Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008876.1 Corchorus capsularis cultivar CVL-1 contig08897, 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: 39002
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:2970 original size:7 final size:7
Alignment explanation
Indices: 2958--2987 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2948 TAATTTACTT
2958 TTGATTA
1 TTGATTA
2965 TTGATTA
1 TTGATTA
2972 TTGATTA
1 TTGATTA
2979 TTGATTA
1 TTGATTA
2986 TT
1 TT
2988 ATGGTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (7 bp):
TTGATTA
Found at i:10373 original size:149 final size:150
Alignment explanation
Indices: 10177--10597 Score: 486
Period size: 149 Copynumber: 2.8 Consensus size: 150
10167 CGCACTGTTC
*
10177 TGGTTTCCCTCTCTTTTTTTTC-GCCAAAAATTGGAAAATTAGCTGAAAATTAACTATAATGGCG
1 TGGTTTCCCTCTCTTTTTTTTCTGCGAAAAATTGGAAAATTAGCTGAAAATTAACTATAATGGCG
* ** * * *
10241 TTTGTTATCGAAAACTTCGTAATAGGGTGAGGGTGGCGGCATTTGTATATAAAAACGCCACCATC
66 TTTGTTATTGAAAACACCGTAATAGGGTGAGGGTGACGGCGTTTGTACATAAAAACGCCACCATC
10306 CTTAAGGCAAAACTTA-TAT
131 CTTAAGGCAAAACTTAGTAT
* * * * *
10325 TGGTTTCCCTCTCTTTTTTTTCTGCGAAAAAATGGAAAATTAGTTGAAAATTAACTATAACGACA
1 TGGTTTCCCTCTCTTTTTTTTCTGCGAAAAATTGGAAAATTAGCTGAAAATTAACTATAATGGCG
* * * * **
10390 TTTGGTATTGAAAACACCATAATAGGGTGAGGGTGACCGCGTTTGTACATAAAAACGTCGTCATC
66 TTTGTTATTGAAAACACCGTAATAGGGTGAGGGTGACGGCGTTTGTACATAAAAACGCCACCATC
*
10455 CTTAAGGCAAAACTTATGGTTT
131 CTTAAGGCAAAACTTA--GTAT
** *** * * * * *
10477 TTCTTTTATTATTTATTTTTTTTTGTGTAAAATTGGAAAATTAGCTGAAAATTAACTATAATGGC
1 TGGTTTCCCTCTCT-TTTTTTTCTGCGAAAAATTGGAAAATTAGCTGAAAATTAACTATAATGGC
* * * * * *
10542 GTGTATTATTTAAAACGCCGTAATAGGGCGAGGGTCACGGCGTTTGTACATAAAAA
65 GTTTGTTATTGAAAACACCGTAATAGGGTGAGGGTGACGGCGTTTGTACATAAAAA
10598 TTATGCCTTA
Statistics
Matches: 225, Mismatches: 43, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
148 22 0.10
149 105 0.47
152 9 0.04
153 89 0.40
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (150 bp):
TGGTTTCCCTCTCTTTTTTTTCTGCGAAAAATTGGAAAATTAGCTGAAAATTAACTATAATGGCG
TTTGTTATTGAAAACACCGTAATAGGGTGAGGGTGACGGCGTTTGTACATAAAAACGCCACCATC
CTTAAGGCAAAACTTAGTAT
Found at i:13871 original size:33 final size:32
Alignment explanation
Indices: 13834--13906 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 32
13824 ACTATGTTAT
*
13834 GGCGTTTGAGAAGGACAAACGCCCCTAAATTGG
1 GGCGTTTCAGAAGGACAAA-GCCCCTAAATTGG
* *
13867 GGCGTTTCTGACGGACAAAGCCCCTAAATTGG
1 GGCGTTTCAGAAGGACAAAGCCCCTAAATTGG
13899 GGCGTTTC
1 GGCGTTTC
13907 CTTTTACAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 21 0.57
33 16 0.43
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (32 bp):
GGCGTTTCAGAAGGACAAAGCCCCTAAATTGG
Found at i:23252 original size:21 final size:21
Alignment explanation
Indices: 23193--23252 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
23183 TTTTACTGAA
* *
23193 TTACTGATTACCATTACTATT
1 TTACTGATTACTATTACTACT
23214 TTACTGATTATTCT-TTACT-CT
