Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014274.1 Corchorus olitorius cultivar O-4 contig14307, 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: 100743
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4987 original size:27 final size:27
Alignment explanation
Indices: 4934--4989 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
4924 AATGGCTGCA
* *
4934 CCCCCGGCGTTGACACCCACAAGTTCT
1 CCCCCGGCATTGACACCCACAACTTCT
* * *
4961 CCCCCTGCATTGACACCGACTACTTCT
1 CCCCCGGCATTGACACCCACAACTTCT
4988 CC
1 CC
4990 TCCGACAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.18, C:0.46, G:0.14, T:0.21
Consensus pattern (27 bp):
CCCCCGGCATTGACACCCACAACTTCT
Found at i:8326 original size:14 final size:14
Alignment explanation
Indices: 8307--8338 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
8297 GGTAGGATCT
8307 TAAGGTTTATTAGA
1 TAAGGTTTATTAGA
8321 TAAGGTTTATTAGA
1 TAAGGTTTATTAGA
8335 TAAG
1 TAAG
8339 AGTAAGACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (14 bp):
TAAGGTTTATTAGA
Found at i:8634 original size:26 final size:26
Alignment explanation
Indices: 8598--8648 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
8588 TTCCATCATA
8598 ATTTTCATGTAATAAACTTGTACATG
1 ATTTTCATGTAATAAACTTGTACATG
8624 ATTTTCATGTAATAAACTTGTACAT
1 ATTTTCATGTAATAAACTTGTACAT
8649 TGCGGTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (26 bp):
ATTTTCATGTAATAAACTTGTACATG
Found at i:9085 original size:18 final size:17
Alignment explanation
Indices: 9062--9099 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
9052 AGAATTCATG
9062 AGAAAAAGGAAAAAAAAA
1 AGAAAAA-GAAAAAAAAA
*
9080 AGAAAAAGAAAAAAGAA
1 AGAAAAAGAAAAAAAAA
9097 AGA
1 AGA
9100 TGGCGTGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AGAAAAAGAAAAAAAAA
Found at i:9091 original size:13 final size:12
Alignment explanation
Indices: 9064--9097 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9054 AATTCATGAG
*
9064 AAAAAGGAAAAA
1 AAAAAGAAAAAA
9076 AAAAAGAAAAAGA
1 AAAAAGAAAAA-A
9089 AAAAAGAAA
1 AAAAAGAAA
9098 GATGGCGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:17679 original size:19 final size:19
Alignment explanation
Indices: 17625--17683 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
17615 CGCTGCTCTA
*
17625 ATAATCTCATCTATACAGT
1 ATAATCTCATCTGTACAGT
* * *
17644 ACCTAATGTAATATGTACAGT
1 A--TAATCTCATCTGTACAGT
17665 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
17684 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:24999 original size:11 final size:11
Alignment explanation
Indices: 24982--25015 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
24972 TCATTGTGTG
24982 AAAAAAAAA-A
1 AAAAAAAAAGA
*
24992 AGAAAAAAAGA
1 AAAAAAAAAGA
25003 AAAAAAAAAGA
1 AAAAAAAAAGA
25014 AA
1 AA
25016 GTGAAGTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:26615 original size:21 final size:21
Alignment explanation
Indices: 26591--26631 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
26581 TTATATGTCA
*
26591 ACATATATTGACTATGGTTGT
1 ACATATAGTGACTATGGTTGT
*
26612 ACATATAGTGACTATTGTTG
1 ACATATAGTGACTATGGTTG
26632 CAACGAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (21 bp):
ACATATAGTGACTATGGTTGT
Found at i:30558 original size:17 final size:17
Alignment explanation
Indices: 30532--30564 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30522 TAATATAAAA
30532 ATCAATGATA-AAATTT
1 ATCAATGATAGAAATTT
30548 ATCAGATGATAGAAATT
1 ATCA-ATGATAGAAATT
30565 GAAAATAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
ATCAATGATAGAAATTT
Found at i:31311 original size:19 final size:17
Alignment explanation
Indices: 31263--31314 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 17
31253 ATAAATTCTG
31263 ATTTTTTTA-TTTTAAT
1 ATTTTTTTATTTTTAAT
31279 ATTTCTTTTAATTTTTAAT
1 ATTT-TTTT-ATTTTTAAT
31298 AATTTTTATTATTTTTA
1 -ATTTTT-TTATTTTTA
31315 TTTATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 1 0.03
19 16 0.52
20 6 0.19
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTATTTTTAAT
Found at i:34203 original size:2 final size:2
Alignment explanation
Indices: 34196--34232 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34186 ACTTGGTATG
34196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34233 TCAAATGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43135 original size:20 final size:20
Alignment explanation
Indices: 43110--43147 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43100 TTTGTTTCAA
*
43110 TTTTATCCTTGAACTTCTTT
1 TTTTATCCTTGAAATTCTTT
43130 TTTTATCCTTGAAATTCT
1 TTTTATCCTTGAAATTCT
43148 AATTGTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTATCCTTGAAATTCTTT
Found at i:43829 original size:91 final size:92
Alignment explanation
Indices: 43642--44281 Score: 871
Period size: 91 Copynumber: 7.0 Consensus size: 92
43632 ATTCTTCCAC
* * *
