Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013888.1 Corchorus capsularis cultivar CVL-1 contig13909, 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: 138463
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
36 TGGAGCTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7718 original size:17 final size:18
Alignment explanation
Indices: 7696--7729 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7686 TTGTAATCTC
7696 TGATTA-TTGATTAAAAG
1 TGATTATTTGATTAAAAG
7713 TGATTATTTGATTAAAA
1 TGATTATTTGATTAAAA
7730 AAACAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (18 bp):
TGATTATTTGATTAAAAG
Found at i:11502 original size:12 final size:12
Alignment explanation
Indices: 11469--11507 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
11459 TCTCTCCGTA
11469 GTGGCGGGCACC
1 GTGGCGGGCACC
11481 GTAGG-GGGCACC
1 GT-GGCGGGCACC
*
11493 GTGGCTGGCACC
1 GTGGCGGGCACC
11505 GTG
1 GTG
11508 TTGGGAGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.10, C:0.28, G:0.49, T:0.13
Consensus pattern (12 bp):
GTGGCGGGCACC
Found at i:20848 original size:1 final size:1
Alignment explanation
Indices: 20842--20881 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
20832 AGAAGGCTAG
20842 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20882 AATTTAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:28885 original size:7 final size:7
Alignment explanation
Indices: 28873--28903 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
28863 TATTATACAT
28873 TGATTGA
1 TGATTGA
28880 TGATTGA
1 TGATTGA
28887 TGATTGA
1 TGATTGA
28894 TGATTGA
1 TGATTGA
28901 TGA
1 TGA
28904 CAAGGTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (7 bp):
TGATTGA
Found at i:44815 original size:21 final size:21
Alignment explanation
Indices: 44789--44832 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
44779 TAAAACTGGA
44789 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
** *
44810 TTGCTATTCACCGTCCCATTT
1 TTGCTAAACACCGCCCCATTT
44831 TT
1 TT
44833 TACGTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:45065 original size:32 final size:33
Alignment explanation
Indices: 45029--45133 Score: 115
Period size: 32 Copynumber: 3.2 Consensus size: 33
45019 TGCCCCAAGA
*
45029 GGGCGGCTT-ACCATGGGCAGGCCGCCCCATTG
1 GGGCGGCTTCACCATGGGCAGGCCGCCCCACTG
* *** *
45061 GGGCGGCTTCACTATGAATAGGCCGCCCCACAG
1 GGGCGGCTTCACCATGGGCAGGCCGCCCCACTG
* **
45094 GGGCGGCTTCGCCA-GGGCAGGCCGCCCCGGTG
1 GGGCGGCTTCACCATGGGCAGGCCGCCCCACTG
45126 GGGCGGCT
1 GGGCGGCT
45134 AGGTTATTTT
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 29 0.50
33 29 0.50
ACGTcount: A:0.12, C:0.34, G:0.40, T:0.13
Consensus pattern (33 bp):
GGGCGGCTTCACCATGGGCAGGCCGCCCCACTG
Found at i:50269 original size:21 final size:21
Alignment explanation
Indices: 50223--50269 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
50213 ACTTTGAAGC
*
50223 CTTACAAGATGAATCTGAGTT
1 CTTACAAGATGAATCTGACTT
* **
50244 TTTACAAGATGAATCTTTCTT
1 CTTACAAGATGAATCTGACTT
50265 CTTAC
1 CTTAC
50270 CTGTAGTCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
CTTACAAGATGAATCTGACTT
Found at i:55194 original size:325 final size:321
Alignment explanation
Indices: 53859--57356 Score: 2788
Period size: 325 Copynumber: 10.9 Consensus size: 321
53849 GCCACATCTA
* * * *
53859 AATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAAATTGAAAAAATGATATTAGAAGCAT
1 AATCTT-TTTCGAATTAATTAGAAATTAATTCGG-AAAAAATTGGAAAAATGATATTAGAAGCGT
* *
53924 GAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTTGCAAAAAGTT
64 GAAAA-ACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
* * * * *
53989 CAGGAAAAAAAATTTCGGATAAGTTTTTAGCCGAAATCGTGTAATAACCCATCACGGTTTTTCGG
128 CA-GAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAA-CCATCACGGTTTTTGGG
* * * *
54054 CAAAAAACGTGTTTCAGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAAACTCTTTGAA
191 CTAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAA
* * **
54119 ATATCTGCATTCATCGAACCAATTCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCACC
256 ATATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCATT
54184 C
321 C
* * **
54185 GAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTTGGAAAAACGATATTAGAAGTT
1 -AATCTT-TTTCGAATTAATTAGAAATTAATTCGGAAAAAA-TTGGAAAAATGATATTAGAAGCG
* * * ** * * * *
54250 TGAAAAACCCTTCAATCTCTTTGGAG-TGAATTATATATATTGTGGTAAAGAATGGAGG-AAAAA
63 TGAAAAA-CCATCAATCTTTTTGGAGTTGAATTATATAT-TTTTTCT-GAGTATTGTGGCAAAAA
* ** * * **
54313 ATTTTC-G-GATCAGTTTAT---G-CAAATTTTTATTCGAAATCGT-TGACT---CATCACGGTT
125 A--TTCAGAAAAAAATTT-TCGGGTC-AGTTTTTAGCCGAAATCGTGT-ACTAACCATCACGGTT
* * * * ** * * **
54368 TAT-GGCTAAAAACGCG-TTCCGAGGCTCCAACTCAGTTTTGCAAGATTTTTAGCTTAAAGACTC
185 TTTGGGCTAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
* * * * * * * * * * * * *
54431 CTTGCAATATCTATATTTACCGAAACAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCG
250 CTTGAAATATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACA
54496 AGCATCTC
315 AGCAT-TC
* * * * *
54504 AATCTTGTTTC-AATACAATTTGAAATTATTTCGGAATAAAACTGGAAAAAAAGATATTAGAAGC
1 AATCTT-TTTCGAAT-TAATTAGAAATTAATTCGGAA-AAAATTGG-AAAAATGATATTAGAAGC
* * * *
54568 GTGAAAAAACACGTCAATCTTTCTGGCA-TTGAATTGTATAATTTTTT-TGAGTATTGTGACAAA
62 GTG-AAAAAC-CATCAATCTTTTTGG-AGTTGAATTATAT-ATTTTTTCTGAGTATTGTGGCAAA
* *
54631 AAATTGAGAAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCATGGTTTT
123 AAATTCAGAAAAAAA-TTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
* * * * * ** * * * *
54696 TGGGC-AAAAACGCG-CTCTGGAGCTCCGAATAAATTTTGCATGTTTTTTTAGC-GCAAAGACTC
187 TGGGCTAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATG-ATTTTTGGCAG-AAAGACTC
* * * ** * * * * *
54758 CTTGAAATATCTATATTAATCGAAGCAAATGTCAACCACATTGGA-TAAAAGAATTTGTTTTTAC
250 CTTGAAATATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACG-ATTAGTTTTTAC
* *
54822 GAGCAACTC
314 AAGC-ATTC
* * * * * *
54831 AATATTTTTTCTATTTAATTAGAAATTAATTCGGAAAAAAGTTGGAAATATGTTATTAGAAGCAT
1 AAT-CTTTTTCGAATTAATTAGAAATTAATTCGGAAAAAA-TTGGAAAAATGATATTAGAAGCGT
* ** *
54896 GAAAAGACCATCAATCTTTTTGGAGTTGAATTATATGTTTTTTCAAAGTATTCTGGCAAAAAATT
64 GAAAA-ACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
* * * * * *
54961 CAGAAAAAAATATTCCGAGTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGATTTTAGGGC
128 CAGAAAAAAAT-TTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGGC
* * * * *
55026 TAAAAAGGTGTTTCCGGGGCCCCAGCTCAATTTTGCATGGTTTTTGGCAGAAAGACTCCATGAAA
192 TAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
*
55091 TATCTACATTCATCGAATCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAA-C---C
257 TATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCATTC
* * * * **
55152 -A-----TTCGATTTTATTAGAAATTAATTCGAAAAAAAATTGGAAAAACGATATTAGAAGTTTG
1 AATCTTTTTCGAATTAATTAGAAATTAATTCG-GAAAAAATTGGAAAAATGATATTAGAAGCGTG
* * * ** * * *
55211 AAAAACCCTTCAATCTTTTTGGTG-TGAATTATATATATTGTGGTAAAGAATTGAGG-AAAAAAT
65 AAAAA-CCATCAATCTTTTTGGAGTTGAATTATATAT-TTTTTCT-GAGTATTGTGGCAAAAAA-
* ** * * ** ** * * * *
55274 TTTC-G--GATCAGTTT-GTG-CAAAATTTTATTCAAAATCATTTACT---CATCACGGTTTAT-
