Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003758.1 Hibiscus syriacus cultivar Beakdansim tig00008050_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: 69537
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:71 original size:19 final size:19
Alignment explanation
Indices: 47--84 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
37 TTCGCATAAA
47 CACTAAACCATGAAAACTG
1 CACTAAACCATGAAAACTG
66 CACTAAACCATGAAAACTG
1 CACTAAACCATGAAAACTG
85 TATCAGCTTT
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:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (19 bp):
CACTAAACCATGAAAACTG
Found at i:2496 original size:29 final size:30
Alignment explanation
Indices: 2463--2526 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
2453 TTGGTAAAGG
2463 ACATTAG-GTGCAAAAGAAAGTTAAGGGCC
1 ACATTAGTGTGCAAAAGAAAGTTAAGGGCC
*
2492 ACATTAGTGTGCAAAAGAAAGTTGAGGGCC
1 ACATTAGTGTGCAAAAGAAAGTTAAGGGCC
2522 ACATT
1 ACATT
2527 GATTTTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (30 bp):
ACATTAGTGTGCAAAAGAAAGTTAAGGGCC
Found at i:10612 original size:33 final size:33
Alignment explanation
Indices: 10550--10617 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
10540 CACTTCCAAA
* * *
10550 ACCTCCCCTACCACCAAAACCGCCGCTTCCGCC
1 ACCTCCCCCACCACCAAAACCACCACTTCCGCC
* * *
10583 ACCTCCCCCACCTCCAAATCCACCACTTCCTCC
1 ACCTCCCCCACCACCAAAACCACCACTTCCGCC
10616 AC
1 AC
10618 TGCCCATACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.22, C:0.59, G:0.04, T:0.15
Consensus pattern (33 bp):
ACCTCCCCCACCACCAAAACCACCACTTCCGCC
Found at i:13738 original size:21 final size:21
Alignment explanation
Indices: 13697--13740 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13687 TTTTCATTTT
* *
13697 AATTTATTTTTTATTTGTAAA
1 AATTAATTTTTTATATGTAAA
13718 AATTAATTTTTTAATAT-TAAA
1 AATTAATTTTTT-ATATGTAAA
13739 AA
1 AA
13741 ATATGTCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
AATTAATTTTTTATATGTAAA
Found at i:17080 original size:21 final size:22
Alignment explanation
Indices: 17031--17081 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
17021 AATTTATCTT
17031 TTGAATATT-TCAAATTAAAAG
1 TTGAATATTATCAAATTAAAAG
* * *
17052 AT-ATTATTATCAACTT-AAAG
1 TTGAATATTATCAAATTAAAAG
17072 TTGAATATTA
1 TTGAATATTA
17082 AAAGATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (22 bp):
TTGAATATTATCAAATTAAAAG
Found at i:17402 original size:6 final size:7
Alignment explanation
Indices: 17386--17410 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17376 TCGATAGCTC
17386 AAAAATA
1 AAAAATA
17393 AAAAATA
1 AAAAATA
17400 AAAAATA
1 AAAAATA
17407 AAAA
1 AAAA
17411 GATTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:19597 original size:35 final size:36
Alignment explanation
Indices: 19553--19621 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
19543 AACAATCTTT
*
19553 AATTTTATTCTAAACCCCAAATTCC-AAAATAATTC
1 AATTATATTCTAAACCCCAAATTCCAAAAATAATTC
*
19588 AATTATATTCTAAACCCTAAATTCCAAAAATAAT
1 AATTATATTCTAAACCCCAAATTCCAAAAATAAT
19622 CAAAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 23 0.74
36 8 0.26
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.33
Consensus pattern (36 bp):
AATTATATTCTAAACCCCAAATTCCAAAAATAATTC
Found at i:20202 original size:35 final size:35
Alignment explanation
Indices: 20156--20229 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
20146 CAATATTATT
* *
20156 TTGAAGTATTTT-AGAATTTTGGGTTTAGAATGTAA
1 TTGAAGTATTTTGA-AATTTGGGGTTTAGAATGAAA
*
20191 TTGAATTATTTTGAAATTTGGGGTTTAGAATGAAA
1 TTGAAGTATTTTGAAATTTGGGGTTTAGAATGAAA
20226 TTGA
1 TTGA
20230 GGACTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (35 bp):
TTGAAGTATTTTGAAATTTGGGGTTTAGAATGAAA
Found at i:30108 original size:2 final size:2
Alignment explanation
Indices: 30101--30126 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30091 ACATCTAGAT
30101 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
30127 GAACAGTGTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31280 original size:57 final size:57
Alignment explanation
Indices: 31192--31308 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
31182 TCAAAATAAG
31192 TTGCAATAAAACTGAGAGTAGATCCAAAGCCATTATTGCATGCAATAAGATTGGCAC
1 TTGCAATAAAACTGAGAGTAGATCCAAAGCCATTATTGCATGCAATAAGATTGGCAC
*
31249 TTGCAATAAAACTGAGAGTAGATCTAAAGCCATTATTGCATGCAATAAGATTGGCAC
1 TTGCAATAAAACTGAGAGTAGATCCAAAGCCATTATTGCATGCAATAAGATTGGCAC
31306 TTG
1 TTG
31309 ATGTTGCTCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (57 bp):
TTGCAATAAAACTGAGAGTAGATCCAAAGCCATTATTGCATGCAATAAGATTGGCAC
Found at i:36261 original size:2 final size:2
Alignment explanation
Indices: 36256--36291 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
36246 ATTTACCCTA