1 TTACTGATTA--CTATTACTACT
23235 TTACTGATTACTAGTTAC
1 TTACTGATTACTA-TTAC
23253 CATTTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
21 25 0.76
22 5 0.15
23 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (21 bp):
TTACTGATTACTATTACTACT
Found at i:23259 original size:29 final size:29
Alignment explanation
Indices: 23227--23359 Score: 98
Period size: 29 Copynumber: 4.7 Consensus size: 29
23217 CTGATTATTC
* *
23227 TTTACTCTTTACTGATTACTAGTTACCAT
1 TTTACTCTTTACTAATTACTATTTACCAT
* *
23256 TTTATTCTTTACTAATTGAC-A-TTA-CTT
1 TTTACTCTTTACTAATT-ACTATTTACCAT
* * * *
23283 TTTACTCATTAATATTTCACTCTTTACCAT
1 TTTACTCTTTACTAATT-ACTATTTACCAT
* *
23313 TTT-TTCCTTTACTAATTACTCTTTACCAT
1 TTTACT-CTTTACTAATTACTATTTACCAT
*
23342 TTT--TCTTTACTGATTACT
1 TTTACTCTTTACTAATTACT
23360 CTTCTCTTTA
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
27 30 0.36
28 4 0.05
29 35 0.42
30 15 0.18
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.53
Consensus pattern (29 bp):
TTTACTCTTTACTAATTACTATTTACCAT
Found at i:23338 original size:7 final size:7
Alignment explanation
Indices: 23328--23437 Score: 51
Period size: 7 Copynumber: 16.6 Consensus size: 7
23318 CCTTTACTAA
23328 TTACTCT
1 TTACTCT
23335 TTAC-CAT
1 TTACTC-T
*
23342 TT-TTCT
1 TTACTCT
**
23348 TTACTGA
1 TTACTCT
23355 TTACTC-
1 TTACTCT
23361 TT-CTCT
1 TTACTCT
23367 TTAC-CAT
1 TTACTC-T
23374 TT--TCT
1 TTACTCT
**
23379 TTACTGA
1 TTACTCT
23386 TTACTCT
1 TTACTCT
23393 TTACTCT
1 TTACTCT
23400 TTAC-CAT
1 TTACTC-T
*
23407 TT-TTCT
1 TTACTCT
*
23413 TTACTGAT
1 TTACT-CT
23421 TT-CTCT
1 TTACTCT
23427 TTACTCT
1 TTACTCT
23434 TTAC
1 TTAC
23438 CATTTTTCTT
Statistics
Matches: 76, Mismatches: 13, Indels: 28
0.65 0.11 0.24
Matches are distributed among these distances:
5 6 0.08
6 17 0.22
7 50 0.66
8 3 0.04
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:23415 original size:20 final size:20
Alignment explanation
Indices: 23390--23451 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
23380 TACTGATTAC
23390 TCTTTACTCTTTACCATTTT
1 TCTTTACTCTTTACCATTTT
* *
23410 TCTTTA--C--T--GATTTC
1 TCTTTACTCTTTACCATTTT
23424 TCTTTACTCTTTACCATTTT
1 TCTTTACTCTTTACCATTTT
23444 TCTTTACT
1 TCTTTACT
23452 GATTACTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
14 10 0.31
16 2 0.06
18 2 0.06
20 18 0.56
ACGTcount: A:0.15, C:0.24, G:0.02, T:0.60
Consensus pattern (20 bp):
TCTTTACTCTTTACCATTTT
Found at i:23416 original size:34 final size:34
Alignment explanation
Indices: 23328--23462 Score: 240
Period size: 34 Copynumber: 4.1 Consensus size: 34
23318 CCTTTACTAA
23328 TTACTCTTTACCATTTTTCTTTACTGATTACTC-
1 TTACTCTTTACCATTTTTCTTTACTGATTACTCT
23361 TT-CTCTTTACCA-TTTTCTTTACTGATTACTCT
1 TTACTCTTTACCATTTTTCTTTACTGATTACTCT
*
23393 TTACTCTTTACCATTTTTCTTTACTGATTTCTCT
1 TTACTCTTTACCATTTTTCTTTACTGATTACTCT
23427 TTACTCTTTACCATTTTTCTTTACTGATTACTCT
1 TTACTCTTTACCATTTTTCTTTACTGATTACTCT
23461 TT
1 TT
23463 TATTTTTTAC
Statistics
