Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018035.1 Corchorus olitorius cultivar O-4 contig18068, 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: 82340
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6159 original size:187 final size:185
Alignment explanation
Indices: 5836--6584 Score: 1216
Period size: 187 Copynumber: 4.0 Consensus size: 185
5826 TAATTATGTT
* *
5836 ATATTATATTTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGCTTTGTGAGAATAACAAAAAA
1 ATATTATAATTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGGTTTGTGAGAATAACAAAAAA
* * *
5901 TCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATGTAGTGATTCGGCTAG
66 CCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGTTAG
*
5966 GAAAAATTTTGAGGGTATTTTAGTAATTACACTTCTTACTATTAGTGTTTTTAATA
131 GAAAAATTTTGAGGGTATTTTAGTAATTACACTTCCTACTATTAGTGTTTTT-ATA
* *
6022 ATATTATAATTTAAAATGCTAGAAATTCAAAAATGCCCTCAGAGGTTTGTGAGAATAACAAAAAG
1 ATATTATAATTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGGTTTGTGAGAATAACAAAAA-
6087 ACCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGTTA
65 ACCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGTTA
* *
6152 TGAAAAATTTTGAGGGTATTTTAGTAATTACACTTCCTGCTATTAGTGTTTTCTAT-
130 GGAAAAATTTTGAGGGTATTTTAGTAATTACACTTCCTACTATTAGTGTTTT-TATA
* * *
6208 A-A-TATAATTTAAAATGTTAGAAAGTCAAAAATGCTCTCAGAGGTTTGTGAGAATAACAAAAAA
1 ATATTATAATTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGGTTTGTGAGAATAAC----AA
* *
6271 AAAACCAAAAGTGAAATGACTAAAAAACCAAGCTGAGTGGTAACAAAATGAATATAGTGATTCGG
62 AAAACCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGG
* *
6336 TTAGGAAAATTTTTGAGGGTATTTTAGTAATTACACTTCTTACTATTAGTGTTTTTATA
127 TTAGGAAAAATTTTGAGGGTATTTTAGTAATTACACTTCCTACTATTAGTGTTTTTATA
*
6395 ATATTATAATTTAAAATGCTAGAAAGTCAAAAAAACCCTCAGAGGTTTGTGAGAATAACAAAAAA
1 ATATTATAATTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGGTTTGTGAGAATAACAAAAAA
*
6460 CCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATGTAGTGATTCGGTTAG
66 CCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGTTAG
* *
6525 GAAAATTTTTGAGGGTACTTTAGTAATTACACTTCCTACTATTAGTGTTTTTTATA
131 GAAAAATTTTGAGGGTATTTTAGTAATTACACTTCCTACTATTAGTG-TTTTTATA
6581 ATAT
1 ATAT
6585 AATGTAAAAA
Statistics
Matches: 525, Mismatches: 28, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
184 52 0.10
185 114 0.22
186 76 0.14
187 225 0.43
188 7 0.01
189 51 0.10
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (185 bp):
ATATTATAATTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGGTTTGTGAGAATAACAAAAAA
CCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGTTAG
GAAAAATTTTGAGGGTATTTTAGTAATTACACTTCCTACTATTAGTGTTTTTATA
Found at i:6583 original size:372 final size:370
Alignment explanation
Indices: 5834--6593 Score: 1272
Period size: 372 Copynumber: 2.0 Consensus size: 370
5824 TATAATTATG
* *
5834 TTATATTATATTTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGCTTTGTGAGAATAACAAAA
1 TTATAATATAATTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGCTTTGTGAGAATAACAAAA
* *
5899 AATCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATGTAGTGATTCGGCT
66 AACCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGCT
5964 AGGAAAAATTTTGAGGGTATTTTAGTAATTACACTTCTTACTATTAGTGTTTTTAATAATATTAT
131 AGGAAAAATTTTGAGGGTATTTTAGTAATTACACTTCTTACTATTAGTGTTTTTAATAATATTAT
* **
6029 AATTTAAAATGCTAGAAATTCAAAAATGCCCTCAGAGGTTTGTGAGAATAACAAAAAGACCAAAA
196 AATTTAAAATGCTAGAAAGTCAAAAAAACCCTCAGAGGTTTGTGAGAATAACAAAAAGACCAAAA
*
6094 GTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGTTATGAAAAA
261 GTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGTTAGGAAAAA
* *
6159 TTTTGAGGGTATTTTAGTAATTACACTTCCTGCTATTAGTGTTTT
326 TTTTGAGGGTACTTTAGTAATTACACTTCCTACTATTAGTGTTTT
* * * * *
6204 CTATAATATAATTTAAAATGTTAGAAAGTCAAAAATGCTCTCAGAGGTTTGTGAGAATAACAAAA
1 TTATAATATAATTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGCTTTGTGAGAATAAC----
* *
6269 AAAAAACCAAAAGTGAAATGACTAAAAAACCAAGCTGAGTGGTAACAAAATGAATATAGTGATTC
62 AAAAAACCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTC
* *
6334 GGTTAGGAAAATTTTTGAGGGTATTTTAGTAATTACACTTCTTACTATTAGTGTTTTT-ATAATA
127 GGCTAGGAAAAATTTTGAGGGTATTTTAGTAATTACACTTCTTACTATTAGTGTTTTTAATAATA
6398 TTATAATTTAAAATGCTAGAAAGTCAAAAAAACCCTCAGAGGTTTGTGAGAATAACAAAAA-ACC
192 TTATAATTTAAAATGCTAGAAAGTCAAAAAAACCCTCAGAGGTTTGTGAGAATAACAAAAAGACC
*
6462 AAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATGTAGTGATTCGGTTAGGA
257 AAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGTTAGGA
*
6527 AAATTTTTGAGGGTACTTTAGTAATTACACTTCCTACTATTAGTGTTTT
322 AAAATTTTGAGGGTACTTTAGTAATTACACTTCCTACTATTAGTGTTTT
*
6576 TTATAATATAATGTAAAA
1 TTATAATATAATTTAAAA
6594 AGAAAAAATT
Statistics
Matches: 363, Mismatches: 23, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
370 54 0.15
372 128 0.35
373 64 0.18
374 117 0.32
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (370 bp):
TTATAATATAATTTAAAATGCTAGAAAGTCAAAAAAGCCCTCAGAGCTTTGTGAGAATAACAAAA
AACCAAAAGTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGCT
AGGAAAAATTTTGAGGGTATTTTAGTAATTACACTTCTTACTATTAGTGTTTTTAATAATATTAT
AATTTAAAATGCTAGAAAGTCAAAAAAACCCTCAGAGGTTTGTGAGAATAACAAAAAGACCAAAA
GTGAAATGACTAAAAAACCAAGCTGAATAGTAACAAAATGAATATAGTGATTCGGTTAGGAAAAA
TTTTGAGGGTACTTTAGTAATTACACTTCCTACTATTAGTGTTTT
Found at i:9110 original size:11 final size:11
Alignment explanation
Indices: 9091--9120 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9081 AGATTTCAAA
9091 TGAAGATTATC
1 TGAAGATTATC
*
9102 TGGAGATTATC
1 TGAAGATTATC
9113 TGAAGATT
1 TGAAGATT
9121 TAAGCATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (11 bp):
TGAAGATTATC
Found at i:13584 original size:11 final size:11
Alignment explanation
Indices: 13565--13594 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
13555 AGATTTCAAA
13565 TGAAGATTATC
1 TGAAGATTATC
*
13576 TGGAGATTATC
1 TGAAGATTATC
13587 TGAAGATT
1 TGAAGATT
13595 TAAGCAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (11 bp):
TGAAGATTATC
Found at i:14668 original size:32 final size:32
Alignment explanation
Indices: 14626--14725 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 32
14616 AAATAAAGAC
14626 CCTCACAAGGCCTCGGCAAGGCTGGCCATGTT
1 CCTCACAAGGCCTCGGCAAGGCTGGCCATGTT
* * * * * *
14658 CCTCAAAAGGCCTTGGCAAAGCAGGCCAAGTG
1 CCTCACAAGGCCTCGGCAAGGCTGGCCATGTT
** * *
14690 CCTTGCCAGGCCTCGGCAAGGCTCGCCCAT-TT
1 CCTCACAAGGCCTCGGCAAGGCT-GGCCATGTT
14722 CCTC
1 CCTC
14726 GCTAGGCTCT
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
32 46 0.92
33 4 0.08
ACGTcount: A:0.20, C:0.36, G:0.26, T:0.18
Consensus pattern (32 bp):
CCTCACAAGGCCTCGGCAAGGCTGGCCATGTT
Found at i:15748 original size:14 final size:15
Alignment explanation
Indices: 15729--15761 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
15719 TGTTCGTTTG
*
15729 TATTATCTATTATT-
1 TATTATATATTATTA
15743 TATTATATATTATTA
1 TATTATATATTATTA
15758 TATT
1 TATT
15762 TTAAACCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTATATATTATTA
Found at i:16849 original size:45 final size:45
Alignment explanation
