Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015536.1 Corchorus olitorius cultivar O-4 contig15569, 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: 37760
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1202 original size:31 final size:31
Alignment explanation
Indices: 1167--1228 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1157 AAAGTTATTA
* *
1167 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
1198 ATGAATATTGTAAATATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
1229 TTCTCTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (31 bp):
ATGAATATTGTAAATATTCATGAATCAAGAG
Found at i:5618 original size:60 final size:60
Alignment explanation
Indices: 5550--5685 Score: 218
Period size: 60 Copynumber: 2.3 Consensus size: 60
5540 AAAGGCTAAT
* * *
5550 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCTAAATAATGACCTAACGTTTGCTAAAA
1 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGACCTAACGTTTGCCAAAA
** *
5610 TGCTCAAATAAGGGCATGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGACCTAACGTTTGCCAAAA
5670 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
5686 TGATATCAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (60 bp):
TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGACCTAACGTTTGCCAAAA
Found at i:5681 original size:31 final size:31
Alignment explanation
Indices: 5584--5686 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
5574 TAATTTGGCT
* *
5584 AAATAATGACCTAACGTTTGCTAAAATGCTC
1 AAATAAGGGCCTAACGTTTGCTAAAATGCTC
* * **
5615 AAATAAGGGCATGATC-TTT--TAATTTGGC-C
1 AAATAAGGGCCT-AACGTTTGCTAAAAT-GCTC
*
5644 AAATAAGGGCCTAACGTTTGCCAAAATGCTC
1 AAATAAGGGCCTAACGTTTGCTAAAATGCTC
5675 AAATAAGGGCCT
1 AAATAAGGGCCT
5687 GATATCAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 2 0.04
29 19 0.35
30 4 0.07
31 28 0.51
32 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (31 bp):
AAATAAGGGCCTAACGTTTGCTAAAATGCTC
Found at i:5805 original size:60 final size:60
Alignment explanation
Indices: 5729--5888 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 60
5719 GATGACAAGT
* * *
5729 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGGC
1 CCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
* **
5789 CCTTATTTGAGTATTTTCGATAACATTAGATCCTTATTTGGCCAAATTAAAAGATCAGAC
1 CCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
* *
5849 CCTTATTTGAGCATTTTGGCA-AACATTAAGCCCTTATTTG
1 CCTTATTTGAGCATTTTCG-ATAACATTAGGCCCTTATTTG
5889 AGCAATTAGC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 87 0.99
61 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
Found at i:5857 original size:29 final size:29
Alignment explanation
Indices: 5759--5857 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
5749 TAACGTTAGG
* *
5759 CCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCAGA
* ** * * *
5788 CCCTTATTTGAG-TATTTTCGATAACATTAGA
1 CCCTTATTTG-GCCAAATT--AAAAGATCAGA
*
