Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016229.1 Corchorus olitorius cultivar O-4 contig16262, 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: 45001
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:650 original size:21 final size:21
Alignment explanation
Indices: 626--692 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
616 AATTCTCTGT
626 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
647 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
668 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
689 AAAT
1 AAAT
693 CCTGGTCCTG
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:672 original size:42 final size:42
Alignment explanation
Indices: 613--693 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
603 GCTAAGTCTT
613 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
655 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
694 CTGGTCCTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:829 original size:55 final size:56
Alignment explanation
Indices: 759--864 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
749 TTTATTTTGT
* *
759 AGAATAATCAAGTAGAGATA-GGGGATAGGATTTACCATAACATTTATTGTGTGAA
1 AGAATAATCAAGTAGAAATAGGGGGATAGAATTTACCATAACATTTATTGTGTGAA
* **
814 AGAATAATTAAGTAGAAATAGGGGGATAGAATTTATTATAACATTTATTGT
1 AGAATAATCAAGTAGAAATAGGGGGATAGAATTTACCATAACATTTATTGT
865 ATGGAGGGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 18 0.40
56 27 0.60
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.32
Consensus pattern (56 bp):
AGAATAATCAAGTAGAAATAGGGGGATAGAATTTACCATAACATTTATTGTGTGAA
Found at i:1774 original size:29 final size:28
Alignment explanation
Indices: 1727--1789 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
1717 CCAGTGTACT
* * * *
1727 GTTGACCGATTTAATCTGCCACATCAGCC
1 GTTGACCGAGTCAACCTGCCACATCA-AC
1756 GTTGACCGAGTCAACCTGCCACATCAAC
1 GTTGACCGAGTCAACCTGCCACATCAAC
1784 GTTGAC
1 GTTGAC
1790 TTTGACTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (28 bp):
GTTGACCGAGTCAACCTGCCACATCAAC
Found at i:2033 original size:27 final size:27
Alignment explanation
Indices: 1995--2062 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
1985 TGACCTTTTT
* *
1995 TGGTCTCGTATTCTGTCCTTGACCTGA
1 TGGTCCCGTATTCTGTCCTTGACCTAA
2022 TGGTCCCGTATTCTGTCCTTGACCTAA
1 TGGTCCCGTATTCTGTCCTTGACCTAA
*
2049 TGGTCCCATATTCT
1 TGGTCCCGTATTCT
2063 TGATGATTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.40
Consensus pattern (27 bp):
TGGTCCCGTATTCTGTCCTTGACCTAA
Found at i:8823 original size:2 final size:2
Alignment explanation
Indices: 8816--8844 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8806 TGGTCAGATT
8816 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 T
8845 GTATGTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8955 original size:27 final size:27
Alignment explanation
Indices: 8925--8976 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
8915 GGTTCGAAAG
* *
8925 AAGCAAGCTCAGGCAAAGGTCCTGCTC
1 AAGCAAGATCAAGCAAAGGTCCTGCTC
8952 AAGCAAGATCAAGCAAAGGTCCTGC
1 AAGCAAGATCAAGCAAAGGTCCTGC
8977 AGTAAGCAAA
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:0.35, C:0.27, G:0.25, T:0.13
Consensus pattern (27 bp):
AAGCAAGATCAAGCAAAGGTCCTGCTC
Found at i:12981 original size:21 final size:22
Alignment explanation
Indices: 12943--12998 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
12933 TACAAAGGGT
* *
12943 TGTTATCAAAGTTTTAATTG-AC
1 TGTTATCAAAATTATAA-TGAAC
12965 -GTTATCAAAATTATAATGAAC
1 TGTTATCAAAATTATAATGAAC
*
12986 TTTTATCAAAATT
1 TGTTATCAAAATT
12999 TTAAATGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 16 0.55
22 11 0.38
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (22 bp):
TGTTATCAAAATTATAATGAAC
Found at i:13038 original size:22 final size:21