Indices: 16798--16894 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
16788 AACAACAATT
* *
16798 AATATTAGCTTTATTTTGATGAATTATATAGAGATGAAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAAATGAAGGAGTAG
* * *
16843 AATATTAGCTTTATTTTTATGAATTACCTAGAAATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAAATGAAGGAGTAG
16888 AAT-TTAG
1 AATATTAG
16895 ATAATGCACT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACATAGAAATGAAGGAGTAG
Found at i:19002 original size:31 final size:32
Alignment explanation
Indices: 18932--19041 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 32
18922 GTTTTTAGTT
* *
18932 AAACGCCACTAAATAAGGGCGTTTTACTTGAAA
1 AAACGCCGCTAAATAAGGGCGTTTCACTT-AAA
* *
18965 AAACGCCGTTAAATAAGGGCGTTTCACTT-CA
1 AAACGCCGCTAAATAAGGGCGTTTCACTTAAA
* * * *
18996 AAACGCCGCTAAAT-AGAGGCATTTTACATGAA
1 AAACGCCGCTAAATAAG-GGCGTTTCACTTAAA
19028 AAACGCCGCTAAAT
1 AAACGCCGCTAAAT
19042 TGGGGTGTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
30 2 0.03
31 23 0.35
32 15 0.23
33 26 0.39
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (32 bp):
AAACGCCGCTAAATAAGGGCGTTTCACTTAAA
Found at i:19034 original size:32 final size:32
Alignment explanation
Indices: 18932--19066 Score: 148
Period size: 32 Copynumber: 4.2 Consensus size: 32
18922 GTTTTTAGTT
* *
18932 AAACGCCACTAAATAAGGGCGTTTTACTTGAAA
1 AAACGCCGCTAAATAAGGGCGTTTTACATG-AA
* * **
18965 AAACGCCGTTAAATAAGGGCGTTTCAC-TTCA
1 AAACGCCGCTAAATAAGGGCGTTTTACATGAA
*
18996 AAACGCCGCTAAAT-AGAGGCATTTTACATGAA
1 AAACGCCGCTAAATAAG-GGCGTTTTACATGAA
** *
19028 AAACGCCGCTAAATTGGGGTGTTTTACATGAA
1 AAACGCCGCTAAATAAGGGCGTTTTACATGAA
19060 AAACGCC
1 AAACGCC
19067 CTATTATATA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.02
31 22 0.26
32 37 0.43
33 25 0.29
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (32 bp):
AAACGCCGCTAAATAAGGGCGTTTTACATGAA
Found at i:21265 original size:30 final size:30
Alignment explanation
Indices: 21169--21523 Score: 449
Period size: 30 Copynumber: 11.7 Consensus size: 30
21159 ACTAATATAT
** *
21169 ATTGACACCAGAAGTTGTCAATGGCCTTCCA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* **
21200 ATTGACACCAGAAATTGTCAATGGCCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* *
21231 ATTGATACCAGAAGTTGTCATGATCTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
*
21261 ATTGACACCAGAAGTTGTCATGATCTTCCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* *
21291 ATTGACACCAAAAGTTGTCATGATCTTCCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * *
21321 ATTGAAACCGGAAGTTGTCATGATCTTCCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
*
21351 ATTGACACCAGAAGTTGTCAATGGTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* *
21382 ATTGACACCAGAAGTTGTCAAGTTCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* *
21412 ATTGACACCAGAAGTTGTCAAGTTCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* *
21442 ATTGACACCAGAAGTTGTCAAGTTCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* *
21472 ATTGACACTAGAAGTTGTCAATGTTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* *
21503 ATTGGCACCAAAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
21524 AATAAATTTC
Statistics
Matches: 298, Mismatches: 24, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
30 198 0.66
31 100 0.34
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATCTTACA
Found at i:21384 original size:121 final size:121
Alignment explanation
Indices: 21169--21523 Score: 469
Period size: 121 Copynumber: 2.9 Consensus size: 121
21159 ACTAATATAT