5819 TCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGGCCAAATTAAAAGATCAGA
5848 CCCTTATTTG
1 CCCTTATTTG
5858 AGCATTTTGG
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
29 30 0.60
30 2 0.04
31 18 0.36
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:6604 original size:8 final size:8
Alignment explanation
Indices: 6591--6625 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
6581 CCTAAAGAAG
6591 TTTTCTTT
1 TTTTCTTT
6599 TTTTCTTT
1 TTTTCTTT
6607 TTTTCTTT
1 TTTTCTTT
6615 TTTTCTTT
1 TTTTCTTT
6623 TTT
1 TTT
6626 GTTCCGCCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:12726 original size:31 final size:28
Alignment explanation
Indices: 12679--12755 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 28
12669 TTAAATAATT
*
12679 AATAAATTACTTTTTTTTGAGG-TAAATA
1 AATAAATTACTTTTTTTTGAGGCGAAA-A
**
12707 AATAAATTACTTAAATTTTTTTTGGCGAAAA
1 AATAAATTACTT---TTTTTTGAGGCGAAAA
12738 AATAAATTACTTTTTTTT
1 AATAAATTACTTTTTTTT
12756 TTTGAAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 18 0.43
31 21 0.50
32 3 0.07
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (28 bp):
AATAAATTACTTTTTTTTGAGGCGAAAA
Found at i:12758 original size:31 final size:33
Alignment explanation
Indices: 12689--12749 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
12679 AATAAATTAC
12689 TTTTTTTTGAGGTAAATAAATAAATTACTTAAA
1 TTTTTTTTGAGGTAAATAAATAAATTACTTAAA
12722 TTTTTTTTG-GCG-AAA-AAATAAATTACTT
1 TTTTTTTTGAG-GTAAATAAATAAATTACTT
12750 TTTTTTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 13 0.48
32 4 0.15
33 10 0.37
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (33 bp):
TTTTTTTTGAGGTAAATAAATAAATTACTTAAA
Found at i:18637 original size:29 final size:30
Alignment explanation
Indices: 18605--18671 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 30
18595 ATGCAATTTG
18605 GGATATAACGTTAC-AAAACAAGCAATTAA
1 GGATATAACGTTACAAAAACAAGCAATTAA
*
18634 GGATATAACGTTACGAAAAACGAGCAATTAA
1 GGATATAACGTTAC-AAAAACAAGCAATTAA
18665 GGATATA
1 GGATATA
18672 GTCCGTCAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
31 21 0.60
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (30 bp):
GGATATAACGTTACAAAAACAAGCAATTAA
Found at i:18849 original size:31 final size:31
Alignment explanation
Indices: 18811--18889 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
18801 CTATATGTCT
*
18811 ATATCCTTAATTGCTTGAAATCGAAAACATC
1 ATATCCTTAATTGCTTGAAATCAAAAACATC
* * *
18842 ATATCCTTAATTGCTTAAAATCAAAAACGTT
1 ATATCCTTAATTGCTTGAAATCAAAAACATC
18873 ATATCCTTAATTGCTTG
1 ATATCCTTAATTGCTTG
18890 TTTTGTAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATCAAAAACATC
Found at i:19607 original size:13 final size:14
Alignment explanation
Indices: 19576--19610 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
19566 ACTATAAAAG
*
19576 TTTAAACAATATCA
1 TTTAAAAAATATCA
19590 TTTAAAAAATAT-A
1 TTTAAAAAATATCA
19603 TTTAAAAA
1 TTTAAAAA