Matches: 97, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
31 19 0.20
32 12 0.12
33 12 0.12
34 54 0.56
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (34 bp):
TTACTCTTTACCATTTTTCTTTACTGATTACTCT
Found at i:23474 original size:22 final size:22
Alignment explanation
Indices: 23446--23742 Score: 202
Period size: 22 Copynumber: 13.5 Consensus size: 22
23436 ACCATTTTTC
*
23446 TTTACTGATTACTCTTTTATTT
1 TTTACTGATTACTCTTTTACTT
* *
23468 TTTACTGATTGC-CTTTTTGCTT
1 TTTACTGATTACTC-TTTTACTT
23490 TTTACTGATTAC-CTTTTTACTT
1 TTTACTGATTACTC-TTTTACTT
** * *
23512 CCTACTGATTACTATTTTACCT
1 TTTACTGATTACTCTTTTACTT
* * *
23534 TTTATTGGTTAC-CTTTTGC-T
1 TTTACTGATTACTCTTTTACTT
* *
23554 CTTACTGATTACTATTTTAC-T
1 TTTACTGATTACTCTTTTACTT
* *
23575 CTTACAGATTA-TCTTTTTACCTTT
1 TTTACTGATTACTC-TTTTA-C-TT
* *
23599 TTTACTAATTACT-ATTTAC-T
1 TTTACTGATTACTCTTTTACTT
* *
23619 CTTGCTGATTAC-CTTCTTACTT
1 TTTACTGATTACTCTT-TTACTT
* *
23641 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTCTTTTACTT
* *
23663 TTTACTGATTACTATTTTACAT
1 TTTACTGATTACTCTTTTACTT
*
23685 TTTACTGATTA-TC-ATTACTTT
1 TTTACTGATTACTCTTTTAC-TT
* *
23706 TTTACTGATTACTATTTTTTCCTTT
1 TTTACTGATTAC--TCTTTTAC-TT
23731 TTTACTGATTAC
1 TTTACTGATTAC
23743 CATTGTACTC
Statistics
Matches: 216, Mismatches: 42, Indels: 31
0.75 0.15 0.11
Matches are distributed among these distances:
20 26 0.12
21 44 0.20
22 111 0.51
23 6 0.03
24 10 0.05
25 19 0.09
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTACTGATTACTCTTTTACTT
Found at i:23537 original size:44 final size:43
Alignment explanation
Indices: 23446--23751 Score: 234
Period size: 44 Copynumber: 7.0 Consensus size: 43
23436 ACCATTTTTC
* * *
23446 TTTACTGATTA-CTCTTTTATTTTTTACTGATTGCCT-TTTTGCTT
1 TTTACTGATTACCT-TTTTACTTTTTACTGATT-ACTATTTTAC-T
**
23490 TTTACTGATTACCTTTTTACTTCCTACTGATTACTATTTTACCT
1 TTTACTGATTACCTTTTTACTTTTTACTGATTACTATTTTA-CT
* * * *
23534 TTTATTGGTTACC-TTTTGC-TCTTACTGATTACTATTTTACT
1 TTTACTGATTACCTTTTTACTTTTTACTGATTACTATTTTACT
* * * *
23575 CTTACAGATTATCTTTTTACCTTTTTTACTAATTACTA-TTTACT
1 TTTACTGATTACCTTTTTA-C-TTTTTACTGATTACTATTTTACT
* * *
23619 CTTGCTGATTACCTTCTTACTTTTTACTGATTACTATTTTACT
1 TTTACTGATTACCTTTTTACTTTTTACTGATTACTATTTTACT
*
23662 CTTTACTGATTA-CTATTTTACATTTTACTGATTA-TCA--TTACTTT
1 -TTTACTGATTACCT-TTTTACTTTTTACTGATTACT-ATTTTAC--T
* * * *
23706 TTTACTGATTACTATTTTTTCCTTTTTTACTGATTACCATTGTACT
1 TTTACTGATTAC--CTTTTTAC-TTTTTACTGATTACTATTTTACT
23752 CCTTGGATTG
Statistics
Matches: 211, Mismatches: 31, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
41 10 0.05
42 42 0.20
43 29 0.14
44 91 0.43
45 21 0.10
46 15 0.07
48 3 0.01
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.56
Consensus pattern (43 bp):
TTTACTGATTACCTTTTTACTTTTTACTGATTACTATTTTACT
Found at i:27940 original size:27 final size:25
Alignment explanation
Indices: 27910--27983 Score: 103
Period size: 27 Copynumber: 2.8 Consensus size: 25
27900 AAGTGAACTT
*
27910 AAAATGACCAAAATACCCCTAAATGCA
