Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008284.1 Corchorus capsularis cultivar CVL-1 contig08305, 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: 57617
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3876 original size:33 final size:30
Alignment explanation
Indices: 3822--3895 Score: 103
Period size: 33 Copynumber: 2.4 Consensus size: 30
3812 ATTAATCTGC
*
3822 TCTAAAAAAAAGTTTTTTTTTTCCGTTTTT
1 TCTAAAAAAAAGTTTTTTTTTTCCGATTTT
3852 TCTAAAAAAAATGTTTTTCCTTTTTCCGATTTT
1 TCTAAAAAAAA-GTTTTT--TTTTTCCGATTTT
*
3885 TATAAAAAAAA
1 TCTAAAAAAAA
3896 AAGCGATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 11 0.28
31 6 0.15
33 22 0.56
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (30 bp):
TCTAAAAAAAAGTTTTTTTTTTCCGATTTT
Found at i:5287 original size:41 final size:41
Alignment explanation
Indices: 5100--5782 Score: 648
Period size: 41 Copynumber: 16.1 Consensus size: 41
5090 TGATGTAAAT
* *
5100 ACAGTCAAAGTCTTAATTCAAGGTAATTAAGAAAAGCAAGCAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAA--AC
* * *
5143 AGTCAAAGTCAAAATCTTAATTCAGGGTAATTAAGAGAAG--AAC
1 A--C--AGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* * *
5186 ACAGTCAAAGTCTTAATTCAGGGTAATTAAGAGAAG-AAGC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
5226 ACAGTTAAAGTCAGAATCTTAATTCAGGGTAGTTAAGAAAAGCAAAC
1 ACAGTT-AA---AG--TCTTAATTCAGGGTAATTAAGAAAAGCAAAC
**
5273 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAGGAG--AAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* * * *
5312 ACAGTCAAAGTCTTAATTAAGGATAATTAAGAGAAA--AAGC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGA-AAAGCAAAC
5352 ACAGTTAAAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAAAC
1 ACAGTTAAAG------TCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
5399 ACAATTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* * * *
5440 ACAATTAAAGTCTTAATTTAGGGTAATTAAGAAAAGAAAAT
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* * * *
5481 GCAGTTAAAGTTTTAATTCTGGGTAATTAAGAAAAGAAGAAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCA-AAC
** * * *
5523 GTAGTCAAAGTTTTAATTCAGGGTAATTAAGAAAAGCAAGC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
5564 ACAGTTAAAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGTAAAC
1 ACAGTTAAAG------TCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
5611 ACAGTTAAAGTCTTAATTCAGGTTAATTAAGAAAAGCAAAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* ** * *
5652 ATAGTCGAAGTCTTAATTTA-GGTAATTAAGAAAAGCAAGC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
5692 ACAGTTAAGGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAAAC
1 ACAG-T----T-AAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* * *
5739 ACAGTTAAAGTCTCAA--CATGGTAATTAAGAAAAGTAAAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
5778 ACAGT
1 ACAGT
5783 CAAGGGTTTA
Statistics
Matches: 543, Mismatches: 61, Indels: 76
0.80 0.09 0.11
Matches are distributed among these distances:
39 91 0.17
40 40 0.07
41 191 0.35
42 37 0.07
43 6 0.01
44 2 0.00
45 5 0.01
46 58 0.11
47 113 0.21
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (41 bp):
ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
Found at i:5325 original size:126 final size:126
