Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012147.1 Corchorus capsularis cultivar CVL-1 contig12168, 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: 52979
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:543 original size:10 final size:10
Alignment explanation
Indices: 527--562 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
517 AATTTAATAT
527 GGATATTTAC
1 GGATATTTAC
* *
537 AGATATTTAT
1 GGATATTTAC
547 GGATATTTAC
1 GGATATTTAC
557 GGATAT
1 GGATAT
563 ATCGAGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:549 original size:20 final size:20
Alignment explanation
Indices: 524--562 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
514 TTTAATTTAA
524 TATGGATATTTACAGATATT
1 TATGGATATTTACAGATATT
*
544 TATGGATATTTACGGATAT
1 TATGGATATTTACAGATAT
563 ATCGAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (20 bp):
TATGGATATTTACAGATATT
Found at i:690 original size:12 final size:12
Alignment explanation
Indices: 673--711 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
663 GTACAGATAT
673 CGGATATATCGA
1 CGGATATATCGA
685 CGGATATATCGA
1 CGGATATATCGA
697 -GG---TATCGA
1 CGGATATATCGA
705 CGGATAT
1 CGGATAT
712 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:7281 original size:24 final size:24
Alignment explanation
Indices: 7249--7296 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
7239 TCCTACCAAA
7249 TCACTTTCCAACATTAGCATGCGT
1 TCACTTTCCAACATTAGCATGCGT
7273 TCACTTTCCAACATTAGCATGCGT
1 TCACTTTCCAACATTAGCATGCGT
7297 AAATGCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (24 bp):
TCACTTTCCAACATTAGCATGCGT
Found at i:12674 original size:87 final size:86
Alignment explanation
Indices: 12460--12763 Score: 450
Period size: 87 Copynumber: 3.5 Consensus size: 86
12450 TTCATTTTTT
* * *
12460 ATATCTTTTAAAACTCCCACAATTTGGCAAGATTTAGAAAATATTTTCATTATTATTAAATCTTT
1 ATATCTTCTAAAACTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
12525 ATAATTTATT-TGTTTCTTAAA
66 ATAATTTATTAT-TTTCTTAAA
* * * * * *
12546 ATA-CTCCTAAACCTTCCACAACTTGACAAGATTTAGAAAATATTATCATCATTATTATATCTTT
1 ATATCTTCTAAAACTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
12610 ATAATTTACTTATTTTCTTAAA
66 ATAATTTA-TTATTTTCTTAAA
* *
12632 ATATCTTCTAAAACTCCCACAACTTGGTAAGATTTAGAAAATATTATCATTATTATTAAATCTTC
1 ATATCTTCTAAAACTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
12697 ATAATTTATTTATTTTCTTAAA
66 ATAATTTA-TTATTTTCTTAAA
* *
12719 ATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATT
1 ATATCTTCTAAAACTCCCACAACTTGGCAAGATTTAGAAAATATT
12764 CTCTTTACAA
Statistics
Matches: 194, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
85 60 0.31
86 17 0.09
87 117 0.60
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (86 bp):
ATATCTTCTAAAACTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
ATAATTTATTATTTTCTTAAA
Found at i:16231 original size:28 final size:27
Alignment explanation
Indices: 16191--16248 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
16181 AATTCTCCCC
16191 TTTATTATTATTATTATTTATTTATT-TA
1 TTTATTATTATTATTA-TTATTT-TTGTA
16219 TTTATT-TTAATTATTATTATTTTTGTA
1 TTTATTATT-ATTATTATTATTTTTGTA
16246 TTT
1 TTT
16249 TTTAAAGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 2 0.07
27 13 0.46
28 13 0.46
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTATTATTATTATTATTATTTTTGTA
Found at i:20556 original size:56 final size:54
Alignment explanation
Indices: 20459--20566 Score: 144
Period size: 56 Copynumber: 2.0 Consensus size: 54
20449 AGTCAACAGG
* * *
20459 ATGACATGGCAGGTGATGTGGCAGAATGACGTGGCATGTTGACTCAGTCAACTA
1 ATGACATGGCAGATGACGTGGCAGAATGACGTGGCAGGTTGACTCAGTCAACTA
