15.1 Consensus size: 13
9126 GATGATTTAG
9136 TAATGATTTGATAA
1 TAATGATTT-ATAA
* *
9150 TAATCATTT-TAG
1 TAATGATTTATAA
*
9162 TAATGCTTTGATAA
1 TAATGATTT-ATAA
*
9176 TAATCA-TTATAA
1 TAATGATTTATAA
9188 TAATGATTTAGTAA
1 TAATGATTTA-TAA
* *
9202 TAATCA-ATATAA
1 TAATGATTTATAA
9214 TAATGATTTAATAA
1 TAATGATTT-ATAA
*
9228 TAATGA-TAATAA
1 TAATGATTTATAA
*
9240 TAAT--TTAATAA
1 TAATGATTTATAA
* *
9251 TAAT-AATGATAA
1 TAATGATTTATAA
*
9263 TAATGATTTAATAG
1 TAATGATTT-ATAA
* *
9277 TAATTA-TT-TAG
1 TAATGATTTATAA
9288 TAATGATTTTATAA
1 TAATGA-TTTATAA
*
9302 TAATGATTTAATAC
1 TAATGATTT-ATAA
9316 TAATGATTTAATAA
1 TAATGATTT-ATAA
9330 T
1 T
9331 TATTACTAAT
Statistics
Matches: 144, Mismatches: 23, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
11 18 0.12
12 43 0.30
13 18 0.12
14 65 0.45
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:9171 original size:26 final size:26
Alignment explanation
Indices: 9136--9330 Score: 166
Period size: 26 Copynumber: 7.6 Consensus size: 26
9126 GATGATTTAG
* *
9136 TAATGATTTGATAATAATCATTTTAG
1 TAATGATTTGATAATAATCATTATAA
*
9162 TAATGCTTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
*
9188 TAATGATTT-AGTAATAATCAATATAA
1 TAATGATTTGA-TAATAATCATTATAA
* *
9214 TAATGA-TT--TAATAATAATGATAA
1 TAATGATTTGATAATAATCATTATAA
* * * *
9237 TAATAATTTAATAATAATAATGATAA
1 TAATGATTTGATAATAATCATTATAA
* * * *
9263 TAATGATTTAATAGTAATTATT-TAG
1 TAATGATTTGATAATAATCATTATAA
* * *
9288 TAATGATTTTATAATAATGATTTAATAC
1 TAATGATTTGATAATAATCA-TT-ATAA
*
9316 TAATGATTTAATAAT
1 TAATGATTTGATAAT
9331 TATTACTAAT
Statistics
Matches: 143, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
23 17 0.12
24 2 0.01
25 22 0.15
26 86 0.60
28 16 0.11
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:9190 original size:3 final size:3
Alignment explanation
Indices: 9172--9266 Score: 63
Period size: 3 Copynumber: 32.7 Consensus size: 3
9162 TAATGCTTTG
* * * * *
9172 ATA ATA ATC ATT ATA ATA ATG AT- TTA GTA ATA ATCA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
* * * * *
9216 ATG AT- TTA ATA ATA ATG ATA ATA ATA AT- TTA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9262 ATA AT
1 ATA AT
9267 GATTTAATAG
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
2 5 0.07
3 63 0.89
4 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:9246 original size:49 final size:49
Alignment explanation
Indices: 9173--9330 Score: 156
Period size: 49 Copynumber: 3.1 Consensus size: 49
9163 AATGCTTTGA
* * * *
9173 TAATAATCATTATAATAATGATTTAGTAATAATCAAT-ATAATAATGATT
1 TAATAATAATGATAATAATAATTTAATAATAAT-AATGATAATAATGATT
9222 TAATAATAATGATAATAATAATTTAATAATAATAATGATAATAATGATT
1 TAATAATAATGATAATAATAATTTAATAATAATAATGATAATAATGATT
* * * * * * * *
9271 TAATAGTAATTATTTAGTAATGATTTTATAATAATGATTTAATACTAATGATT
1 TAATAATAATGA--TAATAATAATTTAATAATAAT-A-ATGATAATAATGATT
9324 TAATAAT
1 TAATAAT
9331 TATTACTAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
48 3 0.03
49 51 0.56
51 18 0.20
52 1 0.01
53 18 0.20
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (49 bp):
TAATAATAATGATAATAATAATTTAATAATAATAATGATAATAATGATT
Found at i:9495 original size:24 final size:24
Alignment explanation
Indices: 9447--9491 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9437 GATTTGATAC
*
9447 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
9471 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
9492 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:9498 original size:17 final size:17
Alignment explanation
Indices: 9458--9499 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
9448 AATGATTTAC
9458 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
9475 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
9492 TAATTATT
1 TAATTATT
9500 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:11863 original size:30 final size:30
Alignment explanation
Indices: 11829--11932 Score: 124
Period size: 30 Copynumber: 3.4 Consensus size: 30