Alignment explanation
Indices: 5102--5844 Score: 676
Period size: 126 Copynumber: 5.9 Consensus size: 126
5092 ATGTAAATAC
* *
5102 AGTCAAAGTCTTAATTCAAGGTAATTAAGAAAAGCAAGCACAGTCAAAGTCAAAATCTTAATTCA
1 AGTCAAA-TCTTAATTCAGGGTAATTAAGAAAAGCAA--ACA--C--AGTCAAAGTCTTAATTCA
* * *
5167 GGGTAATTAAGAGAAG-AACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAGAAGAAGCACAGT
59 GGGTAATTAAGAAAAGCAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAACACAGT
5231 TAA
124 TAA
* *
5234 AGTCAGAATCTTAATTCAGGGTAGTTAAGAAAAGCAAACACAGTTAAAGTCTTAATTCAGGGTAA
1 AGTCA-AATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCAAAGTCTTAATTCAGGGTAA
** * * *
5299 TTAAGAGGAG-AACACAGTCAAAGTCTTAATTAAGGATAATTAAGAGAAA-AAGCACAGTTAA
65 TTAAGAAAAGCAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGA-AAAGAAACACAGTTAA
* *
5360 AGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAATTAAAGTCTTAATTCAGGGTAA
1 AGTC-AAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCAAAGTCTTAATTCAGGGTAA
* * *
5425 TTAAGAAAAGCAAACACAATTAAAGTCTTAATTTAGGGTAATTAAGAAAAGAAA-ATGCAGTTAA
65 TTAAGAAAAGC-AACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAACA--CAGTTAA
* * ** *
5489 AGT----T-TTAATTCTGGGTAATTAAGAAAAGAAGAACGTAGTCAAAGTTTTAATTCAGGGTAA
1 AGTCAAATCTTAATTCAGGGTAATTAAGAAAAGCA-AACACAGTCAAAGTCTTAATTCAGGGTAA
*
5549 TTAAGAAAAGCAAGCACAGTTAAAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGTAAACACA
65 TTAAGAAAAGCAA-CAC------AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAG-AAACACA
5614 GTTAA
122 GTTAA
* * * *
5619 AG-----TCTTAATTCAGGTTAATTAAGAAAAGCAAACATAGTCGAAGTCTTAATTTA-GGTAAT
1 AGTCAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCAAAGTCTTAATTCAGGGTAAT
*
5678 TAAGAAAAGCAAGCACAGTTAAGGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAG
66 TAAGAAAAGCAA-CAC-----A-GTCAAAGTCTTAATTCAGGGTAATTAAGAAAAG-AAACACAG
5743 TTAA
123 TTAA
* * * * *
5747 AGTC---TC--AA--CATGGTAATTAAGAAAAGTAAACACAGTCAAGGGT-TTAATTCAAGGAAA
1 AGTCAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCAA-AGTCTTAATTCAGGGTAA
* * * * *
5804 TTCAGTAAAG----GCAGTCAAAGACTTAATTCAAGGTAATTAAG
65 TTAAGAAAAGCAACACAGTCAAAGTCTTAATTCAGGGTAATTAAG
5845 TAAACATAGT
Statistics
Matches: 534, Mismatches: 53, Indels: 64
0.82 0.08 0.10
Matches are distributed among these distances:
116 25 0.05
117 1 0.00
122 1 0.00
123 26 0.05
124 39 0.07
126 178 0.33
127 24 0.04
128 105 0.20
129 30 0.06
130 67 0.13
131 3 0.01
132 33 0.06
133 2 0.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (126 bp):
AGTCAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCAAAGTCTTAATTCAGGGTAAT
TAAGAAAAGCAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAACACAGTTAA
Found at i:5621 original size:212 final size:208
Alignment explanation
Indices: 5100--5782 Score: 831
Period size: 212 Copynumber: 3.2 Consensus size: 208
5090 TGATGTAAAT
* *
5100 ACAGTCAAAGTCTTAATTCAAGGTAATTAAGAAAAGCAAGCACAGTCAAAGTCAAAATCTTAATT
1 ACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAGCACAGTTAAAGTCAAAATCTTAATT
* * * *
5165 CAGGGTAATTAAGAGAAG-AACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAGAAG-AAGCAC
66 CAGGGTAATTAAGAAAAGAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACAC
* * *
5228 AGTTAAAGTCAGAATCTTAATTCAGGGTAGTTAAGAAAAGCAAACACAGTTAAAGTCTTAATTCA
