Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018844.1 Corchorus olitorius cultivar O-4 contig18877, 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: 107840
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:4757 original size:3 final size:3
Alignment explanation
Indices: 4749--4847 Score: 198
Period size: 3 Copynumber: 33.0 Consensus size: 3
4739 TTTGGGTAAC
4749 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4797 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4845 ATA
1 ATA
4848 GTGAAGTATA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5674 original size:38 final size:38
Alignment explanation
Indices: 5623--5790 Score: 264
Period size: 38 Copynumber: 4.4 Consensus size: 38
5613 CTTGCAACCA
*
5623 GGCCTGCTAGCGGCCCAGCGTGCCAGGCCAGGCGCGCG
1 GGCCTGCAAGCGGCCCAGCGTGCCAGGCCAGGCGCGCG
*
5661 GGCCTACAAGCGGCCCAGCGTGCCAGGCCAGGCGCGCG
1 GGCCTGCAAGCGGCCCAGCGTGCCAGGCCAGGCGCGCG
5699 GGCCTGCAAGCGGCCCAGCGTGCCAGGCCAGGCGCGCG
1 GGCCTGCAAGCGGCCCAGCGTGCCAGGCCAGGCGCGCG
* ** *
5737 GGCCTGCAAGCGGCGCAGCGCACCAGGCCAGGCACGCG
1 GGCCTGCAAGCGGCCCAGCGTGCCAGGCCAGGCGCGCG
* *
5775 GGCCAGCAGGCGGCCC
1 GGCCTGCAAGCGGCCC
5791 GGCGCTCCGG
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 120 1.00
ACGTcount: A:0.14, C:0.40, G:0.41, T:0.05
Consensus pattern (38 bp):
GGCCTGCAAGCGGCCCAGCGTGCCAGGCCAGGCGCGCG
Found at i:5852 original size:2 final size:2
Alignment explanation
Indices: 5847--5877 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5837 GAATAATAAC
*
5847 AT AT AT AT AA 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 A
5878 ATTGGACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:7048 original size:13 final size:12
Alignment explanation
Indices: 7030--7074 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
7020 ATTTTATTAC
7030 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
7043 TGTTTTATAAAT
1 TGTTTTATAAAT
*
7055 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
7069 TGTTTT
1 TGTTTT
7075 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:10769 original size:2 final size:2
Alignment explanation
Indices: 10764--10798 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10754 TTTTCTTTGG
10764 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10799 TTGTTGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13296 original size:15 final size:16
Alignment explanation
Indices: 13272--13309 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
13262 AGAGGTTGAA
*
13272 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
13287 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
13303 AGAAAAC
1 AGAAAAC
13310 TAAACAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.61, C:0.13, G:0.11, T:0.16
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:13950 original size:33 final size:33
Alignment explanation
Indices: 13913--13978 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
13903 CAAAGGATTA
13913 GAAGTATAAGAATTTAGCTACTCATGGATTTTC
1 GAAGTATAAGAATTTAGCTACTCATGGATTTTC
13946 GAAGTATAAGAATTTAGCTACTCATGGATTTTC
1 GAAGTATAAGAATTTAGCTACTCATGGATTTTC
13979 CAAATCCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (33 bp):
GAAGTATAAGAATTTAGCTACTCATGGATTTTC
Found at i:19718 original size:31 final size:27
Alignment explanation
Indices: 19683--19749 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
19673 CTAAAACAAA
*
19683 TTTTTTTTCGACGCAAAAACTAAACAGGTT
1 TTTTTTTTTGACGCAAAAAC--AA-AGGTT
* *
19713 TTTTTTTCTTGACGCTAAAACAAAGTTT
1 TTTTTTT-TTGACGCAAAAACAAAGGTT
19741 TTTTTTTTT
1 TTTTTTTTT
19750 AAAAACGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 2 0.06
28 11 0.33
29 2 0.06
30 7 0.21
31 11 0.33
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.49
Consensus pattern (27 bp):
TTTTTTTTTGACGCAAAAACAAAGGTT
Found at i:19795 original size:23 final size:22
Alignment explanation
Indices: 19747--19787 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19737 GTTTTTTTTT
*
19747 TTTAAAAACGCAACAACAAAAA
1 TTTAAAAACGCAACAAAAAAAA
19769 TTTAAAAACGCAA-AAAAAA
1 TTTAAAAACGCAACAAAAAA
19788 TCAATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.66, C:0.15, G:0.05, T:0.15
Consensus pattern (22 bp):
TTTAAAAACGCAACAAAAAAAA
Found at i:20196 original size:15 final size:16
Alignment explanation
Indices: 20176--20213 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
20166 AGAGGTTGAA
*
20176 AGAAAACAGTTAAAC-
1 AGAAAACAATTAAACT
*
20191 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