1 AAAATGACCAAAATGCCCCTAAA--CA
*
27937 AAAATGACCAAAATGCCCCTGAACA
1 AAAATGACCAAAATGCCCCTAAACA
27962 ACAAATGACCAAAATGCCCCTA
1 A-AAATGACCAAAATGCCCCTA
27984 TGTGACCCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.07
26 19 0.44
27 21 0.49
ACGTcount: A:0.49, C:0.28, G:0.09, T:0.14
Consensus pattern (25 bp):
AAAATGACCAAAATGCCCCTAAACA
Found at i:31089 original size:21 final size:21
Alignment explanation
Indices: 31050--31089 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31040 CCATTACTAT
* *
31050 TTTACTGATTATTCTTTACTC
1 TTTACTGATTACTCGTTACTC
*
31071 TTTACTGATTACTGGTTAC
1 TTTACTGATTACTCGTTAC
31090 CATTTTATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTACTGATTACTCGTTACTC
Found at i:31150 original size:35 final size:35
Alignment explanation
Indices: 31037--31150 Score: 99
Period size: 35 Copynumber: 3.2 Consensus size: 35
31027 TAATTACTTA
*
31037 TTACCATTACTATTTTACTGATTAT-TCTTTACTCT
1 TTACCATTACT-TTTTACTCATTATATCTTTACTCT
* ** * **
31072 TTACTGATTACTGGTTAC-CATTTTATTCTTTACTAA
1 TTAC-CATTACTTTTTACTCATTATA-TCTTTACTCT
*
31108 TTGCCATTACTTTTTACTCATTAATAT-TTTACTCT
1 TTACCATTACTTTTTACTCATT-ATATCTTTACTCT
31143 TTACCATT
1 TTACCATT
31151 TTTTCCTTTA
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
34 4 0.07
35 31 0.53
36 22 0.37
37 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.53
Consensus pattern (35 bp):
TTACCATTACTTTTTACTCATTATATCTTTACTCT
Found at i:31175 original size:14 final size:14
Alignment explanation
Indices: 31152--31203 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
31142 TTTACCATTT
31152 TTTC-CTTTACTGA
1 TTTCTCTTTACTGA
* *
31165 TTACTCTTTAC-CA
1 TTTCTCTTTACTGA
*
31178 TTTTTCTTTACTGA
1 TTTCTCTTTACTGA
31192 TTTCTCTTTACT
1 TTTCTCTTTACT
31204 CTCTACCATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 13 0.42
14 18 0.58
ACGTcount: A:0.15, C:0.23, G:0.04, T:0.58
Consensus pattern (14 bp):
TTTCTCTTTACTGA
Found at i:31189 original size:27 final size:27
Alignment explanation
Indices: 31136--31234 Score: 108
Period size: 34 Copynumber: 3.3 Consensus size: 27
31126 CATTAATATT
31136 TTACTCTTTACCATTTTTTCCTTTACTGA
1 TTACTCTTTACCA-TTTTT-CTTTACTGA
31165 TTACTCTTTACCATTTTTCTTTACTGA
1 TTACTCTTTACCATTTTTCTTTACTGA
*
31192 TTTCTCTTTACTCTCTACCATTTTTCTTTACTGA
1 -------TTACTCTTTACCATTTTTCTTTACTGA
31226 TTACTCTTT
1 TTACTCTTT
31235 TATTTTTTAC
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
27 17 0.28
28 5 0.08
29 13 0.21
34 26 0.43
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (27 bp):
TTACTCTTTACCATTTTTCTTTACTGA
Found at i:31203 original size:34 final size:34
Alignment explanation
Indices: 31165--31234 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
31155 CCTTTACTGA
* *
31165 TTACTCTTTACCATTTTTCTTTACTGATTTCTCT
1 TTACTCTCTACCATTTTTCTTTACTGATTACTCT
31199 TTACTCTCTACCATTTTTCTTTACTGATTACTCT
1 TTACTCTCTACCATTTTTCTTTACTGATTACTCT
31233 TT
1 TT
31235 TATTTTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (34 bp):