11819 TTCCTTAAAC
11829 AACTAATAAACTATTCTTTAATATAACGTT-
1 AACTAATAAACTATTCTTTAATATAAC-TTA
11859 AACTAATAAACTATTCTTTAATATAACTTA
1 AACTAATAAACTATTCTTTAATATAACTTA
*
11889 AACTAATAAA-TGATT-TTTAATTATAATTTA
1 AACTAATAAACT-ATTCTTTAA-TATAACTTA
* *
11919 CTACTAAAAAACTA
1 -AACTAATAAACTA
11933 ATTAACTAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
29 8 0.12
30 48 0.73
31 9 0.14
32 1 0.02
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAACTTA
Found at i:12044 original size:41 final size:38
Alignment explanation
Indices: 11989--12102 Score: 115
Period size: 40 Copynumber: 2.9 Consensus size: 38
11979 CTTAACTATT
*
11989 TAACTAAC--ACAAACTAATTACATATTTTTTTATATA
1 TAACTAACAAACAAACTAATTAAATATTTTTTTATATA
* *
12025 TAACTAACGACTAACAAACTAACTAAATATTTTTATTAATATG
1 TAACTAAC-A--AACAAACTAATTAAATATTTTT-TT-ATATA
* * *
12068 TAACTATCAAACATACTAATTAAATAATTTTTTAT
1 TAACTAACAAACAAACTAATTAAATATTTTTTTAT
12103 TTCTATATGA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
36 8 0.12
38 2 0.03
39 2 0.03
40 19 0.30
41 19 0.30
42 3 0.05
43 11 0.17
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (38 bp):
TAACTAACAAACAAACTAATTAAATATTTTTTTATATA
Found at i:12136 original size:21 final size:21
Alignment explanation
Indices: 12112--12151 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
12102 TTTCTATATG
12112 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
12133 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
12152 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:12392 original size:27 final size:29
Alignment explanation
Indices: 12357--12421 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
12347 AAAATATAAC
*
12357 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAATTATTTAGACTAACTAACAAACTAA
*
12384 TTCAA-TA-TTAGACTAACTAACACACTAA
1 TT-AATTATTTAGACTAACTAACAAACTAA
12412 TTAATTATTT
1 TTAATTATTT
12422 TTTTAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAATTATTTAGACTAACTAACAAACTAA
Found at i:12535 original size:9 final size:9
Alignment explanation
Indices: 12503--12540 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
12493 CTAACAAACT
12503 AATAATTTAA
1 AATAA-TTAA
12513 AATAA-TAA
1 AATAATTAA
*
12521 ACTAATTAA
1 AATAATTAA
12530 AATAATTAA
1 AATAATTAA
12539 AA
1 AA
12541 AAACTTACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:12625 original size:26 final size:25
Alignment explanation
Indices: 12562--12625 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
12552 GATGTTGTGC
12562 TCTCCCTTTCTTCTTCCTTATCTTT
1 TCTCCCTTTCTTCTTCCTTATCTTT
* *
12587 TCTCTGCTATCTTC-TCCTT-TGCTATTT
1 TCTC-CCTTTCTTCTTCCTTAT-C--TTT
12614 TCTCCCTTTCTT
1 TCTCCCTTTCTT
12626 TATCTCTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 1 0.03
25 10 0.32
26 13 0.42
27 7 0.23
ACGTcount: A:0.05, C:0.34, G:0.03, T:0.58
Consensus pattern (25 bp):
TCTCCCTTTCTTCTTCCTTATCTTT
Found at i:12945 original size:8 final size:9
Alignment explanation
Indices: 12934--12977 Score: 56
Period size: 8 Copynumber: 5.0 Consensus size: 9
12924 ATGCCATGTT
12934 GCCATGC-C
1 GCCATGCAC
12942 GCCATGCAC
1 GCCATGCAC
*
12951 AGCCATGCAT
1 -GCCATGCAC
12961 GCCATGC-C
1 GCCATGCAC
12969 GCCATGCAC
1 GCCATGCAC
12978 AGCTATACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 14 0.45
9 9 0.29
10 8 0.26
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.14
Consensus pattern (9 bp):
GCCATGCAC
Found at i:25970 original size:22 final size:23
Alignment explanation
Indices: 25942--25990 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
25932 TAATAATAAT
* *
25942 AATAATAAAATAGATAACAAAGAAA
1 AATAA-AAGATAG-TAAAAAAGAAA
25967 AATAAAAGATAGTAAAAAAGAAA
1 AATAAAAGATAGTAAAAAAGAAA
25990 A
1 A
25991 TAATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 6 0.27
25 5 0.23
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.14
Consensus pattern (23 bp):
AATAAAAGATAGTAAAAAAGAAA
Found at i:25991 original size:22 final size:25
Alignment explanation
