Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023822.1 Corchorus olitorius cultivar O-4 contig23855, 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: 57449
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:2334 original size:86 final size:86
Alignment explanation
Indices: 2242--2457 Score: 414
Period size: 86 Copynumber: 2.5 Consensus size: 86
2232 ATTTCTACAT
*
2242 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCATTCTTTATGATTTATTTAT
1 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCAATCTTTATGATTTATTTAT
2307 TTCTTAAAATATATCCTAAAC
66 TTCTTAAAATATATCCTAAAC
2328 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCAATCTTTATGATTTATTTAT
1 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCAATCTTTATGATTTATTTAT
2393 TTCTTAAAATATATCCTAAAC
66 TTCTTAAAATATATCCTAAAC
*
2414 CTTCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATT
1 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATT
2458 TATTGATTAT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 128 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.44
Consensus pattern (86 bp):
CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCAATCTTTATGATTTATTTAT
TTCTTAAAATATATCCTAAAC
Found at i:4522 original size:1 final size:1
Alignment explanation
Indices: 4516--4541 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4506 TGTTCCGCGC
4516 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
4542 GAAGACTCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4709 original size:51 final size:50
Alignment explanation
Indices: 4621--4723 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 50
4611 GTTCTTCATA
** *
4621 TTTTTCTTGTTTAGATCCTGTCTCAGGACATTCAAACACTC-TTTTAGTGT
1 TTTTTCTTGTTTAGATCCTGTCTCAGGACATAAAAACAC-CGTATTAGTGT
* *
4671 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACCGTATTAGTGT
1 TTTT-TCTTGTTT-AGATCCTGTCTCAGGACATAAAAACACCGTATTAGTGT
4722 TT
1 TT
4724 CTCTTTCATC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
50 5 0.11
51 39 0.87
52 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCCTGTCTCAGGACATAAAAACACCGTATTAGTGT
Found at i:8305 original size:40 final size:40
Alignment explanation
Indices: 8219--8307 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
8209 CCTGAAAAAT
* * * *
8219 CGTCTTCCGATTGGCTTCTGAATATCTAAATCTGATAAAC
1 CGTCTTCTGATTGACTTCTGAAAATCTAAATCTAATAAAC
* **
8259 CTTCTTCTGATTGACTTCTGAAAATCTATTTCTAA-ATAAC
1 CGTCTTCTGATTGACTTCTGAAAATCTAAATCTAATA-AAC
8299 CGTCTTCTG
1 CGTCTTCTG
8308 GTGCATCTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.39
Consensus pattern (40 bp):
CGTCTTCTGATTGACTTCTGAAAATCTAAATCTAATAAAC
Found at i:8453 original size:64 final size:64
Alignment explanation
Indices: 8296--8737 Score: 562
Period size: 64 Copynumber: 6.9 Consensus size: 64
8286 ATTTCTAAAT
* * * *
8296 AACCGTCTTCTGGTGCA-TCTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAACCTTTTTGAG
1 AACCATCTTCTGGTGTACT-TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTTTTGAG
8360 A
64 A
* * * * *
8361 AACGATCTTCTGTTGTACTTTTTAACAAGATCATCTTCCGATCAACTTCTGAAAATTTTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGA
* * * * * * *
8425 AACCATCTTTTGGCGTACTTCTTGACAAGATTGTCTTCCGATCAACTTATGAAAACTCTCGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGA
* * * * * * *
8489 AACCATCTTCTGGTGCACTTCTTGACGAGACCGCCTTCCAATCAACTTCTGAAAACTCTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGA
* * *
8553 AACCATCTTCTGGTGCACTTCTTGACCAGATCGTCTTCCGATCATCTTCTGAAAATTTTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGA
* * * *