36256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36292 GGTAAGGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36512 original size:116 final size:116
Alignment explanation
Indices: 36352--37345 Score: 1522
Period size: 116 Copynumber: 8.6 Consensus size: 116
36342 ATTAATTAAA
* * * *
36352 TTATGGATGGCCCTGAGGTCTTATCATCTTGCATTGTAGGTCTTACAGATGATCCGAAGGATTTA
1 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
*
36417 AATATCAAAAAGCTCCCGAAGGTTTTTTGAAAACATCCTGCACTGTAGGTC
66 AATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC
* * * ** *
36468 TTATGGATGGCCCTGAGGTCTTATCATCTTGGATTGTAGATCTTACAGATGAATCGAAGGCTTTA
1 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
* * * ***
36533 AATATCAAAAATCTCCCGAAGGATTTTTGAAAATATCCTGCACTACCGGTC
66 AATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC
* * *
36584 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATAACCCGAAGACTTTA
1 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
* *
36649 AATATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCCTACACTGTAGGTC
66 AATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC
* *
36700 TTATGGATGGCCCTGAGGTTTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTA
1 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
* * * *
36765 ATTATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATCTTGCGCTGTAGGTC
66 AATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC
* *
36816 TTATGGATGGCCTTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGACTTTA
1 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
* * *
36881 AATATCAAAAAGCTTCCGAAGGATTTTTGAAAACATCCTACACTGTAGGTC
66 AATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC
* *
36932 TTATGGATGGCCCTGAGGTCTTATCATCTTACACTGTAGGTCTTACAGATTACCCGGAGGCTTTA
1 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
* *
36997 AATATTAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAAGTC
66 AATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC
* *
37048 TTATAGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGATCCGGAGGCTTTA
1 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
* * * *
37113 AATATCAAAAAACTCTCGAAGGCTTTTTGAAAACATTCTGCACTGTATGTC
66 AATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC
* *
37164 TTATGGATGGCCTTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGAACCGGAGGCTTTA
1 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
** * * *
37229 AATATCAAAAATATCCCGAAGGCTTTTTGAAAATAACCTGCATTGTAGGTC
66 AATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC
*
37280 TTATGGATGG-CCTGAGGTCTTATCATCTTGCACTATAGGTCTTACAGATGACCCGGAGGCTTTA
1 TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
37344 AA
66 AA
37346 AACATCATGC
Statistics
Matches: 800, Mismatches: 78, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
115 53 0.07
116 747 0.93
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (116 bp):
TTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTA
AATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC
Found at i:38043 original size:22 final size:22
Alignment explanation
Indices: 38018--38063 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
38008 AATAAAGCTT
*
38018 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAAAATCTA
*
38040 TCATCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
38062 TC
1 TC
38064 TATGAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:38504 original size:54 final size:54
Alignment explanation
Indices: 38417--38572 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 54
38407 ATAATCACTG
* * * *
38417 GTTCATAAAATATTTAACAACACATTCATCCTTTCATGTGGCTTCTGCTCAGAT
1 GTTCGTAAAATATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCACAAAT
*
38471 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCACAAAT
1 GTTCGTAAAATATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCACAAAT
* *
38525 GTTCGTAAAATATTTGACAAGACATTCATTCTTTC-TAGTGGCTTCTGC
1 GTTCGTAAAATATTTGACAACACATTCATCCTTTCAT-GTGGCTTCTGC
38573 CCATATTTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.01
54 92 0.99
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAATATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCACAAAT
Found at i:43021 original size:19 final size:18
Alignment explanation
Indices: 42989--43024 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42979 TGTTGATCAT
*
42989 ATTTTCAATTAATTCTCC
1 ATTTTCAATAAATTCTCC
43007 ATTTATCAATAAATTCTC
1 ATTT-TCAATAAATTCTC
43025 AAATTCCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTCAATAAATTCTCC
Found at i:49515 original size:21 final size:21
Alignment explanation
Indices: 49486--49538 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
49476 ATTCTGACTA
49486 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
49507 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