Indices: 25942--26012 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
25932 TAATAATAAT
*
25942 AATAATAAAATAGATAACAAAGAAA
1 AATAATAAAATAGATAAAAAAGAAA
*
25967 AATAA-AAGATAG-TAAAAAAGAAAA
1 AATAATAAAATAGATAAAAAAG-AAA
*
25991 TAATAAAAAAATAGATAAAAAA
1 -AATAATAAAATAGATAAAAAA
26013 TAAATAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
23 7 0.18
24 9 0.23
25 10 0.26
26 6 0.15
27 7 0.18
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.15
Consensus pattern (25 bp):
AATAATAAAATAGATAAAAAAGAAA
Found at i:26008 original size:15 final size:15
Alignment explanation
Indices: 25917--26018 Score: 50
Period size: 15 Copynumber: 6.6 Consensus size: 15
25907 TAAAAAAAAG
*
25917 AAAAAAATA-TTAAT
1 AAAAAAATAGATAAT
* *
25931 ATAATAATA-ATAAT
1 AAAAAAATAGATAAT
* *
25945 AATAAAATAGATAACA
1 AAAAAAATAGATAA-T
*
25961 AAGAAAAATAAAAGATAGT
1 AA-AAAAAT---AGATAAT
*
25980 AAAAAAGA-AAATAAT
1 AAAAAA-ATAGATAAT
25995 AAAAAAATAGATAA-
1 AAAAAAATAGATAAT
26009 AAAATAAATA
1 AAAA-AAATA
26019 AAGAAAATGA
Statistics
Matches: 66, Mismatches: 13, Indels: 17
0.69 0.14 0.18
Matches are distributed among these distances:
14 22 0.33
15 25 0.38
16 2 0.03
17 5 0.08
18 4 0.06
19 3 0.05
20 5 0.08
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.21
Consensus pattern (15 bp):
AAAAAAATAGATAAT
Found at i:26034 original size:23 final size:22
Alignment explanation
Indices: 25987--26043 Score: 53
Period size: 24 Copynumber: 2.4 Consensus size: 22
25977 AGTAAAAAAG
*
25987 AAAATAATAAAAAAATAGATAA
1 AAAATAATAAAAAAATAGACAA
26009 AAAATAAATAAAGAAAAT-GACCAA
1 AAAAT-AATAAA-AAAATAGA-CAA
26033 AATGAATAATA
1 AA--AATAATA
26044 TTTAAAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 5 0.17
23 8 0.28
24 9 0.31
25 4 0.14
26 3 0.10
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.18
Consensus pattern (22 bp):
AAAATAATAAAAAAATAGACAA
Found at i:27481 original size:83 final size:83
Alignment explanation
Indices: 27332--27602 Score: 380
Period size: 83 Copynumber: 3.2 Consensus size: 83
27322 CTGAATGAAA
* * *
27332 TCGAACTCGTCAGGTCTTTAGTTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 TCGAACTCG-AAGGTCTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
27397 TGCCTTGGAGCTGAGCGTAG
64 TGCCTTGGAGCTGAGCGTAG
* * * * * * *
27417 TCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* *
27482 CCTTTGAGCTGAGCGTGG
66 CCTTGGAGCTGAGCGTAG
* * * *
27500 TCGAACTCGAAGGTTTTTGTTGGCAGATATCCCTTCTAGCCTTGAGTTATGCTATGAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
27565 CCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
27583 TCGAACTCGAAGGTCTTTGT
1 TCGAACTCGAAGGTCTTTGT
27603 GTTTCAAGAG
Statistics
Matches: 161, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
83 144 0.89
84 8 0.05
85 9 0.06
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:27650 original size:28 final size:28
Alignment explanation
Indices: 27604--27694 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 28
27594 GGTCTTTGTG
*
27604 TTTCAAGAGAAA-TATTTTCAAAGGTTTT
1 TTTCAAGAGAAACGA-TTTCAAAGGTTTT
27632 TTTCAAGAGAAACGATTTCAAAGGTTTTTTGT
1 TTTCAAGAGAAACGATTTCAAAGG---TTT-T
* *
27664 GTTTCAAGAGAAACGACTTCAAAGGATTT
1 -TTTCAAGAGAAACGATTTCAAAGGTTTT
27693 TT
1 TT
27695 GTGTTTCAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
28 23 0.43
29 2 0.04
30 2 0.04
31 3 0.06
32 1 0.02
33 23 0.43
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (28 bp):
TTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:27673 original size:33 final size:32
Alignment explanation
Indices: 27592--27710 Score: 149
Period size: 33 Copynumber: 3.8 Consensus size: 32
27582 GTCGAACTCG
* *
27592 AAGGTCTTTGTGTTTCAAGAGAAA-TATTTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGA-TTTCA
27624 AAGG--TTT-T-TTTCAAGAGAAACGATTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
*
27652 AAGGTTTTTTGTGTTTCAAGAGAAACGACTTCA
1 AAGG-TTTTTGTGTTTCAAGAGAAACGATTTCA
27685 AAGGATTTTTGTGTTTCAAGAGAAAC
1 AAGG-TTTTTGTGTTTCAAGAGAAAC
