Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004333.1 Hibiscus syriacus cultivar Beakdansim tig00009500_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: 67946
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5985 original size:19 final size:19
Alignment explanation
Indices: 5932--5999 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
5922 AACCCAACCT
**
5932 GTTGACTTTGACCCGACTC
1 GTTGACTTTGACATGACTC
* * *
5951 ATTAAC-TTGACTTGACTC
1 GTTGACTTTGACATGACTC
*
5969 GTTGACTTTGACATGACTT
1 GTTGACTTTGACATGACTC
5988 GTTGACTTTGAC
1 GTTGACTTTGAC
6000 TAGAGTTGAC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.35
19 26 0.65
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (19 bp):
GTTGACTTTGACATGACTC
Found at i:7365 original size:24 final size:24
Alignment explanation
Indices: 7319--7367 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
7309 CATCCTTGTT
* *
7319 TATAAATGTATTTATGCTATATAG
1 TATAAACGTATTTATGATATATAG
7343 TATAAACGTATTATATGATTATATA
1 TATAAACGTATT-TATGA-TATATA
7368 TTTATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (24 bp):
TATAAACGTATTTATGATATATAG
Found at i:21589 original size:15 final size:16
Alignment explanation
Indices: 21564--21593 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21554 CCTAAGTCGA
21564 AAAAGAAAAAGAAAAC
1 AAAAGAAAAAGAAAAC
21580 AAAA-AAAAAGAAAA
1 AAAAGAAAAAGAAAA
21594 AAGATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAC
Found at i:24253 original size:14 final size:13
Alignment explanation
Indices: 24204--24258 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
24194 TATCTTTATC
* *
24204 AATATTATTATTA
1 AATATTATAACTA
*
24217 AATATTATATCTA
1 AATATTATAACTA
24230 AATATTATAACTA
1 AATATTATAACTA
* *
24243 CAATTTTATAAATA
1 -AATATTATAACTA
24257 AA
1 AA
24259 AATATTAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 24 0.69
14 11 0.31
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATTATAACTA
Found at i:24324 original size:37 final size:38
Alignment explanation
Indices: 24283--24379 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 38
24273 TATATGTTAT
* *
24283 TTAAAATAA-AATTATTATAAATTATATTAATTATTTA
1 TTAAAATAATAATTATTATAAATTAGATTAATTACTTA
* *
24320 TTAAAATAAGAATAATATATTATTAATTAGATTAATTACTTG
1 TTAAAAT---AATAAT-TATTATAAATTAGATTAATTACTTA
24362 TTAAAATAATAA-TATTAT
1 TTAAAATAATAATTATTAT
24380 TAAAATATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
37 13 0.25
39 5 0.10
40 2 0.04
41 3 0.06
42 28 0.55
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (38 bp):
TTAAAATAATAATTATTATAAATTAGATTAATTACTTA
Found at i:24348 original size:42 final size:42
Alignment explanation
Indices: 24295--24426 Score: 135
Period size: 42 Copynumber: 3.2 Consensus size: 42
24285 AAAATAAAAT
24295 TATTATAAATTATATTAATTATTTATTAAAATAAGAATAATA
1 TATTATAAATTATATTAATTATTTATTAAAATAAGAATAATA
* * * * *
24337 TATTATTAATTAGATTAATTACTTGTTAAAATAATAAT-AT-
1 TATTATAAATTATATTAATTATTTATTAAAATAAGAATAATA
* ** * *
24377 TATTA-AAATATTTAAAAATTATAATATTAAAATAAGAATATTA
1 TATTATAAAT-TATATTAATTAT-TTATTAAAATAAGAATAATA
24420 TATTATA
1 TATTATA
24427 TTTTAAATAT
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
39 3 0.04
40 12 0.17
41 15 0.21
42 34 0.49
43 5 0.07
44 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.45
Consensus pattern (42 bp):
TATTATAAATTATATTAATTATTTATTAAAATAAGAATAATA
Found at i:24432 original size:41 final size:42
