Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007831.1 Corchorus capsularis cultivar CVL-1 contig07852, 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: 93342
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3186 original size:2 final size:2
Alignment explanation
Indices: 3179--3209 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3169 GAAATATGAT
3179 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3210 AGTCTAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3921 original size:5 final size:5
Alignment explanation
Indices: 3911--3942 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3901 AATTTCTTTC
3911 TTTAT TTTAT TTTAT TTTAT TTTAT TTT-T TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3943 GTGAAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTAT
Found at i:7761 original size:21 final size:21
Alignment explanation
Indices: 7731--7771 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7721 TTATAATACT
* *
7731 ATAACATTTTTTATAACCTTC
1 ATAACATTTTTAACAACCTTC
*
7752 ATAACTTTTTTAACAACCTT
1 ATAACATTTTTAACAACCTT
7772 AAGCATTGGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAACATTTTTAACAACCTTC
Found at i:9695 original size:19 final size:19
Alignment explanation
Indices: 9673--9709 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
9663 TTCTTCTATG
*
9673 TTCTTCTTCGCGAGCCTCT
1 TTCTTCTTCACGAGCCTCT
9692 TTCTTCTTCACGAGCCTC
1 TTCTTCTTCACGAGCCTC
9710 CTCTGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.38, G:0.14, T:0.41
Consensus pattern (19 bp):
TTCTTCTTCACGAGCCTCT
Found at i:12306 original size:7 final size:7
Alignment explanation
Indices: 12293--12353 Score: 88
Period size: 7 Copynumber: 8.7 Consensus size: 7
12283 ACTTTGTGAT
12293 TTTTTCTG
1 TTTTT-TG
*
12301 TTTTCTG
1 TTTTTTG
*
12308 TTTTCTG
1 TTTTTTG
12315 TTTTTTG
1 TTTTTTG
12322 TTTTTTG
1 TTTTTTG
12329 TTTTTTG
1 TTTTTTG
12336 TTTTTTG
1 TTTTTTG
12343 TTTTTT-
1 TTTTTTG
12349 TTTTT
1 TTTTT
12354 ACTTTTATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
6 5 0.10
7 42 0.82
8 4 0.08
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (7 bp):
TTTTTTG
Found at i:14516 original size:32 final size:32
Alignment explanation
Indices: 14475--14653 Score: 209
Period size: 32 Copynumber: 5.3 Consensus size: 32
14465 TTTTTTATTG
14475 ACCCTGAATTAAGTTCTTTATTCTACTTAATT
1 ACCCTGAATTAAGTTCTTTATTCTACTTAATT
**
14507 ACCCTGAATTAA-ACCTTTTATTGACTCCACTTAATT
1 ACCCTGAATTAAGTTC-TTTATT--CT--ACTTAATT
14543 ACCCTGAATTAAGTTCTTTATTCTACTTAATT
1 ACCCTGAATTAAGTTCTTTATTCTACTTAATT
* *
14575 ACCCTGAATTAAG-CCTTTTATTGACTCCACTTGATT
1 ACCCTGAATTAAGTTC-TTTATT--CT--ACTTAATT
*
14611 ACCCTGAATTAAATTCTTTATTCTACTTAATT
1 ACCCTGAATTAAGTTCTTTATTCTACTTAATT
14643 ACCCTGAATTA
1 ACCCTGAATTA
14654 TGCCCTTCAT
Statistics
Matches: 126, Mismatches: 9, Indels: 24
0.79 0.06 0.15
Matches are distributed among these distances:
31 2 0.02
32 63 0.50
34 8 0.06
36 51 0.40
37 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (32 bp):
ACCCTGAATTAAGTTCTTTATTCTACTTAATT
Found at i:14584 original size:68 final size:68
Alignment explanation
Indices: 14475--14653 Score: 331
Period size: 68 Copynumber: 2.6 Consensus size: 68
14465 TTTTTTATTG
14475 ACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAAACCTTTTATTGACTCCACTTA
1 ACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAAACCTTTTATTGACTCCACTTA
14540 ATT
66 ATT
* *
14543 ACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAAGCCTTTTATTGACTCCACTTG
1 ACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAAACCTTTTATTGACTCCACTTA
14608 ATT
66 ATT
*
14611 ACCCTGAATTAAATTCTTTATTCTACTTAATTACCCTGAATTA
1 ACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTA
14654 TGCCCTTCAT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 108 1.00
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (68 bp):
ACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAAACCTTTTATTGACTCCACTTA
ATT
