Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022417.1 Corchorus olitorius cultivar O-4 contig22450, 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: 54833
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6753 original size:22 final size:21
Alignment explanation
Indices: 6712--6753 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
6702 TATTCACTAT
*
6712 AAGAAAATATAGAGATAAACC
1 AAGAAAATATAGAGAAAAACC
6733 AAGAACAATA-AGAAGAAAAAC
1 AAGAA-AATATAG-AGAAAAAC
6754 ACACTTCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.10, G:0.14, T:0.10
Consensus pattern (21 bp):
AAGAAAATATAGAGAAAAACC
Found at i:13500 original size:29 final size:30
Alignment explanation
Indices: 13450--13512 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 30
13440 TGACACTTTA
*
13450 CATCCAATTTTTTTTATTTTGATCAAAACG
1 CATCCAATCTTTTTTATTTTGATCAAAACG
13480 CATCCAA-CTTTTTTATTTTGATCAAAACG
1 CATCCAATCTTTTTTATTTTGATCAAAACG
13509 CATC
1 CATC
13513 TTAAAGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (30 bp):
CATCCAATCTTTTTTATTTTGATCAAAACG
Found at i:13522 original size:29 final size:29
Alignment explanation
Indices: 13461--13527 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
13451 ATCCAATTTT
**
13461 TTTTATTTTGATCAAAACGCATCCAACTT
1 TTTTATTTTGATCAAAACGCATCCAACAG
*
13490 TTTTATTTTGATCAAAACGCATCTTAA-AG
1 TTTTATTTTGATCAAAACGCATC-CAACAG
13519 TTTTATTTT
1 TTTTATTTT
13528 TGTATCACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 32 0.94
30 2 0.06
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (29 bp):
TTTTATTTTGATCAAAACGCATCCAACAG
Found at i:15589 original size:20 final size:22
Alignment explanation
Indices: 15549--15590 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
15539 GTTTTAAACA
*
15549 ATGATTTAATTTTTAAATTATG
1 ATGATTTAATTGTTAAATTATG
15571 ATGA-TTAATTGTT-AATTATG
1 ATGATTTAATTGTTAAATTATG
15591 CACTTAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
ATGATTTAATTGTTAAATTATG
Found at i:19524 original size:23 final size:23
Alignment explanation
Indices: 19490--19535 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
19480 TTCATGTATG
*
19490 GCGAAAGTGGTTTGTAAGAAATT
1 GCGAAAGGGGTTTGTAAGAAATT
*
19513 GCGAAAGGGGTTTGTGAGAAATT
1 GCGAAAGGGGTTTGTAAGAAATT
19536 ATATCATCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (23 bp):
GCGAAAGGGGTTTGTAAGAAATT
Found at i:20080 original size:35 final size:36
Alignment explanation
Indices: 20005--20090 Score: 165
Period size: 36 Copynumber: 2.4 Consensus size: 36
19995 CACCTTGCTT
20005 AACAATTTTCATTGGCTAATTTAAAAAGAAAAAAAA
1 AACAATTTTCATTGGCTAATTTAAAAAGAAAAAAAA
20041 AACAATTTTCATTGGCTAATTTAAAAAG-AAAAAAA
1 AACAATTTTCATTGGCTAATTTAAAAAGAAAAAAAA
20076 AACAATTTTCATTGG
1 AACAATTTTCATTGG
20091 GCAAGATATC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 22 0.44
36 28 0.56
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (36 bp):
AACAATTTTCATTGGCTAATTTAAAAAGAAAAAAAA
Found at i:25057 original size:3 final size:3
Alignment explanation
Indices: 25049--25102 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
25039 CACTAACCAT
25049 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
25097 TTC TTC
1 TTC TTC
25103 CTACTGCTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:27178 original size:12 final size:12
Alignment explanation
Indices: 27161--27185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27151 AAGGTTTGAG
27161 GTTAGCAGGAAT
1 GTTAGCAGGAAT
27173 GTTAGCAGGAAT
1 GTTAGCAGGAAT
27185 G
1 G
27186 GTGAATTTAG
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:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (12 bp):
GTTAGCAGGAAT
Found at i:32974 original size:15 final size:15
Alignment explanation
Indices: 32954--32984 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
32944 AAATCTCTTA
32954 AACAAATATGCTTTC
1 AACAAATATGCTTTC
32969 AACAAATATGCTTTC
1 AACAAATATGCTTTC
32984 A
1 A
32985 GGTTATCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (15 bp):
AACAAATATGCTTTC
Found at i:33229 original size:32 final size:32
Alignment explanation
Indices: 33166--33233 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
33156 ATGATTTTAT
* *
33166 AAATAATAAAATTGCAATTTTGTTGTCAAAAA
1 AAATAATAAAATTGCAATTTTGATGTAAAAAA
33198 AAATAATAAAATTGCAATTTATGATG-AAAAAA