19611 GTTCCGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTAAAAAATATCA
Found at i:19931 original size:31 final size:31
Alignment explanation
Indices: 19890--20026 Score: 116
Period size: 31 Copynumber: 4.5 Consensus size: 31
19880 GCCAAATAAT
* * ***
19890 CAATTTAGGATATAACGTTTGCTCCCACAAG
1 CAATTAAGGATATAACGTTTACTAAAACAAG
*
19921 CAATTAAGGATATAACG-TTAC-AAAACAAT
1 CAATTAAGGATATAACGTTTACTAAAACAAG
* ***
19950 CAATTAAGGATATAACGTTTTCTATTTCAAG
1 CAATTAAGGATATAACGTTTACTAAAACAAG
* * * ***
19981 CAATTAAGGATATGACGTTTTCGATTTCAAG
1 CAATTAAGGATATAACGTTTACTAAAACAAG
20012 CAATTAAGGATATAA
1 CAATTAAGGATATAA
20027 TCAGTAGGGC
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.23
30 6 0.07
31 63 0.70
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (31 bp):
CAATTAAGGATATAACGTTTACTAAAACAAG
Found at i:19981 original size:60 final size:60
Alignment explanation
Indices: 19887--19999 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
19877 TATGCCAAAT
* *
19887 AATCAATTTAGGATATAACGTTTGCTCCCACAAGCAATTAAGGATATAACGTTACAAAAC
1 AATCAATTAAGGATATAACGTTTGCTACCACAAGCAATTAAGGATATAACGTTACAAAAC
* *** *
19947 AATCAATTAAGGATATAACGTTTTCTATTTCAAGCAATTAAGGATATGACGTT
1 AATCAATTAAGGATATAACGTTTGCTACCACAAGCAATTAAGGATATAACGTT
20000 TTCGATTTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (60 bp):
AATCAATTAAGGATATAACGTTTGCTACCACAAGCAATTAAGGATATAACGTTACAAAAC
Found at i:20199 original size:29 final size:31
Alignment explanation
Indices: 20133--20199 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
20123 CCTAACGGAC
20133 TATATCCTTAATTGCTCACTTTTCGTAACGT
1 TATATCCTTAATTGCTCACTTTTCGTAACGT
**
20164 TATATCCTTAATTGCT-TGTTTT-GTAACGT
1 TATATCCTTAATTGCTCACTTTTCGTAACGT
20193 TATATCC
1 TATATCC
20200 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCACTTTTCGTAACGT
Found at i:21952 original size:33 final size:34
Alignment explanation
Indices: 21907--21978 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
21897 AAAAAATTTG
*
21907 CAACACCAGATTCAACGAAATACAACACCAGATT
1 CAACACCAGATTCAACAAAATACAACACCAGATT
*
21941 CAACA-CAGATTCAACAAAATACAGCACCAGATT
1 CAACACCAGATTCAACAAAATACAACACCAGATT
21974 CAACA
1 CAACA
21979 AAATTGCAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 31 0.86
34 5 0.14
ACGTcount: A:0.49, C:0.29, G:0.08, T:0.14
Consensus pattern (34 bp):
CAACACCAGATTCAACAAAATACAACACCAGATT
Found at i:21989 original size:33 final size:33
Alignment explanation
Indices: 21907--21989 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
21897 AAAAAATTTG
* *
21907 CAACACCAGATTCAACGAAATACAACACCAGATT
1 CAACA-CAAATTCAACAAAATACAACACCAGATT
* *
21941 CAACACAGATTCAACAAAATACAGCACCAGATT
1 CAACACAAATTCAACAAAATACAACACCAGATT
21974 CAACA-AAATTGCAACA
1 CAACACAAATT-CAACA
21990 CCAGAAACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 4 0.09
33 36 0.80
34 5 0.11
ACGTcount: A:0.49, C:0.28, G:0.08, T:0.14
Consensus pattern (33 bp):
CAACACAAATTCAACAAAATACAACACCAGATT
