Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_50 ID=scaffold_50-JGI_221_v2.0
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: 23619
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.31
Warning! 620 characters in sequence are not A, C, G, or T
Found at i:1798 original size:22 final size:22
Alignment explanation
Indices: 1768--1813 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1758 ACACCAAAAC
*
1768 AGGCTTTTA-GCGGCGCTTTTTT
1 AGGCCTTTAGGCGGCG-TTTTTT
1790 AGGCCTTTAGGCGGCGTTTTTT
1 AGGCCTTTAGGCGGCGTTTTTT
1812 AG
1 AG
1814 CGCCGCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.11, C:0.17, G:0.30, T:0.41
Consensus pattern (22 bp):
AGGCCTTTAGGCGGCGTTTTTT
Found at i:1960 original size:43 final size:43
Alignment explanation
Indices: 1905--2132 Score: 275
Period size: 43 Copynumber: 5.3 Consensus size: 43
1895 TTTTATAAAT
1905 AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
1 AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
* * * *
1948 AAACGCCGCTAAAGACCATAACCTTTTAGCGGCGCTTTTACAAA
1 AAACGCCACTAAAGACCATGACC-TTTAGCGGCGCTTTTCCAAC
* * * *
1992 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTACAA-
1 AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
* * *
2034 AAAGCGCCACTAAAGACCAGGACCTTTAGTGGCGCTTTTCCCAC
1 AAA-CGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
* *
2078 AAACGCCGCTATAGA--ATAGACCTTTAGCGGCGCTTTTCTC-AC
1 AAACGCCACTAAAGACCAT-GACCTTTAGCGGCGCTTTTC-CAAC
2120 AAACGCCACTAAA
1 AAACGCCACTAAA
2133 AATATATCTT
Statistics
Matches: 161, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
41 1 0.01
42 35 0.22
43 83 0.52
44 42 0.26
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (43 bp):
AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
Found at i:2005 original size:87 final size:86
Alignment explanation
Indices: 1883--2132 Score: 292
Period size: 87 Copynumber: 2.9 Consensus size: 86
1873 GCGTCGCTAA
* * * *
1883 CTTTAGCGGAGTTTTTATAAATAAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
1 CTTTAGCGGCGCTTTTACAAA-AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
* *
1948 AAACGCCGCTAAAGACCATAAC
65 AAACGCCACTAAAGACCAGAAC
* * *
1970 CTTTTAGCGGCGCTTTTACAAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTACAA-
1 C-TTTAGCGGCGCTTTTACAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
*
2034 AAAGCGCCACTAAAGACCAGGAC
65 AAA-CGCCACTAAAGACCAGAAC
* * * * *
2057 CTTTAGTGGCGCTTTTCCCACAAACGCCGCTATAGA--ATAGACCTTTAGCGGCGCTTTTCTC-A
1 CTTTAGCGGCGCTTTTACAAAAAACGCCGCTAAAGACCAT-GACCTTTAGCGGCGCTTTTC-CAA
2119 CAAACGCCACTAAA
64 CAAACGCCACTAAA
2133 AATATATCTT
Statistics
Matches: 140, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 29 0.21
86 37 0.26
87 56 0.40
88 17 0.12
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTTACAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCAACA
AACGCCACTAAAGACCAGAAC
Found at i:2224 original size:25 final size:25
Alignment explanation
Indices: 2183--2242 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
2173 TTATTTAAAT
2183 TAAATA-T-TATTATGTTTTAAGGA
1 TAAATATTATATTATGTTTTAAGGA
2206 TAAATATTATATTATGTTTTAAGGA
1 TAAATATTATATTATGTTTTAAGGA
2231 TAAATATTATAT
1 TAAATATTATAT
2243 AAATATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 6 0.17
24 1 0.03
25 28 0.80
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (25 bp):
TAAATATTATATTATGTTTTAAGGA
Found at i:6267 original size:44 final size:44
Alignment explanation
Indices: 6210--6505 Score: 425
Period size: 44 Copynumber: 6.7 Consensus size: 44
6200 GTATGGGAAC
6210 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
* *
6254 ATAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
*
6298 ACAAAATCTGCTATCATT-GATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATC-TTCGATCTACTTCACGCCAATACATGAAG
*
6342 ACAAGATCTGCTAT-TATTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCT-TCGATCTACTTCACGCCAATACATGAAG
* * * * * * *
6386 ACAAGATTTGCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAG
6431 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
* * *
6475 ACAAGATTTACTTTCTTCGATCTACTTCACG
1 ACAAGATCTGCTATCTTCGATCTACTTCACG
6506 ACAACTCAGG
Statistics
Matches: 224, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 182 0.81
