Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_201 ID=scaffold_201-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: 10365
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.25
Warning! 971 characters in sequence are not A, C, G, or T
Found at i:3477 original size:22 final size:21
Alignment explanation
Indices: 3446--3492 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3436 AGTCAAAGTC
* *
3446 AAAATGAAAATGAAAAAAATCA
1 AAAATCAAAAT-AAAAAAAACA
3468 AAAATCAAAATAAAAAAAACA
1 AAAATCAAAATAAAAAAAACA
3489 AAAA
1 AAAA
3493 GAAGAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.11
Consensus pattern (21 bp):
AAAATCAAAATAAAAAAAACA
Found at i:3532 original size:50 final size:52
Alignment explanation
Indices: 3461--3560 Score: 134
Period size: 50 Copynumber: 2.0 Consensus size: 52
3451 GAAAATGAAA
3461 AAAATCAAAAATCAAAATAAAAAAAACAAAAAG-AAGAAAGAA-GAAAAAATC
1 AAAATCAAAAATCAAAATAAAAAAAACAAAAAGAAAG-AAGAATGAAAAAATC
* ** *
3512 AAAATC-AAGATCAAAATAAAAATGAGAAAAAGAAAGAAGAATGAAAAAA
1 AAAATCAAAAATCAAAATAAAAAAAACAAAAAGAAAGAAGAATGAAAAAA
3561 GAGAAATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 27 0.63
51 16 0.37
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (52 bp):
AAAATCAAAAATCAAAATAAAAAAAACAAAAAGAAAGAAGAATGAAAAAATC
Found at i:5576 original size:5 final size:5
Alignment explanation
Indices: 5561--5589 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5551 GGATCATTCT
5561 TAAAA -AAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
5590 ATTTTGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:6007 original size:99 final size:99
Alignment explanation
Indices: 5779--6262 Score: 659
Period size: 100 Copynumber: 4.9 Consensus size: 99
5769 AAAACAAAAC
*
5779 CTTACTTCCCAGGCGGTGCAGTAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACAT
1 CTTACCTCCCAGGCGGTGCAGTAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACAT
* * *
5844 TGCGGTTAAAAAGATTAAAGCTACATCAG-AAAT
66 TGCAGTTAAAAAGATTAAAGCTACAGCAGCGAAT
* * * * * * *
5877 CCTACCTCTCAGGCGGTGTAGTGGAATAGATTAAAGCCACAACGGTGAATCTTGCATCTTTGACA
1 CTTACCTCCCAGGCGGTGCAGT-AAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACA
*
5942 TTGCAGTTAAAAAGATTAAAGCTACAGTAGCGAAT
65 TTGCAGTTAAAAAGATTAAAGCTACAGCAGCGAAT
*
5977 CTTATCTCCCAGGCGGTGCAGTAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACAT
1 CTTACCTCCCAGGCGGTGCAGTAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACAT
*
6042 TGCGGTTAAAAAGATTAAAGCTACAGCAGCGAAT
66 TGCAGTTAAAAAGATTAAAGCTACAGCAGCGAAT
* * * *
6076 CTTATCTCCCAGGTGGTGCAGTAAAAAACATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACA
1 CTTACCTCCCAGGCGGTGCAGT-AAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACA
* *
6141 TTAC-GATTAAAAAGATTAAAGCTACAGCACCGAAT
65 TTGCAG-TTAAAAAGATTAAAGCTACAGCAGCGAAT
* * * * * *
6176 CTTACCTCTCAGGCGGTGCAGTAGAACAGATTAAAACCACATCGGTGAATCTTGCTTCTCCT-AG
1 CTTACCTCCCAGGCGGTGCAGTA-AAAAGATTAAAGCCACAACGGTGAATCTTGCCTCT-CTGAC
*
6240 ATTACAGTTAAAAAGATTAAAGC
64 ATTGCAGTTAAAAAGATTAAAGC
6263 CACATCGGTG
Statistics
Matches: 342, Mismatches: 37, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
98 18 0.05
99 159 0.46
100 162 0.47
101 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (99 bp):
CTTACCTCCCAGGCGGTGCAGTAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACAT
TGCAGTTAAAAAGATTAAAGCTACAGCAGCGAAT
Found at i:6266 original size:50 final size:50
Alignment explanation
Indices: 5795--6279 Score: 230
Period size: 50 Copynumber: 9.8 Consensus size: 50
5785 TCCCAGGCGG
* *
5795 TGCAG-TAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCT-CTGACAT
1 TGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCT-AGAT
* * * * * * * * **
5844 TGCGGTTAAAAAGATTAAAGCTACATCAG-AAATCCTACCTCT-C-AGGCGG
1 TGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCTA-G-AT
* ** * * *
5893 TGTAGTGGAATAGATTAAAGCCACAACGGTGAATCTTGCATCT-TTGACAT
1 TGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCT-AGAT
