Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013677.1 Corchorus capsularis cultivar CVL-1 contig13698, 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: 56332
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2993 original size:2 final size:2
Alignment explanation
Indices: 2986--3025 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2976 ACAGAACATC
2986 AT AT 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 AT AT
3026 GCAGTGGCGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4423 original size:29 final size:30
Alignment explanation
Indices: 4376--4438 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
4366 CGTTAGGTTG
4376 AGGGGGCAAAACGTCCCAAAATTGAAATTC
1 AGGGGGCAAAACGTCCCAAAATTGAAATTC
* * * *
4406 AGGGGGTAAAATGT-CCAAGATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAATTC
4435 AGGG
1 AGGG
4439 AACAAAACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTGAAATTC
Found at i:4933 original size:27 final size:27
Alignment explanation
Indices: 4869--4933 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
4859 TGGATATGAT
* * *
4869 TATTTAATTTAGGATATCGATTGCAAA
1 TATTTAATTTAGGAAACCGACTGCAAA
**
4896 TATTTTTTTTAGGGAAACCGACTGCAAA
1 TATTTAATTTA-GGAAACCGACTGCAAA
4924 TA-TTAATTTA
1 TATTTAATTTA
4934 TACACAGAGT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (27 bp):
TATTTAATTTAGGAAACCGACTGCAAA
Found at i:5252 original size:103 final size:100
Alignment explanation
Indices: 5143--5420 Score: 344
Period size: 103 Copynumber: 2.7 Consensus size: 100
5133 TTTCTAACAT
* *
5143 TTAAAATAAAATTTTAATTTTAGTTTAGGTTAAACTTAGTG-AATTAGTTATATATTTTATTTCT
1 TTAAAATAAAATTTTAATTTT-G----GGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCT
* * *
5207 AGAACCCTATAACAAT-ATTATTAATTATGGAATTTACCC
61 AAAACCCTATAACAATAATTATTAATTATGAAATTTACCA
*** *
5246 TTAAAATAAAAAAATAATTTTGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAAC
1 TTAAAATAAAATTTTAATTTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
* *
5311 CCTACAACAATAAATTATTAATTTTGAAATTTACCA
66 CCTATAACAAT-AATTATTAATTATGAAATTTACCA
* *
5347 TTAAAATAAAAATATTTAATTTGGGGCTAAATTTAGTGAAATTAGTTTTATATTTTATTTCTAAA
1 TTAAAAT-AAAAT-TTTAATTTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAA
*
5412 ACTCTATAA
64 ACCCTATAA
5421 TTATAAAAAT
Statistics
Matches: 151, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
98 13 0.09
99 35 0.23
101 27 0.18
102 5 0.03
103 71 0.47
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (100 bp):
TTAAAATAAAATTTTAATTTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
CCTATAACAATAATTATTAATTATGAAATTTACCA
Found at i:5304 original size:99 final size:102
Alignment explanation
Indices: 5173--5420 Score: 360
Period size: 103 Copynumber: 2.5 Consensus size: 102
5163 TAGTTTAGGT
* *
5173 TAAACTTAGTG-AATTAGTTATATATTTTATTTCTAGAACCCTATAACAAT-ATTATTAATTATG
1 TAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAATTATTAATTATG
* * *
5236 GAATTTACCCTTAAAATAAAAA-A-ATAATTTTGGGC
66 AAATTTACCATTAAAATAAAAATATATAATTTGGGGC
* * *
5271 TAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTACAACAATAAATTATTAATTTT
1 TAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAAT-AATTATTAATTAT
*
5336 GAAATTTACCATTAAAATAAAAATATTTAATTTGGGGC
65 GAAATTTACCATTAAAATAAAAATATATAATTTGGGGC
* *
5374 TAAATTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACTCTATAA
1 TAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA
5421 TTATAAAAAT
Statistics
Matches: 132, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