43642 TTAATTTAACAAATGGCAAATTTGTGTCAACA-AGAGAATTAGAGTTGTCAAATTTATTATATTG
1 TTAATTTAACGAACGGCAAATTTGTGTCAACAGA-AGAATTACAGTTGTCAAATTTATTATATTG
* ** * *
43706 ACAAATGAAATTTACAAAATAATTACTG
65 ACAAATGGAATTTACGGAAGAATTACAG
* * * * ** *
43734 TTAATTTAACAAATGGCAAATTTGTGTCAACAGACGAATTATA-TCATCCAATTTATTATATTGA
1 TTAATTTAACGAACGGCAAATTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
* * *
43798 CAAATAGAATTTACGGAATAATTACAA
66 CAAATGGAATTTACGGAAGAATTACAG
* * *
43825 TTAATTTAACGAACGACAAACTTGTGTCAACAGAAGAATTACAATTGTCAAATTTATTATATTGA
1 TTAATTTAACGAACGGCAAATTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
* *
43890 CAAATGAAATTTAC-AAAGAATTACAG
66 CAAATGGAATTTACGGAAGAATTACAG
* * * * *
43916 TTAATTTAACGAATGACAAATTTGTGTCAACAGACGAATTACAGTTGTCCAATTTATTATACTGA
1 TTAATTTAACGAACGGCAAATTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
* * *
43981 CAAATAGAATTTACGAAAAAATTACAG
66 CAAATGGAATTTACGGAAGAATTACAG
* *
44008 TTAA-TTAACGAACGGTAAACTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
1 TTAATTTAACGAACGGCAAATTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
44072 CAAATGGAATTTACGGAAGAATTACAG
66 CAAATGGAATTTACGGAAGAATTACAG
* * *
44099 TTAATTTAACGAACGACAAACTTT-TGCCAACAGAAGAATTACAGTTGTCATATTTATTATATTG
1 TTAATTTAACGAACGGCAAA-TTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTG
44163 ACAAATGGAATTTACGGAAGAATTA-AG
65 ACAAATGGAATTTACGGAAGAATTACAG
*
44190 TTAATTTAACGAACGGCAAACTTT-TGCCAACAGAAGAATTACAGTTGTCAAATTTATTATATTG
1 TTAATTTAACGAACGGCAAA-TTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTG
44254 ACAAATGGAATTTACGGAAGAATTACAG
65 ACAAATGGAATTTACGGAAGAATTACAG
44282 GTGTTCAATT
Statistics
Matches: 491, Mismatches: 51, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
91 326 0.66
92 162 0.33
93 3 0.01
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (92 bp):
TTAATTTAACGAACGGCAAATTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
CAAATGGAATTTACGGAAGAATTACAG
Found at i:43969 original size:183 final size:184
Alignment explanation
Indices: 43642--44379 Score: 936
Period size: 183 Copynumber: 4.0 Consensus size: 184
43632 ATTCTTCCAC
* * * *
43642 TTAATTTAACAAATGGCAAATTTGTGTCAACA-AGAGAATTAGAGTTGTCAAATTTATTATATTG
1 TTAATTTAACGAACGGCAAACTTGTGTCAACAGA-AGAATTACAGTTGTCAAATTTATTATATTG
* * * * *
43706 ACAAATGAAATTTACAAAATAATTACTGTTAATTTAACAAATGGCAAATTTGTGTCAACAGACGA
65 ACAAATGAAATTTACGAAAGAATTACAGTTAATTTAACGAATGACAAATTTGTGTCAACAGACGA
* ** * *
43771 ATTATA-TCATCCAATTTATTATATTGACAAATAGAATTTACGGAATAATTACAA
130 ATTACAGTTGTCCAATTTATTATATTGACAAATAGAATTTACGGAAAAATTACAG
* *
43825 TTAATTTAACGAACGACAAACTTGTGTCAACAGAAGAATTACAATTGTCAAATTTATTATATTGA
1 TTAATTTAACGAACGGCAAACTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
43890 CAAATGAAATTTAC-AAAGAATTACAGTTAATTTAACGAATGACAAATTTGTGTCAACAGACGAA
66 CAAATGAAATTTACGAAAGAATTACAGTTAATTTAACGAATGACAAATTTGTGTCAACAGACGAA
* *
43954 TTACAGTTGTCCAATTTATTATACTGACAAATAGAATTTACGAAAAAATTACAG
131 TTACAGTTGTCCAATTTATTATATTGACAAATAGAATTTACGGAAAAATTACAG
*
44008 TTAA-TTAACGAACGGTAAACTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
1 TTAATTTAACGAACGGCAAACTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
* * * * *
44072 CAAATGGAATTTACGGAAGAATTACAGTTAATTTAACGAACGACAAACTTT-TGCCAACAGAAGA
66 CAAATGAAATTTACGAAAGAATTACAGTTAATTTAACGAATGACAAA-TTTGTGTCAACAGACGA
* *
44136 ATTACAGTTGT-CATATTTATTATATTGACAAATGGAATTTACGGAAGAATTA-AG
130 ATTACAGTTGTCCA-ATTTATTATATTGACAAATAGAATTTACGGAAAAATTACAG
* *
44190 TTAATTTAACGAACGGCAAACTTTTGCCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
1 TTAATTTAACGAACGGCAAACTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
* * * * * ** ** *
44255 CAAATGGAATTTACGGAAGAATTACAGGTGTTCAATTTATTA-TATTGACAAA-TGGAATTTACG
66 CAAATGAAATTTACGAAAGAATTACA---GTT-AATTTA--ACGAATGACAAATTTGTGTCAACA
* * * * **
44318 GAAGAATTACAGGTGTTCAATTTATTATATTGACAAATAGAATTTACAGAAAGTTTACAG
125 GACGAATTACAGTTGTCCAATTTATTATATTGACAAATAGAATTTACGGAAAAATTACAG
44378 TT
1 TT
44380 GTCCAATTTA
Statistics
Matches: 492, Mismatches: 48, Indels: 25
0.87 0.08 0.04
Matches are distributed among these distances:
182 128 0.26
183 286 0.58
184 4 0.01
186 4 0.01
187 56 0.11
188 13 0.03
189 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (184 bp):
TTAATTTAACGAACGGCAAACTTGTGTCAACAGAAGAATTACAGTTGTCAAATTTATTATATTGA
CAAATGAAATTTACGAAAGAATTACAGTTAATTTAACGAATGACAAATTTGTGTCAACAGACGAA
TTACAGTTGTCCAATTTATTATATTGACAAATAGAATTTACGGAAAAATTACAG
Found at i:44132 original size:274 final size:272
Alignment explanation
Indices: 43642--44281 Score: 910
Period size: 274 Copynumber: 2.3 Consensus size: 272
43632 ATTCTTCCAC
* *
43642 TTAATTTAACAAATGGCAAATTTGTGTCAACAAGAGAATTAGAGTTGTCAAATTTATTATATTGA
1 TTAATTTAACGAATGGCAAATTTGTGTCAAC-AGAGAATTACAGTTGTCAAATTTATTATATTGA
* * * *
43707 CAAATGAAATTTAC-AAAATAATTACTGTTAATTTAACAAATGGCAAATTTGTGTCAACAGACGA
65 CAAATG-AATTTACGAAAA-AATTACAGTTAATTTAACAAACGGCAAACTTGTGTCAACAGAAGA