Found at i:14693 original size:68 final size:68
Alignment explanation
Indices: 14475--14678 Score: 327
Period size: 68 Copynumber: 3.0 Consensus size: 68
14465 TTTTTTATTG
* *
14475 ACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAAACCTTTTATTGACTCCACTTA
1 ACCCTGAATTAAATTCTTTATTCTACTTAATTACCCTGAATTAAGCCTTTTATTGACTCCACTTA
14540 ATT
66 ATT
* *
14543 ACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAAGCCTTTTATTGACTCCACTTG
1 ACCCTGAATTAAATTCTTTATTCTACTTAATTACCCTGAATTAAGCCTTTTATTGACTCCACTTA
14608 ATT
66 ATT
* * * * *
14611 ACCCTGAATTAAATTCTTTATTCTACTTAATTACCCTGAATTATGCCCTTCATTTACTCTACTTA
1 ACCCTGAATTAAATTCTTTATTCTACTTAATTACCCTGAATTAAGCCTTTTATTGACTCCACTTA
14676 ATT
66 ATT
14679 TCCTTCCTTG
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 127 1.00
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (68 bp):
ACCCTGAATTAAATTCTTTATTCTACTTAATTACCCTGAATTAAGCCTTTTATTGACTCCACTTA
ATT
Found at i:14762 original size:83 final size:82
Alignment explanation
Indices: 14662--14864 Score: 300
Period size: 83 Copynumber: 2.5 Consensus size: 82
14652 TATGCCCTTC
* *
14662 ATTTACTCTACTTAATTTCCTTCCTTGAAATTAAGTCTATGCTTTTCTTTACCTAATTTCCTTCC
1 ATTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTATGCTTTTCTTTACCTAATTTCCTTCC
* *
14727 TTGAAATTAAGTATAATG
66 CTGAAATTAAGTAT-ATA
* * *
14745 CTTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTATGTGCTTTTCTTTACCTAATTTCCTTCC
1 ATTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTATGCTTTTCTTTACCTAATTTCCTTCC
* *
14810 CTGAAATTAAGTCTGTA
66 CTGAAATTAAGTATATA
14827 ATTTACTTTACCTAATTAT-CTTCCTTGAAATTAAGTCT
1 ATTTACTTTACCTAATT-TCCTTCCTTGAAATTAAGTCT
14865 GTGTTTGCCT
Statistics
Matches: 108, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
82 35 0.32
83 73 0.68
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (82 bp):
ATTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTATGCTTTTCTTTACCTAATTTCCTTCC
CTGAAATTAAGTATATA
Found at i:14885 original size:41 final size:41
Alignment explanation
Indices: 14663--14884 Score: 286
Period size: 41 Copynumber: 5.4 Consensus size: 41
14653 ATGCCCTTCA
* * *
14663 TTTACTCTACTTAATTTCCTTCCTTGAAATTAAGTCTATGC
1 TTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGC
* * *
14704 TTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTATAATGC
1 TTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCT-GTGC
*
14746 TTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTATGTGC
1 TTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGC
* * **
14787 TTTTCTTTACCTAATTTCCTTCCCTGAAATTAAGTCTGTAA
1 TTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGC
14828 TTTACTTTACCTAATTAT-CTTCCTTGAAATTAAGTCTGTG-
1 TTTACTTTACCTAATT-TCCTTCCTTGAAATTAAGTCTGTGC
* *
14868 TTTGCCTTTACTTAATT
1 TTT-ACTTTACCTAATT
14885 ACCATGAATC
Statistics
Matches: 162, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
40 3 0.02
41 118 0.73
42 41 0.25
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (41 bp):
TTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGC
Found at i:14919 original size:37 final size:36
Alignment explanation
Indices: 14874--15578 Score: 852
Period size: 37 Copynumber: 18.8 Consensus size: 36
14864 TGTGTTTGCC
* *
14874 TTTACTTAATTACCATGAATCAAGTCCTTTAATAGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAAT-GCT
* *
14911 TTTACTTAATTACCTTGAAATAAGTCCTTTGACTGCTGT
1 TTTACTTAATTACCTTGAATTAAGTCCTTT-AATGC--T
*
14950 GTTTACTTAATTTCCTTGAATTAAGTCCTTTAAATGCT
1 -TTTACTTAATTACCTTGAATTAAGTCCTTT-AATGCT
* *
14988 TTTACTTAATTTCCCTGAATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAA-TGCT
* * *
15025 TTTACTTAATTTCCATGGATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAA-TGCT
* *
15062 TTTACTTAATTACATTGAATTAAGTCCTTTAATTGTT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAA-TGCT
*
15099 TTTACTTAATTACCTTGAATTAAGTCCTTTGACTGCTGT
1 TTTACTTAATTACCTTGAATTAAGTCCTTT-AATGC--T
*
15138 GTTTACTTAATTTCCTTGAATTAAGTCCTTTAACTGCT