45 40 0.18
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (44 bp):
ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
Found at i:6276 original size:117 final size:118
Alignment explanation
Indices: 6070--6417 Score: 342
Period size: 117 Copynumber: 2.8 Consensus size: 118
6060 TACAATTTTA
* * * * * *
6070 TACTTCGCCACCAGTATGGGAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGATACATGA
1 TACTTCACCACCAGTATGGGAACACAAGATCTGCTACCTTCGATCTACTTCACGCCAATACATGA
* * * *
6135 AGACAATATTTGCTTTCTTCGATCTACTT-CGCCAATACATGAAGACAAGATC
66 AGACAAGATCTGCTATCTTCGATCTACTTACGCCAATACATGAAGACAAAATC
*
6187 TACTTCACCACCAGTATGGGAACACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGA
1 TACTTCACCACCAGTATGGGAACACAAGATCTGCTACCTTCGATCTACTTCACGCCAATACATGA
* *
6252 AGATAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAAATCTGC
66 AGACAAGATCTGCTATCTTCGATCTACTT-ACGCCAATACATGAAGACAAAA--T-C
* *** * * *
6309 TATCATTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTA-TTATTGATCTACTTCACG
1 TA-C--T--TC-AC--CA--CCAGTATGGGAACACAAGATCTGCTACCT-TCGATCTACTTCACG
* *
6373 CCAATACATGAAGACAAGATTTGCTTTCTTCGATCTACTT-CGCCA
55 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTACGCCA
6418 CCAGTATAGG
Statistics
Matches: 191, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
117 82 0.43
119 20 0.10
121 1 0.01
122 3 0.02
123 1 0.01
125 1 0.01
127 2 0.01
128 2 0.01
130 7 0.04
131 1 0.01
132 71 0.37
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (118 bp):
TACTTCACCACCAGTATGGGAACACAAGATCTGCTACCTTCGATCTACTTCACGCCAATACATGA
AGACAAGATCTGCTATCTTCGATCTACTTACGCCAATACATGAAGACAAAATC
Found at i:6692 original size:88 final size:88
Alignment explanation
Indices: 6506--7493 Score: 1516
Period size: 88 Copynumber: 11.2 Consensus size: 88
6496 CTACTTCACG
* * *
6506 ACAACTCAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTATCGGAT--AGGAAGGCAAGAT
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTC-GATGCAGGAAGGCAAGAT
6569 CTGCTATCTTCAACCTGCTCCACT
65 CTGCTATCTTCAACCTGCTCCACT
* ** *
6593 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTATAGGAAAGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC
6658 TGCTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * * * * * *
6681 ACGACCTAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTATTGGTACAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC
6746 TGCTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
*
6769 ACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCGA-TGTCGATGCAGGAAGGCAAGAT
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTC-ACTGTCGATGCAGGAAGGCAAGAT
6833 CTGCTATCTTCAACCTGCTCCACT
65 CTGCTATCTTCAACCTGCTCCACT
* * *
6857 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGACAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC
6922 TGCTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
*
6945 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGTAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC
*
7010 TGCTATCTTCAACCTACTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* *
7033 ACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC
*
7098 TGCTATCTTCAACCTACTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* *
7121 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTATCGATGTAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC
*
7186 TACTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* *
7209 ACAACCTAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC
* *
7274 TGCTGTCTTCAACTTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * *
7297 ACAACCGAGGGAGGCAAGGCTAGTATCTTCGATCTGCTTCACTCTCGATGCAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC
*
7362 TGCTATCTTCAAGCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * * * *
7385 ACAACCCAGGGAGGAAAGGCTGGTATCTTCGATATGCTTCGCCGTC-AGTACAGGAAGGCAAGAT
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGA-TGCAGGAAGGCAAGAT
* * *
7449 CTGTTATTTTCAACCTGCTTCACT
65 CTGCTATCTTCAACCTGCTCCACT
* * *
7473 GCAAACCAGAGAGGCAAGGCT
1 ACAACCCAGGGAGGCAAGGCT
7494 TTGTGATTTC
Statistics
Matches: 830, Mismatches: 66, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
86 2 0.00
87 45 0.05
88 782 0.94
89 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (88 bp):
ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC
TGCTATCTTCAACCTGCTCCACT
Found at i:9116 original size:11 final size:10
Alignment explanation
Indices: 9100--9127 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
9090 CCTGGAAGAG
9100 TTTTTTTTTC
1 TTTTTTTTTC
9110 TTTTTTTTTC
1 TTTTTTTTTC
9120 TTTTTTTT
1 TTTTTTTT
9128 GCACCATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:14441 original size:21 final size:19
Alignment explanation
Indices: 14404--14478 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
14394 AATCATATCT
14404 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
14423 TCCAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
14444 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
14463 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
14479 CTTGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:15110 original size:3 final size:3
Alignment explanation
Indices: 15093--15136 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
15083 ATTTCAATAG
*
15093 TAT TA- TAT TATT TAT TATT TAT TAT TAT TAT TGT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
15137 TCTATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:15310 original size:24 final size:22
Alignment explanation
Indices: 15254--15314 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
15244 TGTACATGGA
15254 TATATATATACA-TTTACATTT
1 TATATATATACATTTTACATTT
*
15275 TATAATGCATATACATTTCCTATATTT
1 TAT-AT--ATATACATTT--TACATTT
15302 TATATATATACAT
1 TATATATATACAT
15315 ATATTTTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
21 3 0.09
22 2 0.06
24 15 0.45
25 2 0.06
26 2 0.06
27 9 0.27
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (22 bp):
TATATATATACATTTTACATTT
Found at i:15352 original size:16 final size:16
Alignment explanation
Indices: 15331--15377 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
15321 TTTCATTTTA
*
15331 TATATATATATATATT
1 TATATATATACATATT
*
15347 TATATACATACATATT
1 TATATATATACATATT
* *
15363 TTTACATATACATAT
1 TATATATATACATAT
15378 ACATACTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATATATACATATT
Found at i:17306 original size:19 final size:19
Alignment explanation
Indices: 17280--17326 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
17270 AATGTCTCTT
*
17280 TATGCATT-CATTTCATGCA
1 TATGCATTACATTGCAT-CA
*
17299 TTTGCATTACATTGCATCA
1 TATGCATTACATTGCATCA
17318 TATGCATTA
1 TATGCATTA
17327 AAATCCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (19 bp):
TATGCATTACATTGCATCA
Found at i:20069 original size:15 final size:15
Alignment explanation
Indices: 20044--20082 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
20034 AAAATGACGA
*
20044 AAAAAT-GAAAATG-
1 AAAAATGGAAAAAGT
20057 AAAAATGGAAAAAGT
1 AAAAATGGAAAAAGT
20072 AAAAATGGAAA
1 AAAAATGGAAA
20083 GGCTAGGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 11 0.48
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (15 bp):
AAAAATGGAAAAAGT
Found at i:20076 original size:22 final size:23
Alignment explanation
Indices: 20033--20078 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
20023 TTGAGTCGTA
*
20033 AAAAATGACGAAAAAATGAAAATG
1 AAAAATGA-GAAAAAATAAAAATG
*
20057 AAAAATG-GAAAAAGTAAAAATG
1 AAAAATGAGAAAAAATAAAAATG
20079 GAAAGGCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.13
Consensus pattern (23 bp):
AAAAATGAGAAAAAATAAAAATG
Found at i:21419 original size:88 final size:88
Alignment explanation
Indices: 21311--21923 Score: 960
Period size: 88 Copynumber: 7.0 Consensus size: 88
21301 GTGAAACTTT
* *
21311 AGCCTTGTCTCCCTGAGTAGTAGTGGAATAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
*
21376 CAGCAAAGTAGATCGAAGACCTC
66 CAGCGAAGTAGATCGAAGACCTC
* * *
21399 AGCCTTGTCTCCCT-AGGTAGTAGTGGAGTAGGTTGAAAGTAGCAGATCTTGTCTTCTTGTATTG
1 AGCCTTGTCTCCCTGA-GCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
21463 GCAGCGAAGTAGATCGAAGACCTC
65 GCAGCGAAGTAGATCGAAGACCTC
* * *
21487 AGCCCTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATATTGTCTTCTTGTATTGG
1 AGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* *
21552 CAGTGAAGTAGATCAAAGACCTC
66 CAGCGAAGTAGATCGAAGACCTC
* *
21575 AGCCTTGTCTCCCT-AGGTAGTAGTGGAGTAGGTTGAAAATAGTAGATCTTGTCTTCCTGTATTG