1 AAATAATAAAATTGCAATTT-TGATGTAAAAAA
33230 AAAT
1 AAAT
33234 GCAATTAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (32 bp):
AAATAATAAAATTGCAATTTTGATGTAAAAAA
Found at i:33545 original size:17 final size:17
Alignment explanation
Indices: 33523--33558 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
33513 TACTAATGTT
33523 TTCTCGTATAGAGCGTA
1 TTCTCGTATAGAGCGTA
33540 TTCTCGTATAGAGCGTA
1 TTCTCGTATAGAGCGTA
33557 TT
1 TT
33559 TTCTAGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (17 bp):
TTCTCGTATAGAGCGTA
Found at i:38591 original size:22 final size:23
Alignment explanation
Indices: 38549--38592 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
38539 TATTGCATGT
*
38549 AATGATAAGTACTTGTTTGATTG
1 AATGATAAGTACTTGTCTGATTG
38572 AATG-TAAGTA-TTGTACTGATT
1 AATGATAAGTACTTGT-CTGATT
38593 TACTACCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (23 bp):
AATGATAAGTACTTGTCTGATTG
Found at i:40491 original size:39 final size:39
Alignment explanation
Indices: 40448--40566 Score: 229
Period size: 39 Copynumber: 3.1 Consensus size: 39
40438 ATGTGTTTTT
*
40448 AGAGAGAGGAGAGAGGAGCATATCAAAGCTAATTTGTTA
1 AGAGAGAGGAGGGAGGAGCATATCAAAGCTAATTTGTTA
40487 AGAGAGAGGAGGGAGGAGCATATCAAAGCTAATTTGTTA
1 AGAGAGAGGAGGGAGGAGCATATCAAAGCTAATTTGTTA
40526 AGAGAGAGGAGGGAGGAGCATATCAAAGCTAATTTGTTA
1 AGAGAGAGGAGGGAGGAGCATATCAAAGCTAATTTGTTA
40565 AG
1 AG
40567 TGTAGCAGAT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (39 bp):
AGAGAGAGGAGGGAGGAGCATATCAAAGCTAATTTGTTA
Found at i:47857 original size:333 final size:330
Alignment explanation
Indices: 46150--51137 Score: 5874
Period size: 332 Copynumber: 15.1 Consensus size: 330
46140 AAAGGATAAT
* ** * **
46150 CATCACGGTTTTTGGCTAACAACGTGTTTCC-AGGCGCCGGCTCAGTTTTTTATGA-TTTTGGCG
1 CATCACGG-TTTTGGCTAAAAACG-CATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCG
* * * * * * * *
46213 CAAAAACTCCATGAAATATCTAAATTTATC-TAACCAAATCTCAGCAGCATTGGATTTAAGAATT
64 CCAAGACTCCGTGAAATATCTATATTCATCTTAA-CAAATCTCAGCAACATAGGATTTAAGGATT
* * * * * *
46277 TGTTTTTACAAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAAATCATAAAAAAATAAG-A
128 TGTTTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAATTCA-GAAAAAATAAGAA
* * * *
46341 AAACGATATTAGAAGCGTGAAAATCCCTCCAATATTGTT-G-GCATTGAATTATATATTATTTAC
192 AAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTT-TTAGTGC--TGAATTATATATTGTTAAC
* *** * * *
46404 AAGTA-TTTTGGCCAGAAATTGAGGAAACATCTTTCGGG--------T-C--AATTTTAGCCGAT
254 GAGTATTTTTGATAACAAATTGAGGAAAAAT-TTTCGGGTCAAATTTTGCAAAATTTTAGCCGAA
**
46457 ATCGTAAACTAA-
318 ATCGTGTACTAAC
* * * * * * * *
46469 CAACACGGTTCTTTTTGGATAAAAACG-AGTTTCGAGACGCTGACTCAGTTTTGTATGATTTTTG
1 CATCACGG----TTTTGGCTAAAAACGCA-TTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTG
* * ** * * *
46533 GTGCCGAGACTCTATGAAAAAATCTATATTCATC-TAACCAAATCTCAGTAACATTGGATTTAAG
61 GCGCCAAGACTCCGTG-AAATATCTATATTCATCTTAA-CAAATCTCAGCAACATAGGATTTAAG
* * * *
46597 GATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTA
124 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAATTCAGAAAAAATAA
* * * * * * *
46662 GAAATACAATGTTAGGAGCGTGAAAAGCCCTCCAATATTTTTG-GCATTGAATTATATATTGTTT
189 GAAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTAGTGC--TGAATTATATATTGTTA
* ** * *
46726 ACGATTATTTTTGCCAA-ATATTGAGGAAAAATCTTTCGGGAC-AATTCTTGCAAAATTTTAGCC
252 ACGAGTATTTTTGATAACAAATTGAGGAAAAAT-TTTCGGGTCAAATT-TTGCAAAATTTTAGCC
46789 GAAATCGTGTACT-AC
315 GAAATCGTGTACTAAC
* * *
46804 CATCACCGTTTTGGCTAAAAACGCGTTCCGGGGTGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* *
46869 AAGACTCCCTGAAATATCTATATTCATC-TAACCAAATCTCAGCAACATTGGATTTAAGGATTTG
66 AAGACTCCGTGAAATATCTATATTCATCTTAA-CAAATCTCAGCAACATAGGATTTAAGGATTTG
* * * * *
46933 CTTTTATGAGCATCTGAATCTTGTTTCTATTTAATTAGAAAATTAATTCAG-------AA-AAAA
130 TTTTTACGAGCATCTGAATCTTGTTTCGATATACTTAG-AAATTAATTCAGAAAAAATAAGAAAA
* * * * * * *
46990 ATGATGTTAGAATCGTGAAAAACCCTTCAATCTTTTTG-GCGTTGAATTATATATTGTTTACGAG
194 ACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTAGTGC--TGAATTATATATTGTTAACGAG
* * * *
47054 TATATTTT-TTCAA-AAATTGAAGAAAAATCTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAA
257 TAT-TTTTGAT-AACAAATTGAGGAAAAAT-TTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAA
*
47117 TCGTGTTCTAAC
