Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021138.1 Corchorus olitorius cultivar O-4 contig21171, 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: 76421
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:26760 original size:15 final size:15
Alignment explanation
Indices: 26740--26772 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
26730 TGGGTTAGAG
26740 ATAATCCGTCTTCAT
1 ATAATCCGTCTTCAT
26755 ATAATCCGTCTTCAT
1 ATAATCCGTCTTCAT
26770 ATA
1 ATA
26773 TATATATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.39
Consensus pattern (15 bp):
ATAATCCGTCTTCAT
Found at i:27094 original size:23 final size:23
Alignment explanation
Indices: 27045--27094 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
27035 GTCAAGTCAG
*
27045 TGAGGTCCACTTTTTGAGTATTG
1 TGAGGTCCACTTTTTGAGTATTA
*
27068 TGAGGTCCACTTTTTGAGTGTTA
1 TGAGGTCCACTTTTTGAGTATTA
27091 TGAG
1 TGAG
27095 TGTTTGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.42
Consensus pattern (23 bp):
TGAGGTCCACTTTTTGAGTATTA
Found at i:35347 original size:24 final size:24
Alignment explanation
Indices: 35320--35365 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
35310 AAAGGAGTTC
*
35320 AAAACAAGCAGCCAGAAATAAGAA
1 AAAAAAAGCAGCCAGAAATAAGAA
* * *
35344 AAAAAAAGGAGGCATAAATAAG
1 AAAAAAAGCAGCCAGAAATAAG
35366 GAAGTAAGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.63, C:0.11, G:0.20, T:0.07
Consensus pattern (24 bp):
AAAAAAAGCAGCCAGAAATAAGAA
Found at i:41772 original size:51 final size:51
Alignment explanation
Indices: 41696--41798 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
41686 AATCCTTGAG
* *
41696 TTCATTACAATCAGAATAAATCTCTATATGTCCAAACATTTAAATGAGAAA
1 TTCATTACAATCAGAATAAATCTCTATATGCCCAAACATCTAAATGAGAAA
41747 TTCATTACAATCAGAATAAATCTCTATATGCCCAAACATCTAAATGAGAAA
1 TTCATTACAATCAGAATAAATCTCTATATGCCCAAACATCTAAATGAGAAA
41798 T
1 T
41799 CAACTCAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (51 bp):
TTCATTACAATCAGAATAAATCTCTATATGCCCAAACATCTAAATGAGAAA
Found at i:41828 original size:25 final size:25
Alignment explanation
Indices: 41800--41850 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
41790 ATGAGAAATC
41800 AACTCAAATTAAAAAACTACCATAA
1 AACTCAAATTAAAAAACTACCATAA
41825 AACTCAAATTAAAAAACTACCATAA
1 AACTCAAATTAAAAAACTACCATAA
41850 A
1 A
41851 TAAACTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.20
Consensus pattern (25 bp):
AACTCAAATTAAAAAACTACCATAA
Found at i:41926 original size:61 final size:61
Alignment explanation
Indices: 41855--41976 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
41845 CATAAATAAA
** *
41855 CTATCTACCTATTAAATACACAAATAAACAAATTACAAACTAAACTCACGTTCCGTGAGAC
1 CTATCTACCTACCAAATACACAAATAAACAAATTACAAACTAAACTCACGCTCCGTGAGAC
41916 CTATCTACCTACCAAATACACAAATAAACAAATTACAAACTAAACTCACGCTCCGTGAGAC
1 CTATCTACCTACCAAATACACAAATAAACAAATTACAAACTAAACTCACGCTCCGTGAGAC
41977 TTGAACCCAG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.44, C:0.27, G:0.07, T:0.22
Consensus pattern (61 bp):
CTATCTACCTACCAAATACACAAATAAACAAATTACAAACTAAACTCACGCTCCGTGAGAC
Found at i:47957 original size:45 final size:45
Alignment explanation
Indices: 47893--47986 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
47883 GGATGTGTTC
47893 AATTTCGGCCTAAATCTAATTTGGCCTAAAAGCTTTCGTCAACCA
1 AATTTCGGCCTAAATCTAATTTGGCCTAAAAGCTTTCGTCAACCA
*
47938 AATTTGGGCCTAAATCTAATTTGGCCTAAAAGCTTTCGTCAACCA
1 AATTTCGGCCTAAATCTAATTTGGCCTAAAAGCTTTCGTCAACCA
47983 AATT
1 AATT
47987 ACGTCATCTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (45 bp):
AATTTCGGCCTAAATCTAATTTGGCCTAAAAGCTTTCGTCAACCA
Found at i:50023 original size:6 final size:6
Alignment explanation
Indices: 50012--50036 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
50002 AAAAAGCCTA
50012 ACTAGT ACTAGT ACTAGT ACTAGT A
1 ACTAGT ACTAGT ACTAGT ACTAGT A
50037 AGCAGTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
ACTAGT
Found at i:50636 original size:3 final size:3
Alignment explanation
Indices: 50628--50661 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
50618 ATCATAATGT
50628 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
50662 TATATATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:55061 original size:2 final size:2
Alignment explanation
Indices: 55054--55080 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55044 TATTAATTAC
55054 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 T
55081 TTGCAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61338 original size:78 final size:80
Alignment explanation
Indices: 61244--61389 Score: 224
Period size: 78 Copynumber: 1.9 Consensus size: 80
61234 TTCACCTTTC
* *
61244 TTTTTTGATCGTGCAAAAGTTCATGA-ATTCTCCATTAATGCTTT-CATGTTTTAATTCTCCATA
1 TTTTTTAATCGTGCAAAAGTTCATGATATTCTCCATTAATGCTTTACAAGTTTTAATTCTCCATA
61307 TTTATACCAATGTTG
66 TTTATACCAATGTTG
* * * *