20207 AGAAAAC
1 AGAAAAC
20214 TAAACAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.61, C:0.13, G:0.11, T:0.16
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:24081 original size:56 final size:56
Alignment explanation
Indices: 23995--24311 Score: 469
Period size: 56 Copynumber: 5.9 Consensus size: 56
23985 TATACAGAAT
* *
23995 AGTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAAGATTAG
1 AGTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTAAAGATTAG
*
24051 AGTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACAGTCCTTTTAAAGATTAG
1 AGTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTAAAGATTAG
*
24107 AGTGAATTGGAAGACAATTCAAAGGATAAGAGGAAGACGGTCCTTTTAAAGATTAG
1 AGTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTAAAGATTAG
24163 AGTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTT-AAG---A-
1 AGTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTAAAGATTAG
*
24214 A-TGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT----A-T-G
1 AGTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTAAAGATTAG
* * * *
24263 AGTGGATTGGAAGACAGTTCAAAGGATAAGAGGAGGACGGTCCTTTTAA
1 AGTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTAA
24312 GGTTAAATTG
Statistics
Matches: 245, Mismatches: 10, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
49 1 0.00
50 86 0.35
51 1 0.00
52 1 0.00
55 3 0.01
56 153 0.62
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.23
Consensus pattern (56 bp):
AGTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTAAAGATTAG
Found at i:24703 original size:29 final size:28
Alignment explanation
Indices: 24609--24706 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 28
24599 ATTTACTTTT
*
24609 ATTTTGGTCATTTTGCTTGACCAAGGGC
1 ATTTTGGTCATTTTGCTAGACCAAGGGC
* *
24637 ATTTTGGTCATTTTG-TACATCCATGGGC
1 ATTTTGGTCATTTTGCTAGA-CCAAGGGC
* * *
24665 ATTTTGGTCATTTTGCTAGGCTAGGGGGC
1 ATTTTGGTCATTTTGCTAGACCA-AGGGC
24694 ATTTTGGTCATTT
1 ATTTTGGTCATTT
24707 CAGGGACACC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 39 0.65
29 19 0.32
ACGTcount: A:0.16, C:0.15, G:0.26, T:0.43
Consensus pattern (28 bp):
ATTTTGGTCATTTTGCTAGACCAAGGGC
Found at i:26209 original size:39 final size:39
Alignment explanation
Indices: 26166--26298 Score: 212
Period size: 39 Copynumber: 3.4 Consensus size: 39
26156 TTTCAAGACC
*
26166 TAGCTATATGCATTTTTCAATCCACTACAACACAAAACT
1 TAGCCATATGCATTTTTCAATCCACTACAACACAAAACT
*
26205 TAGCTATATGCATTTTTCAATCCACTACAACACAAAACT
1 TAGCCATATGCATTTTTCAATCCACTACAACACAAAACT
* * * *
26244 TAGCCATATGCATTTTTCAATCCACTGCATCTCAAAACC
1 TAGCCATATGCATTTTTCAATCCACTACAACACAAAACT
26283 TAGCCATATGCATTTT
1 TAGCCATATGCATTTT
26299 GCAGTTCACT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (39 bp):
TAGCCATATGCATTTTTCAATCCACTACAACACAAAACT
Found at i:34421 original size:22 final size:21
Alignment explanation
Indices: 34381--34443 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
34371 ATTGAATAGA
* * *
34381 ACTTCCATATGAAACTTTGTT
1 ACTTCCCTATAAAATTTTGTT
34402 GACTTCCCTATAAAATTTTGTT
1 -ACTTCCCTATAAAATTTTGTT
*
34424 ACCCTCCCTATAAAATTTTG
1 A-CTTCCCTATAAAATTTTG
34444 AAAACCTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (21 bp):
ACTTCCCTATAAAATTTTGTT
Found at i:34722 original size:86 final size:85
Alignment explanation
Indices: 34544--34773 Score: 212
Period size: 85 Copynumber: 2.7 Consensus size: 85
34534 AAGCGCACAT
* * ** * * * * * **
34544 TATGAAAATTTGATAACGTTTCGATAAAATATTGGTAATCACATTATGAAATTTTGATAACCATA
1 TATGAAATTTTGATAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATTTTGACCACC-T-
*
34609 CCATGAAATTGTGATAATATCAC
64 -CATGAAATTGTGATAACATCAC
* * *
34632 TATGAAATTTTTATAAAGCTCCCTATAAAATTTTGATAACTTCCATT-TGAAATTTTGACCACCT
1 TATGAAATTTTGAT-AACCTCCCTATAAAATTTTGATAACCT-CATTATGAAATTTTGACCACCT
* *
34696 CATGAAATTTTGATAACCATC-T
64 CATGAAATTGTGATAA-CATCAC
* * *
34718 TATGAAATTTTGATAACCTCCCTATGAATTTTTGATAACCTCTTTATGAAATTTTG
1 TATGAAATTTTGATAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATTTTG
34774 TTAACCTTCT
Statistics
Matches: 115, Mismatches: 23, Indels: 11
0.77 0.15 0.07
Matches are distributed among these distances:
84 3 0.03
85 33 0.29
86 28 0.24
87 3 0.03
88 13 0.11
89 31 0.27
90 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (85 bp):
TATGAAATTTTGATAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATTTTGACCACCTCA
TGAAATTGTGATAACATCAC
Found at i:34751 original size:63 final size:63
Alignment explanation
Indices: 34658--34797 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 63
