Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022783.1 Corchorus olitorius cultivar O-4 contig22816, 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: 45904
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--74 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
1 CTTG
5 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
75 TTTTAAGATC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3381 original size:36 final size:37
Alignment explanation
Indices: 3313--3385 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
3303 GTTAAAGAAG
3313 GCAATATTCTAGTTGTCTTTCCCCTTACATCCCAACT
1 GCAATATTCTAGTTGTCTTTCCCCTTACATCCCAACT
3350 GCAATATTCTAGTTGTCTTT-CCCTTACATCCCAACT
1 GCAATATTCTAGTTGTCTTTCCCCTTACATCCCAACT
3386 TTTCAGGGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 16 0.44
37 20 0.56
ACGTcount: A:0.22, C:0.32, G:0.08, T:0.38
Consensus pattern (37 bp):
GCAATATTCTAGTTGTCTTTCCCCTTACATCCCAACT
Found at i:8130 original size:22 final size:22
Alignment explanation
Indices: 8096--8138 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
8086 TGGTAAGCAA
* *
8096 TTTTTTTTTTTTACTTTTTTTG
1 TTTTATTTATTTACTTTTTTTG
*
8118 TTTTATTTATTTATTTTTTTT
1 TTTTATTTATTTACTTTTTTT
8139 ACCTTTCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.86
Consensus pattern (22 bp):
TTTTATTTATTTACTTTTTTTG
Found at i:9798 original size:14 final size:14
Alignment explanation
Indices: 9779--9807 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9769 AAATGATAGC
9779 ATGTACAAGGTAGA
1 ATGTACAAGGTAGA
9793 ATGTACAAGGTAGA
1 ATGTACAAGGTAGA
9807 A
1 A
9808 CATGATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.21
Consensus pattern (14 bp):
ATGTACAAGGTAGA
Found at i:14491 original size:23 final size:23
Alignment explanation
Indices: 14465--14513 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
14455 TCGTTGAATT
14465 TTATCAATTTCTAATATATGATG
1 TTATCAATTTCTAATATATGATG
14488 TTATCAATTTCTAATATATGATG
1 TTATCAATTTCTAATATATGATG
14511 TTA
1 TTA
14514 CATGAAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (23 bp):
TTATCAATTTCTAATATATGATG
Found at i:16732 original size:47 final size:47
Alignment explanation
Indices: 16668--16783 Score: 137
Period size: 47 Copynumber: 2.5 Consensus size: 47
16658 TGATATGAGA
* * * *
16668 ACAAAGGTGGAACAAGAAAGGGT-GTGCCGCAGAAG-GGAGAAAATAGG
1 ACAAAAGTGGAAGAAGAAAGGGTAG-GCCGCAGAAGAAG-GAAAAGAGG
* * *
16715 AGAAAAGTGGAAGAAGAAGGGGTAGGTCGCAGAAGAAGGAAAAGAGG
1 ACAAAAGTGGAAGAAGAAAGGGTAGGCCGCAGAAGAAGGAAAAGAGG
16762 ACAAAAGTGGAAGAAGAAAGGG
1 ACAAAAGTGGAAGAAGAAAGGG
16784 CTCTTTTTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
47 56 0.97
48 2 0.03
ACGTcount: A:0.47, C:0.07, G:0.40, T:0.07
Consensus pattern (47 bp):
ACAAAAGTGGAAGAAGAAAGGGTAGGCCGCAGAAGAAGGAAAAGAGG
Found at i:17531 original size:17 final size:18
Alignment explanation
Indices: 17509--17560 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 18
17499 AAGCATATGG
17509 ACTATTTAT-TTTAATAT
1 ACTATTTATATTTAATAT
* *
17526 ACTATTTATATGTACTAT
1 ACTATTTATATTTAATAT
17544 A-TATTTATATTT-ATAT
1 ACTATTTATATTTAATAT
17560 A
1 A
17561 TTTATGAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 4 0.13
17 19 0.63
18 7 0.23