* * *
43771 ATTATATCATCCAATTTATTATATTGACAAATAGAATTTACGGAATAATTACAATTAATTTAACG
128 ATTACATCATCAAATTTATTATATTGACAAATAGAATTTACGGAAGAATTACAATTAATTTAACG
*
43836 AACGACAAACTTGTGTCAACAGAAGAATTACAATTGTCAAATTTATTATATTGACAAATGAAATT
193 AACGACAAACTTGTGCCAACAGAAGAATTACAATTGTCAAATTTATTATATTGACAAATGAAATT
43901 TAC-AAAGAATTACAG
258 TACGAAAGAATTA-AG
* * *
43916 TTAATTTAACGAATGACAAATTTGTGTCAACAGACGAATTACAGTTGTCCAATTTATTATACTGA
1 TTAATTTAACGAATGGCAAATTTGTGTCAACAGA-GAATTACAGTTGTCAAATTTATTATATTGA
* *
43981 CAAATAGAATTTACGAAAAAATTACAGTTAA-TTAACGAACGGTAAACTTGTGTCAACAGAAGAA
65 CAAAT-GAATTTACGAAAAAATTACAGTTAATTTAACAAACGGCAAACTTGTGTCAACAGAAGAA
** * *
44045 TTACAGTTGTCAAATTTATTATATTGACAAATGGAATTTACGGAAGAATTACAGTTAATTTAACG
129 TTACA-TCATCAAATTTATTATATTGACAAATAGAATTTACGGAAGAATTACAATTAATTTAACG
* * * *
44110 AACGACAAACTTTTGCCAACAGAAGAATTACAGTTGTCATATTTATTATATTGACAAATGGAATT
193 AACGACAAACTTGTGCCAACAGAAGAATTACAATTGTCAAATTTATTATATTGACAAATGAAATT
*
44175 TACGGAAGAATTAAG
258 TACGAAAGAATTAAG
* *
44190 TTAATTTAACGAACGGCAAACTTT-TGCCAACAGAAGAATTACAGTTGTCAAATTTATTATATTG
1 TTAATTTAACGAATGGCAAA-TTTGTGTCAACAG-AGAATTACAGTTGTCAAATTTATTATATTG
* *
44254 ACAAATGGAATTTACGGAAGAATTACAG
64 ACAAAT-GAATTTACGAAAAAATTACAG
44282 GTGTTCAATT
Statistics
Matches: 327, Mismatches: 32, Indels: 14
0.88 0.09 0.04
Matches are distributed among these distances:
273 35 0.11
274 275 0.84
275 17 0.05
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (272 bp):
TTAATTTAACGAATGGCAAATTTGTGTCAACAGAGAATTACAGTTGTCAAATTTATTATATTGAC
AAATGAATTTACGAAAAAATTACAGTTAATTTAACAAACGGCAAACTTGTGTCAACAGAAGAATT
ACATCATCAAATTTATTATATTGACAAATAGAATTTACGGAAGAATTACAATTAATTTAACGAAC
GACAAACTTGTGCCAACAGAAGAATTACAATTGTCAAATTTATTATATTGACAAATGAAATTTAC
GAAAGAATTAAG
Found at i:44187 original size:48 final size:47
Alignment explanation
Indices: 44039--44398 Score: 285
Period size: 48 Copynumber: 7.7 Consensus size: 47
44029 TGTGTCAACA
44039 GAAGAATTACAGTTGTCAAATTTATTATATTGACAAATGGAATTTACG
1 GAAGAATTACAGTTGTC-AATTTATTATATTGACAAATGGAATTTACG
* ** ******* *
44087 GAAGAATTACAG-T-T-AATTTA--ACGAACGACAAACTTTTGCCAACA
1 GAAGAATTACAGTTGTCAATTTATTA-TATTGACAAA-TGGAATTTACG
44131 GAAGAATTACAGTTGTCATATTTATTATATTGACAAATGGAATTTACG
1 GAAGAATTACAGTTGTCA-ATTTATTATATTGACAAATGGAATTTACG
* ** * ******* *
44179 GAAGAATTA-AG-T-T-AATTTA--ACGAACGGCAAACTTTTGCCAACA
1 GAAGAATTACAGTTGTCAATTTATTA-TATTGACAAA-TGGAATTTACG
44222 GAAGAATTACAGTTGTCAAATTTATTATATTGACAAATGGAATTTACG
1 GAAGAATTACAGTTGTC-AATTTATTATATTGACAAATGGAATTTACG
*
44270 GAAGAATTACAGGTGTTCAATTTATTATATTGACAAATGGAATTTACG
1 GAAGAATTACAGTTG-TCAATTTATTATATTGACAAATGGAATTTACG
* * *
44318 GAAGAATTACAGGTGTTCAATTTATTATATTGACAAATAGAATTTACA
1 GAAGAATTACAGTTG-TCAATTTATTATATTGACAAATGGAATTTACG
*
44366 GAA-AGTTTACAGTTGTCCAATTTATTATATTGA
1 GAAGA-ATTACAGTTGT-CAATTTATTATATTGA
44399 GTAGAATCTA
Statistics
Matches: 241, Mismatches: 51, Indels: 40
0.73 0.15 0.12
Matches are distributed among these distances:
41 1 0.00
42 7 0.03
43 24 0.10
44 24 0.10
45 3 0.01
46 4 0.02
47 6 0.02
48 155 0.64
49 15 0.06
50 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (47 bp):
GAAGAATTACAGTTGTCAATTTATTATATTGACAAATGGAATTTACG
Found at i:47525 original size:30 final size:30
Alignment explanation
Indices: 47489--47549 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
47479 CGCTGTCTTT
47489 ATTTATCGACTACGTTGACAGAGGAAGTTC
1 ATTTATCGACTACGTTGACAGAGGAAGTTC
*
47519 ATTTATCGACTATGTTGACAGAGGAAGTTC
1 ATTTATCGACTACGTTGACAGAGGAAGTTC
47549 A
1 A
47550 ACCCATGGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (30 bp):
ATTTATCGACTACGTTGACAGAGGAAGTTC
Found at i:58192 original size:21 final size:24
Alignment explanation
Indices: 58140--58187 Score: 78
Period size: 26 Copynumber: 1.9 Consensus size: 24
58130 AAAATTCGTG
58140 ATTAAACTTACATATTCAATTCTATA
1 ATTAAACTTACATATTCAA-T-TATA
58166 ATTAAACTTACATATTCAATTA
1 ATTAAACTTACATATTCAATTA
58188 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.09
25 1 0.05
26 19 0.86
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTAAACTTACATATTCAATTATA
Found at i:63314 original size:26 final size:26
Alignment explanation
Indices: 63278--63329 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
63268 CATCAAACAC
63278 CCTTATATATATATCTATATAGTCAT
1 CCTTATATATATATCTATATAGTCAT
63304 CCTTATATATATATCTATATAGTCAT
1 CCTTATATATATATCTATATAGTCAT
63330 GTACAAGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (26 bp):
CCTTATATATATATCTATATAGTCAT
Found at i:64118 original size:2 final size:2
Alignment explanation
Indices: 64111--64145 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
64101 CATCACAATC
64111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64146 GCATTAATCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:79978 original size:104 final size:105
Alignment explanation
Indices: 79796--79986 Score: 321