34648 AGCTCCCTAT
* * * *
34658 AAAATTTTGATAACTTCCATTTGAAATTTTGACCACCTC-ATGAAATTTTGATAACCATCTTAT
1 AAAATTTTGATAACCTCCATATGAAATTTTGACAACCTCTATGAAATTTTGATAACCATC-TAC
* * * * * *
34721 GAAATTTTGATAACCTCCCTATGAATTTTTGATAACCTCTTTATGAAATTTTGTTAACCTTCTAC
1 AAAATTTTGATAACCTCCATATGAAATTTTGACAACCTC--TATGAAATTTTGATAACCATCTAC
34786 AAAATTTTGATA
1 AAAATTTTGATA
34798 CGAACATTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 32 0.51
65 13 0.21
66 18 0.29
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (63 bp):
AAAATTTTGATAACCTCCATATGAAATTTTGACAACCTCTATGAAATTTTGATAACCATCTAC
Found at i:34773 original size:44 final size:44
Alignment explanation
Indices: 34414--35435 Score: 323
Period size: 44 Copynumber: 23.2 Consensus size: 44
34404 CTTCCCTATA
* * * * *
34414 AAATTTTGTTACCCTCCCTATAAAATTTTGAAAACCTCAATATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCATTATG
* * *
34458 AAATTTTAATAACCACCCAATGAAATTTTGATAA--TCATCCTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAT--TATG
* * * * *
34502 AAATTTTGATAACTTGCCAATGAAATGTTGATAAGCGCACATTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAA-C-CTCATTATG
* * ** * * * * * *
34548 AAAATTTGATAACGTTTCGATAAAATATTGGTAATCACATTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCATTATG
* * ** *
34592 AAATTTTGATAACCATACC-ATGAAATTGTGATAATATCACTATG
1 AAATTTTGATAACC-TCCCTATGAAATTTTGATAACCTCATTATG
* * * *
34636 AAATTTTTATAAAGCTCCCTATAAAATTTTGATAACTTCCATT-TG
1 AAATTTTGAT-AACCTCCCTATGAAATTTTGATAACCT-CATTATG
**
34681 AAATTTTGACCACCT--C-ATGAAATTTTGATAACCATC-TTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCATTATG
* *
34722 AAATTTTGATAACCTCCCTATGAATTTTTGATAACCTCTTTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCATTATG
* * ** **
34766 AAATTTTGTTAACCT-TCTACAAAATTTTGAT-ACGAACA-T-TG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAAC-CTCATTATG
* **
34807 AAATTTTGAT-A-C-CCCTAAATGAAATTTTGATGATTAGCTACACCATG
1 AAATTTTGATAACCTCCCT--ATGAAATTTTGAT-A--ACCT-CATTATG
** * * * * ** *
34854 AAATTACGACAA-CTAGCCTATGAAA-TTTGTTAATCTCCCTATA
1 AAATTTTGATAACCT-CCCTATGAAATTTTGATAACCTCATTATG
* * * * * * *
34897 AAATTTTGAGAACCACACTATCAAATTTTGTTAATCTCACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCATTATG
* ** * * ** ** *
34941 AAATTTTGATAAACTCATTATGAAATTTTAATTACCAAACAATA
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCATTATG
** * * * * ** * *
34985 AAAACTTGATAACAT-TCTAATAAAATTTTGGTAACGACACTATA
1 AAATTTTGATAACCTCCCT-ATGAAATTTTGATAACCTCATTATG
* * *
35029 AAATTTTTATAACCTCTCCCTATG-AA-----AT-ACCACACTATG
1 AAATTTTGATAA-C-CTCCCTATGAAATTTTGATAACCTCATTATG
* * * * **
35068 AAAATTTGACAATCTCCCTATGAAATTTCGATAACCTCCCTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCATTATG
* *
35112 AAATTTTGATAATGTCACTCTATCTCACTATGAAATTTTGATAATCTTC-CTATG
1 AAATTTTGAT-A----AC-C--TC-C-CTATGAAATTTTGATAA-CCTCATTATG
** ** * * *
35166 AAATTTTGATAACGACATTATGAAATTTCGATGACCTC-TATATA
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAT-TATG
* * * * * * *
35210 AAATATCGATAATCGT-GCTATGAAATTTTGTTAGCCTCA--CTG
1 AAATTTTGATAA-CCTCCCTATGAAATTTTGATAACCTCATTATG
*** * * ** *
35252 AAATTTTGATAA-CTAAAGTATGAAAATTT-AGTAAGCTCCCTGTG
1 AAATTTTGATAACCT-CCCTATGAAATTTTGA-TAACCTCATTATG
* * * * * * *
35296 AAATTTTGATATCATTCATATGAAATTCTGATAACATCCTTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCATTATG
* * * *
35340 AAATTTTAATAACCTCCATATGAAA-TTTGATAACATTCA-TAGG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAAC-CTCATTATG
* * *
35383 AAATTTTAATAACCTCCCTATGAAATTTTGATAACATC-TCATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCATTATG
*
35426 AAATTGTGAT
1 AAATTTTGAT
35436 GACTACACAC
Statistics
Matches: 724, Mismatches: 187, Indels: 135
0.69 0.18 0.13
Matches are distributed among these distances:
37 9 0.01
38 2 0.00
39 21 0.03
40 5 0.01
41 53 0.07
42 34 0.05
43 89 0.12
44 361 0.50
45 40 0.06
46 38 0.05
47 16 0.02
48 11 0.02
49 3 0.00
50 4 0.01
52 2 0.00
53 2 0.00
54 31 0.04
55 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCATTATG
Found at i:34778 original size:22 final size:21
Alignment explanation
Indices: 34436--34797 Score: 160
Period size: 22 Copynumber: 16.5 Consensus size: 21
34426 CCTCCCTATA
* *
34436 AAATTTTGAAAACCTCAATATG
1 AAATTTTGATAACCTC-TTATG
* * **
34458 AAATTTTAATAACCACCCAATG
1 AAATTTTGATAACC-TCTTATG
* *
34480 AAATTTTGATAATCATCCTATG
1 AAATTTTGATAA-CCTCTTATG
* **
34502 AAATTTTGATAACTTGCCAATG
1 AAATTTTGATAACCT-CTTATG
* *
34524 AAATGTTGATAAGCGCACATTATG
1 AAATTTTGATAA-C-CTC-TTATG