* * *
20513 ATGACATGGCATGATGCCGTGGCAGAGCTGACGTGGCAGGTTGACTTAGTCAAC
1 ATGACATGGCA-GATGACGTGGCAGA-ATGACGTGGCAGGTTGACTCAGTCAAC
20567 AGTCAACAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 11 0.24
55 11 0.24
56 24 0.52
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (54 bp):
ATGACATGGCAGATGACGTGGCAGAATGACGTGGCAGGTTGACTCAGTCAACTA
Found at i:21927 original size:66 final size:67
Alignment explanation
Indices: 21849--21973 Score: 180
Period size: 66 Copynumber: 1.9 Consensus size: 67
21839 ATTTGATAAT
* *
21849 TACTATAAAATTTCGATAACCTCCATATGAAATTTTAATAA-TTACACTATAAAATTTTTATGAC
1 TACTATAAAATTTCGAGAACATCCATATGAAATTTTAATAACTTACACTATAAAATTTTTATGAC
21913 GA
66 GA
* ** * *
21915 TACTATAGAATTTCGAGAACATCCATATGAAATTTTGTTAACTTTCCCTATAAAATTTT
1 TACTATAAAATTTCGAGAACATCCATATGAAATTTTAATAACTTACACTATAAAATTTT
21974 AATAACCACC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
66 36 0.71
67 15 0.29
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (67 bp):
TACTATAAAATTTCGAGAACATCCATATGAAATTTTAATAACTTACACTATAAAATTTTTATGAC
GA
Found at i:22011 original size:22 final size:22
Alignment explanation
Indices: 21937--22283 Score: 88
Period size: 22 Copynumber: 15.9 Consensus size: 22
21927 TCGAGAACAT
* **
21937 CCATATGAAATTTTGTTAACTTT
1 CCATATGAAATTTTGATAAC-CA
* * *
21960 CCCTATAAAATTTTAATAACCA
1 CCATATGAAATTTTGATAACCA
21982 CC-TAATGAAATTTTGATAACCA
1 CCAT-ATGAAATTTTGATAACCA
* * *
22004 CCATATGACATTTCGATAACCT
1 CCATATGAAATTTTGATAACCA
* * *
22026 CTCA-ATGAAATGTTGGTAATCA
1 C-CATATGAAATTTTGATAACCA
*
22048 CACATTATGAAGA-TTTGATAACCTTT
1 C-CA-TATGAA-ATTTTGATAACC--A
* * * *
22074 CGATA--AAATATTGGTAATCA
1 CCATATGAAATTTTGATAACCA
*
22094 -CATTATGAAATTTTGA-AATCATA
1 CCA-TATGAAATTTTGATAA-C-CA
*
22117 CC--ATGAAATTATGAT-ACTTCA
1 CCATATGAAATTTTGATAAC--CA
*
22138 -C-TATGAAACTTTT-ATAAACCTC
1 CCATATGAAA-TTTTGAT-AACC-A
*
22160 CCA-ATAAAATTTTGATAACC-
1 CCATATGAAATTTTGATAACCA
*
22180 TC--ATGAAATTTTGATAA-CA
1 CCATATGAAATTTTGATAACCA
* * * *
22199 TCCCTAT-AATTTTTTTATAACCT
1 -CCATATGAA-ATTTTGATAACCA
* * *
22222 CCTTATAAAATTTTGATAA-GA
1 CCATATGAAATTTTGATAACCA
* * *
22243 GCACTATTAAATTTTGATAACCC
1 CCA-TATGAAATTTTGATAACCA
22266 CCA-ATGAAATTTTGATAA
1 CCATATGAAATTTTGATAA
22284 TTAACTACAC
Statistics
Matches: 234, Mismatches: 56, Indels: 70
0.65 0.16 0.19
Matches are distributed among these distances:
18 1 0.00
19 15 0.06
20 6 0.03
21 43 0.18
22 116 0.50
23 35 0.15
24 15 0.06
25 2 0.01
26 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
CCATATGAAATTTTGATAACCA
Found at i:22068 original size:46 final size:44
Alignment explanation
Indices: 22007--22106 Score: 121
Period size: 46 Copynumber: 2.2 Consensus size: 44
21997 ATAACCACCA
* * *
22007 TATGACATTTCGATAACCTCTCAATGAAATGTTGGTAATCACACAT
1 TATGAAATTTCGATAACCTCTCAATAAAATATTGGTAAT--CACAT
* *
22053 TATGAAGATTT-GATAACCTTTCGATAAAATATTGGTAATCACAT
1 TATGAA-ATTTCGATAACCTCTCAATAAAATATTGGTAATCACAT
22097 TATGAAATTT
1 TATGAAATTT
22107 TGAAATCATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
43 4 0.08
44 11 0.23
46 29 0.60
47 4 0.08
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (44 bp):
TATGAAATTTCGATAACCTCTCAATAAAATATTGGTAATCACAT
Found at i:22195 original size:63 final size:63
Alignment explanation
Indices: 22118--22240 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
22108 GAAATCATAC
*
22118 CATGAAATTATGAT-ACTTCACTATGAAACTTTTATA-AACCTCCCAATAAAATTTTGATAACCT
1 CATGAAATTATGATAACATCACTAT--AACTTTTATATAACCTCCCAATAAAATTTTGATAACCT
* * * * **
22181 CATGAAATTTTGATAACATCCCTATAATTTTTTTATAACCTCCTTATAAAATTTTGATAA
1 CATGAAATTATGATAACATCACTATAACTTTTATATAACCTCCCAATAAAATTTTGATAA