131 AGTT-AA---AG--TCTTAATTTAGGGTAATTAAGAAAAGAAAACACAGTTAAAGTCTTAATTCA
*
5293 GGGTAATTAAGAGGAGAAC
190 GGGTAATTAAGAGAAGAAC
* *
5312 ACAGTCAAAGTCTTAATTAAGGATAATTAAGAGAAA--AAGCACAGTTAAAGTCAAAATCTTAAT
1 ACAGTCAAAGTCTTAATTCAGGGTAATTAAGA-AAAGCAAGCACAGTTAAAGTCAAAATCTTAAT
*
5375 TCAGGGTAATTAAGAAAAGCAAACACAATTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
65 TCAGGGTAATTAAGAAAAG-AAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* ** * *
5440 ACAATTAAAGTCTTAATTTAGGGTAATTAAGAAAAGAAAATGCAGTTAAAGTTTTAATTCTGGGT
129 ACAGTTAAAGTCTTAATTTAGGGTAATTAAGAAAAGAAAACACAGTTAAAGTCTTAATTCAGGGT
5505 AATTAAGAAAAGAAGAAC
194 AATTAAG---AGAAGAAC
** *
5523 GTAGTCAAAGTTTTAATTCAGGGTAATTAAGAAAAGCAAGCACAGTTAAAGTCAAAATCTTAATT
1 ACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAGCACAGTTAAAGTCAAAATCTTAATT
*
5588 CAGGGTAATTAAGAAAAGTAAACACAGTTAAAGTCTTAATTCAGGTTAATTAAGAAAAGCAAACA
66 CAGGGTAATTAAGAAAAG-AAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACA
* ** * * *
5653 TAGTCGAAGTCTTAATTTA-GGTAATTAAGAAAAGCAAGCACAGTTAAGGTCAAAATCTTAATTC
130 CAGTTAAAGTCTTAATTTAGGGTAATTAAGAAAAGAAAACACAG-T----T-AAAGTCTTAATTC
*
5717 AGGGTAATTAAGAAAAGCAAAC
189 AGGGTAATTAAGAGAAG--AAC
* * * * *
5739 ACAGTTAAAGTCTCAA--CATGGTAATTAAGAAAAGTAAACACAGT
1 ACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAGCACAGT
5783 CAAGGGTTTA
Statistics
Matches: 408, Mismatches: 46, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
208 55 0.13
210 5 0.01
211 98 0.24
212 135 0.33
213 41 0.10
214 37 0.09
216 15 0.04
217 22 0.05
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (208 bp):
ACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAGCACAGTTAAAGTCAAAATCTTAATT
CAGGGTAATTAAGAAAAGAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACAC
AGTTAAAGTCTTAATTTAGGGTAATTAAGAAAAGAAAACACAGTTAAAGTCTTAATTCAGGGTAA
TTAAGAGAAGAAC
Found at i:5819 original size:36 final size:36
Alignment explanation
Indices: 5790--5906 Score: 128
Period size: 36 Copynumber: 3.2 Consensus size: 36
5780 AGTCAAGGGT
*
5790 TTAATTCAAGGAAATTCAGTAAAGGCAGTCAAAGAC
1 TTAATTCAAGGAAATTAAGTAAAGGCAGTCAAAGAC
* ***
5826 TTAATTCAAGGTAATTAAGTAAACATAGT-AAAGAAC
1 TTAATTCAAGGAAATTAAGTAAAGGCAGTCAAAG-AC
* * * *
5862 TTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGAC
1 TTAATTCAAGGAAATTAAGTAAAGGCAGTCAAA-GAC
5899 TTAATTCA
1 TTAATTCA
5907 GAAGGACTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
35 4 0.06
36 51 0.74
37 13 0.19
38 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.27
Consensus pattern (36 bp):
TTAATTCAAGGAAATTAAGTAAAGGCAGTCAAAGAC
Found at i:5986 original size:42 final size:41
Alignment explanation
Indices: 5939--6081 Score: 202
Period size: 39 Copynumber: 3.5 Consensus size: 41
5929 TAAGTGAAAG
5939 CAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAACA
1 CAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAA-A
*
5981 CAAGCACATACTTAATTTTAAGGAAGGAAATTAGGT--AAA
1 CAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAAA
* **
6020 CAAGCACATACTTAATTTCAAGGAAGAAAATTAGGTAAAGG
1 CAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAAA
* *
6061 CAAGCAAAGACTTAA-TTCAAG
1 CAAGCACATACTTAATTTCAAG
6082 ATAATTAAGT
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
39 35 0.38
