Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007314.1 Hibiscus syriacus cultivar Beakdansim tig00019484_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: 56267
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2433 original size:21 final size:23
Alignment explanation
Indices: 2384--2437 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2374 CCTTATAAAG
*
2384 GTATCGATACACATTCAAAGAGG
1 GTATCGATACACATTCAAAGAGA
* *
2407 GTATCGATACACGTT-GAAG-GA
1 GTATCGATACACATTCAAAGAGA
2428 GTATCGATAC
1 GTATCGATAC
2438 CTAGCAAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.39
22 3 0.11
23 14 0.50
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (23 bp):
GTATCGATACACATTCAAAGAGA
Found at i:8279 original size:73 final size:74
Alignment explanation
Indices: 8179--8360 Score: 253
Period size: 73 Copynumber: 2.5 Consensus size: 74
8169 GTTAAATGAC
* *
8179 TAGGGGTATCGGTACCTCTA--AGAGGTATCGGTACCCATTGGGCATTCTATTTTTCTTAGAGCC
1 TAGGGGTATCGATACC-CTATGAGAGGTATCGGTACCCATTGGGCATTCTATTTTTCTCAGAGCC
8242 AAAATTGGCA
65 AAAATTGGCA
* * * * *
8252 TA-GGGTATCGATACCCTATGAGGGGTATCAGTACCCATTTGGCATTCTGTTTTTCTCGGAGCCA
1 TAGGGGTATCGATACCCTATGAGAGGTATCGGTACCCATTGGGCATTCTATTTTTCTCAGAGCCA
8316 AAATTGGCA
66 AAATTGGCA
* *
8325 TAGGGGTATCGGTACCTTATGAGAGGTATCGGTACC
1 TAGGGGTATCGATACCCTATGAGAGGTATCGGTACC
8361 TTCCTATTTA
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
71 3 0.03
72 12 0.13
73 51 0.54
74 29 0.31
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (74 bp):
TAGGGGTATCGATACCCTATGAGAGGTATCGGTACCCATTGGGCATTCTATTTTTCTCAGAGCCA
AAATTGGCA
Found at i:12279 original size:21 final size:20
Alignment explanation
Indices: 12249--12289 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
12239 TATCGGATTT
12249 GTTTAAATGGTCTGTAATAG
1 GTTTAAATGGTCTGTAATAG
12269 GTTTAAAATGGTCTGTAATAG
1 GTTT-AAATGGTCTGTAATAG
12290 TAAACTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTTAAATGGTCTGTAATAG
Found at i:12503 original size:23 final size:22
Alignment explanation
Indices: 12468--12510 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
12458 ATGGTTTTAT
* *
12468 GTTGTTAATGAAATAGTTTTAAA
1 GTTGATAAAGAAATA-TTTTAAA
12491 GTTGATAAAGAAATATTTTA
1 GTTGATAAAGAAATATTTTA
12511 TAATGGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (22 bp):
GTTGATAAAGAAATATTTTAAA
Found at i:14995 original size:131 final size:130
Alignment explanation
Indices: 14802--15293 Score: 508
Period size: 131 Copynumber: 3.8 Consensus size: 130
14792 ATAGATTTTT
* * * * * *
14802 GAAGATCAAATCT-AAAAAGAGATATGCTCCTCTACTCTTCAGGGTATATCAGATCT-AGAAACA
1 GAAGATCAAATATGAAAAAGGGATATGCTCCGCTTCTCTTTAGGGTAGATCAGATCTGA-AAACA
* * *
14865 TTGATTCATTCCACTACTCTTTAGGGAAGATTGAATTGAAGTAGATTTGTTCCACTGCTCCTTAA
65 TTGATTCATTCCACTACTCTTTAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTGCTCCTCAG
14930 G
130 G
* * *
14931 GAAGATCAAATATGAAAAAAGGGATTTGCTCCGCTTCTCTTTAGGTTAGATCAGATTTGAAAACA
1 GAAGATCAAATATG-AAAAAGGGATATGCTCCGCTTCTCTTTAGGGTAGATCAGATCTGAAAACA
* * * * * * *
14996 TTAATTCACTCAACTACACTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTACTGCTCAG
65 TTGATTCATTCCACTACTCTTTAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTGCTCCTCAG
15061 G
130 G
* * * ** * *
15062 GAAAATCAAATCTGAAAAAGGGATTTGCTTTG-TTGGTCTTTAGGGTAGATCAGATCTGAAAATA
1 GAAGATCAAATATGAAAAAGGGATATGCTCCGCTT-CTCTTTAGGGTAGATCAGATCTGAAAACA
* *
15126 TTGATTCATTCCAC-AGCT-TTTCAGGGAAGATTGAATTGAGGAAGACTTGTTCCACTGCTCCTC
65 TTGATTCATTCCACTA-CTCTTT-AGGGAAGATTGAATTGAGGTAGATTTGTTCCACTGCTCCTC
15189 AGG
128 AGG
* * * * * *
15192 GAAGATCAAATATAGAAAAAGGGGATATGCTTCACTGCTCTTCAGGGCAGATCAGATCTGGAAAC
1 GAAGATCAAATAT-GAAAAA-GGGATATGCTCCGCTTCTCTTTAGGGTAGATCAGATCTGAAAAC
* * * * * * * *
15257 GTTTATTAACTCTACTACTATTTAGGGTAGTTTGAAT
