Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006231.1 Hibiscus syriacus cultivar Beakdansim tig00014851_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: 58899
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:325 original size:30 final size:30
Alignment explanation
Indices: 286--342 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
276 AATCGGTCAT
* *
286 TAATGTTATCATTGTTTTA-AAAATGATCAC
1 TAATATTATCATT-TGTTACAAAATGATCAC
*
316 TAATATTATCGTTTGTTACAAAATGAT
1 TAATATTATCATTTGTTACAAAATGAT
343 AATCGACGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.44
Consensus pattern (30 bp):
TAATATTATCATTTGTTACAAAATGATCAC
Found at i:391 original size:3 final size:3
Alignment explanation
Indices: 383--449 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
373 ATTGCAGTAA
383 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
431 TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC T
450 CACCCATTAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1407 original size:3 final size:3
Alignment explanation
Indices: 1399--1518 Score: 210
Period size: 3 Copynumber: 40.7 Consensus size: 3
1389 GGTAATTTAT
1399 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A-G AGG -GG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1445 AGG AGGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG A-GG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1491 AGG AGG AGG AGG AGG AGG AGG A-G AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1519 AACGATTTGT
Statistics
Matches: 113, Mismatches: 0, Indels: 8
0.93 0.00 0.07
Matches are distributed among these distances:
2 6 0.05
3 104 0.92
4 3 0.03
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:1572 original size:30 final size:30
Alignment explanation
Indices: 1537--1601 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
1527 GTTAACGTCA
* * *
1537 AGTGACTATTTTATAACTAACGATAACGTT
1 AGTGACCATTTTATAACAAACGATAACATT
* * *
1567 AGTGACCATTTTGTAAGAAATGATAACATT
1 AGTGACCATTTTATAACAAACGATAACATT
1597 AGTGA
1 AGTGA
1602 TTAATTGGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (30 bp):
AGTGACCATTTTATAACAAACGATAACATT
Found at i:3433 original size:40 final size:40
Alignment explanation
Indices: 3386--3491 Score: 135
Period size: 40 Copynumber: 2.6 Consensus size: 40
3376 TGTTCAGGGG
3386 TAAATCAGTGTTTTTTCAGGCTTTTCATCGTATGCTTAGT
1 TAAATCAGTGTTTTTTCAGGCTTTTCATCGTATGCTTAGT
** ** *
3426 TAAATCAGTGTCTTGATC--TTTATTTCTTCGTATGCTTAGT
1 TAAATCAGTGT-TTTTTCAGGCT-TTTCATCGTATGCTTAGT
3466 TAAATCAGTGTTTTTTCAGGCTTTTC
1 TAAATCAGTGTTTTTTCAGGCTTTTC
3492 CATGGAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
39 5 0.09
40 43 0.81
41 5 0.09
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (40 bp):
TAAATCAGTGTTTTTTCAGGCTTTTCATCGTATGCTTAGT
Found at i:5753 original size:21 final size:20
Alignment explanation
Indices: 5729--5792 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
5719 TTTAACAATA
5729 AATTTATTATTTTTATAATTT
1 AATTTATT-TTTTTATAATTT
*
5750 AATTTCTTTATTTTAT-ATTT
1 AATTTATTT-TTTTATAATTT
*
5770 TATTTCATTTTTTATTATAATTT
1 AATTT-A-TTTTT-TTATAATTT
5793 TTATTTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 9 0.26
21 15 0.43
22 7 0.20
23 4 0.11
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
AATTTATTTTTTTATAATTT
Found at i:8465 original size:22 final size:21
Alignment explanation
Indices: 8426--8466 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
8416 AGTAAAAAAA
**
8426 CCAGATCGATTTTTATCCGAT
1 CCAGATCGATTTAAATCCGAT
8447 CCAGATCGAATTTAAATCCG
1 CCAGATCG-ATTTAAATCCG
8467 GCTATGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (21 bp):
CCAGATCGATTTAAATCCGAT
Found at i:9209 original size:35 final size:35
Alignment explanation
Indices: 9160--9230 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
9150 GTTAAAAATT
* *
9160 ATATTAATATACTAAATTAAAAGCATGGTCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGTCCATAA
*
9195 ATATTAATAAACTAAATTAGAAGCAGGGTCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGTCCATAA
9230 A
1 A
9231 CTTATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAAAAGCAGGGTCCATAA
Found at i:15018 original size:3 final size:3
Alignment explanation
Indices: 15010--15042 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
15000 TAGAAACTCA
15010 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
