Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014234.1 Corchorus olitorius cultivar O-4 contig14267, 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: 57350
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:15210 original size:12 final size:13
Alignment explanation
Indices: 15183--15211 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15173 AGGGAGTGAG
15183 TTATTTACTCTAT
1 TTATTTACTCTAT
15196 TTATTTACT-TAT
1 TTATTTACTCTAT
15208 TTAT
1 TTAT
15212 GAATCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTTACTCTAT
Found at i:19630 original size:60 final size:60
Alignment explanation
Indices: 19555--19719 Score: 208
Period size: 60 Copynumber: 2.8 Consensus size: 60
19545 CTAATTGCTT
* * *
19555 AAATAAGAGCTTAATGTTTGCCGAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACC
1 AAATAAGAGCATAATGTTTGCCAAAATGCTCAAATAAGGGACTGATCTTTTAATTTGACC
* * ** *
19615 AAATAAGGGCATAATGTCTGCCAAAATGCTCAAATAA-GGACCCAGTCTTTTAATTTGGCC
1 AAATAAGAGCATAATGTTTGCCAAAATGCTCAAATAAGGGACTGA-TCTTTTAATTTGACC
* * *
19675 AAATAAGAGCCTAACGTTTGCCAAAATG-TCAAATAAGGGCCTGAT
1 AAATAAGAGCATAATGTTTGCCAAAATGCTCAAATAAGGGACTGAT
19720 AACGAAAATT
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 13 0.15
60 75 0.85
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (60 bp):
AAATAAGAGCATAATGTTTGCCAAAATGCTCAAATAAGGGACTGATCTTTTAATTTGACC
Found at i:20367 original size:72 final size:72
Alignment explanation
Indices: 20253--20655 Score: 563
Period size: 72 Copynumber: 5.5 Consensus size: 72
20243 AGAGAACTTT
* * * **
20253 CTATGAGATTGGACGGCGGTTAAATTCCAAAATAGTCGGGATTCGAGTTTTGTTAATGGTTTGAA
1 CTATGAGATTGGAC-GCGATTAAACTCCGAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAA
*
20318 AGAGCACC
65 AGAGCTCC
*
20326 CTATGAGATTGGACACGATTAAACTCCGAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAA
1 CTATGAGATTGGACGCGATTAAACTCCGAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAA
20391 GAGCTCC
66 GAGCTCC
* *
20398 CTATGAGATTGGACGCGGTTAAACTCCGAAATAGTCGGGATTCGAGTTTTGTTAATGGCTTGAAA
1 CTATGAGATTGGACGCGATTAAACTCCGAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAA
*
20463 GAGCACC
66 GAGCTCC
* *
20470 CCATGAGATTGGACACGATTAAACTCCGAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAA
1 CTATGAGATTGGACGCGATTAAACTCCGAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAA
20535 GAGCTCC
66 GAGCTCC
* *
20542 CTATGAGATTAGACGCGGTTAAACTCTGAAATCTCTGAAATAGTCGGGATTCGAGTTTTGTTAAT
1 CTATGAGATTGGACGC-G----A-T-T-AAA-CTCCGAAATAGTCGGGATTCGAGTTTTGTTAAT
20607 GACTTGAAAGAGCTCC
57 GACTTGAAAGAGCTCC
* * *
20623 CTGTGAGATTAGACGCGGTTAAACTCCGAAATA
1 CTATGAGATTGGACGCGATTAAACTCCGAAATA
20656 ATCAAGCTCA
Statistics
Matches: 298, Mismatches: 23, Indels: 19
0.88 0.07 0.06
Matches are distributed among these distances:
72 208 0.70
73 18 0.06
74 1 0.00
75 1 0.00
77 1 0.00
78 1 0.00
79 1 0.00
80 4 0.01
81 63 0.21