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (18 bp):
ACTATTTATATTTAATAT
Found at i:17649 original size:27 final size:27
Alignment explanation
Indices: 17619--17682 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
17609 CCATTGCTTT
*
17619 TGTCTCATGTCCCATGATTTTGTCCCA
1 TGTCCCATGTCCCATGATTTTGTCCCA
* *
17646 TGTCCCATGTCCCTTGCTTTTGTCCCA
1 TGTCCCATGTCCCATGATTTTGTCCCA
17673 TGTCCCATGT
1 TGTCCCATGT
17683 GCGAAAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.11, C:0.33, G:0.16, T:0.41
Consensus pattern (27 bp):
TGTCCCATGTCCCATGATTTTGTCCCA
Found at i:17651 original size:20 final size:20
Alignment explanation
Indices: 17603--17654 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
17593 TAGACGGGCT
*
17603 CCATGT-CCATTGCTTTTGTC
1 CCATGTCCCA-TGATTTTGTC
*
17623 TCATGTCCCATGATTTTGTC
1 CCATGTCCCATGATTTTGTC
17643 CCATGTCCCATG
1 CCATGTCCCATG
17655 TCCCTTGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.13, C:0.31, G:0.15, T:0.40
Consensus pattern (20 bp):
CCATGTCCCATGATTTTGTC
Found at i:19696 original size:25 final size:25
Alignment explanation
Indices: 19668--19727 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
19658 ACTGCCTTGT
* *
19668 GTCATAAAAAGGGT-TGATTTGATGG
1 GTCATAAAAA-GATATGATTTAATGG
19693 GTCA-AAGAAAGATATGATTTAATGG
1 GTCATAA-AAAGATATGATTTAATGG
*
19718 GTCATCAAAA
1 GTCATAAAAA
19728 TCTAGCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 4 0.14
25 24 0.83
26 1 0.03
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (25 bp):
GTCATAAAAAGATATGATTTAATGG
Found at i:19743 original size:34 final size:35
Alignment explanation
Indices: 19700--19770 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 35
19690 TGGGTCAAAG
*
19700 AAAGATATGATTTAATGGGTCAT-CAAAATCTAGC
1 AAAGATATGATTTAATGGGTCATAAAAAATCTAGC
* *
19734 AAAGTTATGATTTGATGGGTCATAAAAAATCTAGC
1 AAAGATATGATTTAATGGGTCATAAAAAATCTAGC
19769 AA
1 AA
19771 TGTCAAGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 21 0.64
35 12 0.36
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (35 bp):
AAAGATATGATTTAATGGGTCATAAAAAATCTAGC
Found at i:19781 original size:35 final size:34
Alignment explanation
Indices: 19708--19781 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
19698 AGAAAGATAT
* * *
19708 GATTTAATGGGTCATCAAAATCTAGCAAAGTTAT
1 GATTTAATGGGTCATAAAAATCTAGCAAAGTCAA
* *
19742 GATTTGATGGGTCATAAAAAATCTAGCAATGTCAA
1 GATTTAATGGGTCAT-AAAAATCTAGCAAAGTCAA
19777 GATTT
1 GATTT
19782 TAACTTTCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.41
35 20 0.59
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (34 bp):
GATTTAATGGGTCATAAAAATCTAGCAAAGTCAA
Found at i:19836 original size:2 final size:2
Alignment explanation
Indices: 19829--19856 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19819 TTATTATGTC
19829 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
19857 TAAATTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21105 original size:22 final size:22
Alignment explanation
Indices: 21075--21133 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
21065 TTGATAACGT
*
21075 TATCATAAACCCAACATCTTTTC
1 TATC-TAAACCCAACATCTTTGC
21098 TATCTAAAACCCAACATCTTTGC
1 TATCT-AAACCCAACATCTTTGC
*
21121 TATCTAAAACCAA
1 TATCTAAACCCAA
