Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021719.1 Corchorus olitorius cultivar O-4 contig21752, 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: 8253
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:4221 original size:2 final size:2
Alignment explanation
Indices: 4214--4249 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4204 TTGCCTTTAG
4214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4250 TCTACTGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4667 original size:13 final size:14
Alignment explanation
Indices: 4637--4680 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
4627 ACATACTTTT
* *
4637 AAAAGGATTTTTCA
1 AAAATGATTTCTCA
4651 AAAATGATTTCTCA
1 AAAATGATTTCTCA
4665 AAAATGATTTC-CA
1 AAAATGATTTCTCA
4678 AAA
1 AAA
4681 TTTGTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (14 bp):
AAAATGATTTCTCA
Found at i:6388 original size:35 final size:35
Alignment explanation
Indices: 6323--7064 Score: 469
Period size: 36 Copynumber: 20.9 Consensus size: 35
6313 ATGTTCAAAG
* * * **
6323 TTTCAGTTGACCCAGGGCGGT-TTCCCTTCAGTAAA
1 TTTCAATTGACCCAGGGTGGTCTT-TCTTCAGTTTA
* *
6358 TTTCAATCGACCCAGGGTGGTCTTTTTTCAGTGGTT-
1 TTTCAATTGACCCAGGGTGGTCTTTCTTCAGT--TTA
* * * * *
6394 TTT-AAGTTGATCCAGGGCGATCATTCTTCAGTCTA
1 TTTCAA-TTGACCCAGGGTGGTCTTTCTTCAGTTTA
* *
6429 TTTCAGTTGACCCAGGGTTGTCTTTCTTCAGTTTA
1 TTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTA
* *
6464 -TTAAAGTTGACCTAGGGTGGTCTTTTCTTCAGTTTA
1 TTTCAA-TTGACCCAGGGTGGTC-TTTCTTCAGTTTA
* * * * * *
6500 TGTCAGAATGATCGAGGGTGGTCGTTCTTCAATTTA
1 TTTCA-ATTGACCCAGGGTGGTCTTTCTTCAGTTTA
*
6536 TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
1 TTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTA
* *
6571 TTTCAGTTGACCCAGGGTGGTCTTTTCTCCAGTTTA
1 TTTCAATTGACCCAGGGTGGTC-TTTCTTCAGTTTA
* * * *
6607 TTTCAAGTGACCTAGGGTGGTCTTTCTTCATTTTG
1 TTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTA
* * * * * *
6642 TGTCGGAA-TGATCGAGGGTGGT-TGTTCCTCAATTCA
1 TTTC--AATTGACCCAGGGTGGTCT-TTCTTCAGTTTA
* * * * *
6678 GTTCGGAA--GATCGATGGCGGTCTTTCTTCAGTTTA
1 TTTC--AATTGACCCAGGGTGGTCTTTCTTCAGTTTA
* * * *
6713 TTTCAGTTGACCCAGGGCGGTCGTCCTTCAGTTTA
1 TTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTA
* *
6748 TTTCAGTCGACCCAGGGTGGTCTTTTCTTCAGTTTA
1 TTTCAATTGACCCAGGGTGGTC-TTTCTTCAGTTTA
* *
6784 TGTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTA
1 TTTCAATTGACCCAGGGTGGTC-TTTCTTCAGTTTA
* * * *
6820 TTTCAAGTAACCCAGGGAGGTCTTTCTTCAGTTTG
1 TTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTA
* *** * *
6855 TGTCGGAA-TGATTGAGGGTGGT-TGTTCCTCAGTTCA
1 TTTC--AATTGACCCAGGGTGGTCT-TTCTTCAGTTTA
* * * * * *
6891 GTTCGAAATGATCGAGGGTGGTCGTTCTTTAGTTTA
1 TTTC-AATTGACCCAGGGTGGTCTTTCTTCAGTTTA
* * * **
6927 TTTTAGTTGACCCAGGGTGGTCTTTCTTTAGTTGG
1 TTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTA
* * * * * *
6962 TGTCGAAATGATCGAGGGTGGTCATTTTTTCGGTTTA
1 TTTC-AATTGACCCAGGGTGGTC-TTTCTTCAGTTTA
* * * * * **
