Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013832.1 Corchorus olitorius cultivar O-4 contig13865, 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: 59530
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:1833 original size:21 final size:21
Alignment explanation
Indices: 1809--1865 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
1799 ATTCAACATC
1809 TGAGGCAGGCACAAGAAGAAA
1 TGAGGCAGGCACAAGAAGAAA
* ** * * *
1830 TGAGACATTCGCAAGATGAGA
1 TGAGGCAGGCACAAGAAGAAA
*
1851 TGAGGCAGGAACAAG
1 TGAGGCAGGCACAAG
1866 GTGTTATAAA
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.14, G:0.33, T:0.11
Consensus pattern (21 bp):
TGAGGCAGGCACAAGAAGAAA
Found at i:3938 original size:14 final size:15
Alignment explanation
Indices: 3919--3948 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3909 GAGAACATGA
3919 TTTGAAAA-ACCTTT
1 TTTGAAAACACCTTT
3933 TTTGAAAACACCTTT
1 TTTGAAAACACCTTT
3948 T
1 T
3949 ATTGCTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (15 bp):
TTTGAAAACACCTTT
Found at i:6330 original size:15 final size:15
Alignment explanation
Indices: 6310--6338 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6300 GAGAGAGCCC
6310 TTTTTCTTTTTGTTT
1 TTTTTCTTTTTGTTT
6325 TTTTTCTTTTTGTT
1 TTTTTCTTTTTGTT
6339 ATTGAATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (15 bp):
TTTTTCTTTTTGTTT
Found at i:7214 original size:28 final size:28
Alignment explanation
Indices: 7182--7282 Score: 168
Period size: 28 Copynumber: 3.6 Consensus size: 28
7172 TTGAATGTGC
7182 AAATGACCAAAATGCCCCTGGATTTTGA
1 AAATGACCAAAATGCCCCTGGATTTTGA
7210 AAATGACCAAAATGCCCCTGGATTTTGA
1 AAATGACCAAAATGCCCCTGGATTTTGA
* * *
7238 AAATGACCAAAATGCCCCT-GAATGTAA
1 AAATGACCAAAATGCCCCTGGATTTTGA
7265 AAATGACCAAAATGCCCC
1 AAATGACCAAAATGCCCC
7283 CTAAATGACC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 23 0.33
28 47 0.67
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.21
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGATTTTGA
Found at i:7275 original size:27 final size:28
Alignment explanation
Indices: 7156--7282 Score: 159
Period size: 28 Copynumber: 4.6 Consensus size: 28
7146 TGGTCTTTAC
* * * *
7156 AATGACTAAAACG-CCCTTGAATGTGCA
1 AATGACCAAAATGCCCCTGGAATGTGAA
* *
7183 AATGACCAAAATGCCCCTGGATTTTGAA
1 AATGACCAAAATGCCCCTGGAATGTGAA
* *
7211 AATGACCAAAATGCCCCTGGATTTTGAA
1 AATGACCAAAATGCCCCTGGAATGTGAA
*
7239 AATGACCAAAATGCCCCT-GAATGTAAA
1 AATGACCAAAATGCCCCTGGAATGTGAA
7266 AATGACCAAAATGCCCC
1 AATGACCAAAATGCCCC
7283 CTAAATGACC
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 34 0.38
28 56 0.62
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.21
Consensus pattern (28 bp):
AATGACCAAAATGCCCCTGGAATGTGAA
Found at i:24472 original size:35 final size:35
