Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020349.1 Corchorus olitorius cultivar O-4 contig20382, 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: 47975
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:12647 original size:3 final size:3
Alignment explanation
Indices: 12639--12666 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12629 TCTATTCTTG
12639 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12667 TGTTAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12964 original size:14 final size:14
Alignment explanation
Indices: 12945--12971 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12935 GAAAAATTGT
12945 TGAGGATTCATATG
1 TGAGGATTCATATG
12959 TGAGGATTCATAT
1 TGAGGATTCATAT
12972 ATATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (14 bp):
TGAGGATTCATATG
Found at i:12975 original size:2 final size:2
Alignment explanation
Indices: 12968--13003 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12958 GTGAGGATTC
12968 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
13004 CACTTCCACG
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:14024 original size:26 final size:27
Alignment explanation
Indices: 13980--14036 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
13970 CTCTAACATT
*
13980 TTTTTGTTTTTGCGTCAACTGCTCTAA
1 TTTTTGTTTTTGCGTCAACTCCTCTAA
14007 CTTTTT-TTTTTGCG-CAACTCCTCTAA
1 -TTTTTGTTTTTGCGTCAACTCCTCTAA
14033 TTTT
1 TTTT
14037 ATAAGTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 4 0.14
26 11 0.39
27 8 0.29
28 5 0.18
ACGTcount: A:0.14, C:0.21, G:0.11, T:0.54
Consensus pattern (27 bp):
TTTTTGTTTTTGCGTCAACTCCTCTAA
Found at i:15953 original size:28 final size:27
Alignment explanation
Indices: 15889--15963 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 27
15879 TCCGGCATTT
15889 AAGGGCAAAACTGTAA-TTTAGTCAACC
1 AAGGGCAAAA-TGTAATTTTAGTCAACC
* * *
15916 AGGGGTAAAATGGTAATTTTAG-CTGACC
1 AAGGGCAAAAT-GTAATTTTAGTC-AACC
*
15944 AAGGGCAAAACAGTAATTTT
1 AAGGGCAAAA-TGTAATTTT
15964 GACATCTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
26 1 0.03
27 13 0.34
28 24 0.63
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (27 bp):
AAGGGCAAAATGTAATTTTAGTCAACC
Found at i:17944 original size:138 final size:131
Alignment explanation
Indices: 17774--18043 Score: 380
Period size: 130 Copynumber: 2.0 Consensus size: 131
17764 ATTTAAGAAA
* *
17774 TATATTTTAAAAATTCTAATATATCTAAGTTTTTTTAATTAATTAAATTAGTCAAATGATAAAAA
1 TATATTTTAAAAATTCTAATATATATAAG-TTTTTTAATT-A--AAA-TAGTAAAATGATAAAAA
* *
17839 TAAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAAATAGAGTTTTTAGTTGAGTAAAA
61 T-AAAATAGGTATAAAGATATTAGATTTAATTAAAT--AAAAATAGAGTTTTTAATTGAGTAAAA
17904 CTATAAAAG
123 CTATAAAAG
* * *
17913 TATA-TTTAAAAGTTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAA
1 TATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAA
* *
17977 TAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAATTATAAAA
66 TAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAA
18042 G
131 G
18043 T
1 T
18044 TTAAACAATG
Statistics
Matches: 122, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
130 35 0.29
132 31 0.25
133 16 0.13
134 3 0.02
136 1 0.01
137 10 0.08
138 22 0.18
139 4 0.03
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (131 bp):
TATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAA
TAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAA
G
Found at i:29252 original size:14 final size:14
Alignment explanation
Indices: 29233--29262 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29223 CAACGTCTGA
29233 TGTGGTATGCCATG
1 TGTGGTATGCCATG
29247 TGTGGTATGCCATG
1 TGTGGTATGCCATG
29261 TG
1 TG
29263 GACAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.37, T:0.37
Consensus pattern (14 bp):
TGTGGTATGCCATG
Found at i:29337 original size:31 final size:31
Alignment explanation
Indices: 29302--29401 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 31
29292 TTTGTGCATG
**
29302 TGGCATGTCACGTGTCACTTTTTGAAACACA
1 TGGCATGTCACGTGTCACTTTTTGGTACACA
* * *
29333 TGGCATGCCACGTGTCAGTTTTTGGTATACA
1 TGGCATGTCACGTGTCACTTTTTGGTACACA
* * *
29364 TGGCGTGAT-ATGTGTCACTTTTTGGTACACG
1 TGGCATG-TCACGTGTCACTTTTTGGTACACA
29395 TGGCATG
1 TGGCATG
29402 ACACCGTCGG
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (31 bp):
TGGCATGTCACGTGTCACTTTTTGGTACACA
Found at i:30683 original size:22 final size:22
Alignment explanation
Indices: 30655--30698 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
30645 CAATTTGGTA
30655 CTTTTTTAAACTTCCGTCAGCG
1 CTTTTTTAAACTTCCGTCAGCG
30677 CTTTTTTAAACTTCCGTCAGCG
1 CTTTTTTAAACTTCCGTCAGCG
30699 ATTGAAACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (22 bp):
CTTTTTTAAACTTCCGTCAGCG
Found at i:30990 original size:42 final size:42
Alignment explanation
Indices: 30933--31028 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
30923 ACACCGACGA
30933 CCCTCCGGCTCCTTCTCCGACA-ACCCCTCTGCCTTCCAAAAT
1 CCCTCCGGCTCCTTCTCCGACATA-CCCTCTGCCTTCCAAAAT
* * *
30975 CCCTCTGGCTTCTTCTCCGACATACCCTTTGCCTTCCAAAAT
1 CCCTCCGGCTCCTTCTCCGACATACCCTCTGCCTTCCAAAAT
* *
31017 CCTTCCCGCTCC
1 CCCTCCGGCTCC
31029 GACAACCTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.15, C:0.48, G:0.09, T:0.28
Consensus pattern (42 bp):
CCCTCCGGCTCCTTCTCCGACATACCCTCTGCCTTCCAAAAT
Found at i:33644 original size:91 final size:91
Alignment explanation
Indices: 33466--33651 Score: 241
Period size: 91 Copynumber: 2.0 Consensus size: 91
33456 GTAAGATTTC
* * * *
33466 GCAACGACTTAATTTGTCGTTTCAAAAGTAACTATATTTTTTGTAGCGACTTTCAAGGTCGCTGT
1 GCAACAACTTAATTTGTCATTTCAAAAGAAACTATATTTTTTGTAACGACTTTCAAGGTCGCTGT
33531 GAAAATCAATTTGTAAAATATATTAA
66 GAAAATCAATTTGTAAAATATATTAA
* * *
33557 GCAACAACTTAATTTGTCATTTCAAAAGAAATTATATTTTTTTGTAACGACTTT-AGATGTCGTT
1 GCAACAACTTAATTTGTCATTTCAAAAGAAACTATA-TTTTTTGTAACGACTTTCA-AGGTCGCT
* * * *
33621 GTGAAATTCATTTTG-GAACTATATTAA
64 GTGAAAATCAATTTGTAAAATATATTAA
33648 GCAA
1 GCAA
33652 TGACTAATAG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
91 47 0.57
92 35 0.43
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (91 bp):
GCAACAACTTAATTTGTCATTTCAAAAGAAACTATATTTTTTGTAACGACTTTCAAGGTCGCTGT
GAAAATCAATTTGTAAAATATATTAA
Found at i:35868 original size:19 final size:19
Alignment explanation
Indices: 35844--35880 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35834 CTTATCTGTA
* *
35844 ACCGTTTTACCATCGTTTG
1 ACCGTTTCACCACCGTTTG
35863 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
35881 TGGGCCCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.32, G:0.14, T:0.38
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:35956 original size:21 final size:19
