Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005302.1 Hibiscus syriacus cultivar Beakdansim tig00011999_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: 64333
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:6594 original size:72 final size:72
Alignment explanation
Indices: 6446--6597 Score: 162
Period size: 72 Copynumber: 2.1 Consensus size: 72
6436 CCTCGACTCG
* * * * ** * *
6446 ACTCGAAAACTCTGAAATGGATCTTGACTCAACTTGAAAACTCGCGAGCCTAAAGTTTTTAAGTT
1 ACTCGAAAACTCTGAAATGGAGCTCGACTCAACTTGAAAACTAGCAAGCCTAAAACTTTCAAGGT
* * *
6511 CGACTCG
66 CAAATCA
* * *
6518 ACTCGAAAATTGTGAAATGGAGCTCGACTCTAC-TGAAAACTAGCAAGCCTAAAACTTTCAAGGT
1 ACTCGAAAACTCTGAAATGGAGCTCGACTCAACTTGAAAACTAGCAAGCCTAAAACTTTCAAGGT
6582 CAAATCAA
66 CAAATC-A
6590 ACTCGAAA
1 ACTCGAAA
6598 TCATGACTTG
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
71 29 0.45
72 36 0.55
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (72 bp):
ACTCGAAAACTCTGAAATGGAGCTCGACTCAACTTGAAAACTAGCAAGCCTAAAACTTTCAAGGT
CAAATCA
Found at i:7640 original size:13 final size:13
Alignment explanation
Indices: 7618--7668 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
7608 TAGTAGTTGG
*
7618 TTTGACTAACTGA
1 TTTGATTAACTGA
7631 TTTGATTAACTGA
1 TTTGATTAACTGA
**
7644 TTTGAAAAACTGA
1 TTTGATTAACTGA
7657 TTTGATTAACTG
1 TTTGATTAACTG
7669 TTTATATAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (13 bp):
TTTGATTAACTGA
Found at i:9296 original size:16 final size:16
Alignment explanation
Indices: 9269--9314 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
9259 CCTTTATTTA
*
9269 TCTTATTTCTCTTGTT
1 TCTTAATTCTCTTGTT
* *
9285 TGTTAATTCTCTT-TG
1 TCTTAATTCTCTTGTT
9300 TCTTAA-TCTCTTGTT
1 TCTTAATTCTCTTGTT
9315 CTTTGTTTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
14 6 0.25
15 7 0.29
16 11 0.46
ACGTcount: A:0.11, C:0.17, G:0.09, T:0.63
Consensus pattern (16 bp):
TCTTAATTCTCTTGTT
Found at i:13382 original size:21 final size:20
Alignment explanation
Indices: 13337--13388 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
13327 TCCCATAGGG
13337 GTATCGATACTCAGGGTCTA
1 GTATCGATACTCAGGGTCTA
*
13357 GTATCGGTACTCAAAGGGTC-A
1 GTATCGATACTC--AGGGTCTA
13378 GTATCGATACT
1 GTATCGATACT
13389 GAGGTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.39
21 11 0.39
22 6 0.21
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (20 bp):
GTATCGATACTCAGGGTCTA
Found at i:15885 original size:58 final size:59
Alignment explanation
Indices: 15763--15873 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 59
15753 CGGTTAGAGT
* *
15763 CATATTATCGAGTTTACCTTTTCATTGCGACTAGGAGAGTTTGATAGGACACTTAGAAC
1 CATATTATCGAGTTTACCTTTTCATTCCGACTAGGAGAGTTCGATAGGACACTTAGAAC
* * * *
15822 CATATTAT-TAGTTTTCCTTTTCATTCCGACTAGGAGGGTTCGATATGACACT
1 CATATTATCGAGTTTACCTTTTCATTCCGACTAGGAGAGTTCGATAGGACACT
15874 AATCCATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 38 0.83
59 8 0.17
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (59 bp):
CATATTATCGAGTTTACCTTTTCATTCCGACTAGGAGAGTTCGATAGGACACTTAGAAC
Found at i:19473 original size:43 final size:48
Alignment explanation
Indices: 19384--19490 Score: 134
Period size: 43 Copynumber: 2.3 Consensus size: 48
19374 AGGATTAGAT
*
19384 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAATATTATTTTTAGTTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAATATTATGTTTAGTTTA
*
19435 TTATTATTTTATTAGGAATT-A-GAGTT-AAA-A-TATGTTTAGTTTG
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAATATTATGTTTAGTTTA
19478 TTATTATTTTATT
1 TTATTATTTTATT
19491 CATTAGTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
43 24 0.44
44 1 0.02
45 3 0.06
46 5 0.09
50 1 0.02
51 20 0.37
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (48 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAATATTATGTTTAGTTTA
Found at i:29307 original size:15 final size:15
Alignment explanation
Indices: 29278--29307 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29268 AATATGAAAC
29278 TATATGATATACAAT
1 TATATGATATACAAT
29293 TATATGATATACAAT
1 TATATGATATACAAT
29308 ACAATTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