22241 GAGCACTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 8 0.16
63 35 0.69
64 8 0.16
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (63 bp):
CATGAAATTATGATAACATCACTATAACTTTTATATAACCTCCCAATAAAATTTTGATAACCT
Found at i:22263 original size:44 final size:41
Alignment explanation
Indices: 22166--22283 Score: 121
Period size: 44 Copynumber: 2.8 Consensus size: 41
22156 CCTCCCAATA
* *
22166 AAATTTTGATAACCT-CATGAAATTTTGATAACATCCCTAT
1 AAATTTTGATAACCTCCATGAAATTTTGATAACAGCACTAT
* * * *
22206 AATTTTTTTATAACCTCCTTATAAAATTTTGATAAGAGCACTATT
1 AA-ATTTTGATAACCTCC--ATGAAATTTTGATAACAGCACTA-T
*
22251 AAATTTTGATAACCCCCAATGAAATTTTGATAA
1 AAATTTTGATAACCTCC-ATGAAATTTTGATAA
22284 TTAACTACAC
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
40 2 0.03
41 11 0.18
42 1 0.02
43 14 0.23
44 31 0.50
45 3 0.05
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (41 bp):
AAATTTTGATAACCTCCATGAAATTTTGATAACAGCACTAT
Found at i:22572 original size:22 final size:22
Alignment explanation
Indices: 22547--23149 Score: 197
Period size: 22 Copynumber: 27.9 Consensus size: 22
22537 ATGATCTCAT
22547 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * ** *
22569 TATGAAATTTTAAAAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
22591 TATGGAATGTTGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
22613 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* * *
22635 TATAAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
22657 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
22679 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * * *
22701 AATGAAATTTTTATAACCAATAC
1 TATGAAATTTTGATAACC-TTCC
* *
22724 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
22745 ATATGATATATTGATAACC-ACA
1 -TATGAAATTTTGATAACCTTCC
* * *
22767 TCATGAAAATTTAAAAACC-TCC
1 T-ATGAAATTTTGATAACCTTCC
* *
22789 GTATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * *
22812 TTTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
22834 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
22856 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
22879 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* *
22902 TATAAAATTTCGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
*
22923 TTATGAAATCTTGATAA-----C
1 -TATGAAATTTTGATAACCTTCC
* *
22941 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
22962 TATGATTTTTTGATAGCC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
22984 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
*
23006 TATGAAATTTTGATAATCC-TCT
1 TATGAAATTTTGATAA-CCTTCC
**
23028 TATGAAATTTTGA-ATA-CTGAAC
1 TATGAAATTTTGATA-ACCT-TCC
*
23050 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
23071 -CTGAAATTTTGATTA-CTCCAC
1 TATGAAATTTTGATAACCTTC-C
* * * *
23092 AATAAAAGTTTAATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
23114 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
23131 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
23150 CCCCAGAAAT
Statistics
Matches: 426, Mismatches: 112, Indels: 86
0.68 0.18 0.14
Matches are distributed among these distances:
16 11 0.03
17 12 0.03
18 3 0.01
19 2 0.00
20 15 0.04
21 23 0.05
22 285 0.67
23 72 0.17
24 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:23007 original size:44 final size:44
Alignment explanation
Indices: 22546--23040 Score: 220
Period size: 44 Copynumber: 11.3 Consensus size: 44
22536 GATGATCTCA
* * * *
22546 TTATGAAATTTTGATAACCTTCCTATGAAATTTT-AAAAACGATAC
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAGC-CT-C
* * * *** **
22591 -TATGGAATGTTGAGAACCTTTTTAT-AAATTTTTTTTAA-CCTTC