* * *
34548 AAAATTTGATAACGT-TTCGATA
1 AAATTTTGATAACCTCTT--ATG
* * * *
34570 AAATATTGGTAATCACATTATG
1 AAATTTTGATAACCTC-TTATG
*
34592 AAATTTTGATAACCATAC-CATG
1 AAATTTTGATAACC-T-CTTATG
* ** *
34614 AAATTGTGATAATATCACTATG
1 AAATTTTGATAACCTC-TTATG
* * * *
34636 AAATTTTTATAAAGCTCCCTATA
1 AAATTTTGAT-AACCT-CTTATG
*
34659 AAATTTTGATAACTTCCATT-TG
1 AAATTTTGATAACCT-C-TTATG
**
34681 AAATTTTGACCACCTC--ATG
1 AAATTTTGATAACCTCTTATG
34700 AAATTTTGATAACCATCTTATG
1 AAATTTTGATAACC-TCTTATG
*
34722 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCT-CTTATG
*
34744 AATTTTTGATAACCTCTTTATG
1 AAATTTTGATAACCTC-TTATG
* **
34766 AAATTTTGTTAACCT-TCTACA
1 AAATTTTGATAACCTCT-TATG
34787 AAATTTTGATA
1 AAATTTTGATA
34798 CGAACATTGA
Statistics
Matches: 256, Mismatches: 60, Indels: 49
0.70 0.16 0.13
Matches are distributed among these distances:
19 14 0.05
20 6 0.02
21 18 0.07
22 179 0.70
23 22 0.09
24 17 0.07
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (21 bp):
AAATTTTGATAACCTCTTATG
Found at i:34957 original size:22 final size:22
Alignment explanation
Indices: 34431--34969 Score: 147
Period size: 22 Copynumber: 24.5 Consensus size: 22
34421 GTTACCCTCC
*
34431 CTATAAAATTTTGA-AAACCTCA
1 CTATGAAATTTTGATAAA-CTCA
* * * * *
34453 ATATGAAATTTTAATAACCACC
1 CTATGAAATTTTGATAAACTCA
* *
34475 CAATGAAATTTTGATAATCATC-
1 CTATGAAATTTTGATAAAC-TCA
34497 CTATGAAATTTTGAT-AACTTGC-
1 CTATGAAATTTTGATAAAC-T-CA
* * * *
34519 CAATGAAATGTTGATAAGCGCA
1 CTATGAAATTTTGATAAACTCA
* **
34541 CATTATGAAAATTTGAT-AACGTTT
1 C--TATGAAATTTTGATAAAC-TCA
* * * * * *
34565 CGATAAAATATTGGTAATCACA
1 CTATGAAATTTTGATAAACTCA
* *
34587 TTATGAAATTTTGATAACCAT-A
1 CTATGAAATTTTGATAAAC-TCA
* *
34609 CCATGAAATTGTGATAATA-TCA
1 CTATGAAATTTTGATAA-ACTCA
* *
34631 CTATGAAATTTTTATAAAGCTCC
1 CTATGAAATTTTGATAAA-CTCA
*
34654 CTATAAAATTTTGAT-AACTTC-
1 CTATGAAATTTTGATAAAC-TCA
* ** *
34675 CATTTGAAATTTTGA-CCAC-CT
1 C-TATGAAATTTTGATAAACTCA
34696 C-ATGAAATTTTGAT-AAC-CA
1 CTATGAAATTTTGATAAACTCA
* *
34715 TCTTATGAAATTTTGATAACCTCC
1 -C-TATGAAATTTTGATAAACTCA
* * *
34739 CTATGAATTTTTGATAACCTCT
1 CTATGAAATTTTGATAAACTCA
* * * *
34761 TTATGAAATTTTGTTAACCT-T
1 CTATGAAATTTTGATAAACTCA
**
34782 CTACAAAATTTTGATACGAA--CA
1 CTATGAAATTTTGATA--AACTCA
*
34804 -T-TGAAATTTTGAT--AC-CC
1 CTATGAAATTTTGATAAACTCA
*
34821 CTAAATGAAATTTTGATGATTAGCTACA
1 CT--ATGAAATTTTGAT-A--AACT-CA
* ** *
34849 CCATGAAATTACGA-CAACT-A
1 CTATGAAATTTTGATAAACTCA
* * *
34869 GCCTATGAAA-TTTGTTAATCTCC
1 --CTATGAAATTTTGATAAACTCA
* * * *
34892 CTATAAAATTTTGAGAACCACA
1 CTATGAAATTTTGATAAACTCA
* * *
34914 CTATCAAATTTTGTTAATCTCA
1 CTATGAAATTTTGATAAACTCA
34936 CTATGAAATTTTGATAAACTCA
1 CTATGAAATTTTGATAAACTCA
*
34958 TTATGAAATTTT
1 CTATGAAATTTT
34970 AATTACCAAA
Statistics
Matches: 371, Mismatches: 102, Indels: 88
0.66 0.18 0.16
Matches are distributed among these distances:
16 1 0.00
17 1 0.00
18 1 0.00
19 14 0.04
20 13 0.04
21 44 0.12
22 243 0.65
23 28 0.08
24 13 0.04
26 11 0.03
28 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAAACTCA
Found at i:35122 original size:22 final size:22
Alignment explanation
Indices: 35063--35123 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
35053 AAATACCACA
* * *
35063 CTATGAAAATTTGACAATCTCC
1 CTATGAAATTTTGATAACCTCC
*
35085 CTATGAAATTTCGATAACCTCC
1 CTATGAAATTTTGATAACCTCC
35107 CTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
35124 TGTCACTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTCC
Found at i:35164 original size:22 final size:21
Alignment explanation
Indices: 35139--35435 Score: 136
Period size: 22 Copynumber: 13.7 Consensus size: 21
35129 CTCTATCTCA
35139 CTATGAAATTTTGATAATCTTC
1 CTATGAAATTTTGATAA-CTTC
**
35161 CTATGAAATTTTGATAACGAC
1 CTATGAAATTTTGATAACTTC
* * * *
35182 ATTATGAAATTTCGATGACCTC
1 -CTATGAAATTTTGATAACTTC
* * * * * *
35204 TATATAAAATATCGATAATCGTG
1 -CTATGAAATTTTGATAA-CTTC
* * *
35227 CTATGAAATTTTGTTAGCCT-
1 CTATGAAATTTTGATAACTTC
**
35247 C-ACTGAAATTTTGATAACTAAA
1 CTA-TGAAATTTTGATAACT-TC
* * *
35269 GTATGAAAATTT-AGTAAGCTCC
1 CTATGAAATTTTGA-TAA-CTTC
* *
35291 CTGTGAAATTTTGATATCATTC
1 CTATGAAATTTTGATAAC-TTC
* * *
35313 ATATGAAATTCTGATAACATC
1 CTATGAAATTTTGATAACTTC
* *
35334 CTTATGAAATTTTAATAACCTC
1 C-TATGAAATTTTGATAACTTC
35356 CATATGAAA-TTTGATAACATTC
1 C-TATGAAATTTTGATAAC-TTC
* * * *
35378 ATAGGAAATTTTAATAACCTCC
1 CTATGAAATTTTGATAA-CTTC
*
35400 CTATGAAATTTTGATAACAT-
1 CTATGAAATTTTGATAACTTC
*
35420 CTCATGAAATTGTGAT
1 CT-ATGAAATTTTGAT
35436 GACTACACAC
Statistics