Found at i:22642 original size:24 final size:24
Alignment explanation
Indices: 22615--22661 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
22605 GAGAAGCATA
22615 GAGGAAGAAAATGGAAGAAAAATC
1 GAGGAAGAAAATGGAAGAAAAATC
*
22639 GAGGAAGAAGATGGAAGAAAAAT
1 GAGGAAGAAAATGGAAGAAAAAT
22662 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.32, T:0.09
Consensus pattern (24 bp):
GAGGAAGAAAATGGAAGAAAAATC
Found at i:31464 original size:22 final size:22
Alignment explanation
Indices: 31439--32387 Score: 203
Period size: 22 Copynumber: 43.1 Consensus size: 22
31429 TATAAGAATA
*
31439 TCCCTATGAAATTTTGTTAACC
1 TCCCTATGAAATTTTGATAACC
* *
31461 TCCCTAT-ACAATTTTGAAAACA
1 TCCCTATGA-AATTTTGATAACC
** * *
31483 TTACTATAAAATTTTGATAATC
1 TCCCTATGAAATTTTGATAACC
* * * * *
31505 TCCATGTGAAATGTTGGTAAGC
1 TCCCTATGAAATTTTGATAACC
* * * *
31527 ACACTATGAACTTTTTTATAACC
1 TCCCTATGAA-ATTTTGATAACC
* * *
31550 TCCCTATAAAATCTT-ACTGACC
1 TCCCTATGAAATTTTGA-TAACC
* * * *
31572 ACACTGTGAAATTTTGATAATC
1 TCCCTATGAAATTTTGATAACC
* * * *
31594 ACACTATGAAATTGT-AAAGACC
1 TCCCTATGAAATTTTGATA-ACC
** * *
31616 TCGGTATAAAATTTTGATAAACA
1 TCCCTATGAAATTTTGAT-AACC
* * * *
31639 TTCATATAAAATTTTTATAAACC
1 TCCCTATGAAATTTTGAT-AACC
*
31662 TCCCTATAAAATTTTTGATAACC
1 TCCCTATGAAA-TTTTGATAACC
*
31685 TCCTTATGAAATTTTGATAA--
1 TCCCTATGAAATTTTGATAACC
* *
31705 T--C-A-CAAATTTCGATAACC
1 TCCCTATGAAATTTTGATAACC
* *
31723 TCCCTATG-ATTTTTCGATAACT
1 TCCCTATGAAATTTT-GATAACC
** *
31745 TCATTATGAAATTTTGTTAACC
1 TCCCTATGAAATTTTGATAACC
31767 TCCCTATGAAATTTTGATAA--
1 TCCCTATGAAATTTTGATAACC
* *
31787 -CCCTATAAAATTTTGA-AAAC
1 TCCCTATGAAATTTTGATAACC
** *
31807 TAAACTATGAAATTTTGATAATAC
1 T-CCCTATGAAATTTTGATAA-CC
* *
31831 -CCCTTTGAAATTTTAATAACC
1 TCCCTATGAAATTTTGATAACC
* * *
31852 TTCATACGAAATTTT-AGTAACC
1 TCCCTATGAAATTTTGA-TAACC
* ** *
31874 GCACAAATGCAATTTTTGATAACC
1 TC-CCTATG-AAATTTTGATAACC
* * **
31898 TCACTTTGAAA---T-ACCACAC
1 TCCCTATGAAATTTTGATAAC-C
* **
31917 T--CTA--AAATTTGGATAATA
1 TCCCTATGAAATTTTGATAACC
* **
31935 ACATTATGAAATTTTGATAACC
1 TCCCTATGAAATTTTGATAACC
* **
31957 TCCTTATGAAATTTTTCTAACC
1 TCCCTATGAAATTTTGATAACC
* * *
31979 TGATCTCTATGAAATTTAGATAATCA
1 ---TCCCTATGAAATTTTGATAA-CC
* *
32005 T-ACTATGAAATTTTAATAACC
1 TCCCTATGAAATTTTGATAACC
* ** *
32026 ACAATATGAAAATTTTTCATAACC
1 TCCCTATG-AAA-TTTTGATAACC
* *
32050 TCACT-GGAAAATTTTGATAACC
1 TCCCTATG-AAATTTTGATAACC
* *
32072 -CCGCTTTAAAATTTTGATAACC
1 TCC-CTATGAAATTTTGATAACC
32094 -CTCCTATGAAATTTTGATAACC
1 TC-CCTATGAAATTTTGATAACC
* * *
32116 -ACATGATG-AA-TTTGATAACT
1 TCCCT-ATGAAATTTTGATAACC
* * ***
32136 TTCCTATGTAATTTTGGTAATATGA
1 TCCCTATGAAATTTT-G--ATAACC
* *
32161 TCTCTATGAATTTTTGATAA-C
1 TCCCTATGAAATTTTGATAACC
* * **
32182 TACTCTATGAGATTTTGAT-TGC
1 T-CCCTATGAAATTTTGATAACC
*
32204 TTCCTAATGAAATTTTGATAACC
1 TCCCT-ATGAAATTTTGATAACC
** *
32227 -AACTAT-AAATTTTGATAACA
1 TCCCTATGAAATTTTGATAACC
* * *