Alignment explanation
Indices: 35931--35988 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
35921 GTTGCTCTAA
*
35931 TAATCTCATTTGTACAGTACC
1 TAATCTCATATGTACAGT--C
* *
35952 TAATCTAATATGTACAGTG
1 TAATCTCATATGTACAGTC
*
35971 TAATCTCATCTGTACAGT
1 TAATCTCATATGTACAGT
35989 TGCTAAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATATGTACAGTC
Found at i:36487 original size:3 final size:3
Alignment explanation
Indices: 36479--36525 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
36469 TCGACCAACC
36479 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
36526 TCAATATTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:36715 original size:69 final size:71
Alignment explanation
Indices: 36614--36751 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 71
36604 AAATGAGTTG
* *
36614 AGAGATTGAAGAATTATTAGATTAAAAAGAGAA-AGATTTGATTTTGAGGGAAACAAA-TTGAGT
1 AGAGATTGAAGAATGA-TAGATTAAAAAGAGAAGAGATTTGA-TTTGAGGGAAAAAAATTTGAGT
36677 AACGGGCA
64 AACGGGCA
*
36685 AGAGATTGAAGAATGA-AGATTAAAACGAGAAGAGATTTGATTTGAGGGAAAAAAATTTGAGTAA
1 AGAGATTGAAGAATGATAGATTAAAAAGAGAAGAGATTTGATTTGAGGGAAAAAAATTTGAGTAA
36749 CGG
66 CGG
36752 CATGGAGATT
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
69 28 0.45
70 19 0.31
71 15 0.24
ACGTcount: A:0.46, C:0.04, G:0.27, T:0.24
Consensus pattern (71 bp):
AGAGATTGAAGAATGATAGATTAAAAAGAGAAGAGATTTGATTTGAGGGAAAAAAATTTGAGTAA
CGGGCA
Found at i:37040 original size:30 final size:31
Alignment explanation
Indices: 36981--37054 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
36971 AGTTTGATTT
* *
36981 TATCCTTAATTGACACAACCTGATAACGTTA
1 TATCCTGAATTGACACAACCAGATAACGTTA
* *
37012 TATCCTGAATTGACACAA-GAGGTAACGTTA
1 TATCCTGAATTGACACAACCAGATAACGTTA
37042 TATCCTGAATTGA
1 TATCCTGAATTGA
37055 ATTTTTGCCC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 22 0.56
31 17 0.44
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (31 bp):
TATCCTGAATTGACACAACCAGATAACGTTA
Found at i:38804 original size:20 final size:20
Alignment explanation
Indices: 38765--38805 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38755 ACATGAATGA
*
38765 TTAAACGTGTTAGCCGTGTT
1 TTAAACGTGTTAGCCATGTT
* *
38785 TTAATCGTGTTAGTCATGTT
1 TTAAACGTGTTAGCCATGTT
38805 T
1 T
38806 GACACAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.46
Consensus pattern (20 bp):
TTAAACGTGTTAGCCATGTT
Found at i:45258 original size:338 final size:318
Alignment explanation
Indices: 43557--45777 Score: 1028
Period size: 334 Copynumber: 6.8 Consensus size: 318
43547 AACCATGATG
* * * * * * *
43557 GTACACAATTTCAGCTAAAACTTTACAAAAATTGACCCGAAATA-TTTT-CTCAATTTTTAGCCA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAAATTTTTCCTCAATTTTT-GCTA
* * * *
43620 CAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGG--TTTCTCACGCTTCTAA
65 AAATACTCATAAAATATATATAATTC-ACGCC-AAAATATTG--AGGACTTT-TCACGCTTTTAA
* * * * * * * *
43683 TATCATTTTTCCTATTTGTTT-TCAAATTAATTTCTAATTAAATTGAAACATGATTCAAATGCTT
125 TATCGTTTTTCATATTT-TTTCT-GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTC
* ** * * * * * *
43747 GTAAAAACAAATCCTTAATTCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGC
188 GTAAAAACAAATCCTTAAATGTAATGTGACTGATATTTGATTAGATGAATAT--ATATCTCAAGT
* * ** ** ** * * *
43812 A-A-TGTTGCCA-CTAAAAATCGTGCAAAACTGACCCGGGGTCCCAGGGCGTGTATTTAGCCAAA