TATATGATATACAAT
Found at i:29427 original size:18 final size:18
Alignment explanation
Indices: 29404--29445 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
29394 ACACTATATG
29404 ATATATGATAT-CTAAACT
1 ATATATGATATAC-AAACT
* *
29422 ATATATTATATACACACT
1 ATATATGATATACAAACT
29440 ATATAT
1 ATATAT
29446 TATACATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATATGATATACAAACT
Found at i:30159 original size:29 final size:31
Alignment explanation
Indices: 30091--30159 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 31
30081 AAATTATACC
* *
30091 TTGGTC-CTTAAACTTTCTAAAGTTTATACTT
1 TTGGTCAC-TAAACTTTCTAAAATTTACACTT
*
30122 TTGAT-ACTAAACTTT-TAAAATTTACA-TT
1 TTGGTCACTAAACTTTCTAAAATTTACACTT
30150 TTGGTCACTA
1 TTGGTCACTA
30160 GTGAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 6 0.19
29 13 0.41
30 8 0.25
31 5 0.16
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.46
Consensus pattern (31 bp):
TTGGTCACTAAACTTTCTAAAATTTACACTT
Found at i:49934 original size:22 final size:22
Alignment explanation
Indices: 49909--49961 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
49899 ACATATATGC
*
49909 TTTTAAAATGTGTATA-ATATAG
1 TTTTAAAA-GTGTATATATATAA
*
49931 TTTTGAAAGTGTATATATATAA
1 TTTTAAAAGTGTATATATATAA
*
49953 TTTTGAAAG
1 TTTTAAAAG
49962 ATTATGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (22 bp):
TTTTAAAAGTGTATATATATAA
Found at i:53503 original size:28 final size:28
Alignment explanation
Indices: 53471--53524 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
53461 ATATAAAATT
*
53471 TAATATTAATTAAA-ATTAAAATAATACA
1 TAATA-TAATTAAATAATAAAATAATACA
*
53499 TAATATATTTAAATAATAAAATAATA
1 TAATATAATTAAATAATAAAATAATA
53525 TATTATCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
TAATATAATTAAATAATAAAATAATACA
Found at i:53510 original size:21 final size:21
Alignment explanation
Indices: 53489--53528 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53479 ATTAAAATTA
*
53489 AAATAAT-ACATAATATATTT
1 AAATAATAAAATAATATATTT
53509 AAATAATAAAATAATATATT
1 AAATAATAAAATAATATATT
53529 ATCGATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAATAAAATAATATATTT
Found at i:53742 original size:21 final size:21
Alignment explanation
Indices: 53712--53764 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
53702 ATTATTACTA
53712 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
*
53733 TCGCATTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
53754 TCGCAATGCGA
1 TCGCAATGCGA
53765 ATAAGTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:53779 original size:20 final size:21
Alignment explanation
Indices: 53754--53805 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
53744 TTTTCCCAAT
*
53754 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
53774 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
53795 TCGCAATGCGA
1 TCGCAATGCGA
53806 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:53886 original size:21 final size:21
Alignment explanation
Indices: 53712--53887 Score: 62
Period size: 21 Copynumber: 8.5 Consensus size: 21
53702 ATTATTACTA
*
53712 TCGCAATGCGATTTTCCA-ATT
1 TCGCAATGCGATTTT-CATAAT
* **
53733 TCGCATTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCATAAT
* * *
53754 TCGCAATGCGA--ATAAGTAAA
1 TCGCAATGCGATTTTCA-TAAT
** *
53774 TCGCAATGCGAATTTGGA-AAA
1 TCGCAATGCG-ATTTTCATAAT
** *
53795 TCGCAATGCGATACTGACT-A-
1 TCGCAATGCGATTTTCA-TAAT
* * * *
53815 TCGCAACGCGATAATACA-AAA
1 TCGCAATGCGAT-TTTCATAAT
* *
53836 TCGCAATGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
53856 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
53877 TCGCAATGCGA
1 TCGCAATGCGA
53888 ATACGTAAAT
Statistics
Matches: 114, Mismatches: 29, Indels: 24
0.68 0.17 0.14
Matches are distributed among these distances:
19 1 0.01
20 47 0.41
21 65 0.57
23 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:53907 original size:20 final size:20
Alignment explanation
Indices: 53874--53970 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
53864 CGATTTTCAT
53874 AATTCGCAATGCGAATACGTA
1 AATT-GCAATGCGAATACGTA
* * *