64 ATTGATTCATTCCACTACTCTTTAGGGAAGATTGAAT
15294 CGGGTTTGAT
Statistics
Matches: 298, Mismatches: 54, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
129 17 0.06
130 104 0.35
131 114 0.38
132 58 0.19
133 5 0.02
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (130 bp):
GAAGATCAAATATGAAAAAGGGATATGCTCCGCTTCTCTTTAGGGTAGATCAGATCTGAAAACAT
TGATTCATTCCACTACTCTTTAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTGCTCCTCAGG
Found at i:15149 original size:130 final size:130
Alignment explanation
Indices: 14802--15256 Score: 499
Period size: 130 Copynumber: 3.5 Consensus size: 130
14792 ATAGATTTTT
* * * * * *
14802 GAAGATCAAATCT-AAAAAGAGATATGC-TCCTCTACTCTTCAGGGTATATCAGATCT-AGAAAC
1 GAAGATCAAATATGAAAAAGGGATTTGCTTCGT-TGCTCTTCAGGGTAGATCAGATCTGA-AAAC
* *
14864 ATTGATTCATTCCACTACTCTTT-AGGGAAGATTGAATTGAAGTAGATTTGTTCCACTGCTCCTT
64 ATTGATTCATTCCACTACT-TTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTGCTCCTC
*
14928 AAG
128 AGG
* * * *
14931 GAAGATCAAATATGAAAAAAGGGATTTGCTCCGCTT-CTCTTTAGGTTAGATCAGATTTGAAAAC
1 GAAGATCAAATATG-AAAAAGGGATTTGCTTCG-TTGCTCTTCAGGGTAGATCAGATCTGAAAAC
* * * ** * *
14995 ATTAATTCACTCAACTACACTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTACTGCTCA
64 ATTGATTCATTCCACTACTTTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTGCTCCTCA
15060 GG
129 GG
* * * * * *
15062 GAAAATCAAATCTGAAAAAGGGATTTGCTTTGTTGGTCTTTAGGGTAGATCAGATCTGAAAATAT
1 GAAGATCAAATATGAAAAAGGGATTTGCTTCGTTGCTCTTCAGGGTAGATCAGATCTGAAAACAT
* *
15127 TGATTCATTCCAC-AGCTTTTCAGGGAAGATTGAATTGAGGAAGACTTGTTCCACTGCTCCTCAG
66 TGATTCATTCCACTA-CTTTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTGCTCCTCAG
15191 G
130 G
* ** * *
15192 GAAGATCAAATATAGAAAAAGGGGATATGCTTCACTGCTCTTCAGGGCAGATCAGATCTGGAAAC
1 GAAGATCAAATAT-GAAAAA-GGGATTTGCTTCGTTGCTCTTCAGGGTAGATCAGATCTGAAAAC
15257 GTTTATTAAC
Statistics
Matches: 269, Mismatches: 47, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
129 15 0.06
130 109 0.41
131 106 0.39
132 38 0.14
133 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (130 bp):
GAAGATCAAATATGAAAAAGGGATTTGCTTCGTTGCTCTTCAGGGTAGATCAGATCTGAAAACAT
TGATTCATTCCACTACTTTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTGCTCCTCAGG
Found at i:16615 original size:1 final size:1
Alignment explanation
Indices: 16609--16672 Score: 65
Period size: 1 Copynumber: 64.0 Consensus size: 1
16599 TTATTTATTC
* * * * * * *
16609 TTTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTATTTTTTATTTTTTATTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16673 CATTATTTCT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.05, C:0.02, G:0.05, T:0.89
Consensus pattern (1 bp):
T
Found at i:16625 original size:7 final size:7
Alignment explanation
Indices: 16594--16664 Score: 69
Period size: 7 Copynumber: 10.4 Consensus size: 7
16584 GAACCACTTA
16594 TTTATTT
1 TTTATTT
16601 ATTTATTCT
1 -TTTATT-T
16610 TTT-TTT
1 TTTATTT
*
16616 TTTGTTT
1 TTTATTT
*
16623 TTT-TTG
1 TTTATTT
16629 TTT-TTT
1 TTTATTT
*
16635 TGT-TTT
1 TTTATTT
16641 TTTATTT
1 TTTATTT
16648 TTTATTT
1 TTTATTT
16655 TTTATTT
1 TTTATTT
16662 TTT
1 TTT
16665 TTCTTTTTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
6 18 0.32
7 28 0.50
8 9 0.16
9 1 0.02
ACGTcount: A:0.08, C:0.01, G:0.04, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:16665 original size:8 final size:8
Alignment explanation
Indices: 16594--16665 Score: 71
Period size: 8 Copynumber: 9.4 Consensus size: 8
16584 GAACCACTTA
*
16594 TTTATTTA
1 TTTATTTT
16602 TTTATTCTT
1 TTTATT-TT
16611 TTT-TTTT
1 TTTATTTT
*
16618 TGT-TTTT
1 TTTATTTT
*
16625 TTTGTTTT
1 TTTATTTT
*
16633 TTTGTTTT
1 TTTATTTT
16641 TTTA-TTT
1 TTTATTTT
16648 TTTA-TTT
1 TTTATTTT
16655 TTTATTTT
1 TTTATTTT