40 8 0.09
41 14 0.15
42 35 0.38
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.22
Consensus pattern (41 bp):
CAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAAA
Found at i:6139 original size:36 final size:36
Alignment explanation
Indices: 6063--6165 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6053 GGTAAAGGCA
*
6063 AGCAAAGACTTAA-TTCA-AGATAATTAAGT-AAATC
1 AGCAAAGACTTAATTTCACA-AGAATTAAGTAAAATC
6097 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATC
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATC
6133 AGCAAAGACTTAATTTCACAAGAATTAAGTAAA
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAA
6166 GATGATTAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
34 13 0.20
35 13 0.20
36 39 0.60
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (36 bp):
AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATC
Found at i:6262 original size:37 final size:37
Alignment explanation
Indices: 6200--6562 Score: 478
Period size: 37 Copynumber: 9.8 Consensus size: 37
6190 GACTTAACCC
* ** * *
6200 AAGGGGATTAAGTA-AAAAAAGGACTTCATTTCAAAG
1 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
6236 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
1 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
* *
6273 AATGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGA
1 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
*
6310 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGA
1 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
*
6347 AAGGAGATTAAGTAGAGTAAATGACTTAATTTCAAGG
1 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
* *
6384 AAGGAAATTAAGTAGAGTCAAGGACTTAATTTCAAGG
1 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
* * * *
6421 AAGGAAATTAAGTGGATTCAAGGACTTAATTTCAAGG
1 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
* * *
6458 AAGGAAATTAAGTAGAATCAAGGACTTAATTTCAAGG
1 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
* * * *
6495 AAGGAAATTAAGTAGAGTCAAGGGCTTAATTTCAGGG
1 AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
* * *
6532 AAGGATATTAAGTCA-AGTCAGGGACTTAATT
1 AAGGAGATTAAGT-AGAGTAAAGGACTTAATT
6563 CAGGGTAATT
Statistics
Matches: 302, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
36 13 0.04
37 288 0.95
38 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.25
Consensus pattern (37 bp):
AAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAGG
Found at i:6312 original size:18 final size:18
Alignment explanation
Indices: 6291--6351 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
6281 TAAGTAGAGT
6291 AAAGGACTTAATTTCAAG
1 AAAGGACTTAATTTCAAG
* *
6309 AAAGGAGATTAA-GT-AGAG
1 AAAGGA-CTTAATTTCA-AG
6327 TAAAGGACTTAATTTCAAG
1 -AAAGGACTTAATTTCAAG
6346 AAAGGA
1 AAAGGA
6352 GATTAAGTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 1 0.03
18 19 0.56
19 13 0.38
20 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.23, T:0.23
Consensus pattern (18 bp):
AAAGGACTTAATTTCAAG
Found at i:6574 original size:32 final size:32
Alignment explanation
Indices: 6538--6608 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
6528 AGGGAAGGAT
6538 ATTAAGTCAAGTCAGGGACTTAATTCAGGGTA
1 ATTAAGTCAAGTCAGGGACTTAATTCAGGGTA
6570 ATTAAGTCAAGTCAGGGACTTAATTCAGGGTA