Alignment explanation
Indices: 24362--24448 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
24352 TAATTACTTG
*
24362 TTAAAATAATAATATTATTAAAATATTTAAAAATT-ATAATA
1 TTAAAATAAGAATATTATTAAAATATTTAAAAATTAATAATA
** *
24403 TTAAAATAAGAATATTA-TATTATATTTTAAATATTCAATAATA
1 TTAAAATAAGAATATTATTAAAATA-TTTAAAAATT-AATAATA
24446 TTA
1 TTA
24449 TTTTTATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 5 0.13
41 25 0.64
43 9 0.23
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (42 bp):
TTAAAATAAGAATATTATTAAAATATTTAAAAATTAATAATA
Found at i:24450 original size:27 final size:27
Alignment explanation
Indices: 24419--24482 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
24409 TAAGAATATT
* *
24419 ATATTATATTT-T-AAA-TATTCAATA
1 ATATTATTTTTATGAAATTATTAAATA
24443 ATATTATTTTTATGAAATTATTAAATA
1 ATATTATTTTTATGAAATTATTAAATA
*
24470 ATATTAATTTTAT
1 ATATTATTTTTAT
24483 TATTAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.29
25 1 0.03
26 3 0.09
27 20 0.59
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
ATATTATTTTTATGAAATTATTAAATA
Found at i:24639 original size:30 final size:28
Alignment explanation
Indices: 24590--24660 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 28
24580 AATATAATTT
**
24590 AATAATTAATATTTTTATTAAAATGTTATTAA
1 AATAA-TAATATTAATATT-AAATG-TA-TAA
24622 AATAAT-ATATTAATATTAAATGTATAA
1 AATAATAATATTAATATTAAATGTATAA
24649 AATAATAATATT
1 AATAATAATATT
24661 TTGAGTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 9 0.25
28 7 0.19
29 5 0.14
30 9 0.25
31 1 0.03
32 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
AATAATAATATTAATATTAAATGTATAA
Found at i:25796 original size:4 final size:4
Alignment explanation
Indices: 25787--25958 Score: 59
Period size: 4 Copynumber: 43.8 Consensus size: 4
25777 TTTTCTACCC
* * * * *
25787 CTCT CTCT CTCT CT-T C-CC CTCT CTCT CCCC CTAT CTCT CTCT C-CC
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* * * * * * *
25832 CATAT ATCT CTCT CTCC CTCC CTCC CTCT CTCT CTCT C-CC CTCT CCCT
1 C-TCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* * * * * * * * * *
25880 CCCT CCCT CCCT CCCT CCCT CCCT CTCT CTCT CCCC CTCT CCCC CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* *
25928 CTC- CATCC CTCT CTC- CATCC CTCT CTCT CTC
1 CTCT C-TCT CTCT CTCT C-TCT CTCT CTCT CTC
25959 AAACACACAC
Statistics
Matches: 129, Mismatches: 30, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
3 9 0.07
4 118 0.91
5 2 0.02
ACGTcount: A:0.03, C:0.61, G:0.00, T:0.35
Consensus pattern (4 bp):
CTCT
Found at i:25810 original size:12 final size:12
Alignment explanation
Indices: 25793--25958 Score: 66
Period size: 12 Copynumber: 13.8 Consensus size: 12
25783 ACCCCTCTCT
*
25793 CTCTCTCTTCCC
1 CTCTCTCTCCCC
25805 CTCTCTCTCCCC
1 CTCTCTCTCCCC
25817 CTATCTCTCTCTCCC
1 C--TCTCTCTC-CCC
*
25832 CATATATCTCTCTCTCC
1 C-----TCTCTCTCCCC
*
25849 CTC-C-CTCCCT
1 CTCTCTCTCCCC
25859 CTCTCTCTCTCCC
1 CTCTCTCTC-CCC
*
25872 CTCTC-C-CTCC
1 CTCTCTCTCCCC
25882 CTC-C-CTCCCTC
1 CTCTCTCTCCC-C
* *
25893 C-CTCCCTCCCT
1 CTCTCTCTCCCC
25904 CTCTCTCTCCCC
1 CTCTCTCTCCCC
*
25916 CTCTC-C-CCCT
1 CTCTCTCTCCCC
*
25926 CTCTC-CATCCCT
1 CTCTCTC-TCCCC
*
25938 CTCTC-CATCCCT
1 CTCTCTC-TCCCC
25950 CTCTCTCTC
1 CTCTCTCTC
25959 AAACACACAC
Statistics
Matches: 126, Mismatches: 11, Indels: 34
0.74 0.06 0.20
Matches are distributed among these distances:
9 2 0.02
10 24 0.19
11 8 0.06
12 59 0.47
13 8 0.06