1 TTATGAAATTTTGATAACCTCCCTATGAAA-TTTTGATAAGCC-TC
* * * *
22634 TTATAAAATTTTGTTAACCTCCCTAAGGAATTTTG--AAGACCTC
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAG-CCTC
* * * *
22677 AATATGAAATTTTGATAACTTCCCAATGAAATTTTTATAA-CCAATAC
1 -TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAGCC--T-C
* * * * * *
22724 -TATGAGATGTTGATAACCTCCATATGATATATTGATAA-CCAC
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAGCCTC
* * * * * * *
22766 ATCATGAAAATTTAAAAACCTCCGTATG-AATTGTT-AGTAATCACAC
1 -TTATGAAATTTTGATAACCTCCCTATGAAATT-TTGA-TAAGC-CTC
* * * *
22812 TT-TGAAATTTTGATAATCACACTATGAAATTGTGATAA-CCTC
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAGCCTC
* * * * *
22854 GCTATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCC
1 -TTATGAAATTTTGAT-AACCTCCCTATGAAATTTTGATAAGCCT-C
* * * * *
22901 CTATAAAATTTCGATAACCTCCTTATGAAATCTTGATAA----C
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAGCCTC
* **
22941 -TA-CAAATTTTGATAACCTCCCTATGATTTTTTGAT-AGCCTC
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAGCCTC
* * *
22982 ATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATAATCCTC
1 -TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAGCCTC
23027 TTATGAAATTTTGA
1 TTATGAAATTTTGA
23041 ATACTGAACT
Statistics
Matches: 335, Mismatches: 81, Indels: 69
0.69 0.17 0.14
Matches are distributed among these distances:
37 1 0.00
38 27 0.08
39 2 0.01
40 1 0.00
41 1 0.00
42 5 0.01
43 13 0.04
44 175 0.52
45 86 0.26
46 22 0.07
47 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (44 bp):
TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAGCCTC
Found at i:23053 original size:44 final size:42
Alignment explanation
Indices: 23005--23087 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 42
22995 GTTAATCTCC
*
23005 CTATGAAATTTTGATAATCCTCTTATGAAATTTTGAATACTGAA
1 CTATGAAATTTTGAT-ATCCTC-CATGAAATTTTGAATACTGAA
* *
23049 CTATGAAATTTTGATATCCTCCCTGAAATTTTGATTACT
1 CTATGAAATTTTGATATCCTCCATGAAATTTTGAATACT
23088 CCACAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 15 0.42
43 6 0.17
44 15 0.42
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (42 bp):
CTATGAAATTTTGATATCCTCCATGAAATTTTGAATACTGAA
Found at i:23214 original size:22 final size:22
Alignment explanation
Indices: 23189--23241 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
23179 AATCAGATTT
* *
23189 TGAAAATTTGAAAACATTTTTA
1 TGAAAATTTGAAAACATATCTA
* * *
23211 TGAAATTTTGATAACCTATCTA
1 TGAAAATTTGAAAACATATCTA
23233 TGAAAATTT
1 TGAAAATTT
23242 TCTTGACCCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGAAAACATATCTA
Found at i:23378 original size:22 final size:22
Alignment explanation
Indices: 23306--23423 Score: 79
Period size: 21 Copynumber: 5.5 Consensus size: 22
23296 GCTTTGAACA
*
23306 CTATGAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAATCACT
*
23327 CCTAT-ATATTTTGATAATCTGATCT
1 -CTATGAAATTTTGATAATC--A-CT
*
23352 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
23374 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
* * *
23394 CTATCAAATTTTGGTACTC-CT
1 CTATGAAATTTTGATAATCACT
23415 -TATGAAATT
1 CTATGAAATT
23424 GAGACTTTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
19 1 0.01
20 16 0.21
21 27 0.35
22 15 0.19
23 1 0.01
24 4 0.05
25 13 0.17
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:23458 original size:22 final size:22
Alignment explanation
Indices: 23307--23480 Score: 74
Period size: 22 Copynumber: 7.7 Consensus size: 22
23297 CTTTGAACAC
*
23307 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATCTTCA
* *
23329 TAT-ATATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATCT--TC-A