251 AGACT-TAG--AGCCAAAAATCAAGCAAAACTGA-CC----T-GAAACGCAT-T-TCTAGCAAAA
43874 AACCGTGATG----
305 AACCGTGATGATTA
* *
43884 GTACACGATTTCGGCTAAAATTTTGCAAAAA-T----------ATTTTTCCTCCATTTTTAGCCA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAAATTTTTCCTCAATTTTT-GCTA
* * * * * * * *
43938 CAATACTCATAGAATATATATAATTAAAAGCCAAAAAGATAGAAGCACTCTTCACGCTTTTAATA
65 AAATACTCATAAAATATATATAATT-CACGCC-AAAATATTG-AGGACTTTTCACGCTTTTAATA
* ** * * * *
44003 CCGTTTTTCATA-TTTTTCAAAATTACTTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAT
127 TCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAA
** * * * *
44067 AAACAAATCCTTAAAT-TGAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
192 AAACAAATCCTTAAATGT-AATGTGACTGATATTTGATTAGATGAATAT--ATATCTCAAGTAGA
** * * * * * * **
44131 CTCGGCGCCAAAAATCATGCAAAACTAAACCGGGGTCCCAAAACGCGTTTTTAGCCCAAAACCGT
254 CTTAGAGCCAAAAATCAAGCAAAACT-GACC----T---GAAACGCATTTCTAGCAAAAAACCGT
44196 GAT-AGTTA
311 GATGA-TTA
* *** * * ** **
44204 GTATACGATTTCGAAAAAAATTTTGTAAAAAATGACCCA-AAATTTTTTTTCCGTCAATTTACGA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCAGAAA-AATTTTTCC-TCAATTTTTG-
* * **
44268 C-ATAAATACTCATAAAATATATATATAACTTAACACCAAAGGATTGGAGGACTTTTCACGCTTT
62 CTA-AAATACTCAT-AAA-ATATATATAA-TTCACGCCAAAATATT-GAGGACTTTTCACGCTTT
* * * * *
44332 TAATATCATTTTTCATA-TTTTTCTAAATTAATTTCTAATTAAATTGAAATAAGATTCAGATGCT
122 TAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCT
* ** * *
44396 CGTAAAAACAAATTCTTAAATCCAATG-CAGCTGAGATTTGATTAGATGAATATGGATATCTCAA
187 CGTAAAAACAAATCCTTAAATGTAATGTGA-CTGATATTTGATTAGATGAATAT--ATATCTC-A
** * * * * * * * * * *
44460 AG-AGTTTTGGCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCAGAACACGTTTTTCGCGAAA
248 AGTAGACTTAGAGCCAAAAATCAAGCAAAACTGA-CC--TG----A-AACGCATTTCTAGCAAAA
**
44524 AACTATGATGATTA
305 AACCGTGATGATTA
* * * * * * * *
44538 TTACACGATTTCGGCTAGAGA-TTTAC-AAAATTGACTC-G-AAAGTTATT--T-ACTTTTAGCC
1 GTACACGATTTCGGCTA-AAATTTTGCAAAAATTGAC-CAGAAAAATTTTTCCTCAATTTTTGCT
* * * * * * * * * *
44596 ACAATACTCA-AAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTATGCATGCTTCTAG
64 AAAATACTCATAAAATA-TATATAATTC-ACGCC-AAAATATTG-AGGACTTTTCACGCTTTTAA
* ** * * * *
44660 TATCGTTTTTCCTATTATTTTCTGAATTAATTTCCCATTAAATAGAAACATGATTCAGATGCTTG
125 TATCGTTTTTCATATT-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG
*** ** * * * *
44725 T-TTTACAAATCCTTAAATCCATTGTGGA-TGAGATTTTG-TTAGATTAATATAAATATTTCAAG
189 TAAAAACAAATCCTTAAATGTAATGT-GACTGATA-TTTGATTAGATGAATAT--ATATCTCAAG
* ** ** * * * * * * * *
44787 GATTCTCGGCGCAAAAAATCATGCAACACTGAACCGGGGCCCCAGAACGCGTTTTTAGGAAAAAA
250 TAGACTTAGAGCCAAAAATCAAGCAAAACTG-ACC--TG----A-AACGCATTTCTAGCAAAAAA
* * *
44852 CCTTGATTTCCACTAA
307 CCGTGA--T-GA-TTA
* * * *
44868 CATACACGATTTCGGCTAATATTTTGCAAAAATTGACCAGAAATAGTTTTCCTCAATTTTTGTCT
1 -GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAAATTTTTCCTCAATTTTTG-CT
44933 AAAATACTCATAAAATATATATAATTCACGTCCAAAATTATTAGAGGACTTTTCACGCTTTTAAT
64 AAAATACTCATAAAATATATATAATTCACG-CCAAAA-TATT-GAGGACTTTTCACGCTTTTAAT
** * * *
44998 ATCGTTTTTCAT-TTTTTTCTGAATTAAAATCTAATTAAATCGAAACAATATTCAGATACTCGTA
126 ATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
* *
45062 AAAACAAATCTTTAAATGTAATGTGACTGATATTTGATTAGATGAATATATATTTCAACG-AGAC
191 AAAACAAATCCTTAAATGTAATGTGACTGATATTTGATTAGATGAATATATATCTCAA-GTAGAC
* * * * *