1 -TTTACTTAATTACCTTGAATTAAGTCCTTTAA-TGCT
* *
15176 TTTACTTAATTACCTTGAATTAAGTCCTTTGACTGTTGT
1 TTTACTTAATTACCTTGAATTAAGTCCTTT-AATG--CT
* *
15215 GTTTACTTAATTTCCTTGAATTAAGTCCTTTTACTGCT
1 -TTTACTTAATTACCTTGAATTAAGTCC-TTTAATGCT
* *
15253 TTTACTTAATTTCCTTAAATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAA-TGCT
**
15290 TTTACTTAATTTGCTTGAATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAA-TGCT
* *
15327 TTTACTTAATTACCCTGAATTAAGTCCTTTGACTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTT-AATGCT
* * *
15364 TTTACTTAATTACCATGAATTAAGTCCATTAGCTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTA-ATGCT
* *
15401 TTTACTTAATTTCCTTAAATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAA-TGCT
*
15438 TTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAA-TGCT
* *
15475 TTTACTTAATTTCCTTGAGTTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAA-TGCT
* *
15512 TTTACTTAATTACCCTGAATTAAGTCCTTTGACTGCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTT-AATGCT
*
15549 TTTACTTAATTACCATGAATTAAGTCCTTT
1 TTTACTTAATTACCTTGAATTAAGTCCTTT
15579 TCTTAATTAC
Statistics
Matches: 595, Mismatches: 53, Indels: 40
0.86 0.08 0.06
Matches are distributed among these distances:
36 7 0.01
37 478 0.80
38 9 0.02
39 4 0.01
40 94 0.16
41 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (36 bp):
TTTACTTAATTACCTTGAATTAAGTCCTTTAATGCT
Found at i:15062 original size:74 final size:74
Alignment explanation
Indices: 14874--15578 Score: 980
Period size: 74 Copynumber: 9.4 Consensus size: 74
14864 TGTGTTTGCC
* * *
14874 TTTACTTAATTACCATGAATCAAGTCCTTTAA-TAGCTTTTACTTAATTACCTTGAAATAAGTCC
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAACT-GCTTTTACTTAATTACCTTGAATTAAGTCC
*
14938 TTTGACTGCTGT
65 TTTAACTGC--T
* * * *
14950 GTTTACTTAATTTCCTTGAATTAAGTCCTTTAAATGCTTTTACTTAATTTCCCTGAATTAAGTCC
1 -TTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCC
15015 TTTAACTGCT
65 TTTAACTGCT
* * * *
15025 TTTACTTAATTTCCATGGATTAAGTCCTTTAACTGCTTTTACTTAATTACATTGAATTAAGTCCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCT
* *
15090 TTAATTGTT
66 TTAACTGCT
* *
15099 TTTACTTAATTACCTTGAATTAAGTCCTTTGACTGCTGTGTTTACTTAATTTCCTTGAATTAAGT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAACTGC--T-TTTACTTAATTACCTTGAATTAAGT
15164 CCTTTAACTGCT
63 CCTTTAACTGCT
* * *
15176 TTTACTTAATTACCTTGAATTAAGTCCTTTGACTGTTGTGTTTACTTAATTTCCTTGAATTAAGT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAACTG--CT-TTTACTTAATTACCTTGAATTAAGT
*
15241 CCTTTTACTGCT
63 CCTTTAACTGCT
* * **
15253 TTTACTTAATTTCCTTAAATTAAGTCCTTTAACTGCTTTTACTTAATTTGCTTGAATTAAGTCCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCT
15318 TTAACTGCT
66 TTAACTGCT
* * * *
15327 TTTACTTAATTACCCTGAATTAAGTCCTTTGACTGCTTTTACTTAATTACCATGAATTAAGTCCA
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCT
*
15392 TTAGCTGCT
66 TTAACTGCT
* * *
15401 TTTACTTAATTTCCTTAAATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTGAATTAAGTCCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCT
15466 TTAACTGCT
66 TTAACTGCT
* * *
15475 TTTACTTAATTTCCTTGAGTTAAGTCCTTTAACTGCTTTTACTTAATTACCCTGAATTAAGTCCT
1 TTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCT
*
15540 TTGACTGCT
66 TTAACTGCT
*
15549 TTTACTTAATTACCATGAATTAAGTCCTTT
1 TTTACTTAATTACCTTGAATTAAGTCCTTT
15579 TCTTAATTAC
Statistics
Matches: 569, Mismatches: 53, Indels: 15
0.89 0.08 0.02
Matches are distributed among these distances:
74 363 0.64
75 2 0.00
76 1 0.00
77 202 0.36
78 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (74 bp):
TTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCT
TTAACTGCT
Found at i:15118 original size:111 final size:111
Alignment explanation
Indices: 14874--15578 Score: 1007
Period size: 111 Copynumber: 6.3 Consensus size: 111
14864 TGTGTTTGCC
* * * *
14874 TTTACTTAATTACCATGAATCAAGTCCTTTAA-TAGCTTTTACTTAATTACCTTGAAATAAGTCC
1 TTTACTTAATTACCCTGAATTAAGTCCTTTAACT-GCTTTTACTTAATTTCCTTGAATTAAGTCC
* * *