* *
23353 TATGAAATTTCGATAATCACTC-
1 TATGAAATTTTGATAATC-TTCA
* *
23375 TATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAATCTTCA
* * *
23395 TATCAAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATAAT-CTTCA
*
23417 TGAAATTGAGACTTTT-ATAATCTTCA
1 T---A-TGA-AATTTTGATAATCTTCA
* *
23443 TATGAAATTTTGATAACCAT-A
1 TATGAAATTTTGATAATCTTCA
*
23464 CTATGAAATCTTGATAA
1 -TATGAAATTTTGATAA
23481 CCTCCCCATG
Statistics
Matches: 115, Mismatches: 21, Indels: 32
0.68 0.12 0.19
Matches are distributed among these distances:
20 7 0.06
21 34 0.30
22 37 0.32
23 3 0.03
24 6 0.05
25 16 0.14
26 7 0.06
27 5 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCA
Found at i:23568 original size:22 final size:22
Alignment explanation
Indices: 23443--23568 Score: 98
Period size: 22 Copynumber: 5.7 Consensus size: 22
23433 ATAATCTTCA
23443 TATGAAATTTTGATAACCAT-AC
1 TATGAAATTTTGATAACC-TCAC
* *
23465 TATGAAATCTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
23487 CATGAAATATT-AGTAACTTC-C
1 TATGAAATTTTGA-TAACCTCAC
* * *
23508 TAATGAAATTTTGTTAACCACAT
1 T-ATGAAATTTTGATAACCTCAC
*
23531 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCAC
*
23553 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
23569 TCTCTTTGAT
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
21 5 0.06
22 73 0.90
23 3 0.04
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:23749 original size:44 final size:45
Alignment explanation
Indices: 23657--23752 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 45
23647 CCTGATCCTG
*
23657 TGAAATTTTGGTAACCACACTAATGATATTTTGATAACGTCCATA
1 TGAAATTTTGGTAACCACACTAATGATATTTTGATAACCTCCATA
23702 TGAAATTTTGGTAACCACACT-ATGGA-ATTTTGATAACCTCC-TCA
1 TGAAATTTTGGTAACCACACTAAT-GATATTTTGATAACCTCCAT-A
23746 TGAAATT
1 TGAAATT
23753 ATCACAACCA
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
43 1 0.02
44 24 0.50
45 23 0.48
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (45 bp):
TGAAATTTTGGTAACCACACTAATGATATTTTGATAACCTCCATA
Found at i:23783 original size:22 final size:22
Alignment explanation
Indices: 23573--23784 Score: 101
Period size: 22 Copynumber: 9.5 Consensus size: 22
23563 TGATAATCTC
* *
23573 TTTGATAACC-TTTCTATAAAAT
1 TTTGATAACCATCT-TATGAAAT
*
23595 TGTGATAACCATAC-TATGAAAT
1 TTTGATAACCAT-CTTATGAAAT
** * * *
23617 TTCAATAAACAACTTAAGAAAT
1 TTTGATAACCATCTTATGAAAT
* * *
23639 TTTAATAACCTGATCCTGTGAAAT
1 TTTGATAACC--ATCTTATGAAAT
* * * *
23663 TTTGGTAACCACACTAATGATAT
1 TTTGATAACCA-TCTTATGAAAT
* *
23686 TTTGATAA-CGTCCATATGAAAT
1 TTTGATAACCAT-CTTATGAAAT
* * *
23708 TTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCATC-TTATGAAAT
*
23730 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCAT-CTTATGAAAT
* * *
23752 TATCACAACCATCTTATGAAAT
1 TTTGATAACCATCTTATGAAAT
23774 TTTGATAACCA
1 TTTGATAACCA
23785 CATAGAGATA
Statistics
Matches: 135, Mismatches: 43, Indels: 24
0.67 0.21 0.12
Matches are distributed among these distances:
21 2 0.01
22 100 0.74
23 17 0.13
24 16 0.12
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
TTTGATAACCATCTTATGAAAT
Found at i:23981 original size:19 final size:20
Alignment explanation
Indices: 23950--23987 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
23940 ATTGACATTT
23950 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
23969 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
23988 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:24076 original size:11 final size:11
Alignment explanation
Indices: 24062--24086 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24052 TCTAAATTTA
24062 AATTTTTAAAT