Period size: 104 Copynumber: 1.8 Consensus size: 105
79786 ATCAAAATTC
79796 TCATAATTATAATTCCATATATTGATAAAATTAAAAAAATATTAATATTAATATTAATATTTGAT
1 TCATAATTATAATTCCATATATTGATAAAATT-AAAAAATATTAATATTAATATTAATATTTGAT
79861 TAAATAATTTGCCATACTAAAATAAGTAGAAGCAAAAAAAA
65 TAAATAATTTGCCATACTAAAATAAGTAGAAGCAAAAAAAA
* * * * *
79902 TCATAATTATAGTTCCATATATTGATAAAATT-AAATATATTATTGTTATTATTAATATTTGATT
1 TCATAATTATAATTCCATATATTGATAAAATTAAAAAATATTAATATTAATATTAATATTTGATT
79966 AAATAATTTGCCATACTAAAA
66 AAATAATTTGCCATACTAAAA
79987 AAAACTAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
104 49 0.61
106 31 0.39
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (105 bp):
TCATAATTATAATTCCATATATTGATAAAATTAAAAAATATTAATATTAATATTAATATTTGATT
AAATAATTTGCCATACTAAAATAAGTAGAAGCAAAAAAAA
Found at i:82168 original size:39 final size:39
Alignment explanation
Indices: 82114--82192 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
82104 CAATTTTCTA
82114 TAATCGTAATAGTAGAACAGTATGCTTTAAAGTTCTGGT
1 TAATCGTAATAGTAGAACAGTATGCTTTAAAGTTCTGGT
*
82153 TAATCGTAATAGTAGAACTGTATGCTTTAAAGTTCTGGT
1 TAATCGTAATAGTAGAACAGTATGCTTTAAAGTTCTGGT
82192 T
1 T
82193 GCATTCTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (39 bp):
TAATCGTAATAGTAGAACAGTATGCTTTAAAGTTCTGGT
Found at i:88469 original size:21 final size:21
Alignment explanation
Indices: 88430--88470 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
88420 TAATAGGGCA
* **
88430 GATGATGATATGGGTGATGAG
1 GATGATGACATGGCAGATGAG
88451 GATGATGACATGGCAGATGA
1 GATGATGACATGGCAGATGA
88471 TGGGGAGGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.39, T:0.24
Consensus pattern (21 bp):
GATGATGACATGGCAGATGAG
Found at i:88481 original size:12 final size:12
Alignment explanation
Indices: 88466--88512 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
88456 TGACATGGCA
*
88466 GATGATGGGGAG
1 GATGATGAGGAG
*
88478 GATGATGAGGAT
1 GATGATGAGGAG
*
88490 GATGATGAGGGG
1 GATGATGAGGAG
*
88502 GAGGATGAGGA
1 GATGATGAGGA
88513 TGAGGATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.53, T:0.17
Consensus pattern (12 bp):
GATGATGAGGAG
Found at i:88493 original size:24 final size:24
Alignment explanation
Indices: 88466--88515 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
88456 TGACATGGCA
*
88466 GATGATG-GGGAGGATGATGAGGAT
1 GATGATGAGGG-GGAGGATGAGGAT
88490 GATGATGAGGGGGAGGATGAGGAT
1 GATGATGAGGGGGAGGATGAGGAT
88514 GA
1 GA
88516 GGATATAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.52, T:0.18
Consensus pattern (24 bp):
GATGATGAGGGGGAGGATGAGGAT
Found at i:88511 original size:6 final size:6
Alignment explanation
Indices: 88481--88519 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
88471 TGGGGAGGAT
* **
88481 GATGAG GATGAT GATGAG GGGGAG GATGAG GATGAG GAT
1 GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG GAT
88520 ATAGCAGAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.51, T:0.18
Consensus pattern (6 bp):
GATGAG
Found at i:97567 original size:332 final size:327
Alignment explanation
Indices: 95719--100739 Score: 3889
Period size: 332 Copynumber: 15.2 Consensus size: 327
95709 TTTGATTAGT
* * * ** * * * *
95719 TAAAATTTTGCAAAAATTTACCCAAAATATTTTTCATTAATTTTTAGCCAAAAATACTCATAAAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGGTTTTTCCTCAATTTTTGGCC-ACAATACTCAT-AAA
* * ** * *
95784 AATTTATAATTCGATGTAAAAAAGATTG-AAGGTTTTTTCACGCTTTTAATATCGTTTTTCCTAT
64 AATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCTAT
* * * * * ** * * *
95848 TTTCTCAGAATTAATTTAC-GATTAAATTGAAACATTATTCAAATGCTTGTAAAAAAAAAAAATC
129 TTTTTCTGAATTAATTT-CTAATAAAATCGAAACAAGATTCAGATGCTCGT---AAAAACAAATC
** * * *
95912 CTTAAATCCAATGTGGCTGAGATTTGGTTAGAAAAATATATATATTTTAATGAGTCTT-GAC-AC
190 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGT-TTGGGCGAC
** * * * * * * ** *
95975 AAAAAATCATGCAAAACTGAATCGAGGCTACGGAATGCATTTTCAACAAAAAACCGTGAT-GCT-
254 AAAAAA-CATGCAAAACTGAGCCG-GGCT-CGAAACGCGTTTTTAGC-CAAAATTGTGATGGATA
*
96038 ACACGATTTCGG-
315 ATACGATTTCGGC
* * * *
96050 TAAAATTTTACAAAAACTTACCCGAAA--TATTTTCCTCAATTTTCGGCCACAATACTCATAAAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGGT-TTTTCCTCAATTTTTGGCCACAATACTCAT-AAA
* * * * * * *
96113 AATAAATAATTAAACG-TAAAATGATTGAAGGGT-TTTTCACACTTCTAATATCGTTTTTCCCTA
64 AATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTT-CCTA
* * * * *
96176 TTTTTTATGAATT-ATTATTTAATAAAATCGAAATAAGATTCCGATGCTTGTAAAAACAAATCCT
128 TTTTTTCTGAATTAATT-TCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
* *
96240 TAAATCCAATGTGGCTGAGATTTGGTTAGAAGAATATAGATATTGTAACGAGTTTGGGC-ACAAA
192 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACAAA
* * * **
96304 AAATCATGCAAAACTGAGTCGAGGCTCGAAACACGTATTTAGCCAAAACACGTGATGGATAGTAT
257 AAA-CATGCAAAACTGAGCCG-GGCTCGAAACGCGTTTTTAGCCAAAA-TTGTGATGGATA--AT
96369 ACGATTTCGGC
317 ACGATTTCGGC
* ** * **