14938 TTTGACTGCTGTGTTTACTTAATTTCCTTGAATTAAGTCCTTTAAATGCT
65 TTTAACTGC--T-TTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCT
* * *
14988 TTTACTTAATTTCCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCATGGATTAAGTCCT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCTTGAATTAAGTCCT
* * *
15053 TTAACTGCTTTTACTTAATTACATTGAATTAAGTCCTTTAATTGTT
66 TTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCT
* *
15099 TTTACTTAATTACCTTGAATTAAGTCCTTTGACTGCTGTGTTTACTTAATTTCCTTGAATTAAGT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTAACTGC--T-TTTACTTAATTTCCTTGAATTAAGT
* *
15164 CCTTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCTTTGACTGTTGT
63 CCTTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCTTTAACTG--CT
* * * *
15215 GTTTACTTAATTTCCTTGAATTAAGTCCTTTTACTGCTTTTACTTAATTTCCTTAAATTAAGTCC
1 -TTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCTTGAATTAAGTCC
**
15280 TTTAACTGCTTTTACTTAATTTGCTTGAATTAAGTCCTTTAACTGCT
65 TTTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCT
* * * *
15327 TTTACTTAATTACCCTGAATTAAGTCCTTTGACTGCTTTTACTTAATTACCATGAATTAAGTCCA
1 TTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCTTGAATTAAGTCCT
* * *
15392 TTAGCTGCTTTTACTTAATTTCCTTAAATTAAGTCCTTTAACTGCT
66 TTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCT
*
15438 TTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCTTGAGTTAAGTCCT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCTTGAATTAAGTCCT
* *
15503 TTAACTGCTTTTACTTAATTACCCTGAATTAAGTCCTTTGACTGCT
66 TTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCT
*
15549 TTTACTTAATTACCATGAATTAAGTCCTTT
1 TTTACTTAATTACCCTGAATTAAGTCCTTT
15579 TCTTAATTAC
Statistics
Matches: 535, Mismatches: 49, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
111 297 0.56
112 2 0.00
113 1 0.00
114 198 0.37
115 2 0.00
116 1 0.00
117 34 0.06
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (111 bp):
TTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCTTGAATTAAGTCCT
TTAACTGCTTTTACTTAATTACCTTGAATTAAGTCCTTTAACTGCT
Found at i:15583 original size:27 final size:26
Alignment explanation
Indices: 15547--15597 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
15537 CCTTTGACTG
15547 CTTTTACTTAATTACCATGAATTAAGTC
1 CTTTTACTTAATTACCA--AATTAAGTC
15575 CTTTT-CTTAATTACCAAATTAAG
1 CTTTTACTTAATTACCAAATTAAG
15598 ACTTTGACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.30
27 11 0.48
28 5 0.22
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (26 bp):
CTTTTACTTAATTACCAAATTAAGTC
Found at i:20340 original size:2 final size:2
Alignment explanation
Indices: 20333--20364 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20323 ACAACAAGGT
20333 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
20365 TTGTGAGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:33379 original size:21 final size:20
Alignment explanation
Indices: 33351--33389 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
33341 ACTAGCGCTG
33351 GGCGCCCATGTGGTTTGCTT
1 GGCGCCCATGTGGTTTGCTT
33371 GGCGTCCCATGTGGTTTGC
1 GGCG-CCCATGTGGTTTGC
33390 CTCACGACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.05, C:0.26, G:0.36, T:0.33
Consensus pattern (20 bp):
GGCGCCCATGTGGTTTGCTT
Found at i:33400 original size:21 final size:21
Alignment explanation
Indices: 33355--33403 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
33345 GCGCTGGGCG
* ** *
33355 CCCATGTGGTTTGCTTGGCGT
1 CCCATGTGGTTTGCCTCACGA
33376 CCCATGTGGTTTGCCTCACGA
1 CCCATGTGGTTTGCCTCACGA
33397 CCCATGT
1 CCCATGT
33404 ACTCCAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.31, G:0.27, T:0.33
Consensus pattern (21 bp):
CCCATGTGGTTTGCCTCACGA
Found at i:35574 original size:18 final size:18
Alignment explanation
Indices: 35551--35587 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35541 TTATAGGCTG
*
35551 TTCATGAAGATCTGAATT
1 TTCATGAAAATCTGAATT
*
35569 TTCATGAAAATCTGGATT
1 TTCATGAAAATCTGAATT
35587 T
1 T