Alignment explanation
Indices: 12988--13068 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 21
12978 TAATGAACTT
*
12988 TTATCAAAATTTT-AAATGATGG
1 TTATC-AAATTTTCAAA-GATGA
*
13010 TTTTCAAATTTTCAAAGAGTGA
1 TTATCAAATTTTCAAAGA-TGA
*
13032 TTATCAAACTTTCATAAGATGA
1 TTATCAAATTTTCA-AAGATGA
* *
13054 TTGTCAAAATTTCAA
1 TTATCAAATTTTCAA
13069 TTGAAGTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 10 0.20
22 36 0.72
23 4 0.08
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (21 bp):
TTATCAAATTTTCAAAGATGA
Found at i:20216 original size:36 final size:36
Alignment explanation
Indices: 20176--20250 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
20166 GATGCATGGC
20176 AATTCTTTTTCCCAAACTCCAAAACCTGAGAATTGA
1 AATTCTTTTTCCCAAACTCCAAAACCTGAGAATTGA
20212 AATTCTTTTTCCCAAACTCCAAAACCTGAGAATTGA
1 AATTCTTTTTCCCAAACTCCAAAACCTGAGAATTGA
20248 AAT
1 AAT
20251 GACTAATGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (36 bp):
AATTCTTTTTCCCAAACTCCAAAACCTGAGAATTGA
Found at i:22682 original size:17 final size:17
Alignment explanation
Indices: 22660--22693 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
22650 GAAAGATACA
22660 ATTTTTT-TTTCTTTTTT
1 ATTTTTTCTTT-TTTTTT
22677 ATTTTTTCTTTTTTTTT
1 ATTTTTTCTTTTTTTTT
22694 GCCAGGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (17 bp):
ATTTTTTCTTTTTTTTT
Found at i:22683 original size:14 final size:14
Alignment explanation
Indices: 22664--22690 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22654 GATACAATTT
22664 TTTTTTCTTTTTTA
1 TTTTTTCTTTTTTA
22678 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
22691 TTTGCCAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.07, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTCTTTTTTA
Found at i:27287 original size:17 final size:17
Alignment explanation
Indices: 27267--27302 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
27257 ACCGGTCCGA
*
27267 CCGTTTCAATCGTCGGT
1 CCGTTTCAACCGTCGGT
27284 CCGTTTCAACCGTCGGT
1 CCGTTTCAACCGTCGGT
27301 CC
1 CC
27303 AATCTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.36, G:0.22, T:0.31
Consensus pattern (17 bp):
CCGTTTCAACCGTCGGT
Found at i:27739 original size:20 final size:20
Alignment explanation
Indices: 27710--27747 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27700 GGTAGAACGT
27710 AGAACAAATGCACATGGTCA
1 AGAACAAATGCACATGGTCA
* *
27730 AGAACGAATGCACGTGGT
1 AGAACAAATGCACATGGT
27748 TTAGACCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.16
Consensus pattern (20 bp):
AGAACAAATGCACATGGTCA
Found at i:28051 original size:3 final size:3
Alignment explanation
Indices: 28043--28068 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28033 ATACTCATAA
28043 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
28069 TGTTACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:30573 original size:18 final size:18
Alignment explanation
Indices: 30543--30582 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
30533 GACCGATTTC
30543 TTTTCCCTCCCTTTTCTTT
1 TTTTCCCTCCCTTTT-TTT
30562 TTTTCCCT-CCTTTTTTT
1 TTTTCCCTCCCTTTTTTT
30579 TTTT
1 TTTT
30583 ATTCTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.33
18 6 0.29
19 8 0.38
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTCCCTCCCTTTTTTT
Found at i:36420 original size:22 final size:22
Alignment explanation
Indices: 36303--36498 Score: 87
Period size: 22 Copynumber: 8.9 Consensus size: 22
36293 ATTACACTAT
* *
36303 TTTTGATGACCTCCTTATGAAA
1 TTTTGATAACCTTCTTATGAAA
* *
36325 TTTTGATAACATTCCTATGAAA
1 TTTTGATAACCTTCTTATGAAA
* * * *
36347 TTTTAATAACGATAC-TATGGAA
1 TTTTGATAAC-CTTCTTATGAAA
* * *
36369 TTTCGAGAACCTT-TTAAT-AAT
1 TTTTGATAACCTTCTT-ATGAAA
**
36390 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAACCTTCTTATGAAA
* * * * *