61322 TTTTTTAATTGTGCAAAAGTTCATGATTTTTTCCATTAATGGTTTACAAGTTTTAATTCTCCATA
1 TTTTTTAATCGTGCAAAAGTTCATGATATTCTCCATTAATGCTTTACAAGTTTTAATTCTCCATA
61387 TTT
66 TTT
61390 TCTACCCATT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
78 24 0.40
79 15 0.25
80 21 0.35
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (80 bp):
TTTTTTAATCGTGCAAAAGTTCATGATATTCTCCATTAATGCTTTACAAGTTTTAATTCTCCATA
TTTATACCAATGTTG
Found at i:61987 original size:19 final size:19
Alignment explanation
Indices: 61965--62001 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
61955 AATTGATATC
61965 ATTACACCAAATAATGATG
1 ATTACACCAAATAATGATG
* *
61984 ATTACAGCAAATATTGAT
1 ATTACACCAAATAATGAT
62002 ATTTTTTCTA
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:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (19 bp):
ATTACACCAAATAATGATG
Found at i:68312 original size:25 final size:25
Alignment explanation
Indices: 68284--68347 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 25
68274 CTAGCTGTTT
68284 AATTTCATCTTTTGCATCTAATCTG
1 AATTTCATCTTTTGCATCTAATCTG
*
68309 AATTTCATTTTTTTTGCATCTAATCTG
1 AATTTCA--TCTTTTGCATCTAATCTG
*
68336 AATTTTATCTTT
1 AATTTCATCTTT
68348 GGACTGGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.32
27 23 0.68
ACGTcount: A:0.23, C:0.16, G:0.06, T:0.55
Consensus pattern (25 bp):
AATTTCATCTTTTGCATCTAATCTG
Found at i:72524 original size:333 final size:330
Alignment explanation
Indices: 71880--76421 Score: 3653
Period size: 333 Copynumber: 13.7 Consensus size: 330
71870 ATGCTTTGTT
* * * * * * * * *
71880 GCCAAAAATCGTGATGGTTAGTATATGATTTCGTCTAAAATTTTGTAAAAATTTATCT-GAAAGA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCGAAA-A
* * * * **
71944 AATTTCCTAAATTTTCT-G-CAACGATACTCATAAAAAATATATAATTTAACGCTGAAAAGATTG
65 ATTTTCCTCAATTTT-TGGCCAA-AATACTCAT-AAAAATATATAATTTAACACAAAAAAGATTG
** * * * * * ** ** * * *
72007 AAAAACTTTTCACGATTCTAATACCGATTTTCCTA-TTTTCCCCAAACTAATTTCTAGTTATATC
127 AAAGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAATC
** * * **
72071 GAAACATA-ATTCAGATGCTCGTAAAAACAAATTTTTAAATCCAATGTGGCTGAGATTTGGTTAG
192 GAAACA-AGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAG
* * * * * *
72135 ATGGATATAGATATTTCAATGAGTCTT-AGCGGCAAAAATGAAGCAAAACGGAGCCGAGGCCCCG
256 ATGAATATAGATATTTCAAGGAGTCTTGA-C-GCCAAAATCATGCAAAACTGAGCCGAGGCCCCG
*
72199 ACACGTGTTTTTTA
319 A-ACGCG-TTTTTA
* * * ** * * * *
72213 GGCAAAAACCGTGGTGGTTAATACATTATTTCGGCTAAAATTTTGCATAAATTGA-CTAGAAAGA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCGAAA-A
** * *
72277 ATTTTCCTCAATTTTTGGCCATGATGCTCATAAGAAATATATAATTCAACACAAAAAAGATTGAA
65 ATTTTCCTCAATTTTTGGCCAAAATACTCATAA-AAATATATAATTTAACACAAAAAAGATTGAA
* * * * * * *
72342 ATGCTATTCACGCTTCTAATATTGGTTTTCCTATTTTTTTC-GAATTAATTTCTAATTAAATCAA
129 AGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAATCGA
* * * * *
72406 AACATGATTCAGATGCTCGTAAAACCAAATCCTTAAATCCAATGTGGGTAAGATTTGATTAGATG
194 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATG
* * * * * * *
72471 AATATAGATATTTCAATGAGACTTGCCGCCAGAGATAATGCAAAACAGAGCCGAGGCTCCAGAAC
259 AATATAGATATTTCAAGGAGTCTTGACGCCA-AAATCATGCAAAACTGAGCCGAGGC-CCCGAAC
72536 GCGTTTTTA
322 GCGTTTTTA
* * * * * *
72545 GTCAACAACTGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAATTGACCT-G-AAAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCGAAAAA
* * * * * ** *
72608 TTTCTCCTCAATTTTGGGCCACAATACTAATAAAAAAAATATATAACTCAATGCCAAAAAGATTG
66 TTT-TCCTCAATTTTTGGCCAAAATACTCAT---AAAAATATATAATTTAACACAAAAAAGATTG
* * *
72673 -AAGAGCTTCTCATGCTTCTT-ATATCAG--TTTCCTATTTTTTT-TCGAATTAATTTCTAATTA
127 AAAG-GCTTTTCACGCTT-TTAATATC-GTTTTTCATATTTTTTTCT-GAATTAATTTCTAATTA
* * * * * * * * *
72733 AATTGAAA-ATGGATTGAGATGCTCATAAAAATAAAGTCCTTAAATCCAATGTGACTGAGATTTC
188 AATCGAAACA-AGATTCAGATGCTCGTAAAAACAAA-TCCTTAAATGCAATGTGGCTAAGATTTT
* * * * * * *
72797 GTTATATGAATATAGATATCTCAATGAGTTTTGGCGCCAAAATCATGCAAAACTGAGCCGGGGCC
251 ATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAATCATGCAAAACTGAGCCGAGGCC
72862 CCAGAACGCGTTTTTA
316 CC-GAACGCGTTTTTA
* * * ** * *** ** ** * * **
72878 GCCGAAGCAAAATTCAGATGCA-CGTAAAAACA-AATCTTTAAATCCAA-CGTGGATGAGATTTG
1 GCC--A--AAAA--CCG-TG-ATGGTTAGTACACGAT-TTTGGCTAAAATTTTGCA--AAAAAT-
** * * * ** * * *
72940 GTTAGAT-GTATATAGATTTT--TCAAGGAGTCTTGGTGCCAAAA-A-TCATGCAAA-A-CTGAG
54 G--ACCTCG-A-A-AAATTTTCCTC-A--A-TTTTTG-GCCAAAATACTCATAAAAATATATAAT
** * * *** * ** * ***
72998 CCAGGGCCCTGAAACGTGTTTTTAGCAAAAAACCCTGAAACGCTTTTAATATCGTTTTTCATATT
109 TTA--ACAC--AAAAAAG--ATT-G---AAAGGCTTTTCACGCTTTTAATATCGTTTTTCATATT
* *
73063 TTTTTCTGAATTGATTTCTAATTTAATCGAAACAAGATTCA-ATTGCTCGTAAAAACAAATCCTT
164 TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA-TGCTCGTAAAAACAAATCCTT
* * *
73127 AAATGCAAAGTGGCTAA-ATTTTTATTAGACGAATATAGATATTTCAAGGAGTCTTAACGCCAAA
228 AAATGCAATGTGGCTAAGA-TTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAA