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (72 bp):
CTATGAGATTGGACGCGATTAAACTCCGAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAA
GAGCTCC
Found at i:20632 original size:81 final size:81
Alignment explanation
Indices: 20497--20654 Score: 298
Period size: 81 Copynumber: 2.0 Consensus size: 81
20487 ATTAAACTCC
20497 GAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAAGAGCTCCCTATGAGATTAGACGCGGTT
1 GAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAAGAGCTCCCTATGAGATTAGACGCGGTT
*
20562 AAACTCTGAAATCTCT
66 AAACTCCGAAATCTCT
*
20578 GAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAAGAGCTCCCTGTGAGATTAGACGCGGTT
1 GAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAAGAGCTCCCTATGAGATTAGACGCGGTT
20643 AAACTCCGAAAT
66 AAACTCCGAAAT
20655 AATCAAGCTC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (81 bp):
GAAATAGTCGGGATTCGAGTTTTGTTAATGACTTGAAAGAGCTCCCTATGAGATTAGACGCGGTT
AAACTCCGAAATCTCT
Found at i:23279 original size:164 final size:166
Alignment explanation
Indices: 23006--23435 Score: 801
Period size: 164 Copynumber: 2.6 Consensus size: 166
22996 TCCTAAAGTC
23006 TGTAAGTTGTGCACCTGAATGCGAAATGTTTGGAACGGTTTTCTGATATAGTTTAGCACATTAGC
1 TGTAAGTTGTGCACCTGAATGCGAAATGTTTGGAACGGTTTTCTGATATAGTTTAGCACATTAGC
*
23071 TGCCTTTGCATGTGTGGTAAAACGAGTATTTTTTAGATGGCTCTTCGACTTAAGCTATCATAACG
66 TGCCTTTGCATGTGTGATAAAACGAGTATTTTTTAGATGGCTCTTCGACTTAAGCTATCATAACG
23136 TATATGGTTATTTAATGCAGGATCTGATAATCAGA-
131 TATATGGTTATTTAATGCAGGATCTGATAATCAGAT
23171 T-TAAGTTGTGCACCTGAATGCGAAATGTTTGGAACGGTTTTCTGATATAGTTTAGCACATTAGC
1 TGTAAGTTGTGCACCTGAATGCGAAATGTTTGGAACGGTTTTCTGATATAGTTTAGCACATTAGC
23235 TGCCTTTGCATGTGTGATAAAACGAGTATTTTTTAGATGGCTCTTCGACTTAAGCTATCATAACG
66 TGCCTTTGCATGTGTGATAAAACGAGTATTTTTTAGATGGCTCTTCGACTTAAGCTATCATAACG
*
23300 TATATGGTTATTTAATGCATGATCTGATAATCAGATT
131 TATATGGTTATTTAATGCAGGATCTGATAATCAGA-T
*
23337 TGTAAGTTGTGCACCTGAATGCGAAATGTTTGGAACGGTTTTTTGATATAGTTTAGCACATTAGC
1 TGTAAGTTGTGCACCTGAATGCGAAATGTTTGGAACGGTTTTCTGATATAGTTTAGCACATTAGC
*
23402 TGCCTTTGCATGTGTGATAAAACGAGTATCTTTT
66 TGCCTTTGCATGTGTGATAAAACGAGTATTTTTT
23436 GTAGGAAAAC
Statistics
Matches: 258, Mismatches: 4, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
164 161 0.62
165 1 0.00
166 1 0.00
167 95 0.37
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (166 bp):
TGTAAGTTGTGCACCTGAATGCGAAATGTTTGGAACGGTTTTCTGATATAGTTTAGCACATTAGC
TGCCTTTGCATGTGTGATAAAACGAGTATTTTTTAGATGGCTCTTCGACTTAAGCTATCATAACG
TATATGGTTATTTAATGCAGGATCTGATAATCAGAT
Found at i:23758 original size:166 final size:166
Alignment explanation
Indices: 23477--23868 Score: 644
Period size: 166 Copynumber: 2.3 Consensus size: 166
23467 TTCCAACATC
* * * *
23477 TTTTAGATGGCTCTTCGACTTAAGGTCTTGTAACGTATATGGTTATTTAATGCAGGAACAGATAA
1 TTTTAGATGGCTCTTCGACTTAAGATATCGTAACGTATATGGTTATTTAATGCAGGAACAGAGAA
*
23542 TCGGATTTGTAAGTTGTGCACCTGAATGCAAAATGTGTGGAACCGTTTTCTGATATAGTTTAGCA