35588 GACTAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (18 bp):
TTCATGAAAATCTGAATT
Found at i:37535 original size:59 final size:59
Alignment explanation
Indices: 37443--37561 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 59
37433 GGCGTGATGG
* * *
37443 AATCAATCAAACAGATCTACCGCAGGATCATGATTGAAGAATGATTACAGTGGGATCCA
1 AATCAATCAAACAGATCCACCGCAGGATCATGATTGAAGAAGGATTACAGCGGGATCCA
* * *
37502 AATCAAT-AAAGCAGGTCCACCGCAGGATCATGATTGACGCAGGATTACAGCGGGATCCA
1 AATCAATCAAA-CAGATCCACCGCAGGATCATGATTGAAGAAGGATTACAGCGGGATCCA
37561 A
1 A
37562 GATTTAAGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 3 0.06
59 50 0.94
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (59 bp):
AATCAATCAAACAGATCCACCGCAGGATCATGATTGAAGAAGGATTACAGCGGGATCCA
Found at i:37792 original size:15 final size:15
Alignment explanation
Indices: 37772--37810 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
37762 GTAAACTATT
37772 ACAAGTGAATGAGAA
1 ACAAGTGAATGAGAA
37787 ACAAGTGAATGAGAA
1 ACAAGTGAATGAGAA
37802 ACAAGTGAA
1 ACAAGTGAA
37811 GGGAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.54, C:0.08, G:0.26, T:0.13
Consensus pattern (15 bp):
ACAAGTGAATGAGAA
Found at i:38503 original size:35 final size:35
Alignment explanation
Indices: 38457--38528 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
38447 GTCCTAGAAA
38457 GAAAACAAATGTATTGAGAAACATGATATCGAGCT
1 GAAAACAAATGTATTGAGAAACATGATATCGAGCT
38492 GAAAACAAATGTATTGAGAAACATGATATCGAGCT
1 GAAAACAAATGTATTGAGAAACATGATATCGAGCT
38527 GA
1 GA
38529 TTTTAAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (35 bp):
GAAAACAAATGTATTGAGAAACATGATATCGAGCT
Found at i:43605 original size:419 final size:420
Alignment explanation
Indices: 42801--43642 Score: 1496
Period size: 419 Copynumber: 2.0 Consensus size: 420
42791 TTAATTGTCT
*
42801 CAACCTCTTGTTCCTTTTTAATTGTCCCCTCTTTATTAAAATGACATATTTGCTCTGCTTTGAAA
1 CAACCTCTTGTTCCTTTTTAATTGTCCCCTCTTTATTAAAATGACATATTTGCTCTACTTTGAAA
*
42866 CCACAAAATCCATTAAATATGATAGTTGACAAGAGTAAATTATACCAATTAAATAGGACAATATG
66 CCACAAAATCCATTAAATATAATAGTTGACAAGAGTAAATTATACCAATTAAATAGGACAATATG
*
42931 GTAAAGTAAAGTAAATTTTGTATAAAATTTAACAAAATAACTATTTTTCTTAAACAAATAAAGTA
131 GTAAAGTAAAGTAAATTTTGTATAAAATTTAACAAAATAACTACTTTTCTTAAACAAATAAAGTA
*
42996 GTTAAAATGGACAATTAAAAAGGAACAAACGGAGTAACTTCCAAGGCCAAATAATTGAAATTAAC
196 GTTAAAATGGACAATTAAAAAGAAACAAACGGAGTAACTTCCAAGGCCAAATAATTGAAATTAAC
43061 AGAAGATTACTTATTTTAATGGGGAATTGCTTGGACATCATTGAATATTACTAGAATAGGGTTCA
261 AGAAGATTACTTATTTTAATGGGGAATTGCTTGGACATCATTGAATATTACTAGAATAGGGTTCA
* *
43126 ACTATGATGATTCAAGCTGCTAATATGGGGGCCGGGGTAAAACAGTAAGAATTCAACTAACACTT
326 ACTATGATGATTCAAGCTGCTAATACGGGGGCCGAGGTAAAACAGTAAGAATTCAACTAACACTT
43191 ATTGGGTTGAGCAAAAGAAACTTGATATCC
391 ATTGGGTTGAGCAAAAGAAACTTGATATCC
43221 CAACCTCTTGTTCCTTTTTAATTGT-CCCTCTTTATTAAAATGACATATTTG-TCCTACTTTGAA
1 CAACCTCTTGTTCCTTTTTAATTGTCCCCTCTTTATTAAAATGACATATTTGCT-CTACTTTGAA
* *
43284 ATCACAAAA-CTCATTAAATATAATAGTTGACAAGAGTAAATTATACCAATTAAATAGGGCAATA
65 ACCACAAAATC-CATTAAATATAATAGTTGACAAGAGTAAATTATACCAATTAAATAGGACAATA
* *
43348 TGGTAAATTAAAGTTAATTTTGTATAAAATTTAACAAAATAACTACTTTTCTTAAACAAATAAAG
129 TGGTAAAGTAAAGTAAATTTTGTATAAAATTTAACAAAATAACTACTTTTCTTAAACAAATAAAG
*
43413 TAGTTAAAA-GGAACAATTAAAAAGAAACAGA-GAGAGTAACTTCCAAGGCCAAATAATTGAAAT
194 TAGTTAAAATGG-ACAATTAAAAAGAAACAAACG-GAGTAACTTCCAAGGCCAAATAATTGAAAT
43476 TAACAGAAGATTACTTATTTTAATGGGGAATTGCTTGGACATCATTGAATATTACTAGAATAGGG
257 TAACAGAAGATTACTTATTTTAATGGGGAATTGCTTGGACATCATTGAATATTACTAGAATAGGG
*
43541 TTCAACTATGATGATTCAAGCTGCTAATACGGGGGTCGAGGTAAAACAGTAAGAATTCAACTAAC
322 TTCAACTATGATGATTCAAGCTGCTAATACGGGGGCCGAGGTAAAACAGTAAGAATTCAACTAAC
*
43606 ACTTATTGGGTTGAGTAAAAGAAACTTGATATCC
387 ACTTATTGGGTTGAGCAAAAGAAACTTGATATCC
43640 CAA
1 CAA
43643 GTTTAATACG
Statistics
Matches: 405, Mismatches: 13, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
418 5 0.01
419 375 0.93
420 25 0.06
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (420 bp):