49528 TCGCAATGCGA
1 TCGCATTGCGA
49539 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:49553 original size:20 final size:20
Alignment explanation
Indices: 49528--49620 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
49518 TTTTCCTAAT
*
49528 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
49548 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
*
49568 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
49588 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
49608 TCGCAATGCGAAT
1 TCGCAATGCGAAT
49621 CTGACTATCG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:49636 original size:40 final size:40
Alignment explanation
Indices: 49528--49620 Score: 186
Period size: 40 Copynumber: 2.3 Consensus size: 40
49518 TTTTCCTAAT
49528 TCGCAATGCGAATACGTAAATCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATAAGTAAA
49568 TCGCAATGCGAATACGTAAATCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATAAGTAAA
49608 TCGCAATGCGAAT
1 TCGCAATGCGAAT
49621 CTGACTATCG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATAAGTAAA
Found at i:49842 original size:22 final size:22
Alignment explanation
Indices: 49817--49882 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
49807 GGCGACATCC
49817 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
49839 GTCCCCATCGCTGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
49861 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
49883 TTCACGGTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:50295 original size:20 final size:20
Alignment explanation
Indices: 50252--50319 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
50242 CGATTCTTGC
** *
50252 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGT
*
50272 GTTGCGATAGTCATTTTTGT
1 GTTGCGATAGTCATTTTCGT
**
50292 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
50312 GTTGCGAT
1 GTTGCGAT
50320 TTAAAGTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.16, C:0.15, G:0.25, T:0.44
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:50329 original size:20 final size:20
Alignment explanation
Indices: 50290--50329 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
50280 AGTCATTTTT
** *
50290 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTAAAGTTTC
50310 GTGTTGCGATTTAAAGTTTC
1 GTGTTGCGATTTAAAGTTTC
50330 AGAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGATTTAAAGTTTC
Found at i:52229 original size:20 final size:20
Alignment explanation
Indices: 52200--52352 Score: 109
Period size: 20 Copynumber: 8.3 Consensus size: 20
52190 AGAATAGTTT
*
52200 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
52220 ACTATTGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
52240 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAACGCGAAAATG
*
52256 A--ATCGCAATGCG-AAATG
1 ACTATCGCAACGCGAAAATG
**
52273 AAAATCGCAA--C-AACAA--
1 ACTATCGCAACGCGAA-AATG
52289 A--ATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
52307 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* **
52327 ACTATCGCAATGCGAATTTG
1 ACTATCGCAACGCGAAAATG
52347 ACTATC
1 ACTATC
52353 ACAATGCGAT
Statistics
Matches: 111, Mismatches: 8, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
14 14 0.13
16 10 0.09
17 8 0.07
18 5 0.05
19 7 0.06
20 67 0.60
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:52357 original size:20 final size:20
Alignment explanation
Indices: 52290--52366 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
52280 CAACAACAAA
* **
52290 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
**
52310 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
52330 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
* *
52350 ATCACAATGCGATTTTG
1 ATCGCAATGCGAATTTG
52367 TTGTTGCGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATTTGACT
Found at i:52426 original size:20 final size:20
Alignment explanation
Indices: 52401--52449 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
52391 GCGATTCTCT
52401 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
52421 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
52441 CGTTACGAT
1 CGTTGCGAT
52450 TTTAAGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:53024 original size:21 final size:21
Alignment explanation
Indices: 52960--53036 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 21
52950 TCCCCTATTA
*
52960 TTCAAGAGGCCCCTATCATCC
1 TTCAAGAGGCCCCTATCATCG
* * * *
52981 CTCAAGAGTCCCCTCTCACCG
1 TTCAAGAGGCCCCTATCATCG
* *
53002 TTCAAGAGGCCACTGTCATCG
1 TTCAAGAGGCCCCTATCATCG
* *
53023 TTGAAGAGGTCCCT
1 TTCAAGAGGCCCCT
53037 CCCAACATTC
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTATCATCG
Found at i:54444 original size:14 final size:14
Alignment explanation
Indices: 54425--54460 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