14 8 0.06
15 4 0.03
17 3 0.02
18 10 0.08
ACGTcount: A:0.04, C:0.61, G:0.00, T:0.35
Consensus pattern (12 bp):
CTCTCTCTCCCC
Found at i:25957 original size:16 final size:16
Alignment explanation
Indices: 25785--25958 Score: 124
Period size: 16 Copynumber: 10.8 Consensus size: 16
25775 GTTTTTCTAC
*
25785 CCCTCTCTCTCTCTCTT
1 CCCTCTCTCTCTC-CCT
25802 CCC-CTCTCTCTCCC-
1 CCCTCTCTCTCTCCCT
*
25816 CCTATCTCTCTCTCCCCAT
1 CC-CTCTCTCTCT-CCC-T
***
25835 ATATCTCTCTCTCCCT
1 CCCTCTCTCTCTCCCT
*
25851 CCCTCCCTCTCTCTCTCT
1 CCCT--CTCTCTCTCCCT
*
25869 CCC-CTCTCCCTCCCT
1 CCCTCTCTCTCTCCCT
* *
25884 CCCTCCCTCCCTCCCT
1 CCCTCTCTCTCTCCCT
25900 CCCTCTCTCTCT-CC-
1 CCCTCTCTCTCTCCCT
* * *
25914 CCCTCTCCCCCTCTCT
1 CCCTCTCTCTCTCCCT
* * *
25930 CCATCCCTCTCTCCAT
1 CCCTCTCTCTCTCCCT
25946 CCCTCTCTCTCTC
1 CCCTCTCTCTCTC
25959 AAACACACAC
Statistics
Matches: 123, Mismatches: 24, Indels: 21
0.73 0.14 0.12
Matches are distributed among these distances:
14 12 0.10
15 17 0.14
16 61 0.50
17 9 0.07
18 24 0.20
ACGTcount: A:0.03, C:0.61, G:0.00, T:0.35
Consensus pattern (16 bp):
CCCTCTCTCTCTCCCT
Found at i:26411 original size:20 final size:22
Alignment explanation
Indices: 26364--26462 Score: 102
Period size: 22 Copynumber: 4.7 Consensus size: 22
26354 AGGGTGTCAA
26364 AGTGCATCCATGCACC-TGCACT
1 AGTGCATCCATGCACCATG-ACT
*
26386 AGTGCATCGATGCACCATG-C-
1 AGTGCATCCATGCACCATGACT
*
26406 AGTGCATCCATGCA-CTTGCACT
1 AGTGCATCCATGCACCATG-ACT
* *
26428 AGTGTATCGATGCACCATG-C-
1 AGTGCATCCATGCACCATGACT
26448 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
26463 TCCATTTCGA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.05
20 26 0.41
21 3 0.05
22 27 0.42
23 5 0.08
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.23
Consensus pattern (22 bp):
AGTGCATCCATGCACCATGACT
Found at i:26426 original size:42 final size:42
Alignment explanation
Indices: 26364--26463 Score: 182
Period size: 42 Copynumber: 2.4 Consensus size: 42
26354 AGGGTGTCAA
*
26364 AGTGCATCCATGCACCTGCACTAGTGCATCGATGCACCATGC
1 AGTGCATCCATGCACTTGCACTAGTGCATCGATGCACCATGC
*
26406 AGTGCATCCATGCACTTGCACTAGTGTATCGATGCACCATGC
1 AGTGCATCCATGCACTTGCACTAGTGCATCGATGCACCATGC
26448 AGTGCATCCATGCACT
1 AGTGCATCCATGCACT
26464 CCATTTCGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (42 bp):
AGTGCATCCATGCACTTGCACTAGTGCATCGATGCACCATGC
Found at i:26507 original size:20 final size:20
Alignment explanation
Indices: 26482--26574 Score: 123
Period size: 20 Copynumber: 4.7 Consensus size: 20
26472 AATGCACTTA
* *
26482 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCATGTT
*
26502 GTGCATCGATGCATCATTTT
1 GTGCATCGATGCATCATGTT
*
26522 GTGCATCGATACATCATGTT
1 GTGCATCGATGCATCATGTT
* *
26542 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCATGTT
*
26562 GTGCATCCATGCA
1 GTGCATCGATGCA
26575 CGAAGGCTGC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCATGTT
Found at i:27458 original size:57 final size:57
Alignment explanation
Indices: 27370--27480 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
27360 TCGTGAGACA
* *
27370 ACAATCTCTGAACGCAAACTACATATCTATCAAAGATAAAGATTAAATTAGATTGGC
1 ACAATCTCTGAACGCAAACCACATATCTATCAAAGATAAAGACTAAATTAGATTGGC
* * * *
27427 ACAATCTTTGAACGCAAACCACATATCTATCAAAGGTATAGACTATATTAGATT
1 ACAATCTCTGAACGCAAACCACATATCTATCAAAGATAAAGACTAAATTAGATT
27481 ATCCAATCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (57 bp):
ACAATCTCTGAACGCAAACCACATATCTATCAAAGATAAAGACTAAATTAGATTGGC
