Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 2 of 32
Found at i:138413 original size:55 final size:55
Alignment explanation
Indices: 138329--138572 Score: 366
Period size: 55 Copynumber: 4.3 Consensus size: 55
138319 TTTCACCCTT
138329 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
*
138384 TAGTCCTCAAAGAGCAGAACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
* * *
138439 TAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTCGGTGGCACCTT-C
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
*
138494 -AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTCC
1 TAGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
138554 TAGTCCTCAAAGAGCAGGA
1 TAGTCCTCAAAGAGCAGGA
138573 TGCTCTCCCC
Statistics
Matches: 171, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
54 19 0.11
55 101 0.59
56 3 0.02
59 3 0.02
60 27 0.16
61 18 0.11
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (55 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
Found at i:138439 original size:582 final size:568
Alignment explanation
Indices: 136911--139165 Score: 2493
Period size: 582 Copynumber: 3.9 Consensus size: 568
136901 TTAGACCTTC
* *
136911 AGTCCTCAAAGAGCAGGACTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCGGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAA
* * * * *
136976 AAGCAAGACTCCTTTTAAAACCCACACATGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG
65 GAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG
*
137041 CTCTCC-CCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGT
130 CTC-CCACCTTTCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGT
*
137105 GGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCA
194 GGCACTTCCTAGTCCTCAAAGAGCAGGACGCC-TTC--A-CCCACAC-A-TT-GT-GCACCTTTA
*
137170 GTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTC
251 GTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCACCTT-CTAGTC
* * ** *
137234 CTCAAAGAGCAGGACG-C---T----CTCTC-C---TT--TCACCCTT--TAGTCCTCAAAGAGC
309 CTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGC
137283 AGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
374 AGGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGA
* * **
137348 ---C---TCATTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTTAAAGAGCAGGATACT
432 CGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCT
** * *
137407 CTCTTCTCTCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTT
497 CTCCCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCC---T--TTT-AAAGCCCACACAAGTT
*
137472 GGTGGCACCTCC-
556 GGTGGCACTTCCT
137484 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
* * *
137549 AGCAGGACACCTTTTCCATTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-GGTCCTCAAAGAG
66 AGCAGGACGCC---T---TTT-AAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAG
* ** *
137613 CAGGACTCCTTTTAAAGCCCACACATGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG-C-
123 CAGGAC-GC---T----CCCAC-C---TT--TCACCCTT-C-AGTCCTCAAAGAGCAGGACGCCT
* ** * * *
137676 TCT-----CC-C-C---TT--TCACCCTT--TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCTC
172 TTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCC--TT-CA-CCC
*
137727 ACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTT
233 ACAC-A-TT-GT-GCACCTT--TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTT
137791 GGTGGCACCTTC-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTT
292 GGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTT
137855 CCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCA
357 CCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCA
*
137920 AAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGA
422 AAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGA
137985 GCAGGACGCTCTCCCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACA
487 GCAGGACGCTCTCCCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACA
*
138050 AGTTGGTGGCACTTCTT
552 AGTTGGTGGCACTTCCT
*
138067 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
138132 AGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
66 AGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG-
*
138197 CTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
130 C--T-----CCCAC-C---TT--T--CACCCTTCAGTCCTCAAAGAGCAGGA---C---GCCTTT
*
138261 TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG-C-TC-TCC-C-C-T
174 TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCACCCACACAT
*
138320 T-T-CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTT
239 TGTGCA-CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
138382 CCTAGTCCTCAAAGAGCAGAACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTC
303 -CTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTC
* *
138447 AAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTCGGTGGCACCTTCAGTCCTCAAAGAGCAGGA
367 AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGA
* *
138512 CGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTCCTAGTCCTCAAAGAGCAGGATGCT
432 CGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCT
138577 CTCCCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGC
497 CTCCCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGC
138642 ACTTCCT
562 ACTTCCT
*
138649 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCTTCAAAG
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
138714 AGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
66 AGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
* * *
138779 TCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
131 TCCCACCTTTCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
*
138844 CACTTCCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGT
196 CACTTCCTAGTCCTCAAAGAGCAGGACGCC-TTC--A-CCCACAC-A-TT-GT-GCACCTTTAGT
* * **
138909 CCTCAAAGAGCAGGACGCCTTTCAAAACCCACACGAGTTGGTGGCATTTTTCTAGTCCTCAAAGA
253 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTCTAGTCCTCAAAGA
* *
138974 GCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT--TAGTCTTCAAAGAGCA
317 GCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCA
*
139037 GGACGCTTTTGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTCAGTCCTCAAAGAGCAGGA
375 GGA--C----GCCTTTCAAAGCCCACACAAGTTGGTGGCAC--CTTCAGTCCTCAAAGAGCAGGA
* * * *
139102 CGCCTTTT-TTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTC-AGTTCTCAAAGAGCAGGACG
432 CGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG
139165 C
495 C
139166 CTTTCAAAGC
Statistics
Matches: 1474, Mismatches: 88, Indels: 223
0.83 0.05 0.12
Matches are distributed among these distances:
561 55 0.04
562 1 0.00
564 3 0.00
566 2 0.00
567 22 0.01
568 3 0.00
569 1 0.00
570 3 0.00
572 21 0.01
573 73 0.05
574 28 0.02
575 30 0.02
576 111 0.08
577 30 0.02
578 10 0.01
579 86 0.06
580 32 0.02
581 60 0.04
582 451 0.31
583 139 0.09
584 3 0.00