6999 TTTGAAGTGACCTAGGCTGGTCTTGCTTCAACTTA
1 TTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTA
*
7034 TTTCAGAATGACCCAGGGTGGTCTTTCTTCA
1 TTTCA-ATTGACCCAGGGTGGTCTTTCTTCA
7065 ATTCTTCAAG
Statistics
Matches: 550, Mismatches: 131, Indels: 51
0.75 0.18 0.07
Matches are distributed among these distances:
33 1 0.00
34 4 0.01
35 248 0.45
36 267 0.49
37 29 0.05
38 1 0.00
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.39
Consensus pattern (35 bp):
TTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTTA
Found at i:6492 original size:71 final size:70
Alignment explanation
Indices: 6327--7064 Score: 468
Period size: 71 Copynumber: 10.4 Consensus size: 70
6317 TCAAAGTTTC
* * ** * * *
6327 AGTTGACCCAGGGCGGT-TTCCCTTCAGTAAATTTCAATCGACCCAGGGTGGTCTTTTTTCAGTG
1 AGTTGACCCAGGGTGGTCTT-TCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGT-
6391 GTT-TTTA
64 -TTATTTA
* * * * * *
6398 AGTTGATCCAGGGCGATCATTCTTCAGTCTATTTCAGTTGACCCAGGGTTGTCTTTCTTCAGTTT
1 AGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
*
6463 ATTAA
66 ATTTA
* * * * * * *
6468 AGTTGACCTAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTCAAT
1 AGTTGACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCTTTCTTCAGT
*
6533 TTATTTC
64 TTATTTA
*
6540 AGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTCCAGTT
1 AGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-TTTCTTCAGTT
6605 TATTTCA
65 TATTT-A
* * * * * * * * * *
6612 AG-TGACCTAGGGTGGTCTTTCTTCATTTTGTGTCGGAATGATCGAGGGTGGT-TGTTCCTCAAT
1 AGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCT-TTCTTCAGT
* * *
6675 TCAGTTC
64 TTATTTA
* ** * * * * * * *
6682 GGAAGATCGATGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCGTCCTTCAGTTT
1 AGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
*
6747 ATTTC
66 ATTTA
* *
6752 AGTCGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTTCAGT
1 AGTTGACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-TTTCTTCAGT
6817 TTATTTCA
64 TTATTT-A
* * * * * * *** *
6825 AG-TAACCCAGGGAGGTCTTTCTTCAGTTTGTGTCGGAATGATTGAGGGTGGT-TGTTCCTCAGT
1 AGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCT-TTCTTCAGT
* *
6888 TCAGTTCGA
64 TTA-TT-TA
* * * * * * *
6897 A-ATGATCGAGGGTGGTCGTTCTTTAGTTTATTTTAGTTGACCCAGGGTGGTCTTTCTTTAGTTG
1 AGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTT-
* **
6961 GTGTCGA
65 -TATTTA
* * * * * * * * * **
6968 A-ATGATCGAGGGTGGTCATTTTTTCGGTTTATTTGAAG-TGACCTAGGCTGGTCTTGCTTCAAC
1 AGTTGACCCAGGGTGGTC-TTTCTTCAGTTTATTT-CAGTTGACCCAGGGTGGTCTTTCTTCAGT
*
7031 TTATTTC
64 TTATTTA
*
7038 AGAATGACCCAGGGTGGTCTTTCTTCA
1 AG-TTGACCCAGGGTGGTCTTTCTTCA
7065 ATTCTTCAAG
Statistics
Matches: 511, Mismatches: 131, Indels: 50
0.74 0.19 0.07
Matches are distributed among these distances:
69 2 0.00
70 69 0.14
71 266 0.52
72 170 0.33
73 4 0.01
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.39
Consensus pattern (70 bp):
AGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
ATTTA
Found at i:6633 original size:142 final size:142