Found at i:30561 original size:36 final size:36
Alignment explanation
Indices: 30513--30584 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
30503 GCTTTTAAAG
30513 AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
1 AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
*
30549 AAAGGGTTTCTTTCGTAAGGATAAGAGAAGGTTGTT
1 AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
30585 TTTTATTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.32
Consensus pattern (36 bp):
AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
Found at i:31175 original size:20 final size:20
Alignment explanation
Indices: 31150--31199 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
31140 ATAAATAAAA
*
31150 TATTTTATTGAAGAAGATAT
1 TATTTTATTGAAAAAGATAT
31170 TATTTTATTGAAAAAGATAT
1 TATTTTATTGAAAAAGATAT
31190 TATTTATATT
1 TATTT-TATT
31200 TTTTAACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
TATTTTATTGAAAAAGATAT
Found at i:31874 original size:21 final size:21
Alignment explanation
Indices: 31850--31920 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
31840 TACCCTTAAC
* * *
31850 TTTAATCCTTAAATTATAAAT
1 TTTAAACCCTAAACTATAAAT
31871 TTTAAACCCTAAACTAT-AAT
1 TTTAAACCCTAAACTATAAAT
* *
31891 TTCTAAACCCTAAACCATAATT
1 TT-TAAACCCTAAACTATAAAT
31913 TTTAAACC
1 TTTAAACC
31921 ATGAACTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
20 5 0.12
21 34 0.79
22 4 0.09
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAACCCTAAACTATAAAT
Found at i:32615 original size:64 final size:63
Alignment explanation
Indices: 32527--32649 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 63
32517 GGTATTTATC
* * *
32527 ATCTATTTAACTTTGAATATTAAAATATAA-TTATATACTTTTGAATATTTCAAATTAAAATAAT
1 ATCTATTTAACTTTAAATAGTAAAAGA-AATTTATAT-CTTTTGAATATTTCAAATTAAAATAAT
* * *
32591 ATCTATTTAAGTTTAAATAGTAAAAGAAGTTTATATCTTTTGAATATTTTAAATTAAAA
1 ATCTATTTAACTTTAAATAGTAAAAGAAATTTATATCTTTTGAATATTTCAAATTAAAA
32650 GATATTTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 23 0.44
64 29 0.56
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (63 bp):
ATCTATTTAACTTTAAATAGTAAAAGAAATTTATATCTTTTGAATATTTCAAATTAAAATAAT
Found at i:32658 original size:34 final size:34
Alignment explanation
Indices: 32545--32723 Score: 101
Period size: 34 Copynumber: 5.4 Consensus size: 34
32535 AACTTTGAAT
* * *
32545 ATTAAAATATAATTATATACTTTTGAATATTTCAA
1 ATTAAAAGATATTTATAT-CTTTTGAATATTTTAA
*
32580 ATT-AAA-ATA---ATATCTATTT--A-AGTTTAA
1 ATTAAAAGATATTTATATCT-TTTGAATATTTTAA
32607 ATAGTAAAAGA-AGTTTATATCTTTTGAATATTTTAA
1 AT--TAAAAGATA-TTTATATCTTTTGAATATTTTAA
* *
32643 ATTAAAAGATATTTATTGTCTTTTTAA-A-TTTAA
1 ATTAAAAGATATTTA-TATCTTTTGAATATTTTAA
* ** * * **
32676 ATATTAAAGATATCAATATCTTTTAAATATATCGA
1 AT-TAAAAGATATTTATATCTTTTGAATATTTTAA
32711 ATTAAAAGATATT
1 ATTAAAAGATATT
32724 GTCTTTAGAG
Statistics
Matches: 112, Mismatches: 15, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
27 7 0.06
28 1 0.01
29 3 0.03
30 11 0.10
31 1 0.01
33 22 0.20
34 41 0.37
35 18 0.16
36 8 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (34 bp):
ATTAAAAGATATTTATATCTTTTGAATATTTTAA
Found at i:32682 original size:35 final size:34
Alignment explanation
Indices: 32509--32703 Score: 113
Period size: 34 Copynumber: 5.8 Consensus size: 34
32499 AATATACCAA
* * * *
32509 ATTAAATAGGTATTTATCATCTATTTAACTTTGAAT
1 ATTAAA-AGATATTTAT-ATCTTTTTAAATTTAAAT
* * * *