8617 AACCATCTTCTGGTGTACTTTTTGACGAGATCGTATTCCGATCAACTTCTGAAAATTGTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGA
* * *
8681 AACCATCTTCTGGTGTACTTCTTGACGAGATCGTCTTCCAATCAACATCTGAAAATT
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATT
8738 CTTTCTAGCT
Statistics
Matches: 330, Mismatches: 46, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
64 283 0.86
65 46 0.14
66 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (64 bp):
AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGA
Found at i:11071 original size:9 final size:9
Alignment explanation
Indices: 11050--11087 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
11040 TTAGGCTGAG
11050 TTTTTCTTT-
1 TTTTT-TTTC
11059 TTTTTTTTC
1 TTTTTTTTC
11068 TTTTTTTTC
1 TTTTTTTTC
11077 -TTTTTTTC
1 TTTTTTTTC
11085 TTT
1 TTT
11088 GAGTTGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 11 0.41
9 16 0.59
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:11083 original size:12 final size:12
Alignment explanation
Indices: 11050--11075 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11040 TTAGGCTGAG
11050 TTTTTCTTTTTT
1 TTTTTCTTTTTT
11062 TTTTTCTTTTTT
1 TTTTTCTTTTTT
11074 TT
1 TT
11076 CTTTTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:13095 original size:31 final size:31
Alignment explanation
Indices: 13055--13117 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
13045 TGAAAATAGA
* * *
13055 ACAATCAAGCCTTAAATTG-AAGCAAATCAAC
1 ACAAACAAGCCTCAAATTGCAA-CAAATAAAC
13086 ACAAACAAGCCTCAAATTGCAACAAATAAAC
1 ACAAACAAGCCTCAAATTGCAACAAATAAAC
13117 A
1 A
13118 TGGTCAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (31 bp):
ACAAACAAGCCTCAAATTGCAACAAATAAAC
Found at i:13674 original size:19 final size:19
Alignment explanation
Indices: 13624--13674 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
13614 TGTTTTTTAT
*
13624 GTGTGTATGGTTTGAATGG
1 GTGTGTGTGGTTTGAATGG
* *
13643 GTGTGGGTCGTTTGAATGG
1 GTGTGTGTGGTTTGAATGG
13662 GTGTGTGTGGTTT
1 GTGTGTGTGGTTT
13675 ATGGGTCGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.10, C:0.02, G:0.45, T:0.43
Consensus pattern (19 bp):
GTGTGTGTGGTTTGAATGG
Found at i:16812 original size:14 final size:13
Alignment explanation
Indices: 16787--16831 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
16777 TAAAAGACTC
16787 AAAACC-TTTTTG
1 AAAACCTTTTTTG
16799 AAAACCTATTTTTG
1 AAAACCT-TTTTTG
16813 AAAACCTTTTCTTG
1 AAAACCTTTT-TTG
16827 AAAAC
1 AAAAC
16832 AATTATCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.20
13 3 0.10
14 21 0.70
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (13 bp):
AAAACCTTTTTTG
Found at i:24329 original size:15 final size:16
Alignment explanation
Indices: 24299--24336 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
24289 GGAAAAAAAT
24299 AGAAAGTGAAGGAGGA
1 AGAAAGTGAAGGAGGA
*
24315 AGAAAG-GAGGGAGGA
1 AGAAAGTGAAGGAGGA
*
24330 AGGAAGT
1 AGAAAGT
24337 ACGGGCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.47, T:0.05
Consensus pattern (16 bp):
AGAAAGTGAAGGAGGA
Found at i:28240 original size:19 final size:18
Alignment explanation
Indices: 28216--28255 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28206 TTGAAGATTT
*
28216 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
28235 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
28253 ATT
1 ATT
28256 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:28843 original size:12 final size:12
Alignment explanation
Indices: 28812--28848 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
28802 TCTTTTCATC
28812 TTTTCTTCTA-T
1 TTTTCTTCTAGT
28823 TTTTC-TCTAGT
1 TTTTCTTCTAGT
28834 TTTTCTTCTAGT