*
73191 ATTCATGCAAAACTTAGCCG-GGACCCCGGAACGCGTTTTTA
292 A-TCATGCAAAACTGAGCCGAGG-CCCC-GAACGCGTTTTTA
* *
73232 GCCAAAAACCGTGAT-G---GTACACGATTTTAGCTAAAATTTTGCAAAAAATGACCGCGAAAAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCGAAAAA
* ** * * *
73293 TGTTTCCTTAATTTTT-GATAAAATACTCATAATATATATATAATTTAACGCCAAAAAATATTG-
66 T-TTTCCTCAATTTTTGGCCAAAATACTCATAA-AAATATATAATTTAAC-ACAAAAAAGATTGA
* * *
73356 GAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTT-TGAATTAATTTCCAATTCAATC
128 AAGG-CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAATC
* *
73419 GAAACAAGATTCAGCTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAA-ATTTTCATTAG
192 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTT-ATTAG
*
73483 ATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACCGAGCC-AGGGCCCCG
256 ATGAATATAGATATTTCAAGGAGTCTTGACGCC-AAAATCATGCAAAACTGAGCCGA-GGCCCC-
73547 GAACGCGTTTTTA
318 GAACGCGTTTTTA
* * * * * * *
73560 GTCAATAACCGTGATGGTTAGTGCACAATTTTGACTAAAATATTGCAAAAAACGA-C-CGAGAAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCGA-AAA
* ** * ** * * *
73623 TTTTTTTTCACTTTTTGGATAAATTACTCAT-AAAATATATAATTTAACGGCTAAAAA-ATTGGA
65 ATTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATATATAATTTAAC-ACAAAAAAGATT-GA
*
73686 GAA--CTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTCTAAATTAATTTCTAATTAAATC
128 -AAGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAATC
* * * * * * *
73748 GAAACAAGATCCAAATGCTCGTAAAAACAAATCCTTAAAGGCGATGTGGCTAGGTTTTTATTTGA
192 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGA
* * * *
73813 TGAATATAGATATTTCAAGGAGACTTAACGCCAAAATTCATGTAAAACTGAGCCGGGGCCCCGGA
257 TGAATATAGATATTTCAAGGAGTCTTGACGCCAAAA-TCATGCAAAACTGAGCCGAGGCCCC-GA
73878 ACGCGTTTTTA
320 ACGCGTTTTTA
* *
73889 GCTAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAG
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCGAAAA-
* * ** ** * *
73954 TTTTTCCTCAATTTTTTGATAAAATACTCATATAATTTATATAATCTT-ACACCAAAAATATTG-
65 ATTTTCCTCAATTTTTGGCCAAAATACTCATA-AAAATATATAAT-TTAACACAAAAAAGATTGA
* *
74017 GAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTCTGAATTAATTTCTAATTTAATC
128 AAGG-CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAATC
*
74081 GAAACAAGATTCA-ACTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAA-ATTTTTATTA
192 GAAACAAGATTCAGA-TGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGA-TTTTATTA
*
74144 GATGAATATAGATATTTCAAGGAGTCTTAACGCCAAAATTCATGCAAAACTGAGCCG-GGACCCC
255 GATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAA-TCATGCAAAACTGAGCCGAGG-CCCC
*
74208 GGGACGCGTTTTTA
318 -GAACGCGTTTTTA
* * *
74222 GCCAAAAACCGTGATGGTTACTACACGATTTTTGCTAAAATTTTGCAAAAAATGACCGCGAAAAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCGAAAAA
* *** * * *
74287 TGTTTCCTTAATTTTT-GATGAAATACTCATAATATATATATAATTTAACGTCAAAAAATATTG-
66 T-TTTCCTCAATTTTTGGCCAAAATACTCATAA-AAATATATAATTTAAC-ACAAAAAAGATTGA
* *
74350 GAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTT-TGAATTAATTTTTAATTAAATC
128 AAGG-CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAATC
* ** *
74413 GAAACAAGATTCA-ACTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAACTTTTTATGAG
192 GAAACAAGATTCAGA-TGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAG
* *
74477 AT-AAGTATAGATATTTCAAGGCA-TCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCC
256 ATGAA-TATAGATATTTCAAGG-AGTCTTGACGCC-AAAATCATGCAAAACTGAGCCGAGGCCCC
* *
74540 ATAACGCGTTTATA
318 -GAACGCGTTTTTA
* * * * * * *
74554 GTCAATAACCGTGAT-GCTAGTGCACAATTTTGACTAAAATTTTGCAAAAAATGACCGCGAAAAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCG-AAAA
* ** **
74618 ATTTTCCTCAAGTTTTGGATAAAATACTCATAAAATATATATAATTTAATGTC-AAAAAGATTTG
65 ATTTTCCTCAATTTTTGGCCAAAATACTCATAAAA-ATATATAATTTAA-CACAAAAAAGA-TTG
* * * *
74682 -AGGGACTTTTCACGCTTTTAATATCGTTTTTCATAATTTTTTCTAAATTAA-TTCTAACTAAAT
127 AAAGG-CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAAT
* * * * *
74745 CGAAACAAGATTCAAATGGTCGTAAAAACAAATCCTTAAATGAAATGTGGCTAAGTTTTTATTAT
191 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAG
* * *
74810 ATGAATATAGATATTTCAAGGAGTCTTGATGCCAAAAATCATGTAAAACTGAGTCG-GAGCCCCG
256 ATGAATATAGATATTTCAAGGAGTCTTGACGCC-AAAATCATGCAAAACTGAGCCGAG-GCCCCG
74874 TAACGCGTTTTTA
319 -AACGCGTTTTTA
* * *
74887 GCCAATAACAGTGAT-G---GTACACGATTTTGGCTAAAATTTTACAAAAAATGACCGT-GAAAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACC-TCGAAAA
* * * * * *
74947 TTTTTTTCCTCAATTTTT-GCATAAAATACTCATAAAATATTTATAATTTAACGCCAAAAGGATT
65 --ATTTTCCTCAATTTTTGGC-CAAAATACTCATAAAA-ATATATAATTTAACACAAAAAAGATT
* * * * *
75011 TAAGGGCTTTTCACGCTTTTAATATCGTCTTTCATA-TTTTTTCTGAATTAATTTGTGATTAAAT
126 GAAAGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAAT
* * * * *
75075 CGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAGGTGGATAGGTTTTTATTAG
191 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAG
* * *
75140 ATGAATATAGATATTTCAAGGAGTCTTGACGCCGAAATTCATGCAAAACTAAGTCG-GGACCCCG
256 ATGAATATAGATATTTCAAGGAGTCTTGACGCC-AAAATCATGCAAAACTGAGCCGAGG-CCCCG
*
75204 AAACACG-TTTTA
319 -AACGCGTTTTTA
** * * ** *
75216 GCCAAAAACCGTGAT-G-CCGTACACGATTTTAGTTAACGTTTTGCAAAAAATGACCATGGAAAT
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACC-TCGAAA-
** * ** * * * *
75279 TTTTTTTCTCAATTTTTGGATAAAATACTCATAAAATTTATATAATTTAATGAAAAAAAATATTG
64 AATTTTCCTCAATTTTTGGCCAAAATACTCATAAAA-ATATATAATTTAA-CACAAAAAAGATTG
* * * * * *
75344 GAGGGCGTTTCACGCTTTTAATATCGTTTTTTCATA--TTTTTCTAAATTAATTACTAATCAAAT
127 AAAGGCTTTTCACGCTTTTAATATCG-TTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAAT
* * * * * * * *
75407 CGAAACAACATCCAAATGCTCGTAAAACCAAATCTTTAAATGCAAGGGGGCTAAGTTTTTATTAG
191 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAG
* *
75472 ATGAATATAGATATTTCAAGGAGTTTTAACGCCAAAATTCATGCAAAACTGAGCC-AGGACCCCA
256 ATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAA-TCATGCAAAACTGAGCCGAGG-CCCC-
75536 GAACGCGTTTTTA
318 GAACGCGTTTTTA
* * *
75549 GCCAAAAACCGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGTAAAAAATGACCGCGAAAAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCGAAAAA
* * ** * * * * *
75614 TTTTTCCTTACTTTTTGGATAAAATACTTAT-AATATATATAATTTAGCGGCAAAAAA-ATTG-G
66 -TTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATATATAATTTAAC-ACAAAAAAGATTGAA
75676 AGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTCTGAATT-ATTTCTAATTAAATCG
129 AGG-CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAATCG
** * * *
75739 AAACAAGATTCAGATAATCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGAC
193 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGAT
* * * *
75804 GAATATAGATATTTCAAAGAGTTTTGACGGCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAA
258 GAATATAGATATTTCAAGGAGTCTTGACGCCAAAA-TCATGCAAAACTGAGCCGAGGCCCC-GAA
75869 CGCGTTTTTA
321 CGCGTTTTTA
* * * * * *
75879 GCAAAAAAAAACGTGATGGTTAGTACATGATTTCGGATAAAATTATT-CAAAAATTGACC-CGAA
1 GC--CAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATT-TTGCAAAAAATGACCTCGAA
* * * * *
75942 AGAA------T---TTTTT-GCCACAATACT-AAAAAATATATATAATTTACCACCAAAAATATT
63 A-AATTTTCCTCAATTTTTGGCCAAAATACTCATAAAA-ATATATAATTTAACACAAAAAAGATT
* * * * * *
75996 GAAAGG-GTTTCACGCTTATAATATTGTTTTTCCTA--TTTTTCTGAGTTAATTTATAATTAAAT
126 GAAAGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAAT
* * * * * **
76058 CGAAATATGATTCAGATGCTCGTAAAAGCAAATCCTTAAATGCAATGTGGGTGAGATTTGGTTAG
191 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAG
* * * * *
76123 ATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCC-AGGGCCCTG
256 ATGAATATAGATATTTCAAGGAGTCTTGACGCC-AAAATCATGCAAAACTGAGCCGA-GGCCCCG
*
76187 AAACGCGTTTATA
319 -AACGCGTTTTTA
** * *** * * *
76200 GTAAAAAACAGTGATAACT--TACACGATTTCGGCTAAAATATTGCAAAAATTTGACC-CGAAAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAA-ATGACCTCGAAAA
* * * * *
76262 ATTTCTCCCCAATTTTTGGCCAAAATACTAATAAGAAAATATATAACTCAACATC-AAAAAGTTT
65 ATTT-TCCTCAATTTTTGGCCAAAATACTCAT-A-AAAATATATAATTTAACA-CAAAAAAGATT
* * * * * * * *
76326 GGAGGGCATCTCACGCTTCTAATATCGTTTTTCCTA--TTTTTCCGAATTAATTTCAAATTAAAT
126 GAAAGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAAT
** *
76389 CGAAACCGGATTGAGATGCTCGTAAAAACAAAT
191 CGAAACAAGATTCAGATGCTCGTAAAAACAAAT
Statistics
Matches: 3502, Mismatches: 520, Indels: 376
0.80 0.12 0.09
Matches are distributed among these distances:
316 2 0.00
317 26 0.01
318 11 0.00
319 12 0.00
320 13 0.00
321 168 0.05
322 26 0.01
323 3 0.00
325 1 0.00
327 9 0.00
328 206 0.06
329 258 0.07
330 425 0.12
331 388 0.11
332 609 0.17
333 883 0.25
334 122 0.03
335 35 0.01
336 10 0.00
337 10 0.00
338 7 0.00
339 13 0.00
340 16 0.00
341 6 0.00
342 4 0.00
343 14 0.00
344 9 0.00
345 6 0.00
346 3 0.00
347 7 0.00
348 11 0.00
349 8 0.00
350 11 0.00
352 5 0.00
353 70 0.02
354 93 0.03
355 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (330 bp):
GCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCTCGAAAAA
TTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATATATAATTTAACACAAAAAAGATTGAAAG
GCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAATCGAAA
CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAA
TATAGATATTTCAAGGAGTCTTGACGCCAAAATCATGCAAAACTGAGCCGAGGCCCCGAACGCGT
TTTTA
Found at i:73019 original size:144 final size:144
Alignment explanation
Indices: 72749--73023 Score: 358
Period size: 143 Copynumber: 1.9 Consensus size: 144
72739 AAATGGATTG
* * * *
72749 AGATGCTCATAAAAATAAAGTCCTTAAATCCAATGTGACTGAGATTTCGTTATATGAATATAGAT
1 AGATGCACATAAAAACAAAGTCCTTAAATCCAACGTGACTGAGATTTCGTTAGATGAATATAGAT
* * *
72814 ATCTCAATGAGTTTTGGCGCCAAAATCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
66 ATCTCAAGGAGTCTTGGCGCCAAAATCATGCAAAACTGAGCCAGGGCCCCAGAACGCGTTTTTAG
72879 CCGAAGCAAAATTC
131 CCGAAGCAAAATTC