CAACCTCTTGTTCCTTTTTAATTGTCCCCTCTTTATTAAAATGACATATTTGCTCTACTTTGAAA
CCACAAAATCCATTAAATATAATAGTTGACAAGAGTAAATTATACCAATTAAATAGGACAATATG
GTAAAGTAAAGTAAATTTTGTATAAAATTTAACAAAATAACTACTTTTCTTAAACAAATAAAGTA
GTTAAAATGGACAATTAAAAAGAAACAAACGGAGTAACTTCCAAGGCCAAATAATTGAAATTAAC
AGAAGATTACTTATTTTAATGGGGAATTGCTTGGACATCATTGAATATTACTAGAATAGGGTTCA
ACTATGATGATTCAAGCTGCTAATACGGGGGCCGAGGTAAAACAGTAAGAATTCAACTAACACTT
ATTGGGTTGAGCAAAAGAAACTTGATATCC
Found at i:51926 original size:24 final size:24
Alignment explanation
Indices: 51899--51945 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
51889 TGACATGTAA
* *
51899 CACGCCACGTGTGCCAAAAAGTGG
1 CACGCCACATGTACCAAAAAGTGG
*
51923 CACGTCACATGTACCAAAAAGTG
1 CACGCCACATGTACCAAAAAGTG
51946 ATACATGGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (24 bp):
CACGCCACATGTACCAAAAAGTGG
Found at i:52243 original size:2 final size:2
Alignment explanation
Indices: 52236--52271 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52226 TAAACGCTCA
52236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52272 CCTTATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52546 original size:17 final size:16
Alignment explanation
Indices: 52506--52568 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 16
52496 TCGTGTCATT
52506 TTCGGGTTCGGGTTTGA
1 TTCGGGTTCGGG-TTGA
*
52523 GTCGGGTTCGGGTTGGA
1 TTCGGGTTCGGGTT-GA
* * *
52540 TTTGGG-TCAGGTTAA
1 TTCGGGTTCGGGTTGA
52555 TTCGGGTTCGGGTT
1 TTCGGGTTCGGGTT
52569 CTATTTGGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 6 0.16
16 14 0.38
17 17 0.46
ACGTcount: A:0.08, C:0.11, G:0.43, T:0.38
Consensus pattern (16 bp):
TTCGGGTTCGGGTTGA
Found at i:52737 original size:16 final size:16
Alignment explanation
Indices: 52716--52822 Score: 92
Period size: 16 Copynumber: 6.7 Consensus size: 16
52706 TTTTCATAAA
52716 TTTTCGGATTCGGGTT
1 TTTTCGGATTCGGGTT
* * * *
52732 TTTTCGGGTTTGAGCT
1 TTTTCGGATTCGGGTT
*
52748 TTTTCGGGTTCGGGTT
1 TTTTCGGATTCGGGTT
* * *
52764 TTTTC-GAGTTTGAGCT
1 TTTTCGGA-TTCGGGTT
52780 TTTTCGTG-TTCGGGTT
1 TTTTCG-GATTCGGGTT
*
52796 TTTTCGGGTTCGGGTT
1 TTTTCGGATTCGGGTT
*
52812 TTTTCAGATTC
1 TTTTCGGATTC
52823 AGGCGGGTTC
Statistics
Matches: 71, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
15 2 0.03
16 68 0.96
18 1 0.01
ACGTcount: A:0.06, C:0.13, G:0.30, T:0.51
Consensus pattern (16 bp):
TTTTCGGATTCGGGTT
Found at i:52760 original size:32 final size:32
Alignment explanation
Indices: 52716--52805 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
52706 TTTTCATAAA
*
52716 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
*
52748 TTTTCGGGTTCGGGTTTTTTCGAGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
*
52780 TTTTCGTGTTCGGGTTTTTTCGGGTT
1 TTTTCGGGTTCGGGTTTTTTCGGGTT
52806 CGGGTTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.04, C:0.12, G:0.31, T:0.52
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
Found at i:54211 original size:2 final size:2
Alignment explanation
Indices: 54194--54230 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
54184 TAAAGGTCAA
* *
54194 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54231 ATTAAGAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:54709 original size:28 final size:27
Alignment explanation
Indices: 54669--54725 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
54659 TCTACAATCA
*
54669 AACATTTGGTTCAATGGTTGTCATGCAT
1 AACATTTGATTCAATGGTT-TCATGCAT
*
54697 AACATTTGATTCAATGGTTTTATGCAT
1 AACATTTGATTCAATGGTTTCATGCAT
54724 AA
1 AA
54726 TATCTCTACG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (27 bp):
AACATTTGATTCAATGGTTTCATGCAT
Found at i:64424 original size:20 final size:21
Alignment explanation
Indices: 64388--64430 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
64378 GAAATATTTC
64388 ATTACAAATTAATTTCTAATA
1 ATTACAAATTAATTTCTAATA
*
64409 ATTACATATT-ATTTCTAATA
1 ATTACAAATTAATTTCTAATA
64429 AT
1 AT