53895 AATTGCAACGCGATTAAGTA
1 AATTGCAATGCGAATACGTA
* * *
53915 AATTGTAATGCGAATTAGGAA
1 AATTGCAATGCGAA-TACGTA
* *
53936 AATCGCAATGCTAATACGTA
1 AATTGCAATGCGAATACGTA
* *
53956 AATCGCAATGTGAAT
1 AATTGCAATGCGAAT
53971 CTGACTATCG
Statistics
Matches: 60, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 41 0.68
21 19 0.32
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (20 bp):
AATTGCAATGCGAATACGTA
Found at i:54137 original size:21 final size:21
Alignment explanation
Indices: 54113--54179 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
54103 TCATTCCTCG
54113 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
54134 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
54155 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
54176 AGAG
1 AGAG
54180 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:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:54137 original size:42 final size:42
Alignment explanation
Indices: 54061--54179 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
54051 GACTCGCCTG
* * * * * * *
54061 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
54103 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
54145 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
54180 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:55550 original size:14 final size:14
Alignment explanation
Indices: 55531--55566 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
55521 ATTGTTTAAT
55531 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
55545 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
55559 TGATTTGT
1 TGATTTGT
55567 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:55723 original size:33 final size:33
Alignment explanation
Indices: 55673--55762 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 33
55663 AAAAATGACT
* * *
55673 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
55706 ATTGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
55739 ATCGCAACGCGAAACT-AAAATCGC
1 ATCGCAACGCGAAA-TGAAAATCGC
55763 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 50 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:55733 original size:19 final size:19
Alignment explanation
Indices: 55673--55733 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
55663 AAAAATGACT
*
55673 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
55692 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
55706 ATTGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
55725 ATCGCAACG
1 ATCGCAACG
55734 ACAAAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:55760 original size:19 final size:19
Alignment explanation
Indices: 55709--55762 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
55699 CGAGAGAATT
55709 GCAACGCGAAA-TGAAAATC
1 GCAACGCGAAACT-AAAATC
55728 GCAA--CG--AC-AAAATC
1 GCAACGCGAAACTAAAATC
55742 GCAACGCGAAACTAAAATC
1 GCAACGCGAAACTAAAATC
55761 GC
1 GC
55763 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
16 2 0.07
17 2 0.07
18 2 0.07
19 12 0.41
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.09
Consensus pattern (19 bp):
GCAACGCGAAACTAAAATC
Found at i:55781 original size:19 final size:19
Alignment explanation
Indices: 55759--55908 Score: 78
Period size: 19 Copynumber: 8.6 Consensus size: 19
55749 GAAACTAAAA
*
55759 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
55778 TCGCTTTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
* * *
55792 CCTCATTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
55811 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
* *
55825 TCGCGTTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
55844 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
55860 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
**
55877 TCGCATTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
*
55896 TCCGCGTTGCGAT
1 T-CGCATTGCGAT
55909 AGACATTAAG
Statistics
Matches: 96, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 22 0.23
16 12 0.12
17 13 0.14
19 39 0.41
20 10 0.10
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:55810 original size:33 final size:33