36412 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCTTATGAAA
*
36434 TTTTGA-AGACC-TCACTATGAAA
1 TTTTGATA-ACCTTC-TTATGAAA
** * *
36456 TTTTGATAACCAACACTATGAGA
1 TTTTGATAACCTTC-TTATGAAA
* *
36479 TGTTGATAACCTTCATATGA
1 TTTTGATAACCTTCTTATGA
36499 TTAGGGGTGA
Statistics
Matches: 131, Mismatches: 34, Indels: 18
0.72 0.19 0.10
Matches are distributed among these distances:
21 16 0.12
22 91 0.69
23 24 0.18
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTTCTTATGAAA
Found at i:36476 original size:23 final size:23
Alignment explanation
Indices: 36446--36489 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
36436 TTGAAGACCT
*
36446 CACTATGAAATTTTGATAACCAA
1 CACTATGAAATGTTGATAACCAA
*
36469 CACTATGAGATGTTGATAACC
1 CACTATGAAATGTTGATAACC
36490 TTCATATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (23 bp):
CACTATGAAATGTTGATAACCAA
Found at i:36744 original size:21 final size:20
Alignment explanation
Indices: 36709--36747 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
36699 GCACATAGGG
*
36709 TTTAGTTATATTATATATTT
1 TTTAATTATATTATATATTT
36729 TTTAATTATAATTATATAT
1 TTTAATTAT-ATTATATAT
36748 ATCTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTAATTATATTATATATTT
Found at i:38156 original size:22 final size:22
Alignment explanation
Indices: 38131--38245 Score: 106
Period size: 22 Copynumber: 5.1 Consensus size: 22
38121 GAATTGTTAG
*
38131 TAATCACACTCTAAAATTTTGA
1 TAATCACACTATAAAATTTTGA
* *
38153 TAATCACACTATGAAATTGTGA
1 TAATCACACTATAAAATTTTGA
* * * *
38175 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATAAAATTTTGA
*
38197 TAAACATTC-CTATAAAATTTTGA
1 TAATCA--CACTATAAAATTTTGA
* *
38220 TAAATCTCCCTATAAAATTTTGA
1 T-AATCACACTATAAAATTTTGA
38243 TAA
1 TAA
38246 CCTCCTTATG
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
22 44 0.57
23 29 0.38
24 4 0.05
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (22 bp):
TAATCACACTATAAAATTTTGA
Found at i:38214 original size:23 final size:23
Alignment explanation
Indices: 38137--38245 Score: 91
Period size: 23 Copynumber: 4.8 Consensus size: 23
38127 TTAGTAATCA
* * *
38137 CACTCTAAAATTTTGATAATC-A
1 CACTATAAAATTTTGATAAACTT
* * *
38159 CACTATGAAATTGTGAT-AACCT
1 CACTATAAAATTTTGATAAACTT
* *
38181 CGCTATGAAATTTTGATAAACATT
1 CACTATAAAATTTTGATAAAC-TT
38205 C-CTATAAAATTTTGATAAA-TCT
1 CACTATAAAATTTTGATAAACT-T
*
38227 CCCTATAAAATTTTGATAA
1 CACTATAAAATTTTGATAA
38246 CCTCCTTATG
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.04
22 31 0.42
23 37 0.51
24 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (23 bp):
CACTATAAAATTTTGATAAACTT
Found at i:38248 original size:68 final size:67
Alignment explanation
Indices: 38142--38267 Score: 182
Period size: 68 Copynumber: 1.9 Consensus size: 67
38132 AATCACACTC
* *
38142 TAAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGC-TATGAAATTTTGATAAACATTC
1 TAAAATTTTGATAATCACACTATAAAATTGTGATAACCTC-CTTATGAAATCTTGATAAACATTC
38206 CTA
65 CTA
* * *
38209 TAAAATTTTGATAAATCTCCCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAA
1 TAAAATTTTGAT-AATCACACTATAAAATTGTGATAACCTCCTTATGAAATCTTGATAA
38268 CTACAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
67 13 0.25
68 39 0.75
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (67 bp):
TAAAATTTTGATAATCACACTATAAAATTGTGATAACCTCCTTATGAAATCTTGATAAACATTCC
TA
Found at i:38259 original size:22 final size:21
Alignment explanation
Indices: 38144--38432 Score: 180
Period size: 22 Copynumber: 13.5 Consensus size: 21
38134 TCACACTCTA
* *
38144 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCTC-CTATG
*
38166 AAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCTC-CTATG
* *
38188 AAATTTTGATAAACATTCCTATA
1 AAATTTTGAT-AAC-CTCCTATG
* *
38211 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGAT-AACCT-CCTATG