* *** * * **
5943 TGCAGTTAAAAAGATTAAAGCTACAGTAGCGAATCTT--ATCTCCCAGGCGG
1 TGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCTA-G-AT
* *
5993 TGCAG-TAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCT-CTGACAT
1 TGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCT-AGAT
* * * * * * *
6042 TGCGGTTAAAAAGATTAAAGCTACAGCAGCGAATCTT--ATCTCCCAGGT
1 TGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCTAGAT
* * * *
6090 GGTGCAGTAAAAAACATTAAAGCCACAACGGTGAATCTTGCCTC-CCTGACAT
1 --TGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCT-AGAT
* * * *** * * **
6142 TAC-GATTAAAAAGATTAAAGCTACAGCACCGAATCTTACCTCT-C-AGGCGG
1 TGCAG-TTAAAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCTA-G-AT
* * * *
6192 TGCAG-TAGAACAGATTAAAACCACATCGGTGAATCTTGCTTCTCCTAGAT
1 TGCAGTTA-AAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCTAGAT
* *
6242 TACAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTG
1 TGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTG
6280 ATTAAAGCTA
Statistics
Matches: 311, Mismatches: 97, Indels: 55
0.67 0.21 0.12
Matches are distributed among these distances:
47 1 0.00
48 11 0.04
49 70 0.23
50 212 0.68
51 11 0.04
52 6 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (50 bp):
TGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTGCATCTCCTAGAT
Found at i:6300 original size:25 final size:25
Alignment explanation
Indices: 6254--6303 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6244 CAGTTAAAAA
* * *
6254 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
6279 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
6304 ACTCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:6376 original size:125 final size:125
Alignment explanation
Indices: 6154--6391 Score: 334
Period size: 125 Copynumber: 1.9 Consensus size: 125
6144 CGATTAAAAA
* * * * *
6154 GATTAAAGCTACAGCACCGAATCTTACCTCTCAGGCGGTGCAGTAGAACAGATTAAAACCACATC
1 GATTAAAGCTACAACACCGAATCTTACCTCCCAAGCGATGCAGTAGAACAGATTAAAACCAAATC
* *
6219 GGTGAATCTTGCTTCTCCTAGATTACAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
66 GGTGAATCTTGCTTCTCCGACATTACAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
* * *
6279 GATTAAAGCTACAACAGCGAATCTTA-CTCCCCAAGCGATGCAGTGGAACAGATTAAAGCCAAAT
1 GATTAAAGCTACAACACCGAATCTTACCT-CCCAAGCGATGCAGTAGAACAGATTAAAACCAAAT
* * * *
6343 TGGTGAATTTTGCTTCTCCGACATTGCAGTTAAAAATATTAAAGCCACA
65 CGGTGAATCTTGCTTCTCCGACATTACAGTTAAAAAGATTAAAGCCACA
6392 ATGGCGAATC
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
124 2 0.02
125 96 0.98
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (125 bp):
GATTAAAGCTACAACACCGAATCTTACCTCCCAAGCGATGCAGTAGAACAGATTAAAACCAAATC
GGTGAATCTTGCTTCTCCGACATTACAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
Found at i:6553 original size:44 final size:43
Alignment explanation
Indices: 6505--7412 Score: 276
Period size: 44 Copynumber: 21.0 Consensus size: 43
6495 AATGGGACAA
* *
6505 ATTGAAGGTACAAATCTTATCTGCCTGAGGTTGCAGTAGAGCAG
1 ATTGAA-GTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * * *
6549 ATTGAAGCAGATAATCCTATTTCCCTGAAGTTGCAG-AGAAGCGG
1 ATTGAAGTACA-AATCTTATCTCCCTGAAGTTGCAGTAG-AGCAG
* * * **
6593 ATTGAAGTAGTAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGG
1 ATTGAAGTA-CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * ** *
6637 ATCGCA-T-CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 ATTGAAGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * * * * * *
6678 ACTG-AGTAATCCAGTCTTAACCCCCTAAAGTTGCAGTGGGGCAG
1 ATTGAAGT-A-CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * *
6722 ATCGAAGATGACAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAA
1 ATTGAAG-T-ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * *
6767 ATTGAAG-CCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGG
1 ATTGAAGTAC-A-AATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* ** * *