Matches: 204, Mismatches: 56, Indels: 31
0.70 0.19 0.11
Matches are distributed among these distances:
19 1 0.00
20 16 0.08
21 35 0.17
22 145 0.71
23 7 0.03
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
CTATGAAATTTTGATAACTTC
Found at i:35328 original size:66 final size:65
Alignment explanation
Indices: 35250--35387 Score: 152
Period size: 66 Copynumber: 2.1 Consensus size: 65
35240 TTAGCCTCAC
* * * * * *
35250 TGAAATTTTGATAAC-TAAAGTATGAAAATTTAGTAAGCTCCCTGTGAAATTTTGATATCATTCA
1 TGAAATTCTGATAACAT-AAGTATGAAAATTTAATAACCTCCATATGAAA-TTTGATAACATTCA
35314 TA
64 TA
*** *
35316 TGAAATTCTGATAACATCCTTATGAAATTTTAATAACCTCCATATGAAATTTGATAACATTCATA
1 TGAAATTCTGATAACATAAGTATGAAAATTTAATAACCTCCATATGAAATTTGATAACATTCATA
*
35381 GGAAATT
1 TGAAATT
35388 TTAATAACCT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
65 21 0.35
66 38 0.63
67 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (65 bp):
TGAAATTCTGATAACATAAGTATGAAAATTTAATAACCTCCATATGAAATTTGATAACATTCATA
Found at i:35386 original size:65 final size:66
Alignment explanation
Indices: 35270--35417 Score: 181
Period size: 65 Copynumber: 2.3 Consensus size: 66
35260 ATAACTAAAG
* * * * * * * *
35270 TATGAAAATTTAGTAAGCTCCCTGTGAAATTTTGATATCATTCATATGAAATTCTGATAACATCC
1 TATGAAATTTTAATAACCTCCATATGAAATTTTGATAACATTCATAGGAAATTCTAATAACATCC
*
35335 T
66 C
* *
35336 TATGAAATTTTAATAACCTCCATATGAAA-TTTGATAACATTCATAGGAAATTTTAATAACCTCC
1 TATGAAATTTTAATAACCTCCATATGAAATTTTGATAACATTCATAGGAAATTCTAATAACATCC
35400 C
66 C
*
35401 TATGAAATTTTGATAAC
1 TATGAAATTTTAATAAC
35418 ATCTCATGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
65 46 0.66
66 24 0.34
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (66 bp):
TATGAAATTTTAATAACCTCCATATGAAATTTTGATAACATTCATAGGAAATTCTAATAACATCC
C
Found at i:35429 original size:43 final size:43
Alignment explanation
Indices: 35294--35430 Score: 170
Period size: 43 Copynumber: 3.2 Consensus size: 43
35284 AAGCTCCCTG
* * * * * *
35294 TGAAATTTTGATATCATTCATATGAAATTCTGATAACATCCTTA
1 TGAAATTTTAATAACCTCCATATGAAATTTTGATAACAT-CTCA
35338 TGAAATTTTAATAACCTCCATATGAAA-TTTGATAACAT-TCA
1 TGAAATTTTAATAACCTCCATATGAAATTTTGATAACATCTCA
*
35379 TAGGAAATTTTAATAACCTCCCTATGAAATTTTGATAACATCTCA
1 T--GAAATTTTAATAACCTCCATATGAAATTTTGATAACATCTCA
35424 TGAAATT
1 TGAAATT
35431 GTGATGACTA
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
41 3 0.04
43 41 0.50
44 34 0.41
45 4 0.05
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (43 bp):
TGAAATTTTAATAACCTCCATATGAAATTTTGATAACATCTCA
Found at i:35453 original size:24 final size:22
Alignment explanation
Indices: 35426--35475 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
35416 ACATCTCATG
35426 AAATTGTGATGACTACACACTATA
1 AAATTGTGATGAC--CACACTATA
* *
35450 AAATTTTGATTACCACACTATA
1 AAATTGTGATGACCACACTATA
35472 AAAT
1 AAAT
35476 CTTAGTAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.54
24 11 0.46
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (22 bp):
AAATTGTGATGACCACACTATA
Found at i:35486 original size:22 final size:21
Alignment explanation
Indices: 35441--35517 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 21
35431 GTGATGACTA
* *
35441 CACACTATAAAATTTTGATTAC
1 CACACTATAAAATTTAG-TAAC
35463 CACACTATAAAATCTTAGTAA-
1 CACACTATAAAAT-TTAGTAAC
*
35484 C-CA-TATAAATTTTAGTAAC
1 CACACTATAAAATTTAGTAAC
* *
35503 CAAACTATGAAATTT
1 CACACTATAAAATTT
35518 CGATAACCTC
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 7 0.16
19 8 0.18
20 3 0.07
21 9 0.20
22 15 0.33
23 3 0.07
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (21 bp):
CACACTATAAAATTTAGTAAC
Found at i:40264 original size:2 final size:2
Alignment explanation
Indices: 40257--40282 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40247 CCATTTTCGG
40257 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
40283 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:51831 original size:21 final size:21
Alignment explanation
Indices: 51807--51902 Score: 149
Period size: 21 Copynumber: 4.6 Consensus size: 21
51797 CTTAGGCAAT
*
51807 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
51828 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
51849 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
51870 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
51891 TCCAATGAGCTT
1 TCCAATGAGCTT
51903 CTAGCATCTT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 3 0.04
21 67 0.96
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:58207 original size:21 final size:21