TTACTCTCTACCATTTTTCTTTACTGATTACTCT
Found at i:31246 original size:22 final size:22
Alignment explanation
Indices: 31218--31541 Score: 255
Period size: 22 Copynumber: 15.0 Consensus size: 22
31208 ACCATTTTTC
* *
31218 TTTACTGATTACTCTTTTATTT
1 TTTACTGATTACTATTTTACTT
* *
31240 TTTACTGATTGCCT-TTTTGCTT
1 TTTACTGATT-ACTATTTTACTT
31262 TTTACTGATTACCT-TTTTACTT
1 TTTACTGATTA-CTATTTTACTT
** *
31284 CCTACTGATTACTATTTTACCT
1 TTTACTGATTACTATTTTACTT
* * *
31306 TTTACTGGTTAC-CTTTTGC-T
1 TTTACTGATTACTATTTTACTT
*
31326 CTTACTGATTACTATTTTAC-T
1 TTTACTGATTACTATTTTACTT
*
31347 CTTACTGATTACTATTTTAC-T
1 TTTACTGATTACTATTTTACTT
* *
31368 CTTATTGATTATCT-TTTTACCTTT
1 TTTACTGATTA-CTATTTTA-C-TT
*
31392 TTTACTAATTACTA-TTTAC-T
1 TTTACTGATTACTATTTTACTT
* *
31412 CTTGCTGATTAC-ATTCTTACTT
1 TTTACTGATTACTATT-TTACTT
31434 TTTACTGATTACTATTTTACTT
1 TTTACTGATTACTATTTTACTT
*
31456 TTTACTGATTACTATTTTACAT
1 TTTACTGATTACTATTTTACTT
*
31478 TTTACTGA--GC-A--TTACTTT
1 TTTACTGATTACTATTTTAC-TT
*
31496 TTTACTGATTACTATTTTTTCCTTT
1 TTTACTGATTACTA--TTTTAC-TT
* *
31521 TTTACTGATTACCATTGTACT
1 TTTACTGATTACTATTTTACT
31542 CCTTGGATTG
Statistics
Matches: 247, Mismatches: 34, Indels: 42
0.76 0.11 0.13
Matches are distributed among these distances:
17 4 0.02
18 9 0.04
19 2 0.01
20 24 0.10
21 54 0.22
22 111 0.45
23 15 0.06
24 9 0.04
25 19 0.08
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTT
Found at i:31451 original size:15 final size:15
Alignment explanation
Indices: 31428--31513 Score: 56
Period size: 15 Copynumber: 5.7 Consensus size: 15
31418 GATTACATTC
31428 TTACT-TTTTACTGA
1 TTACTATTTTACTGA
**
31442 TTACTATTTTACTTT
1 TTACTATTTTACTGA
31457 TTACTGA--TTACT-A
1 TTACT-ATTTTACTGA
31470 TTTTAC-ATTTTACTGAGCA
1 --TTACTATTTTACT--G-A
*
31489 TTACTTTTTTACTGA
1 TTACTATTTTACTGA
31504 TTACTATTTT
1 TTACTATTTT
31514 TTCCTTTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 21
0.68 0.06 0.26
Matches are distributed among these distances:
13 1 0.02
14 10 0.18
15 31 0.55
16 2 0.04
17 4 0.07
18 7 0.12
19 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (15 bp):
TTACTATTTTACTGA
Found at i:36726 original size:22 final size:21
Alignment explanation
Indices: 36694--36819 Score: 72
Period size: 22 Copynumber: 5.8 Consensus size: 21
36684 CTTTGTGTGA
36694 TTATCAAAATTCCATAAGATGG
1 TTATCAAAATTCCATAAGA-GG
* * * *
36716 TTATTATAATTTCATGAGGAGG
1 TTATCAAAATTCCAT-AAGAGG
* *
36738 TTATCAAAATTCCATAGTGTGG
1 TTATCAAAATTCCATA-AGAGG
* * * **
36760 TTACCAAAATTTCATATGGAAC
1 TTATCAAAATTCCATA-AGAGG
* *
36782 TTATCAAAATTTCATAAGAATG
1 TTATCAAAATTCCATAAG-AGG
* *
36804 TTCTCAAAATTTCATA
1 TTATCAAAATTCCATA
36820 GTATGATTAC
Statistics
Matches: 80, Mismatches: 21, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
21 2 0.03
22 75 0.94
23 3 0.04
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTCCATAAGAGG
Found at i:36761 original size:44 final size:43
Alignment explanation
Indices: 36694--36819 Score: 114