38234 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCC-TATG
* *
38256 AAATCTTGATAA----CTA-C
1 AAATTTTGATAACCTCCTATG
38272 AAATTTTGATAACCTCCCTA-G
1 AAATTTTGATAACCT-CCTATG
** *
38293 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTC-CTATG
* *
38315 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCT-CCTATG
* * * *
38337 AAATTTCGATCTACATGCTATG
1 AAATTTTGAT-AACCTCCTATG
*
38359 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAA-CCTCCTATG
* *
38381 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT--CCTATG
* * *
38403 AAATTTTAATATCCTCC-CTG
1 AAATTTTGATAACCTCCTATG
38423 AAATTTTGAT
1 AAATTTTGAT
38433 TACTCCGTAA
Statistics
Matches: 207, Mismatches: 43, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
20 14 0.07
21 24 0.12
22 111 0.54
23 42 0.20
24 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTATG
Found at i:38562 original size:22 final size:22
Alignment explanation
Indices: 38513--38751 Score: 148
Period size: 22 Copynumber: 10.8 Consensus size: 22
38503 GAAATACCAC
* *
38513 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCAC-TT
* *
38536 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCACTT
*
38557 TATGAAATTTTGATAACCACTC
1 TATGAAATTTTGATAACCACTT
* * * * *
38579 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCACTT
* * *
38601 AATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCACTT
* * *
38623 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCAC-TT
* **
38646 T-TGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCACTT
*
38667 TATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAACCACTT
*
38687 CCTAT-AAATTTTGATAATCCGATCTC
1 --TATGAAATTTTGATAA-CC-A-CTT
* * *
38713 TATGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAACCACTT
*
38735 TATGAGA-TTTGATAACC
1 TATGAAATTTTGATAACC
38752 TTCTATCAAA
Statistics
Matches: 166, Mismatches: 39, Indels: 24
0.72 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 24 0.14
22 120 0.72
23 4 0.02
24 4 0.02
25 11 0.07
26 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACTT
Found at i:38563 original size:44 final size:44
Alignment explanation
Indices: 38513--38705 Score: 166
Period size: 44 Copynumber: 4.4 Consensus size: 44
38503 GAAATACCAC
* *
38513 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
* * * * *
38557 TATGAAATTTTGATAACCAC-TCTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACAT-TATGAAAA-TTTGATAACCTCTT
* * * *
38601 AATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-TT
* *
38646 T-TGAAATTTTGATAA-CAACACTATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAATC-ACATTATGAAAATTTGATAACCTCTT
38687 CCTAT-AAATTTTGATAATC
1 --TATGAAATTTTGATAATC
38706 CGATCTCTAT
Statistics
Matches: 119, Mismatches: 20, Indels: 20
0.75 0.13 0.13
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 19 0.16
44 94 0.79
45 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
Found at i:38675 original size:88 final size:88
Alignment explanation
Indices: 38514--38678 Score: 242
Period size: 88 Copynumber: 1.9 Consensus size: 88
38504 AAATACCACT
* * * * *
38514 ATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCACTC
1 ATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACAC
38579 TATAAAATTTTGTTGACCCCTCA
66 TATAAAATTTTGTTGACCCCTCA
* *
38602 ATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACA
1 ATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAACA
*
38666 CTATGAAATTTTG
65 CTATAAAATTTTG
38679 ATAATCTTCC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
88 66 0.97
89 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (88 bp):
ATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACAC
TATAAAATTTTGTTGACCCCTCA
Found at i:38828 original size:22 final size:22
Alignment explanation