15043 CTGAAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19113 original size:2 final size:2
Alignment explanation
Indices: 19100--19148 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
19090 ACAAAGCATA
* * * *
19100 AG AG AG AC AG AG AG AC AG AG AG AG AG AG GG GG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19142 AG AG AG A
1 AG AG AG A
19149 TAAGAGTCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.04, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25686 original size:26 final size:27
Alignment explanation
Indices: 25631--25687 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
25621 TATTATATTT
*
25631 AAAAAATTATAATTTCTCTAAAATTAC
1 AAAAAATTATAATTTCTCTAAAAATAC
25658 AAAAAATTCA-AA-TTC-CTAAAAATATC
1 AAAAAATT-ATAATTTCTCTAAAAATA-C
25684 AAAA
1 AAAA
25688 TCATCCCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.30
26 8 0.30
27 10 0.37
28 1 0.04
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAAATTATAATTTCTCTAAAAATAC
Found at i:26770 original size:13 final size:12
Alignment explanation
Indices: 26731--26771 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
26721 ATGTAATTTC
26731 AATTTATATTTTT
1 AATTTA-ATTTTT
26744 AA-TT-ATTTTT
1 AATTTAATTTTT
26754 AATTTAATTTCTT
1 AATTTAATTT-TT
26767 AATTT
1 AATTT
26772 TATATTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.32
11 2 0.08
12 6 0.24
13 9 0.36
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
AATTTAATTTTT
Found at i:31482 original size:60 final size:60
Alignment explanation
Indices: 31387--31685 Score: 402
Period size: 60 Copynumber: 5.0 Consensus size: 60
31377 AAACCCCAGA
* * * *
31387 ACAGGCATCTATAAGGACTTTCCCTAGACCACTAAGATCTAGGAGTCCATTATGGAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
* *
31447 AAAGGCATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
* * * *
31507 ACATG-ATCCATAAGGACTTACCGTAGATCATTAAGATCTAAGAGTCCAATATGGAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
* * * * *
31566 GCAGACATCCATAAGGACTTACTGTAAACCACTAAGATCTAGGAGTCTAATATGGAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
** * * * *
31626 ACATACATCCATAAGGACTTACCGTAAACCACTAAGATATAGGAGTCTAATATGAAAGAT
1 ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
31686 CAGAACATAC
Statistics
Matches: 214, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
59 52 0.24
60 162 0.76
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (60 bp):
ACAGGCATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
Found at i:31608 original size:119 final size:119
Alignment explanation
Indices: 31392--31689 Score: 409
Period size: 119 Copynumber: 2.5 Consensus size: 119
31382 CCAGAACAGG
* * * * * *
31392 CATCTATAAGGACTTTCCCTAGACCACTAAGATCTAGGAGTCCATTATGGAAGATAAAGGCATCC
1 CATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT-CAGACATCC
*
31457 ATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATACAT-
65 ATAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACATA
* * * *
31511 GATCCATAAGGACTTACCGTAGATCATTAAGATCTAAGAGTCCAATATGGAAGATGCAGACATCC
1 CATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT-CAGACATCC
** *
31576 ATAAGGACTTACTGTAAACCACTAAGATCTAGGAGTCTAATATGGAAGATACATA
65 ATAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACATA
* * * *
31631 CATCCATAAGGACTTACCGTAAACCACTAAGATATAGGAGTCTAATATGAAAGATCAGA
1 CATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATCAGA
31690 ACATACATGA
Statistics
Matches: 155, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
119 108 0.70
120 47 0.30
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (119 bp):
CATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATCAGACATCCA
TAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACATA
Found at i:32991 original size:16 final size:17
Alignment explanation
Indices: 32970--33002 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32960 AGGTGTCACG
32970 TTGACT-TTTCAAAACT
1 TTGACTCTTTCAAAACT
*
32986 TTGACTCTTTTAAAACT
1 TTGACTCTTTCAAAACT
33003 CATTGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (17 bp):
TTGACTCTTTCAAAACT
Found at i:33632 original size:24 final size:25
Alignment explanation
Indices: 33600--33673 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
33590 TGCCACATAT
* * * *
33600 ATTTATCCCGAAGGACCGTGTA-TA
1 ATTTGTCCCGAAAGACCGCGTAGAA
*
33624 ATTTGTCCCGAAAGACCACGTAGAA