319 TCGTGTACTAAC
* * * * *
47129 CGTCAGGGTTTTGGCTAAAAACGCATTCCGGGGCGCCAGCTCAGTTTTGCATGATTTTTGGTGTC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * * * *
47194 AAGACTCCGTGAAATATCTGTATTCATCTTAACAAATCTCTGCATCATAGGATCTAAGGAGTTGT
66 AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
* * *
47259 TTTTACGAGCATCTTAATCTTGTTTCGATATACTTAGAAATCAATTCAGAAAAATTTTTTTAA-A
131 TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAATTCAGAAAAA-----ATAAGA
* * * *
47323 AAAATGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGCTGAACTATATATTGTTAACG
191 AAAACGATATTAGAAGCGTGAAAAGCCCTCCAATC-TTTTAGTGCTGAATTATATATTGTTAACG
* * * *
47388 AGTATTTTTTATGAAAAAATTGAGGAAAAATCTTTCCGGAC-AATTCTTGCAAAATTTTAGCCGA
255 AGTATTTTTGAT-AACAAATTGAGGAAAAAT-TTTCGGGTCAAATT-TTGCAAAATTTTAGCCGA
47452 AATCGTGTACTAAC
317 AATCGTGTACTAAC
* *
47466 CATCACGGTTTTGGCAAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGACGCC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * * * * ** * * * * *
47531 AAGACTTCGTGAAATAACTTTATCCATATTCCCAAATATCAACAACATTGGGTTTAAGGAGTTGT
66 AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
* *
47596 TTTTACGAGCATTTGAATCTTGTTTCGATATACGTAGAAATTAATTCAGAAAAAATAAGAAAAAC
131 TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAATTCAGAAAAAATAAGAAAAAC
*
47661 GATATTAGAAGCGTGAAAAGCACTCCAATCTTTATAGTGCTGAATTATATATTGTTAACGAGTAT
196 GATATTAGAAGCGTGAAAAGCCCTCCAATCTTT-TAGTGCTGAATTATATATTGTTAACGAGTAT
** *
47726 TTTTGATAACAAATTGAGGAAAAAATTTTCTTGTCAAAATTTGCAAAATTTTAGCCGAAATCGTG
260 TTTTGATAACAAATTGAGG-AAAAATTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCGTG
*
47791 TAGTAAC
324 TACTAAC
*** * *
47798 CATCACGGTGAAAGGCCAAAAACGCATTTCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGC
1 CATCACGGT-TTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGC
* * * *
47863 CAAGAATCTGTGAAATATCTATATTCATTTTAACAAATCTCAGTAACATAGGATTTAAGGATTTG
65 CAAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTG
* *
47928 TTTTTACGAGCATCTGAATCTTGTTTCGATATTCTTAGAAATTAAATCAGAAAAAATAAGAAAAA
130 TTTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAATTCAGAAAAAATAAGAAAAA
* * *
47993 CGACATTAGAAGCGTGAAAAGCCCTCCAATCGTTTTAGTGTTGAATCATATATTGTTAACGAGTA
195 CGATATTAGAAGCGTGAAAAGCCCTCCAATC-TTTTAGTGCTGAATTATATATTGTTAACGAGTA
* * * *
48058 TTTTTGATGAA-AAATTGAGGAAATATTTTTCTGGTCAAAATTTGCAAAATTTTAGCCGAAATTG
259 TTTTTGAT-AACAAATTGAGGAAA-AATTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCG
*
48122 TGTACAAAC
322 TGTACTAAC
* * * * *
48131 CATCACGGTTTTGCCCAAAAACGCATTCCGGGGCGCCGGCTCCGTTTTGCATAATTTTTGGCGTC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * * * * *
48196 AAGACTCCGTCAAATATCTATATTCATC-TAACCATATATCAACAACTTTGGATTTAAGGATTTG
66 AAGACTCCGTGAAATATCTATATTCATCTTAA-CAAATCTCAGCAACATAGGATTTAAGGATTTG
* * *
48260 TTTTTACGACCATCTGAATCTTCTTTCGATATAATTAGAAAATTAA-TCAGAAAAAATAAGAAAA
130 TTTTTACGAGCATCTGAATCTTGTTTCGATATACTTAG-AAATTAATTCAGAAAAAATAAGAAAA
* * **
48324 ACTATATTAGAAGTGTGAAAAGCATTCCAATCATTTTAGTGCTGAATTATATATTGTTAACGAGT
194 ACGATATTAGAAGCGTGAAAAGCCCTCCAATC-TTTTAGTGCTGAATTATATATTGTTAACGAGT
* *
48389 ATTTTTGATGAA-AAATTGAGGAAAAATTTCTCGGGTCAAGTTTTGTAAAATTTTAGCCGAAATC
258 ATTTTTGAT-AACAAATTGAGGAAAAATTT-TCGGGTCAAATTTTGCAAAATTTTAGCCGAAATC
48453 GTGTACTAAC
321 GTGTACTAAC
* * * *
48463 CATCACGGTTTTGGCTAAAAACGCGTTCTGGGGCGCCAGCTCAGTTTTGCATGATTTTTGGTGCC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* *
48528 AAGACTCCGTGAAATATCTATATTCATTTTAACAAATCTCAGCAACATAGGATTTATGGATTTGT
66 AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
* * * *
48593 TTTTACGAGGATCTGAATCTTGTTTCGATATTCATAGAAATTGAA-TCTGAAAAAAATAAGAAAA
131 TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATT-AATTCAG-AAAAAATAAGAAAA
* * *
48657 ACGACATTAGAAGCGTGAAATGCCCTCCAATCGTTTTAGTGTTGAATTATATATTGTTAACGAGT
194 ACGATATTAGAAGCGTGAAAAGCCCTCCAATC-TTTTAGTGCTGAATTATATATTGTTAACGAGT
* *
48722 ATTTTTGATAACAAATTGAGGAAAAACTTTTAGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
258 ATTTTTGATAACAAATTGAGGAAAAA-TTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCG
48787 TGTACTAAC
322 TGTACTAAC
* * *
48796 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCTGCTCAGCTTTGCATGATTTTTGGCGGC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * *
48861 AAGACTCCGTGAAATATCTATATTCATTTTAACAAATCTCAGAAACATAGGATTTAAGTATTTGT