Alignment explanation
Indices: 58183--58299 Score: 182
Period size: 21 Copynumber: 5.6 Consensus size: 21
58173 CTTAGGCAAT
*
58183 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
58204 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
58225 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
58246 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
58267 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
58288 TCCAATGAGCTT
1 TCCAATGAGCTT
58300 CTAGCATCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 3 0.03
21 88 0.97
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:60892 original size:15 final size:14
Alignment explanation
Indices: 60854--60893 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
60844 CACCACAGAA
60854 AAAAGAAAGAAAAAG
1 AAAAG-AAGAAAAAG
*
60869 AAAAAAAGAAAAAG
1 AAAAGAAGAAAAAG
60883 ACAAAGAAGAA
1 A-AAAGAAGAA
60894 GAAAAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAAG
Found at i:67095 original size:3 final size:3
Alignment explanation
Indices: 67089--67148 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
67079 ATGACAAAAA
67089 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
67137 AAG AAG AAG AAG
1 AAG AAG AAG AAG
67149 GAACCTGATG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:69769 original size:11 final size:11
Alignment explanation
Indices: 69755--69779 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
69745 AAAATATTTC
69755 AAAAATAAAAA
1 AAAAATAAAAA
69766 AAAAATAAAAA
1 AAAAATAAAAA
69777 AAA
1 AAA
69780 TTTTACGACC
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:71247 original size:33 final size:32
Alignment explanation
Indices: 71188--71273 Score: 84
Period size: 33 Copynumber: 2.7 Consensus size: 32
71178 CTAAATCTGT
* * * *
71188 TTTAGATGTTGTTTGCGATAATACTAAACCTAA
1 TTTAGGTGTTGTTTGTGATGACACTAAACCT-A
* *
71221 TTT-GAGTGTTGTTTGTGATGACACTAAATCTG
1 TTTAG-GTGTTGTTTGTGATGACACTAAACCTA
*
71253 TTTAGGTGCTGTTTGTGATGA
1 TTTAGGTGTTGTTTGTGATGA
71274 AACAAATTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 19 0.43
33 25 0.57
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.43
Consensus pattern (32 bp):
TTTAGGTGTTGTTTGTGATGACACTAAACCTA
Found at i:71268 original size:32 final size:32
Alignment explanation
Indices: 71230--71320 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
71220 ATTTGAGTGT
*
71230 TGTTTGTGATGACACTAAATCTGTTTAGG-TGC
1 TGTTTGTGATGAAAC-AAATCTGTTTAGGATGC
*
71262 TGTTTGTGATGAAACAAATTCTGTTTTGGATGC
1 TGTTTGTGATGAAACAAA-TCTGTTTAGGATGC
**
71295 TAATTGTGATGTAAACAAATCTGTTT
1 TGTTTGTGATG-AAACAAATCTGTTT
71321 TGGTTGATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.06
32 23 0.44
33 19 0.37
34 7 0.13
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (32 bp):
TGTTTGTGATGAAACAAATCTGTTTAGGATGC
Found at i:71305 original size:33 final size:31
Alignment explanation
Indices: 71233--71324 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 31
71223 TGAGTGTTGT
* * **
71233 TTGTGATGACACTAAATCTGTTTAGGTGCTGT
1 TTGTGATGAAAC-AAATCTGTTTTGGTGCTAA
71265 TTGTGATGAAACAAATTCTGTTTTGGATGCTAA
1 TTGTGATGAAACAAA-TCTGTTTTGG-TGCTAA
71298 TTGTGATGTAAACAAATCTGTTTTGGT
1 TTGTGATG-AAACAAATCTGTTTTGGT
71325 TGATCATAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
31 3 0.06
32 21 0.40
33 22 0.42
34 7 0.13
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (31 bp):
TTGTGATGAAACAAATCTGTTTTGGTGCTAA
Found at i:73156 original size:21 final size:21
Alignment explanation
Indices: 73130--73242 Score: 149
Period size: 21 Copynumber: 5.4 Consensus size: 21
73120 TGCTAGAAGT
73130 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
73151 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* * *
73172 TCATTGGAGCAGGTTACAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
73193 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
73214 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
73235 TCATTGGA
1 TCATTGGA
73243 AATGCCTAAG
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 1 0.01
21 82 0.99
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:74304 original size:10 final size:11
Alignment explanation
Indices: 74284--74308 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
74274 AAATTATTTC
74284 AAAAATAAAAA
1 AAAAATAAAAA
74295 AAAAATAAAAA
1 AAAAATAAAAA
74306 AAA
1 AAA
74309 TTTTCGACCA
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:75776 original size:33 final size:32
Alignment explanation
