Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008065.1 Hibiscus syriacus cultivar Beakdansim tig00110562_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: 676718
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
File 3 of 3
Found at i:577420 original size:10 final size:10
Alignment explanation
Indices: 577407--577464 Score: 62
Period size: 10 Copynumber: 5.8 Consensus size: 10
577397 CTTCCCCTCC
*
577407 CTTCCATATT
1 CTTCCATACT
*
577417 CTTCTATACT
1 CTTCCATACT
*
577427 CTTCCATATT
1 CTTCCATACT
*
577437 ATTCCATACT
1 CTTCCATACT
*
577447 CTTTCATACT
1 CTTCCATACT
*
577457 CTTTCATA
1 CTTCCATA
577465 AGGTTCCACA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.48
Consensus pattern (10 bp):
CTTCCATACT
Found at i:577430 original size:20 final size:20
Alignment explanation
Indices: 577407--577464 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
577397 CTTCCCCTCC
*
577407 CTTCCATATTCTTCTATACT
1 CTTCCATATTCTTCCATACT
*
577427 CTTCCATATTATTCCATACT
1 CTTCCATATTCTTCCATACT
* * *
577447 CTTTCATACTCTTTCATA
1 CTTCCATATTCTTCCATA
577465 AGGTTCCACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.48
Consensus pattern (20 bp):
CTTCCATATTCTTCCATACT
Found at i:577442 original size:30 final size:30
Alignment explanation
Indices: 577408--577464 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
577398 TTCCCCTCCC
*
577408 TTCCATATTC-TTCTATACTCTTCCATATTA
1 TTCCATACTCTTTC-ATACTCTTCCATATTA
*
577438 TTCCATACTCTTTCATACTCTTTCATA
1 TTCCATACTCTTTCATACTCTTCCATA
577465 AGGTTCCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (30 bp):
TTCCATACTCTTTCATACTCTTCCATATTA
Found at i:581471 original size:27 final size:27
Alignment explanation
Indices: 581441--581497 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
581431 CAGCACGTGA
*
581441 TCCATCACTACATCGTGTTCCACCGCT
1 TCCAGCACTACATCGTGTTCCACCGCT
*
581468 TCCAGCACTACCTCGTGTTCCACCGCT
1 TCCAGCACTACATCGTGTTCCACCGCT
581495 TCC
1 TCC
581498 TCGATTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.16, C:0.44, G:0.12, T:0.28
Consensus pattern (27 bp):
TCCAGCACTACATCGTGTTCCACCGCT
Found at i:590960 original size:7 final size:7
Alignment explanation
Indices: 590958--591018 Score: 56
Period size: 7 Copynumber: 9.1 Consensus size: 7
590948 TAATATTTTA
590958 TATATTT
1 TATATTT
*
590965 TATATTA
1 TATATTT
* *
590972 TATCTAT
1 TATATTT
*
590979 AATATTT
1 TATATTT
590986 TATATTT
1 TATATTT
590993 TATA-TT
1 TATATTT
*
590999 TATA-TA
1 TATATTT
591005 TAT-TTT
1 TATATTT
591011 TATATTT
1 TATATTT
591018 T
1 T
591019 TTATATTAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
6 14 0.33
7 28 0.67
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (7 bp):
TATATTT
Found at i:590961 original size:14 final size:14
Alignment explanation
Indices: 590942--591015 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
590932 ATTATATATA
590942 TATATATAATATTT
1 TATATATAATATTT
* *
590956 TATATATTTTATATTA
1 TATATA--TAATATTT
*
590972 TATCTATAATATTT
1 TATATATAATATTT
* *
590986 TATATTTTATA-TT
1 TATATATAATATTT
590999 TATATAT-AT-TTT
1 TATATATAATATTT
591011 TATAT
1 TATAT
591016 TTTTTATATT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
12 9 0.19
13 8 0.17
14 20 0.42
16 11 0.23
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (14 bp):
TATATATAATATTT
Found at i:590983 original size:23 final size:22
Alignment explanation
Indices: 590934--591016 Score: 82
Period size: 21 Copynumber: 3.8 Consensus size: 22
590924 CCACCCCGAT
* *
590934 TATATATA-TATATATAATAT-
1 TATATATATTTTATATTATATC
*
590954 TTTATATATTTTATATTATATC
1 TATATATATTTTATATTATATC
*
590976 TATA-ATATTTTATATTTTATATT