1 ATTAAGTCAAGTCAGGGACTTAATTCAGGGTA
6602 ATTAAGT
1 ATTAAGT
6609 AGCGTCAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (32 bp):
ATTAAGTCAAGTCAGGGACTTAATTCAGGGTA
Found at i:6670 original size:36 final size:35
Alignment explanation
Indices: 6554--6774 Score: 261
Period size: 36 Copynumber: 6.2 Consensus size: 35
6544 TCAAGTCAGG
**
6554 GACTTAATTCAGGGTAATTAAGTCA-AGTC---AGG
1 GACTTAATTCAGGGTAATTAAGT-AGAGTCAATAAA
*
6586 GACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
** *
6621 GGGACTTAATTCAGGACAATTAAGTAGCGTCAATAAAA
1 --GACTTAATTCAGGGTAATTAAGTAGAGTCAAT-AAA
*
6659 GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
*
6694 GAACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
1 G-ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
* *
6730 GAACTTAATTCAGGGTAATTAAGTGGAATCAATAAA
1 G-ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
6766 GAACTTAAT
1 G-ACTTAAT
6775 CTAAAAAGAG
Statistics
Matches: 171, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
31 1 0.01
32 26 0.15
35 5 0.03
36 106 0.62
37 30 0.18
38 3 0.02
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (35 bp):
GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
Found at i:10554 original size:363 final size:363
Alignment explanation
Indices: 9889--10615 Score: 1242
Period size: 363 Copynumber: 2.0 Consensus size: 363
9879 TTAATTTTAA
* *
9889 ACTAGATATTTTCCCCGCGCATTCGTGTCGGATTTTTCAGTTTATGATTAGAATTGAGTAATTTC
1 ACTAGATATTTTCCCCGCGCATTCGCGTCGGATTTTTCAGTTTATGATTAGAACTGAGTAATTTC
* *
9954 AATTCTAAGTAAAATTTTATGTTATGTAATCACAATTAAGTTAGATAGGAGGAAATATTGTTAGA
66 AATTCTAAGTAAAATTTTATCTTATGTAATCACAATTAAGTTAAATAGGAGGAAATATTGTTAGA
**
10019 AATATAATATTTATTCAAATAATTATTTGTTGGAAAAAAGGAAATGGAGGTTTACTTTGATTATA
131 AATATAATATTTATTCAAATAATTATTTGCCGGAAAAAAGGAAATGGAGGTTTACTTTGATTATA
*
10084 ATTCAATGTTCTAAATATTATTTATAAATATTATATTTCGAATTTTAAATATATAATAATATATA
196 ATTCAATGTTCTAAATATTAATTATAAATATTATATTTCGAATTTTAAATATATAATAATATATA
10149 TTGGTTTTCTCCCAACCAATCAACATTGTACAAATGTCAGCATGAGAAATACT-AAATGCTGAGC
261 TTGGTTTTCTCCCAACCAATCAACATTGTACAAATGTCAGCATGAGAAA-ACTCAAATGCTGAGC
10213 ATATAGACGTTTGGGGATAACTTTAATAGTAGGGTATAG
325 ATATAGACGTTTGGGGATAACTTTAATAGTAGGGTATAG
*
10252 ACTAGATATTTTCCCCGCGCATTCGCGTCGGGTTTTTTCAGTTTATGATTAGAACTGAGTAATTT
1 ACTAGATATTTTCCCCGCGCATTCGCGTC-GGATTTTTCAGTTTATGATTAGAACTGAGTAATTT
** * *
10317 CAATTCTAAGTAAAATTTTATCTTATGTAATCGTAATTAAGTTAAATGGGGGGAAATATTGTTAG
65 CAATTCTAAGTAAAATTTTATCTTATGTAATCACAATTAAGTTAAATAGGAGGAAATATTGTTAG
* * *
10382 -AATATAATGTTTATTCAAATAATTATTTGCCGGAAAAAAGGAAATGGAGTTTTATTTTGATTAT
130 AAATATAATATTTATTCAAATAATTATTTGCCGGAAAAAAGGAAATGGAGGTTTACTTTGATTAT
* * *
10446 AATTCAATGTTCTAAATATTAATTATAAATATTATATTTGGAATTTTAAGTATATAATAATCTAT
195 AATTCAATGTTCTAAATATTAATTATAAATATTATATTTCGAATTTTAAATATATAATAATATAT
* *
10511 ATTGGTTTTCTCCCAACCAATCAACGTTGTACAAATGTCAGCATGAGAAAAGTCAAATGCTGAGC
260 ATTGGTTTTCTCCCAACCAATCAACATTGTACAAATGTCAGCATGAGAAAACTCAAATGCTGAGC
10576 ATATAGACGTTTGGGGATAACTTTAATAGTAGGGTATAG
325 ATATAGACGTTTGGGGATAACTTTAATAGTAGGGTATAG
10615 A
1 A
10616 TTTAAAATAG
Statistics
Matches: 342, Mismatches: 20, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
362 2 0.01
363 248 0.73
364 92 0.27
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (363 bp):