66 TCGGATTTGTAAGTTGTGCACCTGAATGCAAAATGTGTGGAACAGTTTTCTGATATAGTTTAGCA
*
23607 CATTA-AGCCTTTGCATGTGTGATTAAACGAGTATTT
131 CATTACAGCCTTTGCATGTGTGATTAAACGAATA-TT
23643 TTTTAGATGGCTCTTCGACTTAAGATATCGTAACGTATATGGTTATTTAATGCAGGAACAGAGAA
1 TTTTAGATGGCTCTTCGACTTAAGATATCGTAACGTATATGGTTATTTAATGCAGGAACAGAGAA
23708 TCGGATTTGTAAGTTGTGCACCTGAATGCAAAATGTGTGGAACAGTTTTCTGATATAGTTTAGCA
66 TCGGATTTGTAAGTTGTGCACCTGAATGCAAAATGTGTGGAACAGTTTTCTGATATAGTTTAGCA
*
23773 CATTAGCTGCCTTTGCATGTGTGATTAAACGAATATT
131 CATTA-CAGCCTTTGCATGTGTGATTAAACGAATATT
* * *
23810 TTTTAGATGGCT-TTTGACTTAAGATATCGTAACATATATGATTATTTTTAATGCAGGAA
1 TTTTAGATGGCTCTTCGACTTAAGATATCGTAACGTATATGGTTA--TTTAATGCAGGAA
23869 TGGATAATCA
Statistics
Matches: 212, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
166 159 0.75
167 14 0.07
168 39 0.18
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.37
Consensus pattern (166 bp):
TTTTAGATGGCTCTTCGACTTAAGATATCGTAACGTATATGGTTATTTAATGCAGGAACAGAGAA
TCGGATTTGTAAGTTGTGCACCTGAATGCAAAATGTGTGGAACAGTTTTCTGATATAGTTTAGCA
CATTACAGCCTTTGCATGTGTGATTAAACGAATATT
Found at i:23794 original size:378 final size:375
Alignment explanation
Indices: 23101--23813 Score: 1140
Period size: 378 Copynumber: 1.9 Consensus size: 375
23091 AACGAGTATT
* *
23101 TTTTAGATGGCTCTTCGACTTAAGCTATCATAACGTATATGGTTATTTAATGCAGGATCTGATAA
1 TTTTAGATGGCTCTTCGACTTAAGCTATCATAACGTATATGGTTATTTAATGCAGGAACAGATAA
* * *
23166 TCAGATTAAGTTGTGCACCTGAATGCGAAATGTTTGGAACGGTTTTCTGATATAGTTTAGCACAT
66 TCAGATTAAGTTGTGCACCTGAATGCAAAATGTGTGGAACCGTTTTCTGATATAGTTTAGCACAT
* *
23231 TAGCTGCCTTTGCATGTGTGATAAAACGAGTATTTTTTAGATGGCTCTTCGACTTAAGCTATCAT
131 TA-CAGCCTTTGCATGTGTGATAAAACGAGTATTTTTTAGATGGCTCTTCGACTTAAGATATCAT
* * * * *
23296 AACGTATATGGTTATTTAATGCATGATCTGATAATCAGATTTGTAAGTTGTGCACCTGAATGCGA
195 AACGTATATGGTTATTTAATGCAGGAACAGAGAATCAGATTTGTAAGTTGTGCACCTGAATGCAA
* * *
23361 AATGTTTGGAACGGTTTTTTGATATAGTTTAGCACATTAGCTGCCTTTGCATGTGTGATAAAACG
260 AATGTGTGGAACAGTTTTCTGATATAGTTTAGCACATTAGCTGCCTTTGCATGTGTGATAAAACG
*
23426 AGTATCTTTTGTAGGAAAACTACAACAAACACGTTGGATTTTTCCAACATC
325 AATATCTTTTGTAGGAAAACTACAACAAACACGTTGGATTTTTCCAACATC
* * **
23477 TTTTAGATGGCTCTTCGACTTAAGGTCTTGTAACGTATATGGTTATTTAATGCAGGAACAGATAA
1 TTTTAGATGGCTCTTCGACTTAAGCTATCATAACGTATATGGTTATTTAATGCAGGAACAGATAA
*
23542 TCGGATTTGTAAGTTGTGCACCTGAATGCAAAATGTGTGGAACCGTTTTCTGATATAGTTTAGCA
66 TCAGA--T-TAAGTTGTGCACCTGAATGCAAAATGTGTGGAACCGTTTTCTGATATAGTTTAGCA
*
23607 CATTA-AGCCTTTGCATGTGTGATTAAACGAGTATTTTTTTAGATGGCTCTTCGACTTAAGATAT
128 CATTACAGCCTTTGCATGTGTGATAAAACGAGTA-TTTTTTAGATGGCTCTTCGACTTAAGATAT
* *
23671 CGTAACGTATATGGTTATTTAATGCAGGAACAGAGAATCGGATTTGTAAGTTGTGCACCTGAATG
192 CATAACGTATATGGTTATTTAATGCAGGAACAGAGAATCAGATTTGTAAGTTGTGCACCTGAATG
*
23736 CAAAATGTGTGGAACAGTTTTCTGATATAGTTTAGCACATTAGCTGCCTTTGCATGTGTGATTAA
257 CAAAATGTGTGGAACAGTTTTCTGATATAGTTTAGCACATTAGCTGCCTTTGCATGTGTGATAAA
*