6811 ATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
1 ATT-GAAGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * **
6855 A-TCACA-TAC-AGTCTTATCTCCCTGAAGTTGCAGTGGAATAG
1 ATTGA-AGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * * * *
6896 A-CGAAAG-AAATCAATCCTATCTCCCTAAAGTTGCAGTGGAG-TG
1 ATTG-AAGTACA--AATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* ** * *
6939 AATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
1 -ATT-GAAGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * * * *
6984 -GTCACA-T-CCAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAG
1 ATTGA-AGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
*** * * * *
7025 ACAAAAG-AAATCAATAC-TATCTCCCTGAAGTTGTAGTGGAGCTG
1 ATTGAAGTACA--AAT-CTTATCTCCCTGAAGTTGCAGTAGAGCAG
* ** * *
7069 ATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
1 ATT-GAAGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * *
7113 A-TCACA-TAC-AGTCTTATCTCTCTGAAGTTACAGT-GAAGCAG
1 ATTGA-AGTACAAATCTTATCTCCCTGAAGTTGCAGTAG-AGCAG
* * * * **
7154 A-CGAAAG-AAATCAATCCTATCTCTCTGAAGTTGCAG-AGGAGTGG
1 ATTG-AAGTACA--AATCTTATCTCCCTGAAGTTGCAGTA-GAGCAG
* *** * *
7198 ATTAAAACCCCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
1 ATT-GAAGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * *
7242 A-TCACA-T-CCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA-
1 ATTGA-AGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
** * * * * * *
7282 AACGAAAG-AAATCAATCCTATCTCTCTAAAGTTACAGTGGAGC-G
1 ATTG-AAGTACA--AATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * **
7326 AATTAAAACTACAGATCTTATCTCAATGAAGTTGCAGTAGAGCAG
1 -ATT-GAAGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * * * * *
7371 ATCGCA-TTC-AGTCTTATCTCCCAGAAGTTACAGTGGAGCAG
1 ATTGAAGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
7412 A
1 A
7413 CGAAAAAAAG
Statistics
Matches: 635, Mismatches: 169, Indels: 123
0.69 0.18 0.13
Matches are distributed among these distances:
40 3 0.00
41 174 0.27
42 15 0.02
43 18 0.03
44 360 0.57
45 55 0.09
46 10 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
ATTGAAGTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
Found at i:6924 original size:218 final size:218
Alignment explanation
Indices: 6514--6934 Score: 589
Period size: 218 Copynumber: 1.9 Consensus size: 218
6504 AATTGAAGGT
* * *
6514 ACAAATCTTATCTGCCTGAGGTTGCAGTAGAGCAGATTGAAGCAGATAATCCTATTTCCCTGAAG
1 ACAAATCTTATCTCCCTGAGGTTGCAGTAGAGCAAATTGAAGCAGATAATCCTATCTCCCTGAAG
* ** * ** *
6579 TTGCAGAGAAGCGGATTGAAGTAGTAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAT
66 TTGCAGAGAAGCGGATTAAACCAGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACAT
* * * *
6644 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAATCCAGTCTTAACCCCCTAAAGT
131 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAGAAATCCAATCCTAACCCCCTAAAGT
6709 TGCAGTGGGGCAGATCGAAGATG
196 TGCAGTGGGGCAGATCGAAGATG
* *
6732 ACAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAAATTGAAGCCGATAATCCTATCTCCCTGAAG
1 ACAAATCTTATCTCCCTGAGGTTGCAGTAGAGCAAATTGAAGCAGATAATCCTATCTCCCTGAAG
* *
6797 TTGCAGTGGAGCGGATTAAAACCA-CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACA
66 TTGCAGAGAAGCGGATT-AAACCAGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACA
* * *
6861 TACA-GTCTTATCTCCCTGAAGTTGCAGTGGAATAGAC-GAAAGAAAT-CAATCCTATCTCCCTA
130 T-CAGGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTG--AGAAATCCAATCCTAACCCCCTA
6923 AAGTTGCAGTGG
192 AAGTTGCAGTGG
6935 AGTGAATTAA
Statistics
Matches: 178, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
217 1 0.01
218 167 0.94
219 10 0.06
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (218 bp):
ACAAATCTTATCTCCCTGAGGTTGCAGTAGAGCAAATTGAAGCAGATAATCCTATCTCCCTGAAG
TTGCAGAGAAGCGGATTAAACCAGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACAT
CAGGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAGAAATCCAATCCTAACCCCCTAAAGT
TGCAGTGGGGCAGATCGAAGATG