98 11 0.08
99 35 0.27
101 32 0.24
102 1 0.01
103 53 0.40
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.42
Consensus pattern (102 bp):
TAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAATTATTAATTATG
AAATTTACCATTAAAATAAAAATATATAATTTGGGGC
Found at i:11201 original size:24 final size:25
Alignment explanation
Indices: 11174--11222 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
11164 CAATTTTTTT
11174 CTTGATTTATT-TTTTTCTCTCTAA
1 CTTGATTTATTATTTTTCTCTCTAA
*
11198 CTTGATTTATTATTTTTTTCTCTAA
1 CTTGATTTATTATTTTTCTCTCTAA
11223 TTTTTTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.18, C:0.14, G:0.04, T:0.63
Consensus pattern (25 bp):
CTTGATTTATTATTTTTCTCTCTAA
Found at i:16930 original size:22 final size:22
Alignment explanation
Indices: 16883--16932 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
16873 TCTTTGTATG
* *
16883 AAATTTTTATAACCATACAATG
1 AAATTTTTATAACCACACAATA
*
16905 AAATTTTTATAACCACACTATA
1 AAATTTTTATAACCACACAATA
16927 AAATTT
1 AAATTT
16933 CGAAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATTTTTATAACCACACAATA
Found at i:16940 original size:31 final size:31
Alignment explanation
Indices: 16905--16966 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
16895 CCATACAATG
*
16905 AAATTTTTATAACCACACTATAAAATTTCGA
1 AAATTTTGATAACCACACTATAAAATTTCGA
* * * *
16936 AAATTTTGATAATCTCCCTATGAAATTTCGA
1 AAATTTTGATAACCACACTATAAAATTTCGA
16967 TAACCATACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (31 bp):
AAATTTTGATAACCACACTATAAAATTTCGA
Found at i:17019 original size:22 final size:22
Alignment explanation
Indices: 16936--17026 Score: 85
Period size: 22 Copynumber: 4.1 Consensus size: 22
16926 AAAATTTCGA
* * *
16936 AAATTTTGATAATCTCCCTATG
1 AAATTTCGATAACCTCCTTATG
*
16958 AAATTTCGATAACCATAC-TATG
1 AAATTTCGATAACC-TCCTTATG
* * *
16980 AAAATTCGGTAACTTCCTTATG
1 AAATTTCGATAACCTCCTTATG
* *
17002 AAATTTTGATAACCTCCTTGTG
1 AAATTTCGATAACCTCCTTATG
17024 AAA
1 AAA
17027 ATTTAATATA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 2 0.04
22 51 0.93
23 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
AAATTTCGATAACCTCCTTATG
Found at i:21217 original size:331 final size:328
Alignment explanation
Indices: 19667--22069 Score: 1876
Period size: 331 Copynumber: 7.4 Consensus size: 328
19657 TCTACTAACA
* * * * * * *
19667 TACACGATTTCAGTTAATATTTTACAAAAATTGACCAG-AAA-TCTTTTTCTTCAATTTTTGTCT
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTTTC-TCAATTTTTGGCT
* * * * *
19730 AAA-A-T-AT---TCATATATAATTCAACTCCAAAAAGATCGAAGGACTTTCCACGCTTTTAATA
65 AAATACTCATAAAT-ATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACAC-TTTAATA
* * * *
19789 TCCTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAGGATTCAGATGCTAGTAAA
128 TCGTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* *
19854 AACAAATCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTTAAGGAGTCT
193 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
*** * * * * * *
19919 TAACGCAAAAAATCATTCAAAACTGAGGCA-GGGTCCCGAAACGCATTTTTAGCAAAAAAAACAA
258 TGGTGCCAAAAATCATGC-AAACTGA-CCATGGG-CCCGGAACGCGTTTTTAGCCAAAAAAAC-A
*
19983 TGATGGTT-T
319 TGATGATTAT
* * * * *
19992 ATACACGATTTCGGCTAAACTTTTGCATAAAATTGACCAGAAAA-TTTTTTTATTAATTTTTGGT
1 -TACACGATTTCGGCTAAAATTTTGCA-AAAATTGACCCGAAAAGTTTTTTTCTCAATTTTTGGC
* * * * *
20056 TAGAATACTCATGAAATATATATAATTTAACGTCAAATAGTTTGGAA-GACTTTTCACTCTTTTC
64 TA-AATACTCAT-AAATATATATAATTTAACGCCAAAAAGATT-GAAGGACTTTTCACAC-TTTA
**
20120 ATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATTAAAACATA-ATTCAGATGCTC
