Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008610.1 Hibiscus syriacus cultivar Beakdansim tig00111566_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: 2108335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2071443 original size:60 final size:60
Alignment explanation
Indices: 2071350--2071482 Score: 239
Period size: 60 Copynumber: 2.2 Consensus size: 60
2071340 GACCAACAAA
*
2071350 ATCGCAATGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTCTGACT
* *
2071410 ATCGCAACGCGATTTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACT
1 ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTCTGACT
2071470 ATCGCAACGCGAT
1 ATCGCAACGCGAT
2071483 AATACAAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (60 bp):
ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTCTGACT
Found at i:2071522 original size:19 final size:20
Alignment explanation
Indices: 2071498--2071545 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
2071488 AAAATCGCAA
2071498 TGCGATTTTCCAAATT-CGT
1 TGCGATTTTCCAAATTACGT
** *
2071517 TGCGATAGTCCAAGTTCACGT
1 TGCGATTTTCCAAATT-ACGT
2071538 TGCGATTT
1 TGCGATTT
2071546 CTTAAGAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TGCGATTTTCCAAATTACGT
Found at i:2071936 original size:19 final size:19
Alignment explanation
Indices: 2071912--2072020 Score: 103
Period size: 19 Copynumber: 5.4 Consensus size: 19
2071902 TTATTTTGGA
2071912 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
2071931 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
2071953 GTTTTTCAAACTCTCGCAACA-
1 -TTTTTC--ACTATCGCAACAC
*
2071974 TATTTTAACTATCGCAACAC
1 T-TTTTCACTATCGCAACAC
* *
2071994 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
2072013 ATTTTTCA
1 -TTTTTCA
2072021 AAATTGCATT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
19 42 0.56
20 6 0.08
21 4 0.05
22 11 0.15
23 6 0.08
25 6 0.08
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:2072054 original size:20 final size:21
Alignment explanation
Indices: 2072029--2072082 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
2072019 CAAAATTGCA
*
2072029 TTGCGAATCT-TACAATCGCG
1 TTGCGAATCTGGACAATCGCG
* *
2072049 TTGCGAATCTGGATATTCGCG
1 TTGCGAATCTGGACAATCGCG
2072070 TTGCGAATCTGGA
1 TTGCGAATCTGGA
2072083 AACTGAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (21 bp):
TTGCGAATCTGGACAATCGCG
Found at i:2073739 original size:24 final size:24
Alignment explanation
Indices: 2073712--2073758 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2073702 TCCGATCGAA
2073712 TTGGAATTATACAAAAATTTGAAT
1 TTGGAATTATACAAAAATTTGAAT
2073736 TTGGAATTATACAAAAATTTGAA
1 TTGGAATTATACAAAAATTTGAA
2073759 GGATGTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (24 bp):
TTGGAATTATACAAAAATTTGAAT
Found at i:2075646 original size:60 final size:59
Alignment explanation
Indices: 2075547--2075683 Score: 193
Period size: 60 Copynumber: 2.3 Consensus size: 59
2075537 AGCAGGCTGG
** * *
2075547 ATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTC
1 ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTC
** *
2075606 ATATTCGGGAATTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTC
1 ATATTCGGGAA-TACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTC
*
2075666 ATATTCGGGATTACACTA
1 ATATTCGGGAATACACTA
2075684 CGGTGCAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 15 0.23
60 51 0.77
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (59 bp):
ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTC
Found at i:2075774 original size:20 final size:20
Alignment explanation
Indices: 2075737--2075779 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2075727 TATATTGGGC
* *
2075737 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
* *
2075757 TATTTTCTATGGTATATGTT
1 TATTGTCTATGGTATATGGT
2075777 TAT
1 TAT
2075780 GGAATAATGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:2076384 original size:6 final size:6
Alignment explanation
Indices: 2076368--2076436 Score: 57
Period size: 6 Copynumber: 10.7 Consensus size: 6
2076358 TTTATGGTAT
* * * *
2076368 TGTTCAC TGTTAC TGTTAAC GGATAC TGTTTAC TGTTAC TGTTCAC GGATAC
1 TGTT-AC TGTTAC TGTT-AC TGTTAC TG-TTAC TGTTAC TGTT-AC TGTTAC
2076420 TGTTTAC TGTTAC TGTT
1 TG-TTAC TGTTAC TGTT
2076437 CACGGGTACT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
6 28 0.56
7 22 0.44
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (6 bp):
TGTTAC
Found at i:2076394 original size:13 final size:13
Alignment explanation