1 AATTTTTAAAT
24073 AATTTTTAAAT
1 AATTTTTAAAT
24084 AAT
1 AAT
24087 AAAATTATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTTTAAAT
Found at i:25402 original size:24 final size:24
Alignment explanation
Indices: 25370--25425 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
25360 GGAGGCTCAA
25370 ACCCGAAATTATCTGAACCATATG
1 ACCCGAAATTATCTGAACCATATG
*
25394 ACCCGAAATTATCTGATCCATATG
1 ACCCGAAATTATCTGAACCATATG
25418 ACCCGAAA
1 ACCCGAAA
25426 CTGAAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (24 bp):
ACCCGAAATTATCTGAACCATATG
Found at i:26991 original size:132 final size:132
Alignment explanation
Indices: 26820--27083 Score: 501
Period size: 132 Copynumber: 2.0 Consensus size: 132
26810 CTTATTTAAA
*
26820 AACAAACCATTAGCACGAATATAGTTGAGTTGAGTGTTTAAACAAATAAATCAAGAAACCCACTG
1 AACAAACCATTAGAACGAATATAGTTGAGTTGAGTGTTTAAACAAATAAATCAAGAAACCCACTG
26885 GCTAAATTCTAACTCTAATTATGAATATAACTATTTAAGTATGAAATTGAAATACAAGTGAGTTT
66 GCTAAATTCTAACTCTAATTATGAATATAACTATTTAAGTATGAAATTGAAATACAAGTGAGTTT
26950 TT
131 TT
*
26952 AACAAACCATTAGAACGAATATAGTTGAGTTGAGTGTTTAAACAAATAAATCAGGAAACCCACTG
1 AACAAACCATTAGAACGAATATAGTTGAGTTGAGTGTTTAAACAAATAAATCAAGAAACCCACTG
*
27017 GCTAAATTCTAACTCTAATTATGAATTTAACTATTTAAGTATGAAATTGAAATACAAGTGAGTTT
66 GCTAAATTCTAACTCTAATTATGAATATAACTATTTAAGTATGAAATTGAAATACAAGTGAGTTT
27082 TT
131 TT
27084 TTTTCTCCGT
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 129 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (132 bp):
AACAAACCATTAGAACGAATATAGTTGAGTTGAGTGTTTAAACAAATAAATCAAGAAACCCACTG
GCTAAATTCTAACTCTAATTATGAATATAACTATTTAAGTATGAAATTGAAATACAAGTGAGTTT
TT
Found at i:39134 original size:30 final size:31
Alignment explanation
Indices: 39100--39173 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
39090 ACTTATCTAC
*
39100 CATTTTCCCCCTCTGAATTTCAATCTT-GGA
1 CATTTTCCCCCTCTGAACTTCAATCTTGGGA
* *
39130 CATTTTGCCCC-CTGAACTTCAATTTTGGGA
1 CATTTTCCCCCTCTGAACTTCAATCTTGGGA
*
39160 CGTTTTACCCCCTC
1 CATTTT-CCCCCTC
39174 AACCTAACGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 13 0.36
30 18 0.50
31 4 0.11
32 1 0.03
ACGTcount: A:0.18, C:0.32, G:0.12, T:0.38
Consensus pattern (31 bp):
CATTTTCCCCCTCTGAACTTCAATCTTGGGA
Found at i:43576 original size:22 final size:22
Alignment explanation
Indices: 43548--43649 Score: 71
Period size: 22 Copynumber: 4.3 Consensus size: 22
43538 TTACTCTGGT
43548 TGATTACCTTTTTACTTTTTAC
1 TGATTACCTTTTTACTTTTTAC
* * *
43570 TGATTACCATTTTATTCTTTTAT
1 TGATTACCTTTTTACT-TTTTAC
* *
43593 TGATTACTATTTTCTGCTCCTTTTTAAC
1 TGATTAC--CTTT-T--TACTTTTT-AC
*
43621 TGATTA-CTCTTTTACTTCTTAC
1 TGATTACCT-TTTTACTTTTTAC
43643 TGATTAC
1 TGATTAC
43650 TATTTGACTC
Statistics
Matches: 60, Mismatches: 11, Indels: 17
0.68 0.12 0.19
Matches are distributed among these distances:
22 22 0.37
23 18 0.30
25 4 0.07
26 3 0.05
27 4 0.07
28 9 0.15
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.56
Consensus pattern (22 bp):
TGATTACCTTTTTACTTTTTAC
Found at i:43663 original size:21 final size:21
Alignment explanation
Indices: 43619--43704 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
43609 CTCCTTTTTA
* *
43619 ACTGATTACTCTTTTACTTCTT
1 ACTGATTACTATTTGAC-TCTT
43641 ACTGATTACTATTTGACTCTT
1 ACTGATTACTATTTGACTCTT
* * *
43662 ACTAATTACCACTTTG-CTCTC
1 ACTGATTACTA-TTTGACTCTT
* * *
43683 ATTGATTACTGTTTTACTCTT
1 ACTGATTACTATTTGACTCTT
43704 A
1 A
43705 ATGACTACCT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
20 3 0.06
21 29 0.57
22 19 0.37
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (21 bp):
ACTGATTACTATTTGACTCTT
Found at i:43733 original size:35 final size:35
