Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000117.1 Hibiscus syriacus cultivar Beakdansim tig00000212_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: 63423
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:16640 original size:33 final size:33
Alignment explanation
Indices: 16555--16642 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
16545 GAGTGACTGA
*
16555 TGATGATGAGGGAGATGGAGACGTGCTCGGGTT
1 TGATGATGAGGGACATGGAGACGTGCTCGGGTT
*
16588 TGATGATGAGGGAGATGGAGACGTGCTCGGGTT
1 TGATGATGAGGGACATGGAGACGTGCTCGGGTT
*
16621 TGATGATG-GGGATCTTGGAGAC
1 TGATGATGAGGGA-CATGGAGAC
16643 ATTTAGTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 4 0.08
33 48 0.92
ACGTcount: A:0.22, C:0.09, G:0.44, T:0.25
Consensus pattern (33 bp):
TGATGATGAGGGACATGGAGACGTGCTCGGGTT
Found at i:16641 original size:39 final size:33
Alignment explanation
Indices: 16555--16632 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
16545 GAGTGACTGA
16555 TGATGATGAGGGAGATGGAGACGTGCTCGGGTT
1 TGATGATGAGGGAGATGGAGACGTGCTCGGGTT
16588 TGATGATGAGGGAGATGGAGACGTGCTCGGGTT
1 TGATGATGAGGGAGATGGAGACGTGCTCGGGTT
16621 TGATGATG-GGGA
1 TGATGATGAGGGA
16633 TCTTGGAGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 4 0.09
33 41 0.91
ACGTcount: A:0.22, C:0.08, G:0.46, T:0.24
Consensus pattern (33 bp):
TGATGATGAGGGAGATGGAGACGTGCTCGGGTT
Found at i:20234 original size:48 final size:48
Alignment explanation
Indices: 20178--20273 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
20168 TCCATCCAGT
20178 CAACTTCTGATAAAATTTCTGGATAATCAGCTCCCATAACCCTATCGA
1 CAACTTCTGATAAAATTTCTGGATAATCAGCTCCCATAACCCTATCGA
* *
20226 CAACTTCTGATAAAATTTCTGGATAATTAGCTCTCATAACCCTATCGA
1 CAACTTCTGATAAAATTTCTGGATAATCAGCTCCCATAACCCTATCGA
20274 ATTTCGCATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (48 bp):
CAACTTCTGATAAAATTTCTGGATAATCAGCTCCCATAACCCTATCGA
Found at i:22662 original size:13 final size:14
Alignment explanation
Indices: 22644--22672 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
22634 TCTTATAGCA
22644 TTTTTATAAAC-TT
1 TTTTTATAAACATT
22657 TTTTTATAAACATT
1 TTTTTATAAACATT
22671 TT
1 TT
22673 AACAGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTATAAACATT
Found at i:24366 original size:10 final size:10
Alignment explanation
Indices: 24336--24360 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
24326 TTGAGTTTGA
24336 GTTTGCATTT
1 GTTTGCATTT
24346 GTTTGCATTT
1 GTTTGCATTT
24356 GTTTG
1 GTTTG
24361 AGTTTGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (10 bp):
GTTTGCATTT
Found at i:28235 original size:42 final size:39
Alignment explanation
Indices: 28179--28257 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 39
28169 CGGGAAGTTC
*
28179 ATTTATGTGCGTTTATTTATTAAATGAACGAACATGAACAAG
1 ATTTATGTGCGTTTA---ATTAAATGAACGAACATAAACAAG
* *
28221 ATTTGTGTTCGTTTAATTAAATGAACGAACATAAACA
1 ATTTATGTGCGTTTAATTAAATGAACGAACATAAACA
28258 TTGGTCTCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 21 0.62
42 13 0.38
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (39 bp):
ATTTATGTGCGTTTAATTAAATGAACGAACATAAACAAG
Found at i:28511 original size:7 final size:7
Alignment explanation
Indices: 28499--28585 Score: 77
Period size: 7 Copynumber: 12.4 Consensus size: 7
28489 TATTAAAAAT
28499 CCTAAAC
1 CCTAAAC
28506 CCTAAAC
1 CCTAAAC
28513 CCTAAAC
1 CCTAAAC
* *
28520 CCTACAT
1 CCTAAAC
28527 CCTAAAC
1 CCTAAAC
* *
28534 CCTACAT
1 CCTAAAC
28541 CCTAAAC
1 CCTAAAC
*
28548 CATAAAC
1 CCTAAAC
* *
28555 ACTAAAA
1 CCTAAAC
*
28562 CCT-ACC
1 CCTAAAC
28568 TCCTAAAC
1 -CCTAAAC
*
28576 CTTAAAC
1 CCTAAAC
28583 CCT
1 CCT
28586 TAATCTAATT
Statistics
Matches: 60, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
6 1 0.02
7 57 0.95
8 2 0.03
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:29844 original size:12 final size:11
Alignment explanation
Indices: 29812--29865 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
29802 GGATTGGGTC
29812 AATCGAGCTTG
1 AATCGAGCTTG
29823 AATCGAGCTTG
1 AATCGAGCTTG
* *
29834 AAATTGAGCTTC
1 -AATCGAGCTTG
*
29846 AATCGAGCTCG
1 AATCGAGCTTG
*
29857 AGTCGAGCT
1 AATCGAGCT
29866 GATGAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
11 27 0.75
12 9 0.25
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (11 bp):
AATCGAGCTTG