Found at i:7506 original size:129 final size:129
Alignment explanation
Indices: 6737--7490 Score: 1037
Period size: 129 Copynumber: 5.8 Consensus size: 129
6727 AGATGACAAA
* * * **
6737 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAATTG-AAGCCGAT-AATCCTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAG-AAATCAATCCTATCTCCCTGAAGTTG
6800 CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATACA
64 CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATACA
6865 G
129 G
** *
6866 TCTTATCTCCCTGAAGTTGCAGTGGAATAGACGAAAGAAATCAATCCTATCTCCCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTGCA
* * * *
6931 GTGGAGTGAATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCACATCCAG
66 GTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATACAG
* * * *
6995 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGACAAAAGAAATCAATACTATCTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTGCA
*
7060 GTGGAGCTGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATACAG
66 GTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATACAG
* * * *
7124 TCTTATCTCTCTGAAGTTACAGTGAAGCAGACGAAAGAAATCAATCCTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTGCA
* * * *
7189 GAGGAGTGGATTAAAACCCCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAG
66 GTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATACAG
* * * *
7253 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACGAAAGAAATCAATCCTATCTCTCTAAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTGCA
* * ** * *
7318 GTGGAGCGAATTAAAACTACAGATCTTATCTCAATGAAGTTGCAGTAGAGCAGATCGCATTCAG
66 GTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATACAG
* * * * *
7382 TCTTATCTCCCAGAAGTTACAGTGGAGCAGACGAAAAAAAGT-AATCCTATCTTCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAA-TCAATCCTATCTCCCTGAAGTTGC
* ** ** * *
7446 AGTGAAGCGGATTAAAATGATGGATCTTATCTATCTGGAGTTGCA
65 AGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
7491 ATATAGCATA
Statistics
Matches: 551, Mismatches: 71, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
128 3 0.01
129 547 0.99
130 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTGCA
GTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATACAG
Found at i:8480 original size:19 final size:19
Alignment explanation
Indices: 8456--8493 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
8446 GTGATTTCAA
*
8456 CTTTTATTTCTCTGTTTCT
1 CTTTTATTTCTCAGTTTCT
*
8475 CTTTTATTTTTCAGTTTCT
1 CTTTTATTTCTCAGTTTCT
8494 TTAGTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.68
Consensus pattern (19 bp):
CTTTTATTTCTCAGTTTCT
Found at i:10248 original size:109 final size:108
Alignment explanation
Indices: 10019--10365 Score: 532
Period size: 109 Copynumber: 3.2 Consensus size: 108
10009 AAAGAAAATT
* * * * * *
10019 TTTCTAAATGAGGCAATATTTAGCATTTGGAAATTCGAGGAAACGTGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGA-GAAACATGCCCTAAGGTGCTGGGTGT
10084 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTAAAAA
65 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTAAAAA
* *
10128 TTCCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAATGTGCTGGGTGTC
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTC
10193 GATTTTTCTCGTTCAACCAAATAGCTAAATATACCTTCTAAAAA
66 GATTTTTCTCGTTCAACCAAATAGCTAAATAT-CCTTCTAAAAA
*
10237 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGCAAGCATGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-AAACATGCCCTAAGGTGCTGGGTGT
* * * * *
10302 CAATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAT
65 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTAAAAA
*
10346 TTTTAAAATAAGGCAATGTT
1 TTTCAAAATAAGGCAATGTT
Statistics
Matches: 219, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
108 57 0.26
109 109 0.50
110 53 0.24
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (108 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTC
GATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTAAAAA
Done.