64431 ATTTATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTACAAATTAATTTCTAATA
Found at i:64463 original size:30 final size:29
Alignment explanation
Indices: 64427--64484 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
64417 TTATTTCTAA
*
64427 TAATATTTATTGCATATCAAATAAATATTC
1 TAATATTTATTACATAT-AAATAAATATTC
*
64457 TAATATTTATTACATATTAATAAATATT
1 TAATATTTATTACATATAAATAAATATT
64485 TCCAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (29 bp):
TAATATTTATTACATATAAATAAATATTC
Found at i:64601 original size:11 final size:10
Alignment explanation
Indices: 64556--64607 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
64546 AATCTTAATT
64556 AACGAACATA
1 AACGAACATA
*
64566 AACGAGCTATA
1 AACGAAC-ATA
*
64577 AACGAGCCATTA
1 AACGA-ACA-TA
64589 AACGAACACTA
1 AACGAACA-TA
64600 AACGAACA
1 AACGAACA
64608 ATAATCGAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 6 0.17
11 21 0.60
12 8 0.23
ACGTcount: A:0.52, C:0.23, G:0.13, T:0.12
Consensus pattern (10 bp):
AACGAACATA
Found at i:66150 original size:30 final size:30
Alignment explanation
Indices: 66114--66175 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
66104 GATCAAGTGG
*
66114 CCGGTTGTGGCCGGATGGCCCGTGCGATGT
1 CCGGTTGTCGCCGGATGGCCCGTGCGATGT
66144 CCGGTTGTCGCCGGATGGCCCGTGCGATGT
1 CCGGTTGTCGCCGGATGGCCCGTGCGATGT
66174 CC
1 CC
66176 CATGCATTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.06, C:0.31, G:0.40, T:0.23
Consensus pattern (30 bp):
CCGGTTGTCGCCGGATGGCCCGTGCGATGT
Found at i:71590 original size:11 final size:10
Alignment explanation
Indices: 71573--71599 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
71563 TCTAGTCGAA
71573 ATTTTTTTTT
1 ATTTTTTTTT
71583 ATTTTTTTTT
1 ATTTTTTTTT
71593 ATTTTTT
1 ATTTTTT
71600 CGATATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:72685 original size:42 final size:42
Alignment explanation
Indices: 72626--72708 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
72616 TCAAGTGGCC
* * * *
72626 GGTTGTGGCCGGATGGCCCATGCAATGGCTCGTGCGATGTCT
1 GGTTGTCGCCGAATGGCCCATGCAATAGCCCGTGCGATGTCT
* *
72668 GGTTGTCGCCGAATGGCCCGTGCGATAGCCCGTGCGATGTC
1 GGTTGTCGCCGAATGGCCCATGCAATAGCCCGTGCGATGTC
72709 CCATGCATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.37, T:0.24
Consensus pattern (42 bp):
GGTTGTCGCCGAATGGCCCATGCAATAGCCCGTGCGATGTCT
Found at i:73137 original size:21 final size:21
Alignment explanation
Indices: 73096--73137 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
73086 GCCACAGCAG
*
73096 TCGCAGATTACTACTCCACTA
1 TCGCAGATTAATACTCCACTA
* *
73117 TCGCAGATTAATGCTCTACTA
1 TCGCAGATTAATACTCCACTA
73138 GATGCTGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (21 bp):
TCGCAGATTAATACTCCACTA
Found at i:79320 original size:1 final size:1
Alignment explanation
Indices: 79314--79344 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
79304 ATTTCATTGC
79314 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
79345 CATTTTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:80974 original size:52 final size:51
Alignment explanation
Indices: 80902--81013 Score: 147
Period size: 52 Copynumber: 2.2 Consensus size: 51
80892 TATGTAATAG
** *
80902 TTCATAAATCATAAAAAAATATAATAAATCACATATTAATTCGTAATCATAA
1 TTCATAAAAAATAAAAAAATATAATAAATCACATAATAATTCGTAAT-ATAA
* * *
80954 TTCATAAAAAATAAATAAATATAATAAATCGCATAATAATTTGTAATATAA
1 TTCATAAAAAATAAAAAAATATAATAAATCACATAATAATTCGTAATATAA
81005 --CATAAAAAA
1 TTCATAAAAAA
81014 AATATAATCT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
49 9 0.17
51 4 0.07
52 41 0.76
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (51 bp):
TTCATAAAAAATAAAAAAATATAATAAATCACATAATAATTCGTAATATAA
Found at i:83555 original size:29 final size:29
Alignment explanation
Indices: 83513--83575 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
83503 TAATCATTAA
* * *
83513 AATTCCGTGTACCAATATACGTGCTACAT
1 AATTCCATCTACCAATAAACGTGCTACAT
*
83542 AATTCCATCTACCAATAAACGTGTTACAT
1 AATTCCATCTACCAATAAACGTGCTACAT