1 TATATATATTTTATA--TTATATC
590999 TATATATATTTTTATATT
1 TATATATA-TTTTATATT
591017 TTTTATATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
20 7 0.13
21 20 0.38
22 3 0.06
23 12 0.23
24 3 0.06
25 7 0.13
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
TATATATATTTTATATTATATC
Found at i:591034 original size:30 final size:29
Alignment explanation
Indices: 590942--591036 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 29
590932 ATTATATATA
590942 TATATATAATATTTTATATATTTTATATTATAT
1 TATATAT-AT-TTTTATAT-TTTTATATTA-AT
590975 CTATA-ATA-TTTTATA-TTTTATA-T--T
1 -TATATATATTTTTATATTTTTATATTAAT
590999 TATATATATTTTTATATTTTTTATATTAAT
1 TATATATATTTTTATA-TTTTTATATTAAT
591029 TATATATA
1 TATATATA
591037 AAATATTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
23 4 0.07
24 4 0.07
25 7 0.13
27 8 0.15
28 8 0.15
30 16 0.30
32 1 0.02
33 2 0.04
34 4 0.07
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (29 bp):
TATATATATTTTTATATTTTTATATTAAT
Found at i:591449 original size:8 final size:9
Alignment explanation
Indices: 591423--591448 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
591413 TTTTAATTTT
591423 TTAAAAAAA
1 TTAAAAAAA
591432 TTAAAAAAA
1 TTAAAAAAA
591441 TTAAAAAA
1 TTAAAAAA
591449 TAATAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:595032 original size:48 final size:48
Alignment explanation
Indices: 594976--595086 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
594966 AAATATTTTA
*
594976 TCTGATTTCCGACT-TGAATTTTGTTCTGCTATATGACCTGAATTCTGT
1 TCTGATTTCCGA-TATGAATTTTGTTCTGATATATGACCTGAATTCTGT
* * * **
595024 TCTGATTTCTGATATGGATTTTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATATGAATTTTGTTCTGATATATGACCTGAATTCTGT
* *
595072 TTTGATTTCTGATAT
1 TCTGATTTCCGATAT
595087 CTCCGTTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 54 0.98
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.50
Consensus pattern (48 bp):
TCTGATTTCCGATATGAATTTTGTTCTGATATATGACCTGAATTCTGT
Found at i:595033 original size:12 final size:12
Alignment explanation
Indices: 595013--595082 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
595003 GCTATATGAC
*
595013 CTGAATTCTGTT
1 CTGATTTCTGTT
*
595025 CTGATTTCTGAT
1 CTGATTTCTGTT
*
595037 ATGGATTT-TGTT
1 CT-GATTTCTGTT
*
595049 CTGATATCTGTT
1 CTGATTTCTGTT
*
595061 CTGAATTCTGTT
1 CTGATTTCTGTT
*
595073 TTGATTTCTG
1 CTGATTTCTG
595083 ATATCTCCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 4 0.09
12 37 0.80
13 5 0.11
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.53
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:595048 original size:24 final size:24
Alignment explanation
Indices: 595014--595086 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
595004 CTATATGACC
595014 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * * * *
595038 TGGATTTTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATA
*
595062 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
595086 T
1 T
595087 CTCCGTTTAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:597845 original size:63 final size:63
Alignment explanation
Indices: 597662--597830 Score: 284
Period size: 63 Copynumber: 2.7 Consensus size: 63
597652 AGGAGGGAAG
*
597662 GGGAAAGGAGAGAGAGAAGCAGTAGCAAGTCGAGAAGGCACGAAAGGGAGGAAGAAAGGGAGA
1 GGGAAAGGAGAGAGAGAAGCAGTAGCAAGTCGAGAAGGCACGAAAGGGAGGAAGAACGGGAGA
597725 GGGAAAGGAGAGAGAGAAGCAGTAGCAAGTCGAGAAGGCACGAAAGGGAGGAAGAACGGGAGA
1 GGGAAAGGAGAGAGAGAAGCAGTAGCAAGTCGAGAAGGCACGAAAGGGAGGAAGAACGGGAGA
* * * * *
597788 TGGAGAGGAGAGAGAGAAGCAGTAGCAGGTCAAGAAGACACGA
1 GGGAAAGGAGAGAGAGAAGCAGTAGCAAGTCGAGAAGGCACGA
597831 GAGTGATCGC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 100 1.00