1 ATTTGTCCCGAAAGACCGCGTAGAA
*
33649 ATTTGTCCCGAATGACCGCGTAGAA
1 ATTTGTCCCGAAAGACCGCGTAGAA
33674 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 18 0.43
25 24 0.57
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (25 bp):
ATTTGTCCCGAAAGACCGCGTAGAA
Found at i:33822 original size:15 final size:15
Alignment explanation
Indices: 33804--33865 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
33794 CACATAGGGT
*
33804 ATTTTCACGTAGAAC
1 ATTTTCACATAGAAC
* *
33819 ATTTTCACTTAGCAC
1 ATTTTCACATAGAAC
*
33834 ATTTTCACATAAAAC
1 ATTTTCACATAGAAC
* *
33849 ATTTTCATATAAAAC
1 ATTTTCACATAGAAC
33864 AT
1 AT
33866 AATCACATAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (15 bp):
ATTTTCACATAGAAC
Found at i:38812 original size:11 final size:11
Alignment explanation
Indices: 38796--38831 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
38786 CGTATTTTGC
*
38796 TTGTTTATGTT
1 TTGTTTTTGTT
38807 TTGTTTTTGTTT
1 TTGTTTTTG-TT
38819 TTGTTTTTGTT
1 TTGTTTTTGTT
38830 TT
1 TT
38832 TTTCACAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.81
Consensus pattern (11 bp):
TTGTTTTTGTT
Found at i:38814 original size:6 final size:6
Alignment explanation
Indices: 38796--38832 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
38786 CGTATTTTGC
*
38796 TTGTTT ATG-TT TTGTTT TTGTTT TTGTTT TTGTTT TT
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TT
38833 TTCACAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.03, C:0.00, G:0.16, T:0.81
Consensus pattern (6 bp):
TTGTTT
Found at i:42291 original size:17 final size:17
Alignment explanation
Indices: 42270--42310 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
42260 AGAGTAATTA
42270 AAATATATAA-ATTATT
1 AAATATATAATATTATT
42286 ATAATATTATAATATT-TT
1 A-AATA-TATAATATTATT
42304 AAATATA
1 AAATATA
42311 ATGTCATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 8 0.36
19 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATATATAATATTATT
Found at i:50609 original size:23 final size:23
Alignment explanation
Indices: 50565--50609 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
50555 TGCTTTCATA
* *
50565 GCACACTTTTTCTCTTCCTTTTG
1 GCACACTTTTTATCTTCATTTTG
* *
50588 GCACGCTTTTTATTTTCATTTT
1 GCACACTTTTTATCTTCATTTT
50610 CGATCATTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.24, G:0.09, T:0.56
Consensus pattern (23 bp):
GCACACTTTTTATCTTCATTTTG
Found at i:54648 original size:2 final size:2
Alignment explanation
Indices: 54641--54674 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
54631 CAGTAATTAA
54641 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54675 GTAAAAGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:54979 original size:21 final size:21
Alignment explanation
Indices: 54955--54996 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54945 AAATGCAAAT
54955 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
54976 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
54997 CCACGACCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:55672 original size:19 final size:19
Alignment explanation
Indices: 55648--55913 Score: 187
Period size: 19 Copynumber: 13.3 Consensus size: 19
55638 TTAACTATCA
55648 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
55667 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
55686 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
55705 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
*
55727 CAACGCGAA-ATGGAAAATCG
1 CAA--CGAATTTGGAAAATCG
* ** *
55747 CAACGCGATTTTCAACTATCG
1 CAACG-AATTTGGAA-AATCG
*
55768 CAACGCGAA-ATGGAAAATCG
1 CAA--CGAATTTGGAAAATCG
* ** *
55788 CAACGCGATTTTCAACTATCG
1 CAACG-AATTTGGAA-AATCG
*
55809 CAACGCGAA-ATGGAAAATCG
1 CAA--CGAATTTGGAAAATCG
* * **
55829 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
55851 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
55870 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
*
55889 CAACTAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
55908 CAACGA
1 CAACGA
55914 CAACTGTAGA
Statistics
Matches: 190, Mismatches: 38, Indels: 38
0.71 0.14 0.14
Matches are distributed among these distances:
18 6 0.03
19 95 0.50
20 34 0.18
21 22 0.12
22 27 0.14
23 4 0.02
24 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:55745 original size:61 final size:61
Alignment explanation
Indices: 55663--55892 Score: 215