96380 TAAAATTTTGCAAAAACTGCCCCGGAAGGTTTTTTCTCAAATTTTT-GCCACAATGTTCATCAAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGGTTTTTCCTC-AATTTTTGGCCACAATACTCAT-AAA
* * * * * **
96444 AATATATAATTCAGTGCCAAAAAGATTG-AAGGGCTTTTAACGCTTCTAATATTGTTCTTATTA-
64 AATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCTAT
*
96507 TTTTTC-GAATTAATTTCTAATAAAATCGAAACAAGAATT-TGATGCTCGTAAAAACAAATCCTT
129 TTTTTCTGAATTAATTTCTAATAAAATCGAAACAAG-ATTCAGATGCTCGTAAAAACAAATCCTT
* *
96570 AAATCCATTGTGGCTGAGATTTGGTTAGATGAATAGAGATATTTTAACGAGTTTGGGC-ACAAAA
193 AAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACAAAA
* * * * *
96634 AATCATGCAAAACTGAGCCCGGATCCGGAACGCGTTTTTAGCCAAAACTCGTGATGGATAGTACA
258 AA-CATGCAAAACTGAGCCGGGCT-CGAAACGCGTTTTTAGCCAAAA-TTGTGATGGATAATAC-
***
96699 TGATTTCATT
319 -GATTTCGGC
* * * *
96709 TAAAATTTTGCAAAAACTGTCCCTAAAGGTTTTTCCTAAAATTTTGGCCACAAAACTCATAAGAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGGTTTTTCCTCAATTTTTGGCCACAATACTCATAA-AA
* * * * * *
96774 ATATATAATTCAATACCAAAAAGATCGAATGG-CGTTTCACGATTCTAATATC-ATTTTCCTATT
65 ATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCTATT
* * * * * * *
96837 TTTTCTGAATTAATTTTTGATTAAATTGACACATGATTCAGATGCTCGTAAGAAA-AATTCCTTA
130 TTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAA-AAACAAATCCTTA
* *
96901 AATCCAATGTGGCTGAGATTTCGTTAGATGAATATAGATATTTTAACGAGTTTTGGC-ACCAAAA
194 AATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGA-CAAAA
* ** * *
96965 ATCATGCAAAACACAGCCGGGGCCCGGAACGCGTTTTTAGCCAAAATTCGTGAT-G------CGA
258 AACATGCAAAACTGAGCC-GGGCTCGAAACGCGTTTTTAGCCAAAATT-GTGATGGATAATACGA
97023 TTTCGGC
321 TTTCGGC
* * * ** * *
97030 AAAAATTTTGTAAAAAGTGACCCGTAAATTTTTTTTCTCAATTTTTGGCCACAATACTCGTAAAA
1 TAAAATTTTGCAAAAACTGACCC-TAAAGGTTTTTCCTCAATTTTTGGCCACAATACTCATAAAA
* * * * * * * * *
97095 GTTTTATAATTTAATGCTAAAAA-ATTG-AAGGGCTTTTCACACTTTTAATATTGTTTTTCCTTT
65 -ATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCC-TA
* * *
97158 TTTTTTCCGAAAT-ATTATCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCT
128 TTTTTTCTGAATTAATT-TCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
* * * *
97222 TAAATCCAATGTGGCTGAGATTTGTTTATATGAATATAGAT-TTTTCAACGCGTTTGGGCGCCAA
192 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTT-AACGAGTTTGGGCGACAA
* * *
97286 AAAACAAGCAAAACTGAGCCGTGGCTCGAAATGCGTTTTTAGGCAAAATGTGTGATGGATAATAC
256 AAAACATGCAAAACTGAGCCG-GGCTCGAAACGCGTTTTTAGCCAAAAT-TGTGATGGATAATAC
97351 GCTATTTCGGC
319 G--ATTTCGGC
* * *
97362 TAAAATTTTGCAAAATCTGACCATAAAGGTTTTTCCTCAATTTTTGGCCACAACACTCATATAAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGGTTTTTCCTCAATTTTTGGCCACAATACTCATA-AAA
* * * *
97427 ATTTATAATTCAACGCC-AAAAGTATTGAAAGGTCTTCTAACGCTTCTAATATCGTTTTTCCTAT
65 ATATATAATTCAATGCCAAAAAG-ATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCTAT
* * ** ** * *
97491 TTTTTCTGAATTAATTTCAAATTAAATTTAAACCTGATTCAGATGCTCGTAAAAACAAATACTCA
129 TTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * *
97556 AATGCAATGTGGCTGAGATTTAGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGTCAAAAA
194 AATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACAAAAA
* * * * * * * * *
97621 TCATGCAAAACTGAGCCGGGACACGGAACGTGTTTTTTTTGTCAAAACCTGTGATGGATGGTACA
259 ACATGCAAAACTGAGCCGGG-CTCGAAACGCG--TTTTTAGCCAAAA-TTGTGATGGAT--AATA
*
97686 CGATTTCGAC
318 CGATTTCGGC
* * * * **
97696 TAAAAGTTTGCAAAAACTG-CCCGAAAGGTTTTTTCTCAAATTTTGGCCACAATTTTCATAAGAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGGTTTTTCCTCAATTTTTGGCCACAATACTCATAA-AA
* * * *
97760 ATATATAACTCAAGGCCAAAAAGATT-AAAGGTCTTTTCACGCTTCTAATATCATTTTTCCGATT
65 ATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCTATT
* * ** * *
97824 TTTTCTGAATAAATTTCTAATTAAATTTAAACATGATTCAGATGCTCGT-AAATCAAATCCTTAA
130 TTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
* * ** * * * * * *
97888 ATCTAATATTACTGAGAATTGGTTAGATGAGTATAAATATTTTAACGAGTTTGGGTGGCAAAAAT
195 ATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACAAAAAA
* * **
97953 CATGCAAAACTGAGCC-GGCACCTGGAACGCGTTTTTAGCCAAAACCCGTGATGGATAGTATACG
260 CATGCAAAACTGAGCCGGGC-TC-GAAACGCGTTTTTAGCCAAAA-TTGTGATGGATA--ATACG
*
98017 ATTT-GACC
320 ATTTCG-GC
* * * * * *
98025 CAAAA-TTT--------T-----T-----TTTTT-CTCAATTCTCGACCATAGTACT-CAT-A-A
1 TAAAATTTTGCAAAAACTGACCCTAAAGGTTTTTCCTCAATTTTTGGCC--A-CAATAC-TCATA
* * * * * *
98067 AAAATATATAATTCAATGCTAAAAACATTG-AAGGGCTTTTCACACTTCTAACATTGTTTTTCCT
62 AAAATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCT
* * * * *
98131 -TTTTTTC-GAAATAATATCTAATAAAATCAAAACCAGATTCTGATGCTCGTAAAAAATCAAATC
127 ATTTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGT-AAAAA-CAAATC
** * * * * * *
98194 CTTGGATCCAATGTAGCTTATATTTGGTTAGATGAATATGGATATTTTAACGAGTTTGGGTGCCA
190 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACA
* * * * *
98259 AAAATA-ATGCAAAACTGAGCCGGGACGCGGAACGAGTTTTTAGCCAAAACCTGTGATGGACAGT
255 AAAA-ACATGCAAAACTGAGCCGGG-CTCGAAACGCGTTTTTAGCCAAAA-TTGTGATGGATA--