66 AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
* *
48926 TTTTACGAGCATTTGAATCTTGTTTCGATATTCTTAGAAATT-ATATCAGAAAAAATAAGAAAAA
131 TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAAT-TCAGAAAAAATAAGAAAAA
* * *
48990 CGACATTAGAAGCATGAAAAG-ACTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTA
195 CGATATTAGAAGCGTGAAAAGCCCTCCAATC-TTTTAGTGCTGAATTATATATTGTTAACGAGTA
* * * * * *
49054 ATTTTGATGACATATTGAGGAAAAATTTTCTGGTCAAAATTTGCAAAATTTTAGCCGAAATTGTG
259 TTTTTGATAACAAATTGAGGAAAAATTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCGTG
49119 TACTAAC
324 TACTAAC
* * * * *
49126 CATCACGGTTTTGCCCAAAAACGTATTCCGGGGCGCCGGCTCTGTTTTTCATGATTTTTGGCGCC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * * * *
49191 AAGACTCTGTGAAATATCTATATTCCTTTTAACAAATCTCAGTAACATAGGATTTAAGTATTTGT
66 AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
* * *
49256 TTTTACGAGCATCTGAATCTTATTTCGATATTCTTAGAAATTAAATCAGAAAAAATAAGAAAAAC
131 TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAATTCAGAAAAAATAAGAAAAAC
* * **
49321 GACATTAGAAGCGTGAAAAGCCCTCCAATCGTTTAAGTATTGAATTATATATTGTTAACGAGTAT
196 GATATTAGAAGCGTGAAAAGCCCTCCAATC-TTTTAGTGCTGAATTATATATTGTTAACGAGTAT
* * *
49386 TTTTTATAACAAATTGAGGAAAAACTTTTAGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
260 TTTTGATAACAAATTGAGGAAAAA-TTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCGTG
49451 TACTAAC
324 TACTAAC
** * *
49458 CATCATAGTTTTGGCTAAAAACGCATTTCGGGGCGCCTGCTCAGTTTTGCATGATTTTTGGCGCC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * * * *
49523 AAGACTCCGTGAAATATCTATATTCATTTTAACAAATCTTAGAAACATAGGATTTAAGTACTTGT
66 AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
* * * *
49588 TTTTACAAGCATCTGAATCTTGTTTCAATAT-TTTAGAAATT-ATATCATAAAAAATAAGAAAAA
131 TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAAT-TCAGAAAAAATAAGAAAAA
**
49651 CGACGTTAGAAGCGTGAAAAGCCCTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTA
195 CGATATTAGAAGCGTGAAAAGCCCTCCAATC-TTTTAGTGCTGAATTATATATTGTTAACGAGTA
* * **
49716 TTTTTGATAACAAATTGAGGAAAAATTTCTCTGGTCAAAATTTGCAAAATTTTAGCAAAAATCGT
259 TTTTTGATAACAAATTGAGGAAAAATTT-TCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCGT
*
49781 GTAGTAAC
323 GTACTAAC
* * *
49789 CATCACGGTTTTGGCCAAAAACGCATTCCGGGGCGCCGCCTCAGTTTTGCATGATTTTTGGCGTC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * * * *
49854 AAGACTCCGTCAAATATCTATATTCATC-TAACCATATCTCAACAACATTGGATTTAAGGATTTA
66 AAGACTCCGTGAAATATCTATATTCATCTTAA-CAAATCTCAGCAACATAGGATTTAAGGATTTG
* * * *
49918 TTTTTACGACCATTTGAATCTTCTTTCGATATAATTAGAAAATTAA-TCAGAAAAAATAAGAAAA
130 TTTTTACGAGCATCTGAATCTTGTTTCGATATACTTAG-AAATTAATTCAGAAAAAATAAGAAAA
* * ** *
49982 ACTATATTAGAAGTGTGAAAAGCATTCCAATCTTTTTAGTGCTGAATTATATATTGCTAACGAGT
194 ACGATATTAGAAGCGTGAAAAGCCCTCCAATC-TTTTAGTGCTGAATTATATATTGTTAACGAGT
* *
50047 ATTTTTGATGAA-AAATTGAGGAAAAATTTCTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATC
258 ATTTTTGAT-AACAAATTGAGGAAAAATTT-TCGGGTCAAATTTTGCAAAATTTTAGCCGAAATC
50111 GT-TAACTAAC
321 GTGT-ACTAAC
* * * **** *
50121 CATCACGGTTTTGGCTAAAAATGCGTTCCGGGGCGGCAAAACAGTTTTGTATGATTTTTGGCGCC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * * *
50186 AAGACTCCGTGAAATATCAATATTCATCTTAACAAATCTCTGCATCATAGGATTTAAGGAGTTGT
66 AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
* *
50251 TTTTACGAGCATCAGAATCTTGTTTCGATATACTTAGAAAATTAATTCAGAAAAAATTTAAAAAA
131 TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAG-AAATTAATTCAGAAAAAA--TAAGAAA
* * ** * *
50316 AATGATATTAGAAGCGTGAAAAG-CCTCCAATCTTTTTGCCACTGAACTATATTTTGTTAACGAG
193 AACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTAG-TGCTGAATTATATATTGTTAACGAG
* * * *
50380 TATTTTTGATTAAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAA
257 TATTTTTGA-T-AACAAATTGAGGAAAAA-TTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAA
* * *
50445 TCCTTTAGTAAC
319 TCGTGTACTAAC
* * * * * * * * *
50457 CATCATGGTTTTGG-TAAAAGCGCGTTCCGAGCCGCCGGCTTAGTTTTACAAGATTTTTGGTGCC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * * * * * * *
50521 AAGACTCCGTGAAATAACTTTATTCATCTTAACAAATCTCAGCAACATTGGGTTTATGTAGTTAT
66 AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
* * * *
50586 TTTTACGTGCATTTGAATCTTGTTTCGATATTCTTAGAAATTAAATCAGTAAAAAATAAGAAAAA