1 TTTTCTTCTAGT
28846 TTT
1 TTT
28849 AGGTTGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.17
11 11 0.46
12 9 0.38
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTCTTCTAGT
Found at i:31352 original size:30 final size:29
Alignment explanation
Indices: 31279--31354 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
31269 ACTTGTAGAC
*
31279 TTTGGTCGTTTTGCCCCATGAACTTCAAT
1 TTTGGACGTTTTGCCCCATGAACTTCAAT
*
31308 TTTGGACATTTTGCCCCATGAACTTCAAT
1 TTTGGACGTTTTGCCCCATGAACTTCAAT
31337 TTTGCGACGTTTTGCCCC
1 TTTG-GACGTTTTGCCCC
31355 CTTAGCCTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
29 31 0.72
30 12 0.28
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.39
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCATGAACTTCAAT
Found at i:31538 original size:29 final size:29
Alignment explanation
Indices: 31488--31563 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
31478 CGTTAGCCTG
* *
31488 AGGGGGCAATACGTCCTAAAATTGAAGTTC
1 AGGGGGCAAAACGTCC-AAAATTGAAATTC
*
31518 AGGGGGCAAAATGTCCAAAATTGAAATTC
1 AGGGGGCAAAACGTCCAAAATTGAAATTC
31547 AGGGGGCAAAACGTCCA
1 AGGGGGCAAAACGTCCA
31564 GACGCTACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 28 0.67
30 14 0.33
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAAATTGAAATTC
Found at i:32896 original size:2 final size:2
Alignment explanation
Indices: 32889--32923 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
32879 GGGAAACCAA
32889 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 A
32924 GGTAAATTTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33640 original size:53 final size:53
Alignment explanation
Indices: 33576--34041 Score: 368
Period size: 53 Copynumber: 9.0 Consensus size: 53
33566 TGTTTATTCA
* *
33576 ATTGAACCTATTAAATAAGAACACATATCAAATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
*
33629 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
* *
33682 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGTAATGAACT
1 ATTGAATCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
* * * * * *** ***** * * * *
33735 ATTGGA--T-TTAAAGAAAAATACA-AGCACCCAAT-TGTGTTG--TTTATTCA
1 ATTGAATCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGA-ACT
*
33782 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
*
33835 ATTGAATCTATTAAATAA-ACACACATACCACATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGA-ACACATACCAAATAATACAAAATGCAATGAACT
* * * * * *** ***** * * * *
33888 ATTGGA--T-TTAAAGAAAAATACA-AGCACCCAAT-TGTGTTG--TTTATTCA
1 ATTGAATCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGA-ACT
* * * *
33935 ATTGAACCTATTAAATAGGAACGCATACCAAATAATACAAAATGTAATGAACT
1 ATTGAATCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
* * *
33988 ATTGAATATATTAAATTAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
34041 A
1 A
34042 CTGGATTTAA
Statistics
Matches: 313, Mismatches: 82, Indels: 36
0.73 0.19 0.08
Matches are distributed among these distances:
46 4 0.01
47 12 0.04
48 4 0.01
49 15 0.05
50 44 0.14
51 15 0.05
52 5 0.02
53 210 0.67
54 4 0.01
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (53 bp):
ATTGAATCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
Found at i:33870 original size:153 final size:153
Alignment explanation
Indices: 33629--34068 Score: 781
Period size: 153 Copynumber: 2.9 Consensus size: 153
33619 GCAATGAACT
* *
33629 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATT
1 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATT
*
33694 AAATAAGCACACATACCAAATAATACAAAATGTAATGAACTATTGGATTTAAAGAAAAATACAAG
66 AAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAG
33759 CACCCAATTGTGTTGTTTATTCA
131 CACCCAATTGTGTTGTTTATTCA
33782 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATT
1 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATT
* *
33847 AAATAAACACACATACCACATAATACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAG
66 AAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAG
33912 CACCCAATTGTGTTGTTTATTCA
131 CACCCAATTGTGTTGTTTATTCA
* * * *
33935 ATTGAACCTATTAAATAGGAACGCATACCAAATAATACAAAATGTAATGAACTATTGAATATATT
1 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATT
* *
34000 AAATTAGCACACATACCAAATAATACAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAG
66 AAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAG
34065 CACC
131 CACC
34069 AAAATGACTA
Statistics
Matches: 274, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
153 274 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (153 bp):
ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATT
AAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAG
CACCCAATTGTGTTGTTTATTCA
Found at i:34658 original size:21 final size:21
Alignment explanation
Indices: 34620--34659 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34610 ATAATTTTTA
*
34620 ACTAATAAAAATATATAAAAT
1 ACTAAAAAAAATATATAAAAT
34641 ACTAAAAATAAATA-ATAAA
1 ACTAAAAA-AAATATATAAA
34660 TTAAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (21 bp):
ACTAAAAAAAATATATAAAAT
Found at i:36355 original size:11 final size:11
Alignment explanation
Indices: 36335--36365 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
36325 TCTCCTAAAC
*
36335 TTTTTGTTTTT
1 TTTTTCTTTTT
36346 TTTTTCTTTTT
1 TTTTTCTTTTT
36357 TTTTTCTTT
1 TTTTTCTTT
36366 CTAGTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.90
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:41744 original size:69 final size:69
Alignment explanation
Indices: 41633--41771 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
41623 TATCCGCATA
41633 TTAGTTTAACGAGTTATGGATTAAGTCAACTAAGCAAGTATAATAAATAAAACATATATTGTGCA
1 TTAGTTTAACGAGTTATGGATTAAGTCAACTAAGCAAGTATAATAAATAAAACATATATTGTGCA
41698 ATGC
66 ATGC
41702 TTAGTTTAACGAGTTATGGATTAAGTCAACTAAGCAAGTATAATAAATAAAACATATATTGTGCA
1 TTAGTTTAACGAGTTATGGATTAAGTCAACTAAGCAAGTATAATAAATAAAACATATATTGTGCA
41767 ATGC
66 ATGC
41771 T
1 T
41772 CTTACCGAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (69 bp):
TTAGTTTAACGAGTTATGGATTAAGTCAACTAAGCAAGTATAATAAATAAAACATATATTGTGCA
ATGC
Found at i:44777 original size:29 final size:31
Alignment explanation
Indices: 44745--44803 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
44735 ACGTTTTATC
* *
44745 CCATGAACTT-CAAA-TCAGGATATTTTACA
1 CCATGAAATTCCAAATTCAGGACATTTTACA
*
44774 CCATGAAATTCCAAATTTAGGACATTTTAC
1 CCATGAAATTCCAAATTCAGGACATTTTAC
44804 TGCCTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 4 0.16
31 12 0.48
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.32
Consensus pattern (31 bp):
CCATGAAATTCCAAATTCAGGACATTTTACA
Found at i:46553 original size:16 final size:16
Alignment explanation
Indices: 46532--46581 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
46522 AGCGCAACAA
46532 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
46548 AAACAAAAACAGAAAAAC-
1 AAAC-AAAAC-G-AAAACG
*
46566 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
46581 A
1 A
46582 TGCCAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
14 5 0.17
15 2 0.07
16 9 0.31
17 5 0.17
18 3 0.10
19 5 0.17
ACGTcount: A:0.72, C:0.16, G:0.12, T:0.00
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:49999 original size:438 final size:435