21134 TCTAAAACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 8 0.24
23 25 0.76
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.31
Consensus pattern (22 bp):
TATCTAAACCCAACATCTTTGC
Found at i:21107 original size:23 final size:23
Alignment explanation
Indices: 21081--21131 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
21071 ACGTTATCAT
*
21081 AAACCCAACATCTTTTCTATCTA
1 AAACCCAACATCTTTGCTATCTA
21104 AAACCCAACATCTTTGCTATCTA
1 AAACCCAACATCTTTGCTATCTA
21127 AAACC
1 AAACC
21132 AATCTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.29
Consensus pattern (23 bp):
AAACCCAACATCTTTGCTATCTA
Found at i:21138 original size:11 final size:11
Alignment explanation
Indices: 21122--21146 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21112 CATCTTTGCT
21122 ATCTAAAACCA
1 ATCTAAAACCA
21133 ATCTAAAACCA
1 ATCTAAAACCA
21144 ATC
1 ATC
21147 CAATTATGGG
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:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (11 bp):
ATCTAAAACCA
Found at i:21844 original size:2 final size:2
Alignment explanation
Indices: 21837--21891 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
21827 ATTTCTTGAC
* *
21837 TA TA TA TA TA -A TA TA -A TA TA -A TA TA TA TT TA AA 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
21876 T- TA TA -A TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
21892 TGATACTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
1 6 0.14
2 37 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:25881 original size:42 final size:42
Alignment explanation
Indices: 25822--25903 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
25812 TAAAAAAGAA
25822 TATTCAATATGGCTAATTATAACAACCTCACTCTTTTTGGCC
1 TATTCAATATGGCTAATTATAACAACCTCACTCTTTTTGGCC
25864 TATTCAATATGGCTAATTATAACAACCTCACTCTTTTTGG
1 TATTCAATATGGCTAATTATAACAACCTCACTCTTTTTGG
25904 GCCATGGGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (42 bp):
TATTCAATATGGCTAATTATAACAACCTCACTCTTTTTGGCC
Found at i:38583 original size:3 final size:3
Alignment explanation
Indices: 38575--38605 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
38565 AATTTATTCC
*
38575 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
38606 CTAGAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:38990 original size:11 final size:11
Alignment explanation
Indices: 38976--39013 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
38966 ATTCATAACA
38976 AATTTATAATT
1 AATTTATAATT
38987 AATTTATAATT
1 AATTTATAATT
38998 -ATTTGATAATT
1 AATTT-ATAATT
*
39009 TATTT
1 AATTT
39014 TATCTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:39960 original size:165 final size:165
Alignment explanation
Indices: 39695--40021 Score: 482
Period size: 165 Copynumber: 2.0 Consensus size: 165
39685 TGAAAGTACA
* * *
39695 AATAATGGAAAACTTTATGTTTTCCGATTGTATCCTTTTTCAAATATATTTCTAAATTGACATTA
1 AATAATGGAAAACTTTATGTTTTCCGATTGCACCCTTTTTCAAATATATTTATAAATTGACATTA
39760 TTAAAATTTATCATTTAAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAA
66 TTAAAATTTATCATTT-AAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAA
39825 ATTGA-TTTTCATTGATAAACATGCAAATTTCCACG
130 ATTGATTTTTCATTGATAAACATGCAAATTTCCACG
* *
39860 AATAATGGGAAACTTTATGTTTTCCGATTGCACCCTTTTTTCAAATATATTTATAAATTGCCATT