Indices: 2076368--2076452 Score: 80
Period size: 13 Copynumber: 6.5 Consensus size: 13
2076358 TTTATGGTAT
* *
2076368 TGTTCACTGTTAC
1 TGTTCACGGATAC
*
2076381 TGTTAACGGATAC
1 TGTTCACGGATAC
* * *
2076394 TGTTTACTGTTAC
1 TGTTCACGGATAC
2076407 TGTTCACGGATAC
1 TGTTCACGGATAC
* * *
2076420 TGTTTACTGTTAC
1 TGTTCACGGATAC
*
2076433 TGTTCACGGGTAC
1 TGTTCACGGATAC
2076446 TGTTCAC
1 TGTTCAC
2076453 TATTCATAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 57 1.00
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (13 bp):
TGTTCACGGATAC
Found at i:2076402 original size:26 final size:26
Alignment explanation
Indices: 2076368--2076449 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
2076358 TTTATGGTAT
* *
2076368 TGTTCACTGTTACTGTTAACGGATAC
1 TGTTTACTGTTACTGTTCACGGATAC
2076394 TGTTTACTGTTACTGTTCACGGATAC
1 TGTTTACTGTTACTGTTCACGGATAC
*
2076420 TGTTTACTGTTACTGTTCACGGGTAC
1 TGTTTACTGTTACTGTTCACGGATAC
2076446 TGTT
1 TGTT
2076450 CACTATTCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (26 bp):
TGTTTACTGTTACTGTTCACGGATAC
Found at i:2076421 original size:39 final size:39
Alignment explanation
Indices: 2076354--2076452 Score: 110
Period size: 39 Copynumber: 2.6 Consensus size: 39
2076344 TCGATTCCCC
* * *
2076354 ACTGTTTA-TGGTATTGTTCACTGTTACTGTTAACGGAT
1 ACTGTTTACTGGTACTGTTCACGGATACTGTTAACGGAT
* * * *
2076392 ACTGTTTACTGTTACTGTTCACGGATACTGTTTACTGTT
1 ACTGTTTACTGGTACTGTTCACGGATACTGTTAACGGAT
* *
2076431 ACTGTTCACGGGTACTGTTCAC
1 ACTGTTTACTGGTACTGTTCAC
2076453 TATTCATAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 8 0.16
39 42 0.84
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (39 bp):
ACTGTTTACTGGTACTGTTCACGGATACTGTTAACGGAT
Found at i:2076518 original size:16 final size:16
Alignment explanation
Indices: 2076497--2076527 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2076487 ATAATAAATC
*
2076497 ATATTTTTATGATATG
1 ATATTTTTATAATATG
2076513 ATATTTTTATAATAT
1 ATATTTTTATAATAT
2076528 CAGTTACCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATATTTTTATAATATG
Found at i:2078738 original size:31 final size:31
Alignment explanation
Indices: 2078703--2078761 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2078693 AGTTGTATGG
* * *
2078703 ATTATTTAAATTTTAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
2078734 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
2078762 TTTTTAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:2078800 original size:16 final size:16
Alignment explanation
Indices: 2078779--2078821 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
2078769 GATTAAAAAA
2078779 TTAGTTTATTTATATT
1 TTAGTTTATTTATATT
2078795 TTAGTTTATTTATATT
1 TTAGTTTATTTATATT
2078811 TTAGTTTATTT
1 TTAGTTTATTT
2078822 TAGCAGTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
TTAGTTTATTTATATT
Found at i:2083141 original size:13 final size:13
Alignment explanation
Indices: 2083123--2083147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2083113 TTTTGTATGG
2083123 ATTATATATGTGA
1 ATTATATATGTGA
2083136 ATTATATATGTG
1 ATTATATATGTG
2083148 TTTTCAGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
ATTATATATGTGA
Found at i:2083997 original size:22 final size:21
Alignment explanation
Indices: 2083939--2084009 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 21
2083929 TGCAAAAATT
*
2083939 GTATCGGTACCATA--ATAGA
1 GTATCGATACCATAGTATAGA
*
2083958 GTATCGATACCCTAGTATAGTA
1 GTATCGATACCATAGTATAG-A
*
2083980 GTATCGATACCATGGTAT-GA
1 GTATCGATACCATAGTATAGA
*
2084000 GCATCGATAC
1 GTATCGATAC
2084010 TAATGAGCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 12 0.27
20 10 0.23
21 5 0.11
22 17 0.39
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (21 bp):
GTATCGATACCATAGTATAGA
Found at i:2084400 original size:54 final size:54
Alignment explanation
Indices: 2084337--2084667 Score: 491
Period size: 54 Copynumber: 6.1 Consensus size: 54
2084327 TTACCAAATA
*
2084337 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTC
2084391 GGCACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* ** *
2084445 GGTACTAAGTGTGCAAATCACATAATTCATCATATGTTAATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * **
2084499 GGCACTAAGTGTGCAAACCACGAAATTCATCATATGTTGATGAATAATTGTTTC
1 GGCACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTC
** * * * *
2084553 GATACTAAGTGTGCAATTCACGAAATTCATCATATGTTAATGAATAACCGTTTT
1 GGCACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * **
2084607 GGTACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACAATTTC
1 GGCACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTC
2084661 GGCACTA
1 GGCACTA
2084668 TTGTACAAAC
Statistics
Matches: 248, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 248 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:2090330 original size:2 final size:2
Alignment explanation
Indices: 2090323--2090381 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2090313 GACTATTTTA
2090323 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2090365 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
2090382 CGTTTTTCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2092773 original size:22 final size:22
Alignment explanation
Indices: 2092743--2092784 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2092733 GAGTAAGTGG
*
2092743 AATATTTAAAAATA-TTATTTAA
1 AATAATTAAAAA-ACTTATTTAA
2092765 AATAATTAAAAAACTTATTT
1 AATAATTAAAAAACTTATTT
2092785 TTAAAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAATTAAAAAACTTATTTAA
Found at i:2094227 original size:229 final size:227
Alignment explanation
Indices: 2093822--2094270 Score: 774
Period size: 229 Copynumber: 2.0 Consensus size: 227
2093812 GTAAATTATC
* * *
2093822 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
2093887 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
2093952 TGTGTAAATGAAATTATTAAATTAATATTGTAGTTGGAAAACATGAAACACTATTAAAAAAAATT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATT
2094017 GAAACATAAA-TACATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
2094050 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
2094115 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
2094180 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
2094245 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
2094271 GCAGTTATAA
Statistics
Matches: 209, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
228 58 0.28
229 151 0.72
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:2094365 original size:20 final size:20
Alignment explanation
Indices: 2094340--2094378 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2094330 ATACCAGGTA
2094340 AAAATGATAAAACCGGTAAC
1 AAAATGATAAAACCGGTAAC
2094360 AAAATGATAAAACCGGTAA
1 AAAATGATAAAACCGGTAA
2094379 ATTTAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATGATAAAACCGGTAAC
Found at i:2094524 original size:20 final size:19
Alignment explanation
Indices: 2094501--2094547 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2094491 CGATATAACA
2094501 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
2094521 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
2094541 GGTAAAA
1 GGTAAAA
2094548 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2094549 original size:17 final size:19
Alignment explanation
Indices: 2094510--2094552 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2094500 AGGTAAAAAT
2094510 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
2094530 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
2094547 ATGATA
1 ATGATA
2094553 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:2096824 original size:21 final size:21
Alignment explanation
Indices: 2096777--2096841 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2096767 AAGACAATCA
* *
2096777 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
2096799 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
2096819 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
2096840 AG
1 AG
2096842 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:2096917 original size:33 final size:33
Alignment explanation
Indices: 2096875--2096940 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2096865 AAATAGATGG
*
2096875 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2096908 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2096941 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2098751 original size:19 final size:19
Alignment explanation
Indices: 2098727--2098775 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
2098717 AATGTAGGGT
2098727 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2098746 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
2098765 T-ATTTTCGTAT
1 TAATTTT-GTAT
2098776 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2099468 original size:197 final size:197
Alignment explanation
Indices: 2098900--2100173 Score: 2430
Period size: 197 Copynumber: 6.5 Consensus size: 197
2098890 GGCCAAAAGG
*
2098900 ATGTAATTTTTCAATATAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
