Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003703.1 Hibiscus syriacus cultivar Beakdansim tig00007918_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: 75759
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7359 original size:18 final size:18
Alignment explanation
Indices: 7336--7428 Score: 63
Period size: 18 Copynumber: 5.5 Consensus size: 18
7326 CATTCCTCCA
7336 ATTCTTCTTCTCCTTCAG
1 ATTCTTCTTCTCCTTCAG
*
7354 ATTCTTCTGCTCCTTC--
1 ATTCTTCTTCTCCTTCAG
*
7370 -TTC-TC--CTCCTTCAA
1 ATTCTTCTTCTCCTTCAG
* * * *
7384 ATGCTTCCTCGCCTTCCG
1 ATTCTTCTTCTCCTTCAG
* * *
7402 ATTCTTCGTCTTCTTCGG
1 ATTCTTCTTCTCCTTCAG
7420 ATTCTTCTT
1 ATTCTTCTT
7429 GACCTGATCC
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
12 7 0.12
14 2 0.03
15 5 0.09
16 2 0.03
18 42 0.72
ACGTcount: A:0.09, C:0.35, G:0.09, T:0.47
Consensus pattern (18 bp):
ATTCTTCTTCTCCTTCAG
Found at i:7399 original size:30 final size:30
Alignment explanation
Indices: 7337--7399 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
7327 ATTCCTCCAA
* * * *
7337 TTCTTCTTCTCCTTCAGATTCTTCTGCTCC
1 TTCTTCTCCTCCTTCAAATGCTTCTGCGCC
7367 TTCTTCTCCTCCTTCAAATGCTTCCT-CGCC
1 TTCTTCTCCTCCTTCAAATGCTT-CTGCGCC
7397 TTC
1 TTC
7400 CGATTCTTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.08, C:0.40, G:0.06, T:0.46
Consensus pattern (30 bp):
TTCTTCTCCTCCTTCAAATGCTTCTGCGCC
Found at i:10794 original size:23 final size:22
Alignment explanation
Indices: 10755--10797 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
10745 TTATAGGTTA
10755 TTTTTTTTGTTTTTTTCCTTTG
1 TTTTTTTTGTTTTTTTCCTTTG
10777 TTTTTTTAT-TTTTATTTCCTT
1 TTTTTTT-TGTTTT-TTTCCTT
10798 CCTCCAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.05, C:0.09, G:0.05, T:0.81
Consensus pattern (22 bp):
TTTTTTTTGTTTTTTTCCTTTG
Found at i:19866 original size:21 final size:22
Alignment explanation
Indices: 19837--19891 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
19827 ATTCTGATTA
19837 TCGCATTGCGA-TTTCCTAAAT
1 TCGCATTGCGATTTTCCTAAAT
*
19858 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
*
19879 TCGCAATGCGATT
1 TCGCATTGCGATT
19892 ACGTAAATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:19900 original size:20 final size:20
Alignment explanation
Indices: 19875--20052 Score: 198
Period size: 20 Copynumber: 8.8 Consensus size: 20
19865 GCGATTTTCC
19875 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
19895 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
19915 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
* * *
19935 TAAATTGCAATACGAATTAGG
1 TAAATCGCAATGCG-ATTACG
* *
19956 AAAATCGCAAAGCGATTACG
1 TAAATCGCAATGCGATTACG
*
19976 TAAATCGCAATGTGATTACG
1 TAAATCGCAATGCGATTACG
* *
19996 T-ATTCGCATTGCGATTTACG
1 TAAATCGCAATGCGA-TTACG
* * *
20016 T-AATCGCATTGCGACTTTCC
1 TAAATCGCAATGCGA-TTACG
* *
20036 TAATTCGCATTGCGATT
1 TAAATCGCAATGCGATT
20053 TACATAGCGT
Statistics
Matches: 136, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.07
20 99 0.73
21 27 0.20
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (20 bp):
TAAATCGCAATGCGATTACG
Found at i:20045 original size:21 final size:21
Alignment explanation
Indices: 19837--20055 Score: 107
Period size: 20 Copynumber: 10.8 Consensus size: 21
19827 ATTCTGATTA
19837 TCGCATTGCGATTT-CCTAAAT
1 TCGCATTGCGATTTACCT-AAT
* * *
19858 TCGCGTTGCGATTTTCCTAAA
1 TCGCATTGCGATTTACCTAAT
* * *
19879 TCGCAATGCGA-TTACGTAAA
1 TCGCATTGCGATTTACCTAAT
* * *
19899 TCGCAATGCGA-TTACGTAAA
1 TCGCATTGCGATTTACCTAAT
* *
19919 TCGCAATGCGA-TTACGTAAAT
1 TCGCATTGCGATTTACCT-AAT
* * * *** *
19940 T-GCAATACGAATTAGGAAAA
1 TCGCATTGCGATTTACCTAAT