ACTAGATATTTTCCCCGCGCATTCGCGTCGGATTTTTCAGTTTATGATTAGAACTGAGTAATTTC
AATTCTAAGTAAAATTTTATCTTATGTAATCACAATTAAGTTAAATAGGAGGAAATATTGTTAGA
AATATAATATTTATTCAAATAATTATTTGCCGGAAAAAAGGAAATGGAGGTTTACTTTGATTATA
ATTCAATGTTCTAAATATTAATTATAAATATTATATTTCGAATTTTAAATATATAATAATATATA
TTGGTTTTCTCCCAACCAATCAACATTGTACAAATGTCAGCATGAGAAAACTCAAATGCTGAGCA
TATAGACGTTTGGGGATAACTTTAATAGTAGGGTATAG
Found at i:11005 original size:12 final size:12
Alignment explanation
Indices: 10979--11017 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10969 CCGTTTTTTT
10979 TTTTATTTTTAAA
1 TTTTATTTTT-AA
*
10992 TTTTATTATTAA
1 TTTTATTTTTAA
*
11004 TTTAATTTTTAA
1 TTTTATTTTTAA
11016 TT
1 TT
11018 GTAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:20675 original size:19 final size:18
Alignment explanation
Indices: 20638--20686 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
20628 CGAAATATAT
20638 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
20656 TAATTATTT-TTCAGAATAA
1 TAATTATTTATT-A-AATAA
*
20675 TTATTATTTATT
1 TAATTATTTATT
20687 TTCCCTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 10 0.37
19 13 0.48
20 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:21653 original size:26 final size:27
Alignment explanation
Indices: 21619--21669 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
21609 AGAAGGAGAA
*
21619 ATTGTCCATCTTCCATCAAGAGGGAAG
1 ATTGTCCATCCTCCATCAAGAGGGAAG
21646 ATTG-CCATCCTCCATCAAGAGGGA
1 ATTGTCCATCCTCCATCAAGAGGGA
21670 TGATGTCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (27 bp):
ATTGTCCATCCTCCATCAAGAGGGAAG
Found at i:35271 original size:27 final size:27
Alignment explanation
Indices: 35240--35291 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
35230 AAGTGGACTC
* *
35240 AAAATGACCA-AAATGTCCCTGAATGCA
1 AAAATGA-CATAAATGCCCCTAAATGCA
35267 AAAATGACATAAATGCCCCTAAATG
1 AAAATGACATAAATGCCCCTAAATG
35292 ACCCTAATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.19
Consensus pattern (27 bp):
AAAATGACATAAATGCCCCTAAATGCA
Found at i:37127 original size:6 final size:6
Alignment explanation
Indices: 37118--37151 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
37108 AAAGCAAAGC
37118 AAATCT AAATCT AAATCTT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATC-T AAATCT AAATCT AAA
37152 GTAGATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:37141 original size:13 final size:13
Alignment explanation
Indices: 37118--37148 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
37108 AAAGCAAAGC
37118 AAATC-TAAATCT
1 AAATCTTAAATCT
37130 AAATCTTAAATCT
1 AAATCTTAAATCT
37143 AAATCT
1 AAATCT
37149 AAAGTAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATCTTAAATCT
Found at i:44856 original size:21 final size:21
Alignment explanation
Indices: 44817--44856 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44807 CAAGCACCAA
* *
44817 GAAGATGCCTTTTGATCCATT
1 GAAGATACCTATTGATCCATT
*
44838 GAAGATACCTATTGGTCCA
1 GAAGATACCTATTGATCCA
44857 ATGACAAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
GAAGATACCTATTGATCCATT
Found at i:45051 original size:21 final size:21
Alignment explanation
Indices: 45021--45063 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
45011 AAAAAAATAG