** * **
21169 ATTGACACCAGAAGTTGTCAATGGCCTTCCAATTGACACCAGAAATTGTCAATGGCCTTACAATT
1 ATTGACACCAGAAGTTGTC-ATGATCTTCCAATTGACACCAGAAGTTGTC-ATGATCTTACAATT
* * *
21234 GATACCAGAAGTTGTC-ATGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTCCA
64 GACACCAGAAGTTGTCAATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTACA
* * * *
21291 ATTGACACCAAAAGTTGTCATGATCTTCCAATTGAAACCGGAAGTTGTCATGATCTTCCAATTGA
1 ATTGACACCAGAAGTTGTCATGATCTTCCAATTGACACCAGAAGTTGTCATGATCTTACAATTGA
* * *
21356 CACCAGAAGTTGTCAATGGTCTTACAATTGACACCAGAAGTTGTCAAGTTCTTACA
66 CACCAGAAGTTGTCAATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTACA
* * * * *
21412 ATTGACACCAGAAGTTGTCAAGTTCTTACAATTGACACCAGAAGTTGTCAAGTTCTTACAATTGA
1 ATTGACACCAGAAGTTGTCATGATCTTCCAATTGACACCAGAAGTTGTCATGATCTTACAATTGA
* * * *
21477 CACTAGAAGTTGTCAATGTTCTTACAATTGGCACCAAAAGTTGTCAT
66 CACCAGAAGTTGTCAATGATCTTACAATTGACACCAGAAGTTGTCAT
21524 AATAAATTTC
Statistics
Matches: 203, Mismatches: 29, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
120 26 0.13
121 159 0.78
122 18 0.09
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (121 bp):
ATTGACACCAGAAGTTGTCATGATCTTCCAATTGACACCAGAAGTTGTCATGATCTTACAATTGA
CACCAGAAGTTGTCAATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTACA
Found at i:23732 original size:33 final size:33
Alignment explanation
Indices: 23669--23732 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
23659 ATACTGAATA
**
23669 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
* *
23702 ATATTGCCCCTGTAGTGGCATAAACCCATGA
1 ATATTGCCCCTGAAGAGGCATAAACCCATGA
23733 AAAGATCACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
Found at i:25716 original size:119 final size:123
Alignment explanation
Indices: 25405--25717 Score: 349
Period size: 119 Copynumber: 2.6 Consensus size: 123
25395 TAAAGTGCGT
**
25405 TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACAGGGTTTTCC-GACTTAAGGTTTTTAATG
1 TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCATTGGGTTTTCCAG-CTTAAGGTTTTTAATG
* * * *
25469 AGGCAACAATAGCACATTTAGATGTAATTGTCCTGAAGACATATACATGGACTTAATTGCTC
65 AGGCAAAAAGAGCACATGTAGA-GTAATTGTCCAGAAGACA-ATACATGGACTTAATTGC-C
* * * **
25531 TAGCACTCTTTTTCCCTTCTGTTCGGTTTT-TCCCATTGGGTTTTCGA-CACAAGGTTTTTAATG
1 T-GCACTCTTTTTCCCTTATGATCGGTTTTGTCCCATTGGGTTTTCCAGCTTAAGGTTTTTAATG
* *
25594 AGGCAATAAAGAGCACATGTA-A-TATTTGTCCAGAAGAC-A-A-ATGGACTTGATATG-C
65 AGGCAA-AAAGAGCACATGTAGAGTAATTGTCCAGAAGACAATACATGGACTTAAT-TGCC
* *
25649 TGCACTCTTTTTTCCTTATGA-CTGGTTTTGTCCCATTGGGTTTTCCAGCTTAAGGTTTTTAACG
1 TGCACTCTTTTTCCCTTATGATC-GGTTTTGTCCCATTGGGTTTTCCAGCTTAAGGTTTTTAATG
25713 AGGCA
65 AGGCA
25718 CTAGCTACAT
Statistics
Matches: 160, Mismatches: 20, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
116 1 0.01
117 23 0.14
118 18 0.11
119 28 0.17
120 3 0.02
121 1 0.01
123 14 0.09
125 21 0.13
126 25 0.16
127 26 0.16
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (123 bp):
TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCATTGGGTTTTCCAGCTTAAGGTTTTTAATGA
GGCAAAAAGAGCACATGTAGAGTAATTGTCCAGAAGACAATACATGGACTTAATTGCC
Found at i:26947 original size:23 final size:25
Alignment explanation
Indices: 26900--26948 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
26890 AAGGCGTTGA
*
26900 AAAAGAATGACATTTTTTTTGTTAC
1 AAAAGAATGACATTTTTTGTGTTAC
26925 AAAAGAATGACA-TTTTTGT-TTAC
1 AAAAGAATGACATTTTTTGTGTTAC
26948 A
1 A
26949 TATTTTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
24 6 0.26
25 12 0.52
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (25 bp):
AAAAGAATGACATTTTTTGTGTTAC