Period size: 44 Copynumber: 2.9 Consensus size: 43
36684 CTTTGTGTGA
** * **
36694 TTATCAAAATTCCATAAGATGGTTATTATAATTTCATGA-GGAGG
1 TTATCAAAATTCCAT-AGATGGTTACCAAAATTTCAT-ATGGAAC
*
36738 TTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGGAAC
1 TTATCAAAATTCCATAG-ATGGTTACCAAAATTTCATATGGAAC
*
36782 TTATCAAAATTTCATAAGAAT-GTT-CTCAAAATTTCATA
1 TTATCAAAATTCCAT-AG-ATGGTTAC-CAAAATTTCATA
36820 GTATGATTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
43 4 0.06
44 62 0.90
45 3 0.04
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (43 bp):
TTATCAAAATTCCATAGATGGTTACCAAAATTTCATATGGAAC
Found at i:36833 original size:22 final size:22
Alignment explanation
Indices: 36742--36841 Score: 82
Period size: 22 Copynumber: 4.5 Consensus size: 22
36732 AGGAGGTTAT
* * *
36742 CAAAATTCCATAGTGTGGTTAC
1 CAAAATTTCATAGTATGATTAC
* *
36764 CAAAATTTCATA-T-GGAACTTAT
1 CAAAATTTCATAGTATG-A-TTAC
*
36786 CAAAATTTCATAAGAATG-TT-C
1 CAAAATTTCAT-AGTATGATTAC
36807 TCAAAATTTCATAGTATGATTAC
1 -CAAAATTTCATAGTATGATTAC
36830 CAAAATTTCATA
1 CAAAATTTCATA
36842 AGATCAGGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.02
21 6 0.10
22 52 0.84
23 2 0.03
25 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTATGATTAC
Found at i:36995 original size:22 final size:22
Alignment explanation
Indices: 36957--37031 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
36947 GGGTTATAAG
*
36957 AATTTCA-AAGTGTGGTTAACAA
1 AATTTCATAAG-GAGGTTAACAA
36979 AATTTCATAAGGAGGTT-ACTAA
1 AATTTCATAAGGAGGTTAAC-AA
* ** *
37001 TATTTCATGGGGAGGTTATCAA
1 AATTTCATAAGGAGGTTAACAA
37023 AATTTCATA
1 AATTTCATA
37032 GTATGATTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 2 0.05
22 37 0.86
23 4 0.09
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (22 bp):
AATTTCATAAGGAGGTTAACAA
Found at i:36996 original size:44 final size:44
Alignment explanation
Indices: 36948--37031 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 44
36938 GTCATAGCAG
* *
36948 GGTTA-TAAGAATTTCAAAGTGTGGTTAACAAAATTTCATAAGGA
1 GGTTACTAA-AATTTCAAAGGGAGGTTAACAAAATTTCATAAGGA
* ** *
36992 GGTTACTAATATTTCATGGGGAGGTTATCAAAATTTCATA
1 GGTTACTAAAATTTCAAAGGGAGGTTAACAAAATTTCATA
37032 GTATGATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
44 30 0.91
45 3 0.09
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (44 bp):
GGTTACTAAAATTTCAAAGGGAGGTTAACAAAATTTCATAAGGA
Found at i:37041 original size:22 final size:22
Alignment explanation
Indices: 37016--37076 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
37006 CATGGGGAGG
37016 TTATCAAAATTTCATAGTATGA
1 TTATCAAAATTTCATAGTATGA
** * *
37038 TTATCAAAAATTTTTTAGTCTGG
1 TTATC-AAAATTTCATAGTATGA
37061 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
37077 TGAAGGTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTATGA
Found at i:37084 original size:22 final size:21
Alignment explanation
Indices: 36928--37090 Score: 71
Period size: 22 Copynumber: 7.4 Consensus size: 21
36918 ATCAAAGAGA
* *