1 AGCCTTGTCTCCCTGA-GCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
*
21639 GCAGCGAAGTAGATCGAAAACCTC
65 GCAGCGAAGTAGATCGAAGACCTC
*
21663 AGCCTCGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
21728 CAGCGAAGTAGATCGAAGACCTC
66 CAGCGAAGTAGATCGAAGACCTC
* * * *
21751 AGCCTTGTCTCCCTAAGCAGTAGCGGAGGAGGTTGAAAATAGCAGATCTTGTCTTCCTGGATTGG
1 AGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
21816 CAGCGAAGTAGATCGAAGACCTC
66 CAGCGAAGTAGATCGAAGACCTC
* * ** *
21839 AGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAATATAGCAGATCTTACCTTCCTGTACTGG
1 AGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* *
21904 CAGTGAAGCAGATCGAAGAC
66 CAGCGAAGTAGATCGAAGAC
21924 ACCAGTTTTA
Statistics
Matches: 483, Mismatches: 38, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
87 2 0.00
88 479 0.99
89 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (88 bp):
AGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
CAGCGAAGTAGATCGAAGACCTC
Found at i:22456 original size:44 final size:41
Alignment explanation
Indices: 22228--22472 Score: 174
Period size: 44 Copynumber: 5.7 Consensus size: 41
22218 ACTGAGAAAG
* * * *
22228 CAAATCTTATCCCCCTGAAGTTGTAGTGGGGCAGATTAAAGATGG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-AAGA--C
* *
22273 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAA-AGC
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAGA-C
* * * * *
22315 CAATAGTCTTACCTCCCTGAGGTTGCAGTGGAGCTGATTAAAAT
1 CAA-A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAGAC
* * * * *
22359 CAGATCTTATCTCCCT-AAGGTTGCAG-AGAGCAGATCACAT
1 CAAATCTTATCTCCCTGAA-GTTGCAGTGGAGCAGATAAGAC
*
22399 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAC
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-AAGAC
*
22442 CTAAATCCTATCTCCCT-AAGGTTGCAGTGGA
1 C-AAATCTTATCTCCCTGAA-GTTGCAGTGGA
22473 ATGGATTAAA
Statistics
Matches: 163, Mismatches: 27, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
40 25 0.15
41 16 0.10
42 22 0.13
43 8 0.05
44 59 0.36
45 33 0.20
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (41 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAGAC
Found at i:22508 original size:126 final size:129
Alignment explanation
Indices: 22277--22570 Score: 311
Period size: 126 Copynumber: 2.3 Consensus size: 129
22267 AGATGGCGAA
* * * *
22277 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAG-CCAATAGTCTTACCTCCCTGAGGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACCAATAGTCCTACCTCCCTAAGGTTGC
* * * * *
22341 AGTGGAGCTGATTAAAATCAGATCTTATCTCCCTAAGGTTGC-A-GAGAGCAGATCACA-T-CAA
66 AGTGGAGATGATTAAAATCAGATCTTATCT-CCTAAAGTTGCAATAAAAGAAGATCA-AGTACAA
22402 G
129 G
* *
22403 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACCTAA-A-TCCTATCTCCCTAAGGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACC-AATAGTCCTACCTCCCTAAGGTTG
* * * *
22466 CAGTGGA-ATGGATTAAAATATCCAGAT-TTATCT-TTAAAGTTGCAATAAAATAAGTTGAAGTC
65 CAGTGGAGAT-GATT-AAA-AT-CAGATCTTATCTCCTAAAGTTGCAATAAAAGAAGATCAAGT-
22528 ACAAG
125 ACAAG
22533 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGA
22571 TAGCAAATTT
Statistics
Matches: 141, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
125 1 0.01
126 69 0.49
127 8 0.06
128 17 0.12
129 5 0.04
130 41 0.29
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACCAATAGTCCTACCTCCCTAAGGTTGC
AGTGGAGATGATTAAAATCAGATCTTATCTCCTAAAGTTGCAATAAAAGAAGATCAAGTACAAG
Found at i:22980 original size:21 final size:21
Alignment explanation
Indices: 22954--22993 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
22944 CACAGTAGTC
*
22954 CCCCGCACGTCGCGCACGTTG
1 CCCCGCACGTCGCACACGTTG
22975 CCCCGCACGTCGCACACGT
1 CCCCGCACGTCGCACACGT
22994 CACCCAGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.50, G:0.25, T:0.12
Consensus pattern (21 bp):
CCCCGCACGTCGCACACGTTG
Found at i:23003 original size:21 final size:21
Alignment explanation
Indices: 22958--23003 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
22948 GTAGTCCCCC
* ** *
22958 GCACGTCGCGCACGTTGCCCC
1 GCACGTCGCACACGTCACCCA
22979 GCACGTCGCACACGTCACCCA
1 GCACGTCGCACACGTCACCCA
23000 GCAC
1 GCAC
23004 AACGGTCGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.48, G:0.24, T:0.11
Consensus pattern (21 bp):
GCACGTCGCACACGTCACCCA
Done.