Alignment explanation
Indices: 55762--55888 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
55752 ACTAAAATCG
* * *
55762 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
* *
55795 CATTGTGATTTTCATTTCGCATTGCGATTCTCG
1 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
55828 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
* *
55861 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGTGATTTTCATTTCGCATTGCGAT
55889 AGTCATTTCC
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
Found at i:55907 original size:20 final size:20
Alignment explanation
Indices: 55882--55954 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
55872 TTATTTCGCA
*
55882 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* **
55902 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
55922 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
55943 TTGCGATAGTCA
1 TTGCGATAGTCA
55955 AATGAATGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:58219 original size:12 final size:12
Alignment explanation
Indices: 58202--58226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58192 TCTTCGGGGA
58202 CTTTTTCTTCTT
1 CTTTTTCTTCTT
58214 CTTTTTCTTCTT
1 CTTTTTCTTCTT
58226 C
1 C
58227 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:59217 original size:20 final size:20
Alignment explanation
Indices: 59140--59222 Score: 130
Period size: 20 Copynumber: 4.2 Consensus size: 20
59130 CAAAAATCGT
*
59140 GATTCTGACTTTCGCAACGT
1 GATTCTGACTTTCGCAACGA
*
59160 GATTCTGACTTTCGCAACGC
1 GATTCTGACTTTCGCAACGA
59180 GATTCTGACTTTCGCAACGA
1 GATTCTGACTTTCGCAACGA
* *
59200 GATTCTGACTATCACAACGA
1 GATTCTGACTTTCGCAACGA
59220 GAT
1 GAT
59223 AATACAGAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (20 bp):
GATTCTGACTTTCGCAACGA
Found at i:59640 original size:20 final size:20
Alignment explanation
Indices: 59565--59633 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
59555 CAACGGGGAA
* *
59565 ATCGCAATGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
59585 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
59605 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
59625 ATCGCAACG
1 ATCGCAACG
59634 AAAAAATCGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:59644 original size:34 final size:35
Alignment explanation
Indices: 59563--59652 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 35
59553 CACAACGGGG
* *
59563 AAATCGCAATGCGAAAATGGCTATCGCAACGCGAAA
1 AAATCGCAACGCGAAAATGACTATCGCAAC-CGAAA
59599 ATGACTATCGCAACGCGAAAATGACTATCGCAA-CGAAA
1 A--A--ATCGCAACGCGAAAATGACTATCGCAACCGAAA
59637 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
59653 TGAAAATCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
34 14 0.29
36 2 0.04
38 7 0.15
40 25 0.52
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (35 bp):
AAATCGCAACGCGAAAATGACTATCGCAACCGAAA
Found at i:59684 original size:14 final size:14
Alignment explanation
Indices: 59665--59717 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
59655 AAAATCGCAC
59665 TGCGATTTTCTCGT
1 TGCGATTTTCTCGT
59679 TGCGATTTTCATTTCGCAT
1 TGCGATTTTC---TCG--T
*
59698 TGCGATTCTCTCGT
1 TGCGATTTTCTCGT
59712 TGCGAT
1 TGCGAT
59718 AGTCAGTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (14 bp):
TGCGATTTTCTCGT
Found at i:61339 original size:41 final size:42
Alignment explanation
Indices: 61294--61372 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
61284 CAATGACAGT
61294 GGCCTCTTGAACG-GTGG-GGGAGACTCTTGAGGGATGATAGG
1 GGCCTCTTGAACGAGTGGAGGG-GACTCTTGAGGGATGATAGG
*
61335 GGCCTCTTGAACGATTGGAGGGGACTCTTGAGGGATGA
1 GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGA
61373 CAGGTGAGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
41 13 0.37
42 19 0.54
43 3 0.09
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.23
Consensus pattern (42 bp):
GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGATAGG
Found at i:61343 original size:21 final size:21
Alignment explanation
Indices: 61315--61372 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
61305 CGGTGGGGGA
*
61315 GACTCTTGAGGGATGATAGGG