* * * *
72893 AGATGCACGTAAAAACAAA-TCTTTAAATCCAACGTGGA-TGAGATTTGGTTAGATGTATATAGA
1 AGATGCACATAAAAACAAAGTCCTTAAATCCAACGT-GACTGAGATTTCGTTAGATGAATATAGA
* * * * *
72956 TTTTTCAAGGAGTCTTGGTGCCAAAAATCATGCAAAACTGAGCCAGGG-CCCTGAAACGTGTTTT
65 TATCTCAAGGAGTCTTGGCGCC-AAAATCATGCAAAACTGAGCCAGGGCCCCAG-AACGCGTTTT
73020 TAGC
128 TAGC
73024 AAAAAACCCT
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
143 57 0.51
144 55 0.49
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (144 bp):
AGATGCACATAAAAACAAAGTCCTTAAATCCAACGTGACTGAGATTTCGTTAGATGAATATAGAT
ATCTCAAGGAGTCTTGGCGCCAAAATCATGCAAAACTGAGCCAGGGCCCCAGAACGCGTTTTTAG
CCGAAGCAAAATTC
Found at i:74645 original size:332 final size:334
Alignment explanation
Indices: 73037--76421 Score: 3978
Period size: 332 Copynumber: 10.3 Consensus size: 334
73027 AAACCCTGAA
* *
73037 ACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTGATTTCTAATTTAATCGAAACAAGATT
1 ACGCTTTTAATATCGTTTTTCATA-TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
* * *
73102 CAATTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTTATTAGACGAATATAGAT
65 CAAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGAT
* * * *
73167 ATTTCAAGGAGTCTTAACGCCAAAATTCATGCAAAACTTAGCCGGGACCCCGGAACGCGTTTTTA
130 ATTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTA
73232 GCCAAAAACCGTGAT-G---GTACACGATTTT-AGCTAAAATTTTGCAAAAAATGACCGCG-AAA
195 GCCAAAAACCGTGATGGTTAGTACACGATTTTGA-CTAAAATTTTGCAAAAAATGACCGCGAAAA
* * *
73291 AATGTTTCCTTAATTTTT-GATAAAATACTCATAATATATATATAATTTAACGCCAAAAAATATT
259 AAT-TTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGTCAAAAAATATT
73355 GGAGGACTTTTC
323 GGAGGACTTTTC
* *
73367 ACGCTTTTAATATCGTTTTTCATATTTTTT-TGAATTAATTTCCAATTCAATCGAAACAAGATTC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
** * *
73431 AGCTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTCATTAGATGAATATAGATA
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
* * * *
73496 TTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACCGAGCCAGGGCCCCGGAACGCGTTTTTAG
131 TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
* * * * * * * *
73561 TCAATAACCGTGATGGTTAGTGCACAATTTTGACTAAAATATTGCAAAAAACGA-C-CGAGAAAT
196 CCAAAAACCGTGATGGTTAGTACACGATTTTGACTAAAATTTTGCAAAAAATGACCGCGAAAAAA
** * * * *
73624 TTTTTTTCACTTTTTGGATAAATTACTCAT-AAA-ATATATAATTTAACGGCTAAAAA-ATTGGA
261 TTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGTCAAAAAATATTGGA
*
73686 GAACTTTTC
326 GGACTTTTC
* *
73695 ACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATCC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * * * *
73760 AAATGCTCGTAAAAACAAATCCTTAAAGGCGATGTGGCTAGGTTTTTATTTGATGAATATAGATA
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
* * * *
73825 TTTCAAGGAGACTTAACGCCAAAATTCATGTAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAG
131 TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
* * **
73890 CTAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAGT
196 CCAAAAACCGTGATGGTTAGTACACGATTTTGACTAAAATTTTGCAAAAAATGACCGCGAAAAAA
* * *
73955 TTTTCCTCAATTTTTTGATAAAATACTCATATAATTTATATAATCTTACAC--C-AAAAATATTG
261 TTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAAT-TTA-ACGTCAAAAAATATTG
74017 GAGGACTTTTC
324 GAGGACTTTTC
*
74028 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* *
74093 AACTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTTATTAGATGAATATAGATA
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
* * * *
74158 TTTCAAGGAGTCTTAACGCCAAAATTCATGCAAAACTGAGCCGGGACCCCGGGACGCGTTTTTAG
131 TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
*
74223 CCAAAAACCGTGATGGTTACTACACGATTTTTG-CTAAAATTTTGCAAAAAATGACCGCG-AAAA
196 CCAAAAACCGTGATGGTTAGTACACGA-TTTTGACTAAAATTTTGCAAAAAATGACCGCGAAAAA
* * *
74286 ATGTTTCCTTAATTTTT-GATGAAATACTCATAATATATATATAATTTAACGTCAAAAAATATTG
260 AT-TTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGTCAAAAAATATTG
74350 GAGGACTTTTC
324 GAGGACTTTTC
*
74361 ACGCTTTTAATATCGTTTTTCATATTTTTT-TGAATTAATTTTTAATTAAATCGAAACAAGATTC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * *
74425 AACTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAACTTTTTATGAGAT-AAGTATAGAT
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAA-TATAGAT
* * * *
74489 ATTTCAAGGCA-TCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCATAACGCGTTTAT
130 ATTTCAAGG-AGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTT
* * * * *
74553 AGTCAATAACCGTGAT-GCTAGTGCACAATTTTGACTAAAATTTTGCAAAAAATGACCGCGAAAA
194 AGCCAAAAACCGTGATGGTTAGTACACGATTTTGACTAAAATTTTGCAAAAAATGACCGCGAAAA
* *
74617 AATTTTCCTCAAGTTTTGGATAAAATACTCATAAAATATATATAATTTAATGTCAAAAAGAT-TT
259 AATTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGTCAAAAA-ATATT
74681 -GAGGGACTTTTC
323 GGA-GGACTTTTC
* *
74693 ACGCTTTTAATATCGTTTTTCATAATTTTTTCTAAATTAA-TTCTAACTAAATCGAAACAAGATT