Found at i:28760 original size:15 final size:15
Alignment explanation
Indices: 28740--28773 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
28730 TATTTTTAAT
28740 ACTATCTATGAACAC
1 ACTATCTATGAACAC
28755 ACTATCTATGAACAC
1 ACTATCTATGAACAC
28770 ACTA
1 ACTA
28774 CTAACACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
ACTATCTATGAACAC
Found at i:37666 original size:125 final size:117
Alignment explanation
Indices: 37402--37713 Score: 319
Period size: 125 Copynumber: 2.6 Consensus size: 117
37392 ATATAGTAAC
* * * *
37402 TGCCTCGTTAAAAAGCTTAAG-CTGGAAAACCCAATGGGATAAAACC-AGACATAAGGAAAAAAG
1 TGCCTCATTAAAAACCTTAAGTCT-GAAAACCCAATGGGACAAAACCGA-ACATAAGGGAAAAAG
* * *
37465 AGTACAACATATTAAGCCCATTGTCTTCTGGACAAATGTAAAATGTGCTCTTAT
64 AGTGCAACATATTAAGCCCATTGTCTTCAGGACAAATGTAAAATGTGCTATTAT
* *
37519 TGCCTCTTTAAAAACCTTAAGTCTGAAAACCCAATGGGACAAAACCGAACAGAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCTGAAAACCCAATGGGACAAAACCGAACATAAGGGAAAAAGAG
* *
37584 TGCATAGCA-ATTAAGTCCATGTAATGTCTTCAGGAC-AAT-TCAATCTAGATGTGCTATTGT
66 TGCA-A-CATATTAAGCCCA--T--TGTCTTCAGGACAAATGT-AA---A-ATGTGCTATTAT
* ** * * *
37644 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCTGTGGGAGAAAACCGATCATAAGGGAAAAATAG
1 TGCCTCATTAAAAACCTTAAGTCTGAAAACCCAATGGGACAAAACCGAACATAAGGGAAAAAGAG
37709 TGCAA
66 TGCAA
37714 TGCCCTTTAA
Statistics
Matches: 164, Mismatches: 18, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
117 58 0.35
118 13 0.08
119 2 0.01
120 2 0.01
121 5 0.03
122 11 0.07
124 2 0.01
125 71 0.43
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23
Consensus pattern (117 bp):
TGCCTCATTAAAAACCTTAAGTCTGAAAACCCAATGGGACAAAACCGAACATAAGGGAAAAAGAG
TGCAACATATTAAGCCCATTGTCTTCAGGACAAATGTAAAATGTGCTATTAT
Found at i:41032 original size:30 final size:30
Alignment explanation
Indices: 40988--41172 Score: 282
Period size: 30 Copynumber: 6.2 Consensus size: 30
40978 TAGTGTATAA
*
40988 GACAACTTCTGGTGTCAATT-CTAAATTCAT
1 GACAACTTCTGGTGTCAATTGC-AAAATCAT
* *
41018 GAAAACTTCCGGTGTCAATTGCAAAATCAT
1 GACAACTTCTGGTGTCAATTGCAAAATCAT
41048 GACAACTTCTGGTGTCAATTGCAAAATCAT
1 GACAACTTCTGGTGTCAATTGCAAAATCAT
*
41078 GACAACTTCTGGTGTCAATTGCAATATCAT
1 GACAACTTCTGGTGTCAATTGCAAAATCAT
41108 GACAACTTCTGGTGTCAATTGCAAAATCAT
1 GACAACTTCTGGTGTCAATTGCAAAATCAT
* ** *
41138 GACAACTTCTAGTGTCAATTATAAGATCAT
1 GACAACTTCTGGTGTCAATTGCAAAATCAT
41168 GACAA
1 GACAA
41173 TTTCGATTAA
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
30 142 0.99
31 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (30 bp):
GACAACTTCTGGTGTCAATTGCAAAATCAT
Found at i:41600 original size:35 final size:36
Alignment explanation
Indices: 41559--41627 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
41549 CTTGATCAAC
* *
41559 ATACATGTCTTTTCATATAGAC-AACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACAAACTTTATGATCA
41594 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACA-AACTTTATGA
41628 AAAATTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 20 0.67
37 10 0.33
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (36 bp):
ATACATGTCTTTCCAAATAGACAAACTTTATGATCA
Found at i:42965 original size:49 final size:49
Alignment explanation
Indices: 42889--42987 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
42879 TTAATAAAGT
* * *
42889 TGTTTTCTCGAACATTAATATATCTCTTTTTCCTTTTGGAATTCAAAAA
1 TGTTGTCTCGAACATTAATATACCTCTTATTCCTTTTGGAATTCAAAAA
42938 TGTTGTCTCGAACATTAATATACCTCTTATTCCTTTTGGAATTCAAAAA
1 TGTTGTCTCGAACATTAATATACCTCTTATTCCTTTTGGAATTCAAAAA
42987 T
1 T