Alignment explanation
Indices: 49056--50159 Score: 1298
Period size: 438 Copynumber: 2.5 Consensus size: 435
49046 AAAATTTCAA
*
49056 AAGCATTTTTTAGAATTGAAACATAAAAATTAGTTTTTGAG-TCTTTCATGAAAGTTGTAGATCA
1 AAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTTC-TTCATGAAAGTTGTAGATCA
* * *
49120 TAAAATTACCTATTAATAGACACTTGAAAT-ACCTTAATTGGACAAATAGAACAAAGAAAATAAC
65 TGAAATTACCTTTTAATAGACA-TTG-AATCACCTTAATCGGACAAATAGAACAAAG--AATAA-
* *
49184 AAAAAATGAAGCGTTAAATCG--AG--TAAGATATAATTTGTAAAGGACTAAGTAGCATAAAATA
125 AAAAAA--AAGC-TTAAA-CGTTAGATTAAGATATAATTTGTAAAGGACTAAATAGCATAAAGT-
* * *
49245 AAAAAAAAGTATGAGGGTGATTTGATAACTAATTCAAATAAGAAAATATTTGTTAATGGAGATCT
185 --AAAAAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCT
* * * * * * *
49310 TGAAACATTAAAATTCCTTTTTGAACTCTTCAAGAAACTCGTAGATCAAATTAACTTTCGGCTTC
248 TGAAACATAAAAATTCCCTTTTGAACCCTTCAAGAAACTCGTAGAACAAATTAACTTTCAGATCC
* * * * *
49375 TTCATGAAAGTCGTAGATCATACAATAACCTTTTAACCGACACTTGAATAACTTTAATTGGACAT
313 TTCATGAAAGTCGTAAATCATACAATAACCATTTAACCAACACTTCAATAACTTCAATTGGACAT
** * * * *
49440 GTGGATTGACAATTATATGGTATTAAATAAACCAACAATCGAAACGACCAAATTTAGG
378 GTGGATCAACAATTATACGATATTAAATAAACCAACAATCAAAACGACAAAATTTAGG
* * * *
49498 AAGCATTTTTTTGAATTGAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTTTAGATCAT
1 AAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTTCTTCATGAAAGTTGTAGATCAT
*
49563 GAAATTACCTTTTAATAGACATATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAA
66 GAAATTACCTTTTAATAGACAT-TGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAA
* * * *
49628 CAAAGCTTAAACGTTAGATTAAGATAGAATTTGTAAAGGACTAACTAGTATAAAGTAGAAAAGTA
130 -AAAGCTTAAACGTTAGATTAAGATATAATTTGTAAAGGACTAAATAGCATAAAGTAAAAAAGTA
*
49693 TGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAAA
194 TGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAA
* * *
49758 AATTCCCTTTTGAACCCTTTACGAAACTCGTAGAACAAATTTAGCTTTCAGATCCTTCATGAAAG
259 AATTCCCTTTTGAACCCTTCAAGAAACTCGTAGAACAAA-TTAACTTTCAGATCCTTCATGAAAG
*
49823 TCGTAAATCATGCAATAACCATTTAACCAACACTTCAATAACTTCAATTGGACATGTGGA-CAAC
323 TCGTAAATCATACAATAACCATTTAACCAACACTTCAATAACTTCAATTGGACATGTGGATCAAC
* ** *
49887 AAATTATACGATATTAAATTAACCGGCAATCAAAATC-ACAAAATTTTGG
388 -AATTATACGATATTAAATAAACCAACAATCAAAA-CGACAAAATTTAGG
** * * * * * *
49936 AAGCATTTTTTAGAATCAAAACATTAAAATTGGGTTTTAAGTTCTTAATGAAAATTGTAGATCAT
1 AAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTTCTTCATGAAAGTTGTAGATCAT
* * * *
50001 GAAATAACCTTTTAATAGACATTTGAATCACCTTAATCAGATAAATAGAA-AAAAAATACAAAAA
66 GAAATTACCTTTTAATAGACA-TTGAATCACCTTAATCGGACAAATAGAACAAAGAATA-AAAAA
* * ** * *
50065 TAAAAGGC--AACGCGTTAAATCGTCCAACCTATAA-TTGTAAAGGACTAAATAGCATAAAGCAT
129 -AAAA-GCTTAA-ACGTTAGAT--T--AAGATATAATTTGTAAAGGACTAAATAGCATAAAGTAA
50127 AAAAGTATGAGGGTCATTAT-ATAAATAATCCAA
187 AAAAGTATGAGGGTCATT-TGATAAATAATCCAA
50160 CAAAAAAAAA
Statistics
Matches: 572, Mismatches: 69, Indels: 43
0.84 0.10 0.06
Matches are distributed among these distances:
436 2 0.00
437 118 0.21
438 232 0.41
439 10 0.02
440 40 0.07
441 59 0.10
442 110 0.19
443 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (435 bp):
AAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTTCTTCATGAAAGTTGTAGATCAT
GAAATTACCTTTTAATAGACATTGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAAA
AAGCTTAAACGTTAGATTAAGATATAATTTGTAAAGGACTAAATAGCATAAAGTAAAAAAGTATG
AGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAAA
TTCCCTTTTGAACCCTTCAAGAAACTCGTAGAACAAATTAACTTTCAGATCCTTCATGAAAGTCG
TAAATCATACAATAACCATTTAACCAACACTTCAATAACTTCAATTGGACATGTGGATCAACAAT
TATACGATATTAAATAAACCAACAATCAAAACGACAAAATTTAGG
Done.