1 AATAATGGAAAACTTTATGTTTTCCGATTGCACCC-TTTTTCAAATATATTTATAAATTGACATT
** *
39925 ATTAAAATTTAGT-ATAATT-TTATTATTTA-AAAATTTCAATTTAGACCGAATTATAAGTTTGT
65 ATTAAAATTTA-TCAT--TTAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGT
* * *
39987 CAAATTGATTTTTCGTTGATGAACATGCAAATTTC
127 AAAATTGATTTTTCATTGATAAACATGCAAATTTC
40022 GTTTACTATT
Statistics
Matches: 146, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
165 72 0.49
166 71 0.49
167 1 0.01
168 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (165 bp):
AATAATGGAAAACTTTATGTTTTCCGATTGCACCCTTTTTCAAATATATTTATAAATTGACATTA
TTAAAATTTATCATTTAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAA
TTGATTTTTCATTGATAAACATGCAAATTTCCACG
Found at i:40072 original size:20 final size:20
Alignment explanation
Indices: 40035--40073 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40025 TACTATTATT
40035 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
40055 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
40074 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:40402 original size:68 final size:66
Alignment explanation
Indices: 40291--40420 Score: 156
Period size: 68 Copynumber: 1.9 Consensus size: 66
40281 GGAGGTGTGC
40291 TTACCAAAATTCAATATGGAAGTTATCAAAATTTCATGAGAAGGTTATCAAAATTGCATAGTATG
1 TTACCAAAATTCAATATGGAAGTTATCAAAATTTCATGAGAAGGTTATCAAAATTGCATAGTATG
40356 G
66 G
* * * ** *
40357 TTACCAAAATTCCAT-TGGATCAGGTTATTAAAATTTC-TTAGGAAGGTTATTGAAATTTCATAG
1 TTACCAAAATTCAATATGGA--A-GTTATCAAAATTTCATGA-GAAGGTTATCAAAATTGCATAG
40420 T
62 T
40421 GTAGTTATCA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
65 4 0.07
66 14 0.26
67 3 0.06
68 33 0.61
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (66 bp):
TTACCAAAATTCAATATGGAAGTTATCAAAATTTCATGAGAAGGTTATCAAAATTGCATAGTATG
G
Found at i:40428 original size:22 final size:22
Alignment explanation
Indices: 40240--40419 Score: 105
Period size: 22 Copynumber: 7.9 Consensus size: 22
40230 GTCTCTGTGT
* *
40240 GGTTATTAAAATTTCATAAGAT
1 GGTTATTAAAATTTCATAGGAA
*
40262 GGTTATTATAATTTCATGAGG-A
1 GGTTATTAAAATTTCAT-AGGAA
* *
40284 GGTGTGCTTACCAAAATTCAATATGGAA
1 GGT-T-ATTA--AAATTTC-ATA-GGAA
*
40312 -GTTATCAAAATTTCAT-GAGAA
1 GGTTATTAAAATTTCATAG-GAA
* * * *
40333 GGTTATCAAAATTGCATAGTAT
1 GGTTATTAAAATTTCATAGGAA
** * *
40355 GGTTACCAAAATTCCATTGGATCA
1 GGTTATTAAAATTTCATAGGA--A
*
40379 GGTTATTAAAATTTCTTAGGAA
1 GGTTATTAAAATTTCATAGGAA
*
40401 GGTTATTGAAATTTCATAG
1 GGTTATTAAAATTTCATAG
40420 TGTAGTTATC
Statistics
Matches: 121, Mismatches: 24, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
20 1 0.01
21 3 0.02
22 72 0.60
23 10 0.08
24 19 0.16
25 2 0.02
26 7 0.06
27 6 0.05
28 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGAA
Found at i:40484 original size:22 final size:22
Alignment explanation
Indices: 40452--40852 Score: 169
Period size: 22 Copynumber: 18.0 Consensus size: 22
40442 AAAGGTTTTC
* *
40452 AAAGAGATTATCAAAATGTCAT
1 AAAGAGGTTATCAAAATTTCAT
*
40474 AACGAGGTTAT-AAGAATTTCAT
1 AAAGAGGTTATCAA-AATTTCAT
** * *
40496 AGTGTGGTTAACAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
** *
40518 AAAGAGGTTA-CTACTATTCCAT
1 AAAGAGGTTATC-AAAATTTCAT
***
40540 GGGGAGGTTATCAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
