Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018652.1 Corchorus olitorius cultivar O-4 contig18685, 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: 46792
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6275 original size:2 final size:2
Alignment explanation
Indices: 6264--6301 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
6254 GTCCAAACCC
6264 AT AT AT -T 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 AT AT A
6302 ATTAGCTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7155 original size:32 final size:32
Alignment explanation
Indices: 7093--7155 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
7083 GGCTTGAGTC
* *
7093 GGGTTAAATTTGGATCAGACTGATTTGGGTTT
1 GGGTTAAATTTGGATCAGACTAATTCGGGTTT
* *
7125 GGGTTAAATTTGGGTCAGATTAATTCGGGTT
1 GGGTTAAATTTGGATCAGACTAATTCGGGTT
7156 CAGGTTAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.22, C:0.06, G:0.32, T:0.40
Consensus pattern (32 bp):
GGGTTAAATTTGGATCAGACTAATTCGGGTTT
Found at i:7162 original size:32 final size:32
Alignment explanation
Indices: 7094--7162 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
7084 GCTTGAGTCG
* * **
7094 GGTTAAATTTGGATCAGACTGATTTGGGTTTG
1 GGTTAAATTTGGATCAGACTAATTCGGGTTCA
* *
7126 GGTTAAATTTGGGTCAGATTAATTCGGGTTCA
1 GGTTAAATTTGGATCAGACTAATTCGGGTTCA
7158 GGTTA
1 GGTTA
7163 GGTTTTAGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.39
Consensus pattern (32 bp):
GGTTAAATTTGGATCAGACTAATTCGGGTTCA
Found at i:7365 original size:22 final size:22
Alignment explanation
Indices: 7337--7378 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7327 TAGTATTGAA
*
7337 TTCGGGTTTTTTCAGGTTCGAG
1 TTCGGGTTTTTACAGGTTCGAG
7359 TTCGGGTTTTTACAGGTTCG
1 TTCGGGTTTTTACAGGTTCG
7379 GGTCTTATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.14, G:0.31, T:0.45
Consensus pattern (22 bp):
TTCGGGTTTTTACAGGTTCGAG
Found at i:8236 original size:65 final size:65
Alignment explanation
Indices: 8132--8264 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 65
8122 CGGAATGTGA
8132 GTTTAATTTGTAATTTGTTTGTTTGTTTATTTGGTTTGTAGGTAGATATAGTTTTCAGTTTCTAG
1 GTTTAATTTGTAATTTGTTTGTTTGTTTATTTGGTTTGTAGGTAGATATAGTTTTCAGTTTCTAG
*
8197 GTTTAATTTGTAATTTGTTTGTTTGTTTATTTGGTTTGTAGGTAGGTATAGTTTTCAGTTTCTAG
1 GTTTAATTTGTAATTTGTTTGTTTGTTTATTTGGTTTGTAGGTAGATATAGTTTTCAGTTTCTAG
8262 GTT
1 GTT
8265 CAAGAGCCAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.57
Consensus pattern (65 bp):
GTTTAATTTGTAATTTGTTTGTTTGTTTATTTGGTTTGTAGGTAGATATAGTTTTCAGTTTCTAG
Found at i:8361 original size:68 final size:68
Alignment explanation
Indices: 8282--8418 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
8272 CAGGTGTTAT
8282 GAGATTTCAATTGTATTTGTTGGGGAAGGGGTTGACTCATAGATTAGCGTTTCGATAAGCATGTA
1 GAGATTTCAATTGTATTTGTTGGGGAAGGGGTTGACTCATAGATTAGCGTTTCGATAAGCATGTA
8347 GCA
66 GCA
8350 GAGATTTCAATTGTATTTGTTGGGGAAGGGGTTGACTCATAGATTAGCGTTTCGATAAGCATGTA
1 GAGATTTCAATTGTATTTGTTGGGGAAGGGGTTGACTCATAGATTAGCGTTTCGATAAGCATGTA
8415 GCA
66 GCA
8418 G
1 G
8419 TGTACGGTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.26, C:0.10, G:0.30, T:0.34
Consensus pattern (68 bp):
GAGATTTCAATTGTATTTGTTGGGGAAGGGGTTGACTCATAGATTAGCGTTTCGATAAGCATGTA
GCA
Found at i:11038 original size:30 final size:32
Alignment explanation
Indices: 10989--11058 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
10979 TAAATGCCCT