54415 ATTGTTTAAT
54425 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
54439 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
54453 TGATTTGT
1 TGATTTGT
54461 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:54579 original size:34 final size:34
Alignment explanation
Indices: 54536--54631 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
54526 GTTGATTTCG
54536 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
54570 CGTTGCGATTTTCA-TTTAGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
54603 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
54632 AGTCATTTCC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:54713 original size:20 final size:20
Alignment explanation
Indices: 54603--54697 Score: 172
Period size: 20 Copynumber: 4.8 Consensus size: 20
54593 GCGATTCTCT
54603 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
54623 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
54643 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
54663 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
54683 TGTTGCGATAGTCAT
1 CGTTGCGATAGTCAT
54698 ATTCACGTTG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:57163 original size:24 final size:24
Alignment explanation
Indices: 57129--57182 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
57119 CTGAAAAATC
57129 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
57153 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
57177 ATCAAA
1 ATCAAA
57183 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:57196 original size:24 final size:24
Alignment explanation
Indices: 57129--57196 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
57119 CTGAAAAATC
* * *
57129 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
57153 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
57177 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
57197 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:58049 original size:20 final size:20
Alignment explanation
Indices: 58024--58070 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
58014 AAATTCAGTA
*
58024 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
58044 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
58064 TTGCGAT
1 TTGCGAT
58071 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:58080 original size:20 final size:20
Alignment explanation
Indices: 58057--58231 Score: 224
Period size: 20 Copynumber: 8.7 Consensus size: 20
58047 CGATAGTCAG
*
58057 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
58077 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
58097 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
58117 ATTCGCATTGCGATATTCCAA
1 ATTCGCATTGCGAT-TTACGT
*
58138 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
58158 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
58178 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
58199 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
58219 ATTCGCATTGCGA
1 ATTCGCATTGCGA
58232 ATTAGGAAAA
Statistics
Matches: 132, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
20 101 0.77
21 31 0.23
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:58088 original size:40 final size:39
Alignment explanation
Indices: 58044--58171 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 39
58034 CAGAATCTCG
*
58044 TTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGTA
1 TTGCGATA-TCAGATTCGCGTTGCGATTTACGTATTCGCA
* **
58084 TTGCGAT-TTACGTATTCGTATTGCGATTTACGTATTCGCA
1 TTGCGATATCA-G-ATTCGCGTTGCGATTTACGTATTCGCA
*
58124 TTGCGATATTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGATA-T-CAGATTCGCGTTGCGATTTACGTATTCGCA
58165 TTGCGAT
1 TTGCGAT
58172 TTACGTAATC
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 38 0.51
41 32 0.43
42 1 0.01
43 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (39 bp):
TTGCGATATCAGATTCGCGTTGCGATTTACGTATTCGCA
Found at i:58142 original size:81 final size:80
Alignment explanation
Indices: 58044--58193 Score: 246
Period size: 81 Copynumber: 1.9 Consensus size: 80
58034 CAGAATCTCG
* * * *
58044 TTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGTATTGCGATTTACGTATTCGTATTGCG
1 TTGCGATAGTCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCG
58109 ATTTACGTATTCGCA
66 ATTTACGTATTCGCA
*
58124 TTGCGATATTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGC
1 TTGCGATAGT-CAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGC
58189 GATTT
65 GATTT
58194 TCCAAATTCG
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
80 9 0.14
81 55 0.86
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (80 bp):
TTGCGATAGTCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCG
ATTTACGTATTCGCA