23801 ACGAATATTTTTT
322 ACGAATATCTTTT
23814 AGATGGCTTT
Statistics
Matches: 307, Mismatches: 26, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
376 63 0.21
377 26 0.08
378 160 0.52
379 58 0.19
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (375 bp):
TTTTAGATGGCTCTTCGACTTAAGCTATCATAACGTATATGGTTATTTAATGCAGGAACAGATAA
TCAGATTAAGTTGTGCACCTGAATGCAAAATGTGTGGAACCGTTTTCTGATATAGTTTAGCACAT
TACAGCCTTTGCATGTGTGATAAAACGAGTATTTTTTAGATGGCTCTTCGACTTAAGATATCATA
ACGTATATGGTTATTTAATGCAGGAACAGAGAATCAGATTTGTAAGTTGTGCACCTGAATGCAAA
ATGTGTGGAACAGTTTTCTGATATAGTTTAGCACATTAGCTGCCTTTGCATGTGTGATAAAACGA
ATATCTTTTGTAGGAAAACTACAACAAACACGTTGGATTTTTCCAACATC
Found at i:25067 original size:25 final size:25
Alignment explanation
Indices: 25033--25082 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
25023 GCTTATGTTT
25033 CGTTCTGTGCCCAAGGCCAAAACAG
1 CGTTCTGTGCCCAAGGCCAAAACAG
25058 CGTTCTGTGCCCAAGGCCAAAACAG
1 CGTTCTGTGCCCAAGGCCAAAACAG
25083 AGAGAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (25 bp):
CGTTCTGTGCCCAAGGCCAAAACAG
Found at i:29577 original size:26 final size:26
Alignment explanation
Indices: 29538--29595 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
29528 TGTTTATTTG
* *
29538 AATTAAAACCTTTCCATTAAAAAAAA
1 AATTAAAACATTTCCATCAAAAAAAA
* * *
29564 AATTATAACATTTCCCTCAAACAAAA
1 AATTAAAACATTTCCATCAAAAAAAA
29590 AATTAA
1 AATTAA
29596 GTAAAACCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (26 bp):
AATTAAAACATTTCCATCAAAAAAAA
Found at i:31973 original size:2 final size:2
Alignment explanation
Indices: 31966--31990 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31956 AGAATTATTT
31966 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 T
31991 TTTTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35984 original size:33 final size:32
Alignment explanation
Indices: 35922--35985 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
35912 AAATGGCATC
*
35922 ATTCGGTTGAGTCTTTTTTTTTGGGCTACTTG
1 ATTCGGTTGAGTCTTTTTTTTTGGACTACTTG
* *
35954 ATTCGGTTGTGTTCTTTCTTTTTT-TACTACTT
1 ATTCGGTTGAG-TCTTT-TTTTTTGGACTACTT
35986 TGGTTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 10 0.37
33 11 0.41
34 6 0.22
ACGTcount: A:0.09, C:0.14, G:0.19, T:0.58
Consensus pattern (32 bp):
ATTCGGTTGAGTCTTTTTTTTTGGACTACTTG
Found at i:36560 original size:79 final size:75
Alignment explanation
Indices: 36445--36599 Score: 256
Period size: 79 Copynumber: 2.0 Consensus size: 75
36435 CAAATGGTAC
36445 ATCAAAAAAATATAGAATTTTTTTTTTGTTTGAAAAAATTTATGGCTAAAACCCAATTGGTTTAG
1 ATCAAAAAAATATAGAATTTTTTTTTTGTTTGAAAAAATTTATGGCTAAAACCCAATTGGTTTAG
*
36510 CGTAAGAAAA
66 CGCAAGAAAA
*
36520 ATCACAAAAATATAGAAAAATTCTTTTTTTTGTTTGAAAAAATTTATGGCTAAAACCCAATTGGT
1 ATCAAAAAAATATAG---AATT-TTTTTTTTGTTTGAAAAAATTTATGGCTAAAACCCAATTGGT
36585 TTAGCGCAAGAAAA
62 TTAGCGCAAGAAAA
36599 A
1 A
36600 GGTAAACAGA
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