126 -TTCAGAAAAAAATTTTCGGGTC-AGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
* * * * ** *
55330 GGCTAAAAACGCG-TTCTGGGGCCCCGGCTCAGTTTTGCAAGATTTTTAGCTTAAAGACTCCTAG
189 GGCTAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTG
* * * * * * * * * * *
55394 AAATATCTATATTTATCGAACAAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCTAGCA
254 AAATATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCA
55459 TATC
319 T-TC
* * * *
55463 AATCTTGTTTC-AATATAATTAGAAATTATTTCGGAATAAAAATGGAAAAACGATATTATAAGCG
1 AATCTT-TTTCGAAT-TAATTAGAAATTAATTCGGAA-AAAATTGGAAAAATGATATTAGAAGCG
* ** * *
55527 TGAAAAACACGTCAAT-TTTTCTGGCA-TTGAATCGTATAATTTTTCTGACTATTGTGGCAAAAA
63 TGAAAAAC-CATCAATCTTTT-TGG-AGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAA
* * * *
55590 ATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTGGG
125 ATTCAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
* * * * * * *
55655 GCTAAAAACGTGTTTCGGGGGTCCAGACTCAGCTTTGCATAATTTTTGGCAGAAAAACTCCTTGA
190 GCTAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGA
* * *
55720 AATATCCACATTCGTCGAAACAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCAT
255 AATATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCAT
*
55785 CC
320 TC
* *
55787 GAATCTTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGGAAAAATGATATTAGAAGCC
1 -AATCTT-TTTCGAATTAATTAGAAATTAATTCGG-AAAAAATTGGAAAAATGATATTAGAAGCG
*
55852 TGAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAGAT
63 TGAAAA-ACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAT
55917 TCAGAAAAAAAATTTT-GGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGG
127 TCAG-AAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGG
* * * * * * *
55981 TTAAAAACGTGTTT-CGGGAGCACCGGCTTAGTTTTGCATGATTTTTGACAAAAAGACTCCATAA
191 CTAAAAACGTGTTTCCGGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGA
* *
56045 AATATCTACATTAATCGAACCAAATCCCAGCCACATTCGATTTTAACTATTAGTTTTTACAA-C-
255 AATATCTACATTCATCGAACCAAATCCCAGCCACATTCGA-TTTAACGATTAGTTTTTACAAGCA
56108 --C
319 TTC
* * * * * * **
56109 -A-----TTCGATTTTATTAGAAATTCATTCGGAAAAAAGTAG-AAAACGATATTAGAAGTTTGA
1 AATCTTTTTCGAATTAATTAGAAATTAATTCGGAAAAAATTGGAAAAATGATATTAGAAGCGTGA
* * * * * *
56167 AAAACCCTTCAATCATTTTGGCG-TGAATTATATA---TAT-TGAG----GT---AAAGAATTGA
66 AAAA-CCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCA
* * * ** * * *
56220 GGAAAAATTTTTCGGATCAGTTTGTGCAAAATTTTATTCAAAATCGTTTACT---CATCAGGGTT
130 GAAAAAAATTTTCGGGTCA----GT------TTTTAGCCGAAATCGTGTACTAACCATCACGGTT
* * * * * **
56282 TAT-GGCTAAAAACGCG-TTCCGGGGCCCCGGCTCAGTTTTGAAAGATTTTTAGCTTAAAGACTC
185 TTTGGGCTAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
* * * * * * * * * * *
56345 CTTGAAATATCTATATTTATAGAAACATATCTCAGCCATATT-GTATATAAGGATTTGTTTTTTC
250 CTTGAAATATCTACATTCATCGAACCAAATCCCAGCCACATTCG-ATTTAACGATTAGTTTTTAC
*
56409 TAGCATCTC
314 AAGCAT-TC
* *
56418 AATCTTGTTTC-AATATAATTAGAAATTATTTCGGAATAAAA-TGGAAAAACGATATTAGAAGCG
1 AATCTT-TTTCGAAT-TAATTAGAAATTAATTCGGAA-AAAATTGGAAAAATGATATTAGAAGCG
* ** * *
56481 TGAAAAA-CAGGTCAATCTTTCTGGCA-TTGAATCGTATAATTTCTCTGAGTATTGTGGCAAAAA
63 TGAAAAACCA--TCAATCTTTTTGG-AGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAA
* * * * *
56544 ATTGAGAAAAAACTTTTCGGGTCAGTTTTTAACCGAAATCGTATACT-ACCATCATGGTTTTT-G
125 ATTCAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
* * ** * * *
56607 GCTAAAAACGCG-TTCCGGAGCCCCGTATAAATTTTGCATGATTTTTAGCGCA-AAA-AGTCCTT
190 GCTAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTT-G-GCAGAAAGACTCCTT
* * * ** * * * * * * *