32247 TTCATATGACATTTAGAATTTT-ATAACA
1 TCCCTATG------A-AATTTTGATAACC
** *
32275 TTACTATGAAATTTT-AGTTACC
1 TCCCTATGAAATTTTGA-TAACC
* * *
32297 ACACTATGAAATCTTTAATAACC
1 TCCCTATGAAAT-TTTGATAACC
* *
32320 -ACCTGATAAAATTTTGATAACC
1 TCCCT-ATGAAATTTTGATAACC
* *
32342 ACACC-ATGAAATTCTGATAACC
1 TC-CCTATGAAATTTTGATAACC
** *
32364 TTGCTATGAAATTTTAATAACC
1 TCCCTATGAAATTTTGATAACC
32386 TC
1 TC
32388 TTTGATAGCC
Statistics
Matches: 668, Mismatches: 185, Indels: 148
0.67 0.18 0.15
Matches are distributed among these distances:
15 3 0.00
16 11 0.02
17 3 0.00
18 6 0.01
19 20 0.03
20 29 0.04
21 37 0.06
22 374 0.56
23 97 0.15
24 38 0.06
25 30 0.04
26 1 0.00
28 13 0.02
29 6 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TCCCTATGAAATTTTGATAACC
Found at i:31677 original size:24 final size:23
Alignment explanation
Indices: 31620--31704 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
31610 AAGACCTCGG
* *
31620 TATAAAATTTTGATAAACATTCA
1 TATAAAATTTTGATAAACCTCCA
* *
31643 TATAAAATTTTTATAAACCTCCC
1 TATAAAATTTTGATAAACCTCCA
*
31666 TATAAAATTTTTGAT-AACCTCCT
1 TATAAAA-TTTTGATAAACCTCCA
*
31689 TATGAAATTTTGATAA
1 TATAAAATTTTGATAA
31705 TCACAAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
22 7 0.13
23 40 0.75
24 6 0.11
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (23 bp):
TATAAAATTTTGATAAACCTCCA
Found at i:31786 original size:44 final size:39
Alignment explanation
Indices: 31674--31827 Score: 116
Period size: 41 Copynumber: 3.8 Consensus size: 39
31664 CCTATAAAAT
*
31674 TTTTGATAACCTCCTTATGAAATTTTGATAA-TCACAAA
1 TTTTGATAACCTCCCTATGAAATTTTGATAACTCACAAA
* * *
31712 TTTCGATAACCTCCCTATG-ATTTTTCGATAACTTCATTATGAAA
1 TTTTGATAACCTCCCTATGAAATTTT-GATAAC-TC---A-CAAA
* * *
31756 TTTTGTTAACCTCCCTATGAAATTTTGATAACCCTATAAAA
1 TTTTGATAACCTCCCTATGAAATTTTGATAACTC-A-CAAA
* **
31797 TTTTGA-AAACTAAACTATGAAATTTTGATAA
1 TTTTGATAACCT-CCCTATGAAATTTTGATAA
31828 TACCCCTTTG
Statistics
Matches: 94, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
37 5 0.05
38 22 0.23
40 6 0.06
41 28 0.30
43 2 0.02
44 26 0.28
45 5 0.05
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (39 bp):
TTTTGATAACCTCCCTATGAAATTTTGATAACTCACAAA
Found at i:32291 original size:29 final size:29
Alignment explanation
Indices: 32234--32288 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
32224 ACCAACTATA
*
32234 AATTTTGATAACATTCATATGACATTTAG
1 AATTTTGATAACATTCATATGAAATTTAG
32263 AATTTT-ATAACATT-ACTATGAAATTT
1 AATTTTGATAACATTCA-TATGAAATTT
32289 TAGTTACCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 17 0.71
29 6 0.25
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (29 bp):
AATTTTGATAACATTCATATGAAATTTAG
Found at i:32461 original size:27 final size:24
Alignment explanation
Indices: 32402--32491 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 24
32392 ATAGCCTCTT
32402 TATGAAATTTTGATAACC--A-CAC
1 TATGAAATTTTGATAACCTAATC-C
*
32424 TATGAAATTTTGATAACTTTAATTTCC