Alignment explanation
Indices: 6398--6853 Score: 544
Period size: 142 Copynumber: 3.2 Consensus size: 142
6388 GTGGTTTTTA
* * * * *
6398 AGTTGATCCAGGGCGATCATTCTTCAGTCTATTTCAGTTGACCCAGGGTTGTCTTTCTTCAGTTT
1 AGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
*
6463 A-TTAAAGTTGACCTAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTC
66 ATTTCAAG-TGACCTAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTC
6527 TTCAATTTATTTC
130 TTCAATTTATTTC
* *
6540 AGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTCCAGTT
1 AGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-TTTCTTCAGTT
* * * *
6605 TATTTCAAGTGACCTAGGGTGGTC-TTTCTTCATTTTGTGTCGGAATGATCGAGGGTGGTTGTTC
65 TATTTCAAGTGACCTAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTC
* * *
6669 CTCAATTCAGTTC
130 TTCAATTTATTTC
* ** * * * * * *
6682 GGAAGATCGATGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCGTCCTTCAGTTT
1 AGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
* * * * *
6747 ATTTC-AGTCGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAG-TTGACCCAGGGTGGTCTTTT
66 ATTTCAAGT-GACCTAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTC-GTT
*
6810 CTTCAGTTTATTTC
129 CTTCAATTTATTTC
* *
6824 AAG-TAACCCAGGGAGGTCTTTCTTCAGTTT
1 -AGTTGACCCAGGGCGGTCTTTCTTCAGTTT
6854 GTGTCGGAAT
Statistics
Matches: 262, Mismatches: 46, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
140 3 0.01
141 39 0.15
142 187 0.71
143 28 0.11
144 5 0.02
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (142 bp):
AGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
ATTTCAAGTGACCTAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCT
TCAATTTATTTC
Found at i:6706 original size:213 final size:214
Alignment explanation
Indices: 6477--6948 Score: 678
Period size: 213 Copynumber: 2.2 Consensus size: 214
6467 AAGTTGACCT
* * * * *
6477 AGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTCAATTTATTTCAG
1 AGGGCGGTC-TTTCTTCAGTTTATGTCAG-ATGACCCAGGGCGGTCGTCCTTCAATTTATTTCAG
* *
6542 TTGACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTCCAGTTT
64 TCGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTCCAGTTT
* * * *
6606 ATTTCAAGTGACCTAGGGTGGTCTTTCTTCATTTTGTGTCGGAATGATCGAGGGTGGTTGTTCCT
129 ATTTCAAGTAACCCAGGGAGGTCTTTCTTCAGTTTGTGTCGGAATGATCGAGGGTGGTTGTTCCT
*
6671 CAATTCAGTTCGGAA-GATCG
194 CAATTCAGTTCGAAATGATCG
* * * *
6691 ATGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCGTCCTTCAGTTTATTTCAGTC
1 AGGGCGGTCTTTCTTCAGTTTATGTCAGATGACCCAGGGCGGTCGTCCTTCAATTTATTTCAGTC
*
6756 GACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTAT
66 GACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTCCAGTTTAT
*
6821 TTCAAGTAACCCAGGGAGGTCTTTCTTCAGTTTGTGTCGGAATGATTGAGGGTGGTTGTTCCTCA
131 TTCAAGTAACCCAGGGAGGTCTTTCTTCAGTTTGTGTCGGAATGATCGAGGGTGGTTGTTCCTCA
*
6886 GTTCAGTTCGAAATGATCG
196 ATTCAGTTCGAAATGATCG
* * * * * * *
6905 AGGGTGGTCGTTCTTTAGTTTATTTTAGTTGACCCAGGGTGGTC
1 AGGGCGGTCTTTCTTCAGTTTATGTCAGATGACCCAGGGCGGTC
6949 TTTCTTTAGT