56669 GAAATATATATATTCATTGAACCAAATGTCAGGCACGTTGGATATAAGGATTTGTTTTTACGAGC
253 GAAATATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGC
*
56734 ATTTA
318 A-TTC
* *
56739 AATCTTGTTTCGATTTAATTA-AAATTAATTCGGAAAAAAATTGAAAAAATGATATTAGAAGCGT
1 AATCTT-TTTCGAATTAATTAGAAATTAATTCGG-AAAAAATTGGAAAAATGATATTAGAAGCGT
* *
56803 AAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATG
64 GAAAA-ACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
* * *
56868 CAGGAAAAAAA-TTTCGGGTCAGTTTTTAGCCGAAATCATGTATTAACCATCACGGTTTTTGTGC
128 CA-GAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGGC
* ** * * *
56932 TAAAAACGTGTTTCGGGGGTTCCGGCTCAGTTTTGCATAATTTTTGGCAGAAAAACTTCTTGAAA
192 TAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
* * * * * *
56997 TATCTACTTTCATCGAATCAAATCCCGGCCACATTCGATTTAATGATTAGATTTTACAAGCATCC
257 TATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCATTC
* *
57062 GAATCTTCTTTCGATTTAATTAGAAATTAATTCGGAATAAGATTGGAAAAATGATATTAGAAGCG
1 -AATCTT-TTTCGAATTAATTAGAAATTAATTCGGAA-AAAATTGGAAAAATGATATTAGAAGCG
* *
57127 TGAAAAGACCATCAAT-TATTTTAGAGCTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA
63 TGAAAA-ACCATCAATCT-TTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA
* * * **
57191 TTCAGGAAAAAAA-TTTCGGGTCAGTTTTTAACCTAAATCATGTACTAACCA-CACTATTTTTGG
126 TTCA-GAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
* * * * * * *
57254 GCTAAAAACGTGTTTCGGGGGTCCAGACTCAGTTTTGCATAATTTTTGGTAGCAAA-ATTCCTTG
190 GCTAAAAACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTG
*
57318 AAATATCCACATTCATCGAACCAAATCCCAGCCACATTC
254 AAATATCTACATTCATCGAACCAAATCCCAGCCACATTC
57357 AGGAAAAAAT
Statistics
Matches: 2527, Mismatches: 486, Indels: 319
0.76 0.15 0.10
Matches are distributed among these distances:
299 9 0.00
300 13 0.01
303 2 0.00
304 18 0.01
305 69 0.03
306 106 0.04
307 27 0.01
308 12 0.00
309 1 0.00
310 18 0.01
311 32 0.01
312 39 0.02
313 22 0.01
314 96 0.04
315 18 0.01
316 28 0.01
317 57 0.02
318 201 0.08
319 72 0.03
320 76 0.03
321 252 0.10
322 39 0.02
323 51 0.02
324 246 0.10
325 571 0.23
326 201 0.08
327 212 0.08
328 11 0.00
329 28 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (321 bp):
AATCTTTTTCGAATTAATTAGAAATTAATTCGGAAAAAATTGGAAAAATGATATTAGAAGCGTGA
AAAACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAG
AAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAA
AACGTGTTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATC
TACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCATTC
Found at i:56423 original size:955 final size:948
Alignment explanation
Indices: 53859--57055 Score: 4576
Period size: 959 Copynumber: 3.3 Consensus size: 948
53849 GCCACATCTA
*
53859 AATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAAATTGAAAAAATGATATTAGAAGCAT
1 AATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAAATGATATTAGAAGCAT
* *
53924 GAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTTGCAAAAAGTT
66 GAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
* * *
53989 CAGGAAAAAAAATTTCGGATAAGTTTTTAGCCGAAATCGTGTAATAACCCATCACGGTTTTTCGG
131 CA-GAAAAAAAATTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAA-CCATCACGGTTTTTGGG
* **
54054 CAAAAAACGTGTTTCAGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAAACTCTTTGAA
194 CTAAAAACGTGTTTC-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCATGAA
* *
54119 ATATCTGCATTCATCGAACCAATTCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCACC
258 ATATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTAC-A--A-C