Found at i:58159 original size:61 final size:61
Alignment explanation
Indices: 58084--58231 Score: 269
Period size: 61 Copynumber: 2.4 Consensus size: 61
58074 CGTATTCGTA
* *
58084 TTGCGATTTACGTATTCGTATTGCGATTTACGTATTCGCATTGCGATATTCCAAATTCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATATTCCAAATTCGCG
*
58145 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATATTCCAAATTCGCG
58206 TTGCGATTTACGTATTCGCATTGCGA
1 TTGCGATTTACGTATTCGCATTGCGA
58232 ATTAGGAAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 84 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (61 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATATTCCAAATTCGCG
Found at i:58203 original size:41 final size:40
Alignment explanation
Indices: 58059--58231 Score: 204
Period size: 41 Copynumber: 4.3 Consensus size: 40
58049 ATAGTCAGAT
* * *
58059 TCGCGTTGCGATTTACGTATTCGTATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
* **
58099 TCGTATTGCGATTTACGTATTCGCATTGCGATATT-CCAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGAT-TTACGTAA
*
58139 TTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAA
1 -TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
* ** * *
58180 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGA-TTTACGTATTCGCATTGCGATTTACGTAA
58221 TCGCATTGCGA
1 TCGCATTGCGA
58232 ATTAGGAAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
40 43 0.38
41 70 0.62
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
Found at i:58251 original size:21 final size:21
Alignment explanation
Indices: 58221--58294 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
58211 ATTTACGTAT
*
58221 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
58242 GCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
58263 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
58284 TCGCAATGCGA
1 TCGCAATGCGA
58295 TAGTCAGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:58252 original size:41 final size:41
Alignment explanation
Indices: 58160--58295 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 41
58150 ATTTACGTAT
* * ** *
58160 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAAT
1 TCGCAATGCGATTTACGTAATCGCATTGCGAATTTGGAAAA
** * *
58201 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGATTTACGTAATCGCATTGCGAATTTGGAAAA
* * * * *
58242 GCGCAATGCGAATTAGGAAAATCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGATTTACG-TAATCGCATTGCGAATTTGGAAAA
58284 TCGCAATGCGAT
1 TCGCAATGCGAT
58296 AGTCAGAATC
Statistics
Matches: 76, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 46 0.61
42 30 0.39
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (41 bp):
TCGCAATGCGATTTACGTAATCGCATTGCGAATTTGGAAAA
Found at i:58322 original size:41 final size:41
Alignment explanation
Indices: 58221--58323 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 41
58211 ATTTACGTAT
*
58221 TCGCATTGCGAATTAGGAAAAGCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGAATT-GGAAAAGCGCAATGCGAATTAGCAAAA
* * *
58263 TCGCAATGCGAATTTGGAAAATCGCAATGCG-A-TAGTCAGAA
1 TCGCATTGCGAA-TTGGAAAAGCGCAATGCGAATTAG-CAAAA
*
58304 TCGCGTTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
58324 CTGATTTGCG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
40 4 0.08
41 20 0.38
42 26 0.50
43 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (41 bp):
TCGCATTGCGAATTGGAAAAGCGCAATGCGAATTAGCAAAA
Found at i:61719 original size:6 final size:6
Alignment explanation
Indices: 61708--61732 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61698 TTTTTATTAA
61708 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
61733 GTGAGAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:62874 original size:49 final size:51
Alignment explanation
Indices: 62786--62884 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 51
62776 ATAAAATAAT
* * *
62786 TTTTTTTTAATTTTACATAATATTCAAAACAATATTAATAT-ATATGTAACA
1 TTTTTTTTAAGTTTACA-AATATTCAAAACAATAATAATATCATAAGTAACA
**
62837 TTTTTTTTAAGTTTAC-AATATT-AAAAGGTATAATAATATCATAAGTAA
1 TTTTTTTTAAGTTTACAAATATTCAAAA-CAATAATAATATCATAAGTAA
62885 TAACATATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
48 4 0.10
49 15 0.37
50 7 0.17
51 15 0.37
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (51 bp):
TTTTTTTTAAGTTTACAAATATTCAAAACAATAATAATATCATAAGTAACA
Found at i:65523 original size:24 final size:24
Alignment explanation
Indices: 65496--65548 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
65486 GTATATAAAA
65496 TTAAAAACAAG-CATATTAATTTTG
1 TTAAAAACAAGACATATTAA-TTTG
**
65520 TTAAAATTAAGAACATATTAATTTG
1 TTAAAAACAAG-ACATATTAATTTG
65545 TTAA
1 TTAA
65549 CATAGGACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 8 0.32
26 8 0.32
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (24 bp):
TTAAAAACAAGACATATTAATTTG
Done.