* * *
98323 AGAAGATTTCAGC
315 ATACGATTTCGGC
* * * * **
98336 TAAAATTTTGCAAAAATTG-CCCGAAAGGTTTTTTTCTCAATTTTTCGCCACAATTTTCATAAGA
1 TAAAATTTTGCAAAAACTGACCCTAAAGG-TTTTTCCTCAATTTTTGGCCACAATACTCATAA-A
* ** * *
98400 AATCTATAAACCAATGCCAAAAAGATTG-AAGGGCTTTTCACGCTTCTAATATC--ATTTCCTCG
64 AATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCT--
* ** * *
98462 ATTTTTTCAT-AA-TAAGCTTT-TAATTAAATTTAAACATGATTCAGATTCTCGTAAAAACAAAT
127 ATTTTTTC-TGAATTAA--TTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * * * * *
98524 CCTTAAATCCAATATGGTTGAGATTTGTTTAGATGAATCTTGATATTTTAATGAGTTTGGGCGCC
189 CCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGAC
* * * * * * * *
98589 AAAAATCATGCAAAACTGAGCCGGGATCCGGAACACGTTTTTTGCCAAAACCTGTGATTGATAGT
254 AAAAAACATGCAAAACTGAGCCGGGCT-CGAAACGCGTTTTTAGCCAAAA-TTGTGATGGATAAT
*
98654 ACATGATTTCGGG
317 AC--GATTTCGGC
* * * **
98667 TAAAATTTTGCAAAAACTGCCCCGAAAGGATTTTTCC-CAAATTTTT-GACACAATTTTCATCAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGG-TTTTTCCTC-AATTTTTGGCCACAATACTCAT-AA
* * * ** * * *
98730 AAATATATAATTCAGTTCCAAAAAGATTG-AAGGACTTTGAACGCTTCTAAAATAGTTCTTCCTA
63 AAATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCTA
* * * * *
98794 TTATTTTTCCGAATTAGTTTCTAATAAAATCGAGACAAGATTCTGATGCACGTAAAAACAAATCC
128 -T-TTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * * * * **
98859 TTAAATGCAACGCGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTAGACTCCAA
191 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACAA
** * * * *
98924 AATTCATGCAAAACTGAGCCAGGAC-CTGGAACGCGTTTTTTGCCAAAACATGTGATGGATAGTA
256 AAAACATGCAAAACTGAGCC-GGGCTC-GAAACGCGTTTTTAGCCAAAA-TTGTGATGGATA--A
*
98988 CACGATTTCGGC
316 TACGATTTCGGC
* * **
99000 TAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCC-CAAATTTTT-GCCACAATTTTCATCAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGG-TTTTTCCTC-AATTTTTGGCCACAATACTCAT-AA
* * * * ** * * *
99063 AACTATATAATTTAGTGCCAAAAAGATTG-GAGGGATTTTAACGCTTCTAATATAGTTCTTCCTA
63 AAATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCTA
** * *
99127 TTATTTTCCAAATTAAATTCTAA-AAAGATCGAAATAAGATT-ATGATGCTCGTAAAAACAAATC
128 TT-TTTTCTGAATTAATTTCTAATAAA-ATCGAAACAAGATTCA-GATGCTCGTAAAAACAAATC
* * **
99190 CTTAAATGCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTAGGCTCCA
190 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACA
* * * * * *
99255 AAAATCATGCAAAACTGAGCTGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGATAGTA
255 AAAAACATGCAAAACTGAGCCGGG-CTCGAAACGCGTTTTTAGCCAAAA-TTGTGATGGATA--A
* **
99320 CACGATTTCAAC
316 TACGATTTCGGC
* * * * **
99332 TAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCC-CAAAATTTT-GACACAATTTTCATCAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGG-TTTTTCCTC-AATTTTTGGCCACAATACTCAT-AA
* * * * ** * * *
99395 AACTATATAATTCAGTGGCAAAGAGATTG-AAGGGATTTTAACGCTTCTAATATAGTTCTTCCTA
63 AAATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCTA
** * *
99459 TTATTTTCCAAATTAAATTCTAA-AAAGATCGAAATAAGATT-ATGATGCTCGTAAAAACAAATC
128 TT-TTTTCTGAATTAATTTCTAATAAA-ATCGAAACAAGATTCA-GATGCTCGTAAAAACAAATC
* * * * * * *
99522 CTTAAATGCAATGTGACTGAGATTTGTTTAAATGAATATAGGTATTTTAACGAGTTTGGACGCCA
190 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACA
* * * * * * * *
99587 AAAATCATGCAAAACTGAGCTGGGACCCGGAACGCGTTTTTTTGCCAAAACCTCTAATGGATAGT
255 AAAAACATGCAAAACTGAGCCGGG-CTCGAAACGCG-TTTTTAGCCAAAA-TTGTGATGGATA--
* *
99652 ACACGATTTCGAC
315 ATACGATTTCGGC
* * **
99665 TAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTCTCCAAAATTTTT-GCCACAAT-CTTCATCAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGGTTTT-TCCTCAATTTTTGGCCACAATAC-TCAT-AA
* * * * * * * **
99728 AAATATATATTTCAGTGCCCAAAAAGATTG-AAGGGCTTTTAACGCTTATAATATTGTTCTAACT
63 AAATATATAATTCAATG-CCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCT
* * * * *
99792 ATTATTTTCCGAATTAAATTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATAC
127 ATT-TTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * * *
99857 TTAAATCCAACGTGGCTAAGA-TTGGCTTAGATAAATATAGATATTTTAACGAGTTTGGGC-TCA
191 TTAAATCCAATGTGGCTGAGATTTGG-TTAGATGAATATAGATATTTTAACGAGTTTGGGCGACA
* * * * * * *
99920 AAAAATCATGCAAAACAGAGCCGGACCCGAAACACGGTTTTTTGCCAAAACCTATGATGGATAGT
255 AAAAA-CATGCAAAACTGAGCCGGGCTCGAAACGC-GTTTTTAGCCAAAA-TTGTGATGGATA--
* *
99985 ACACGATTTCGGT
315 ATACGATTTCGGC
* * ** *
99998 TAAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTT-GCCACAAT-TTCCATCA
1 T-AAAATTTTGCAAAAACTGACCCTAAAGG-TTTTTCCTCAATTTTTGGCCACAATACT-CAT-A
* * * * * *
100061 AAAATATATAATTCAGTGCCAAAAAGATTG-AAGGGCATTTAACGCTTCTAATATAGTTCTTCCT
62 AAAATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCT
* * *
100125 ATTATTTTCCGAATTAAATTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCC
127 ATT-TTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * **
100190 TTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAATTTGGGCTCCAA
191 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACAA
* * * * * * *
100255 AAATCATGGAAAACTGAGCCGGGACTCGGAATGCGTTTTTTGCCAAAACCTGTGATTGATAGTAT
256 AAAACATGCAAAACTGAGCCGGG-CTCGAAACGCGTTTTTAGCCAAAA-TTGTGATGGATA--AT
**
100320 ACGATTTCGAT
317 ACGATTTCGGC
* * ** **
100331 TAAAATTTTGCAAATACT-ACCCCGAAAGGTTTTTTTTTCCAAATTTTT-GCCACAATTTTCATC
1 TAAAATTTTGCAAAAACTGA-CCCTAAAGG-TTTTTCCT-C-AATTTTTGGCCACAATACTCAT-
* ** * * * * **
100394 AAAAATATATAATTCAGTGCCAAAAAGATTG-AAGGGATTTTAACGCATCTAAAATGGTTCATCC
61 AAAAATATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCC
* *
100458 TATTATTTTCTGAATTATTTTCTAATAAAATCGAAA-AAGATTCTA-ATGCTCGTAAATACAAAT
126 TATT-TTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTC-AGATGCTCGTAAAAACAAAT
* * * *
100521 CCTTAAATGCAATGTGGCTGCGATTTGGCT--ATGAATATAGATATTTTAACGAGTTTGGGC-TC
189 CCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGAC
* * * * * * *
100583 AAAAAATCATGCAACACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATCGTTAG
254 AAAAAA-CATGCAAAACTGAGCCGGG-CTCGAAACGCGTTTTTAGCCAAAA-TTGTGATGGATA-
* *
100648 TACACGATTTCGGT
315 -ATACGATTTCGGC
* * * * ** **
100662 TAAAATTTTGCAAATACTGTCTCGAAAGGTTTTTTTTCCAAATTTTT-GCCACAATTTTCATCAA
1 TAAAATTTTGCAAAAACTGACCCTAAAGGTTTTTCCT-C-AATTTTTGGCCACAATACTCAT-AA
100726 AAATATATAATTCA
63 AAATATATAATTCA
100740 GTTC
Statistics
Matches: 3968, Mismatches: 562, Indels: 321
0.82 0.12 0.07
Matches are distributed among these distances:
308 34 0.01
309 7 0.00
310 65 0.02
311 129 0.03
312 8 0.00
313 4 0.00
320 5 0.00
321 45 0.01
322 66 0.02
323 144 0.04
324 6 0.00
325 18 0.00
326 95 0.02
327 3 0.00
328 58 0.01
329 381 0.10
330 260 0.07
331 587 0.15
332 814 0.21
333 814 0.21
334 410 0.10
335 11 0.00
336 4 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (327 bp):
TAAAATTTTGCAAAAACTGACCCTAAAGGTTTTTCCTCAATTTTTGGCCACAATACTCATAAAAA
TATATAATTCAATGCCAAAAAGATTGAAAGGTCTTTTCACGCTTCTAATATCGTTTTTCCTATTT
TTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
TCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCGACAAAAAAC
ATGCAAAACTGAGCCGGGCTCGAAACGCGTTTTTAGCCAAAATTGTGATGGATAATACGATTTCG
GC
Found at i:98963 original size:333 final size:332
Alignment explanation
Indices: 98061--100741 Score: 3523
Period size: 333 Copynumber: 8.1 Consensus size: 332
98051 ACCATAGTAC
* * * * * * * * * *
98061 TCATAAAAAATATATAATTCAATGCTAAAAACATTGAAGGGCTTTTCACACTTCTAACATTGTTT
1 TCATCAAAAATATATAATTCAGTGCCAAAAAGATTGAAGGACTTTTAACGCTTCTAATATAGTTC
* * *
98126 TTCCT-TT-TTTT-CGAAAT-AATATCTAATAAAATCAAAACCAGATTCTGATGCTCGTAAAAAA
66 TTCCTATTATTTTCCGAATTAAAT-TCTAATAAAATCGAAACAAGATTCTGATGCTCGT-AAAAA
** * * * *
98187 TCAAATCCTTGGATCCAATGTAGCTTATATTTGGTTAGATGAATATGGATATTTTAACGAGTTTG
129 -CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTG
* * * *
98252 GG-TGCCAAAAATAATGCAAAACTGAGCCGGGACGCGGAACGAGTTTTTAGCCAAAACCTGTGAT
193 GGCT-CCAAAAATCATGCAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGAT
* * * * * *
98316 GGACAGTAGAAGATTTCAGCTAAAATTTTGCAAAAATTG-CCCGAAAGGTTTTTTTCTC-AATTT
257 GGATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGCCCCGAAAGG-TTTTTTCCCAAATTT
98379 TTCGCCACAATTT
321 TT-GCCACAATTT
* ** * * * *
98392 TCAT-AAGAAATCTATAAACCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATT
1 TCATCAA-AAATATATAATTCAGTGCCAAAAAGATTGAAGGACTTTTAACGCTTCTAATAT-AGT
* * ** * * * ** * * *
98456 TCCT-CGATT-TTTTCATAA-TAAGCTTTTAATTAAATTTAAACATGATTCAGATTCTCGTAAAA
64 TCTTCCTATTATTTTCCGAATTAA-ATTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAA
* * * * * *
98518 ACAAATCCTTAAATCCAATATGGTTGAGATTTGTTTAGATGAATCTTGATATTTTAATGAGTTTG
128 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTG
* * * *
98583 GGCGCCAAAAATCATGCAAAACTGAGCCGGGATCCGGAACACGTTTTTTGCCAAAACCTGTGATT
193 GGCTCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATG
* * *
98648 GATAGTACATGATTTCGGGTAAAATTTTGCAAAAACTGCCCCGAAAGGATTTTTCCCAAATTTTT
258 GATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCCAAATTTTT
*
98713 GACACAATTT
323 GCCACAATTT
* * *
98723 TCATCAAAAATATATAATTCAGTTCCAAAAAGATTGAAGGACTTTGAACGCTTCTAAAATAGTTC
1 TCATCAAAAATATATAATTCAGTGCCAAAAAGATTGAAGGACTTTTAACGCTTCTAATATAGTTC
** * *
98788 TTCCTATTATTTTTCCGAATTAGTTTCTAATAAAATCGAGACAAGATTCTGATGCACGTAAAAAC
66 TTCCTATTA-TTTTCCGAATTAAATTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAAC
* * * * *
98853 AAATCCTTAAATGCAACGCGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTAGA
130 AAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGG
* * * *
98918 CTCCAAAATTCATGCAAAACTGAGCCAGGACCTGGAACGCGTTTTTTGCCAAAACATGTGATGGA
195 CTCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGA
98983 TAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCCAAATTTTTGC
260 TAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCCAAATTTTTGC
99048 CACAATTT
325 CACAATTT
* * *