Indices: 38803--38928 Score: 114
Period size: 22 Copynumber: 5.7 Consensus size: 22
38793 ATGACCTTCA
*
38803 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTCAC
*
38825 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
38847 CATGAAATATT-AGTAACCTTC-T
1 TATGAAATTTTGA-TAACC-TCAC
* * *
38869 TATAAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCTCAC
*
38891 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCAC
*
38913 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
38929 TCTCTTTGAT
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
21 4 0.05
22 74 0.90
23 4 0.05
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:38877 original size:66 final size:65
Alignment explanation
Indices: 38796--39167 Score: 273
Period size: 66 Copynumber: 5.4 Consensus size: 65
38786 GACTTTTATG
* *
38796 ACCTTCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATTAGT
1 ACCTTCTTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAAT-TTAGT
38861 A
65 A
* * * * *
38862 ACCTTCTTATAAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCTCGCTATGACATTTTGA
1 ACCTTCTTATAAAATTTTGATAACCACACTATGAAATT-TTGATAACCTCCCCATGAAATTTAG-
38926 TA
64 TA
* * * * * **
38928 ATCTCTTTGATAATCTTTTATAAAATTGTGATGACCACACTATG-AATTTTCAATAATCTTCGTA
1 A-C-C-----T--TC--TTATAAAATTTTGATAACCACACTATGAAATTTT-GATAACCTCCCCA
* *
38992 AGAAATTTGAATA
54 TGAAATTT-AGTA
* * * * *
39005 ACCTGATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTG
1 ACCT--TCTTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATTTAG
39070 ATA
64 -TA
* * * * * *
39073 A-CTTCCATATAAAATTTTGGTAATCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAA
1 ACCTT-CTTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATT-TAG
39137 TA
64 TA
* *
39139 ACCATCTTATCAAATTTTGATAACCACAC
1 ACCTTCTTATAAAATTTTGATAACCACAC
39168 AGAGACAAGA
Statistics
Matches: 241, Mismatches: 44, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
65 4 0.02
66 125 0.52
67 8 0.03
68 42 0.17
69 6 0.02
70 4 0.02
73 1 0.00
75 5 0.02
76 5 0.02
77 41 0.17
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (65 bp):
ACCTTCTTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATTTAGTA
Found at i:39041 original size:22 final size:22
Alignment explanation
Indices: 39013--39167 Score: 122
Period size: 22 Copynumber: 7.0 Consensus size: 22
39003 TAACCTGATC
*
39013 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
39035 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
39057 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
* * *
39080 -TATAAAATTTTGGTAATCACA
1 CTATGAAATTTTGATAACCACA
* *
39101 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
39122 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
* *
39145 TTATCAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
39167 C
1 C
39168 AGAGACAAGA
Statistics
Matches: 103, Mismatches: 21, Indels: 18
0.73 0.15 0.13
Matches are distributed among these distances:
20 1 0.01
21 5 0.05
22 93 0.90
23 3 0.03
24 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:39362 original size:19 final size:20
Alignment explanation
Indices: 39331--39368 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39321 ATTGACATTT
39331 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
39350 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
39369 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:44855 original size:21 final size:21
Alignment explanation
Indices: 44830--44878 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
44820 ACTGAGATGG
* *
44830 TGAGATTAGTTACTTTACAGA
1 TGAGATTAGATACTGTACAGA
44851 TGAGATTAGATACTGTACAGA
1 TGAGATTAGATACTGTACAGA
44872 TGAGATT
1 TGAGATT
44879 GTAATCAGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (21 bp):
TGAGATTAGATACTGTACAGA
Done.