Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022444.1 Corchorus olitorius cultivar O-4 contig22477, 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: 23266
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1970 original size:2 final size:2
Alignment explanation
Indices: 1916--1956 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1906 TGAGCATGAG
1916 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
1957 TATGACAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4947 original size:32 final size:31
Alignment explanation
Indices: 4909--4998 Score: 109
Period size: 29 Copynumber: 3.0 Consensus size: 31
4899 ATGTTAAATT
4909 AAGATTAGTATATTTTTTTTCTCAAAAAAAA
1 AAGATTAGTATATTTTTTTTCTCAAAAAAAA
*
4940 GAAGATTAGTATATTTTTGGTTCT---AAAAAA
1 -AAGATTAGTATATTTTT-TTTCTCAAAAAAAA
*
4970 AAGATTAGTATA-TTTTTCT-TCAAAAAAAA
1 AAGATTAGTATATTTTTTTTCTCAAAAAAAA
4999 TTGTATATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 4 0.08
29 18 0.35
30 6 0.12
32 17 0.33
33 4 0.08
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (31 bp):
AAGATTAGTATATTTTTTTTCTCAAAAAAAA
Found at i:7303 original size:332 final size:332
Alignment explanation
Indices: 6659--7910 Score: 1233
Period size: 332 Copynumber: 3.8 Consensus size: 332
6649 TCTTTTGGGG
* * * * * *
6659 CAATTTTTACAAAATTTTAGTCGAAATCGTGTAAAAACCATCACAATTTTTGGCTAAAAAAGCGT
1 CAATTTTTGCAAAA-TTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTAAAAACGCGT
* * * * *
6724 TTCGGGGCCTCGGCTCAGTTTTGCATGATTTTTAGTG-TGAAGACTCCTTGAGATAT-TCATATT
65 TTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCCTTGAAATATCT-ATATT
* * * * * * * *
6787 CATCTAACCAAATCTCACCCATATTGGATTTAAGAATTTGTTTTTACGAGCATCTCAATCTTGTT
129 CATCTAATCAAATCTCAGCCACAATGCATTTAATAATTTGTTTTTAAGAGCATCTGAATCTTGTT
*
6852 TCGATTTAATTAGAAATTAATTCAGAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
194 TCGATTTAATTAGAAATTAATTCAG-AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCC
* * * * *
6917 TCCAATCTTTTTGGCGTTAAATTATATA--TATTAGGATTATTTTAT-TCAAAAAATTGAGGAAA
258 TTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGATTA--TTATGGCAAAAAATTGAGGAAA
*
6979 AATTTTTCGGGT
321 AATATTTCGGGT
* * * * *
6991 CATTTTTTGCAAAATTTCAACCAAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGCGT
1 CAATTTTTGCAAAATTT-AGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTAAAAACGCGT
* * * *
7056 TTCGGGGCCCCAGCTCAGTTTTGCATGATTTTGGGCGTCGAA-ACTCCTTGAAACATCTATATTC
65 TTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCCTTGAAATATCTATATTC
* * * * *
7120 ATCTAATAAAATTTTAGCCACAATGCATTTAATAATTTGTTTTTAAGAGCATTTGATTCTTGTTT
130 ATCTAATCAAATCTCAGCCACAATGCATTTAATAATTTGTTTTTAAGAGCATCTGAATCTTGTTT
* * **
7185 CGATTTAATTAGAAATTTATTCTGAAAAAATATGAAAAACGATATTAAAAATGTGAAAAGCCCTT
195 CGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTT
* * * * * * *
7250 CAATCTTTTAGCCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATATC
260 CAATCTTTTTGGCGTTGAATTATATATTTTTTATGATTATTATGGCAAAAAATTGAGGAAAAATA
7315 TTTCGGGT
325 TTTCGGGT
* * *