*
10989 TTTGCCCCCTTACCTTTTCAAAAAT-GGACAC
1 TTTGCCCCCTTACCTTTTCAAAAATGGGACAA
* **
11020 TTTGCCCCCTTAGC-TTTCAAATTTGGGACAA
1 TTTGCCCCCTTACCTTTTCAAAAATGGGACAA
11051 TTTGCCCC
1 TTTGCCCC
11059 AAAAGGACGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.34
Consensus pattern (32 bp):
TTTGCCCCCTTACCTTTTCAAAAATGGGACAA
Found at i:26646 original size:14 final size:15
Alignment explanation
Indices: 26629--26657 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
26619 ATTGACAATA
26629 TTAAAATTT-ATTAT
1 TTAAAATTTAATTAT
26643 TTAAAATTTAATTAT
1 TTAAAATTTAATTAT
26658 AAATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAAATTTAATTAT
Found at i:27041 original size:22 final size:22
Alignment explanation
Indices: 27009--27108 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
26999 ATTTCATATG
* **
27009 AAAATTCCATAGTTTGGTTACC
1 AAAATTTCATAGTAAGGTTACC
* *
27031 AAAATTTCATA-TGAAAGTTATC
1 AAAATTTCATAGT-AAGGTTACC
* * * *
27053 AAAATTTCATGGGAAGATTATC
1 AAAATTTCATAGTAAGGTTACC
**
27075 AAAATTTCATAGTGTGGTTACC
1 AAAATTTCATAGTAAGGTTACC
27097 AAAATTTCATAG
1 AAAATTTCATAG
27109 GATCAAGTTA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 1 0.02
22 60 0.98
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGTAAGGTTACC
Found at i:27124 original size:24 final size:22
Alignment explanation
Indices: 27031--27154 Score: 90
Period size: 22 Copynumber: 5.5 Consensus size: 22
27021 TTTGGTTACC
* *
27031 AAAATTTCATATGAAAGTTATC
1 AAAATTTCATAGGAAAGTTATT
* *
27053 AAAATTTCAT-GGGAAGATTATC
1 AAAATTTCATAGGAAAG-TTATT
** **
27075 AAAATTTCATAGTG-TGGTTACC
1 AAAATTTCATAG-GAAAGTTATT
27097 AAAATTTCATAGGATCAAGTTATT
1 AAAATTTCATAGGA--AAGTTATT
** *
27121 AAAATTTTTTAGGAAGGTTATT
1 AAAATTTCATAGGAAAGTTATT
*
27143 GAAATTTCATAG
1 AAAATTTCATAG
27155 TGTGGTTATC
Statistics
Matches: 81, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.06
22 57 0.70
23 2 0.02
24 17 0.21
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGGAAAGTTATT
Found at i:27149 original size:68 final size:66
Alignment explanation
Indices: 27009--27189 Score: 211
Period size: 68 Copynumber: 2.7 Consensus size: 66
26999 ATTTCATATG
* * * *
27009 AAAATTCCATAGTTTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATGGGAAGATTAT
1 AAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAAAGTTATCAAAATTTCATAGGAAGATTAT
27074 C
66 C
* ** *
27075 AAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAAGTTATTAAAATTTTTTAGGAAGGTT
1 AAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA--AAGTTATCAAAATTTCATAGGAAGATT
*
27140 ATT
64 ATC
* * * *
27143 GAAATTTCATAGTGTGGTTATCACAATTTTATA-GAAAGGTTATCAAA
1 AAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAAA-GTTATCAAA
27190 GAGATTATCA
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 2 0.02
66 41 0.42
67 2 0.02
68 53 0.54
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (66 bp):
AAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAAAGTTATCAAAATTTCATAGGAAGATTAT
C
Found at i:27219 original size:22 final size:22
Alignment explanation
Indices: 27194--28161 Score: 266
Period size: 22 Copynumber: 43.7 Consensus size: 22
27184 ATCAAAGAGA
* *
27194 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
27216 TTAT-AAGAATTTCATAATGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
27238 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