75 14 0.19
78 4 0.05
79 56 0.76
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (75 bp):
ATCAAAAAAATATAGAATTTTTTTTTTGTTTGAAAAAATTTATGGCTAAAACCCAATTGGTTTAG
CGCAAGAAAA
Found at i:37753 original size:13 final size:13
Alignment explanation
Indices: 37720--37746 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37710 CTGCATAAAA
37720 TAATTAATAGTAT
1 TAATTAATAGTAT
37733 TAATTAATAGTAT
1 TAATTAATAGTAT
37746 T
1 T
37747 GCATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TAATTAATAGTAT
Found at i:39733 original size:22 final size:22
Alignment explanation
Indices: 39685--39735 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
39675 AAATTACATT
*
39685 AAGGAAAATATCATTAATGGAG
1 AAGGAAAATATCATTAATGGAC
*
39707 TAGGAAAATATCATTAA-GGAAC
1 AAGGAAAATATCATTAATGG-AC
39729 AAGGAAA
1 AAGGAAA
39736 TTAAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.20
Consensus pattern (22 bp):
AAGGAAAATATCATTAATGGAC
Found at i:43117 original size:6 final size:6
Alignment explanation
Indices: 43106--43130 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43096 AATTAACAGC
43106 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
43131 TTTGCTATAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:54637 original size:24 final size:24
Alignment explanation
Indices: 54605--54683 Score: 113
Period size: 24 Copynumber: 3.1 Consensus size: 24
54595 CTCTTCAATA
*
54605 CAAAACAGAGATACAGCGAAATCC
1 CAAAACAGAGATACAGCAAAATCC
54629 CAAAACAGAGATACATACAGCAAAATCC
1 CAAAACAGAG----ATACAGCAAAATCC
54657 CAAAACAGAGATACAGCAAAATCC
1 CAAAACAGAGATACAGCAAAATCC
54681 CAA
1 CAA
54684 TCATTTATGG
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
24 27 0.54
28 23 0.46
ACGTcount: A:0.53, C:0.25, G:0.13, T:0.09
Consensus pattern (24 bp):
CAAAACAGAGATACAGCAAAATCC
Found at i:54655 original size:28 final size:28
Alignment explanation
Indices: 54615--54671 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
54605 CAAAACAGAG
*
54615 ATACAGCGAAATCCCAAAACAGAGATAC
1 ATACAGCAAAATCCCAAAACAGAGATAC
54643 ATACAGCAAAATCCCAAAACAGAGATAC
1 ATACAGCAAAATCCCAAAACAGAGATAC
54671 A
1 A
54672 GCAAAATCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.53, C:0.25, G:0.12, T:0.11
Consensus pattern (28 bp):
ATACAGCAAAATCCCAAAACAGAGATAC
Found at i:55113 original size:16 final size:17
Alignment explanation
Indices: 55092--55165 Score: 64
Period size: 16 Copynumber: 4.3 Consensus size: 17
55082 TAGGGTTTTA
55092 ATATAAAAT-ATATTAT
1 ATATAAAATAATATTAT
*
55108 ATATAATACTAATATTAAT
1 ATATAA-AATAATATT-AT
*
55127 ATATATATATAATGA-TAT
1 ATATA-AAATAAT-ATTAT
*
55145 ATATAAAA-AATATAAT
1 ATATAAAATAATATTAT
55161 ATATA
1 ATATA
55166 TAATTTGTCG
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
15 1 0.02
16 16 0.34
17 4 0.09
18 12 0.26
19 12 0.26
20 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
ATATAAAATAATATTAT
Done.