Indices: 75717--75802 Score: 84
Period size: 33 Copynumber: 2.7 Consensus size: 32
75707 CTAAATCTGT
* * * *
75717 TTTAGATGTTGTTTGCGATAATACTAAACCTAA
1 TTTAGGTGTTGTTTGTGATGACACTAAACCT-A
* *
75750 TTT-GAGTGTTGTTTGTGATGACACTAAATCTG
1 TTTAG-GTGTTGTTTGTGATGACACTAAACCTA
*
75782 TTTAGGTGCTGTTTGTGATGA
1 TTTAGGTGTTGTTTGTGATGA
75803 AACAAATTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 19 0.43
33 25 0.57
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.43
Consensus pattern (32 bp):
TTTAGGTGTTGTTTGTGATGACACTAAACCTA
Found at i:75797 original size:32 final size:32
Alignment explanation
Indices: 75759--75849 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
75749 ATTTGAGTGT
*
75759 TGTTTGTGATGACACTAAATCTGTTTAGG-TGC
1 TGTTTGTGATGAAAC-AAATCTGTTTAGGATGC
*
75791 TGTTTGTGATGAAACAAATTCTGTTTTGGATGC
1 TGTTTGTGATGAAACAAA-TCTGTTTAGGATGC
**
75824 TAATTGTGATGTAAACAAATCTGTTT
1 TGTTTGTGATG-AAACAAATCTGTTT
75850 TGGTTGATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.06
32 23 0.44
33 19 0.37
34 7 0.13
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (32 bp):
TGTTTGTGATGAAACAAATCTGTTTAGGATGC
Found at i:75834 original size:33 final size:31
Alignment explanation
Indices: 75762--75853 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 31
75752 TGAGTGTTGT
* * **
75762 TTGTGATGACACTAAATCTGTTTAGGTGCTGT
1 TTGTGATGAAAC-AAATCTGTTTTGGTGCTAA
75794 TTGTGATGAAACAAATTCTGTTTTGGATGCTAA
1 TTGTGATGAAACAAA-TCTGTTTTGG-TGCTAA
75827 TTGTGATGTAAACAAATCTGTTTTGGT
1 TTGTGATG-AAACAAATCTGTTTTGGT
75854 TGATCATAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
31 3 0.06
32 21 0.40
33 22 0.42
34 7 0.13
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (31 bp):
TTGTGATGAAACAAATCTGTTTTGGTGCTAA
Found at i:77682 original size:21 final size:21
Alignment explanation
Indices: 77658--77770 Score: 149
Period size: 21 Copynumber: 5.4 Consensus size: 21
77648 TGCTAGAAGT
77658 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
77679 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* * *
77700 TCATTGGAGCAGGTTACAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
77721 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
77742 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
77763 TCATTGGA
1 TCATTGGA
77771 AATGCCTAAG
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 1 0.01
21 82 0.99
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:78688 original size:175 final size:175
Alignment explanation
Indices: 78397--78746 Score: 682
Period size: 175 Copynumber: 2.0 Consensus size: 175
78387 GTTTGTGAAT
78397 CTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGAT
1 CTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGAT
78462 TCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAG
66 TCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAG
*
78527 ATATTCAAGGCTAGATTTGAATCTAACACAACTAGATTCGTATCA
131 ATATTCAAGGCTAGATTTGAATCTAACACAACTAAATTCGTATCA
78572 CTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGAT
1 CTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGAT
78637 TCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAG
66 TCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAG
*
78702 ATATTCAAGGCTAGATTTGAATCTAACACAACTAAATTTGTATCA
131 ATATTCAAGGCTAGATTTGAATCTAACACAACTAAATTCGTATCA
78747 ATTCCATGAC
Statistics
Matches: 173, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 173 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (175 bp):
CTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGAT
TCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAG
ATATTCAAGGCTAGATTTGAATCTAACACAACTAAATTCGTATCA
Found at i:80587 original size:2 final size:2
Alignment explanation
Indices: 80580--80616 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
80570 GTTTTGCAAG
80580 AT AT AT AT AT 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
80617 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:87049 original size:45 final size:45
Alignment explanation
Indices: 86985--87081 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 45
86975 AATAACAATT
*
86985 AATATTAGCTTTATTTTGATGAATTATATAGAGATGGAGAAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAGAAGTAG
* * *
87030 AATATTAGTTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAGAAGTAG
87075 AAT-TTAG
1 AATATTAG
87082 GTAATGCACT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
44 4 0.08
45 44 0.92
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAGAAGTAG
Found at i:89596 original size:3 final size:3
Alignment explanation
Indices: 89588--89632 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
89578 GCTTTGCTAG
* * *
89588 AGA AGA AGA AGA AGA AGA A-A AGA AGA GGA AGG AGA AAA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
89633 ACCCTAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:89685 original size:18 final size:19
Alignment explanation
Indices: 89662--89701 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
89652 GAGAGGGATG
89662 AAATTAAATGGG-TTAAAA
1 AAATTAAATGGGTTTAAAA
89680 AAATTAAATGGGTTTAAAA
1 AAATTAAATGGGTTTAAAA
89699 AAA
1 AAA
89702 ATTTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (19 bp):
AAATTAAATGGGTTTAAAA
Found at i:91083 original size:12 final size:12
Alignment explanation
Indices: 91066--91090 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
91056 ATTATGCAAA
91066 AATGCAAATGAT
1 AATGCAAATGAT
91078 AATGCAAATGAT
1 AATGCAAATGAT
91090 A
1 A
91091 GAGTATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
AATGCAAATGAT
Found at i:94861 original size:39 final size:39
Alignment explanation
Indices: 94804--94885 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
94794 CTTATGAGCC
*
94804 TAAGTGAAATGTAGGAATAAAATGAGACTAAATGAAATA
1 TAAGTGAAATGTAAGAATAAAATGAGACTAAATGAAATA
*
94843 TAAGTGAAATGTAAGAATAAAATGAGACTAAATGAAATG
1 TAAGTGAAATGTAAGAATAAAATGAGACTAAATGAAATA
94882 TAAG
1 TAAG
94886 AACAAAGGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.54, C:0.02, G:0.21, T:0.23
Consensus pattern (39 bp):
TAAGTGAAATGTAAGAATAAAATGAGACTAAATGAAATA
Found at i:94863 original size:28 final size:26
Alignment explanation
Indices: 94832--94898 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
94822 AAAATGAGAC
94832 TAAATGAAATATAAGTGAAATGTAAGAA
1 TAAATGAAATA-AA-TGAAATGTAAGAA
*
94860 TAAAATGAGACTAAATGAAATGTAAGAA
1 T-AAATGA-AATAAATGAAATGTAAGAA
* *
94888 CAAAGGAAATA
1 TAAATGAAATA
94899 CAACCTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 3 0.09
27 5 0.15
28 14 0.42
29 8 0.24
30 3 0.09
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.21
Consensus pattern (26 bp):
TAAATGAAATAAATGAAATGTAAGAA
Found at i:94939 original size:33 final size:34
Alignment explanation
Indices: 94902--94968 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
94892 GGAAATACAA
*
94902 CCTTAATGTGACTAGAATGGAAC-AAAAATATTT
1 CCTTAATGTGACTAGAATGAAACAAAAAATATTT
* *
94935 CCTTAATGTTATTAGAATGAAACAAAAAATATTT
1 CCTTAATGTGACTAGAATGAAACAAAAAATATTT
94969 TTAGATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 20 0.67
34 10 0.33
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (34 bp):
CCTTAATGTGACTAGAATGAAACAAAAAATATTT
Found at i:99084 original size:76 final size:76
Alignment explanation
Indices: 98945--99085 Score: 194
Period size: 76 Copynumber: 1.9 Consensus size: 76
98935 TGACAAGGGC
* * * *
98945 CCCGACTCCTCCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTTAAGACCCAG
1 CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG
99010 CTGGGCAATGT
66 CTGGGCAATGT
* * * *
99021 CCCGACTCCACCTGGGTGCCCACATGGTTTGTC-TGAGGACCCATGTGATTTGCCTGATCACCCA
1 CCCGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCA
99085 G
65 G
99086 GTAGGCTGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 52 0.93
77 4 0.07
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.24
Consensus pattern (76 bp):
CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG
CTGGGCAATGT
Found at i:101942 original size:18 final size:18
Alignment explanation
Indices: 101919--101953 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
101909 CACCAGACAA
101919 TGAGCATCATGGACATCC
1 TGAGCATCATGGACATCC
*
101937 TGAGCATCATGGCCATC
1 TGAGCATCATGGACATC
101954 AAGTTTGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (18 bp):
TGAGCATCATGGACATCC
Found at i:102670 original size:16 final size:16
Alignment explanation
Indices: 102642--102674 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
102632 TTTTGGCTTG
102642 ATTATTAAAGAAAAGA
1 ATTATTAAAGAAAAGA
102658 ATTA-TAAAGGAAAAGA
1 ATTATTAAA-GAAAAGA
102674 A
1 A
102675 AAACATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (16 bp):
ATTATTAAAGAAAAGA
Found at i:107475 original size:5 final size:6
Alignment explanation
Indices: 107460--107484 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
107450 TTGTGTATTA
107460 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
107485 ATATTAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Done.