Alignment explanation
Indices: 24426--24708 Score: 273
Period size: 35 Copynumber: 7.7 Consensus size: 35
24416 AAATCAATAA
**
24426 TTTCAAAAGTTGGCATCGGTTGGCCTTCTAAATTGT
1 TTTC-AAAGTTGGCATCGGTTGGCCTTCTAAAAAGT
* *
24462 TTTCAAAGTTGGCATCGGTGGGGCTTCTTGAAGAAAAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTC-T--A-AAAAGT
* * *
24501 TTCCAAAAGTTGGCACCGGTTGGCCTTCTAAAATGT
1 TTTC-AAAGTTGGCATCGGTTGGCCTTCTAAAAAGT
*
24537 TTTCAAAATTGGCATCGGTTGGCCTTCTTGAAGAAAAAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTC-T----AAAAAGT
* * *
24577 TTCCAAAAGTTGGCATCGGTTGGCCTTTTAAAATGT
1 TTTC-AAAGTTGGCATCGGTTGGCCTTCTAAAAAGT
24613 TTTCAAAGTTGGCATCGGTTGGCCTTCTACAAAA-T
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTA-AAAAGT
*
24648 TTTCAAAGTTGGCATCAGTTGGCCTTCTTGAAAGGAAG-
1 TTTCAAAGTTGGCATCGGTTGGCCTTC-T-AAA--AAGT
* *
24686 TTTCCAATTTGGCATCGGTTGGC
1 TTTCAAAGTTGGCATCGGTTGGC
24709 TTTATTGTAA
Statistics
Matches: 206, Mismatches: 24, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
35 93 0.45
36 29 0.14
37 2 0.01
38 23 0.11
39 8 0.04
40 30 0.15
41 21 0.10
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (35 bp):
TTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGT
Found at i:24609 original size:76 final size:75
Alignment explanation
Indices: 24429--24675 Score: 369
Period size: 76 Copynumber: 3.3 Consensus size: 75
24419 TCAATAATTT
* * *
24429 CAAAAGTTGGCATCGGTTGGCCTTCTAAATTGTTTTCAAAGTTGGCATCGGTGGGGCTTCTTGAA
1 CAAAAGTTGGCATCGGTTGGCCTTCTAAAATGTTTTCAAAGTTGGCATCGGTTGGCCTTCTTGAA
24494 GAAAAGTTTC
66 GAAAAGTTTC
* *
24504 CAAAAGTTGGCACCGGTTGGCCTTCTAAAATGTTTTCAAAATTGGCATCGGTTGGCCTTCTTGAA
1 CAAAAGTTGGCATCGGTTGGCCTTCTAAAATGTTTTCAAAGTTGGCATCGGTTGGCCTTCTTGAA
24569 GAAAAAGTTTC
66 G-AAAAGTTTC
*
24580 CAAAAGTTGGCATCGGTTGGCCTTTTAAAATGTTTTCAAAGTTGGCATCGGTTGGCCTTC-T--A
1 CAAAAGTTGGCATCGGTTGGCCTTCTAAAATGTTTTCAAAGTTGGCATCGGTTGGCCTTCTTGAA
* *
24642 CAAAA-TTTT
66 GAAAAGTTTC
*
24651 C-AAAGTTGGCATCAGTTGGCCTTCT
1 CAAAAGTTGGCATCGGTTGGCCTTCT
24676 TGAAAGGAAG
Statistics
Matches: 159, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
70 22 0.14
71 4 0.03
72 4 0.03
73 1 0.01
75 62 0.39
76 66 0.42
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (75 bp):
CAAAAGTTGGCATCGGTTGGCCTTCTAAAATGTTTTCAAAGTTGGCATCGGTTGGCCTTCTTGAA
GAAAAGTTTC
Found at i:25248 original size:6 final size:6
Alignment explanation
Indices: 25228--25267 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
25218 TAATTCATTT
25228 AAAAA- AAAGAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
25268 GAGGAGCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 3 0.09
6 27 0.82
7 3 0.09
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:25955 original size:7 final size:7