Statistics
Matches: 231, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
212 44 0.19
213 137 0.59
214 50 0.22
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (214 bp):
AGGGCGGTCTTTCTTCAGTTTATGTCAGATGACCCAGGGCGGTCGTCCTTCAATTTATTTCAGTC
GACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTCCAGTTTAT
TTCAAGTAACCCAGGGAGGTCTTTCTTCAGTTTGTGTCGGAATGATCGAGGGTGGTTGTTCCTCA
ATTCAGTTCGAAATGATCG
Found at i:6823 original size:107 final size:105
Alignment explanation
Indices: 6323--6853 Score: 464
Period size: 107 Copynumber: 5.0 Consensus size: 105
6313 ATGTTCAAAG
* * ** * * *
6323 TTTCAGTTGACCCAGGGCGGT-TTCCCTTCAGTAAATTTCAATCGACCCAGGGTGGTCTTTT-TT
1 TTTCAGTTGACCCAGGGTGGTCTT-TCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTT
* * * * *
6386 CAGTGGTT-TTTAAGTTGATCCAGGGCGATCATTCTTCAGTCTA
65 CAGT--TTATTTCAG-TGACCCAGGGCGGTCGTTCTTCAGTTTA
* * *
6429 TTTCAGTTGACCCAGGGTTGTCTTTCTTCAGTTTAT-TAAAGTTGACCTAGGGTGGTCTTTTCTT
1 TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATGT-CAGTTGACCCAGGGTGGTCTTTTCTT
* * * * *
6493 CAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTCAATTTA
65 CAGTTTATTTCAG--TGACCCAGGGCGGTCGTTCTTCAGTTTA
* *
6536 TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTCC
1 TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTTC
* * * * *
6601 AGTTTATTTCAAGTGACCTAGGGTGGTCTTTCTTCATTTTG
66 AGTTTATTTC-AGTGACCCAGGGCGGTCGTTCTTCAGTTTA
* * * * * * * * * ** * * * *
6642 TGTCGGAATGATCGAGGGTGGT-TGTTCCTCAATTCA-GTTCGGAAGATCGATGGCGGTC-TTTC
1 TTTCAG-TTGACCCAGGGTGGTCT-TTCTTCAGTTTATG-TCAGTTGACCCAGGGTGGTCTTTTC
*
6704 TTCAGTTTATTTCAGTTGACCCAGGGCGGTCGTCCTTCAGTTTA
63 TTCAGTTTATTTCAG-TGACCCAGGGCGGTCGTTCTTCAGTTTA
*
6748 TTTCAGTCGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTT
1 TTTCAGTTGACCCAGGGTGGTC-TTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTT
* * *
6813 CAGTTTATTTCAAGTAACCCAGGGAGGTCTTTCTTCAGTTT
65 CAGTTTATTTC-AGTGACCCAGGGCGGTCGTTCTTCAGTTT
6854 GTGTCGGAAT
Statistics
Matches: 338, Mismatches: 71, Indels: 31
0.77 0.16 0.07
Matches are distributed among these distances:
105 16 0.05
106 143 0.42
107 174 0.51
108 5 0.01
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.40
Consensus pattern (105 bp):
TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTTCTTC
AGTTTATTTCAGTGACCCAGGGCGGTCGTTCTTCAGTTTA
Found at i:6887 original size:107 final size:108
Alignment explanation
Indices: 6468--7064 Score: 448
Period size: 107 Copynumber: 5.6 Consensus size: 108
6458 AGTTTATTAA
* * * * * * *
6468 AGTTGACCTAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTCAAT
1 AGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCA-AGTGACCCAGGGTGGTCTTTCTTCAGT
* * * * * * * * *
6533 TTATTTCAG-TTGACCCAGGGTGGTCT-TTCTTCAGTTTATTTC
65 TTGTGTCGGAATGATCGAGGGTGGTCTGTTCCTCAGTTCAGTTC
* * *
6575 AGTTGACCCAGGGTGGTCTTTTCTCCAGTTTATTTCAAGTGACCTAGGGTGGTCTTTCTTCATTT
1 AGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAGTGACCCAGGGTGGTCTTTCTTCAGTT
*
6640 TGTGTCGGAATGATCGAGGGTGGT-TGTTCCTCAATTCAGTTC