45021 GACAAGTCCTGCCCAGGACTT
1 GACAAGTCCTGCCCAGGACTT
* *
45042 GACAATTCCTGCCTAGGACTT
1 GACAAGTCCTGCCCAGGACTT
45063 G
1 G
45064 GTCTGTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (21 bp):
GACAAGTCCTGCCCAGGACTT
Found at i:45116 original size:21 final size:21
Alignment explanation
Indices: 45092--45134 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
45082 AGAGTTGCAG
* *
45092 GACAAGTCCGGCCCAGGACTT
1 GACAACTCCGGCCCAGAACTT
*
45113 GACAACTCCTGCCCAGAACTT
1 GACAACTCCGGCCCAGAACTT
45134 G
1 G
45135 TTCCGGGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16
Consensus pattern (21 bp):
GACAACTCCGGCCCAGAACTT
Found at i:51678 original size:30 final size:30
Alignment explanation
Indices: 51644--51715 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
51634 CCACAATTTT
* *
51644 GGATTAGGGTTTCTTATCTAGGTTATTTGG
1 GGATTAGGGTTTCTTATCCAGGTGATTTGG
51674 GGATTAGGGTTTCTTATCCAGGTGATTTGG
1 GGATTAGGGTTTCTTATCCAGGTGATTTGG
*
51704 GAATTAGGGTTT
1 GGATTAGGGTTT
51716 TGCTTAGTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.18, C:0.07, G:0.32, T:0.43
Consensus pattern (30 bp):
GGATTAGGGTTTCTTATCCAGGTGATTTGG
Found at i:53110 original size:33 final size:33
Alignment explanation
Indices: 53034--53136 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
53024 GCAAAGAGTG
* * * *
53034 TTTTAGATGTTGTTTGCAATGATACTAAACCTA
1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
* * *
53067 ATTT-GAGTGTTGTTTGCGATGACACTAAATCTG
1 TTTTAG-GTGTTGTTTGCGATGAAACTAAATCTA
* *
53100 TTTTAGGTGTTGTTTGTGATGAAACAAAATCTA
1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
53133 TTTT
1 TTTT
53137 GGATGCTAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 1 0.02
33 55 0.96
34 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (33 bp):
TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
Found at i:53615 original size:30 final size:30
Alignment explanation
Indices: 53579--53641 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
53569 TCTTCAAGGG
*
53579 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATCATGCG-CCAAGGACTTATCAT
*
53609 GGAGGGAATCATGCGCTAAGGACTTATCAT
1 GGAGGGAATCATGCGCCAAGGACTTATCAT
53639 GGA
1 GGA
53642 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.21
Consensus pattern (30 bp):
GGAGGGAATCATGCGCCAAGGACTTATCAT
Found at i:53708 original size:18 final size:19
Alignment explanation
Indices: 53685--53722 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
53675 GTGCATGGGC
*
53685 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
53703 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
53722 T
1 T
53723 AACGATGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:55987 original size:35 final size:36
Alignment explanation
Indices: 55909--55992 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 36
55899 CCAACCAAAA
* * * *
55909 ACCAGCAAGCAAAAGCAATTATGTTCCTATTTAACT
1 ACCAACAAGCAAAACCAATCATGTTCCTATTCAACT
*
55945 AACAACAAGCAAAACCAATCATGTTCCTA-TCAACT
1 ACCAACAAGCAAAACCAATCATGTTCCTATTCAACT
*
55980 ACCAACAATCAAA
1 ACCAACAAGCAAA
55993 TCCACTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 16 0.39
36 25 0.61
ACGTcount: A:0.45, C:0.26, G:0.07, T:0.21
Consensus pattern (36 bp):
ACCAACAAGCAAAACCAATCATGTTCCTATTCAACT
Done.