27711 TGTCTCCAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
28 21 0.27
29 2 0.03
30 3 0.04
31 3 0.04
32 5 0.06
33 44 0.56
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (32 bp):
AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
Found at i:28125 original size:105 final size:106
Alignment explanation
Indices: 27810--28870 Score: 1626
Period size: 105 Copynumber: 10.2 Consensus size: 106
27800 AGCACGATTC
** * * * *
27810 CCTTCGTCATGAAGTTGAAATTGACTC-AAGAATTGGAAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTTATTGACAACCAGCGGTCC
27874 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
27916 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
* * **
27981 TTCGTCGTGAAGTTAAACATGCGTTGTCAAGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
28022 CCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
28086 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * *
28127 CCTTCGCTCTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTG-TTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
*
28191 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
28232 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGAAAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
28296 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
28337 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA---GTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
*
28399 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
28440 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
28504 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
28545 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
*
28609 TTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
28650 CCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
* *
28715 TTTGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
28756 CCTTCGCTGTGAAGTTGAAATTGG----G--A-----AA-TTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
* *
28809 TTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT-CAAGAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
28849 CCTTCGTTGAGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAAATT
28871 TACTCTCGAG
Statistics
Matches: 896, Mismatches: 54, Indels: 23
0.92 0.06 0.02
Matches are distributed among these distances:
93 25 0.03
94 55 0.06
95 2 0.00
100 1 0.00
102 1 0.00
103 99 0.11
104 2 0.00
105 494 0.55
106 216 0.24
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:28471 original size:313 final size:312
Alignment explanation
Indices: 27819--28870 Score: 1689
Period size: 313 Copynumber: 3.4 Consensus size: 312
27809 CCCTTCGTCA
* * *
27819 TGAAGTTGAAATTGACTCAAGAATTGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCGA-AATTGG-AAAGTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
27884 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
64 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
* * * * * **
27949 TGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACATGCGTTGTCAAGAG
129 TGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
*
28014 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAGTTGTTGTTGACAACCAG
193 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG-T-TTGTTGACAACCAG
* *
28079 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTC
256 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTG
*
28136 TGAAGTTGAAATTGGCTCTGAAATTGGAAAGT-TGTTGTTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTC-GAAATTGGAAAGTGT-TTATTGACAACCAGCGGTCCCTTCGTCGTG
* *
28200 AAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAAT
64 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
*
28265 TGGGAAATGTTTATTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
129 TGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
28330 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTGTTGACAACCAGCGG
194 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTGTTGACAACCAGCGG
28395 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTG
259 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTG
28449 TGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTC-GAAATT-GGAAAGTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
28513 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
64 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
*
28578 TGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGT
129 TGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
28643 CCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
194 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA---GTTTGTTGACAACCAG
*
28708 CGGTCCCTTTGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTG
256 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTG
28765 TGAAGTTGAAATTGG---GAAA-T------TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 TGAAGTTGAAATTGGCTCGAAATTGGAAAGTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
* * *
28820 GTTGAACTTGCGTTGTCTAGAGT-CAAGATCCTTCGTTGAGAAGTTGAAATT
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
28871 TACTCTCGAG
Statistics
Matches: 700, Mismatches: 28, Indels: 27
0.93 0.04 0.04
Matches are distributed among these distances:
304 26 0.04
305 57 0.08
311 1 0.00
312 4 0.01
313 294 0.42
314 7 0.01
315 99 0.14
316 188 0.27
317 23 0.03
318 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (312 bp):
TGAAGTTGAAATTGGCTCGAAATTGGAAAGTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG
GGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTGTTGACAACCAGCGGTC
CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTG
Found at i:28636 original size:418 final size:417
Alignment explanation
Indices: 27819--28870 Score: 1653
Period size: 418 Copynumber: 2.5 Consensus size: 417
27809 CCCTTCGTCA
* * *
27819 TGAAGTTGAAATTGACTC-AAGAATTGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
1 TGAAGTTGAAATTGGCTCTGA-AATTGGGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGT
27883 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
64 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
* * *
27948 TTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACATGCGTTGTCAAGA
129 TTG-GAA---GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGA
* * *
28013 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAGTTGTTGTTGACAACCA
190 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTATTGACAACCA
28078 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTCTGAAGTT
255 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTCTGAAGTT
* *
28143 GAAATTGGCTCTGAAATTGGAAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
320 GAAATTGGCTCTGAAATTGGAAAGTTGTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAA
*
28208 CTTACGTTGTCTGGAGTCCAATATCCTTCGCTG
385 CTTACGTTGTCTGGAGTCCAATATCCTCCGCTG
*
28241 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGAAAACCAGCGGTCCCTTCGTCGTGA
1 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
28306 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
66 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
* *
28371 GGGAAGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCA
131 -GGAAGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCA
*
28436 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAACCAGCGG
195 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTATTGACAACCAGCGG
* *
28500 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
259 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTCTGAAGTTGAAA
28565 TTGGCTCTGAAATTGGGAAA--TGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACT
324 TTGGCTCTGAAATT-GGAAAGTTG-TTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACT
* *
28628 TGCGTTGTCTGGAGTCCAATATCCTCCGTTG
387 TACGTTGTCTGGAGTCCAATATCCTCCGCTG
* * * *
28659 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTTGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
* *