Alignment explanation
Indices: 43685--43773 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
43675 TTGCTCTCAT
*
43685 TGATTACTGTTTTACTCTTAATGACTACCTTCTAC
1 TGATTACTATTTTACTCTTAATGACTACCTTCTAC
* * ** * *
43720 TGATCACTATTTTACTCTTAATGGCTGTCTTTTGC
1 TGATTACTATTTTACTCTTAATGACTACCTTCTAC
43755 TGATTACTATTTTACTCTT
1 TGATTACTATTTTACTCTT
43774 TACTGATTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.49
Consensus pattern (35 bp):
TGATTACTATTTTACTCTTAATGACTACCTTCTAC
Found at i:43810 original size:21 final size:22
Alignment explanation
Indices: 43764--43812 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
43754 CTGATTACTA
*
43764 TTTTACTCTTTACTGATTATTC
1 TTTTACTCTTTACTCATTATTC
*
43786 -TTTACTCTTTAC-CATTTTTC
1 TTTTACTCTTTACTCATTATTC
43806 TTTTACT
1 TTTTACT
43813 AATTACTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTACTCTTTACTCATTATTC
Found at i:43984 original size:31 final size:31
Alignment explanation
Indices: 43930--43995 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
43920 AATTACTGAT
43930 TTACTGATTACTATTTTTACCTTGACTCTTAA
1 TTACTGATTAC-ATTTTTACCTTGACTCTTAA
43962 TTACTGATTA-ATTTCTTACCTTGACTCTTAA
1 TTACTGATTACATTT-TTACCTTGACTCTTAA
43993 TTA
1 TTA
43996 TCAATTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 4 0.12
31 19 0.58
32 10 0.30
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (31 bp):
TTACTGATTACATTTTTACCTTGACTCTTAA
Found at i:44065 original size:55 final size:55
Alignment explanation
Indices: 44016--44145 Score: 235
Period size: 55 Copynumber: 2.4 Consensus size: 55
44006 GATTACTATG
44016 TTTTTACTTGA-TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTC
1 TTTTTAC-TGATTTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTC
*
44071 TTTTTACTGATTTACTGATTTACTGATTACCATCACTTTGATTTTGATTAATCTC
1 TTTTTACTGATTTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTC
44126 TTTTTACTGATTTACTGATT
1 TTTTTACTGATTTACTGATT
44146 ACCATCACCT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
54 3 0.04
55 70 0.96
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (55 bp):
TTTTTACTGATTTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTC
Found at i:44086 original size:8 final size:8
Alignment explanation
Indices: 44073--44098 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
44063 TTAATCTCTT
44073 TTTACTGA
1 TTTACTGA
44081 TTTACTGA
1 TTTACTGA
44089 TTTACTGA
1 TTTACTGA
44097 TT
1 TT
44099 ACCATCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (8 bp):
TTTACTGA
Found at i:44132 original size:47 final size:47
Alignment explanation
Indices: 44081--44194 Score: 167
Period size: 47 Copynumber: 2.4 Consensus size: 47
44071 TTTTTACTGA
* * * * *
44081 TTTACTGATTTACTGATTACCATCACTTTGATTTTGATTAATCTCTT
1 TTTACTGATTTACTGATTACCATCACCTTCACTCTGATTAAGCTCTT
*
44128 TTTACTGATTTACTGATTACCATCACCTTCACTCTGTTTAAGCTCTT
1 TTTACTGATTTACTGATTACCATCACCTTCACTCTGATTAAGCTCTT
44175 TTTACTGA-TTACTGATTACC
1 TTTACTGATTTACTGATTACC
44195 CCTTTTTACT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
46 12 0.20
47 49 0.80
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (47 bp):
TTTACTGATTTACTGATTACCATCACCTTCACTCTGATTAAGCTCTT
Found at i:45027 original size:51 final size:50
Alignment explanation
Indices: 44844--45403 Score: 579
Period size: 51 Copynumber: 11.1 Consensus size: 50
44834 AAGGTAACAT
* *
44844 TTTATTTACTAATTACTTAAAAATTCAATCTTTCATTCAAAGGTTAAAGC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* * ** * ** * *
44894 TTTATTTACTAATCACTCTAAAGATTCAATCTTTTACCCTAACATGACAT-
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* *
44944 TATTACTTACCAATTACTT-AAAATTCAATCTTTTATTCAAAGGTTAAATC