** *
40562 AGTGTGGTTATCAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
* *
40584 -ATGAAGGTTATAAAAGTCTCAATTTCAT
1 AAAG-AGGTTAT-CAA-----AATTTCAT
* * *
40612 AAGGA-G-TACCAAAATTTGAT
1 AAAGAGGTTATCAAAATTTCAT
* *
40632 AGA-AGGTTATC-AAATCTCAT
1 AAAGAGGTTATCAAAATTTCAT
* * * *
40652 AGAGTGATTATCGAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
* **
40674 AGAGATCGGATTATCAAAATTAAAT
1 AAAGA--GG-TTATCAAAATTTCAT
*
40699 GGAAGA--TTATCAAAATTTCA-
1 -AAAGAGGTTATCAAAATTTCAT
*
40719 AAGCGAGGTTATCAAAATTAT-AT
1 AA-AGAGGTTATCAAAATT-TCAT
* * *
40742 AATGTGATTATCAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
* * * *
40764 AAAGGGGTCAACAAAATTTTAT
1 AAAGAGGTTATCAAAATTTCAT
* *
40786 AGAGATGTTATCAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
*
40808 AAAGAGGTTATCAAATTTTCA-
1 AAAGAGGTTATCAAAATTTCAT
* * *
40829 AAATGTGATTACCAAAATTTCAT
1 AAA-GAGGTTATCAAAATTTCAT
40852 A
1 A
40853 GTGGTATTTC
Statistics
Matches: 281, Mismatches: 70, Indels: 55
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.01
20 21 0.07
21 30 0.11
22 187 0.67
23 9 0.03
24 1 0.00
25 14 0.05
26 5 0.02
27 1 0.00
28 9 0.03
29 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (22 bp):
AAAGAGGTTATCAAAATTTCAT
Found at i:40592 original size:44 final size:43
Alignment explanation
Indices: 40544--41177 Score: 156
Period size: 44 Copynumber: 14.9 Consensus size: 43
40534 TTCCATGGGG
40544 AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATA-GA
* * * *
40588 AGGTTATAAAAGTCTCAATTTCATAAG-G-AG-TACCAAAATTTGATAGA
1 AGGTTAT-CAA-----AATTTCAT-AGTGTGGTTATCAAAATTTCATAGA
* * * *
40635 AGGTTATC-AAATCTCATAGAGTGATTATCGAAATTTCATAGA
1 AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGA
** * * * *
40677 GATCGGATTATCAAAATTAAAT-G-GAAGATTATCAAAATTTCAAAGCG
1 -A--GG-TTATCAAAATTTCATAGTG-TGGTTATCAAAATTTCATAG-A
* *
40724 AGGTTATCAAAATTAT-ATAATGTGATTATCAAAATTTCATA-A
1 AGGTTATCAAAATT-TCATAGTGTGGTTATCAAAATTTCATAGA
* * * * *
40766 AGGGGTCAACAAAATTTTATAGAGAT-GTTATCAAAATTTCATAAA
1 A--GGTTATCAAAATTTCATAGTG-TGGTTATCAAAATTTCATAGA
* * * * *
40811 GAGGTTATCAAATTTTCAAAATGTGATTACCAAAATTTCATAG-
1 -AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGA
* *
40854 TGG---T----ATTTC-TCAG-GAGGTTATCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCAT-AGTGTGGTTATCAAAATTTCATAG-A
* * ** * * ** *
40890 TGGTTA-CCAAA-TT-A-AG-AAGGTTATTAAACTTTTGTTATGG
1 AGGTTATCAAAATTTCATAGTGTGGTTATCAAA-ATTTCATA-GA
* * * * *
40930 A-GTAATCAAAATTTC--AGGGAGGATATCAAAACTTCATATGA
1 AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATA-GA
* * * *
40971 AGGTTATCAAAATTTCATAGTAT-GTAGATCAACATTTCATAGGG
1 AGGTTATCAAAATTTCATAGTGTGGT-TATCAAAATTTCATA-GA
* * * * **
41015 AGATTA-AAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGA
1 AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATA--GA
* * * *
41059 A-GTTATCAAAA--T--T--TGTAGTTATCAAGATTTCAAAAGG
1 AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTC-ATAGA
* * *
41096 AGGTTATCAAAATTTTATAG-GAAGGTTTATCAAAATTTTATA-A
1 AGGTTATCAAAATTTCATAGTG-TGG-TTATCAAAATTTCATAGA
* *
41139 TGAGGTTATCACAATTTCATAGTGTGATTATCAAAATTT
1 --AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTT
41178 TAGAGTGTGA
Statistics