2098965 TGTCGACACT-A-ATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
2099028 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
2099093 AT
196 AT
2099095 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTTATGTGAGAATATGTCTAAATAAT
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTTATGTGAGAATATGTCTAAATAAT
2099160 GTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
65 GTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
*
2099225 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAACATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
2099290 AAT
195 AAT
2099293 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
2099358 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
2099423 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
2099488 AT
196 AT
*
2099490 ATGTAATTTTTCAATCTAACCAGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
2099555 TGTCGATACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
*
2099620 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAACATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
2099685 AT
196 AT
2099687 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
2099752 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
2099817 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
2099882 AT
196 AT
2099884 ATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
2099948 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
2100013 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
2100077 AAT
195 AAT
*
2100080 ATGTAATTTTTCAATCTAAACGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
2100145 TGTCGACACTAATATAGTTTGTGTCGATA
66 TGTCGACACTAATATAGTTTGTGTCGATA
2100174 CTAATTTAAA
Statistics
Matches: 1062, Mismatches: 12, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
195 36 0.03
196 177 0.17
197 695 0.65
198 154 0.15
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (197 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
AT
Found at i:2101652 original size:18 final size:18
Alignment explanation
Indices: 2101631--2101692 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
2101621 AGCGGTCGCA
2101631 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
2101649 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
2101667 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
2101685 GAAGATGA
1 GAAGATGA
2101693 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:2101655 original size:6 final size:6
Alignment explanation
Indices: 2101631--2101716 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
2101621 AGCGGTCGCA
* * * * * *
2101631 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * *
2101679 GGCGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
2101717 TGATCCAAAC
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:2101666 original size:3 final size:3
Alignment explanation
Indices: 2101646--2101720 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
2101636 TGAAGCTGAC
* * * * * ** *
2101646 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
2101694 GAC GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
2101721 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:2101685 original size:36 final size:36
Alignment explanation
Indices: 2101634--2101712 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
2101624 GGTCGCAGAA
*
2101634 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
2101670 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
2101706 GATGAAG
1 GATGAAG
2101713 ATGATGATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.20
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:2101720 original size:12 final size:12
Alignment explanation
Indices: 2101634--2101716 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
2101624 GGTCGCAGAA
*
2101634 GATGAAGCTGAC
1 GATGAAGATGAC
2101646 GATGAAGATGAC
1 GATGAAGATGAC
*
2101658 GATGATGATGAC
1 GATGAAGATGAC
* *
2101670 GATGAAGCTGGC
1 GATGAAGATGAC
*
2101682 GATGAAGATGAT
1 GATGAAGATGAC
* * *
2101694 GACGATGATGAT
1 GATGAAGATGAC
2101706 GATGAAGATGA
1 GATGAAGATGA
2101717 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:2103498 original size:181 final size:182
Alignment explanation
Indices: 2103185--2103805 Score: 1077
Period size: 181 Copynumber: 3.4 Consensus size: 182
2103175 CTTTCAACAT
** * * * * * *
2103185 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
2103250 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACC-ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