1 ACGCTTTTAATATCGTTTTTCAT-ATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
* *
74757 CAAATGGTCGTAAAAACAAATCCTTAAATG-AAATGTGGCTAAGTTTTTATTATATGAATATAGA
65 CAAATGCTCGTAAAAACAAATCCTTAAATGCAAA-GTGGCTAAGTTTTTATTAGATGAATATAGA
* * * * *
74821 TATTTCAAGGAGTCTTGATGCCAAAAATCATGTAAAACTGAGTCGGAGCCCC-GTAACGCGTTTT
129 TATTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAG-AACGCGTTTT
* * * * *
74885 TAGCCAATAACAGTGAT-G---GTACACGATTTTGGCTAAAATTTTACAAAAAATGACCGTGAAA
193 TAGCCAAAAACCGTGATGGTTAGTACACGATTTTGACTAAAATTTTGCAAAAAATGACCGCGAAA
** * * * *
74946 ATTTTTTTCCTCAATTTTTGCATAAAATACTCATAAAATATTTATAATTTAACGCCAAAAGGAT-
258 A-AATTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGTCAAAA-AATA
* *
75010 TT-AAGGGCTTTTC
321 TTGGAGGACTTTTC
* * *
75023 ACGCTTTTAATATCGTCTTTCATATTTTTTCTGAATTAATTTGTGATTAAATCGAAACAAGATTC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * *
75088 AAATGCTCGTAAAAACAAATCCTTAAATGCAAGGTGGATAGGTTTTTATTAGATGAATATAGATA
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
* * * * *
75153 TTTCAAGGAGTCTTGACGCCGAAATTCATGCAAAACTAAGTCGGGACCCC-GAAACACG-TTTTA
131 TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAG-AACGCGTTTTTA
** * **
75216 GCCAAAAACCGTGAT-G-CCGTACACGATTTT-AGTTAACGTTTTGCAAAAAATGACCATG-GAA
195 GCCAAAAACCGTGATGGTTAGTACACGATTTTGA-CTAAAATTTTGCAAAAAATGACC--GCGAA
*** * * * **
75277 ATTTTTTTTCTCAATTTTTGGATAAAATACTCATAAAATTTATATAATTTAATGAAAAAAAATAT
257 AAAATTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGTCAAAAAATAT
* *
75342 TGGAGGGCGTTTC
322 TGGAGGACTTTTC
* * * * *
75355 ACGCTTTTAATATCGTTTTTTCATA-TTTTTCTAAATTAATTACTAATCAAATCGAAACAACATC
1 ACGCTTTTAATATCG-TTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * *
75419 CAAATGCTCGTAAAACCAAATCTTTAAATGCAAGGGGGCTAAGTTTTTATTAGATGAATATAGAT
65 CAAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGAT
* * * *
75484 ATTTCAAGGAGTTTTAACGCCAAAATTCATGCAAAACTGAGCCAGGACCCCAGAACGCGTTTTTA
130 ATTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTA
*
75549 GCCAAAAACCGTGATGGTTAGTACACGATTTT-AGCTAAAATTTTGTAAAAAATGACCGCGAAAA
195 GCCAAAAACCGTGATGGTTAGTACACGATTTTGA-CTAAAATTTTGCAAAAAATGACCGCGAAAA
* * * * * *
75613 ATTTTTCCTTACTTTTTGGATAAAATACT--TATAATATATATAATTTAGCGGCAAAAAA-ATTG
259 AATTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGTCAAAAAATATTG
75675 GAGGACTTTTC
324 GAGGACTTTTC
75686 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATT-ATTTCTAATTAAATCGAAACAAGATTC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* ** *
75750 AGATAATCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGACGAATATAGATA
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
* * *
75815 TTTCAAAGAGTTTTGACGGCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
131 TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
* * * * *
75880 CAAAAAAAAACGTGATGGTTAGTACATGATTTCGGA-TAAAATTATT-CAAAAATTGACC-CGAA
196 C--CAAAAACCGTGATGGTTAGTACACGATTT-TGACTAAAATT-TTGCAAAAAATGACCGCGAA
* ** * * ** *
75942 AGAA------T---TTTTT-GCCACAATACT-AAAAAATATATATAATTT-ACCACCAAAAATAT
257 AAAATTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGTCAAAAAATAT
* *
75995 TGAAAGG--GTTTC
322 TG-GAGGACTTTTC
* * * * * * *
76007 ACGCTTATAATATTGTTTTTCCTA-TTTTTCTGAGTTAATTTATAATTAAATCGAAATATGATTC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * * * * * **
76071 AGATGCTCGTAAAAGCAAATCCTTAAATGCAATGTGGGTGAGATTTGGTTAGATGAATATAGATA
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
* * * * * * * *
76136 TTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCCAGGG-CCCTGAAACGCGTTTATA
131 TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAG-AACGCGTTTTTA
** * *** * * * *
76200 GTAAAAAACAGTGATAACT--TACACGATTTCGGCTAAAATATTGCAAAAATTTGACC-CG-AAA
195 GCCAAAAACCGTGATGGTTAGTACACGATTTTGACTAAAATTTTGCAAAAA-ATGACCGCGAAAA
* ** * * * * * *
76261 AATTTCTCCCCAATTTTTGGCCAAAATACTAATAAGAAAATATATAACTCAACATCAAAAAGT-T
259 AATTT-TCCTCAATTTTTGGATAAAATACTCATAA-AATATATATAATTTAACGTCAAAAAATAT
* * *
76325 TGGAGGGCATCTC
322 TGGAGGACTTTTC
* * * * ** *
76338 ACGCTTCTAATATCGTTTTTCCTA-TTTTTCCGAATTAATTTCAAATTAAATCGAAACCGGATTG
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
*
76402 AGATGCTCGTAAAAACAAAT
66 AAATGCTCGTAAAAACAAAT
Statistics
Matches: 2655, Mismatches: 320, Indels: 159
0.85 0.10 0.05
Matches are distributed among these distances:
316 3 0.00
317 25 0.01
318 8 0.00
319 12 0.00
320 15 0.01
321 169 0.06
322 24 0.01
323 3 0.00
325 1 0.00
327 5 0.00
328 217 0.08
329 259 0.10
330 409 0.15
331 373 0.14
332 542 0.20
333 507 0.19
334 48 0.02
335 35 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (334 bp):
ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
CCAAAAACCGTGATGGTTAGTACACGATTTTGACTAAAATTTTGCAAAAAATGACCGCGAAAAAA
TTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGTCAAAAAATATTGGA
GGACTTTTC
Found at i:75448 original size:662 final size:661
Alignment explanation