Found at i:30099 original size:10 final size:10
Alignment explanation
Indices: 30084--30157 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
30074 GGCCTCTAAA
30084 GTTTATGTTC
1 GTTTATGTTC
30094 GTTTATGTTC
1 GTTTATGTTC
*
30104 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
**
30116 GTTCGTGTTC
1 GTTTATGTTC
30126 GTTTATGTT-
1 GTTTATGTTC
*
30135 -TGTA--TTC
1 GTTTATGTTC
30142 GTTTATGTTC
1 GTTTATGTTC
30152 GTTTAT
1 GTTTAT
30158 TTATTAAATG
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 2 0.04
8 6 0.12
10 29 0.60
11 7 0.15
12 4 0.08
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:30114 original size:16 final size:16
Alignment explanation
Indices: 30089--30153 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
30079 CTAAAGTTTA
30089 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
30105 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
30121 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
30137 TATTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
30153 T
1 T
30154 TTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:30203 original size:31 final size:31
Alignment explanation
Indices: 30168--30241 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
30158 TTATTAAATG
*
30168 AACGAATATGAATAAGTTATATTCCTTAATA
1 AACGAACATGAATAAGTTATATTCCTTAATA
30199 AACGAACATGAATAAGTTATATTCCTTAATA
1 AACGAACATGAATAAGTTATATTCCTTAATA
30230 AACGAACATGAA
1 AACGAACATGAA
30242 CAAAAAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (31 bp):
AACGAACATGAATAAGTTATATTCCTTAATA
Found at i:30878 original size:20 final size:20
Alignment explanation
Indices: 30853--30970 Score: 137
Period size: 20 Copynumber: 5.9 Consensus size: 20
30843 ACGATTTTCC
* * *
30853 GACTATCGCAATGCGAGTAT
1 GACTATCGCAACGCGATTCT
*
30873 GACTATTGCAACGCGATTCT
1 GACTATCGCAACGCGATTCT
* * * *
30893 GACTGTCGCAAAGGGATTTT
1 GACTATCGCAACGCGATTCT
30913 GACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTCT
* *
30933 GACTGTCGCAACGCGATGCT
1 GACTATCGCAACGCGATTCT
*
30953 GACTATCGCAATGCGATT
1 GACTATCGCAACGCGATT
30971 TTCAAAGCGC
Statistics
Matches: 80, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (20 bp):
GACTATCGCAACGCGATTCT
Found at i:30923 original size:60 final size:60
Alignment explanation
Indices: 30844--30972 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
30834 AGTCGCGTTA
* * * *
30844 CGATTTTCCGACTATCGCAATGCGAGTATGACTATTGCAACGCGATTCTGACTGTCGCAAAG
1 CGATTTT--GACTATCGCAACGCGAGTATGACTATCGCAACGCGATGCTGACTATCGCAAAG
* * * * *
30906 GGATTTTGACTATCGCAACGCGATTCTGACTGTCGCAACGCGATGCTGACTATCGCAATG
1 CGATTTTGACTATCGCAACGCGAGTATGACTATCGCAACGCGATGCTGACTATCGCAAAG
30966 CGATTTT
1 CGATTTT
30973 CAAAGCGCCA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 51 0.89
62 6 0.11
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (60 bp):
CGATTTTGACTATCGCAACGCGAGTATGACTATCGCAACGCGATGCTGACTATCGCAAAG
Found at i:31674 original size:20 final size:19
Alignment explanation
Indices: 31571--31691 Score: 101
Period size: 20 Copynumber: 6.5 Consensus size: 19
31561 AGAATCGAAA
31571 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
31590 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
31609 TGCGA--TTC---TCGCGT
1 TGCGATTTTCATTTCGCGT
** *
31623 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTC-ATTTCGCGT
** *
31643 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
*
31663 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
31683 TGCGATTTT
1 TGCGATTTT
31692 AAGTTTCAGA
Statistics
Matches: 89, Mismatches: 5, Indels: 15
0.82 0.05 0.14
Matches are distributed among these distances:
14 11 0.12
16 2 0.02
17 3 0.03
19 23 0.26
20 50 0.56
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:31698 original size:20 final size:20
Alignment explanation
Indices: 31655--31698 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
31645 CGATAGTCAT
* *
31655 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
31675 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
31695 TTTC
1 TTTC
31699 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:33207 original size:20 final size:20
Alignment explanation
Indices: 33182--33249 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
33172 TAGTTTACTT