ACGTcount: A:0.43, C:0.09, G:0.43, T:0.04
Consensus pattern (63 bp):
GGGAAAGGAGAGAGAGAAGCAGTAGCAAGTCGAGAAGGCACGAAAGGGAGGAAGAACGGGAGA
Found at i:601459 original size:18 final size:18
Alignment explanation
Indices: 601436--601471 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
601426 ATTTAGAGGT
601436 ACATTTTT-TTTCTCTTGA
1 ACATTTTTCTTT-TCTTGA
601454 ACATTTTTCTTTTCTTGA
1 ACATTTTTCTTTTCTTGA
601472 TATTAATGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.61
Consensus pattern (18 bp):
ACATTTTTCTTTTCTTGA
Found at i:605073 original size:32 final size:32
Alignment explanation
Indices: 605029--605093 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
605019 TACATTTGGT
* *
605029 TACTAAATGACAAGTTGAAACTCTCAATCGTA
1 TACTAAAGGACAAGTCGAAACTCTCAATCGTA
* *
605061 TACTAAAGGACAAGTCGAAACTTTCAATTGTA
1 TACTAAAGGACAAGTCGAAACTCTCAATCGTA
605093 T
1 T
605094 CTCTTCTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (32 bp):
TACTAAAGGACAAGTCGAAACTCTCAATCGTA
Found at i:625019 original size:22 final size:22
Alignment explanation
Indices: 624976--625018 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
624966 AAATTTAAAT
* *
624976 GAGACAATTTAAATATGCAAAA
1 GAGACAAATTAAATATGAAAAA
624998 GAGACAAATTAAATA-GAAAAA
1 GAGACAAATTAAATATGAAAAA
625019 ATATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (22 bp):
GAGACAAATTAAATATGAAAAA
Found at i:627488 original size:39 final size:39
Alignment explanation
Indices: 627402--627474 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
627392 ATCTTTTAAG
*
627402 GAGAACA--ACTTTGAAAGATTCTCATAGGGATAGATAA
1 GAGAACATGACTTTGAAAGATTCTCATAGGGATAAATAA
*
627439 GAGAACATGACTTTGGAAGATTCTCATAGGGA-AAAT
1 GAGAACATGACTTTGAAAGATTCTCATAGGGATAAAT
627475 TTAATATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 7 0.22
38 3 0.09
39 22 0.69
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (39 bp):
GAGAACATGACTTTGAAAGATTCTCATAGGGATAAATAA
Found at i:628367 original size:2 final size:2
Alignment explanation
Indices: 628356--628403 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
628346 ATTTGAGTAC
628356 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
628397 TA TA TA T
1 TA TA TA T
628404 CGATTAGGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:630762 original size:23 final size:25
Alignment explanation
Indices: 630709--630762 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
630699 CTTATAAAAT
630709 TTTAAAAATAGAAATAAATTATTAA
1 TTTAAAAATAGAAATAAATTATTAA
* * *
630734 -TAAAAAAT-GCAATATATTA-TAA
1 TTTAAAAATAGAAATAAATTATTAA
630756 TTTAAAA
1 TTTAAAA
630763 TCTTCAGAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 3 0.12
23 14 0.58
24 7 0.29
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
TTTAAAAATAGAAATAAATTATTAA
Found at i:632498 original size:9 final size:9
Alignment explanation
Indices: 632484--632577 Score: 62
Period size: 9 Copynumber: 9.8 Consensus size: 9
632474 GGCTGATGGA
632484 AACCGGTTT
1 AACCGGTTT
632493 AACCGGTTTT
1 AACCGG-TTT
632503 CAACCGGTTCT
1 -AACCGGTT-T
*
632514 GACCGGTTT
1 AACCGGTTT
*
632523 GACCGGTTT
1 AACCGGTTT
* **
632532 CAATCGGCTCG
1 -AACCGG-TTT
632543 AACCGGTTT
1 AACCGGTTT
* *
632552 GACCGGTCTG
1 AACCGGT-TT
632562 AACCGGTTT
1 AACCGGTTT
*
632571 GACCGGT
1 AACCGGT
632578 CTGACTCGAC
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
9 30 0.45
10 28 0.42
11 8 0.12
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:632509 original size:20 final size:21
Alignment explanation
Indices: 632484--632522 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
632474 GGCTGATGGA
632484 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