27260 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
27282 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
27304 TTATCAAAATTTCAT-TTGAAGC
1 TTATCAAAATTTCATAGTG-AGG
* *
27326 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
27351 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
*
27373 TTATC-AAATCTCATA--GA-G
1 TTATCAAAATTTCATAGTGAGG
* * *
27391 TGCATCGAAATTTCATAGAGATCGG
1 T-TATCAAAATTTCATAGTGA--GG
*
27416 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
**
27438 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* *
27460 TTATCAAAATTTGAAAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
*
27482 TTATCAAAATTACATGATGTGA--
1 TTATCAAAATTTCAT-A-GTGAGG
27504 TTATCAAAATTTCATAGAT-AGG
1 TTATCAAAATTTCATAG-TGAGG
* * * *
27526 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
27548 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
27570 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
27592 TTA-CTAAATTTCATAGTG-GTAT
1 TTATCAAAATTTCATAGTGAG--G
** ** *
27614 TTATGGGGAGGTTATCA-A---A-A
1 TTAT--CAAAATT-TCATAGTGAGG
*
27634 TT-TCATAGTATGGTTACCAAATTAG-GAAGG
1 TTATCA-A-AAT--TT--C--A-TAGTG-AGG
* *
27664 TTATTAAACTCTT-ATTA-TGGAGG
1 TTATCAAAAT-TTCA-TAGT-GAGG
* *
27687 ATATCAAAATTTCATA-TGAATG
1 TTATCAAAATTTCATAGTG-AGG
*
27709 TTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG-TGAGG
* *
27731 TTTTCAAAATTTCATA-AGAGGG
1 TTATCAAAATTTCATAGTGA-GG
* *
27753 TTATCAAAATTTTATAGT-ATG
1 TTATCAAAATTTCATAGTGAGG
* * *
27774 TAGATCAAAATTTCATAGGGAGA
1 T-TATCAAAATTTCATAGTGAGG
* * *
27797 TTAACAAAATTCCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
** *
27819 TTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
27841 TTATCAAAA-TT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
*
27857 TTATCAAGATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
27879 TTATCAAAATTTTACT-GGGAGAT
1 TTATCAAAATTTCA-TAGTGAG-G
*
27902 TTATCAAAATTTTATAG-GAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
27924 TTTATCAAAATTTCATGGCGAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
27947 TTATCACAATTTCATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
27969 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
27991 TTA-CTAACAA-TTCATA-TGAAGG
1 TTATC-AA-AATTTCATAGTG-AGG
* * * ** *
28013 TTTTTAAATTTTCATAACGTGG
1 TTATCAAAATTTCATAGTGAGG
*
28035 TTATCAATATATT-ATA-TGGAGG
1 TTATCAAAAT-TTCATAGT-GAGG
* * *
28057 TTATCAATATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AGG
* *
28080 TTATCAAAATTTCATTCG-GAAG
1 TTATCAAAATTTCA-TAGTGAGG
* *
28102 TTATCATAATTTCTTAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
28124 TCT-TCAAAATTCCTTAGGGAGG
1 T-TATCAAAATTTCATAGTGAGG
*
28146 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
28162 AGAAGGTTAA
Statistics
Matches: 696, Mismatches: 155, Indels: 190
0.67 0.15 0.18
Matches are distributed among these distances:
16 9 0.01
17 3 0.00
18 4 0.01
19 8 0.01
20 24 0.03
21 54 0.08
22 453 0.65
23 85 0.12
24 15 0.02
25 18 0.03
26 10 0.01
27 4 0.01
28 2 0.00
29 2 0.00
30 3 0.00
31 2 0.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:27909 original size:23 final size:23
Alignment explanation
Indices: 27879--27936 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
27869 CATAAGGAGG
*
27879 TTATCAAAATTTTACT-GGGAGAT
1 TTATCAAAATTTTA-TAGGAAGAT
*
27902 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGAT
27925 TTATCAAAATTT
1 TTATCAAAATTT
27937 CATGGCGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:27951 original size:45 final size:45
Alignment explanation
Indices: 27855--27982 Score: 136
Period size: 45 Copynumber: 2.8 Consensus size: 45
27845 CAAAATTTGT
* *
27855 AGTTATCAAGATTTCATAAGGAGGTTATCAAAATTTTACTGGGAG
1 AGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCACTGGGAG
* *
27900 ATTTATCAAAATTTTAT-AGGAAGGTTTATCAAAATTTCA-TGGCGAG
1 AGTTATCAAAATTTCATAAGG-AGG-TTATCAAAATTTCACTGG-GAG
* * * *
27946 -GTTATCACAATTTCATAATGTGATTATCAAAATTTCA
1 AGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCA
27983 GAGTGTGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
44 17 0.25
45 34 0.49
46 18 0.26
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (45 bp):
AGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCACTGGGAG
Found at i:28168 original size:22 final size:22
Alignment explanation
Indices: 28143--28184 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28133 TTCCTTAGGG
*
28143 AGGTTAACA-AAATTTCATAAGA
1 AGGTTAAAAGAAATTT-ATAAGA
28165 AGGTTAAAAGAAATTTATAA
1 AGGTTAAAAGAAATTTATAA
28185 AAAGATTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (22 bp):
AGGTTAAAAGAAATTTATAAGA
Found at i:29045 original size:43 final size:42
Alignment explanation
Indices: 28962--29047 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
28952 TCAAAATCAA
* * * * *
28962 TGGTATATTATCCTTTTAAATTGCACAATTTGTATTAATTAT
1 TGGTATATTATCCTTTTAAATCGCAAAATCTATATCAATTAT
29004 TGGTATTATTATCCTTTTAAATCGCAAAATCTATATCAATTAT
1 TGGTA-TATTATCCTTTTAAATCGCAAAATCTATATCAATTAT
29047 T
1 T
29048 TTATCACTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 5 0.13
43 33 0.87
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (42 bp):
TGGTATATTATCCTTTTAAATCGCAAAATCTATATCAATTAT
Found at i:34186 original size:22 final size:23
Alignment explanation
Indices: 34161--34213 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 23
34151 AGGGAACGTT
*
34161 AATTTCATAGGTA-GGTTACCAG
1 AATTTCATAGGTATGGTTACCAA
*
34183 AATTTC--A-GTATGGTTATCAA
1 AATTTCATAGGTATGGTTACCAA
34203 AATTTCATAGG
1 AATTTCATAGG
34214 GAAGTTTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
22 7 0.28
23 1 0.04
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (23 bp):
AATTTCATAGGTATGGTTACCAA
Found at i:35943 original size:21 final size:24
Alignment explanation
Indices: 35914--35964 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
35904 TTTTGAACTC
35914 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
35937 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
35960 ATTAT
1 ATTAT
35965 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:35959 original size:25 final size:25
Alignment explanation
Indices: 35914--35962 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
35904 TTTTGAACTC
*
35914 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
35939 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
35963 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:42471 original size:30 final size:30
Alignment explanation
Indices: 42435--42494 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
42425 TGGAATTGCT
* * *
42435 AATCTAAACTAAGATTATGACTAAGATGAC
1 AATCTAAACTAAAAGTATAACTAAGATGAC
42465 AATCTAAACTAAAAGTATAACTAAGATGAC
1 AATCTAAACTAAAAGTATAACTAAGATGAC