33182 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
33202 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
33222 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
33242 TCGCAACG
1 TCGCAACG
33250 AAAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:33317 original size:20 final size:20
Alignment explanation
Indices: 33292--33347 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
33282 GCGATTCTCT
33292 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
33312 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
33332 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
33348 CGTGTTGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:33354 original size:18 final size:19
Alignment explanation
Indices: 33292--33358 Score: 100
Period size: 20 Copynumber: 3.5 Consensus size: 19
33282 GCGATTCTCT
33292 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
33312 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
33332 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
33350 TGTTGCGAT
1 CGTTGCGAT
33359 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
18 12 0.26
20 34 0.74
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:33939 original size:21 final size:21
Alignment explanation
Indices: 33848--33944 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
33838 GACTCACCTG
*
33848 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
33870 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
33890 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
33911 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
33932 TCATCGTTGAAGA
1 TCATCGTTCAAGA
33945 CGTCCCTCCC
Statistics
Matches: 58, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.05
21 54 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:35390 original size:14 final size:14
Alignment explanation
Indices: 35356--35417 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
35346 TTGCTTGTTT
*
35356 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
35370 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
35384 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
35399 TATTGATGTGTAAA
1 AATTGATTTGTAAA
35413 TAATT
1 -AATT
35418 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:36298 original size:20 final size:20
Alignment explanation
Indices: 36273--36340 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
36263 TAGTTTACTT
36273 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
36293 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
36313 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
36333 TCGCAACG
1 TCGCAACG
36341 AAAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:36408 original size:20 final size:20
Alignment explanation
Indices: 36383--36438 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
36373 GCGATTCTCT
36383 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
36403 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
36423 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
36439 CGTGTTGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:36445 original size:18 final size:19
Alignment explanation
Indices: 36383--36449 Score: 100
Period size: 20 Copynumber: 3.5 Consensus size: 19
36373 GCGATTCTCT
36383 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
36403 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
36423 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
36441 TGTTGCGAT
1 CGTTGCGAT
36450 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
18 12 0.26
20 34 0.74
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:37029 original size:21 final size:21
Alignment explanation
Indices: 36938--37034 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
36928 GACTCACCTG
*
36938 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
36960 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
36980 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
37001 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
37022 TCATCGTTGAAGA
1 TCATCGTTCAAGA
37035 CGTCCCTCCC
Statistics
Matches: 58, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.05
21 54 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:38478 original size:14 final size:14
Alignment explanation