83571 AATTC
1 AATTC
83576 TTTAGTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.32
Consensus pattern (29 bp):
AATTCCATCTACCAATAAACGTGCTACAT
Found at i:87313 original size:76 final size:77
Alignment explanation
Indices: 87216--87366 Score: 259
Period size: 76 Copynumber: 2.0 Consensus size: 77
87206 GTTTGAACCA
* ** *
87216 AATAATGTTTCGATTTTCCTTGTTTTTTTAATTCTTTAGAAATTTTGATTATTGAAGATTTGCTT
1 AATAATGTTTCGATTTTCCTTGATTTTTTAATTCTTTAGAAATTTAAATTATTGAAAATTTGCTT
87281 TGGAGTTTTCCC
66 TGGAGTTTTCCC
87293 AATAAT-TTTCGATTTTCCTTGATTTTTTAATTCTTTAGAAATTTAAATTATTGAAAATTTGCTT
1 AATAATGTTTCGATTTTCCTTGATTTTTTAATTCTTTAGAAATTTAAATTATTGAAAATTTGCTT
87357 TGGAGTTTTC
66 TGGAGTTTTC
87367 AAGGAAATCC
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
76 64 0.91
77 6 0.09
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.53
Consensus pattern (77 bp):
AATAATGTTTCGATTTTCCTTGATTTTTTAATTCTTTAGAAATTTAAATTATTGAAAATTTGCTT
TGGAGTTTTCCC
Found at i:87393 original size:76 final size:75
Alignment explanation
Indices: 87239--87396 Score: 176
Period size: 76 Copynumber: 2.1 Consensus size: 75
87229 TTTTCCTTGT
** * * * * *
87239 TTTTTTAATTCTTTAGAAATTTTGATTATTGAAGATTTGCTTTGGAGTTTTCCCAATAATTTTCG
1 TTTTTTAATTCTTTAGAAATTTAAATTATTGAAAATTTGCTTTGGAGTTTT-CCAAGAATATCCA
** *
87304 ATTTTCCTTGA
65 ATTTGACTCGA
87315 TTTTTTAATTCTTTAGAAATTTAAATTATTGAAAATTTGCTTTGGAGTTTT-CAAGGAA-ATCCA
1 TTTTTTAATTCTTTAGAAATTTAAATTATTGAAAATTTGCTTTGGAGTTTTCCAA-GAATATCCA
87378 AGTTTGGACTCGA
65 A-TTT-GACTCGA
87391 TTTTTT
1 TTTTTT
87397 TAGAAATTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
74 6 0.09
75 5 0.07
76 58 0.84
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (75 bp):
TTTTTTAATTCTTTAGAAATTTAAATTATTGAAAATTTGCTTTGGAGTTTTCCAAGAATATCCAA
TTTGACTCGA
Found at i:87822 original size:56 final size:60
Alignment explanation
Indices: 87734--87860 Score: 174
Period size: 56 Copynumber: 2.2 Consensus size: 60
87724 ACACACACAC
* *
87734 CAGAGGAACCTCTCTACAAGTCCTCAAACACAAGGGCAT-T-CA-T-AAGTCCCTAAACA
1 CAGAGGCATCTCTCTACAAGTCCTCAAACACAAGGGCATCTACACTAAAGTCCCTAAACA
* *
87790 CAGAGGCATCTCTCT-CAAAGTCCTCAAGCACAAGGGCATCTATACTAAAGTCCCTAAACA
1 CAGAGGCATCTCTCTAC-AAGTCCTCAAACACAAGGGCATCTACACTAAAGTCCCTAAACA
87850 CAGAGGCATCT
1 CAGAGGCATCT
87861 AGACTAAAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
55 1 0.02
56 34 0.55
57 1 0.02
58 1 0.02
59 1 0.02
60 24 0.39
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (60 bp):
CAGAGGCATCTCTCTACAAGTCCTCAAACACAAGGGCATCTACACTAAAGTCCCTAAACA
Found at i:87840 original size:30 final size:30
Alignment explanation
Indices: 87777--87881 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
87767 GGGCATTCAT
**
87777 AAGTCCCTAAACAC-AGAGGCATCT-CTCTCA
1 AAGTCCC-AAACACAAGAGGCATCTAGACT-A
* *
87807 AAGTCCTCAAGCACAAG-GGCATCTATACTA
1 AAGTCC-CAAACACAAGAGGCATCTAGACTA
87837 AAGTCCCTAAACAC-AGAGGCATCTAGACTA
1 AAGTCCC-AAACACAAGAGGCATCTAGACTA
87867 AAGTCCCCAAACACA
1 AAGT-CCCAAACACA
87882 TATAACACAG
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
29 3 0.05
30 52 0.83
31 8 0.13
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.17
Consensus pattern (30 bp):
AAGTCCCAAACACAAGAGGCATCTAGACTA
Found at i:87870 original size:60 final size:56
Alignment explanation
Indices: 87751--87881 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 56
87741 ACCTCTCTAC
*
87751 AAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTCTCA
1 AAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCACTCA
* * *
87807 AAGTCCTCAAGCACAAGGGCATCTATACTAAAGTCCCTAAACACAGAGGCATCTAGACT-A
1 AAGTCCTCAAACACAAGGGCAT-T-CA-T-AAGTCCCTAAACACAGAGGCATCT-CACTCA
*
87867 AAGTCCCCAAACACA
1 AAGTCCTCAAACACA
87882 TATAACACAG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
56 21 0.33
57 1 0.02
58 1 0.02
59 1 0.02
60 38 0.59
61 2 0.03
ACGTcount: A:0.38, C:0.30, G:0.15, T:0.18
Consensus pattern (56 bp):
AAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCACTCA
Done.