32545 ATTAAAATATAATTATATACTTTTGAATATTTCAA-
1 ATTAAAAGATATTTATAT-CTTTTTAA-ATTTAAAT
* *
32580 ATT-AAA-ATA---ATATCTATTTAAGTTTAAAT
1 ATTAAAAGATATTTATATCTTTTTAAATTTAAAT
* * *
32609 AGTAAAAGA-AGTTTATATCTTTTGAATATTTTAA-
1 ATTAAAAGATA-TTTATATCTTTTTAA-ATTTAAAT
*
32643 ATTAAAAGATATTTATTGTCTTTTTAAATTTAAAT
1 ATTAAAAGATATTTA-TATCTTTTTAAATTTAAAT
**
32678 ATT-AAAGATATCAATATC-TTTTAAAT
1 ATTAAAAGATATTTATATCTTTTTAAAT
32704 ATATCGAATT
Statistics
Matches: 123, Mismatches: 23, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
28 5 0.04
29 8 0.07
30 8 0.07
31 1 0.01
32 8 0.07
33 6 0.05
34 42 0.34
35 34 0.28
36 11 0.09
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (34 bp):
ATTAAAAGATATTTATATCTTTTTAAATTTAAAT
Found at i:34648 original size:57 final size:56
Alignment explanation
Indices: 34502--34652 Score: 187
Period size: 56 Copynumber: 2.7 Consensus size: 56
34492 GAACAATTTC
* * ** **
34502 ATTTTGTAGAAGAAATAAATTGTTAAATTTATTT-TCACAGAATCTTGTATGATTCT
1 ATTTTGTAAAAGAAATAAATCGTTAAATTTATTTCT-TGAGAATCAAGTATGATTCT
* * * *
34558 ATTTTGCAAAAGAATTAAATCATTGAATTTATTTCTTGAGAATCAAGTATGATTCT
1 ATTTTGTAAAAGAAATAAATCGTTAAATTTATTTCTTGAGAATCAAGTATGATTCT
34614 ATTTTGTAAAAAGAAATAAATCGTTAAATTTATTTCTTG
1 ATTTTGT-AAAAGAAATAAATCGTTAAATTTATTTCTTG
34653 GAAGTATCGA
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
56 50 0.63
57 29 0.37
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (56 bp):
ATTTTGTAAAAGAAATAAATCGTTAAATTTATTTCTTGAGAATCAAGTATGATTCT
Found at i:36390 original size:130 final size:130
Alignment explanation
Indices: 36220--36456 Score: 350
Period size: 130 Copynumber: 1.8 Consensus size: 130
36210 ATTTAAGAGA
* * * *
36220 TAATTATTTTCAATCGAGAATAAACAACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATC
1 TAATTATTTCCAATCGAGAATAAACAACCTCTCATGCCTTAAAGCAATCATTTATCACTCCAACC
* *
36285 GAAAT-AAAGAGATATAACTATTTCATCTTAAAATTCAATATTGATTTAGAGAAAATGATAATAT
66 AAAATGAAA-AGATATAACTATTTCATCCTAAAATTCAATATTGATTTAGAGAAAATGATAATAT
36349 C
130 C
* *
36350 TAATTATTTCCAATCGAGAATAAATAACCTCTCATTCCTTAAAGCAATCATTTATCACTCCAACC
1 TAATTATTTCCAATCGAGAATAAACAACCTCTCATGCCTTAAAGCAATCATTTATCACTCCAACC
* * * *
36415 AAAATGAAAATATATTATTATTTCGTCCTAAAATTCAATATT
66 AAAATGAAAAGATATAACTATTTCATCCTAAAATTCAATATT
36457 AATTCGAGTG
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
130 91 0.97
131 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (130 bp):
TAATTATTTCCAATCGAGAATAAACAACCTCTCATGCCTTAAAGCAATCATTTATCACTCCAACC
AAAATGAAAAGATATAACTATTTCATCCTAAAATTCAATATTGATTTAGAGAAAATGATAATATC
Found at i:39462 original size:13 final size:13
Alignment explanation
Indices: 39444--39475 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
39434 AACTTTGGAA
39444 ATCGAAAGTCTTT
1 ATCGAAAGTCTTT
39457 ATCGAAAGTCTTT
1 ATCGAAAGTCTTT
39470 AT-GAAA
1 ATCGAAA
39476 ACATATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (13 bp):
ATCGAAAGTCTTT
Found at i:39624 original size:205 final size:206
Alignment explanation
Indices: 39267--39650 Score: 599
Period size: 205 Copynumber: 1.9 Consensus size: 206
39257 CATTTTTCGA
* * * * *
39267 AAAACATATGAAAACACCCTGCTCGAAGGTCTTATGTATGGCCCGAAGGACTTATCCTCTTGCTC
1 AAAACATATGAAAACACCCTGCCCGAAGGTCTTATGTATGCCCCAAAGGACTTATCATCTTGATC
* * *
39332 GAAAGACTCATAGATGACCTGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAA
66 GAAAGACTCATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAA
* *