125 ATATCGTTTTTCATATTTTTT-TGAATTAATTTCTAATTAAATCGAAACA-AGATTCAGATGCTC
* * * * *
20184 AT-AAAA-AAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGGTGAATATGGATATTTCAAGG
188 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGG
* * ** * *
20247 AGTATTAGCACAAAAAATCATGCAAAACTGA-CATGGGGCCCCGCAACGCGTTTTTAG-CAAAAA
253 AGTCTTGGTGCCAAAAATCATGC-AAACTGACCAT-GGG-CCCGGAACGCGTTTTTAGCCAAAAA
*
20310 ACCATGATGATTAT
315 AACATGATGATTAT
* * * *
20324 TACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CTGGAAAGATATTTT-TCAATTTTTGGCTA
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTTTCTCAATTTTTGGCT-
* * * * * * *
20387 AAATAATCATAAAATAATATATAATTCAACGCCAAAAATATTGATTGG-TTTTTTACGCTTCTAA
65 AAATACTCAT-AAAT-ATATATAATTTAACGCCAAAAAGATTGA-AGGACTTTTCACACTT-TAA
* ** * * *
20451 TATCGTTTTCCATACTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGACTT-AGATGCTTG
126 TATCGTTTTTCATA-TTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGA-TTCAGATGCTCG
* * *
20515 TCAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTAATTAGATG-ATAATAGATATTTCAAGG
189 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT-ATAGATATTTCAAGG
* * *
20579 AGTCTTGGCGCCAAAAATCATGCACAACTGACGC--GGGACCCTGCAATGCGTTTTTAGCCAAAA
253 AGTCTTGGTGCCAAAAATCATGCA-AACTGAC-CATGGG-CCC-GGAACGCGTTTTTAGCCAAAA
* *
20642 AAAAACTG-TGA-TGT
314 AAACA-TGATGATTAT
* * * * * * * *
20656 TACATGATTTCGGCTAATATTATGCAAAAATGGACTCGAAATATTTTTTTTCTCAAATTTTAGCC
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-AGTTTTTTTCTC-AATTTTTGGC
* * * * *
20721 AAAATGCTCATAAAAAGTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACACTTT--TA
64 TAAATACTCATAAATA-TATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACACTTTAATA
* * *
20784 ---ATTTTCATATTTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG-TACATA
128 TCGTTTTTCATATTTTTT-TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT-CGTA
* * * * *
20845 ATAACAAATCCTTAAATCCAATGTAGCTGATATTTTATTAGATGAATAAAGATATTTCAAGGAGT
191 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
* * * * *
20910 CTCGGTGCCAAAAATCATGCAAACAGAACCATGGTCCCGGAACGCGTTTTTAGCCAAAAAATCGT
256 CTTGGTGCCAAAAATCATGCAAACTG-ACCATGGGCCCGGAACGCGTTTTTAGCCAAAAAAACAT
*
20975 GATGATTAG
320 GATGATTAT
* * * * *
20984 TACACGATTTCGGCTAAAAATTTGCAAAAAATGACCCGAAAAGTTTTTCTGTCAATTTTTTGCTA
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTTTCTCAATTTTTGGCTA
* *
21049 AACTACTCATAAACTATATTTAATTTAACGCCAAAAAGATTGGAGGACTTTTCACACTTTAATAT
66 AA-TACTCATAAA-TATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACACTTTAATAT
* *
21114 CGTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCGTAAAA
129 CGTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * * * **
21179 ACAAAAT-TTTAAATCCAATGTAGCTGAGATTTTATTAGATGAATA-AGGTTATCTCAAATAGTC
194 AC-AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA-GATATTTCAAGGAGTC
* * *
21242 TTGGTGCCATAAATCATGCAAAACTTAGC-TGGGGCCTCAGG-ACGCGTTTTTAGCC--AAAAAC
257 TTGGTGCCAAAAATCATGC-AAACTGACCAT-GGGCC-C-GGAACGCGTTTTTAGCCAAAAAAAC
21303 TATGATGATTAT
318 -ATGATGATTAT
* ** * * * * *
21315 TACACGATTTCGGTTAGTATTTTGCAAAAATTGTCTCG-AAAGTTATTTTCTCAAATTTTAG-TC
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTTTCTCAATTTTTGGCT-
* *
21378 ACAATACTCATGAAA-AGTATATAATTTAACGCCAAAAAGATTGAAGGGCTTTTCAGACTTCTAA
65 A-AATACTCAT-AAATA-TATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACACTT-TAA
** * * * * *
21442 TATCGTTTTTCCCATTTTTTCGAATTAATTTCTAATTAAAAC--AA-AACATTCAAATGCTAGT-