36928 TTATCAAAATGTCATAGCAGGG
1 TTATCAAAATTTCATAG-AAGG
* **
36950 TTAT-AAGAATTTCAAAGTGTGG
1 TTATCAA-AATTTCATAG-AAGG
* *
36972 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGAAGG
* * *
36994 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGAAGG
* *
37016 TTATCAAAATTTCATAGTATGA
1 TTATCAAAATTTCATAG-AAGG
** **
37038 TTATCAAAAATTTTTTAGTCTGG
1 TTATC-AAAATTTCATAG-AAGG
37061 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GAAGG
37083 TTAT-AAAA
1 TTATCAAAA
37091 GTCTCAATTT
Statistics
Matches: 109, Mismatches: 24, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
21 8 0.07
22 77 0.71
23 24 0.22
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGAAGG
Found at i:37298 original size:22 final size:22
Alignment explanation
Indices: 37144--37309 Score: 113
Period size: 22 Copynumber: 7.6 Consensus size: 22
37134 AGAGATTGGA
* *
37144 TTATCAAAATTT-AT-AGGAAGT
1 TTATCAAAATTTCATAAAG-AGG
** **
37165 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
37187 TTATCAAAATTTCA-AAGTGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * * *
37209 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* * *
37231 TTATCGAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * * *
37253 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
37275 TTATCAAAATTGCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
37297 TTATCAAATTTTC
1 TTATCAAAATTTC
37310 CAAATGTGAT
Statistics
Matches: 112, Mismatches: 29, Indels: 7
0.76 0.20 0.05
Matches are distributed among these distances:
21 13 0.12
22 96 0.86
23 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:37663 original size:22 final size:20
Alignment explanation
Indices: 37635--37714 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 20
37625 CAGGAGGATA
37635 TCAAAATTTCATATGAAGGTTG
1 TCAAAATTTCATA-G-AGGTTG
* *
37657 TCAAAATTTCATAAGAGAATTA
1 TCAAAATTTCAT-AGAG-GTTG
* *
37679 TCAAAATTTCATAGTATGTAG
1 TCAAAATTTCATAG-AGGTTG
37700 ATCAAAATTTCATAG
1 -TCAAAATTTCATAG
37715 GGAGATTAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 5 0.10
22 42 0.88
23 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (20 bp):
TCAAAATTTCATAGAGGTTG
Found at i:37686 original size:44 final size:44
Alignment explanation
Indices: 37633--37733 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
37623 TCCAGGAGGA
*
37633 TATCAAAATTTCATATGAAGGTTG-TCAAAATTTCATA-AGAGAAT
1 TATCAAAATTTCATA-GAAGGTAGATCAAAATTTCATAGAGAG-AT
* * *
37677 TATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATAGAAGGTAGATCAAAATTTCATAGAGAGAT
*
37721 TAACAAAATTTCA
1 TATCAAAATTTCA
37734 CAATGAGGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
43 5 0.10
44 42 0.84
45 3 0.06
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (44 bp):
TATCAAAATTTCATAGAAGGTAGATCAAAATTTCATAGAGAGAT
Found at i:37833 original size:22 final size:23
Alignment explanation
Indices: 37808--37877 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
37798 TATAGCGAGC
* *