** * *
19960 TCGCAAAGCGA-TTACGTAAA
1 TCGCATTGCGATTTACCTAAT
* * *
19980 TCGCAATGTGA-TTACGT-AT
1 TCGCATTGCGATTTACCTAAT
*
19999 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
20019 TCGCATTGCGACTTT-CCTAAT
1 TCGCATTGCGA-TTTACCTAAT
20040 TCGCATTGCGATTTAC
1 TCGCATTGCGATTTAC
20056 ATAGCGTCAT
Statistics
Matches: 168, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
19 10 0.06
20 101 0.60
21 54 0.32
22 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATTTACCTAAT
Found at i:20607 original size:20 final size:19
Alignment explanation
Indices: 20584--20655 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
20574 TTCTAAACTT
*
20584 AAAATCGCAACATTAAAATG
1 AAAATCGCAACA-GAAAATG
20604 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
20624 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
20645 AAAATCGCAAC
1 AAAATCGCAAC
20656 GAGAGAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:20645 original size:21 final size:21
Alignment explanation
Indices: 20599--20662 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
20589 CGCAACATTA
20599 AAATGAAAATCGCAAC-ACGA-
1 AAATGAAAATCGCAACGA-GAG
**
20619 AAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
20640 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
20661 AA
1 AA
20663 TCATATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAG
Found at i:21501 original size:94 final size:94
Alignment explanation
Indices: 21286--21753 Score: 734
Period size: 94 Copynumber: 5.1 Consensus size: 94
21276 TAGATTGCTT
* *
21286 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
21347 ATTTGTCTTT-TGTTGTCTTTTGCTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
21374 AGTAAATTTATTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
21439 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
21468 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
21533 ATTTGTCTTTGTTTTGTTTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
21562 AGTAAATTTCTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTTTTTAACACTGTGAATTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
21627 ATTTGTCTTTGTTTTATCCTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
21656 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
21721 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
21749 AGTAA
1 AGTAA
21754 TGCAATCCAT
Statistics
Matches: 350, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
88 34 0.10
90 3 0.01
91 2 0.01
92 29 0.08
93 20 0.06
94 262 0.75
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:21871 original size:20 final size:20
Alignment explanation
Indices: 21846--21907 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
21836 TTTTGGTTGA
21846 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
21866 AATGAAAATTGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
21885 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
21905 AAT
1 AAT
21908 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.50, C:0.16, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:21893 original size:19 final size:19
Alignment explanation
Indices: 21844--21903 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
21834 TTTTTTGGTT
21844 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
21863 GAGAATGAAAATTGCAACGC
1 GA-AATGAAAATCGCAACGA
*
21883 GAAACGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
21902 GA
1 GA
21904 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.50, C:0.17, G:0.23, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:21953 original size:19 final size:19
Alignment explanation
Indices: 21931--22016 Score: 110