126 TATCGTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * *
21503 ------AA-----AAA--CAA--TGGCTGGGGTTTGATTAGATGATTATAGATATTTCAAGGAGT
191 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
* * ** * * * *
21553 CTTGGTGTCAAAAATTATTTAAAACTGAACC--GGGCTCAGGAATGTGTTTTCAGCC-AAAAAAC
256 CTTGGTGCCAAAAATCA-TGCAAACTG-ACCATGGGC-CCGGAACGCGTTTTTAGCCAAAAAAAC
*
21615 TGTGATGATTAT
318 -ATGATGATTAT
* * * * *
21627 TACACGATTT-GGATTAAAATTTTGCAAAAATTGACAC-AAAAGATATTTCCTCAA----T---T
1 TACACGATTTCGG-CTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTTTCTCAATTTTTGGCT
* *
21683 -AAT--TC----A-AT-T-CAA--T---GCCAAAAA-ATTTGAAGGGCTTTTCACACTTCTAATA
65 AAATACTCATAAATATATATAATTTAACGCCAAAAAGA-TTGAAGGACTTTTCACACTT-TAATA
* * *
21732 TCGTTTTTCATATTTTATTTCTAAATTAATTTCTAATTAAATCGGAACAAGATTCAGATGCTTGT
128 TCGTTTTTCATA-TTT-TTT-TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * * * *
21797 AAAAACAAATCCTTAAATGCAATGTGACTAAAATTTTATTAGATGAATATAGGTATTTCAAGGAT
190 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* * ** * * * *
21862 TGTCGGTGCCAAAAATCATGCAAAACTGAGTAAGGGCCCTGAAACACGTTTTTAGCC-AAAAACC
255 TCTTGGTGCCAAAAATCATGC-AAACTGACCATGGGCCC-GGAACGCGTTTTTAGCCAAAAAAAC
*
21926 GTGATGATTAT
318 ATGATGATTAT
* * * *
21937 TACATGATTTTGGCTAAAATTTTGCAGAAAA-TGACCC-AAAATTTTTTTTCTCAA-TTTTGGAT
1 TACACGATTTCGGCTAAAATTTTGCA-AAAATTGACCCGAAAAGTTTTTTTCTCAATTTTTGGCT
* ** *
21999 AAAATACTCATAAAATATATATAATTTAACGCCAAAAAAATTGAAAAACTTTTTCACGATTTTAA
65 -AAATACTCAT-AAATATATATAATTTAACGCCAAAAAGATTGAAGGAC-TTTTCAC-ACTTTAA
22064 TATCGT
126 TATCGT
22070 CCTCTACTTT
Statistics
Matches: 1677, Mismatches: 268, Indels: 256
0.76 0.12 0.12
Matches are distributed among these distances:
287 1 0.00
288 43 0.03
289 3 0.00
290 3 0.00
291 20 0.01
293 4 0.00
294 15 0.01
295 1 0.00
296 2 0.00
301 4 0.00
303 3 0.00
306 4 0.00
308 4 0.00
309 2 0.00
310 105 0.06
311 45 0.03
312 112 0.07
313 5 0.00
314 3 0.00
316 4 0.00
318 3 0.00
320 4 0.00
325 1 0.00
326 35 0.02
327 119 0.07
328 184 0.11
329 43 0.03
330 164 0.10
331 260 0.16
332 165 0.10
333 132 0.08
334 121 0.07
335 55 0.03
336 8 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (328 bp):
TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTTTCTCAATTTTTGGCTA
AATACTCATAAATATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACACTTTAATATCG
TTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGG
TGCCAAAAATCATGCAAACTGACCATGGGCCCGGAACGCGTTTTTAGCCAAAAAAACATGATGAT
TAT
Found at i:22473 original size:66 final size:66
Alignment explanation
Indices: 22401--22532 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
22391 TTATATATAT
*
22401 TATAATATATACAAATATATATATA-ATTAACAAAATAATAGAATTTTCAACAAGCAGGAAAGAA
1 TATAATATATACAAATATATATATATA-TAACAAAATAATAGAATTTTCAAAAAGCAGGAAAGAA
22465 AG
65 AG
* *
22467 TATAATATATATATATATATATATATATAACAAAATAATAGAATTTTCAAAAAGCAGGAAAGAAA
1 TATAATATATACAAATATATATATATATAACAAAATAATAGAATTTTCAAAAAGCAGGAAAGAAA
22532 G
66 G
22533 AAGCAAATTC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 61 0.98
67 1 0.02
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (66 bp):
TATAATATATACAAATATATATATATATAACAAAATAATAGAATTTTCAAAAAGCAGGAAAGAAA
G
Found at i:22478 original size:2 final size:2
Alignment explanation
Indices: 22467--22495 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
22457 GGAAAGAAAG
22467 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22496 ACAAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:24481 original size:3 final size:3
Alignment explanation