16663 TTT
1 TTT
16666 TCTTTTTCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
7 24 0.42
8 29 0.51
9 4 0.07
ACGTcount: A:0.08, C:0.01, G:0.04, T:0.86
Consensus pattern (8 bp):
TTTATTTT
Found at i:16685 original size:23 final size:23
Alignment explanation
Indices: 16637--16694 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
16627 TGTTTTTTTG
* * *
16637 TTTTTTTATTTTTTATTTTTTAT
1 TTTTTTTCTTTTTCATTATTTAT
*
16660 TTTTTTTCTTTTTCATTATTTCT
1 TTTTTTTCTTTTTCATTATTTAT
*
16683 TTTCCTTTCTTT
1 TTT-TTTTCTTT
16695 CTTTCTTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.09, C:0.10, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTTCTTTTTCATTATTTAT
Found at i:16704 original size:23 final size:22
Alignment explanation
Indices: 16659--16738 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 22
16649 TTATTTTTTA
16659 TTTT-TTTTC-TT-TTTCATT-
1 TTTTCTTTTCTTTCTTTCATTC
* *
16677 ATTTCTTTTCCTTTCTTTCTTTC
1 TTTTCTTTT-CTTTCTTTCATTC
16700 TTTTCTTTTC-TT-TTTCATTC
1 TTTTCTTTTCTTTCTTTCATTC
16720 TTCTTCCTTTTTCTTTCTT
1 TT-TT-C-TTTTCTTTCTT
16739 CAGGAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
18 3 0.06
19 4 0.08
20 10 0.21
21 6 0.12
22 8 0.17
23 13 0.27
24 2 0.04
25 2 0.04
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTCTTTTCTTTCTTTCATTC
Found at i:16709 original size:28 final size:28
Alignment explanation
Indices: 16678--16735 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
16668 TTTTTCATTA
* *
16678 TTTCTTTTCCTTTCTTTCTTTC-TTTTCT
1 TTTCTTTTCCATTC-TTCTTCCTTTTTCT
*
16706 TTTCTTTTTCATTCTTCTTCCTTTTTCT
1 TTTCTTTTCCATTCTTCTTCCTTTTTCT
16734 TT
1 TT
16736 CTTCAGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTCTTTTCCATTCTTCTTCCTTTTTCT
Found at i:16736 original size:41 final size:39
Alignment explanation
Indices: 16645--16738 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 39
16635 TGTTTTTTTA
* *
16645 TTTTTTATTT-TTTATTTTTTTTCTTTTTCATTATTTCT
1 TTTTTTCTTTCTTTATTTTTTTTCTTTTTCATTACTTCT
*
16683 TTTCCTTTCTTTCTTTCTTTTCTTTTCTTTTTCATT-CTTCT
1 TTT--TTTCTTTCTTTATTTT-TTTTCTTTTTCATTACTTCT
16724 TCCTTTTTCTTTCTT
1 T--TTTTTCTTTCTT
16739 CAGGAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
38 3 0.06
40 6 0.13
41 22 0.47
42 14 0.30
43 2 0.04
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (39 bp):
TTTTTTCTTTCTTTATTTTTTTTCTTTTTCATTACTTCT
Found at i:19766 original size:6 final size:6
Alignment explanation
Indices: 19755--20914 Score: 2190
Period size: 6 Copynumber: 195.7 Consensus size: 6
19745 AAATCCTCGA
19755 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
19803 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
19851 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
19899 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
19947 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
19995 ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20041 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20087 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20135 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20183 ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20229 ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20275 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20323 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20371 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20417 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20465 ACATAT AC--AT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20511 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20559 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20607 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20655 ACATAT ACATAT ACATAT --ATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20701 ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT ACATATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--ATAT ACATAT