131 TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAATTCAG-AAAAAATAAGAAAAA
50651 CGATATTAGAAGCGTGAAAAGCCCTCCAATCCTTTTAGTGCTGAATTATATATTGTTAACGAGTA
195 CGATATTAGAAGCGTGAAAAGCCCTCCAAT-CTTTTAGTGCTGAATTATATATTGTTAACGAGTA
* * *
50716 GTTTTGATAACAAATTGAGGAAAAAAATTTCGGGTCAAAATTTGCAAAATTTTAGCCGAAATCGT
259 TTTTTGATAACAAATTGAGG-AAAAATTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCGT
50781 GTACTAAC
323 GTACTAAC
* ** * * *
50789 CATCACGGTTTTGGCCAAAAACAAATTCCGGGACGCCGACTCAATTTTGCATGATTTTTGGCGCC
1 CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* * * * ** * * * * *
50854 AAGACTCAGTGAAATAACTTTATTCATATTCCCAAATATCAGCAACATTGGGTTTGAGGAGTTGT
66 AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
* * * * *
50919 TTTTACGAGCATTTGAATCTTGTTTCGATATAGTTAGAAATTAATTTAGAGAAAATAAGAATAAC
131 TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAATTCAGAAAAAATAAGAAAAAC
* *
50984 GATATTAGAAGCGTGAAAAGCCCTCCAATCTTTATAGTGCTCAATTATATATTGTTAACGATTAT
196 GATATTAGAAGCGTGAAAAGCCCTCCAATCTTT-TAGTGCTGAATTATATATTGTTAACGAGTAT
* * * *
51049 CTTTT-ATAACAAATTAAGGAAAAACTTTTAGGGTCAATTTTTGCAAAATTTTAGCAGAAATCGT
260 -TTTTGATAACAAATTGAGGAAAAA-TTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCGT
51113 GTACTAAC
323 GTACTAAC
51121 CATCACGGTTTTGGCTA
1 CATCACGGTTTTGGCTA
51138 GGGCTATTCG
Statistics
Matches: 4064, Mismatches: 513, Indels: 171
0.86 0.11 0.04
Matches are distributed among these distances:
319 7 0.00
321 3 0.00
322 34 0.01
323 88 0.02
324 240 0.06
325 154 0.04
326 3 0.00
330 332 0.08
331 497 0.12
332 1195 0.29
333 873 0.21
334 94 0.02
335 195 0.05
336 127 0.03
337 220 0.05
338 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (330 bp):
CATCACGGTTTTGGCTAAAAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
AAGACTCCGTGAAATATCTATATTCATCTTAACAAATCTCAGCAACATAGGATTTAAGGATTTGT
TTTTACGAGCATCTGAATCTTGTTTCGATATACTTAGAAATTAATTCAGAAAAAATAAGAAAAAC
GATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTAGTGCTGAATTATATATTGTTAACGAGTATT
TTTGATAACAAATTGAGGAAAAATTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCGTGTA
CTAAC
Found at i:49474 original size:995 final size:993
Alignment explanation
Indices: 46182--51133 Score: 5881
Period size: 995 Copynumber: 5.0 Consensus size: 993
46172 CGTGTTTCCA
* * * * * * *
46182 GGCGCCGGCTCAGTTTTTTATGA-TTTTGGCGCAAAAACTCCATGAAATATCTAAATTTA-TCTA
1 GGCGCCGGCTCAGTTTTTCATGATTTTTGGCGCCAAGACTCCGTGAAATATCTATATTCATTTTA
* * * * * *
46245 ACCAAATCTCAGCAGCATTGGATTTAAGAATTTGTTTTTACAAGCATTTGAATCTTGTTTCGATT
66 A-CAAATCTCAGCAACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATA
* * *
46310 TAATTAGAAATTAAATCATAAAAAAATAAG-AAAACGATATTAGAAGCGTGAAAATCCCTCCAAT
130 TACTTAGAAATTAAATCA-GAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTCCAAT
* * * * * * * *
46374 -ATTGTTGGCATTGAATTATATATTATTTACAAGTA-TTTTG--GCCAGAAATTGAGGAAACATC
194 CATT-TTAGCACTGAATTATATATTGTTAACGAGTATTTTTGATG-AAAAAATTGAGGAAAAAT-
* ** * * *
46435 TTTCGGG--------T-C--AATTTTAGCCGATATCGTAAACTAA-CAACACGGTTCTTTTTGGA
256 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGG----TTTTGGC
* * * * * * * **
46488 TAAAAACGAGTT-TCGAGACGCTGACTCAGTTTTGTATGATTTTTGGTGCCGAGACTCTATGAAA
317 TAAAAACGCGTTCT-GGGGCGCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCGTG-AA
* * * * *
46552 AAATCTATATTCA-TCTAACCAAATCTCAGTAACATTGGATTTAAGGATTTGTTTTTACAAGCAT
380 ATATCTATATTCATTTTAA-CAAATCTCAGCAACATTGGATTTAAGGAGTTGTTTTTACGAGCAT
* * * * * *
46616 CTGAATCTTGTTTCGAT-TTAATTAGAAATTAAT-TCAGAAAAAATTAGAAATACAATGTTAGGA
444 CTGAATCTTGTTTCGATATTCA-TAGAAATTAATCTCAGAAAAAATAAGAAAAACGATATTAGAA
* * * * **
46679 GCGTGAAAAGCCCTCCAAT-ATTTTTG-GCATTGAATTATATATTGTTTACGATTATTTTTGCCA
508 GCGTGAAAAGCCCTCCAATCGTTTTAGTGC--TGAATTATATATTGTTAACGAGTATTTTTGATA
* * *
46742 A-ATATTGAGGAAAAATCTTTCGGGAC-AATTCTTGCAAAATTTTAGCCGAAATCGTGTACT-AC
571 ACAAATTGAGGAAAAAT-TTTCGGGTCAAAAT-TTGCAAAATTTTAGCCGAAATCGTGTACTAAC
* * * *
46804 CATCACCGTTTTGGCTAAAAACGCGTTCCGGGGTGCCGGCTCAGTTTTGCATGATTTTTGGCGCC
634 CATCACGGTTTTGGCCAAAAACGCATTCCGGGGCGCC-GCTCAGTTTTGCATGATTTTTGGCGCC
* * *
46869 AAGACTCCCTGAAATATCTATATTCA-TCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTG
698 AAGACTCCGTGAAATATCTATATTCATTTTAA-CAAATCTCAGAAACATTGGATTTAAGGATTTG
* * * * *
46933 CTTTTATGAGCATCTGAATCTTGTTTCTAT-TTAATTAGAAAATTAATTCAGAAAAAA-ATG---