28724 AAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG----GAAAT
65 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
*
28785 T----GTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT-CA
130 TGGAAGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCA
* *
28845 AGATCCTTCGTTGAGAAGTTGAAATT
195 ATATCCTTCGTTGTGAAGTTGAAATT
28871 TACTCTCGAG
Statistics
Matches: 591, Mismatches: 33, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
409 25 0.04
410 54 0.09
415 6 0.01
417 4 0.01
418 284 0.48
419 89 0.15
421 101 0.17
422 27 0.05
423 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (417 bp):
TGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
GGAAGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAA
TATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTATTGACAACCAGCGGTC
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTCTGAAGTTGAAATT
GGCTCTGAAATTGGAAAGTTGTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTACG
TTGTCTGGAGTCCAATATCCTCCGCTG
Found at i:28843 original size:94 final size:93
Alignment explanation
Indices: 28677--28870 Score: 298
Period size: 94 Copynumber: 2.1 Consensus size: 93
28667 AAATTGGCTC
* * *
28677 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTACGTTGT
1 TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
* * *
28742 CTGGAGTCCAATATCCTTCGCTGTGAAGT
66 CTAGAGT-CAAGATCCTTCGCTGAGAAGT
* *
28771 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
*
28836 CTAGAGTCAAGATCCTTCGTTGAGAAGT
66 CTAGAGTCAAGATCCTTCGCTGAGAAGT
28864 TGAAATT
1 TGAAATT
28871 TACTCTCGAG
Statistics
Matches: 91, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 25 0.27
94 66 0.73
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (93 bp):
TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
CTAGAGTCAAGATCCTTCGCTGAGAAGT
Found at i:32588 original size:22 final size:23
Alignment explanation
Indices: 32560--32608 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
32550 TAATAATAAT
* *
32560 AATAATAAAATAGATAACAAAGAAA
1 AATAA-AAGATAG-TAAAAAAGAAA
32585 AATAAAAGATAGTAAAAAAGAAA
1 AATAAAAGATAGTAAAAAAGAAA
32608 A
1 A
32609 TAATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 6 0.27
25 5 0.23
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.14
Consensus pattern (23 bp):
AATAAAAGATAGTAAAAAAGAAA
Found at i:32609 original size:22 final size:25
Alignment explanation
Indices: 32560--32631 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 25
32550 TAATAATAAT
*
32560 AATAATAAAATAGATAACAAAGAAA
1 AATAATAAAATAGATAAAAAAGAAA
*
32585 AATAA-AAGATAG-TAAAAAAGAAAA
1 AATAATAAAATAGATAAAAAAG-AAA
*
32609 TAATAAAAAAAATAGATAAAAAA
1 -AAT-AATAAAATAGATAAAAAA
32632 TAAATAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 7 0.18
24 9 0.23
25 8 0.21
26 2 0.05
27 6 0.15
28 7 0.18
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.15
Consensus pattern (25 bp):
AATAATAAAATAGATAAAAAAGAAA
Found at i:32619 original size:11 final size:11
Alignment explanation
Indices: 32508--32645 Score: 50
Period size: 13 Copynumber: 11.5 Consensus size: 11
32498 ATTATATTAT
32508 AAAATAA-AAA
1 AAAATAATAAA
*
32518 CAAAT-ATAAA
1 AAAATAATAAA
*
32528 AAAA-AGAAAAA
1 AAAATA-ATAAA
32539 AAATATTAATATAA
1 AAA-A-TAATA-AA
*
32553 TAATAATAATAAT
1 -AA-AATAATAAA
32566 AAAATAGATAACA
1 AAAATA-ATAA-A
*
32579 AAGAAAAATAAA
1 AA-AATAATAAA
* *
32591 AGATAGTAAAAAA
1 A-A-AATAATAAA
32604 GAAAATAATAAAA
1 -AAAATAAT-AAA
32617 AAAATAGAT-AA
1 AAAATA-ATAAA
32628 AAAATAAATAAA
1 AAAAT-AATAAA
32640 GAAAAT
1 -AAAAT
32646 GACCAAAATG
Statistics
Matches: 96, Mismatches: 13, Indels: 35
0.67 0.09 0.24
Matches are distributed among these distances:
9 1 0.01
10 10 0.10
11 20 0.21
12 22 0.23
13 27 0.28
14 12 0.12
15 3 0.03
16 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (11 bp):
AAAATAATAAA
Found at i:32627 original size:13 final size:12
Alignment explanation
Indices: 32510--32645 Score: 68
Period size: 12 Copynumber: 11.0 Consensus size: 12
32500 TATATTATAA