99056 TCATCAAAACTATATAATTTAGTGCCAAAAAGATTGGAGGGA-TTTTAACGCTTCTAATATAGTT
1 TCATCAAAAATATATAATTCAGTGCCAAAAAGATT-GAAGGACTTTTAACGCTTCTAATATAGTT
* * *
99120 CTTCCTATTATTTTCCAAATTAAATTCTAA-AAAGATCGAAATAAGATTATGATGCTCGTAAAAA
65 CTTCCTATTATTTTCCGAATTAAATTCTAATAAA-ATCGAAACAAGATTCTGATGCTCGTAAAAA
* *
99184 CAAATCCTTAAATGCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTAG
129 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGG
*
99249 GCTCCAAAAATCATGCAAAACTGAGCTGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGG
194 GCTCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGG
** *
99314 ATAGTACACGATTTCAACTAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCCAAAATTTTG
259 ATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCCAAATTTTTG
*
99379 ACACAATTT
324 CCACAATTT
* * *
99388 TCATCAAAACTATATAATTCAGTGGCAAAGAGATTGAAGGGA-TTTTAACGCTTCTAATATAGTT
1 TCATCAAAAATATATAATTCAGTGCCAAAAAGATTGAA-GGACTTTTAACGCTTCTAATATAGTT
* * *
99452 CTTCCTATTATTTTCCAAATTAAATTCTAA-AAAGATCGAAATAAGATTATGATGCTCGTAAAAA
65 CTTCCTATTATTTTCCGAATTAAATTCTAATAAA-ATCGAAACAAGATTCTGATGCTCGTAAAAA
* * * * *
99516 CAAATCCTTAAATGCAATGTGACTGAGATTTGTTTAAATGAATATAGGTATTTTAACGAGTTTGG
129 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGG
* * * * *
99581 ACGCCAAAAATCATGCAAAACTGAGCTGGGACCCGGAACGCGTTTTTTTGCCAAAACCTCTAATG
194 GCTCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAACGCG-TTTTTTGCCAAAACCTGTGATG
* * *
99646 GATAGTACACGATTTCGACTAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTCTCCAAAATTTTT
258 GATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCCAAATTTTT
*
99711 GCCACAATCT
323 GCCACAATTT
* * * *
99721 TCATCAAAAATATATATTTCAGTGCCCAAAAAGATTGAAGGGCTTTTAACGCTTATAATATTGTT
1 TCATCAAAAATATATAATTCAGTG-CCAAAAAGATTGAAGGACTTTTAACGCTTCTAATATAGTT
** *
99786 CTAACTATTATTTTCCGAATTAAATTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAAC
65 CTTCCTATTATTTTCCGAATTAAATTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAAC
* * * *
99851 AAATACTTAAATCCAACGTGGCTAAGA-TTGGCTTAGATAAATATAGATATTTTAACGAGTTTGG
130 AAATCCTTAAATCCAATGTGGCTGAGATTTGG-TTAGATGAATATAGATATTTTAACGAGTTTGG
* * * * *
99915 GCTCAAAAAATCATGCAAAACAGAGCC-GGACCCGAAACACGGTTTTTTGCCAAAACCTATGATG
194 GCTCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAACGC-GTTTTTTGCCAAAACCTGTGATG
* *
99979 GATAGTACACGATTTCGGTTAAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTT
258 GATAGTACACGATTTCGGCT-AAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCCAAATTTT
100044 TGCCACAATTT
322 TGCCACAATTT
* * *
100055 CCATCAAAAATATATAATTCAGTGCCAAAAAGATTGAAGGGCATTTAACGCTTCTAATATAGTTC
1 TCATCAAAAATATATAATTCAGTGCCAAAAAGATTGAAGGACTTTTAACGCTTCTAATATAGTTC
100120 TTCCTATTATTTTCCGAATTAAATTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACA
66 TTCCTATTATTTTCCGAATTAAATTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACA
* *
100185 AATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAATTTGGGC
131 AATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGC
* * * *
100250 TCCAAAAATCATGGAAAACTGAGCCGGGACTCGGAATGCGTTTTTTGCCAAAACCTGTGATTGAT
196 TCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGAT
* ** * * *
100315 AGTATACGATTTCGATTAAAATTTTGCAAATACTACCCCGAAAGGTTTTTTTTTCCAAATTTTTG
261 AGTACACGATTTCGGCTAAAATTTTGCAAAAACTGCCCCGAAAGG--TTTTTTCCCAAATTTTTG
100380 CCACAATTT
324 CCACAATTT
* * *
100389 TCATCAAAAATATATAATTCAGTGCCAAAAAGATTGAAGGGA-TTTTAACGCATCTAAAATGGTT
1 TCATCAAAAATATATAATTCAGTGCCAAAAAGATTGAA-GGACTTTTAACGCTTCTAATATAGTT
* * ** * *
100453 CATCCTATTATTTTCTGAATTATTTTCTAATAAAATCGAAA-AAGATTCTAATGCTCGTAAATAC
65 CTTCCTATTATTTTCCGAATTAAATTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAAC
* * *
100517 AAATCCTTAAATGCAATGTGGCTGCGATTTGGCT--ATGAATATAGATATTTTAACGAGTTTGGG
130 AAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGG
* * * *
100580 CTCAAAAAATCATGCAACACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATCGT
195 CTCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGA
* * * * *
100645 TAGTACACGATTTCGGTTAAAATTTTGCAAATACTGTCTCGAAAGGTTTTTTTTCCAAATTTTTG
260 TAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGCCCCGAAAGG-TTTTTTCCCAAATTTTTG
100710 CCACAATTT
324 CCACAATTT
100719 TCATCAAAAATATATAATTCAGT
1 TCATCAAAAATATATAATTCAGT
100742 TC
Statistics
Matches: 2087, Mismatches: 234, Indels: 59
0.88 0.10 0.02
Matches are distributed among these distances:
330 58 0.03
331 392 0.19
332 515 0.25
333 743 0.36
334 374 0.18
335 5 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (332 bp):
TCATCAAAAATATATAATTCAGTGCCAAAAAGATTGAAGGACTTTTAACGCTTCTAATATAGTTC
TTCCTATTATTTTCCGAATTAAATTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACA
AATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGC
TCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGAT
AGTACACGATTTCGGCTAAAATTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCCAAATTTTTGCC
ACAATTT
Done.