45126 -TCGATGCCAAAAATCATGCAAAACTTAGTTGGAGCTCGAAACGCGTTTTTAGCAAAAAAAAAAA
255 TTAGA-GCCAAAAATCAAGCAAAAC-----T-GACCT-GAAACGCATTTCTAGC---------AA
*
45190 AAAACCCGTGATGGTTA
303 AAAA-CCGTGATGATTA
* * *
45207 GTACACGATTTCGTCTAAAATTTTGCAAAAAATGACCACAAAAATTTTTCCTCAATTTTTGCCTA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAAATTTTTCCTCAATTTTTG-CTA
* * * * * * * * *
45272 AAATACTTATGAAATATATATAATTTAACGCCAAAAAGATTGGAGGACGTCTCAAGATTTTCATA
65 AAATACTCATAAAATATATATAA-TTCACGCC-AAAATATT-GAGGACTTTTCACGCTTTTAATA
* * *
45337 TCGTTTTTCATAATTTTTCTGAAATAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAA
127 TCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAA
* * * ** * * * *
45402 AATCAGATCCATAAATGTAATGTTTCTGAGATTTGATTTGACGAATATGGATATCTCAAGTAGTC
192 AAACAAATCCTTAAATGTAATGTGACTGATATTTGATTAGATGAATAT--ATATCTCAAGTAGAC
* * * *
45467 TTAGAGCCAAAAATCAAGCAAAACTGACCTGGAATGCATTTCTAGCCAAAAACTGTGATGATTA
255 TTAGAGCCAAAAATCAAGCAAAACTGACCTGAAACGCATTTCTAGCAAAAAACCGTGATGATTA
* * * * * * *
45531 TTACACGATTTCGGCTAAAGTTTTGCAAAAATTGAACGGAAAGATAATTT-CTCATTTTTTGCTA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAAAT-TTTTCCTCAATTTTTGCTA
* *
45595 AATTA-TCATAAAAAATATATATAATTCTACGCCGAAAATATTGAAGGA-TTTTAAACGCTTCTA
65 AAATACTCAT--AAAATATATATAATTC-ACGCC-AAAATATTG-AGGACTTTT-CACGC-T-T-
* * *
45658 TTAATATCGTTTTTCCTATTTTTTCCGAATGAATTTCTAATTAAATCGAAACAAGATTTAGATGC
121 TTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGC
** * *
45723 TCGTAAAAACAAATCCTTAAATCCAATGTGACTGATATTTGAGTAGATAAATATA
186 TCGTAAAAACAAATCCTTAAATGTAATGTGACTGATATTTGATTAGATGAATATA
45778 GATAGTTCAA
Statistics
Matches: 1492, Mismatches: 285, Indels: 236
0.74 0.14 0.12
Matches are distributed among these distances:
316 139 0.09
317 12 0.01
318 79 0.05
319 2 0.00
320 26 0.02
321 1 0.00
322 3 0.00
323 16 0.01
324 101 0.07
325 46 0.03
326 108 0.07
327 180 0.12
328 3 0.00
329 1 0.00
330 4 0.00
331 25 0.02
332 24 0.02
333 45 0.03
334 241 0.16
335 73 0.05
336 49 0.03
337 51 0.03
338 119 0.08
339 98 0.07
340 2 0.00
341 30 0.02
342 9 0.01
343 5 0.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (318 bp):
GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAAATTTTTCCTCAATTTTTGCTAA
AATACTCATAAAATATATATAATTCACGCCAAAATATTGAGGACTTTTCACGCTTTTAATATCGT
TTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAC
AAATCCTTAAATGTAATGTGACTGATATTTGATTAGATGAATATATATCTCAAGTAGACTTAGAG
CCAAAAATCAAGCAAAACTGACCTGAAACGCATTTCTAGCAAAAAACCGTGATGATTA
Found at i:46986 original size:13 final size:13
Alignment explanation
Indices: 46953--47005 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
46943 GCACCCAAAA
46953 CATTTAT-TAAAG
1 CATTTATATAAAG
46965 CATTT-TATAAAG
1 CATTTATATAAAG
*
46977 CCTTTATATAAAG
1 CATTTATATAAAG
*
46990 CAGTTATA-AAA-
1 CATTTATATAAAG
47001 CATTT
1 CATTT
47006 CCTCAACGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.49
13 13 0.37
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:47219 original size:19 final size:19
Alignment explanation
Indices: 47178--47219 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
47168 TAGATCATAG
* *
47178 CAAAACCAAGATAATCAAT
1 CAAAACCAAGATAATAAAC
*
47197 CAAAACCGAGATAATAAAC
1 CAAAACCAAGATAATAAAC
47216 CAAA
1 CAAA
47220 TCAATCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.21, G:0.07, T:0.12
Consensus pattern (19 bp):
CAAAACCAAGATAATAAAC
Done.