Alignment explanation
Indices: 25943--25969 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25933 TTTGAGTCGA
25943 AGTGGAG
1 AGTGGAG
25950 AGTGGAG
1 AGTGGAG
25957 AGTGGAG
1 AGTGGAG
25964 AGTGGA
1 AGTGGA
25970 AAGCGGCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.56, T:0.15
Consensus pattern (7 bp):
AGTGGAG
Found at i:30360 original size:62 final size:62
Alignment explanation
Indices: 30262--30515 Score: 298
Period size: 62 Copynumber: 4.1 Consensus size: 62
30252 ATTCTCGGTT
* * * * *
30262 GTAAGACCTACTTGGGCATCCCTTACCTAGGCCATAAGACCGATCGACCATTACTCTCGTCT
1 GTAAGACCTAGTTGGGCATCCCTCACTTAGGCCATAAGACCGATCGACCATTACTCTCGGCC
* * * **
30324 GTAAGAGCTAGTTGGGCATCCCTCGCTTAGGTCATAAGATTGATCGACCATTACTCTCGGCC
1 GTAAGACCTAGTTGGGCATCCCTCACTTAGGCCATAAGACCGATCGACCATTACTCTCGGCC
* * * ***
30386 GTAAGACCTAGTTGGGCATCCCTCGCTTGGGTCATAAGATTAATCGACCATTACTCTCGGCC
1 GTAAGACCTAGTTGGGCATCCCTCACTTAGGCCATAAGACCGATCGACCATTACTCTCGGCC
* * *
30448 GTAAGACCTAGTTGGGCAACTC-CAC-TATGGCCATAAGACCGATCGACCATAACT-TCCGGCC
1 GTAAGACCTAGTTGGGCATCCCTCACTTA-GGCCATAAGACCGATCGACCATTACTCT-CGGCC
30509 GTAAGAC
1 GTAAGAC
30516 TCAATTGGAC
Statistics
Matches: 168, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
60 2 0.01
61 35 0.21
62 131 0.78
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (62 bp):
GTAAGACCTAGTTGGGCATCCCTCACTTAGGCCATAAGACCGATCGACCATTACTCTCGGCC
Found at i:30547 original size:123 final size:124
Alignment explanation
Indices: 30304--30547 Score: 273
Period size: 123 Copynumber: 2.0 Consensus size: 124
30294 CATAAGACCG
* * * * * * **
30304 ATCGACCATTACTCTCGTCTGTAAGAGCTAGTTGGGCATCCCTCGCTTAGGTCATAAGATTGATC
1 ATCGACCATTACTCTCGGCCGTAAGACCTAGTTGGGCAACCCTCACTTAGGCCATAAGACCGATC
* * * * * **
30369 GACCATTACTCTCGGCCGTAAGACCTAGTTGGGCATCCCTCGCTTGGGTCATAAGATTA
66 GACCATAACTCTCGGCCGTAAGACCTAATTGGACATCCCTCACTCGGGAAATAAGATTA
*
30428 ATCGACCATTACTCTCGGCCGTAAGACCTAGTTGGGCAACTC-CAC-TATGGCCATAAGACCGAT
1 ATCGACCATTACTCTCGGCCGTAAGACCTAGTTGGGCAACCCTCACTTA-GGCCATAAGACCGAT
30491 CGACCATAACT-TCCGGCCGTAAGA-CTCAATTGGACATCCCAT-ACTCGGGAAATAAGA
65 CGACCATAACTCT-CGGCCGTAAGACCT-AATTGGACATCCC-TCACTCGGGAAATAAGA
30548 CTATTTGACC
Statistics
Matches: 100, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
122 5 0.05
123 57 0.57
124 38 0.38
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (124 bp):
ATCGACCATTACTCTCGGCCGTAAGACCTAGTTGGGCAACCCTCACTTAGGCCATAAGACCGATC
GACCATAACTCTCGGCCGTAAGACCTAATTGGACATCCCTCACTCGGGAAATAAGATTA
Found at i:30956 original size:22 final size:21
Alignment explanation
Indices: 30913--30996 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 21
30903 CATACAATAG
*
30913 TCACGCTTTTGGCACTACACC
1 TCACGCTCTTGGCACTACACC
*