*
54184 CGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTTGGAAAAACGATATTAGAAGT
319 C--A------TTCGATTTTATTAGAAATTAATTCGGAAAAAA-TTGGAAAAACGATATTAGAAGT
*
54249 TTGAAAAACCCTTCAATCTCTTTGGAGTGAATTATATATATTGTGGTAAAGAATGGAGGAAAAAA
375 TTGAAAAACCCTTCAATCT-TTTGGAGTGAATTATATATATTGTGGTAAAGAATTGAGGAAAAAA
* * * *
54314 TTTTCGGATCAGTTTATGCAAATTTTTATTCGAAATCGTTGACTCATCACGGTTTATGGCTAAAA
439 TTTTCGGATCAGTTTGTGCAAAATTTTATTCAAAATCGTTTACTCATCACGGTTTATGGCTAAAA
* * ** *
54379 ACGCGTTCCGAGGCTCCAACTCAGTTTTGCAAGATTTTTAGCTTAAAGACTCCTTGCAATATCTA
504 ACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGATTTTTAGCTTAAAGACTCCTTGAAATATCTA
* *
54444 TATTTACCGAAACAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCT
569 TATTTATCGAAACAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCTAGCATCTCAATCT
* * * *
54509 TGTTTCAATACAATTTGAAATTATTTCGGAATAAAACTGGAAAAAAAGATATTAGAAGCGTGAAA
634 TGTTTCAATATAATTAGAAATTATTTCGGAATAAAAATGG-AAAAACGATATTAGAAGCGTG-AA
* * *
54574 AAACACGTCAATCTTTCTGGCATTGAATTGTATAATTTTTTTGAGTATTGTGACAAAAAATTGAG
697 AAACACGTCAATCTTTCTGGCATTGAATCGTATAATTTTTCTGAGTATTGTGGCAAAAAATTGAG
54639 AAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGGC-AA
762 -AAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCATGG-TTTTGGGCTAA
* * * ** *
54703 AAACGCGCTCTGGAGCTCCGAATAAATTTTGCATGTTTTTTTAGCGCAAAGACTCCTTGAAATAT
825 AAACGCGTTC-GGGGGTCCG-ATAAATTTTGCAT-AATTTTTAGCGCAAAAACTCCTTGAAATAT
* * * * *
54768 CTATATTAATCGAAGCAAATGTCAACCACATTGGA-TAAAAGAATTTGTTTTTACGAGCAACTC
887 CTATATTCATCGAAACAAATGTCAGCCACATTGGATTTAAAG-ATTTGTTTTTACGAGCATC-C
* * * * * * *
54831 AATATTTTTTCTATTTAATTAGAAATTAATTCGGAAAAAAGTTGGAAATATGTTATTAGAAGCAT
1 AATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAAATGATATTAGAAGCAT
* ** *
54896 GAAAAGACCATCAATCTTTTTGGAGTTGAATTATATGTTTTTTCAAAGTATTCTGGCAAAAAATT
66 GAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
* * * * *
54961 CAGAAAAAAATATTCCGAGTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGATTTTAGGGC
131 CAGAAAAAAA-ATTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGGC
* * * * *
55026 TAAAAAGGTGTTTCCGGGGCCCCAGCTCAATTTTGCATGGTTTTTGGCAGAAAGACTCCATGAAA
195 TAAAAACGTGTTT-CGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCATGAAA
*
55091 TATCTACATTCATCGAATCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAACCATTC
259 TATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAACCATTC
*
55156 GATTTTATTAGAAATTAATTCGAAAAAAAATTGGAAAAACGATATTAGAAGTTTGAAAAACCCTT
324 GATTTTATTAGAAATTAATTCG-GAAAAAATTGGAAAAACGATATTAGAAGTTTGAAAAACCCTT
*
55221 CAATCTTTTTGGTGTGAATTATATATATTGTGGTAAAGAATTGAGGAAAAAATTTTCGGATCAGT
388 CAATC-TTTTGGAGTGAATTATATATATTGTGGTAAAGAATTGAGGAAAAAATTTTCGGATCAGT
* *
55286 TTGTGCAAAATTTTATTCAAAATCATTTACTCATCACGGTTTATGGCTAAAAACGCGTTCTGGGG
452 TTGTGCAAAATTTTATTCAAAATCGTTTACTCATCACGGTTTATGGCTAAAAACGCGTTCCGGGG
*
55351 CCCCGGCTCAGTTTTGCAAGATTTTTAGCTTAAAGACTCCTAGAAATATCTATATTTATCG-AAC
517 CCCCGGCTCAGTTTTGCAAGATTTTTAGCTTAAAGACTCCTTGAAATATCTATATTTATCGAAAC
*
55415 AAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCTAGCATATCAATCTTGTTTCAATATA
582 -AAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCTAGCATCTCAATCTTGTTTCAATATA
* *
55480 ATTAGAAATTATTTCGGAATAAAAATGGAAAAACGATATTATAAGCGTGAAAAACACGTCAATTT
646 ATTAGAAATTATTTCGGAATAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACACGTCAATCT
*
55545 TTCTGGCATTGAATCGTATAATTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGG
711 TTCTGGCATTGAATCGTATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGG
** *
55610 GTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTGGGGCTAAAAACGTGTTTCGGGG
776 GTCAGTTTTTAGCCGAAATCGTGTACTAACCATCATGGTTTT-GGGCTAAAAACGCG-TTCGGGG
* ** * * * *
55675 GTCCAGACTCAGCTTTGCATAATTTTTGGCAG-AAAAACTCCTTGAAATATCCACATTCGTCGAA
839 GTCC-GA-TAAATTTTGCATAATTTTTAGC-GCAAAAACTCCTTGAAATATCTATATTCATCGAA
** * * * *
55739 ACAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAAGCATCC
901 ACAAATGTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCC
* * *
55787 GAATCTTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGGAAAAATGATATTAGAAGCC
1 -AATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAAATGATATTAGAAGCA
*
55852 TGAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAGAT
65 TGAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAT
* * *
55917 TCAGAAAAAAAATTTTGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGGT
130 TCAGAAAAAAAATTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGGC
* * * *
55982 TAAAAACGTGTTTCGGGAGCACCGGCTTAGTTTTGCATGATTTTTGACA-AAAAGACTCCATAAA
195 TAAAAACGTGTTTCGGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAA-ACTCCATGAA
* *
56046 ATATCTACATTAATCGAACCAAATCCCAGCCACATTCGATTTTAACTATTAGTTTTTACAACCAT
258 ATATCTACATTCATCGAACCAAATCCCAGCCACATTCGA-TTTAACGATTAGTTTTTACAACCAT
* * *
56111 TCGATTTTATTAGAAATTCATTCGGAAAAAAGTAG-AAAACGATATTAGAAGTTTGAAAAACCCT
322 TCGATTTTATTAGAAATTAATTCGGAAAAAATTGGAAAAACGATATTAGAAGTTTGAAAAACCCT
* * *
56175 TCAATCATTTTGGCGTGAATTATATATATTGAGGTAAAGAATTGAGGAAAAATTTTTCGGATCAG
387 TCAATC-TTTTGGAGTGAATTATATATATTGTGGTAAAGAATTGAGGAAAAAATTTTCGGATCAG
*
56240 TTTGTGCAAAATTTTATTCAAAATCGTTTACTCATCAGGGTTTATGGCTAAAAACGCGTTCCGGG
451 TTTGTGCAAAATTTTATTCAAAATCGTTTACTCATCACGGTTTATGGCTAAAAACGCGTTCCGGG
* *
56305 GCCCCGGCTCAGTTTTGAAAGATTTTTAGCTTAAAGACTCCTTGAAATATCTATATTTATAGAAA
516 GCCCCGGCTCAGTTTTGCAAGATTTTTAGCTTAAAGACTCCTTGAAATATCTATATTTATCGAAA
* *
56370 CATATCTCAGCCATATTGTATATAAGGATTTGTTTTTTCTAGCATCTCAATCTTGTTTCAATATA
581 CAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCTAGCATCTCAATCTTGTTTCAATATA
*
56435 ATTAGAAATTATTTCGGAAT-AAAATGGAAAAACGATATTAGAAGCGTGAAAAACAGGTCAATCT
646 ATTAGAAATTATTTCGGAATAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACACGTCAATCT
*
56499 TTCTGGCATTGAATCGTATAATTTCTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGG
711 TTCTGGCATTGAATCGTATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGG
* * * * *
56564 GTCAGTTTTTAACCGAAATCGTATACT-ACCATCATGGTTTTTGGCTAAAAACGCGTTCCGGAGC
776 GTCAGTTTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTGGGCTAAAAACGCGTT-CGGGGG
* * * * * *
56628 CCCGTATAAATTTTGCATGATTTTTAGCGCAAAAAGTCCTTGAAATATATATATTCATTGAACCA
840 TCCG-ATAAATTTTGCATAATTTTTAGCGCAAAAACTCCTTGAAATATCTATATTCATCGAAACA
* * * * **
56693 AATGTCAGGCACGTTGGATATAAGGATTTGTTTTTACGAGCATTTA
904 AATGTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCA-TCC
*
56739 AATCTTGTTTCGATTTAATTA-AAATTAATTCGGAAAAAAATTGAAAAAATGATATTAGAAGCGT
1 AATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAAATGATATTAGAAGCAT
* *
56803 AAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATG
66 GAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
* * * * *
56868 CAGGAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCATGTATTAACCATCACGGTTTTTGTGCT
131 CAGAAAAAAAATTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGGCT
** * * *
56933 AAAAACGTGTTTCGGGGGTTCCGGCTCAGTTTTGCATAATTTTTGGCAGAAAAACTTCTTGAAAT
196 AAAAACGTGTTTC-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCATGAAAT
* * * * *
56998 ATCTACTTTCATCGAATCAAATCCCGGCCACATTCGATTTAATGATTAGATTTTACAA