Indices: 73037--76421 Score: 3978
Period size: 662 Copynumber: 5.1 Consensus size: 661
73027 AAACCCTGAA
* *
73037 ACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTGATTTCTAATTTAATCGAAACAAGATT
1 ACGCTTTTAATATCGTTTTTCATA-TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
* * *
73102 CAATTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTTATTAGACGAATATAGAT
65 CAAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGAT
* * * *
73167 ATTTCAAGGAGTCTTAACGCCAAAATTCATGCAAAACTTAGCCGGGACCCCGGAACGCGTTTTTA
130 ATTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTA
*
73232 GCCAAAAACCGTGATG--GTACACGATTTTAGCTAAAATTTTGCAAAAAATGACCGCGAAAAATG
195 GCCAAAAACCGTGATGCAGTACACGATTTTAGCTAAAATTTTGCAAAAAATGACCGCGAAAAATT
* * * **
73295 TTTCCTTAATTTTT-GATAAAATACTCATAATATATATATAATTTAACGCCAAAAAATATTGGAG
260 TTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAATGAAAAAAAATATTGGAG
* *
73359 GACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTT-TGAATTAATTTCCAATTC-AATCGAA
325 GACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTTCTAA-TCAAATCGAA
** *
73422 ACAAGATTCAGCTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTCATTAGATGA
389 ACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTTATTAGATGA
* *
73487 ATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACCGAGCCAGGGCCCCGGAACG
454 ATATAGATATTTCAAGGAGTCTTAACGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGGAACG
* * * * * *
73552 CGTTTTTAGTCAATAACCGTGATGGTTAGTGCACAATTTTGACTAAAATATTGCAAAAAACGA-C
519 CGTTTTTAGCCAAAAACCGTGATGGTTA---CACGATTTTGGCTAAAATTTTGCAAAAAATGACC
* ** * * *
73616 -CGAGAAATTTTTTTTCACTTTTTGGATAAATTACTCAT-AAA-ATATATAATTTAACGGCTAAA
581 GCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAAC-GCCAAA
*
73678 AAATTGGAGAACTTTTC
645 AAATTGGAGGACTTTTC
* *
73695 ACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATCC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * * * *
73760 AAATGCTCGTAAAAACAAATCCTTAAAGGCGATGTGGCTAGGTTTTTATTTGATGAATATAGATA
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
* * * *
73825 TTTCAAGGAGACTTAACGCCAAAATTCATGTAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAG
131 TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAG
* * * *
73890 CTAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAGT
196 CCAAAAACCGTGAT-G-CAGTACACGATTTTAGCTAAAATTTTGCAAAAAATGACCGCGAAAAAT
* * * * **
73955 TTTTCCTCAATTTTTTGATAAAATACTCATATAATTTATATAATCTT-A-CACCAAAAATATTGG
259 TTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAAT-TTAATGAAAAAAAATATTGG
* **
74018 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTTAATCGA
323 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTTCTAATCAAATCGA
*
74083 AACAAGATTCAACTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTTATTAGATG
388 AACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTTATTAGATG
* *
74148 AATATAGATATTTCAAGGAGTCTTAACGCCAAAATTCATGCAAAACTGAGCC-GGGACCCCGGGA
453 AATATAGATATTTCAAGGAGTCTTAACGCCAAAAATCATGCAAAACTGAGCCAGGG-CCCCGGAA
*
74212 CGCGTTTTTAGCCAAAAACCGTGATGGTTACTACACGATTTTTGCTAAAATTTTGCAAAAAATGA
517 CGCGTTTTTAGCCAAAAACCGTGATGG-T--TACACGATTTTGGCTAAAATTTTGCAAAAAATGA
* * * * *
74277 CCGCGAAAAATGTTTCCTTAATTTTT-GATGAAATACTCATAATATATATATAATTTAACGTCAA
579 CCGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACG-CCA
74341 AAAATATTGGAGGACTTTTC
643 AAAA-ATTGGAGGACTTTTC
*
74361 ACGCTTTTAATATCGTTTTTCATATTTTTT-TGAATTAATTTTTAATTAAATCGAAACAAGATTC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * *
74425 AACTGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAACTTTTTATGAGAT-AAGTATAGAT
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAA-TATAGAT
* * *
74489 ATTTCAAGGCA-TCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCC-ATAACGCGTTTA
130 ATTTCAAGG-AGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCGA-AACGCGTTTT
* * * *
74552 TAGTCAATAACCGTGATGCTAGTGCACAATTTT-GACTAAAATTTTGCAAAAAATGACCGCGAAA
193 TAGCCAAAAACCGTGATGC-AGTACACGATTTTAG-CTAAAATTTTGCAAAAAATGACCGCGAAA
* * * *
74616 AAATTTTCCTCAAGTTTTGGATAAAATACTCATAAAATATATATAATTTAATGTCAAAAAGAT-T
256 AATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAATG-AAAAAAAATAT
74680 T-GAGGGACTTTTCACGCTTTTAATATCGTTTTTCATAATTTTTTCTAAATTAA-TTCTAA-CTA
320 TGGA-GGACTTTTCACGCTTTTAATATCGTTTTTCAT-ATTTTTTCTAAATTAATTTCTAATC-A
* *
74742 AATCGAAACAAGATTCAAATGGTCGTAAAAACAAATCCTTAAATG-AAATGTGGCTAAGTTTTTA
382 AATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAA-GTGGCTAAATTTTTA
* * * * *
74806 TTATATGAATATAGATATTTCAAGGAGTCTTGATGCCAAAAATCATGTAAAACTGAGTC-GGAGC
446 TTAGATGAATATAGATATTTCAAGGAGTCTTAACGCCAAAAATCATGCAAAACTGAGCCAGG-GC
* * * *
74870 CCCGTAACGCGTTTTTAGCCAATAACAGTGATGG-TACACGATTTTGGCTAAAATTTTACAAAAA
510 CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTACACGATTTTGGCTAAAATTTTGCAAAAA
* * * *
74934 ATGACCGTGAAAATTTTTTTCCTCAATTTTTGCATAAAATACTCATAAAATATTTATAATTTAAC