Period size: 19 Copynumber: 4.8 Consensus size: 19
21921 TATAATCGCG
21931 TTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTCCGCA
*
21950 TTGCGATTCTC--T-CG--
1 TTGCGATTTTCATTCCGCA
*
21964 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTCCGCA
*
21983 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTCCGCA
22002 TTGCGATTTTCATTC
1 TTGCGATTTTCATTC
22017 TCTCGTTGCG
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.17
16 3 0.05
17 3 0.05
19 43 0.73
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTCCGCA
Found at i:22529 original size:21 final size:21
Alignment explanation
Indices: 22505--22571 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
22495 TCATTCCTCG
22505 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
22526 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
22547 AGATGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
22568 AGAG
1 AGAG
22572 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:22529 original size:42 final size:42
Alignment explanation
Indices: 22453--22571 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
22443 GACTCGCCTG
* * * * * *
22453 TCATCCCTCGAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
22495 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
22537 TCA-TCGTTGAAGATGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
22572 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.06
42 59 0.91
43 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:23956 original size:14 final size:14
Alignment explanation
Indices: 23921--23957 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
23911 GATTGTTTAA
*
23921 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
*
23935 ATGATTTGTAAAAG
1 TTGATTTGTAAAAG
23949 TTGATTTGT
1 TTGATTTGT
23958 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:24088 original size:19 final size:19
Alignment explanation
Indices: 24066--24155 Score: 83
Period size: 19 Copynumber: 5.3 Consensus size: 19
24056 AAATGACTAG
24066 CGCAATGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
*
24085 CGCAAT--G--A-GAGAAT
1 CGCAATGCGAAATGAAAAT
*
24099 CACAATGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
*
24118 CGTAA--CG--A-GAAAAT
1 CGCAATGCGAAATGAAAAT
24132 CGCAATGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
24151 CGCAA
1 CGCAA
24156 CGACAAAATC
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
14 20 0.36
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 25 0.45
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
CGCAATGCGAAATGAAAAT
Found at i:24105 original size:33 final size:33
Alignment explanation
Indices: 24068--24176 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
24058 ATGACTAGCG
* *
24068 CAATGCGAAATGAAAATCGCAATGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCA
* *
24101 CAATGCGAAATGAAAATCGTAACGAGAAAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCA
* *
24134 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCA
*
24167 CAACGCGAAA
1 CAATGCGAAA
24177 CTAAATCCGC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAAAATCA
Found at i:24143 original size:14 final size:14
Alignment explanation
Indices: 24112--24176 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
24102 AATGCGAAAT
*
24112 GAAAATCGTAACGA
1 GAAAATCGCAACGA
24126 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
24144 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
24159 CAAAATCGCAACGC
1 GAAAATCGCAACGA
24173 GAAA
1 GAAA
24177 CTAAATCCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 25 0.60
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 11 0.26