Indices: 24473--24507 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
24463 CCACCCTTTA
24473 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
24508 GGGAAATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:24949 original size:24 final size:24
Alignment explanation
Indices: 24917--24966 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
24907 CCGCCCATTT
*
24917 TTAATTTTTAAAAT-AAAATAATAA
1 TTAAATTTTAAAATAAAAATAA-AA
**
24941 TTAAATTTTTTAATAAAAATAAAA
1 TTAAATTTTAAAATAAAAATAAAA
24965 TT
1 TT
24967 TAAACATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAAATTTTAAAATAAAAATAAAA
Found at i:26958 original size:3 final size:3
Alignment explanation
Indices: 26950--26985 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
26940 CTAGTTTGGT
26950 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
26986 CTCTGTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29498 original size:45 final size:45
Alignment explanation
Indices: 29442--29531 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
29432 AATTACTTCT
*
29442 CCAGCTCATCATGAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATGAATTCGGGGTAAGGATCTTTTAGTAATTCCAC
* *
29487 CCAGCTTATCATTAATTCGGGGTAAGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATGAATTCGGGGTAAGGATCTTTTAGTAATTCCAC
29532 TACTCTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (45 bp):
CCAGCTCATCATGAATTCGGGGTAAGGATCTTTTAGTAATTCCAC
Found at i:33815 original size:2 final size:2
Alignment explanation
Indices: 33808--33847 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
33798 TACTAACGTG
33808 AT AT 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 AT AT
33848 TATTTTAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43450 original size:60 final size:60
Alignment explanation
Indices: 43365--43527 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
43355 GCTAATTGCT
* * * * *
43365 CAAATAAGGGCCCAACATTTTCCAAAATGCTCAAATAAGGGCCCGATCCTTT-AATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCAT-CTTTGAATTTGAC
43425 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC
43485 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
43528 TGTCTCACTC
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
59 4 0.04
60 93 0.96
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC
Found at i:43496 original size:29 final size:28
Alignment explanation
Indices: 43396--43496 Score: 80
Period size: 29 Copynumber: 3.4 Consensus size: 28
43386 CCAAAATGCT
*
43396 CAAATAAGGGCCCGATCCTTT-AATTTGGC
1 CAAATAAGGGCCCCAT-CTTTGAATTT-GC
* * **
43425 CAAATAAGGG-CCTAACGTTTGCCAAAATGC
1 CAAATAAGGGCCCCATC-TTTG--AATTTGC
43455 TCAAATAAGGGCCCCATCTTTGAATTTGAC
1 -CAAATAAGGGCCCCATCTTTGAATTTG-C
43485 CAAATAAGGGCC
1 CAAATAAGGGCC
43497 TAACGTTTGC
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
27 1 0.02
28 6 0.11
29 26 0.46
30 3 0.05
31 17 0.30
32 4 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (28 bp):
CAAATAAGGGCCCCATCTTTGAATTTGC
Found at i:43528 original size:31 final size:31
Alignment explanation
Indices: 43361--43528 Score: 136
Period size: 31 Copynumber: 5.5 Consensus size: 31
43351 AAAGGCTAAT
* * *
43361 TGCTCAAATAAGGGCCCAACATTTTCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * **
43392 TGCTCAAATAAGGGCCCGATCCTTT---AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
43421 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * **
43452 TGCTCAAATAAGGGCCCCATC-TTTG--AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
43481 TGAC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 TG-CTCAAATAAGGGCCTAACGTTTGCCAAAA