20749 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20797 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20845 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
20893 ACATAT ACATAT ACATAT ACAT
1 ACATAT ACATAT ACATAT ACAT
20915 GAGAGTCTAT
Statistics
Matches: 1136, Mismatches: 0, Indels: 36
0.97 0.00 0.03
Matches are distributed among these distances:
4 32 0.03
6 1098 0.97
8 6 0.01
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:24831 original size:19 final size:20
Alignment explanation
Indices: 24789--24835 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
24779 CTAGATCATT
*
24789 TTTCAAAATTTCATTTTGAT
1 TTTCAAAATTTCATTTTGAC
24809 TTTCAAAA-TTCATTTTTG-C
1 TTTCAAAATTTCA-TTTTGAC
24828 TTTCAAAA
1 TTTCAAAA
24836 GAAAATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTCAAAATTTCATTTTGAC
Found at i:27664 original size:18 final size:18
Alignment explanation
Indices: 27632--27675 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
27622 GACTATTAAT
27632 AAATAAAATGCAATGCAAA
1 AAAT-AAATGCAATGCAAA
* *
27651 AAGTAAATGTAATGCAAA
1 AAATAAATGCAATGCAAA
27669 AAATAAA
1 AAATAAA
27676 AATATACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.64, C:0.07, G:0.11, T:0.18
Consensus pattern (18 bp):
AAATAAATGCAATGCAAA
Found at i:30934 original size:14 final size:14
Alignment explanation
Indices: 30915--30941 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30905 AATGAATTTA
30915 ATTTTTAAAATATG
1 ATTTTTAAAATATG
30929 ATTTTTAAAATAT
1 ATTTTTAAAATAT
30942 CTCGACTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
ATTTTTAAAATATG
Found at i:33779 original size:21 final size:20
Alignment explanation
Indices: 33749--33787 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
33739 TATCGAAATT
33749 GTTTAAATGGTCTGTAATAG
1 GTTTAAATGGTCTGTAATAG
33769 GTTTAAAATGGTCTGTAAT
1 GTTT-AAATGGTCTGTAAT
33788 GGTAAACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (20 bp):
GTTTAAATGGTCTGTAATAG
Found at i:34230 original size:81 final size:83
Alignment explanation
Indices: 34075--34235 Score: 227
Period size: 81 Copynumber: 1.9 Consensus size: 83
34065 ATGTTCAACG
* * * *
34075 AATGTCTGTAAGATTTATGTAACATCTTTAACTCGTATTTCGAGATGTATATGTGTTATGGGTTT
1 AATGTCTGTAAGATTTATGTAACATCTTTAA--C-TATTTCGAGATGTATACGGGTTATAGGTAT
*
34140 TGCAATGGTCAGATCCCAGAC
63 TACAATGGTCAGATCCCAGAC
*
34161 AATGTCTGTAAGGTTTATGTAACATCTTT-A-TATTTCGAGATGTATACGGGTTATAGGTATTAC
1 AATGTCTGTAAGATTTATGTAACATCTTTAACTATTTCGAGATGTATACGGGTTATAGGTATTAC
34224 AATGGTCAGATC
66 AATGGTCAGATC
34236 TAGACGACAA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 40 0.58
85 1 0.01
86 28 0.41
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (83 bp):
AATGTCTGTAAGATTTATGTAACATCTTTAACTATTTCGAGATGTATACGGGTTATAGGTATTAC
AATGGTCAGATCCCAGAC
Found at i:38559 original size:16 final size:17
Alignment explanation
Indices: 38534--38569 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
38524 ACCCGACCCG
*
38534 ATTATTTTATATTT-AT
1 ATTATATTATATTTAAT
38550 ATTATATTATATTTAAT
1 ATTATATTATATTTAAT
38567 ATT
1 ATT
38570 TTATGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATATTATATTTAAT
Found at i:55081 original size:20 final size:20
Alignment explanation
Indices: 55033--55083 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
55023 ACGTGAGAAG
*
55033 CAGATTTAACTCACCGAGGC
1 CAGATTTATCTCACCGAGGC
**
55053 CAGATTTATCTCGTCGAGGC
1 CAGATTTATCTCACCGAGGC
55073 CAGATTTATCT
1 CAGATTTATCT
55084 GAAGAAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (20 bp):
CAGATTTATCTCACCGAGGC
Done.