7323 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCAAAAAAGGCCT
1 CAATTTTTGCAAAA-TTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTAAAAACGCGT
* * * * * * *
7388 TCCGAGG-CCTGGTTCAGTTTTGCAAGATTTTTGGTGCCG-AGA-TACCTTGAAAAATCTATATT
65 TTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAAGACT-CCTTGAAATATCTATATT
* **
7450 CATCTAACCAAATCTCAG------T-C--------A-TTGTTTTTACA-AGCATCTGAATCACGT
129 CATCTAATCAAATCTCAGCCACAATGCATTTAATAATTTGTTTTTA-AGAGCATCTGAATCTTGT
* * *
7498 TTCGATTTAATTAGAGATTAATT-AGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCC
193 TTCGATTTAATTAGAAATTAATTCA-GAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* * *
7562 CCTCAATCTTTTTGGCATTGAATTATATATTTTTTATGATTATTATGGAAAAAAATTGAGGAAAA
257 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGATTATTATGGCAAAAAATTGAGGAAAA
*
7627 ATATTTCGAGT
322 ATATTTCGGGT
** *** *
7638 CAATTTTTGCAAAATATTAGCCGAAATCGTGT-ACCATCA-CGGTGTTTATTTGCTAAAAACGCG
1 CAATTTTTGCAAAAT-TTAGCCGAAATCGTGTAATAATCATCACAGTTT-TTGGCTAAAAACGCG
* * * * * *
7701 TTACAGGGCTCCGGGC-CAGTTTTGCATGA-TTTTGGC-CCCAAGGCTCCTTGAAATATTTATAT
64 TTTCGGGGC-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCCTTGAAATATCTATAT
* * * * * *
7763 TCATCTAATCAAATCTCAGCCACATTGGATTGAA-AGATTTATTTTTACGAGCATCT-AAACATT
128 TCATCTAATCAAATCTCAGCCACAATGCATTTAATA-ATTTGTTTTTAAGAGCATCTGAATC-TT
* * * * * **
7826 GTTTCGATTTAATTAGAAATTAATTCAGAAAAAGTA-GGAAAACTATATTAGAAGCGTAAAAAAT
191 GTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGC
* * *
7890 CTTTCAATATTTTTGGTGTTG
256 CCTTCAATCTTTTTGGCGTTG
7911 GTTTCAATAT
Statistics
Matches: 752, Mismatches: 132, Indels: 75
0.78 0.14 0.08
Matches are distributed among these distances:
313 7 0.01
314 63 0.08
315 185 0.25
316 6 0.01
320 1 0.00
324 1 0.00
325 1 0.00
329 43 0.06
330 49 0.07
331 124 0.16
332 257 0.34
333 15 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (332 bp):
CAATTTTTGCAAAATTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTAAAAACGCGTT
TCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCCTTGAAATATCTATATTCA
TCTAATCAAATCTCAGCCACAATGCATTTAATAATTTGTTTTTAAGAGCATCTGAATCTTGTTTC
GATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTC
AATCTTTTTGGCGTTGAATTATATATTTTTTATGATTATTATGGCAAAAAATTGAGGAAAAATAT
TTCGGGT
Found at i:8551 original size:334 final size:331
Alignment explanation
Indices: 7920--8551 Score: 806
Period size: 333 Copynumber: 1.9 Consensus size: 331
7910 GGTTTCAATA
* * * *
7920 TTTCGGATCAATTTGTGCAGAATTTTAGCCGAAATCCTATAATAATCATCACAGTTTTTGGCTAA
1 TTTCGGATCAATTTGTGCAAAATTTAAGCCGAAATCATATAATAACCATCACAGTTTTTGGC-AA
*
7985 AAAACGTTCCAGGGCCCCGGGTCAGTTTTGCATGAATTCTGACATCAAGACTCCTTGAGATATAT
65 AAAACGTTCCAGGGCCCCGGCTCAGTTTTGCATGAATTCTGACATCAAGACTCCTT-AGATATAT
*
8050 ATCCATATTCATCTAATCAAATCTCAGCCACATTACATTTAAGGATTTTTTTTAAGAGCATTTGA
129 ATCCATATTCATCTAATCAAATCTCAGCCACATTACATTTAAGGATTTTTTTTAAGAGCATCTGA
* * *
8115 ATCTTGTTTCAATTTAATTACAAATTTATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGA
194 ATCTTGTTTCAATTTAATTACAAATTAATTCAGAAAAAATATGAAAAACAATATGAAAAACGTGA
* * *