30934 TCACGCTTCTTAGG-ATTACACC
1 TCACGC-TCTT-GGCACTACACC
30956 TCACGCTCTTGGCACTACACC
1 TCACGCTCTTGGCACTACACC
* *
30977 TCATGCTCTTGGCGCTACAC
1 TCACGCTCTTGGCACTACAC
30997 TCTAATTGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 2 0.04
21 35 0.64
22 16 0.29
23 2 0.04
ACGTcount: A:0.19, C:0.37, G:0.15, T:0.29
Consensus pattern (21 bp):
TCACGCTCTTGGCACTACACC
Found at i:34002 original size:21 final size:21
Alignment explanation
Indices: 33978--34022 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33968 GGCGCCCACA
* *
33978 TGGTTACCTTGAGCACCCATG
1 TGGTTACCTTGAGAACCCAGG
**
33999 TGGTTTGCTTGAGAACCCAGG
1 TGGTTACCTTGAGAACCCAGG
34020 TGG
1 TGG
34023 GCAGTGTCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.22, G:0.31, T:0.29
Consensus pattern (21 bp):
TGGTTACCTTGAGAACCCAGG
Found at i:42232 original size:22 final size:21
Alignment explanation
Indices: 42207--42459 Score: 153
Period size: 22 Copynumber: 11.6 Consensus size: 21
42197 TGTGATTACT
*
42207 AAAATTTCATTGTGTGGTTATC
1 AAAATTTCATAG-GTGGTTATC
* *
42229 AAAATTTTATAGAGTGGTTACC
1 AAAATTTCATAG-GTGGTTATC
42251 AAAATTTCATAGGTAGGATT-TC
1 AAAATTTCATAGGT-GG-TTATC
*
42273 AAAATTTTAT-GGTGTAGTTATC
1 AAAATTTCATAGGTG--GTTATC
42295 AAAATTTCAT--GTGATGTTATC
1 AAAATTTCATAGGTG--GTTATC
* *
42316 AAATTTTCATAGGGAGGTTAT-
1 AAAATTTCATA-GGTGGTTATC
*
42337 AAAATTTTATAGG-GATGTTATC
1 AAAATTTCATAGGTG--GTTATC
* *
42359 AGAATTTCATATGGAGGTTATC
1 AAAATTTCATA-GGTGGTTATC
* * *
42381 AGAACTTCATAGGAAGGTTATC
1 AAAATTTCATAGG-TGGTTATC
*
42403 AAAATTTCACAGG-GAAGTTA-C
1 AAAATTTCATAGGTG--GTTATC
**
42424 TAAAATTTCATACTCTGGTTATC
1 -AAAATTTCATA-GGTGGTTATC
*
42447 AAAATTCCATAGG
1 AAAATTTCATAGG
42460 GAGTCTAACA
Statistics
Matches: 185, Mismatches: 26, Indels: 41
0.73 0.10 0.16
Matches are distributed among these distances:
19 1 0.01
20 4 0.02
21 42 0.23
22 129 0.70
23 5 0.03
24 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
AAAATTTCATAGGTGGTTATC
Found at i:42391 original size:65 final size:65
Alignment explanation
Indices: 42223--42449 Score: 191
Period size: 66 Copynumber: 3.5 Consensus size: 65
42213 TCATTGTGTG
* * *
42223 GTTATCAAAATTTTATA-GAGTGGTTACCAAAAT-TTCATAGGTAGGATT-TCAAAATTTTAT-G
1 GTTATCAAAATTTCATATGA--GGTTATC-AAATCTTCATAGGAAGG-TTATCAAAATTTTATAG
42284 GTG-T
62 G-GAT
* * * *
42288 AGTTATCAAAATTTCATGTGATGTTATCAAATTTTCATAGGGAGGTTAT-AAAATTTTATAGGGA
1 -GTTATCAAAATTTCATATGAGGTTATCAAATCTTCATAGGAAGGTTATCAAAATTTTATAGGGA
42352 T
65 T
* * *
42353 GTTATCAGAATTTCATATGGAGGTTATCAGAA-CTTCATAGGAAGGTTATCAAAATTTCACAGGG
1 GTTATCAAAATTTCATAT-GAGGTTATCA-AATCTTCATAGGAAGGTTATCAAAATTTTATAGGG
*
42417 AA
64 AT
**
42419 GTTA-CTAAAATTTCATACTCTGGTTATCAAA
1 GTTATC-AAAATTTCATA-TGAGGTTATCAAA
42450 ATTCCATAGG
Statistics