43512 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
43529 GTCTCACTCG
Statistics
Matches: 107, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 11 0.10
29 31 0.29
30 6 0.06
31 48 0.45
32 11 0.10
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:43597 original size:31 final size:31
Alignment explanation
Indices: 43559--43680 Score: 160
Period size: 31 Copynumber: 4.0 Consensus size: 31
43549 TGACACCAGA
43559 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
43590 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
* ** * * *
43621 CCCTTATTTGACCAAATT--A-AAAGATCGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
43649 ACCCTTATTTGAGCATTTTCGATAACGTTAGG
1 -CCCTTATTTGAGCATTTTCGATAACGTTAGG
43681 TCCCGGGTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
28 6 0.08
29 16 0.21
31 47 0.63
32 6 0.08
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGG
Found at i:44339 original size:45 final size:44
Alignment explanation
Indices: 44218--44344 Score: 114
Period size: 44 Copynumber: 2.9 Consensus size: 44
44208 TTACACTATT
44218 TTTTA-TAATCCA-ATTATGAAATTTTGATAACCTTCCTATAAAA
1 TTTTATTAAT-CATATTATGAAATTTTGATAACCTTCCTATAAAA
* * * * ** *
44261 TTTTATTAATGATACTATGAAATTTCGAGAACCTTTTTATAAATT
1 TTTTATTAATCATATTATGAAATTTTGATAACCTTCCTATAAA-A
* * * * *
44306 TTTTTTTAATCTTTTTATGAAATTTTGTTAACCTCCCTA
1 TTTTATTAATCATATTATGAAATTTTGATAACCTTCCTA
44345 AGGAATTTTG
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
43 6 0.10
44 29 0.46
45 28 0.44
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (44 bp):
TTTTATTAATCATATTATGAAATTTTGATAACCTTCCTATAAAA
Found at i:44458 original size:22 final size:22
Alignment explanation
Indices: 44396--44451 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
44386 CAATGAAATT
*
44396 TTGATAACCAACACTATGAGATA
1 TTGATAACC-ACAATATGAGATA
* * * *
44419 TTGCTAACCTCCATATGATATA
1 TTGATAACCACAATATGAGATA
44441 TTGATAACCAC
1 TTGATAACCAC
44452 GTTATGAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (22 bp):
TTGATAACCACAATATGAGATA
Found at i:44572 original size:23 final size:23
Alignment explanation
Indices: 44496--44791 Score: 134
Period size: 22 Copynumber: 13.7 Consensus size: 23
44486 TAGCAATCAT
*
44496 ACTATGAAATTTTGATAATC-AC
1 ACTATGAAATTTTGATAATCTTC
*
44518 ACTATGAAATTTTGATAA-CCTC
1 ACTATGAAATTTTGATAATCTTC
*
44540 GCTATGAAATTTTGATAAATCTTC
1 ACTATGAAATTTTGAT-AATCTTC
* * * *
44564 -CTATAAAATTTTTATAAACCTC
1 ACTATGAAATTTTGATAATCTTC
* * *
44586 CCTATAAAATTTT--TAAACTTTC
1 ACTATGAAATTTTGATAATC-TTC
* **
44608 -TTATGAAATCATGATAA-C-T-
1 ACTATGAAATTTTGATAATCTTC
*
44627 AC----AAATTTTGATAACCTTC
1 ACTATGAAATTTTGATAATCTTC
* ** *
44646 -GTATGATTTTTTGATAA-CCTC
1 ACTATGAAATTTTGATAATCTTC
* *
44667 ATTATGAAATTTTGTTAATC-TC
1 ACTATGAAATTTTGATAATCTTC
* * *
44689 CCTATGAAATTTTGAT-CTGCAT-
1 ACTATGAAATTTTGATAAT-CTTC
*
44711 ACTATGAAATTTTGATAACCTTC
1 ACTATGAAATTTTGATAATCTTC
* * **
44734 -TTATGAAATTTTGA-AAACTAA
1 ACTATGAAATTTTGATAATCTTC
*
44755 ACTATGAAATTTTGAT-ATCCTC
1 ACTATGAAATTTTGATAATCTTC
*
44777 -C-CTGAAATTTTGATA
1 ACTATGAAATTTTGATA
44792 TCCTCCATAA
Statistics
Matches: 209, Mismatches: 41, Indels: 49
0.70 0.14 0.16
Matches are distributed among these distances:
16 10 0.05
17 1 0.00
18 1 0.00
20 13 0.06
21 23 0.11
22 126 0.60
23 32 0.15
24 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (23 bp):
ACTATGAAATTTTGATAATCTTC
Found at i:44759 original size:44 final size:44
Alignment explanation
Indices: 44321--44789 Score: 134