632504 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
632523 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:632529 original size:19 final size:18
Alignment explanation
Indices: 632505--632582 Score: 77
Period size: 19 Copynumber: 4.1 Consensus size: 18
632495 CCGGTTTTCA
*
632505 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTCTG
* *
632524 ACCGGTTTCAATCGG-CTCG
1 ACCGGTTT-GACCGGTCT-G
632543 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
632562 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
632581 AC
1 AC
632583 TCGACCCGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.08
19 36 0.72
20 10 0.20
ACGTcount: A:0.15, C:0.28, G:0.29, T:0.27
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCTG
Found at i:632547 original size:29 final size:30
Alignment explanation
Indices: 632484--632567 Score: 100
Period size: 29 Copynumber: 2.8 Consensus size: 30
632474 GGCTGATGGA
* *
632484 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGCTCTG
*
632515 -ACCGGTTTGACCGGTTTCAATCGGCTC-G
1 AACCGGTTTGACCGGTTTCAACCGGCTCTG
* *
632543 AACCGGTTTGACCGGTCTGAACCGG
1 AACCGGTTTGACCGGTTTCAACCGG
632568 TTTGACCGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.02
29 32 0.70
30 13 0.28
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGCTCTG
Found at i:632582 original size:9 final size:9
Alignment explanation
Indices: 632544--632582 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
632534 ATCGGCTCGA
*
632544 ACCGGTTTG
1 ACCGGTCTG
632553 ACCGGTCTG
1 ACCGGTCTG
*
632562 AACCGGTTTG
1 -ACCGGTCTG
632572 ACCGGTCTG
1 ACCGGTCTG
632581 AC
1 AC
632583 TCGACCCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:632604 original size:17 final size:17
Alignment explanation
Indices: 632579--632617 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
632569 TTGACCGGTC
*
632579 TGACTCGACCCGAACGT
1 TGACCCGACCCGAACGT
* *
632596 TGACCCGACCGGACCGT
1 TGACCCGACCCGAACGT
632613 TGACC
1 TGACC
632618 GTTGACTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCGAACGT
Found at i:639840 original size:29 final size:28
Alignment explanation
Indices: 639785--639883 Score: 117
Period size: 29 Copynumber: 3.4 Consensus size: 28
639775 GCTGCTAGAA
*
639785 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTT-TG
* *
639815 ATCGGTTTGATCGGTTTCAACCGGTTTG
1 ACCGGTTTGACCGGTTTCAACCGGTTTG
* *
639843 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTTG
*
639872 ACCGGTCTGACC
1 ACCGGTTTGACC
639884 TGACCCGACC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.22
29 36 0.60
30 11 0.18
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTTG
Found at i:639881 original size:19 final size:19
Alignment explanation
Indices: 639784--639877 Score: 100
Period size: 19 Copynumber: 4.8 Consensus size: 19
639774 GGCTGCTAGA
* *
639784 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TTTG
*
639804 AACCGGTTCTGATCGGTTTG
1 AACCGGTT-TGACCGGTTTG
* *
639824 -ATCGGTTTCAACCGGTTTG
1 AACCGGTTT-GACCGGTTTG
*
639843 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTTTG
639862 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
639878 CTGACCTGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.02
19 38 0.61
20 18 0.29
21 5 0.08
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTG
Found at i:639882 original size:9 final size:9
Alignment explanation
Indices: 639785--639883 Score: 81
Period size: 10 Copynumber: 10.3 Consensus size: 9
639775 GCTGCTAGAA
*
639785 ACCGGTTTA
1 ACCGGTTTG
*
639794 ACCGGTTTTCA
1 ACCGG-TTT-G
639805 ACCGGTTCTG
1 ACCGGTT-TG
*
639815 ATCGGTTTG
1 ACCGGTTTG
* *