66 TGTGTCGGAATGATCGAGGGTGGTCTGTTCCTCAGTTCAGTTC
* ** * * * * * * *
6682 GGAAGATCGATGGCGGTC-TTTCTTCAGTTTATTTC-AGTTGACCCAGGGCGGTCGTCCTTCAGT
1 AGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAG-TGACCCAGGGTGGTCTTTCTTCAGT
* * * * * * * *
6745 TTATTTC--AGTCGACCCAGGGTGGTCTTTTCTTCAGTTTA-TGTC
65 TTGTGTCGGAAT-GATCGAGGGTGGTCTGTTCCTCAGTTCAGT-TC
* *
6788 AGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAGTAACCCAGGGAGGTCTTTCTTCAGTT
1 AGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAGTGACCCAGGGTGGTCTTTCTTCAGTT
*
6853 TGTGTCGGAATGATTGAGGGTGGT-TGTTCCTCAGTTCAGTTC
66 TGTGTCGGAATGATCGAGGGTGGTCTGTTCCTCAGTTCAGTTC
** * * * * * *
6895 GAAATGATCGAGGGTGGTC-GTTCTTTAGTTTATTT-TAGTTGACCCAGGGTGGTCTTTCTTTAG
1 -AGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAG-TGACCCAGGGTGGTCTTTCTTCAG
* * ** * * * *
6958 TTGGTGTCGAAATGATCGAGGGTGGTCAT-TTTTTCGGTTTATTTGA
64 TTTGTGTCGGAATGATCGAGGGTGGTC-TGTTCCTCAGTTCAGTT-C
* * * ** *
7004 AG-TGACCTAGGCTGGTC-TTGCTTCAACTTATTTCAGAATGACCCAGGGTGGTCTTTCTTCA
1 AGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCA-AGTGACCCAGGGTGGTCTTTCTTCA
7065 ATTCTTCAAG
Statistics
Matches: 381, Mismatches: 91, Indels: 35
0.75 0.18 0.07
Matches are distributed among these distances:
104 2 0.01
105 14 0.04
106 95 0.25
107 206 0.54
108 60 0.16
109 4 0.01
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (108 bp):
AGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAGTGACCCAGGGTGGTCTTTCTTCAGTT
TGTGTCGGAATGATCGAGGGTGGTCTGTTCCTCAGTTCAGTTC
Found at i:7054 original size:179 final size:179
Alignment explanation
Indices: 6726--7055 Score: 385
Period size: 179 Copynumber: 1.8 Consensus size: 179
6716 CAGTTGACCC
* **
6726 AGGGCGGTCGTCCTTCAGTTTATTTCAGTCGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGT
1 AGGGCGGTCGTCCTTCAGTTTATTTCAGTCGACCCAGGGTGGTCTTTTCTTCAGTTGATGTCAAA
* * ** *
6791 TGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAGTAACCCAGGGAGGTCTTTCTTCAGTTTGT
66 TGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAGTAACCCAGGCAGGTCTTGCTTCAACTTAT
* ***
6856 GTCGGAATGATTGAGGGTGGTTGTTCCTCAGTTCAGTTCGAAATGATCG
131 GTCAGAATGACCCAGGGTGGTTGTTCCTCAGTTCAGTTCGAAATGATCG
* * * * * * *
6905 AGGGTGGTCGTTCTTTAGTTTATTTTAGTTGACCCAGGGTGGTC-TTTCTTTAGTTGGTGTCGAA
1 AGGGCGGTCGTCCTTCAGTTTATTTCAGTCGACCCAGGGTGGTCTTTTCTTCAGTTGATGTC-AA
* * * * * * *
6969 ATGATCGAGGGTGGTCATTTT-TTCGGTTTATTTGAAGTGACCTAGGCTGGTCTTGCTTCAACTT
65 ATGACCCAGGGTGGTC-TTTTCTTCAGTTTATTTCAAGTAACCCAGGCAGGTCTTGCTTCAACTT
*
7033 ATTTCAGAATGACCCAGGGTGGT
129 ATGTCAGAATGACCCAGGGTGGT
7056 CTTTCTTCAA
Statistics
Matches: 122, Mismatches: 27, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
178 14 0.11
179 104 0.85
180 4 0.03
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (179 bp):
AGGGCGGTCGTCCTTCAGTTTATTTCAGTCGACCCAGGGTGGTCTTTTCTTCAGTTGATGTCAAA
TGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAGTAACCCAGGCAGGTCTTGCTTCAACTTAT
GTCAGAATGACCCAGGGTGGTTGTTCCTCAGTTCAGTTCGAAATGATCG
Done.