1 GACTCTTGAGGGATGAGAGGG
* **
61336 GCCTCTTGAACGATTG-GAGGG
1 GACTCTTGAGGGA-TGAGAGGG
61357 GACTCTTGAGGGATGA
1 GACTCTTGAGGGATGA
61373 CAGGTGAGTC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.22, C:0.14, G:0.40, T:0.24
Consensus pattern (21 bp):
GACTCTTGAGGGATGAGAGGG
Found at i:61737 original size:20 final size:20
Alignment explanation
Indices: 61712--61749 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
61702 AAGAAAAGTT
61712 TACTTTCGCAACACGAAACA
1 TACTTTCGCAACACGAAACA
*
61732 TACTTTCGCAACGCGAAA
1 TACTTTCGCAACACGAAA
61750 ATGACCATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (20 bp):
TACTTTCGCAACACGAAACA
Found at i:61851 original size:19 final size:19
Alignment explanation
Indices: 61829--61925 Score: 83
Period size: 19 Copynumber: 5.6 Consensus size: 19
61819 GAAACATAAA
61829 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
61848 TCGCGTTGCGA---TC-TT
1 TCGCATTGCGATTTTCATT
61863 GTCG--TTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
61881 TCGCATTGCGA---TC-TT
1 TCGCATTGCGATTTTCATT
61896 GTCG--TTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
61914 TCGCATTGCGAT
1 TCGCATTGCGAT
61926 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 1, Indels: 28
0.68 0.01 0.30
Matches are distributed among these distances:
14 12 0.19
15 4 0.06
16 10 0.16
17 10 0.16
18 4 0.06
19 23 0.37
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:61870 original size:14 final size:14
Alignment explanation
Indices: 61851--61906 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 14
61841 TTTCATTTCG
61851 CGTTGCGATCTTGT
1 CGTTGCGATCTTGT
61865 CGTTGCGATTTTCATT-T
1 CGTTGCGA---TC-TTGT
61882 CGCATTGCGATCTTGT
1 CG--TTGCGATCTTGT
61898 CGTTGCGAT
1 CGTTGCGAT
61907 TTTCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
14 15 0.43
15 2 0.06
16 5 0.14
17 5 0.14
18 2 0.06
19 6 0.17
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (14 bp):
CGTTGCGATCTTGT
Found at i:61876 original size:33 final size:33
Alignment explanation
Indices: 61834--61925 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
61824 ATAAATCGCA
*
61834 TTGCGATTTTCATTTCGCGTTGCGATCTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATCTTGTCG
61867 TTGCGATTTTCATTTCGCATTGCGATCTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATCTTGTCG
61900 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
61926 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATCTTGTCG
Found at i:61944 original size:20 final size:19
Alignment explanation
Indices: 61910--61964 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
61900 TTGCGATTTT
*
61910 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
61929 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
61949 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
61965 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:62525 original size:18 final size:18
Alignment explanation
Indices: 62502--62549 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
62492 CGGGTCGATT
62502 AGGTGATGGCTCTAGGTG
1 AGGTGATGGCTCTAGGTG
* *
62520 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTAGGTG
62538 AGGTGATGGCTC
1 AGGTGATGGCTC
62550 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTAGGTG
Found at i:63894 original size:19 final size:19
Alignment explanation
Indices: 63840--63894 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
63830 TAGTTTCTGA
* *
63840 AAATGAAAATCGCAACACG
1 AAATGACAATCGCAACGCG
63859 AAATGACAATCGCAACGCG
1 AAATGACAATCGCAACGCG
* **
63878 AATTGATTATCGCAACG
1 AAATGACAATCGCAACG
63895 AGAGAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (19 bp):
AAATGACAATCGCAACGCG
Found at i:64037 original size:26 final size:26
Alignment explanation
Indices: 64001--64053 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
63991 TATTATTGAA
64001 ATACCAGTAAACTTATCATCAATTTC
1 ATACCAGTAAACTTATCATCAATTTC
64027 ATACCAGTAAACTTATCATCAATTTC
1 ATACCAGTAAACTTATCATCAATTTC
64053 A
1 A
64054 ATATGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.34
Consensus pattern (26 bp):
ATACCAGTAAACTTATCATCAATTTC
Done.