39397 GGACTTACCAATTTTAGAAATAGTTTACTAGGTAATAAACTTTGGAAATCGAAAGTCTTTATCGA
131 GGACTTACCAATTTGAGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGAAAGTCTTTATCGA
39462 AAGTCTTTATG
196 AAGTCTTTATG
* * *
39473 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATG-GTGCCCCAAAGGACTTATCATCTTTATC
1 AAAACATATGAAAACACCCTGCCCGAAGGTCTTATGTATGCCCCAAAGGACTTATCATCTTGATC
* * *
39537 GAAAGGCTTATAGATGACCCGAAAGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAA
66 GAAAGACTCATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAA
* *
39602 GGACTTATCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAAT
131 GGACTTACCAATTTGAGAAATAGTTTACTAGGTAAGAAACTTTGGAAAT
39651 TGTTTTCTTA
Statistics
Matches: 160, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
205 126 0.79
206 34 0.21
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (206 bp):
AAAACATATGAAAACACCCTGCCCGAAGGTCTTATGTATGCCCCAAAGGACTTATCATCTTGATC
GAAAGACTCATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAA
GGACTTACCAATTTGAGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGAAAGTCTTTATCGA
AAGTCTTTATG
Found at i:40258 original size:177 final size:176
Alignment explanation
Indices: 39984--40338 Score: 498
Period size: 177 Copynumber: 2.0 Consensus size: 176
39974 TCTCATTTTT
* * * * * *
39984 TTTTCAAAAAACATGTGAAAACATCATACTCGAAGGTCTTATGAATGGCCCGAATGACTATTATC
1 TTTTCAAAAAACATATAAAAACATCATACCCGAAGGCCTTATGAATGGCCCAAAGGACTATTATC
*
40049 CTCCTCGAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTC-AAAAGACTTACTGATG
66 CTCCTCAAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCGAAAA-ACTTACTGATG
* *
40113 TCTCGAAGGACTTACTAAGTAAGAAACTTTGGAAAACATCTTCTTAC
130 GCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAAACATCTTCTTAC
* * * * *
40160 TTTTCGAAAAACATATAAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCAAAGGACTTTTCAT
1 TTTTCAAAAAACATATAAAAACATCATACCCGAAGGCCTTATGAATGGCCCAAAGGACTATT-AT
* * *
40225 CTTGCTCAAAAGGCTTATAGATGA-CTCGAAGGATTTAATCATCATGCTCGAATAACTTACTGAT
65 CCTCCTCAAAAGGCTTATAGATGACCT-GAAGGATTTAATCATCATGCTCGAAAAACTTACTGAT
* *
40289 GGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTAC
129 GGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAAACATCTTCTTAC
40337 TT
1 TT
40339 CTTAACTTAT
Statistics
Matches: 157, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
176 53 0.34
177 101 0.64
178 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (176 bp):
TTTTCAAAAAACATATAAAAACATCATACCCGAAGGCCTTATGAATGGCCCAAAGGACTATTATC
CTCCTCAAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCGAAAAACTTACTGATGG
CCCGAAGGACTTACTAAGTAAGAAACTTTGGAAAACATCTTCTTAC
Found at i:41930 original size:2 final size:2
Alignment explanation
Indices: 41923--41983 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
41913 AACTTTATTG
41923 TA TA TA 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
41965 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
41984 CACCTTTATC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48244 original size:130 final size:130
Alignment explanation
Indices: 48000--48258 Score: 344
Period size: 130 Copynumber: 2.0 Consensus size: 130
47990 GGATTTTAAG
* *
48000 AGAGAAAATGATAATATATAATTATTTCCAATGAGAATAAACAACCTCATATGTCTTAAAGCAGT
1 AGAGAAAATGATAATATATAATTATTTCCAATGAGAATAAACAACCTCATATGACCTAAAGCAGT
* * * * *
48065 CATTTATTACTCCAATCGAAATGAAGAGATATCACTATGTCGTCTTAAAATTCAATATTGATTCA
66 CATTTATTACTCCAATCGAAATGAAAAGAAATCACTATGTCATCCTAAAATTCAATATTAATTCA