42988 TATGTTTAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.44
Consensus pattern (49 bp):
TGTTGTCTCGAACATTAATATACCTCTTATTCCTTTTGGAATTCAAAAA
Found at i:47590 original size:16 final size:16
Alignment explanation
Indices: 47569--47599 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47559 AATTAAGAAG
47569 GAATTGAAAGGGAACT
1 GAATTGAAAGGGAACT
*
47585 GAATTGAGAGGGAAC
1 GAATTGAAAGGGAAC
47600 GGAAAAAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.35, T:0.16
Consensus pattern (16 bp):
GAATTGAAAGGGAACT
Found at i:48772 original size:10 final size:11
Alignment explanation
Indices: 48752--48777 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48742 ATTAAGACCA
48752 TTTTTCTTTTT
1 TTTTTCTTTTT
48763 TTTTTCTTTTT
1 TTTTTCTTTTT
48774 TTTT
1 TTTT
48778 ATAGCCACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:54338 original size:40 final size:41
Alignment explanation
Indices: 54290--54384 Score: 113
Period size: 46 Copynumber: 2.2 Consensus size: 41
54280 CAATCAATTA
54290 CAAT-CAACAATCATAACAA-TAGCAAACTCTCAATCTAAT
1 CAATCCAACAATCATAACAACTAGCAAACTCTCAATCTAAT
*
54329 CAATCCAACATTCATAACAATCTCTCTAGCAAACTCTCAATCTAAT
1 CAATCCAACAATCATAACAA-----CTAGCAAACTCTCAATCTAAT
*
54375 CAACCCAACA
1 CAATCCAACA
54385 TGGGTGATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
39 4 0.09
40 14 0.30
46 29 0.62
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.23
Consensus pattern (41 bp):
CAATCCAACAATCATAACAACTAGCAAACTCTCAATCTAAT
Found at i:65395 original size:21 final size:22
Alignment explanation
Indices: 65369--65418 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
65359 ACCCTAATCG
**
65369 TAATTTTCTTTTTCTTT-CTTT
1 TAATTTTCAATTTCTTTGCTTT
65390 TAATTTTCAATTTCTTTGCTTT
1 TAATTTTCAATTTCTTTGCTTT
65412 TAATTTT
1 TAATTTT
65419 GGTTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (22 bp):
TAATTTTCAATTTCTTTGCTTT
Found at i:67412 original size:17 final size:17
Alignment explanation
Indices: 67387--67430 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
67377 GTTTTAGACT
*
67387 AAGAAAAAAATAAACAG
1 AAGATAAAAATAAACAG
67404 AAGATAAAAATAAACAG
1 AAGATAAAAATAAACAG
*
67421 AAGTTAAAAA
1 AAGATAAAAA
67431 AAGGTAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.11
Consensus pattern (17 bp):
AAGATAAAAATAAACAG
Found at i:67558 original size:20 final size:20
Alignment explanation
Indices: 67535--67572 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
67525 TTAGTTTTTG
67535 TAGGCATATTCTGATTTTAT
1 TAGGCATATTCTGATTTTAT
*
67555 TAGGCTTATTCTGATTTT
1 TAGGCATATTCTGATTTT
67573 CTGTTTTTTT
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:0.21, C:0.11, G:0.16, T:0.53
Consensus pattern (20 bp):
TAGGCATATTCTGATTTTAT
Found at i:69496 original size:42 final size:42
Alignment explanation
Indices: 69437--69516 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
69427 CTAAATTCTA
* *
69437 CTCCATCTATAGGTAATTCATCAAAATAAAGCTAATATACTC
1 CTCCATCTATAGATAATTCATCAAAATAAAACTAATATACTC
*
69479 CTCCATCTCTAGATAATTCATCAAAATAAAACTAATAT
1 CTCCATCTATAGATAATTCATCAAAATAAAACTAATAT
69517 TAATTGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.31
Consensus pattern (42 bp):
CTCCATCTATAGATAATTCATCAAAATAAAACTAATATACTC
Found at i:70123 original size:295 final size:293
Alignment explanation
Indices: 69590--70179 Score: 919
Period size: 295 Copynumber: 2.0 Consensus size: 293
69580 AATCTTGATT
** * *
69590 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCATTAATCCTTTGGAATTTCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACAAATCCTTTGGAATTCCGACA
* * **
69655 GAGGAGTTCAACCGATAAATCCTAATATCCACACATAATCAATATGTAATTAAAACACACTTAAT
66 AAGGAGTTCAACCGATAAATCCTAATATCCACACACAATCAATACATAATTAAAACACACTTAAT
* * * *
69720 CATAAAAATAAAAATAGTAAATTATAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCATCG
131 CATAAAAACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCAGCA
*
69785 AGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAGTCAAAAGGAAGCACCACAT
196 AGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGAC-AAAAAAAAGCCAAAAGGAAGCACCACAT
*
69850 TAATCCTCAATTTGGCCTTTTAGGTAATTTCCATA
260 TAATCCTCAATTTGGCC-TTTAAGTAATTTCCATA
* * *
69885 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACAAATCCTTTGGAATTCCGACA
1 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACAAATCCTTTGGAATTCCGACA
* * * *
69950 AAGGAGTTGAATCGGTAAATCCTAATATCCACACACAATTAATACATAATTAAAACACACTTAAT
66 AAGGAGTTCAACCGATAAATCCTAATATCCACACACAATCAATACATAATTAAAACACACTTAAT
* * *
70015 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGGAGGAAAAGTAAGGGAGGAAATTTAGCA
131 CATAAAAACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCAGCA
* * *
70080 AGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCGCATT
196 AGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAAGCACCACATT
70145 AATCCTCAATTTGGCCTTTAAGTAATTTCCATA
261 AATCCTCAATTTGGCCTTTAAGTAATTTCCATA
70178 GC
1 GC
70180 CACTAAAAAT
Statistics
Matches: 268, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
293 18 0.07
294 41 0.15
295 209 0.78
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (293 bp):
GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACAAATCCTTTGGAATTCCGACA
AAGGAGTTCAACCGATAAATCCTAATATCCACACACAATCAATACATAATTAAAACACACTTAAT
CATAAAAACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCAGCA
AGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAAGCACCACATT
AATCCTCAATTTGGCCTTTAAGTAATTTCCATA
Found at i:72717 original size:251 final size:253
Alignment explanation
Indices: 72274--72803 Score: 974
Period size: 251 Copynumber: 2.1 Consensus size: 253
72264 TTATCTGGTA
*
72274 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCTTGTACTTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
* **
72339 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGTGTGCCGT
66 TCCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
*
72404 GACAGACCCGTCAAATATGCTGATGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
131 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
72469 ACGTGGAATAAAAATTAAATATTTTTT-AATATA-TTTATTTTATTGAAATTTATTTT
196 ACGTGGAATAAAAATTAAATATTTTTTGAATATATTTTATTTTATTGAAATTTATTTT
72525 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
*
72590 TCCTACAAATTTGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
66 TCCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
*
72655 GACAGACCCGTCAAATATGTTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
131 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
72720 ACGTGGAATAAAAATTAAATATTTTTTGAATATATTTTATTTTATTGAAATTTATTTT
196 ACGTGGAATAAAAATTAAATATTTTTTGAATATATTTTATTTTATTGAAATTTATTTT
*
72778 GGTAAAAGTACCCGGGAGATCCCTGT
1 GGTAAAAGTACCCGGGAGGTCCCTGT
72804 CTAACTTTTA
Statistics
Matches: 269, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
251 215 0.80
252 6 0.02
253 48 0.18
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (253 bp):
GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
TCCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
ACGTGGAATAAAAATTAAATATTTTTTGAATATATTTTATTTTATTGAAATTTATTTT