Period size: 61 Copynumber: 3.8 Consensus size: 61
55653 AATTTGGAAA
55663 ATCGCAA--CGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGCGAA-TTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
* * ** * * **
55723 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGCGAATTGGAAAATCGCAACG-AATTTGGAA-AATCGCAACGAC-AACTGTAGACT
* ** * *
55784 ATCGCAACGCGATTTTCAACTATCGCAACGCGAA-ATGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGCGAATTGGAA-AATCGCAA--CGAATTTGGAAAATCGCAACGACAACTGTAGACT
55847 ATCGCAA--CGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAAC
1 ATCGCAACGCGAA-TTGGAAAATCGCAACGAATTTGGAAAATCGCAAC
55893 TAATTTGGAA
Statistics
Matches: 131, Mismatches: 26, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
59 4 0.03
60 21 0.16
61 55 0.42
62 26 0.20
63 23 0.18
64 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (61 bp):
ATCGCAACGCGAATTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
Found at i:55765 original size:41 final size:41
Alignment explanation
Indices: 55720--55998 Score: 331
Period size: 41 Copynumber: 6.9 Consensus size: 41
55710 ACAACTGTAG
55720 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
55761 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* * *
55802 ACTATCGCAACGCGAAATGGAAAATCGCAACGACAACTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG-CGATTTTCA
* * **
55843 GACTATCGCAA--CGAATTTGGAAAATCGCAACG-AATTTGGA
1 -ACTATCGCAACGCGAA-ATGGAAAATCGCAACGCGATTTTCA
* * * * * *
55883 A-AATCGCAA--CTAATTTGGAAAATCGCAACGACAACTGT-A
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA
55922 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
55964 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
55999 ATTTGCGATA
Statistics
Matches: 209, Mismatches: 18, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
38 27 0.13
39 5 0.02
40 9 0.04
41 135 0.65
42 30 0.14
43 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:55769 original size:21 final size:21
Alignment explanation
Indices: 55743--55816 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
55733 GAAATGGAAA
55743 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
55764 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
55784 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
55805 ATCGCAACGCGA
1 ATCGCAACGCGA
55817 AATGGAAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:55929 original size:162 final size:163
Alignment explanation
Indices: 55682--55995 Score: 474
Period size: 162 Copynumber: 1.9 Consensus size: 163
55672 AATTTGGAAA
**
55682 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGAATTTGGAAAATCGCAACGA-AACTGTAGAAAATCGCAAC-CGAAATGGAAAATCG
* * *
55747 CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAA
64 CAACGCAACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAA
55812 CGCGAAATGGAAAATCGCAACGACAACTGTAGACT
129 CGCGAAATGGAAAATCGCAACGACAACTGTAGACT
* * * *
55847 ATCGCAACGAATTTGGAAAATCGCAACG-AA-TTTGGAAAATCGCAA-CTAATTTGGAAAATCGC
1 ATCGCAACGAATTTGGAAAATCGCAACGAAACTGTAGAAAATCGCAACCGAA-ATGGAAAATCGC
55909 AACGACAACTGT-AGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
65 AACG-CAACTGTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
55973 ACGCGAAATGGAAAATCGCAACG
128 ACGCGAAATGGAAAATCGCAACG
55996 CGAATTTGCG
Statistics
Matches: 137, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
160 3 0.02
161 16 0.12
162 88 0.64
163 2 0.01
165 28 0.20
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (163 bp):
ATCGCAACGAATTTGGAAAATCGCAACGAAACTGTAGAAAATCGCAACCGAAATGGAAAATCGCA
ACGCAACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACG
CGAAATGGAAAATCGCAACGACAACTGTAGACT
Found at i:56432 original size:39 final size:39
Alignment explanation
Indices: 56389--56500 Score: 109
Period size: 39 Copynumber: 2.9 Consensus size: 39
56379 ATGAATACTT
*
56389 CACGACTGCATGACGTATTCAGGCCAATGAAGAAGACCC
1 CACGACTGCATGACGTCTTCAGGCCAATGAAGAAGACCC
* * * * * * *
56428 CACGACTGTATGGCATCTTCAGACAAATGGAGAAGACCT
1 CACGACTGCATGACGTCTTCAGGCCAATGAAGAAGACCC
* * **
56467 CAAGAGTGCACAACGTCTTCAGGCCAAT-AAGAAG
1 CACGACTGCATGACGTCTTCAGGCCAATGAAGAAG
56501 TCATAGTTCG
Statistics
Matches: 55, Mismatches: 18, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
38 5 0.09
39 50 0.91
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (39 bp):
CACGACTGCATGACGTCTTCAGGCCAATGAAGAAGACCC
Done.