260 ATCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAA
57056 GCATCCGAAT
Statistics
Matches: 2000, Mismatches: 202, Indels: 69
0.88 0.09 0.03
Matches are distributed among these distances:
949 18 0.01
950 244 0.12
951 108 0.05
952 20 0.01
953 12 0.01
954 129 0.06
955 303 0.15
956 195 0.10
957 318 0.16
958 39 0.02
959 320 0.16
960 7 0.00
965 1 0.00
967 2 0.00
968 1 0.00
970 1 0.00
971 131 0.07
972 151 0.08
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (948 bp):
AATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAAATGATATTAGAAGCAT
GAAAAGACCATCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
CAGAAAAAAAATTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGGCT
AAAAACGTGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCATGAAATA
TCTACATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTAGTTTTTACAACCATTCGA
TTTTATTAGAAATTAATTCGGAAAAAATTGGAAAAACGATATTAGAAGTTTGAAAAACCCTTCAA
TCTTTTGGAGTGAATTATATATATTGTGGTAAAGAATTGAGGAAAAAATTTTCGGATCAGTTTGT
GCAAAATTTTATTCAAAATCGTTTACTCATCACGGTTTATGGCTAAAAACGCGTTCCGGGGCCCC
GGCTCAGTTTTGCAAGATTTTTAGCTTAAAGACTCCTTGAAATATCTATATTTATCGAAACAAAT
CTCAGCCATATTGGATATAAGGATTTGTTTTTTCTAGCATCTCAATCTTGTTTCAATATAATTAG
AAATTATTTCGGAATAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACACGTCAATCTTTCTG
GCATTGAATCGTATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAG
TTTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTGGGCTAAAAACGCGTTCGGGGGTCCGAT
AAATTTTGCATAATTTTTAGCGCAAAAACTCCTTGAAATATCTATATTCATCGAAACAAATGTCA
GCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCC
Found at i:57463 original size:262 final size:262
Alignment explanation
Indices: 57103--57618 Score: 711
Period size: 262 Copynumber: 2.0 Consensus size: 262
57093 TCGGAATAAG
* *
57103 ATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATTATTTTAGAGCTGAATTATATATTT
1 ATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATAAATTATTTTAGAGATGAATTATATATTT
* * * *
57168 TTTCTGAGTATTGTGGCAAAAAATTCAGGAAAAAAATTTCGGGTCAGTTTTT-AACCTAAATCAT
66 TTTATGAGTATTGTGGCAAAAAATTCAGGAAAAAAATTTCAGGTCAGTTTTTCAA-CGAAAACAT
* * *
57232 GTACTAACCA-CACT-ATTTTTGGGCTAAAAACGTGTTTCGGGGGTCCAGACTCAGTTTTGCATA
130 GTACTAACCATCA-TGATTTTGGGGCTAAAAACGTGTTTCAGGGGTCCAG-CTCAATTTTGCATA
* * * *
57295 ATTTTTGGTAGCAAAATTCCTTGAAATATCCACATTCATCGAACCAAATCCCAGCCACATTCAGG
193 ATTTTTGGCAGAAAAAATCCTTGAAATATCCACATTCATCGAACAAAATCCCAGCCACATTCAGG
57360 AAAAA
258 AAAAA
*
57365 ATTGG-AAAATGATATTAGGAGCGTGAAAAGACCATAAATCT-TTTT-GAAGATGAATTATATAT
1 ATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATAAAT-TATTTTAG-AGATGAATTATATA-
* *
57427 TTTTTTATGAGTATTGTGGCAAAAAATTCAGGAAAAAATTTTCAGGTCAGTTTTTCGACGAAAAC
63 TTTTTTATGAGTATTGTGGCAAAAAATTCAGGAAAAAAATTTCAGGTCAGTTTTTCAACGAAAAC
* * * * *
57492 GTGTACTAACCATCATGGTTTTGGGGCTAAAAACTTGTTTCAGGGGTCCCGTTCAATTTTGCATA
128 ATGTACTAACCATCATGATTTTGGGGCTAAAAACGTGTTTCAGGGGTCCAGCTCAATTTTGCATA
* * * *
57557 ATTTTTGGCAGAAAAAATCCTTGAAATATCTACATTTATCGAGCAAAATCCCTGCCACATTC
193 ATTTTTGGCAGAAAAAATCCTTGAAATATCCACATTCATCGAACAAAATCCCAGCCACATTC
57619 GATTTAACGA
Statistics
Matches: 223, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
260 1 0.00
261 49 0.22
262 141 0.63
263 32 0.14
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (262 bp):
ATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATAAATTATTTTAGAGATGAATTATATATTT
TTTATGAGTATTGTGGCAAAAAATTCAGGAAAAAAATTTCAGGTCAGTTTTTCAACGAAAACATG
TACTAACCATCATGATTTTGGGGCTAAAAACGTGTTTCAGGGGTCCAGCTCAATTTTGCATAATT