1 TATGAAATTTTGATAAC-CTAA--TCC
*
32451 TATGAAATTTTAATAACCTAATCC
1 TATGAAATTTTGATAACCTAATCC
32475 ATATGAAATTTTGATAA
1 -TATGAAATTTTGATAA
32492 TCACTCAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
22 17 0.30
24 3 0.05
25 16 0.28
26 3 0.05
27 17 0.30
28 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (24 bp):
TATGAAATTTTGATAACCTAATCC
Found at i:32632 original size:22 final size:22
Alignment explanation
Indices: 32615--32735 Score: 88
Period size: 22 Copynumber: 5.5 Consensus size: 22
32605 GATAACCTTT
32615 CTATGAAATTTTAGTAACCGCA
1 CTATGAAATTTTAGTAACCGCA
* *
32637 CTATGAAATTTTGGTAACCACAA
1 CTATGAAATTTTAGTAACCGC-A
* * * *
32660 C-ATGAATTTTTAATAACCTCC
1 CTATGAAATTTTAGTAACCGCA
* * * *
32681 CTAT-AAAATTTGGTAACTGAA
1 CTATGAAATTTTAGTAACCGCA
*
32702 CTATGAAATTTT-GATAACCTC-
1 CTATGAAATTTTAG-TAACCGCA
32723 CTTATGAAATTTT
1 C-TATGAAATTTT
32736 GATAATGTTA
Statistics
Matches: 75, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
21 16 0.21
22 57 0.76
23 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTAGTAACCGCA
Found at i:32708 original size:43 final size:44
Alignment explanation
Indices: 32615--32734 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 44
32605 GATAACCTTT
* * * *
32615 CTATGAAATTTTAGTAACCGCACTATGAAATTTTGGTAACCACAA
1 CTATGAAATTTTAATAACCTCCCTAT-AAAATTTGGTAACCACAA
* **
32660 C-ATGAATTTTTAATAACCTCCCTATAAAATTTGGTAA-CTGAA
1 CTATGAAATTTTAATAACCTCCCTATAAAATTTGGTAACCACAA
* * *
32702 CTATGAAATTTTGATAACCTCCTTATGAAATTT
1 CTATGAAATTTTAATAACCTCCCTATAAAATTT
32735 TGATAATGTT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 4 0.06
43 38 0.60
44 20 0.32
45 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (44 bp):
CTATGAAATTTTAATAACCTCCCTATAAAATTTGGTAACCACAA
Found at i:32736 original size:22 final size:22
Alignment explanation
Indices: 32576--32760 Score: 87
Period size: 22 Copynumber: 8.5 Consensus size: 22
32566 TAATCCCTAT
* *
32576 AAATTTTGATAA-CTACTCGATG
1 AAATTTTGATAACCTCCT-TATG
* *
32598 AAAATTTGATAACCT-TTCTATG
1 AAATTTTGATAACCTCCT-TATG
*
32620 AAATTTT-AGTAACCGCAC-TATG
1 AAATTTTGA-TAACCTC-CTTATG
* * ***
32642 AAATTTTGGTAACCACAACATG
1 AAATTTTGATAACCTCCTTATG
* * *
32664 AATTTTTAATAACCTCCCTAT-
1 AAATTTTGATAACCTCCTTATG
* * *
32685 AAAATTTGGTAA-CTGAAC-TATG
1 AAATTTTGATAACCT--CCTTATG
32707 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCCTTATG
** **
32729 AAATTTTGATAATGTTATTATG
1 AAATTTTGATAACCTCCTTATG
32751 AAATTTTGAT
1 AAATTTTGAT
32761 TACCACACAA
Statistics
Matches: 123, Mismatches: 29, Indels: 22
0.71 0.17 0.13
Matches are distributed among these distances:
20 2 0.02
21 13 0.11
22 104 0.85
23 4 0.03
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCCTTATG
Found at i:32862 original size:22 final size:22
Alignment explanation
Indices: 32836--32886 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
32826 TAAATTTTCC
32836 TCATGAAAACTTGATAATCTCA
1 TCATGAAAACTTGATAATCTCA