32510 AATAAAAACAAAT
1 AATAAAAA-AAAT
*
32523 -ATAAAAAAAAG
1 AATAAAAAAAAT
*
32534 AA-AAAAAATATT
1 AATAAAAAA-AAT
*
32546 AATATAATAATAAT
1 AATA-AA-AAAAAT
*
32560 AAT-AATAAAAT
1 AATAAAAAAAAT
32571 AGATAACAAAGAAA-
1 A-ATAA-AAA-AAAT
* *
32585 AATAAAAGATAGT
1 AATAAAA-AAAAT
32598 AA-AAAAGAAAAT
1 AATAAAA-AAAAT
32610 AATAAAAAAAAT
1 AATAAAAAAAAT
*
32622 AGATAAAAAATA-
1 A-ATAAAAAAAAT
*
32634 AATAAAGAAAAT
1 AATAAAAAAAAT
32646 GACCAAAATG
Statistics
Matches: 94, Mismatches: 15, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
11 22 0.23
12 35 0.37
13 22 0.23
14 10 0.11
15 5 0.05
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.18
Consensus pattern (12 bp):
AATAAAAAAAAT
Found at i:32635 original size:20 final size:19
Alignment explanation
Indices: 32508--32635 Score: 64
Period size: 20 Copynumber: 6.4 Consensus size: 19
32498 ATTATATTAT
*
32508 AAAATAAAAACAAATATAAAA
1 AAAATAAAAA-AAATA-ATAA
* *
32529 AAAAGAAAAAAAATATTAA
1 AAAATAAAAAAAATAATAA
* * *
32548 TATAATAATAATAATAATAA
1 -AAAATAAAAAAAATAATAA
32568 AATAGATAACAAAGAAA-AATAA
1 AA-A-ATAA-AAA-AAATAATAA
* * *
32590 AAGATAGTAAAAAA-GA-AA
1 AAAATA-AAAAAAATAATAA
*
32608 ATAATAAAAAAAATAGATAA
1 AAAATAAAAAAAATA-ATAA
32628 AAAATAAA
1 AAAATAAA
32636 TAAAGAAAAT
Statistics
Matches: 79, Mismatches: 19, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
17 6 0.08
18 6 0.08
19 8 0.10
20 35 0.44
21 13 0.16
22 9 0.11
23 2 0.03
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAATAAAAAAAATAATAA
Found at i:32644 original size:27 final size:27
Alignment explanation
Indices: 32554--32631 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
32544 TTAATATAAT
*
32554 AATAATAATAATAAAATAGATAACAAAG-A
1 AATAATAA-AA-AAAATAG-TAAAAAAGAA
*
32583 AA-AAT--AAAAGATAGTAAAAAAGAA
1 AATAATAAAAAAAATAGTAAAAAAGAA
32607 AATAATAAAAAAAATAGATAAAAAA
1 AATAATAAAAAAAATAG-TAAAAAA
32632 TAAATAAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
23 7 0.17
24 9 0.22
25 5 0.12
27 8 0.20
28 10 0.24
29 2 0.05
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (27 bp):
AATAATAAAAAAAATAGTAAAAAAGAA
Found at i:32644 original size:28 final size:27
Alignment explanation
Indices: 32588--32644 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
32578 AAAGAAAAAT
* *
32588 AAAAGATAGTAAAAAAGAAAATAATAA
1 AAAAAATAGTAAAAAAGAAAATAAGAA
*
32615 AAAAAATAGATAAAAAA-TAAATAAAGAA
1 AAAAAATAG-TAAAAAAGAAAAT-AAGAA
32643 AA
1 AA
32645 TGACCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (27 bp):
AAAAAATAGTAAAAAAGAAAATAAGAA
Found at i:32653 original size:24 final size:23
Alignment explanation
Indices: 32605--32662 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
32595 AGTAAAAAAG
*
32605 AAAATAATAAAAAAAATAGATAA
1 AAAATAATAAAAAAAATAGACAA
*
32628 AAAATAAATAAAGAAAAT-GACCAA
1 AAAAT-AATAAAAAAAATAGA-CAA
32652 AATGAATAATA
1 AA--AATAATA
32663 TTTAAAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 7 0.24
24 15 0.52
25 4 0.14
26 3 0.10
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.17
Consensus pattern (23 bp):
AAAATAATAAAAAAAATAGACAA
Found at i:38758 original size:23 final size:23
Alignment explanation
Indices: 38724--38773 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
38714 GCAAGCCCTG
*
38724 ATAAATTGAATTACATTTAAAAT
1 ATAAATTAAATTACATTTAAAAT
*
38747 ATAAATTAAATTACGTTTAAAAT
1 ATAAATTAAATTACATTTAAAAT
38770 ATAA
1 ATAA
38774 TTTTAGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (23 bp):
ATAAATTAAATTACATTTAAAAT
Found at i:40731 original size:17 final size:17
Alignment explanation
Indices: 40709--40746 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
40699 TATTTAATAG
40709 AAAATACA-AAAAAATCT
1 AAAATACATAAAAAAT-T
*
40726 AAAATATATAAAAAATT
1 AAAATACATAAAAAATT
40743 AAAA
1 AAAA
40747 GTTTTAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATACATAAAAAATT
Found at i:47568 original size:15 final size:15
Alignment explanation
Indices: 47550--47587 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