762 TTTTTACGAGCATTTGAATCTTGTTTCGATATT-ATTAG-AAATTAA-TCAGAAAAAATAAGAAA
* * * * * * * * * *
46993 -ATG---TTAGAATCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTGTTTACGAG
824 AACGACATTAGAAGCGTGAAAAGCACTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAG
* * * *
47054 TATATTTT-TTCAAAAATTGAAGAAAAATCTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAAT
889 TA-ATTTTGATGAAAAATTGAGGAAAAAT-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
* * * * *
47118 CGTGTTCTAACCGTCAGGGTTTTGGCTAAAAACGCATTCCGG
952 CGTGTACTAACCATCACGGTTTTGCCCAAAAACGCATTCCGG
* * * * * *
47160 GGCGCCAGCTCAGTTTTGCATGATTTTTGGTGTCAAGACTCCGTGAAATATCTGTATTCATCTTA
1 GGCGCCGGCTCAGTTTTTCATGATTTTTGGCGCCAAGACTCCGTGAAATATCTATATTCATTTTA
* * * * *
47225 ACAAATCTCTGCATCATAGGATCTAAGGAGTTGTTTTTACGAGCATCTTAATCTTGTTTCGATAT
66 ACAAATCTCAGCAACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATAT
* * * *
47290 ACTTAGAAATCAATTCAGAAAAATTTTTTTAA-AAAAATGATATTAGAAGCGTGAAAAGCCCTCC
131 ACTTAGAAATTAAATCAGAAAAA-----ATAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTCC
* * * * *
47354 AATCTTTTTGGCGCTGAACTATATATTGTTAACGAGTATTTTTTATGAAAAAATTGAGGAAAAAT
191 AATCATTTTAGCACTGAATTATATATTGTTAACGAGTATTTTTGATGAAAAAATTGAGGAAAAAT
* * * * *
47419 CTTTCCGGACAATTCTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTGGCAAA
256 -TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTGGCTAA
* * ** * *
47484 AAACGCATTCCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGACGCCAAGACTTCGTGAAATAAC
320 AAACGCGTTCTGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCGTGAAATATC
* * * ** * * * *
47549 TTTATCCATATTCCCAAATATCAACAACATTGGGTTTAAGGAGTTGTTTTTACGAGCATTTGAAT
385 TATATTCATTTTAACAAATCTCAGCAACATTGGATTTAAGGAGTTGTTTTTACGAGCATCTGAAT
* *
47614 CTTGTTTCGATATACGTAGAAATTAAT-TCAGAAAAAATAAGAAAAACGATATTAGAAGCGTGAA
450 CTTGTTTCGATATTCATAGAAATTAATCTCAGAAAAAATAAGAAAAACGATATTAGAAGCGTGAA
*
47678 AAGCACTCCAATC-TTTATAGTGCTGAATTATATATTGTTAACGAGTATTTTTGATAACAAATTG
515 AAGCCCTCCAATCGTTT-TAGTGCTGAATTATATATTGTTAACGAGTATTTTTGATAACAAATTG
** *
47742 AGGAAAAAATTTTCTTGTCAAAATTTGCAAAATTTTAGCCGAAATCGTGTAGTAACCATCACGGT
579 AGG-AAAAATTTTCGGGTCAAAATTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
*** * * *
47807 GAAAGGCCAAAAACGCATTTCGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAATCT
643 -TTTGGCCAAAAACGCATTCCGGGGCGCC-GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* *
47872 GTGAAATATCTATATTCATTTTAACAAATCTCAGTAACATAGGATTTAAGGATTTGTTTTTACGA
706 GTGAAATATCTATATTCATTTTAACAAATCTCAGAAACATTGGATTTAAGGATTTGTTTTTACGA
* *
47937 GCATCTGAATCTTGTTTCGATATTCTTAGAAATTAAATCAGAAAAAATAAGAAAAACGACATTAG
771 GCATTTGAATCTTGTTTCGATATTATTAGAAATT-AATCAGAAAAAATAAGAAAAACGACATTAG
* * * *
48002 AAGCGTGAAAAGCCCTCCAATCGTTTTAGTGTTGAATCATATATTGTTAACGAGTATTTTTGATG
835 AAGCGTGAAAAGCACTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTAATTTTGATG
* * ** * *
48067 AAAAATTGAGGAAATATTTTTCTGGTCAAAATTTGCAAAATTTTAGCCGAAATTGTGTACAAACC
900 AAAAATTGAGGAAA-AATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
48132 ATCACGGTTTTGCCCAAAAACGCATTCCGG
964 ATCACGGTTTTGCCCAAAAACGCATTCCGG
* * * * * *
48162 GGCGCCGGCTCCGTTTTGCATAATTTTTGGCGTCAAGACTCCGTCAAATATCTATATTCA-TCTA
1 GGCGCCGGCTCAGTTTTTCATGATTTTTGGCGCCAAGACTCCGTGAAATATCTATATTCATTTTA
* * * * * * *
48226 ACCATATATCAACAACTTTGGATTTAAGGATTTGTTTTTACGACCATCTGAATCTTCTTTCGATA
66 A-CAAATCTCAGCAACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATA
* * * **
48291 TAATTAGAAAATT-AATCAGAAAAAATAAGAAAAACTATATTAGAAGTGTGAAAAGCATTCCAAT
130 TACTTAG-AAATTAAATCAGAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTCCAAT
**
48355 CATTTTAGTGCTGAATTATATATTGTTAACGAGTATTTTTGATG-AAAAATTGAGGAAAAATTTC
194 CATTTTAGCACTGAATTATATATTGTTAACGAGTATTTTTGATGAAAAAATTGAGGAAAAATTT-
* * *
48419 TCGGGTCAAGTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTGGCTAAAAA
258 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTGGCTAAAAA
*
48484 CGCGTTCTGGGGCGCCAGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCGTGAAATATCTAT
323 CGCGTTCTGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCGTGAAATATCTAT
* * * *
48549 ATTCATTTTAACAAATCTCAGCAACATAGGATTTATGGATTTGTTTTTACGAGGATCTGAATCTT
388 ATTCATTTTAACAAATCTCAGCAACATTGGATTTAAGGAGTTGTTTTTACGAGCATCTGAATCTT
* * *