8180 AAAGTCCTCGAATCTTTTTGGCGTTAAATTATATATATTTCATTAGTATTTTAGCCAAAAAATGA
259 AAAGTCCTCCAATCATTTTAGCGTTAAATTATATATATTTCATTAGTATTTTAGCCAAAAAATGA
8245 GGAAAATT
324 GGAAAATT
* * * * * *
8253 TTTCGGATCATTTTTTGCAAAATTTAAGCCGAAATCATGTAGTAACCATCACGGTTTTTTG-AAA
1 TTTCGGATCAATTTGTGCAAAATTTAAGCCGAAATCATATAATAACCATCACAGTTTTTGGCAAA
* * ** * * * * *
8317 AAACGCGTTTCGGGGTTCCGGCTCAGTTTTGCATTATTTTTGGCATCGAGACTCCTT-GA-A-AT
66 AAA--CGTTCCAGGGCCCCGGCTCAGTTTTGCATGAATTCTGACATCAAGACTCCTTAGATATAT
* * * *
8379 ATCTATATTCATCTAATCAAATCTTAGCCACATTGAAATATATTTAAGGATTTGTTTTTACGAGC
129 ATCCATATTCATCTAATCAAATCTCAGCCACA-T----TACATTTAAGGATTT-TTTTTAAGAGC
* * * *
8444 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAATAATATTAAAA
188 ATCTGAATCTTGTTTCAATTTAATTACAAATTAATTCAGAAAAAATATGAAAAACAATATGAAAA
* *
8508 ACGTGAAAAGTCCTCCAATCATTTTAGCGTTGAATTTTATATAT
253 ACGTGAAAAGTCCTCCAATCATTTTAGCGTTAAATTATATATAT
8552 ATATATATAT
Statistics
Matches: 254, Mismatches: 37, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
329 32 0.13
330 2 0.01
331 8 0.03
333 93 0.37
334 74 0.29
335 45 0.18
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (331 bp):
TTTCGGATCAATTTGTGCAAAATTTAAGCCGAAATCATATAATAACCATCACAGTTTTTGGCAAA
AAACGTTCCAGGGCCCCGGCTCAGTTTTGCATGAATTCTGACATCAAGACTCCTTAGATATATAT
CCATATTCATCTAATCAAATCTCAGCCACATTACATTTAAGGATTTTTTTTAAGAGCATCTGAAT
CTTGTTTCAATTTAATTACAAATTAATTCAGAAAAAATATGAAAAACAATATGAAAAACGTGAAA
AGTCCTCCAATCATTTTAGCGTTAAATTATATATATTTCATTAGTATTTTAGCCAAAAAATGAGG
AAAATT
Found at i:8552 original size:2 final size:2
Alignment explanation
Indices: 8545--8577 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8535 CGTTGAATTT
8545 TA TA TA TA 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 TA TA TA TA T
8578 TATGAGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9936 original size:330 final size:330
Alignment explanation
Indices: 8702--9984 Score: 1206
Period size: 330 Copynumber: 3.9 Consensus size: 330
8692 CAGGTCAATC
* * *
8702 TTTTGATGTCAAATTATATA-TTTTTATGGGTA-TTTAGCCAAAAAATTGAGGAAATATCTTTCG
1 TTTTGATGTCGAATTATATATTTTTTATGAGTATTTTAGCC-AAAAATTAAGGAAATATCTTTCG
* * * * *
8765 GG-AAATTTTTTGCAAAATTTTAGCAGAAATCGTGT--ATGTTATCACGGTTTTTGGCT-AAAAC
65 GGTCAA-TTTTTGCAAAATTTTAGCTGAAATCGTGTACATATTATCACGTTTTTTGGCTAAAAAT
* * *
8826 GTGTTCC-GGAGCCACGGCTG-TGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTA
129 GCGTTCCTGGA-CC-C-GCTGCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTA
* * * * * *
8889 TATTCATCTAACCAAATCTTAGTCACATTAGATTTAAGGATTTATTTTTTACGAGCATTTGAATC
191 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT-GTTTTTACGAGCATCTAAATC
* * ** * * * * * *
8954 ATGTTTTGATTTAATTTAGAAATTAATT-TGAAAAATAGGGAAAATGTTATTATAAGCATGAGAA
255 TTGTTTCGATTTAA-TTAGAAATTAATTAAAAAAAATAGGAAAAATGATATTAGAAGCGTAAAAA
* *
9018 GCCCGTCAATCT
319 GCCCTTCAATTT
* * * * * *
9030 TTTTGGTGTTGAATTATATATTTTTTATGAGGATTGTAGCTAAAAAAATTAAGTAAA-A-CATTT
1 TTTTGATGTCGAATTATATATTTTTTATGAGTATTTTAGC--CAAAAATTAAGGAAATATC-TTT
* * * * **** *