47540 TCTGCGGCCC
47550 TCGACTCTGTCACCA
1 TCGACTCTGTCACCA
*
47565 TCGACTCTGTCGCCA
1 TCGACTCTGTCACCA
47580 TCGACTCT
1 TCGACTCT
47588 AACTGCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.39, G:0.16, T:0.29
Consensus pattern (15 bp):
TCGACTCTGTCACCA
Found at i:50706 original size:201 final size:201
Alignment explanation
Indices: 50361--50762 Score: 795
Period size: 201 Copynumber: 2.0 Consensus size: 201
50351 TAAATTGAAT
50361 TCAATTAAAACCCAAAGAACAAATTACTTTATGTTTCTTTGGTGGGGATTGATGACGTGGCTTCG
1 TCAATTAAAACCCAAAGAACAAATTACTTTATGTTTCTTTGGTGGGGATTGATGACGTGGCTTCG
50426 TGAGGGCTATTTGATCAAGGTCCATATATGTTTGTTTTGTTTCACTTGGATTGAAACATCCATAG
66 TGAGGGCTATTTGATCAAGGTCCATATATGTTTGTTTTGTTTCACTTGGATTGAAACATCCATAG
50491 CCTTTGGATCAAGGTTAATCAATGATGGATATTGTTTTGTGCTTTTAGCCATGAATTGATGATGT
131 CCTTTGGATCAAGGTTAATCAATGATGGATATTGTTTTGTGCTTTTAGCCATGAATTGATGATGT
50556 AAGCAA
196 AAGCAA
50562 TCAATTAAAACCCAAAGAACAAATTACTTTATGTTTCTTTGGTGGGGATTGATGACGTGGCTTCG
1 TCAATTAAAACCCAAAGAACAAATTACTTTATGTTTCTTTGGTGGGGATTGATGACGTGGCTTCG
*
50627 TGAGGGCTATTTGATCAAGGTCCATATATGTTTGTTTTGTTTCAGTTGGATTGAAACATCCATAG
66 TGAGGGCTATTTGATCAAGGTCCATATATGTTTGTTTTGTTTCACTTGGATTGAAACATCCATAG
50692 CCTTTGGATCAAGGTTAATCAATGATGGATATTGTTTTGTGCTTTTAGCCATGAATTGATGATGT
131 CCTTTGGATCAAGGTTAATCAATGATGGATATTGTTTTGTGCTTTTAGCCATGAATTGATGATGT
50757 AAGCAA
196 AAGCAA
50763 AATCCCCCCT
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 200 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (201 bp):
TCAATTAAAACCCAAAGAACAAATTACTTTATGTTTCTTTGGTGGGGATTGATGACGTGGCTTCG
TGAGGGCTATTTGATCAAGGTCCATATATGTTTGTTTTGTTTCACTTGGATTGAAACATCCATAG
CCTTTGGATCAAGGTTAATCAATGATGGATATTGTTTTGTGCTTTTAGCCATGAATTGATGATGT
AAGCAA
Found at i:51164 original size:65 final size:61
Alignment explanation
Indices: 51083--51219 Score: 211
Period size: 65 Copynumber: 2.2 Consensus size: 61
51073 AACATGTGGC
*
51083 TTTCATTCAACAATTATTTATGATCTATCACATCCGACTTCCTAAAATAAAGGGGACAAACATTG
1 TTTCATTCAACAATTATTTATGATCTATCACATCCGACTACCTAAAATAAA--GG--AAACATTG
* *
51148 TTTCATTCAACGATTATTTCTGATCTATCACATCCGACTACCTAAAATAAAGGAAACATTG
1 TTTCATTCAACAATTATTTATGATCTATCACATCCGACTACCTAAAATAAAGGAAACATTG
51209 TTTCATTCAAC
1 TTTCATTCAAC
51220 TTAGCTTTCT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
61 19 0.28
63 2 0.03
65 48 0.70
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (61 bp):
TTTCATTCAACAATTATTTATGATCTATCACATCCGACTACCTAAAATAAAGGAAACATTG
Found at i:70078 original size:22 final size:22
Alignment explanation
Indices: 70060--70126 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
70050 AATCGTTAAG
70060 CGTTGAATGTTGAAACGTTCAA
1 CGTTGAATGTTGAAACGTTCAA
*
70082 CGCTT-AATGTTGAACCGTTCAA
1 CG-TTGAATGTTGAAACGTTCAA
* *
70104 CGCTGAATGCTG-AACTGTTCAA
1 CGTTGAATGTTGAAAC-GTTCAA
70126 C
1 C
70127 ATTCAAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 3 0.08
22 33 0.87
23 2 0.05
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (22 bp):
CGTTGAATGTTGAAACGTTCAA
Found at i:70327 original size:15 final size:16
Alignment explanation
Indices: 70291--70328 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
70281 AGAGCCTCTG
*
70291 AATCATTCAGCGTTTA
1 AATCATTCAGCGCTTA
70307 AATCATTCAGCGCTT-
1 AATCATTCAGCGCTTA
70322 AATCATT
1 AATCATT
70329 TTGAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (16 bp):
AATCATTCAGCGCTTA
Found at i:82493 original size:2 final size:2
Alignment explanation
Indices: 82486--82515 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
82476 GATAGTTTTA
82486 AT 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 AT
82516 TAGTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82827 original size:2 final size:2
Alignment explanation
Indices: 82820--82847 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
82810 ATGATTTTTA
82820 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
82848 GAACTAAGTA
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
Done.