Indices: 38444--38505 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
38434 TTGCTTGTTT
*
38444 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
38458 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
38472 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
38487 TATTGATGTGTAAA
1 AATTGATTTGTAAA
38501 TAATT
1 -AATT
38506 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:38723 original size:20 final size:20
Alignment explanation
Indices: 38700--38864 Score: 131
Period size: 20 Copynumber: 8.8 Consensus size: 20
38690 GCGATTTTCT
* *
38700 CGTTGCGATAGTCAAATACT
1 CGTTGCGATAGTCAAATTCG
* *
38720 CGTTGGGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
38740 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* * *
38754 TGTTGTGATAGTCAAATAAC-
1 CGTTGCGATAGTCAAAT-TCG
38774 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
38794 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
38814 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
38828 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
38848 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
38865 GAATGTGTAA
Statistics
Matches: 114, Mismatches: 17, Indels: 28
0.72 0.11 0.18
Matches are distributed among these distances:
14 22 0.19
16 2 0.02
18 1 0.01
19 1 0.01
20 87 0.76
21 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:38746 original size:54 final size:54
Alignment explanation
Indices: 38666--38802 Score: 186
Period size: 54 Copynumber: 2.5 Consensus size: 54
38656 AGTCAATTCG
* * * *
38666 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAAT-AC
1 CGTTGCGATAATCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAAC
* * *
38719 TCGTTGGGATAATCAAATTCGCGTTGCGATTTTCTTGTTGTGATAGTCAAATAAC
1 -CGTTGCGATAATCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAAC
*
38774 CGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAATCAAATTCGCGTTGCGAT
38803 AGACAAATTC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 71 0.97
55 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAAC
Found at i:38784 original size:74 final size:74
Alignment explanation
Indices: 38700--38864 Score: 219
Period size: 74 Copynumber: 2.2 Consensus size: 74
38690 GCGATTTTCT
* * * *
38700 CGTTGCGATAGTCAAATACTCGTTGGGATA-ATCAAATTCGCGTTGCGATTTTCT-TGTTGTGAT
1 CGTTGCGATAGTCAAATACGCGTTGCGATAGA-CAAATTCGCGTTGCGATTTT-TGCGTTGCGAT
38763 AGTCAAATAAC-
64 AGTCAAAT-ACG
*
38774 CGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTTGCGTTGCGATAG
1 CGTTGCGATAGTCAAATACGCGTTGCGATAGACAAATTCGCGTTGCGATTTTTGCGTTGCGATAG
*
38839 TCAAATTCG
66 TCAAATACG
*
38848 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
38865 GAATGTGTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
73 2 0.02
74 78 0.96
75 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (74 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATAGACAAATTCGCGTTGCGATTTTTGCGTTGCGATAG
TCAAATACG
Found at i:39186 original size:18 final size:18
Alignment explanation
Indices: 39163--39197 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39153 AAGCCGGTTC
39163 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
39181 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
39198 GCTTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:41716 original size:20 final size:20
Alignment explanation
Indices: 41692--41758 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
41682 AAATTCAGTG
* *
41692 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
*
41712 TTGCGATAGTCAGAATCACA
1 TTGCGATAGTCAGAATCGCA
*
41732 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
41752 TTGCGAT
1 TTGCGAT
41759 TTACATATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:43691 original size:18 final size:20
Alignment explanation
Indices: 43668--43708 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
43658 ATGACTTGGT
*
43668 TATATATGT-CATA-TGAAA
1 TATATACGTGCATATTGAAA
43686 TATATACGTGCATATTGAAA
1 TATATACGTGCATATTGAAA
43706 TAT
1 TAT
43709 CATGATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 8 0.40
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (20 bp):
TATATACGTGCATATTGAAA
Found at i:55109 original size:19 final size:19
Alignment explanation
Indices: 55087--55141 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