9093 CAGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTACCATTACAGTTTTTTTTTTTTTTTGCT
63 CGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTA-CA-T--A-TTATCACGTTTTTTGGCT
* * ** * ** *
9158 AAAAA-CCTGTT-ATAGGACCCGGGGTCAGTTTTGCATTATTTTTTACGCCAAGACTCCTTAAAA
123 AAAAATGC-GTTCCT-GGACCCGCTG-CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-GAA
* * * * *
9221 TATATCTATATTCATCTAACCAAACCTCAGGCACATCGTATTTAAGGATTTGTTTTTACGAGTAT
184 -ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * * *
9286 CTAAATCTTCTATCGATTTTATCAGAAATTAATTTGGAAATAAAATAGGAAAAATGATATTAGAA
248 CTAAATCTTGTTTCGATTTAATTAGAAATTAA-TT--AAAAAAAATAGGAAAAATGATATTAGAA
* * *
9351 GAGTGAAAAAGACTTTCAATTT
310 GCGT-AAAAAGCCCTTCAATTT
* * * * * * * *
9373 TTTTG-CGTTGAATTATATATTTTTTATGAATATTTTCGCTAGAAATTGAGGAAAAATCTTTCGG
1 TTTTGATGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTAAGGAAATATCTTTCGG
* * * * * *
9437 GTCAATTTTTGCAAAACTTTAGCTAAAATCGTGTAC--GTT-GC-GGTTTTTTGGCTAAAAATGT
66 GTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTACATATTATCACGTTTTTTGGCTAAAAATGC
* * * * * *
9498 GTTTCGGGACCCGGTTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATTTATATTC
131 GTTCCTGGACCCGCTGCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTC
* * *
9563 ATCTAACTAAATCTCAGCCACATTGGGTTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTT
196 ATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTT
** * *
9628 CGATTTAATTAGAAATTAATTAAAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAATCCCTTC
261 CGATTTAATTAGAAATTAATTAAAAAAAATAGGAAAAATGATATTAGAAGCGTAAAAAGCCCTTC
9693 AATTT
326 AATTT
*
9698 TTTTGATGTCGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTAAGGAAATATCCTTCGG
1 TTTTGATGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTAAGGAAATATCTTTCGG
* * * *
9762 GTCAATTTTTGTAAAATTTTAGCTGAAATCGTGTAC-TAATCATCACGATTTTTGCCTAAAAATG
66 GTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTACAT-ATTATCACGTTTTTTGGCTAAAAATG
** * *
9826 CGTTCCTGTG-CCACAGCTGC-GTTTTGCATGATTTTTGGCGCCGGGACTCCTTGAATTATCTTT
130 CGTTCCTG-GACC-C-GCTGCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTAT
* * * **
9889 ATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGTTCATCTAAATCTT
192 ATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTT
9954 GTTTCGATTTAATTAGAAATTAATTAAAAAA
257 GTTTCGATTTAATTAGAAATTAATTAAAAAA
9985 TATGAAACAA
Statistics
Matches: 766, Mismatches: 151, Indels: 74
0.77 0.15 0.07
Matches are distributed among these distances:
325 88 0.11
326 40 0.05
327 1 0.00
328 20 0.03
329 117 0.15
330 168 0.22
331 47 0.06
332 25 0.03
333 1 0.00
334 3 0.00
336 2 0.00
337 12 0.02
338 47 0.06
339 33 0.04
340 56 0.07
341 37 0.05
342 53 0.07
343 16 0.02
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (330 bp):
TTTTGATGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTAAGGAAATATCTTTCGG
GTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTACATATTATCACGTTTTTTGGCTAAAAATGC
GTTCCTGGACCCGCTGCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTC
ATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTT
CGATTTAATTAGAAATTAATTAAAAAAAATAGGAAAAATGATATTAGAAGCGTAAAAAGCCCTTC
AATTT
Found at i:10499 original size:14 final size:14
Alignment explanation
Indices: 10480--10507 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10470 TTAACATTCT
10480 TCCCACATTGCAGG
1 TCCCACATTGCAGG
10494 TCCCACATTGCAGG
1 TCCCACATTGCAGG
10508 GTAAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (14 bp):
TCCCACATTGCAGG
Found at i:13127 original size:165 final size:164
Alignment explanation
Indices: 12842--13427 Score: 572
Period size: 165 Copynumber: 3.5 Consensus size: 164
12832 GGGTTCCTGA
* * * *
12842 AAAAGTTGGAAACTTTGGAGATAA-AGAAATGTGGTATCCTGAAATCTGTCTTTCCACTATCGGT
1 AAAAGTTGGAAACTTTGGAGATAAGAG-GATGTGGTAGCCTGAAATCTCTCTTTCCACCATC-GT
* *
12906 TGCTAAAAATCTCGAGCAATTAAAAAGTGTCAAAATAGTTGACTGCAATATGTTGGAGCAAATTT
64 TGCTAAAAATCTCGTGCAATTGAAAAGTGTCAAAATAGTTGACTGCAATATGTTGGAGCAAATTT
*
12971 TCGAGCAGATGGAGGGTGCTAATGATGAGGTGCTAC
129 TCGAGGAGATGGAGGGTGCTAATGATGAGGTGCTAC
* * **
13007 AAAAGTTGGAAACATTGGAGATAAGAGGATGTGGCAGCCTGAAATCTCTCTTTCCACCGCCAGTT
1 AAAAGTTGGAAACTTTGGAGATAAGAGGATGTGGTAGCCTGAAATCTCTCTTTCCACCATC-GTT
* * * ** * *
13072 GCTAAATATCTTGTTCAATTGAAAAGTGTCAAAATAACT-ACATGCGATGTGTTGGAGCAAATTT
65 GCTAAAAATCTCGTGCAATTGAAAAGTGTCAAAATAGTTGAC-TGCAATATGTTGGAGCAAATTT
* * * *
13136 TTGAGGAGATGG-GAGGTGTTAATCATGACCGGGTGCTAT
129 TCGAGGAGATGGAG-GGTGCTAATGATGA---GGTGCTAC
** ** * * ** * *
13175 GGAAGTTGGAAACTTTGGAGATATCAGTATGTGGTAGGCTGAGGTGTCTCTTTCCACCTTCGATT
1 AAAAGTTGGAAACTTTGGAGATAAGAGGATGTGGTAGCCTGAAATCTCTCTTTCCACCATCG-TT
* * * * * * *
13240 ACTAAACATCTCATGCAATTGAACAGTGTGAAAATAGTTGACTGCCATATGTTGGAGAAAATTTT
65 GCTAAAAATCTCGTGCAATTGAAAAGTGTCAAAATAGTTGACTGCAATATGTTGGAGCAAATTTT
* *
13305 CGAGGAGATGGAAGGTGCTAATGA-G-GG-GCTCC
130 CGAGGAGATGGAGGGTGCTAATGATGAGGTGCTAC
* * * ** * *
13337 AAAAGCTGGAATCTTTGGAGATAAGAAGATGCAGTAGCTTGAAATCTCTCTTCCCACCATCGGTT
1 AAAAGTTGGAAACTTTGGAGATAAGAGGATGTGGTAGCCTGAAATCTCTCTTTCCACCATC-GTT
* * *
13402 GCTGAAAAGCTTGTGCAATTAGAAAA
65 GCTAAAAATCTCGTGCAATT-GAAAA
13428 ACTCCATATA
Statistics
Matches: 332, Mismatches: 78, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
162 63 0.19
163 7 0.02
164 3 0.01
165 127 0.38
166 2 0.01
167 2 0.01
168 126 0.38
169 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (164 bp):
AAAAGTTGGAAACTTTGGAGATAAGAGGATGTGGTAGCCTGAAATCTCTCTTTCCACCATCGTTG
CTAAAAATCTCGTGCAATTGAAAAGTGTCAAAATAGTTGACTGCAATATGTTGGAGCAAATTTTC
GAGGAGATGGAGGGTGCTAATGATGAGGTGCTAC
Found at i:19212 original size:57 final size:57
Alignment explanation
Indices: 19124--19238 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
19114 ATTGTTCCAG
* * * *
19124 CTTAAGTTATGCAGTTGCTCCTGTTGCTAGACTCACCGATCGAAACCAGGTGTGCGA
1 CTTAAGTTACGCAGCTGCTCCTGTTGCTAGACTCACCGACCGAAACCAAGTGTGCGA
* *
19181 CTTAAGTTACGCAGCTGTTTCTGTTGCTAGACTCACCGACCGAAACCAAGTGTGCGA
1 CTTAAGTTACGCAGCTGCTCCTGTTGCTAGACTCACCGACCGAAACCAAGTGTGCGA
19238 C
1 C
19239 GACAGGGTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (57 bp):
CTTAAGTTACGCAGCTGCTCCTGTTGCTAGACTCACCGACCGAAACCAAGTGTGCGA
Done.