639824 ATCGGTTTCA
1 ACCGGTTT-G
639834 ACCGGTTTG
1 ACCGGTTTG
639843 AACCGGTTTG
1 -ACCGGTTTG
*
639853 ACCGGTCTG
1 ACCGGTTTG
639862 AACCGGTTTG
1 -ACCGGTTTG
*
639872 ACCGGTCTG
1 ACCGGTTTG
639881 ACC
1 ACC
639884 TGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:654608 original size:20 final size:21
Alignment explanation
Indices: 654570--654608 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
654560 ATAATAATGG
**
654570 AAATTTTACAAAATTTATAGT
1 AAATTTTACAAAAGATATAGT
654591 AAATTTTA-AAAAGATATA
1 AAATTTTACAAAAGATATA
654609 TATATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (21 bp):
AAATTTTACAAAAGATATAGT
Found at i:655786 original size:18 final size:17
Alignment explanation
Indices: 655763--655801 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
655753 TATATATATG
*
655763 ATTATCCTCTTCCTTATC
1 ATTATCCTCTT-ATTATC
655781 ATTATCCTCTTATTATC
1 ATTATCCTCTTATTATC
655798 ATTA
1 ATTA
655802 ATACCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATCCTCTTATTATC
Found at i:656156 original size:31 final size:31
Alignment explanation
Indices: 656118--656211 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
656108 CCCGAAGGAC
* * *
656118 CAGTCCATAGGTTCCGAAGAACCTAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
656149 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
656180 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
656211 C
1 C
656212 CCACGACCCT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:664973 original size:22 final size:22
Alignment explanation
Indices: 664940--664995 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
664930 AAAATGATGG
* *
664940 ATGTTCTT-TTTACTATTGTAGT
1 ATGTT-TTCTTTACTATTATAAT
*
664962 ATGTTTTCTTTATTATTATAAT
1 ATGTTTTCTTTACTATTATAAT
664984 ATAGTTTTCTTT
1 AT-GTTTTCTTT
664996 TTAAAATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 18 0.62
23 9 0.31
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.62
Consensus pattern (22 bp):
ATGTTTTCTTTACTATTATAAT
Found at i:668904 original size:5 final size:5
Alignment explanation
Indices: 668894--668934 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
668884 AACGGTCAAC
*
668894 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
668935 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:668955 original size:19 final size:19
Alignment explanation
Indices: 668933--669010 Score: 97
Period size: 19 Copynumber: 4.1 Consensus size: 19
668923 TCGGGTCGGG
668933 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
668952 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
668971 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
668990 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
669010 T
1 T
669011 GAAAACCGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.06
19 39 0.76
20 9 0.18
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:668961 original size:10 final size:9
Alignment explanation
Indices: 668931--669009 Score: 86
Period size: 10 Copynumber: 8.3 Consensus size: 9
668921 GGTCGGGTCG
*
668931 GGTCAGACC
1 GGTCAAACC
668940 GGTCAAACC
1 GGTCAAACC
*
668949 GGTTCAGACC
1 GG-TCAAACC
668959 GGTCAAACC
1 GGTCAAACC
*
668968 GGTTCGAACC
1 GG-TCAAACC
*
668978 GGTTGAAACC
1 GG-TCAAACC
668988 GGTCAAACC
1 GGTCAAACC
668997 GGTCAGAACC
1 GGTCA-AACC
669007 GGT
1 GGT
669010 TGAAAACCGG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
9 29 0.48
10 31 0.52
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:668988 original size:29 final size:28
Alignment explanation
Indices: 668932--669029 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 28
668922 GTCGGGTCGG
* *