**
48130 AGAGAAAATGATAATA-ACTAATTATTTCCAATCGAGAATAAATGACCTC-TCAT-ACCTAAAGC
1 AGAGAAAATGATAATATA-TAATTATTTCCAAT-GAGAATAAACAACCTCAT-ATGACCTAAAGC
* * * * *
48192 AGTCATTTATTACTCCAATTGAAATGAAAATAAATTACTTTTTCATCCTAAAATTCAATATTAAT
63 AGTCATTTATTACTCCAATCGAAATGAAAAGAAATCACTATGTCATCCTAAAATTCAATATTAAT
48257 TC
128 TC
48259 GAGTGTTGCT
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
129 1 0.01
130 95 0.85
131 16 0.14
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (130 bp):
AGAGAAAATGATAATATATAATTATTTCCAATGAGAATAAACAACCTCATATGACCTAAAGCAGT
CATTTATTACTCCAATCGAAATGAAAAGAAATCACTATGTCATCCTAAAATTCAATATTAATTCA
Found at i:50099 original size:15 final size:16
Alignment explanation
Indices: 50079--50108 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50069 TGACGGCTGG
50079 AAACCCTAGG-GTTTT
1 AAACCCTAGGTGTTTT
50094 AAACCCTAGGTGTTT
1 AAACCCTAGGTGTTT
50109 AGTTTAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (16 bp):
AAACCCTAGGTGTTTT
Found at i:50243 original size:6 final size:6
Alignment explanation
Indices: 50232--50281 Score: 66
Period size: 6 Copynumber: 8.3 Consensus size: 6
50222 AAGGCTTGTA
* *
50232 AAAAAT AAAAAT AAAAAT AAAAAT AAAACA- AAAAAT AATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT
50280 AA
1 AA
50282 TTAATAATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
5 1 0.02
6 39 0.95
7 1 0.02
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:50273 original size:3 final size:3
Alignment explanation
Indices: 50235--50292 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
50225 GCTTGTAAAA
* * * *
50235 AAT AAA AAT AAA AAT AAA AAT AA- AAC AA- AA- AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
50280 AATT AAT AAT AAT
1 AA-T AAT AAT AAT
50293 GTTAATGGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 6 0.13
3 37 0.80
4 3 0.07
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:50282 original size:12 final size:12
Alignment explanation
Indices: 50235--50288 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
50225 GCTTGTAAAA
*
50235 AATAAAAATAAA
1 AATAAAAATAAT
50247 AATAAAAATAA-
1 AATAAAAATAAT
*
50258 AACAAAAAATAAT
1 AA-TAAAAATAAT
*
50271 AATAATAATAATT
1 AATAAAAATAA-T
50284 AATAA
1 AATAA
50289 TAATGTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 2 0.06
12 26 0.72
13 8 0.22
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:51091 original size:36 final size:36
Alignment explanation
Indices: 51051--51121 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
51041 CATGATATGA
*
51051 GATTAG-TCGATACAATTTTGGACATCCAAATTAAAC
1 GATTAGCT-GATACAATTCTGGACATCCAAATTAAAC
* *
51087 GATTAGCTTATACAATTCTGGGCATCCAAATTAAA
1 GATTAGCTGATACAATTCTGGACATCCAAATTAAA
51122 AGGTCATCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (36 bp):
GATTAGCTGATACAATTCTGGACATCCAAATTAAAC
Found at i:53010 original size:2 final size:2
Alignment explanation
Indices: 53003--53067 Score: 50
Period size: 2 Copynumber: 34.5 Consensus size: 2
52993 ATGATACATG
* * *
53003 TA TA TA TA -A TG TA TA T- TA CA -A TA TA T- TA TA TA CA -A GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
53041 TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
53068 TGTAATTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
1 5 0.10
2 45 0.88
3 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:53184 original size:99 final size:101
Alignment explanation