TTTGGCAGAAAAAATCCTTGAAATATCCACATTCATCGAACAAAATCCCAGCCACATTCAGGAAA
AA
Found at i:76031 original size:6 final size:6
Alignment explanation
Indices: 76020--76056 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
76010 AGATTAAACA
76020 AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG A
1 AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG A
76057 AGGCGTGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.19, C:0.00, G:0.65, T:0.16
Consensus pattern (6 bp):
AGGGTG
Found at i:77155 original size:31 final size:33
Alignment explanation
Indices: 77117--77199 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
77107 AGAAGCCATC
* *
77117 ATTCTTCAAATCTTTTTTCTTTTTGG-G-TAGA
1 ATTCTTCAAATCTTTTTTCTTTTTGGTGAAAAA
*
77148 ATTCTTCAAATCCTTTTTTTTTTTTTGGTGAAAAA
1 ATTCTTCAAAT-C-TTTTTTCTTTTTGGTGAAAAA
77183 ATTCTTCAAATCTTTTT
1 ATTCTTCAAATCTTTTT
77200 GCTACAATGC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 11 0.24
32 1 0.02
33 18 0.40
34 2 0.04
35 13 0.29
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.55
Consensus pattern (33 bp):
ATTCTTCAAATCTTTTTTCTTTTTGGTGAAAAA
Found at i:97643 original size:35 final size:35
Alignment explanation
Indices: 97597--97665 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
97587 AATGCTAACA
97597 GAGATTTAGTGCTTCTTGATTCTTGAAGGGCCAAC
1 GAGATTTAGTGCTTCTTGATTCTTGAAGGGCCAAC
97632 GAGATTTAGTGCTTCTTGATTCTTGAAGGGCCAA
1 GAGATTTAGTGCTTCTTGATTCTTGAAGGGCCAA
97666 GCGCTGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (35 bp):
GAGATTTAGTGCTTCTTGATTCTTGAAGGGCCAAC
Found at i:101950 original size:7 final size:7
Alignment explanation
Indices: 101940--101970 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
101930 AAAATTAAAG
101940 AAACCCA
1 AAACCCA
101947 AAACCCA
1 AAACCCA
101954 AAACCCA
1 AAACCCA
*
101961 AAACACA
1 AAACCCA
101968 AAA
1 AAA
101971 TTACTTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (7 bp):
AAACCCA
Found at i:103845 original size:16 final size:17
Alignment explanation
Indices: 103811--103847 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
103801 AATTATATTT
103811 AAATAATCTGAATCCGA
1 AAATAATCTGAATCCGA
103828 AAATAAT-TGAA-CCTGA
1 AAATAATCTGAATCC-GA
103844 AAAT
1 AAAT
103848 CGGAGGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.11
16 10 0.53
17 7 0.37
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (17 bp):
AAATAATCTGAATCCGA
Found at i:108112 original size:12 final size:12
Alignment explanation
Indices: 108097--108121 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
108087 ATGTACTAAT
108097 TAATTAATTATA
1 TAATTAATTATA
108109 TAATTAATTATA
1 TAATTAATTATA
108121 T
1 T
108122 TACATTCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATTAATTATA
Found at i:115187 original size:2 final size:2
Alignment explanation
Indices: 115180--115215 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
115170 GCAGCAATGC
115180 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
115216 GAGTAGCGTA
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:120389 original size:42 final size:42
Alignment explanation
Indices: 120343--120429 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
120333 TACCGGCCAA
*
120343 AAAAAAAAGTTTTCATTTTTAGTTTTTTTAAAAAATCTAACT
1 AAAAAAAAGTTTTCATTTTTAGTTTTTTAAAAAAATCTAACT
120385 AAAAAAAAGTTTTCATTTTTAGTTTTTTAAAAAAATCTAACT
1 AAAAAAAAGTTTTCATTTTTAGTTTTTTAAAAAAATCTAACT
120427 AAA
1 AAA
120430 TGCATATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (42 bp):
AAAAAAAAGTTTTCATTTTTAGTTTTTTAAAAAAATCTAACT
Done.