2103315 AATGTGTCGATACGATTTAAAAAAGTGTCGACTTTTACACATCGGAACCCATA
130 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
2103368 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
2103433 GGTCTACAACC-TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GGTCTACAACCATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
2103497 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
2103549 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTAT-AA-ATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
2103612 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACC-ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
2103677 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
130 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * * *
2103730 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
*
2103795 TGTCTACAACC
66 GGTCTACAACC
2103806 TAAAATGTGT
Statistics
Matches: 420, Mismatches: 14, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
179 33 0.08
180 2 0.00
181 286 0.68
182 2 0.00
183 97 0.23
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (182 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
GGTCTACAACCATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:2106316 original size:22 final size:22
Alignment explanation
Indices: 2106285--2106336 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
2106275 TAACTACAAG
* *
2106285 TATATAATGTAATAGGTATCGTT
1 TATAT-ATGTAATAGGTAACGCT
2106308 TATATATGTAATAGGTAACGCT
1 TATATATGTAATAGGTAACGCT
2106330 TATATAT
1 TATATAT
2106337 ATTGTAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (22 bp):
TATATATGTAATAGGTAACGCT
Found at i:2106783 original size:18 final size:18
Alignment explanation
Indices: 2106762--2106798 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2106752 GTAATTGGAG
2106762 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2106780 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2106798 T
1 T
2106799 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2106806 original size:24 final size:24
Alignment explanation
Indices: 2106754--2106800 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2106744 TTTCATATGT
* *
2106754 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
2106778 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
2106801 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:2107095 original size:38 final size:39
Alignment explanation
Indices: 2107053--2107138 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
2107043 TCCGATGCTC
*
2107053 ATCAAAATCCAAAGCTCATATGGT-CCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
2107091 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
2107130 ATCAAAATC
1 ATCAAAATC
2107139 TACAACTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 21 0.49
39 22 0.51
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.19
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:2107602 original size:21 final size:23
Alignment explanation
Indices: 2107552--2107622 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
2107542 TAGGTAAAAA
*
2107552 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
2107575 ATATAATGTAATAGGTATCG-TT
1 ATATAATGTAATAGGTAGCGCTT
* *
2107597 -TATAATGTAATAGGTAGGGGTT
1 ATATAATGTAATAGGTAGCGCTT
2107619 ATAT
1 ATAT
2107623 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.40
22 4 0.10
23 21 0.50
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2107626 original size:21 final size:21
Alignment explanation
Indices: 2107558--2107627 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
2107548 AAAAATATGA
2107558 TGTAATAGGTAGCGCTTATAT
1 TGTAATAGGTAGCGCTTATAT
* * *
2107579 AATGTAATAGGTATCGTTTATAA
1 --TGTAATAGGTAGCGCTTATAT
* *
2107602 TGTAATAGGTAGGGGTTATAT
1 TGTAATAGGTAGCGCTTATAT
2107623 TGTAA
1 TGTAA
2107628 AGTGTCTATC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 22 0.55
23 18 0.45
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (21 bp):
TGTAATAGGTAGCGCTTATAT
Found at i:2108009 original size:22 final size:22
Alignment explanation
Indices: 2107981--2108037 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
2107971 TAAAAATATG
2107981 ATGTAATAGGTAGCGCTTTATA
1 ATGTAATAGGTAGCGCTTTATA
* *
2108003 ATGTAATAGGTATCGTTTTATA
1 ATGTAATAGGTAGCGCTTTATA
2108025 ATGTAATAGGTAG
1 ATGTAATAGGTAG
2108038 TGGTTATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (22 bp):
ATGTAATAGGTAGCGCTTTATA
Done.