Indices: 53070--53267 Score: 292
Period size: 101 Copynumber: 2.0 Consensus size: 101
53060 ATATATATTG
* * * * *
53070 TAATTATGTATGATCAATAATGTATGTTTTATA-G-GTGTATATAAGCCTATTTATGCATGTATG
1 TAATTATGTATGATCAATAATATATGTTTTATATGTATATATATAAGCATATATATGCATGTATG
53133 TACATATGTATGATGTATGCATGATGCATGTATATA
66 TACATATGTATGATGTATGCATGATGCATGTATATA
* * *
53169 TAATTATGTATGATCAATGATATATGTTTTATATGTATATATATAAGTATATATATGCATTTATG
1 TAATTATGTATGATCAATAATATATGTTTTATATGTATATATATAAGCATATATATGCATGTATG
* *
53234 TACATATGTATTATGTATGTATGATGCATGTATA
66 TACATATGTATGATGTATGCATGATGCATGTATA
53268 CACATATATT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 31 0.36
100 1 0.01
101 55 0.63
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (101 bp):
TAATTATGTATGATCAATAATATATGTTTTATATGTATATATATAAGCATATATATGCATGTATG
TACATATGTATGATGTATGCATGATGCATGTATATA
Found at i:53343 original size:2 final size:2
Alignment explanation
Indices: 53336--53438 Score: 63
Period size: 2 Copynumber: 52.0 Consensus size: 2
53326 AAATTAATGT
* *
53336 TA TA TA TA TA TA TA TA TA -A GT- TA TA CA CA TA TA TA -A GTA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
53377 TA TG TA TGA TG TA TGA TG TA TG TA CA TA AA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53421 TA TA TA TA T- TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA
53439 CATTATACGC
Statistics
Matches: 78, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
1 5 0.06
2 68 0.87
3 5 0.06
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (2 bp):
TA
Found at i:53360 original size:17 final size:16
Alignment explanation
Indices: 53340--53438 Score: 57
Period size: 17 Copynumber: 6.2 Consensus size: 16
53330 TAATGTTATA
53340 TATATATATATATAAG
1 TATATATATATATAAG
* *
53356 TTATACACATATATAAG
1 -TATATATATATATAAG
*
53373 TATATATGTATGAT--G
1 TATATATATAT-ATAAG
* * *
53388 TATGATGTATGTACATAAA
1 TAT-A--TATATATATAAG
53407 TATATATATATAT-A-
1 TATATATATATATAAG
53421 TATATATAT-TATAA-
1 TATATATATATATAAG
53435 TATA
1 TATA
53439 CATTATACGC
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
13 3 0.05
14 14 0.21
15 5 0.08
16 16 0.24
17 18 0.27
18 7 0.11
19 3 0.05
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (16 bp):
TATATATATATATAAG
Found at i:53367 original size:21 final size:21
Alignment explanation
Indices: 53321--53370 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
53311 ATGATATATG
* *
53321 CATATAAATTAATGTTATATA
1 CATATATATTAATGTTATACA
*
53342 TATATATATATAA-GTTATACA
1 CATATATAT-TAATGTTATACA
53363 CATATATA
1 CATATATA
53371 AGTATATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (21 bp):
CATATATATTAATGTTATACA
Found at i:56469 original size:20 final size:21
Alignment explanation
Indices: 56424--56473 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
56414 AGTCCAATCG
56424 TTTGTAACTCATGCAATTACC
1 TTTGTAACTCATGCAATTACC
* *
56445 TTTGTAACTCTTGCATTTA-C
1 TTTGTAACTCATGCAATTACC
56465 TTTGTAACT
1 TTTGTAACT
56474 GGCAGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTGTAACTCATGCAATTACC
Found at i:62306 original size:18 final size:18
Alignment explanation
Indices: 62269--62306 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
62259 TTTTAAGATT
*
62269 TTATATTCGATTTAAATA
1 TTATATTCGATTCAAATA
*
62287 TTATATTCGATTCAATTA
1 TTATATTCGATTCAAATA
62305 TT
1 TT
62307 CGAATATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATATTCGATTCAAATA
Done.