668932 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTAAGACCG
*
668960 GTCAAACCGGTTCGAACCGGTTGAA-ACCG
1 GTCAAACCGG-TCAAACCGGTT-AAGACCG
*
668989 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTT-AAGACCG
* *
669019 GTTAAAACGGT
1 GTCAAACCGGT
669030 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.18
29 35 0.58
30 14 0.23
ACGTcount: A:0.30, C:0.27, G:0.28, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTAAGACCG
Found at i:669025 original size:10 final size:10
Alignment explanation
Indices: 668937--669030 Score: 90
Period size: 9 Copynumber: 9.7 Consensus size: 10
668927 GTCGGGTCAG
668937 ACCGG-TCAA
1 ACCGGTTCAA
*
668946 ACCGGTTCAG
1 ACCGGTTCAA
668956 ACCGG-TCAA
1 ACCGGTTCAA
*
668965 ACCGGTTCGA
1 ACCGGTTCAA
*
668975 ACCGGTTGAA
1 ACCGGTTCAA
668985 ACCGG-TCAA
1 ACCGGTTCAA
668994 ACCGG-TCAGA
1 ACCGGTTCA-A
*
669004 ACCGGTTGAAA
1 ACCGGTT-CAA
669015 ACCGGTT-AA
1 ACCGGTTCAA
*
669024 AACGGTT
1 ACCGGTT
669031 TCCAGCAGCC
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 32 0.44
10 30 0.42
11 9 0.12
12 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:676136 original size:5 final size:5
Alignment explanation
Indices: 676126--676166 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
676116 AATGGTCAAC
*
676126 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
676167 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:676147 original size:22 final size:22
Alignment explanation
Indices: 676119--676167 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
676109 AACGGTCAAT
676119 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
676141 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
676163 GGTCA
1 GGTCA
676168 GACCGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:676181 original size:9 final size:9
Alignment explanation
Indices: 676163--676252 Score: 72
Period size: 10 Copynumber: 9.3 Consensus size: 9
676153 GGTCGGGTCG
*
676163 GGTCAGACC
1 GGTCAAACC
676172 GGTCAAACC
1 GGTCAAACC
*
676181 GGTTCAGACC
1 GG-TCAAACC
676191 GGTCAAACC
1 GGTCAAACC
*
676200 GGTTCGAACC
1 GG-TCAAACC
*
676210 GGTTGAAACC
1 GG-TCAAACC
676220 GGTCAGAACC
1 GGTCA-AACC
*
676230 GGTTGAAAACC
1 GG-T-CAAACC
*
676241 GGTTAAACC
1 GGTCAAACC
676250 GGT
1 GGT
676253 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
9 28 0.42
10 31 0.46
11 7 0.10
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.29, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:676187 original size:19 final size:20
Alignment explanation
Indices: 676165--676232 Score: 90
Period size: 19 Copynumber: 3.5 Consensus size: 20
676155 TCGGGTCGGG
676165 TCAG-ACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
676184 TCAG-ACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
*
676203 TC-GAACCGGTTGAAACCGG-
1 TCAGAACCGG-TCAAACCGGT
676222 TCAGAACCGGT
1 TCAGAACCGGT
676233 TGAAAACCGG
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
18 1 0.02
19 29 0.64
20 15 0.33
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.16
Consensus pattern (20 bp):
TCAGAACCGGTCAAACCGGT
Found at i:676220 original size:20 final size:20
Alignment explanation
Indices: 676176--676253 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
676166 CAGACCGGTC
*
676176 AAACCGGTTC-AGACCGG-TC
1 AAACCGGTTCGA-ACCGGTTG
676195 AAACCGGTTCGAACCGGTTG
1 AAACCGGTTCGAACCGGTTG
676215 AAACCGG-TCAGAACCGGTTG
1 AAACCGGTTC-GAACCGGTTG
*
676235 AAAACCGGTT-AAACCGGTT
1 -AAACCGGTTCGAACCGGTT
676254 TCCAGCAGCC
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
19 17 0.33
20 27 0.52
21 7 0.13
22 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (20 bp):
AAACCGGTTCGAACCGGTTG
Done.