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:24226 original size:33 final size:33
Alignment explanation
Indices: 24184--24293 Score: 184
Period size: 33 Copynumber: 3.3 Consensus size: 33
24174 AAACTAAATC
* *
24184 CGCATTGCGATTCTCTTGTTGCGGTTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
24217 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
* *
24250 CGCATTGCGATTCTCTCGTTACGATTTTCAGTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
24283 CGCATTGCGAT
1 CGCATTGCGAT
24294 AGTCATTTCC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
Found at i:24259 original size:19 final size:19
Alignment explanation
Indices: 24202--24313 Score: 73
Period size: 19 Copynumber: 6.4 Consensus size: 19
24192 GATTCTCTTG
*
24202 TTGCGGTTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
24221 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
24235 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
24254 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
* *
24268 TTACGATTTTCAGTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
24287 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
24307 TTGCGAT
1 TTGCGAT
24314 AGACATTAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
14 11 0.16
16 14 0.20
17 13 0.19
19 22 0.31
20 10 0.14
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:24359 original size:20 final size:20
Alignment explanation
Indices: 24287--24359 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
24277 TCAGTTCGCA
**
24287 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCATG
* ***
24307 TTGCGATAGACATTAAGATG
1 TTGCGATAGTCATTTCCATG
24327 ATTGCGA-ACGTCATTTCCATG
1 -TTGCGATA-GTCATTTCCATG
24348 TTGCGATAGTCA
1 TTGCGATAGTCA
24360 AATGAATGCC
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCATG
Found at i:26859 original size:24 final size:24
Alignment explanation
Indices: 26825--26878 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
26815 CTGAAAAATC
26825 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
26849 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
26873 ATCAAA
1 ATCAAA
26879 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:27764 original size:20 final size:20
Alignment explanation
Indices: 27741--27807 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
27731 AGAATCTCGT
27741 TGCGATTTACTAAATCGCAA
1 TGCGATTTACTAAATCGCAA
27761 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTAC-TAAATCGCAA
* ***
27781 CGCGAATTTGGGAAATCGCAA
1 TGCG-ATTTACTAAATCGCAA
27802 TGCGAT
1 TGCGAT
27808 AGTCAGAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 13 0.33
22 2 0.05
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (20 bp):
TGCGATTTACTAAATCGCAA
Found at i:27828 original size:41 final size:41
Alignment explanation
Indices: 27687--27828 Score: 105
Period size: 41 Copynumber: 3.5 Consensus size: 41
27677 TGTTGCGAAT
* * *
27687 TCAGAAATCGAGTTGCGAATTT--GAAATTCAGTATTGCGATAG
1 TCAG-AATCGCGTTGCGAATTTACGAAA-TC-GCAATGCGATAG
* *
27729 TCAGAATCTCGTTGCG-ATTTACTAAATCGCAATGCGATTACG
1 TCAGAATCGCGTTGCGAATTTACGAAATCGCAATGCGA-TA-G
*** **
27771 T-A-AATCGCAACGCGAATTTGGGAAATCGCAATGCGATAG
1 TCAGAATCGCGTTGCGAATTTACGAAATCGCAATGCGATAG
*
27810 TCAGAATCGCGTTACGAAT
1 TCAGAATCGCGTTGCGAAT
27829 CTGGAAACTG
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
39 2 0.03
40 22 0.29
41 44 0.57
42 9 0.12
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (41 bp):
TCAGAATCGCGTTGCGAATTTACGAAATCGCAATGCGATAG
Found at i:48998 original size:289 final size:289
Alignment explanation
Indices: 48468--49014 Score: 753
Period size: 289 Copynumber: 1.9 Consensus size: 289
48458 CCTGCTTCCA