Period size: 44 Copynumber: 10.8 Consensus size: 44
44311 TTAATCTTTT
* * * * * * *
44321 TATGAAATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCT-CAG
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGAA-AACTAAAC
* * *
44365 TATGAAATTTTGATAA-CTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTT-CCTATGAAATTTTGAAAACTAA-AC
* * * * * * * ***
44410 TATGAGATATTGCTAACC-TCCATATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTTCC-TATGAAATTTTGAAAACTAAAC
* * * * * * *
44454 TATGAAAATTTAAAAACC-TCCATATG-GATTATTAGCAATC-ATAC
1 TATGAAATTTTGATAACCTTCC-TATGAAATT-TT-GAAAACTAAAC
* * * **
44498 TATGAAATTTTGATAATC-ACACTATGAAATTTTGATAACCT-CGC
1 TATGAAATTTTGATAACCTTC-CTATGAAATTTTGA-AAACTAAAC
* * * **
44542 TATGAAATTTTGATAAATCTTCCTATAAAATTTTTATAAACCT-CCC
1 TATGAAATTTTGAT-AACCTTCCTATGAAATTTTGA-AAA-CTAAAC
* * * * **
44588 TATAAAATTTTTA-AACTTTCTTATGAAATCATG---A-T-AAC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGAAAACTAAAC
* * ** * * *
44626 TA-CAAATTTTGATAACCTTCGTATGATTTTTTGATAACCT-CAT
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGA-AAACTAAAC
* * * * *
44669 TATGAAATTTTGTTAATCTCCCTATGAAATTTTG--ATCTGCATAC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGAAAACT--AAAC
*
44713 TATGAAATTTTGATAACCTTCTTATGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGAAAACTAAAC
* *
44757 TATGAAATTTTGATATCC-TCC-CTGAAATTTTGA
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGA
44790 TATCCTCCAT
Statistics
Matches: 310, Mismatches: 89, Indels: 54
0.68 0.20 0.12
Matches are distributed among these distances:
37 8 0.03
38 18 0.06
40 1 0.00
41 3 0.01
42 11 0.04
43 13 0.04
44 179 0.58
45 57 0.18
46 20 0.06
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTTCCTATGAAATTTTGAAAACTAAAC
Found at i:44784 original size:20 final size:20
Alignment explanation
Indices: 44759--44797 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
44749 AACTAAACTA
44759 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
44779 TGAAATTTTGATATCCTCC
1 TGAAATTTTGATATCCTCC
44798 ATAATAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:45035 original size:22 final size:21
Alignment explanation
Indices: 44873--45042 Score: 87
Period size: 22 Copynumber: 7.8 Consensus size: 21
44863 GAAATACCAC
*
44873 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAA-CACGT
* *
44895 TCTGAAAATTTGATAAC-CTGTT
1 TATGAAATTTTGATAACAC-G-T
*
44917 TCTGAAATTTTGATAAC-CTGTT
1 TATGAAATTTTGATAACAC-G-T
* * * * *
44939 TATAAAATTTTGTTGACCCCT
1 TATGAAATTTTGATAACACGT
* *
44960 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAA-CACGT
* *
44983 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAA-CACG-T
*
45006 T-TGGAATTTTGATAACAACGT
1 TATGAAATTTTGATAAC-ACGT
45027 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
45043 TCTTCCTATA
Statistics
Matches: 116, Mismatches: 23, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.01
21 9 0.08
22 100 0.86
23 6 0.05
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTGATAACACGT
Found at i:45255 original size:22 final size:21
Alignment explanation
Indices: 44919--45485 Score: 140
Period size: 22 Copynumber: 25.9 Consensus size: 21
44909 AACCTGTTTC
***
44919 TGAAATTTTGATAACCTGTTTA
1 TGAAATTTTGATAACC-ACCTA
* * * *
44941 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCAC-CTA
* * *
44963 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCAC-CTA
* * *
44985 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCAC-CTA
* * *
45007 TGGAATTTTGATAACAACGTTA