Found at i:73236 original size:15 final size:15
Alignment explanation
Indices: 73216--73244 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
73206 TTCAGATTTC
73216 TTTTTTTT-AAAATA
1 TTTTTTTTAAAAATA
73230 TTTTTTTTAAAAATA
1 TTTTTTTTAAAAATA
73245 AAATTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTTTAAAAATA
Found at i:77281 original size:20 final size:21
Alignment explanation
Indices: 77251--77311 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 21
77241 AGCAAAGCTG
*
77251 TAGAAAACAGCCGCCTACCTC
1 TAGAGAACAGCCGCCTACCTC
*
77272 -AGAGAACAGCCGCCTACCCC
1 TAGAGAACAGCCGCCTACCTC
77292 TAGAGAACAGCCGCCT-CCTC
1 TAGAGAACAGCCGCCTACCTC
77312 CACCTGAGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.30, C:0.41, G:0.18, T:0.11
Consensus pattern (21 bp):
TAGAGAACAGCCGCCTACCTC
Found at i:78556 original size:42 final size:45
Alignment explanation
Indices: 78471--78558 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 45
78461 GAAATGGTAA
* *
78471 GTAATTTGGACTAACTACTTTTCTGCTAATTGTGTTACATAATTCT
1 GTAATTTGGACTAACTAC-ATTCTGCAAATTGTGTTACATAATTCT
78517 GTAATTTGGACTAACTA-ATT-TG-AAATTGTGTTACATAATTCT
1 GTAATTTGGACTAACTACATTCTGCAAATTGTGTTACATAATTCT
78559 ATTATCTACC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 19 0.47
43 2 0.05
44 2 0.05
46 17 0.43
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (45 bp):
GTAATTTGGACTAACTACATTCTGCAAATTGTGTTACATAATTCT
Found at i:79844 original size:30 final size:30
Alignment explanation
Indices: 79810--79869 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
79800 ATGAAAGATA
*
79810 AATTATTTGGAGAAG-CTAAAAAGAAAAAAG
1 AATTATTTGAAGAAGTC-AAAAAGAAAAAAG
* *
79840 AATTATTTTAAGGAGTCAAAAAGAAAAAAG
1 AATTATTTGAAGAAGTCAAAAAGAAAAAAG
79870 TTCAACGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.57, C:0.03, G:0.18, T:0.22
Consensus pattern (30 bp):
AATTATTTGAAGAAGTCAAAAAGAAAAAAG
Found at i:80119 original size:72 final size:74
Alignment explanation
Indices: 80038--80194 Score: 210
Period size: 72 Copynumber: 2.1 Consensus size: 74
80028 AAATTTTTAA
*
80038 GGGGCCAAATTAGAAACTTTCCAATTTTTTTAGTTGAAATGC-AT-ATATATGAAAGAATTCTTG
1 GGGGCCAAATTAGAAACTTTCCAATTTTTTCAGTTGAAATGCAATAATATATGAAAGAATTCTTG
80101 GCAATTTGG
66 GCAATTTGG
* * * *
80110 GGGGCCAAATTATAAATTTTCCAATTTTTTCATTTGAAGTGCATATATACATATATGAAAGAATT
1 GGGGCCAAATTAGAAACTTTCCAATTTTTTCAGTTGAAATGC--A-ATA-ATATATGAAAGAATT
*
80175 CTTGGCAGTTTGG
62 CTTGGCAATTTGG
80188 GGGGCCA
1 GGGGCCA
80195 TGGCCCCTGT
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
72 37 0.51
76 2 0.03
78 34 0.47
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (74 bp):
GGGGCCAAATTAGAAACTTTCCAATTTTTTCAGTTGAAATGCAATAATATATGAAAGAATTCTTG
GCAATTTGG
Found at i:81948 original size:20 final size:20
Alignment explanation
Indices: 81923--81960 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
81913 ATATAGTGGA
81923 TTACTAAACACCGCCCCCTT
1 TTACTAAACACCGCCCCCTT
**
81943 TTACTAGCCACCGCCCCC
1 TTACTAAACACCGCCCCC
81961 CTTGGACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.50, G:0.08, T:0.21
Consensus pattern (20 bp):
TTACTAAACACCGCCCCCTT
Found at i:81969 original size:21 final size:20
Alignment explanation
Indices: 81931--81969 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
81921 GATTACTAAA
**
81931 CACCGCCCCCTTTTACTAGC
1 CACCGCCCCCTTGGACTAGC
81951 CACCGCCCCCCTTGGACTA
1 CACCG-CCCCCTTGGACTA
81970 TTTTGCCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.15, C:0.51, G:0.13, T:0.21
Consensus pattern (20 bp):
CACCGCCCCCTTGGACTAGC
Done.