Matches: 135, Mismatches: 16, Indels: 21
0.78 0.09 0.12
Matches are distributed among these distances:
64 33 0.24
65 47 0.35
66 52 0.39
67 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (65 bp):
GTTATCAAAATTTCATATGAGGTTATCAAATCTTCATAGGAAGGTTATCAAAATTTTATAGGGAT
Found at i:42824 original size:22 final size:22
Alignment explanation
Indices: 42798--42896 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
42788 TGTGGTAATT
*
42798 AAAATTTCATAATGAG-TTGATC
1 AAAATTTCATAATGAGATT-AAC
*
42820 AAAATTTCATAGTGAGATTAAC
1 AAAATTTCATAATGAGATTAAC
* ** **
42842 AAAATTTAATTGTGTAG-TTCTC
1 AAAATTTCATAATG-AGATTAAC
* **
42864 AAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAATGAGATTAAC
42886 AAAATTTCATA
1 AAAATTTCATA
42897 GGAAAGTTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 2 0.03
22 56 0.90
23 4 0.06
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAATGAGATTAAC
Found at i:42846 original size:44 final size:44
Alignment explanation
Indices: 42798--42896 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
42788 TGTGGTAATT
*
42798 AAAATTTCATAATG-AGTTGATCAAAATTTCATAGTGAGATTAAC
1 AAAATTTCATAATGTAGTT-ATCAAAATTTCATAGGGAGATTAAC
* ** * *
42842 AAAATTTAATTGTGTAGTTCTCAAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAATGTAGTTATCAAAATTTCATAGGGAGATTAAC
42886 AAAATTTCATA
1 AAAATTTCATA
42897 GGAAAGTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 42 0.91
45 4 0.09
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.36
Consensus pattern (44 bp):
AAAATTTCATAATGTAGTTATCAAAATTTCATAGGGAGATTAAC
Found at i:42897 original size:22 final size:22
Alignment explanation
Indices: 42819--42898 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
42809 ATGAGTTGAT
*
42819 CAAAATTTCATAGTGAGATTAA
1 CAAAATTTCATAGGGAGATTAA
* * * **
42841 CAAAATTTAATTGTGTAG-TTCT
1 CAAAATTTCATAG-GGAGATTAA
*
42863 CAAAATTTTATAGGGAGATTAA
1 CAAAATTTCATAGGGAGATTAA
42885 CAAAATTTCATAGG
1 CAAAATTTCATAGG
42899 AAAGTTATCG
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
21 3 0.07
22 39 0.89
23 2 0.05
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGATTAA
Found at i:43033 original size:22 final size:21
Alignment explanation
Indices: 42970--43156 Score: 137
Period size: 22 Copynumber: 8.7 Consensus size: 21
42960 AATAGTGTTC
* *
42970 TTATCAAAATTTCGTAGGAGG
1 TTATAAAAATTTCATAGGAGG
*
42991 TTA-ACAAAATTTTATAGGAGG
1 TTATA-AAAATTTCATAGGAGG
*
43012 TTATAAAAAATTCATAGTGAGG
1 TTATAAAAATTTCATAG-GAGG
* *
43034 TTATCAAAATTTCATAAGGTGG
1 TTATAAAAATTTCAT-AGGAGG
**
43056 TTACCAAAATTTCAT--GAGG
1 TTATAAAAATTTCATAGGAGG
* * *
43075 TTATCAAAATTTCAAATGGATG
1 TTATAAAAATTTCATA-GGAGG
* * **
43097 TTATCAAAATTTTATAAAATGG
1 TTATAAAAATTTCATAGGA-GG
*
43119 TTTATAAAAATTTCATAGTGTGG