1 TGAAATTTTGATAACCAC-CTA
**
45029 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAA-CCACCTA
*
45051 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C-CA-C-CTA
* *
45075 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCAC-CTA
* **
45097 TGAGA-TTTGATAACCTTCTA
1 TGAAATTTTGATAACCACCTA
* *
45117 TCAAATTTTGAT-ACTC-CTTA
1 TGAAATTTTGATAAC-CACCTA
* * *
45137 TGAAATTGAGACTTTTATAACCTTCATA
1 TGAAA-T-----TTTGATAACC-ACCTA
*
45165 TGGAATTTTGATAACCACGCTA
1 TGAAATTTTGATAACCAC-CTA
* * *
45187 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACC-ACCTA
* *
45209 TGAAATATT-AGTAACCTCCTAA
1 TGAAATTTTGA-TAACCACCT-A
*
45231 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCAC-CTA
45253 TGAAATTCTT-ATAA--ATCGCTA
1 TGAAATT-TTGATAACCA-C-CTA
* * * *
45274 TGACATTTTGATAATC-TCTT
1 TGAAATTTTGATAACCACCTA
** *
45294 TGATAACCTTTAT-ATAA--AATTG
1 TGA-AA--TTT-TGATAACCACCTA
*
45316 TGAAA--AT--TAACCACCCTA
1 TGAAATTTTGATAACCA-CCTA
** *
45334 TGAAATTTCAATAACCAATCTA
1 TGAAATTTTGATAACC-ACCTA
* *
45356 AGAAATTTTAATAACCTGATCCTA
1 TGAAATTTTGATAACC--A-CCTA
**
45380 TGAAATTTTGATAACTTCCATA
1 TGAAATTTTGATAACCACC-TA
*
45402 TGAAATTTTGGTAACCACGCTA
1 TGAAATTTTGATAACCAC-CTA
* *
45424 TGGAATTTTGATAACCTCCTCA
1 TGAAATTTTGATAACCACCT-A
* * * *
45446 TGAAATTATAATAAACATCTTA
1 TGAAATTTTGATAACCA-CCTA
45468 TGAAATTTTGATAACCAC
1 TGAAATTTTGATAACCAC
45486 ATAGAGACAA
Statistics
Matches: 397, Mismatches: 101, Indels: 95
0.67 0.17 0.16
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 1 0.00
18 6 0.02
20 22 0.06
21 56 0.14
22 239 0.60
23 21 0.05
24 21 0.05
25 11 0.03
26 6 0.02
27 3 0.01
28 7 0.02
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (21 bp):
TGAAATTTTGATAACCACCTA
Found at i:45690 original size:30 final size:32
Alignment explanation
Indices: 45645--45710 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
45635 TGGTAATTTA
* *
45645 GAAATATGTTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
45676 GAAATAT-ATTTTAAAAATAAGGGTACAATCG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
45707 GAAA
1 GAAA
45711 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (32 bp):
GAAATATGATTTTAAAAATAAGGGTACAATCG
Found at i:46276 original size:111 final size:109
Alignment explanation
Indices: 46079--46299 Score: 361
Period size: 111 Copynumber: 2.0 Consensus size: 109
46069 GGGTCTAGTT
* *
46079 ATAATTTTTGCTAGTATTTTTCGGATAAGGGCATCTTTTGAATATAATAAACTGTCAGAAACTGT
1 ATAATTTTTGCTAGTATTTTTCGGATAAGGGCATCTTTTGAATATAATAAACTGTCAAAAAATGT
* *
46144 AAATACAGTTTTTCAAGTTTCAAGTTTAATAGATCTCTGTTGAC
66 AAATACAGTTTTTCAAATTTCAAGTTTAATAGATATCTGTTGAC
* *
46188 ATAATTTTTGCTAGTATTTTTTGGATAAGAGGCATTTTTTTGAATATAATAAACTGTCAAAAAAT
1 ATAATTTTTGCTAGTATTTTTCGGATAAG-GGCA-TCTTTTGAATATAATAAACTGTCAAAAAAT
*
46253 GTAAATACAGTTTTTCAAATTTCAAGTTTAATAGATATTTGTTGAC
64 GTAAATACAGTTTTTCAAATTTCAAGTTTAATAGATATCTGTTGAC
46299 A
1 A
46300 AAGAGATGTC
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
109 28 0.27
110 4 0.04
111 71 0.69
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (109 bp):
ATAATTTTTGCTAGTATTTTTCGGATAAGGGCATCTTTTGAATATAATAAACTGTCAAAAAATGT
AAATACAGTTTTTCAAATTTCAAGTTTAATAGATATCTGTTGAC
Found at i:53214 original size:21 final size:21
Alignment explanation
Indices: 53188--53227 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
53178 GGAGGATAAA
53188 GAAACCCCAAGGTTTCAAGTT
1 GAAACCCCAAGGTTTCAAGTT
53209 GAAACCCCAAGGTTTCAAG
1 GAAACCCCAAGGTTTCAAG
53228 CTTTTACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
GAAACCCCAAGGTTTCAAGTT
Done.