1 T-TTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* ** * ** * * *
44994 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTACCCTAACATGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* *
45045 TTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* * * * * *
45095 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTACCCTCACA--TGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTA--TTCAAAGGTTAAATC
* *
45146 TTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* * * * * *
45196 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTACTCAAAGATGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTAAATC
*
45247 TTTATTTACCAATTTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
1 TTTATTTACTAA-TTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* * * * * *
45298 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTACTCAAAGATGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* *
45349 TTTATTTACCAATTTACTTAAAAATTCAATCTTTTATTCAAAGGTTGAATC
1 TTTATTTACTAA-TTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
45400 TTTA
1 TTTA
45404 AGCCAAAGGT
Statistics
Matches: 406, Mismatches: 90, Indels: 27
0.78 0.17 0.05
Matches are distributed among these distances:
48 4 0.01
49 36 0.09
50 100 0.25
51 252 0.62
52 10 0.02
53 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (50 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
Found at i:45333 original size:102 final size:101
Alignment explanation
Indices: 44843--45403 Score: 953
Period size: 101 Copynumber: 5.5 Consensus size: 101
44833 AAAGGTAACA
* * * * *
44843 TTTTATTTACTAATTACTTAAAAATTCAATCTTTCATTCAAAGGTTAAAGCTTTATTTACTAATC
1 TTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
44908 ACTCTAAAGATTCAATCTTTTACCCTAACATGACAT
66 ACTCTAAAGATTCAATCTTTTACCCTAACATGACAT
*
44944 TATTACTTACCAATTACTT-AAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
1 TTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
45008 ACTCTAAAGATTCAATCTTTTACCCTAACATGACAT
66 ACTCTAAAGATTCAATCTTTTACCCTAACATGACAT
45044 TTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
1 TTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
*
45109 ACTCTAAAGATTCAATCTTTTACCCTCACATGACAT
66 ACTCTAAAGATTCAATCTTTTACCCTAACATGACAT
45145 TTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
1 TTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
* * *
45210 ACTCTAAAGATTCAATCTTTTACTCAAAGATGACAT
66 ACTCTAAAGATTCAATCTTTTACCCTAACATGACAT
*
45246 TTTTATTTACCAATTTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAAT
1 TTTTACTTACCAA-TTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAAT
* * *
45311 TACTCTAAAGATTCAATCTTTTACTCAAAGATGACAT
65 TACTCTAAAGATTCAATCTTTTACCCTAACATGACAT
* *
45348 TTTTATTTACCAATTTACTTAAAAATTCAATCTTTTATTCAAAGGTTGAATCTTTA
1 TTTTACTTACCAA-TTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTA
45404 AGCCAAAGGT
Statistics
Matches: 444, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
100 96 0.22
101 205 0.46
102 143 0.32
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (101 bp):
TTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
ACTCTAAAGATTCAATCTTTTACCCTAACATGACAT
Found at i:48465 original size:27 final size:27
Alignment explanation
Indices: 48435--48486 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
48425 CAGGTGAACA
*
48435 CAAAAATGACCAAAATGCCCCTGGGTG
1 CAAAAATGACCAAAATACCCCTGGGTG
*
48462 CAAAAATGACCAAAATACCCTTGGG
1 CAAAAATGACCAAAATACCCCTGGG
48487 CGGCCCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.15
Consensus pattern (27 bp):
CAAAAATGACCAAAATACCCCTGGGTG
Done.