42495 CAAAGAGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (30 bp):
AATCTAAACTAAAAGTATAACTAAGATGAC
Found at i:42639 original size:30 final size:30
Alignment explanation
Indices: 42557--42712 Score: 219
Period size: 30 Copynumber: 5.3 Consensus size: 30
42547 AGGTGACCGA
* *
42557 AATGCCCCCAGATATGCAA-AAATTACCAT
1 AATGCCCCTAGATATGCAAGAAATTATCAT
*
42586 AATGCCCCTGGATATGC-AGAAATTATCAT
1 AATGCCCCTAGATATGCAAGAAATTATCAT
42615 AATGCCCCTAGATATGCAAGAAATTATCAT
1 AATGCCCCTAGATATGCAAGAAATTATCAT
42645 AATGCCCCTAGATATGCAAGAAATTATCAT
1 AATGCCCCTAGATATGCAAGAAATTATCAT
* * * *
42675 AATGCCCCTGGATACGCAA-AAATGACCAT
1 AATGCCCCTAGATATGCAAGAAATTATCAT
42704 AATGTCCCC
1 AATG-CCCC
42713 GGATCTGTAA
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
28 1 0.01
29 52 0.45
30 63 0.54
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (30 bp):
AATGCCCCTAGATATGCAAGAAATTATCAT
Found at i:42659 original size:59 final size:59
Alignment explanation
Indices: 42557--42712 Score: 233
Period size: 59 Copynumber: 2.6 Consensus size: 59
42547 AGGTGACCGA
* *
42557 AATGCCCCCAGATATGCAAAAATTACCATAATGCCCCTGGATATGC-AGAAATTATCAT
1 AATGCCCCTAGATATGCAAAAATTACCATAATGCCCCTAGATATGCAAGAAATTATCAT
*
42615 AATGCCCCTAGATATGCAAGAAATTATCATAATGCCCCTAGATATGCAAGAAATTATCAT
1 AATGCCCCTAGATATGCAA-AAATTACCATAATGCCCCTAGATATGCAAGAAATTATCAT
* * *
42675 AATGCCCCTGGATACGCAAAAATGACCATAATGTCCCC
1 AATGCCCCTAGATATGCAAAAATTACCATAATG-CCCC
42713 GGATCTGTAA
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
58 18 0.20
59 37 0.42
60 33 0.38
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (59 bp):
AATGCCCCTAGATATGCAAAAATTACCATAATGCCCCTAGATATGCAAGAAATTATCAT
Found at i:42759 original size:29 final size:29
Alignment explanation
Indices: 42511--42803 Score: 126
Period size: 29 Copynumber: 10.0 Consensus size: 29
42501 GAACCCAGAG
* * *
42511 TATGCAAAAATGACCAAAATACCCCTGGA
1 TATGCGAAAATGACCAAAATGCCCTTGGA
* * * * ***
42540 CATAC-AAAGGTGACCGAAATGCCCCCAGA
1 TATGCGAAA-ATGACCAAAATGCCCTTGGA
* * * *
42569 TATGCAAAAATTACCATAATGCCCCTGGA
1 TATGCGAAAATGACCAAAATGCCCTTGGA
* * * * *
42598 TATGC-AGAAATTATCATAATGCCCCTAGA
1 TATGCGA-AAATGACCAAAATGCCCTTGGA
* * * * * *
42627 TATGCAAGAAATTATCATAATGCCCCTAGA
1 TATGCGA-AAATGACCAAAATGCCCTTGGA
* * * * *
42657 TATGCAAGAAATTATCATAATGCCCCTGGA
1 TATGCGA-AAATGACCAAAATGCCCTTGGA
* * * *
42687 TACGCAAAAATGACCATAATGTCCC-CGGA
1 TATGCGAAAATGACCAAAATG-CCCTTGGA
* * * *
42716 TCTG-TAAACACGACCAAAATGCCTTTGGA
1 TATGCGAAA-ATGACCAAAATGCCCTTGGA
*
42745 TATGCGAAAATGACCAAGATGCCCTTGGA
1 TATGCGAAAATGACCAAAATGCCCTTGGA
* * *
42774 TTTGCGTAAATGACCAAAATGCCCCTGGA
1 TATGCGAAAATGACCAAAATGCCCTTGGA
42803 T
1 T
42804 TCACAAAAGG
Statistics
Matches: 218, Mismatches: 38, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
28 9 0.04
29 141 0.65
30 68 0.31
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (29 bp):
TATGCGAAAATGACCAAAATGCCCTTGGA
Found at i:43411 original size:22 final size:20
Alignment explanation
Indices: 43384--43437 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
43374 GTAATTATTA
43384 AAATTTCATAGCATGATTATC
1 AAATTTCATAGCAT-ATTATC
* *
43405 AACATTTAATAGGATAGTTATC
1 AA-ATTTCATAGCATA-TTATC
43427 ATAATTTCATA
1 A-AATTTCATA
43438 AAAATATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 23 0.85
23 1 0.04
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (20 bp):
AAATTTCATAGCATATTATC
Done.