48614 GTTTCGATATTCATAGAAATTGAATCTGA-AAAAAATAAGAAAAACGACATTAGAAGCGTGAAAT
453 GTTTCGATATTCATAGAAATT-AATCTCAGAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAA
*
48678 GCCCTCCAATCGTTTTAGTGTTGAATTATATATTGTTAACGAGTATTTTTGATAACAAATTGAGG
517 GCCCTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTATTTTTGATAACAAATTGAGG
* **
48743 AAAAACTTTTAGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
582 AAAAA-TTTTCGGGTCAAAATTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
* * *
48808 GGCTAAAAACGCATTCCGGGGCGCCTGCTCAGCTTTGCATGATTTTTGGCGGCAAGACTCCGTGA
646 GGCCAAAAACGCATTCCGGGGCGCC-GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCGTGA
* *
48873 AATATCTATATTCATTTTAACAAATCTCAGAAACATAGGATTTAAGTATTTGTTTTTACGAGCAT
710 AATATCTATATTCATTTTAACAAATCTCAGAAACATTGGATTTAAGGATTTGTTTTTACGAGCAT
*
48938 TTGAATCTTGTTTCGATATTCTTAGAAATTATATCAGAAAAAATAAGAAAAACGACATTAGAAGC
775 TTGAATCTTGTTTCGATATTATTAGAAATTA-ATCAGAAAAAATAAGAAAAACGACATTAGAAGC
* * *
49003 ATGAAAAG-ACTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTAATTTTGATGACAT
839 GTGAAAAGCACTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTAATTTTGATGAAAA
* ** *
49067 ATTGAGGAAAAATTTTCTGGTCAAAATTTGCAAAATTTTAGCCGAAATTGTGTACTAACCATCAC
904 ATTGAGGAAAAATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
*
49132 GGTTTTGCCCAAAAACGTATTCCGG
969 GGTTTTGCCCAAAAACGCATTCCGG
* * *
49157 GGCGCCGGCTCTGTTTTTCATGATTTTTGGCGCCAAGACTCTGTGAAATATCTATATTCCTTTTA
1 GGCGCCGGCTCAGTTTTTCATGATTTTTGGCGCCAAGACTCCGTGAAATATCTATATTCATTTTA
* * *
49222 ACAAATCTCAGTAACATAGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTATTTCGATAT
66 ACAAATCTCAGCAACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATAT
* * *
49287 TCTTAGAAATTAAATCAGAAAAAATAAGAAAAACGACATTAGAAGCGTGAAAAGCCCTCCAATCG
131 ACTTAGAAATTAAATCAGAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATCA
* * * * * *
49352 TTTAAGTATTGAATTATATATTGTTAACGAGTATTTTTTAT-AACAAATTGAGGAAAAACTTTTA
196 TTTTAGCACTGAATTATATATTGTTAACGAGTATTTTTGATGAAAAAATTGAGGAAAAA-TTTTC
*
49416 GGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTGGCTAAAAACG
260 GGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTGGCTAAAAACG
* * *
49481 CATT-TCGGGGCGCCTGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCGTGAAATATCTATA
325 CGTTCT-GGGGCGCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCGTGAAATATCTATA
* * * * * *
49545 TTCATTTTAACAAATCTTAGAAACATAGGATTTAAGTACTTGTTTTTACAAGCATCTGAATCTTG
389 TTCATTTTAACAAATCTCAGCAACATTGGATTTAAGGAGTTGTTTTTACGAGCATCTGAATCTTG
* * * * **
49610 TTTCAATATT-TTAGAAATT-ATATCATAAAAAATAAGAAAAACGACGTTAGAAGCGTGAAAAGC
454 TTTCGATATTCATAGAAATTAATCTCAGAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGC
49673 CCTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTATTTTTGATAACAAATTGAGGAA
519 CCTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTATTTTTGATAACAAATTGAGGAA
* ** *
49738 AAATTTCTCTGGTCAAAATTTGCAAAATTTTAGCAAAAATCGTGTAGTAACCATCACGGTTTTGG
584 AAATTT-TCGGGTCAAAATTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTGG
* *
49803 CCAAAAACGCATTCCGGGGCGCCGCCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCGTCAAA
648 CCAAAAACGCATTCCGGGGCGCCG-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCGTGAAA
* * * *
49868 TATCTATATTCA-TCTAACCATATCTCA-ACAACATTGGATTTAAGGATTTATTTTTACGACCAT
712 TATCTATATTCATTTTAA-CAAATCTCAGA-AACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * * *
49931 TTGAATCTTCTTTCGATATAATTAGAAAATTAATCAGAAAAAATAAGAAAAACTATATTAGAAGT
775 TTGAATCTTGTTTCGATATTATTAG-AAATTAATCAGAAAAAATAAGAAAAACGACATTAGAAGC
* * * *
49996 GTGAAAAGCATTCCAATCTTTTTAGTGCTGAATTATATATTGCTAACGAGTATTTTTGATGAAAA
839 GTGAAAAGCACTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTAATTTTGATGAAAA
*
50061 ATTGAGGAAAAATTTCTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGT-TAACTAACCATC
904 ATTGAGGAAAAATTT-TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ACTAACCATC
* * * *
50125 ACGGTTTTGGCTAAAAATGCGTTCCGG
967 ACGGTTTTGCCCAAAAACGCATTCCGG
* **** * *
50152 GGCGGCAAAACAGTTTTGT-ATGATTTTTGGCGCCAAGACTCCGTGAAATATCAATATTCATCTT
1 GGCGCCGGCTCAGTTTT-TCATGATTTTTGGCGCCAAGACTCCGTGAAATATCTATATTCATTTT
* * * *
50216 AACAAATCTCTGCATCATAGGATTTAAGGAGTTGTTTTTACGAGCATCAGAATCTTGTTTCGATA
65 AACAAATCTCAGCAACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATA
* * *
50281 TACTTAGAAAATTAATTCAGAAAAAATTTAAAAAAAATGATATTAGAAGCGTGAAAAG-CCTCCA
130 TACTTAG-AAATTAAATCAGAAAAAA--TAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTCCA
* * * * *
50345 ATC-TTTTTGCCACTGAACTATATTTTGTTAACGAGTATTTTTGATTAAAAAAATTGAGAAAAAA
192 ATCATTTTAG-CACTGAATTATATATTGTTAACGAGTATTTTTGA-TGAAAAAATTGAGGAAAAA
* * * *
50409 CTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCCTTTAGTAACCATCATGGTTTTGG-TA
255 -TTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTGGCTA
* * * * * * * *
50473 AAAGCGCGTTCCGAGCCGCCGGCTTAGTTTTACAAGATTTTTGGTGCCAAGACTCCGTGAAATAA
319 AAAACGCGTTCTGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCGTGAAATAT
* * * * * * * *
50538 CTTTATTCATCTTAACAAATCTCAGCAACATTGGGTTTATGTAGTTATTTTTACGTGCATTTGAA
384 CTATATTCATTTTAACAAATCTCAGCAACATTGGATTTAAGGAGTTGTTTTTACGAGCATCTGAA
* *
50603 TCTTGTTTCGATATTCTTAGAAATTAA-ATCAGTAAAAAATAAGAAAAACGATATTAGAAGCGTG
449 TCTTGTTTCGATATTCATAGAAATTAATCTCAG-AAAAAATAAGAAAAACGATATTAGAAGCGTG
* *
50667 AAAAGCCCTCCAATCCTTTTAGTGCTGAATTATATATTGTTAACGAGTAGTTTTGATAACAAATT
513 AAAAGCCCTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTATTTTTGATAACAAATT
*
50732 GAGGAAAAAAATTTCGGGTCAAAATTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG
578 GAGG-AAAAATTTTCGGGTCAAAATTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG
** * * *
50797 TTTTGGCCAAAAACAAATTCCGGGACGCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCA
642 TTTTGGCCAAAAACGCATTCCGGGGCGCCG-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * * ** * * * * *
50862 GTGAAATAACTTTATTCATATTCCCAAATATCAGCAACATTGGGTTTGAGGAGTTGTTTTTACGA
706 GTGAAATATCTATATTCATTTTAACAAATCTCAGAAACATTGGATTTAAGGATTTGTTTTTACGA
* * * *
50927 GCATTTGAATCTTGTTTCGATA-TAGTTAGAAATTAATTTAGAGAAAATAAGAATAACGATATTA
771 GCATTTGAATCTTGTTTCGATATTA-TTAGAAATTAA-TCAGAAAAAATAAGAAAAACGACATTA
* * * *
50991 GAAGCGTGAAAAGCCCTCCAATC-TTTATAGTGCTCAATTATATATTGTTAACGA-TTATCTTTT
834 GAAGCGTGAAAAGCACTCCAATCGTTT-TAGTGCTGAATTATATATTGTTAACGAGTAAT-TTTG
* * *
51054 AT-AACAAATTAAGGAAAAACTTTTAGGGTCAATTTTTGCAAAATTTTAGCAGAAATCGTGTACT
897 ATGAA-AAATTGAGGAAAAA-TTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
51118 AACCATCACGGTTTTG
960 AACCATCACGGTTTTG
51134 GCTAGGGCTA
Statistics
Matches: 3442, Mismatches: 440, Indels: 162
0.85 0.11 0.04
Matches are distributed among these distances:
978 25 0.01
979 96 0.03
980 3 0.00
983 60 0.02
984 6 0.00
985 22 0.01
986 1 0.00
992 166 0.05
993 419 0.12
994 123 0.04
995 792 0.23
996 120 0.03
997 448 0.13
998 364 0.11
999 106 0.03
1000 413 0.12
1001 19 0.01
1002 253 0.07
1003 6 0.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (993 bp):
GGCGCCGGCTCAGTTTTTCATGATTTTTGGCGCCAAGACTCCGTGAAATATCTATATTCATTTTA
ACAAATCTCAGCAACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATAT
ACTTAGAAATTAAATCAGAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATCA
TTTTAGCACTGAATTATATATTGTTAACGAGTATTTTTGATGAAAAAATTGAGGAAAAATTTTCG
GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTGGCTAAAAACGC
GTTCTGGGGCGCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCGTGAAATATCTATATT
CATTTTAACAAATCTCAGCAACATTGGATTTAAGGAGTTGTTTTTACGAGCATCTGAATCTTGTT
TCGATATTCATAGAAATTAATCTCAGAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGCCC
TCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTATTTTTGATAACAAATTGAGGAAAA
ATTTTCGGGTCAAAATTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTGGCCA
AAAACGCATTCCGGGGCGCCGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCGTGAAATATC
TATATTCATTTTAACAAATCTCAGAAACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAAT
CTTGTTTCGATATTATTAGAAATTAATCAGAAAAAATAAGAAAAACGACATTAGAAGCGTGAAAA
GCACTCCAATCGTTTTAGTGCTGAATTATATATTGTTAACGAGTAATTTTGATGAAAAATTGAGG
AAAAATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTG
CCCAAAAACGCATTCCGG
Found at i:51398 original size:30 final size:29
Alignment explanation
Indices: 51362--51423 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
51352 CATACATACA
*
51362 AATCACTGAAATCAGAATACTTAAAACTTC
1 AATCACTGAAATCAGAAAACTT-AAACTTC
*
51392 AATCACTGAAGTCAGAAAACTTAAACTTC
1 AATCACTGAAATCAGAAAACTTAAACTTC
51421 AAT
1 AAT
51424 AGCTAGCTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.26
Consensus pattern (29 bp):
AATCACTGAAATCAGAAAACTTAAACTTC
Done.