37808 TTATCACAATTGCATAG-AGTGA
1 TTATCAAAATTGCAGAGTAGTGA
**
37830 TTATCAAAATTTTAGAGTAGTGA
1 TTATCAAAATTGCAGAGTAGTGA
**
37853 TTATCAAAATTTTAGAGT-GTGA
1 TTATCAAAATTGCAGAGTAGTGA
37875 TTA
1 TTA
37878 CTAACAATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 20 0.47
23 23 0.53
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTGCAGAGTAGTGA
Found at i:37886 original size:23 final size:23
Alignment explanation
Indices: 37825--37877 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
37815 AATTGCATAG
37825 AGTGATTATCAAAATTTTAGAGT
1 AGTGATTATCAAAATTTTAGAGT
37848 AGTGATTATCAAAATTTTAGAGT
1 AGTGATTATCAAAATTTTAGAGT
37871 -GTGATTA
1 AGTGATTA
37878 CTAACAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 7 0.23
23 23 0.77
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.40
Consensus pattern (23 bp):
AGTGATTATCAAAATTTTAGAGT
Found at i:37983 original size:23 final size:23
Alignment explanation
Indices: 37935--38050 Score: 91
Period size: 22 Copynumber: 5.2 Consensus size: 23
37925 ATATATCCTA
* *
37935 TCATA-TGGAGGTTATCAACATC
1 TCATAGTGGAGGTTATCAAAATT
**
37957 TCATAGTGTTGGTTATCAAAATT
1 TCATAGTGGAGGTTATCAAAATT
* *
37980 TCATTG-GGAAGTTATCAAAATT
1 TCATAGTGGAGGTTATCAAAATT
* *
38002 TTATAGT-GAGGTCT-TTAAAA-T
1 TCATAGTGGAGGT-TATCAAAATT
*
38023 TCATTA-TGGAGGTTAACAAAATT
1 TCA-TAGTGGAGGTTATCAAAATT
38046 TCATA
1 TCATA
38051 AGAAGGTTAA
Statistics
Matches: 72, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
21 5 0.07
22 44 0.61
23 23 0.32
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (23 bp):
TCATAGTGGAGGTTATCAAAATT
Found at i:38110 original size:22 final size:22
Alignment explanation
Indices: 38082--38135 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
38072 AAAAATTTCG
* *
38082 AAATTTCATA-GTATAGTTATTA
1 AAATTTCATAGGAAT-GTTATCA
38104 AAATTTCATAGGAATGTTATCA
1 AAATTTCATAGGAATGTTATCA
38126 AAATTTCATA
1 AAATTTCATA
38136 AAGAGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATTTCATAGGAATGTTATCA
Found at i:38144 original size:22 final size:22
Alignment explanation
Indices: 37967--38150 Score: 73
Period size: 22 Copynumber: 8.5 Consensus size: 22
37957 TCATAGTGTT
**
37967 GGTTATCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCA-TAAGAA
* *
37990 -GTTATCAAAATTTTAT-AGTGA
1 GGTTATCAAAATTTCATAAG-AA
* * *
38011 GGTCT-TTAAAA-TTCATTATGGA
1 GGT-TATCAAAATTTCA-TAAGAA
*
38033 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
** * *
38055 GGTTA--AAAAAATGATAAAAA
1 GGTTATCAAAATTTCATAAGAA
** *
38075 AATT-TCGAAATTTCAT-AGTATA
1 GGTTATCAAAATTTCATAAG-A-A
* *
38097 -GTTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGAA
*
38118 TGTTATCAAAATTTCATAA-AGA
1 GGTTATCAAAATTTCATAAGA-A
38140 GGTTATCAAAA
1 GGTTATCAAAA
38151 ATAGTATAAT
Statistics
Matches: 118, Mismatches: 28, Indels: 31
0.67 0.16 0.18
Matches are distributed among these distances:
20 15 0.13
21 17 0.14
22 79 0.67
23 7 0.06
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Done.