**
32858 TCATG-AAGTTTGATAATCTCA
1 TCATGAAAACTTGATAATCTCA
*
32879 TTATGAAA
1 TCATGAAA
32887 TTTTTTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATGAAAACTTGATAATCTCA
Found at i:32872 original size:21 final size:21
Alignment explanation
Indices: 32846--32885 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
32836 TCATGAAAAC
32846 TTGATAATCTCATCATGAAGT
1 TTGATAATCTCATCATGAAGT
*
32867 TTGATAATCTCATTATGAA
1 TTGATAATCTCATCATGAA
32886 ATTTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (21 bp):
TTGATAATCTCATCATGAAGT
Found at i:33550 original size:22 final size:22
Alignment explanation
Indices: 33522--33638 Score: 74
Period size: 22 Copynumber: 5.4 Consensus size: 22
33512 TGAGATTTTT
*
33522 AAAATTTCACAGTGTGGTTATC
1 AAAATTTCATAGTGTGGTTATC
* *
33544 AAAATTTCATTGTGTGGTTGTC
1 AAAATTTCATAGTGTGGTTATC
** * * * *
33566 GGATTTTCATAGGGAGATTATC
1 AAAATTTCATAGTGTGGTTATC
* * * * *
33588 GAAATTCCATAATGAGATTATC
1 AAAATTTCATAGTGTGGTTATC
* *
33610 -AATTTTCACAGTGTGGTTATC
1 AAAATTTCATAGTGTGGTTATC
*
33631 AATATTTC
1 AAAATTTC
33639 TACGTTGGAG
Statistics
Matches: 70, Mismatches: 24, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
21 15 0.21
22 55 0.79
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (22 bp):
AAAATTTCATAGTGTGGTTATC
Found at i:36321 original size:12 final size:11
Alignment explanation
Indices: 36305--36355 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
36295 CAGATTTTGA
36305 TAATTTTATTT
1 TAATTTTATTT
*
36316 ATAA-TTAATTT
1 -TAATTTTATTT
*
36327 CAATTATTATTT
1 TAATT-TTATTT
*
36339 TAATTTTCTTT
1 TAATTTTATTT
36350 TAATTT
1 TAATTT
36356 AAACACGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.06
11 18 0.56
12 12 0.38
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (11 bp):
TAATTTTATTT
Found at i:37630 original size:45 final size:45
Alignment explanation
Indices: 37565--37655 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
37555 TTTTCGAAGC
*
37565 AGTTGAATTTTTAAATGTATAATCATACTATAAGAACTAAACCGG
1 AGTTGAATTTTTAAAAGTATAATCATACTATAAGAACTAAACCGG
* *
37610 AGTTGAATTTTTAAAAGTATAATCATACTATAAGAGCTAAATCGG
1 AGTTGAATTTTTAAAAGTATAATCATACTATAAGAACTAAACCGG
37655 A
1 A
37656 TTAGATTGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (45 bp):
AGTTGAATTTTTAAAAGTATAATCATACTATAAGAACTAAACCGG
Found at i:37671 original size:45 final size:45
Alignment explanation
Indices: 37581--37671 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
37571 ATTTTTAAAT
***
37581 GTATAATCATACTATAAGAACTAAACCGGAGTTGAATTTTTAAAA
1 GTATAATCATACTATAAGAACTAAACCGGAGTTGAATTCCAAAAA
* *
37626 GTATAATCATACTATAAGAGCTAAATCGGA-TT-AGATTGCCAAAAA
1 GTATAATCATACTATAAGAACTAAACCGGAGTTGA-ATT-CCAAAAA
37671 G
1 G
37672 AAAAGCCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
43 1 0.03
44 5 0.13
45 33 0.85
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (45 bp):
GTATAATCATACTATAAGAACTAAACCGGAGTTGAATTCCAAAAA
Done.