575 ATGACCGCGAAAA-ATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAAC
* ** *
74999 GCCAAAAGGATTTAAGGGCTTTTC
639 GCCAAAA-AATTGGAGGACTTTTC
* * *
75023 ACGCTTTTAATATCGTCTTTCATATTTTTTCTGAATTAATTTGTGATTAAATCGAAACAAGATTC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * *
75088 AAATGCTCGTAAAAACAAATCCTTAAATGCAAGGTGGATAGGTTTTTATTAGATGAATATAGATA
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
* * * * *
75153 TTTCAAGGAGTCTTGACGCCGAAATTCATGCAAAACTAAGTCGGGACCCCGAAACACG-TTTTAG
131 TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAG
* * ** **
75217 CCAAAAACCGTGATGCCGTACACGATTTTAGTTAACGTTTTGCAAAAAATGACCATG-GAAATTT
196 CCAAAAACCGTGATGCAGTACACGATTTTAGCTAAAATTTTGCAAAAAATGACC--GCGAAAAAT
* *
75281 TTTTTCTCAATTTTTGGATAAAATACTCATAAAATTTATATAATTTAATGAAAAAAAATATTGGA
259 TTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAATGAAAAAAAATATTGGA
* * *
75346 GGGCGTTTCACGCTTTTAATATCGTTTTTTCATA-TTTTTCTAAATTAATTACTAATCAAATCGA
324 GGACTTTTCACGCTTTTAATATCG-TTTTTCATATTTTTTCTAAATTAATTTCTAATCAAATCGA
* * * * * * *
75410 AACAACATCCAAATGCTCGTAAAACCAAATCTTTAAATGCAAGGGGGCTAAGTTTTTATTAGATG
388 AACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTTATTAGATG
* * * *
75475 AATATAGATATTTCAAGGAGTTTTAACGCCAAAATTCATGCAAAACTGAGCCAGGACCCCAGAAC
453 AATATAGATATTTCAAGGAGTCTTAACGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGGAAC
* *
75540 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGTAAAAAATGAC
518 GCGTTTTTAGCCAAAAACCGTGATGG-T--TACACGATTTTGGCTAAAATTTTGCAAAAAATGAC
* * * * *
75605 CGCGAAAAATTTTTCCTTACTTTTTGGATAAAATACT--TATAATATATATAATTTAGCGGCAAA
580 CGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAAC-GCCAA
75668 AAAATTGGAGGACTTTTC
644 AAAATTGGAGGACTTTTC
75686 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATT-ATTTCTAATTAAATCGAAACAAGATTC
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* ** *
75750 AGATAATCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGACGAATATAGATA
66 AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
* * *
75815 TTTCAAAGAGTTTTGACGGCAAAATTCATGCAAAACTGAGCCGGGGCCCC-AGAACGCGTTTTTA
131 TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCGA-AACGCGTTTTTA
* * * * ** * *
75879 GCAAAAAAAAACGTGATGGTTAGTACATGATTTCGGATAAAATTATT-CAAAAATTGACC-CGAA
195 GC--CAAAAACCGTGAT-G-CAGTACACGATTTTAGCTAAAATT-TTGCAAAAAATGACCGCGAA
** * * ** **
75942 AGAA-------T---TTTTT-GCCACAATACT-AAAAAATATATATAATTT-ACCACCAAAAATA
255 A-AATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAATGAAAAAAAATA
* * * * * * * * *
75994 TTGAAAGG--GTTTCACGCTTATAATATTGTTTTTCCTA-TTTTTCTGAGTTAATTTATAATTAA
319 TTG-GAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTTCTAATCAA
* * * * * * * **
76056 ATCGAAATATGATTCAGATGCTCGTAAAAGCAAATCCTTAAATGCAATGTGGGTGAGA-TTTGGT
383 ATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCT-AAATTTTTAT
* * ** *
76120 TAGATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCCAGGGCCC
447 TAGATGAATATAGATATTTCAAGGAGTCTTAACGCCAAAAATCATGCAAAACTGAGCCAGGGCCC
* * * ** * ** * *
76185 TGAAACGCGTTTATAGTAAAAAACAGTGATAACTTACACGATTTCGGCTAAAATATTGCAAAAAT
512 CGGAACGCGTTTTTAGCCAAAAACCGTGAT-GGTTACACGATTTTGGCTAAAATTTTGCAAAAA-
* * * ** * * * *
76250 TTGACC-CGAAAAATTTCTCCCCAATTTTTGGCCAAAATACTAATAAGAAAATATATAACTCAAC
575 ATGACCGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAA-AATATATATAATTTAAC
** * * * *
76314 ATCAAAAAGTTTGGAGGGCATCTC
639 GCCAAAAA-ATTGGAGGACTTTTC
* * * * ** *
76338 ACGCTTCTAATATCGTTTTTCCTA-TTTTTCCGAATTAATTTCAAATTAAATCGAAACCGGATTG
1 ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
*
76402 AGATGCTCGTAAAAACAAAT
66 AAATGCTCGTAAAAACAAAT
Statistics
Matches: 2354, Mismatches: 302, Indels: 148
0.84 0.11 0.05
Matches are distributed among these distances:
649 55 0.02
650 5 0.00
651 175 0.07
652 106 0.05
653 12 0.01
654 19 0.01
655 8 0.00
656 5 0.00
657 168 0.07
658 25 0.01
659 1 0.00
661 205 0.09
662 648 0.28
663 272 0.12
664 119 0.05
665 396 0.17
666 106 0.05
667 27 0.01
668 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (661 bp):
ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTC
AAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAGTTTTTATTAGATGAATATAGATA
TTTCAAGGAGTCTTGACGCCAAAATTCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAG
CCAAAAACCGTGATGCAGTACACGATTTTAGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTT
TTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAATGAAAAAAAATATTGGAGG
ACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTTCTAATCAAATCGAAAC
AAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAAGTGGCTAAATTTTTATTAGATGAAT
ATAGATATTTCAAGGAGTCTTAACGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGGAACGCG
TTTTTAGCCAAAAACCGTGATGGTTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAA
AAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGCCAAAAAATTG
GAGGACTTTTC
Done.