1 -TTATAAAAATTTCATAG-GAGG
*
43142 TTATCAAAATTTCAT
1 TTATAAAAATTTCAT
43157 GTTATGGTTT
Statistics
Matches: 132, Mismatches: 24, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
19 16 0.12
21 31 0.23
22 67 0.51
23 18 0.14
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.37
Consensus pattern (21 bp):
TTATAAAAATTTCATAGGAGG
Found at i:43083 original size:41 final size:41
Alignment explanation
Indices: 42970--43157 Score: 150
Period size: 41 Copynumber: 4.4 Consensus size: 41
42960 AATAGTGTTC
* * * *
42970 TTATCAAAATTTCGTAGGAGGTTAACAAAATTTTAT-AGGAGG
1 TTATCAAAATTTC--ATGAGGTTATCAAAATTTCATAAGGTGG
* *
43012 TTATAAAAAATTCATAGTGAGGTTATCAAAATTTCATAAGGTGG
1 TTATCAAAATTTC--A-TGAGGTTATCAAAATTTCATAAGGTGG
*
43056 TTACCAAAATTTCATGAGGTTATCAAAATTTCA-AATGGAT-G
1 TTATCAAAATTTCATGAGGTTATCAAAATTTCATAA-GG-TGG
* * *
43097 TTATCAAAATTTTATAAAATGGTTTATAAAAATTTCAT-AGTGTGG
1 TTATCAAAATTTCAT--GA-GG-TTATCAAAATTTCATAAG-GTGG
43142 TTATCAAAATTTCATG
1 TTATCAAAATTTCATG
43158 TTATGGTTTG
Statistics
Matches: 119, Mismatches: 16, Indels: 21
0.76 0.10 0.13
Matches are distributed among these distances:
40 2 0.02
41 35 0.29
42 15 0.13
43 18 0.15
44 19 0.16
45 30 0.25
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (41 bp):
TTATCAAAATTTCATGAGGTTATCAAAATTTCATAAGGTGG
Found at i:43339 original size:22 final size:22
Alignment explanation
Indices: 43311--43362 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
43301 TTGAGGTTTT
**
43311 CAAAATTTTATAGGGATGCTAA
1 CAAAATTTTATAGAAATGCTAA
*
43333 CAAAATTTTATAGAAATGTTAA
1 CAAAATTTTATAGAAATGCTAA
43355 CAAAATTT
1 CAAAATTT
43363 CATATGGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (22 bp):
CAAAATTTTATAGAAATGCTAA
Found at i:43959 original size:14 final size:13
Alignment explanation
Indices: 43916--43963 Score: 78
Period size: 13 Copynumber: 3.6 Consensus size: 13
43906 TGTTGTCTAA
43916 TCTTTGTTTTGCT
1 TCTTTGTTTTGCT
43929 TCTTTGTTTTGCT
1 TCTTTGTTTTGCT
*
43942 TCTTTGTCTTTACT
1 TCTTTGT-TTTGCT
43956 TCTTTGTT
1 TCTTTGTT
43964 CGTTTTAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 21 0.64
14 12 0.36
ACGTcount: A:0.02, C:0.17, G:0.12, T:0.69
Consensus pattern (13 bp):
TCTTTGTTTTGCT
Found at i:47142 original size:51 final size:51
Alignment explanation
Indices: 47079--47181 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
47069 CATACTCACA
* *
47079 AGATTCAATTATGGTTCCTAATCTGGTTTTAGAGGCACAAAGAAACAAGTC
1 AGATTCAATTATGGTTCCTAATCTGGTTTTAAAGGCACAAAAAAACAAGTC
47130 AGATTCAATTATGGTTCCTAATCTGGTTTTAAAGGCACAAAAAAACAAGTC
1 AGATTCAATTATGGTTCCTAATCTGGTTTTAAAGGCACAAAAAAACAAGTC
47181 A
1 A
47182 TGATAGAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (51 bp):
AGATTCAATTATGGTTCCTAATCTGGTTTTAAAGGCACAAAAAAACAAGTC
Done.