Matches: 425, Mismatches: 101, Indels: 128
0.65 0.15 0.20
Matches are distributed among these distances:
34 18 0.04
35 5 0.01
36 3 0.01
37 2 0.00
38 23 0.05
39 20 0.05
40 19 0.04
41 14 0.03
42 42 0.10
43 44 0.10
44 130 0.31
45 39 0.09
46 26 0.06
47 15 0.04
48 13 0.03
49 1 0.00
50 9 0.02
51 2 0.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (43 bp):
AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGA
Found at i:41121 original size:22 final size:21
Alignment explanation
Indices: 40865--41179 Score: 96
Period size: 22 Copynumber: 15.0 Consensus size: 21
40855 GGTATTTCTC
*
40865 AGGAGGTTATCAAAATTTCAT
1 AGGAGGTTATCAAAATTTTAT
* *
40886 AGTATGGTTA-CCAAA--TTA-
1 AGGA-GGTTATCAAAATTTTAT
* * * *
40904 AGAAGGTTATTAAACTTTTGTT
1 AGGAGGTTATCAAAATTTT-AT
* *
40926 ATGGA-GTAATCAAAATTTCA-
1 A-GGAGGTTATCAAAATTTTAT
* * * *
40946 GGGAGGATATCAAAACTTCAT
1 AGGAGGTTATCAAAATTTTAT
* *
40967 ATGAAGGTTATCAAAATTTCAT
1 A-GGAGGTTATCAAAATTTTAT
* * * * *
40989 AGTATGTAGATCAACATTTCAT
1 AGGAGGT-TATCAAAATTTTAT
* * *
41011 AGGGAGATTA-AAAAATTTCAT
1 A-GGAGGTTATCAAAATTTTAT
* ** *
41032 AATGAGGTTATCAAAAAATCAT
1 -AGGAGGTTATCAAAATTTTAT
*
41054 AGGGAAGTTATCAAAA--TT-T
1 A-GGAGGTTATCAAAATTTTAT
* * * *
41073 -GTA-GTTATCAAGATTTCAAA
1 AGGAGGTTATCAAAATTT-TAT
41093 AGGAGGTTATCAAAATTTTAT
1 AGGAGGTTATCAAAATTTTAT
41114 AGGAAGGTTTATCAAAATTTTAT
1 AGG-AGG-TTATCAAAATTTTAT
* * *
41137 AATGAGGTTATCACAATTTCAT
1 -AGGAGGTTATCAAAATTTTAT
* *
41159 AGTGTGATTATCAAAATTTTA
1 AG-GAGGTTATCAAAATTTTA
41180 GAGTGTGATT
Statistics
Matches: 213, Mismatches: 56, Indels: 49
0.67 0.18 0.15
Matches are distributed among these distances:
16 9 0.04
17 7 0.03
18 6 0.03
19 6 0.03
20 15 0.07
21 34 0.16
22 111 0.52
23 23 0.11
24 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.35
Consensus pattern (21 bp):
AGGAGGTTATCAAAATTTTAT
Found at i:41184 original size:22 final size:22
Alignment explanation
Indices: 41099--41190 Score: 87
Period size: 22 Copynumber: 4.1 Consensus size: 22
41089 CAAAAGGAGG
* *
41099 TTATCAAAATTTTATAG-GAAGGT
1 TTATCAAAATTTTATAGTG--TGA
* * *
41122 TTATCAAAATTTTATAATGAGG
1 TTATCAAAATTTTATAGTGTGA
* *
41144 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTTATAGTGTGA
*
41166 TTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTTATAGTGTGA
41188 TTA
1 TTA
41191 CTAACAATTC
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
22 40 0.70
23 16 0.28
24 1 0.02
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTTATAGTGTGA
Found at i:41302 original size:45 final size:45
Alignment explanation
Indices: 41229--41317 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
41219 TTTCATAACG
* * *
41229 TGGTTATCAATATATCATATGGATGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
41274 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGTG
41318 AGATCTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:41457 original size:22 final size:22
Alignment explanation
Indices: 41413--41460 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
41403 TATCGTTATT
* *
41413 AAAATTTCATAAAAAGGTTATC
1 AAAATTTCATAAAAAGATCATC
**
41435 AAAATTTCATAATGAGATCATC
1 AAAATTTCATAAAAAGATCATC
41457 AAAA
1 AAAA
41461 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAAAAAGATCATC
Done.