55077 GATTGTTTCC
55087 TACAGTCTGTTTTCTACTA
1 TACAGTCTGTTTTCTACTA
* *
55106 TACAATCTGTTTTCTTTCTA
1 TACAGTCTGTTTTC-TACTA
55126 T--AGTCTGATTTTCTAC
1 TACAGTCTG-TTTTCTAC
55142 ATGGTATCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.23
19 18 0.60
20 5 0.17
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.51
Consensus pattern (19 bp):
TACAGTCTGTTTTCTACTA
Found at i:57264 original size:36 final size:36
Alignment explanation
Indices: 57208--57278 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
57198 CTAGCATTCG
* *
57208 CCAAGAACCAAATTCAGATCCTGTTGCCTCTGAAAA
1 CCAAAAACCAAATTCAGATCCTGTTGCATCTGAAAA
* *
57244 CCAAAAACCAGATTCGGATCCTGTTGCATCTGAAA
1 CCAAAAACCAAATTCAGATCCTGTTGCATCTGAAA
57279 CAGAAGGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (36 bp):
CCAAAAACCAAATTCAGATCCTGTTGCATCTGAAAA
Found at i:59222 original size:19 final size:19
Alignment explanation
Indices: 59200--59254 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
59190 GACTATTTCC
59200 TACAGTCTGTTTTCTACTA
1 TACAGTCTGTTTTCTACTA
*
59219 TACAGTCTGTTTTCTTTCTA
1 TACAGTCTGTTTTC-TACTA
59239 T--AGTCTGATTTTCTAC
1 TACAGTCTG-TTTTCTAC
59255 AATTAACTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.25
19 19 0.59
20 5 0.16
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (19 bp):
TACAGTCTGTTTTCTACTA
Found at i:60402 original size:15 final size:14
Alignment explanation
Indices: 60372--60431 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
60362 TATCAAACGT
60372 AATAATAAAA-TAA
1 AATAATAAAATTAA
60385 AATAATAATAATTAA
1 AATAATAA-AATTAA
60400 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
60415 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
60430 AA
1 AA
60432 ACTAATGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 25 0.62
16 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:61761 original size:15 final size:15
Alignment explanation
Indices: 61707--61768 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
61697 TTTGGGCTTG
* *
61707 TAATATATATTTATAT
1 TAATATA-ATTAATAA
61723 TAATAATAA-TAATAA
1 TAAT-ATAATTAATAA
61738 TAAT-T--TTAATAA
1 TAATATAATTAATAA
*
61750 TAATATAATTAAAAA
1 TAATATAATTAATAA
61765 TAAT
1 TAAT
61769 TTTAATGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
12 10 0.26
13 2 0.05
15 18 0.47
16 5 0.13
17 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATATAATTAATAA
Found at i:62209 original size:75 final size:76
Alignment explanation
Indices: 61928--62258 Score: 526
Period size: 76 Copynumber: 4.4 Consensus size: 76
61918 GAGGTCTTAA
61928 AAACATCATGCACTGCAGGACTTACAGATGACCCT-AGGCTTTG-AAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
61990 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
62001 AAACATCATGCACTACAAGATTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
62066 AGGCTTTTTTGG
66 AGGC-TTTTTGG
* *
62078 AAACATCATGCACTGCA-GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
62142 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
62153 AAACATCATGCACTGTATGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
62218 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
62229 AAACATCATGCACTGTAGGACTTATAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
62259 TGGGAAATAG
Statistics
Matches: 241, Mismatches: 12, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
73 32 0.13
74 7 0.03
75 38 0.16
76 141 0.59
77 23 0.10
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:62507 original size:76 final size:76
Alignment explanation
Indices: 62382--62666 Score: 522
Period size: 76 Copynumber: 3.8 Consensus size: 76
62372 TCAAAGTAAC
62382 AACATCAAAAAGCT-CCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
*
62446 AAGGTTTTGAA
66 AAGGCTTTGAA
*
62457 AACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
62522 AAGGCTTTGAA
66 AAGGCTTTGAA
62533 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
62598 AAGGCTTTGAA
66 AAGGCTTTGAA
*
62609 AACA-CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTA-GACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
62667 TGGGAAATAG
Statistics
Matches: 205, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
74 12 0.06
75 54 0.26
76 139 0.68
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
AAGGCTTTGAA
Done.