* * *
48468 AGTTTTTATAATTGTTTAAATTCTATTATTAGTTCTTCTATAATGTGAAAATTAAACATTTAGTC
1 AGTTTTTATAATTGTTCAAATTCTATTATTAGTCCTTCTATAATGTCAAAATTAAACATTTAGTC
* * * * * *
48533 TTTATAGACTAATTTGGTTAATTTTGATCTCTATTCTTTTATAACTTTAAACTTCAATCATTACT
66 CTTATACACTAATTTGATTAATTTTGATCCCTATACTTTTATAACTTTAAACTTCAATCATTACC
* * * *
48598 CAAATAGTATATTAACAATATTATTAAAAGCATAATGACTAAAAAATTATAAATTTGGAGAAAAA
131 CAAATAGTATATTAACAATATGAATAAAAGCATAAGGACTAAAAAATTATAAATATGGAGAAAAA
* * *
48663 TAATTAAGGGTATATTTGGACATGATAGGCTGCAAGAATATGTACTTGCTAGAGCAGTAATTACT
196 TAAATAAGGGTATATTTGGACATGATAGGCTGCAAGAATATGTACTTACTAGAACAGTAATTACT
48728 GTGTGCAAAACCTAAATCCTCATTTTCTT
261 GTGTGCAAAACCTAAATCCTCATTTTCTT
* * **
48757 AGTTTTTATAGTT-TCTCAAATTCTATTATTAGTCCTTCTATAATG-CAATTATTTCACATTTAG
1 AGTTTTTATAATTGT-TCAAATTCTATTATTAGTCCTTCTATAATGTCAA-AATTAAACATTTAG
* *
48820 TCCTTATACACTAATTTGATTAATTTTTATCCCTATACTTTCT-TAACTTTAAATTTCAATCATT
64 TCCTTATACACTAATTTGATTAATTTTGATCCCTATACTTT-TATAACTTTAAACTTCAATCATT
*
48884 ACCCAAAT-GATATATTAACAATATGAATAAAAGTATAAGGACTAAAAAATTACTAAA-ATGGAG
128 ACCCAAATAG-TATATTAACAATATGAATAAAAGCATAAGGACTAAAAAATTA-TAAATATGGAG
* * ** * *
48947 AAAAATAAATAAGGGTGTATTTGGACATGATAGGTTGTGAGGATGTGTACTTACTAGAACAGTAA
191 AAAAATAAATAAGGGTATATTTGGACATGATAGGCTGCAAGAATATGTACTTACTAGAACAGTAA
49012 TTA
256 TTA
49015 TCGTGTCTTG
Statistics
Matches: 224, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
288 4 0.02
289 215 0.96
290 5 0.02
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (289 bp):
AGTTTTTATAATTGTTCAAATTCTATTATTAGTCCTTCTATAATGTCAAAATTAAACATTTAGTC
CTTATACACTAATTTGATTAATTTTGATCCCTATACTTTTATAACTTTAAACTTCAATCATTACC
CAAATAGTATATTAACAATATGAATAAAAGCATAAGGACTAAAAAATTATAAATATGGAGAAAAA
TAAATAAGGGTATATTTGGACATGATAGGCTGCAAGAATATGTACTTACTAGAACAGTAATTACT
GTGTGCAAAACCTAAATCCTCATTTTCTT
Found at i:50164 original size:2 final size:2
Alignment explanation
Indices: 50157--50190 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
50147 ACTAAGATCC
*
50157 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
50191 GATGAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:50332 original size:14 final size:14
Alignment explanation
Indices: 50313--50340 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50303 GGATTGCTTT
50313 TTCTTATCAACCAC
1 TTCTTATCAACCAC
50327 TTCTTATCAACCAC
1 TTCTTATCAACCAC
50341 AAATTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (14 bp):
TTCTTATCAACCAC
Found at i:59145 original size:18 final size:19
Alignment explanation
Indices: 59122--59166 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
59112 ATTTAAGTAG
59122 AAATAAAAACGATT-AAAT
1 AAATAAAAACGATTAAAAT
*
59140 AAATAAAAGCGATTAAAAT
1 AAATAAAAACGATTAAAAT
59159 AAA-AAAAA
1 AAATAAAAA
59167 TAAGAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (19 bp):
AAATAAAAACGATTAAAAT
Found at i:60041 original size:26 final size:26
Alignment explanation
Indices: 60012--60074 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
60002 AGGATGAAGT
*
60012 CTTCTAGAAACCGCTGTTGACTGGAC
1 CTTCTAGAAACCGCTGTTAACTGGAC
60038 CTTCTAGAAACCGCTGTTAACTGGAC
1 CTTCTAGAAACCGCTGTTAACTGGAC
60064 CTTCTAGAAAC
1 CTTCTAGAAAC
60075 TGCCACGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (26 bp):
CTTCTAGAAACCGCTGTTAACTGGAC
Found at i:67870 original size:20 final size:20
Alignment explanation
Indices: 67833--67875 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
67823 AAATCCACAC
*
67833 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
67853 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
67873 ATG
1 ATG
67876 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Done.