585 6 0.00
586 3 0.00
587 9 0.01
588 126 0.09
589 31 0.02
590 71 0.05
591 6 0.00
593 10 0.01
594 1 0.00
595 25 0.02
596 1 0.00
597 21 0.01
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.23
Consensus pattern (568 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
AGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
TCCCACCTTTCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
CACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCACCCACACATTGTGCACCTTTAGTCCTCAAAG
AGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGC
CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
CCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACA
CAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCCCCTTTCACCCTTTAGTCCTC
AAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCT
Found at i:138567 original size:115 final size:110
Alignment explanation
Indices: 138329--138575 Score: 372
Period size: 115 Copynumber: 2.2 Consensus size: 110
138319 TTTCACCCTT
* * *
138329 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTCCTAGTCCTCAA
*
138394 AGAGCAGAACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
66 AGAGCAGAACGCCTTTTAAAGCCCACACAAGTTAGTGGCACTTCC
138439 TAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTCGGTGGCACCTT-C-AGTCCTCA
1 TAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTCGGTGGCA-CTTCCTAGTCCTCA
*
138502 AAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTCC
65 AAGAGCAGAACG------CCTTTTAAAGCCCACACAAGTTAGTGGCACTTCC
138554 TAGTCCTCAAAGAGCAGGATGC
1 TAGTCCTCAAAGAGCAGGATGC
138576 TCTCCCCTTT
Statistics
Matches: 125, Mismatches: 5, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
109 19 0.15
110 48 0.38
111 3 0.02
115 55 0.44
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (110 bp):
TAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTCCTAGTCCTCAA
AGAGCAGAACGCCTTTTAAAGCCCACACAAGTTAGTGGCACTTCC
Found at i:138733 original size:54 final size:55
Alignment explanation
Indices: 138593--138778 Score: 331
Period size: 55 Copynumber: 3.4 Consensus size: 55
138583 TTTCACCCTT
138593 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
*
138648 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-C
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
*
138703 -AGTCTTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
138757 TAGTCCTCAAAGAGCAGGACGC
1 TAGTCCTCAAAGAGCAGGACGC
138779 TCTCTCCTTT
Statistics
Matches: 124, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
53 3 0.02
54 48 0.39
55 70 0.56
56 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (55 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
Found at i:138810 original size:148 final size:148
Alignment explanation
Indices: 138648--138926 Score: 483
Period size: 148 Copynumber: 1.9 Consensus size: 148
138638 TGGCACTTCC
*
138648 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-C-AGTCTTCA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCA
*
138711 AAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGG
65 AAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-C-AGTCCTCAAAGAGCAGG
138775 ACGCTCTCTCCTTTCACCCTT
128 ACGCTCTCTCCTTTCACCCTT
*
138796 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
138861 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG
66 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG
138926 C
131 C
138927 CTTTCAAAAC
Statistics
Matches: 125, Mismatches: 3, Indels: 6
0.93 0.02 0.04
Matches are distributed among these distances:
147 3 0.02
148 71 0.57
149 48 0.38
150 3 0.02
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (148 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG
CTCTCTCCTTTCACCCTT
Found at i:138846 original size:203 final size:203
Alignment explanation
Indices: 138384--138982 Score: 1027
Period size: 203 Copynumber: 2.9 Consensus size: 203
138374 TGGCACTTCC
*
138384 TAGTCCTCAAAGAGCAGAACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
* *
138449 AGAGCAGGATGCCTTTCAAAGCCCACACAAGTCGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG
66 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG
* *
138514 CCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTCCTAGTCCTCAAAGAGCAGGATGCTCT
131 ------CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCT
138579 CCCCTTTCACCCTT
190 CCCCTTTCACCCTT
138593 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
*
138658 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCTTCAAAGAGCAGGACG
66 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG
*
138723 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
131 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCCCCTT
138788 TCACCCTT
196 TCACCCTT
138796 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
138861 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG
66 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG
* * * * *
138926 CCTTTCAAAACCCACACGAGTTGGTGGCATTTTTCTAGTCCTCAAAGAGCAGGACGC
131 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGC
138983 CTTTTCCTTT
Statistics
Matches: 376, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
203 225 0.60
204 25 0.07
209 126 0.34
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (203 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCCCCTT
TCACCCTT
Found at i:138882 original size:55 final size:56
Alignment explanation
Indices: 138796--139334 Score: 594
Period size: 55 Copynumber: 9.3 Consensus size: 56
138786 TTTCACCCTT
* *
138796 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
138851 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * **
138906 -AGTCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACGAGTTGGTGGCATTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
138961 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACC-TT-
1 TAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
139021 TAGTCTTCAAAGAGCAGGACGCTTTTGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTT
1 TAGTCCTCAAAGAGCAGGA--C----GCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
139082 TCAGTCCTCAAAGAGCAGGACGCCTTTTTTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTC
1 T-AGTCCTCAAAGAGCAGGACGCC------TTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
139145 -AGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
139199 TCAATCCTCAAATAACAGGACGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTC
1 T-AGTCCTCAAAGAGCAGGACG-C----C-TTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
139262 -AGTTCTCAAAGAGCAGGACGCCTTCCAAAGCCCACACGAGTTGGTGGCA-CTTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
139316 TAGTCCTCAAAGAGCAGGA
1 TAGTCCTCAAAGAGCAGGA
139335 TACACTTTAT
Statistics
Matches: 417, Mismatches: 32, Indels: 70
0.80 0.06 0.13
Matches are distributed among these distances:
54 55 0.13
55 123 0.29
56 43 0.10
57 4 0.01
58 1 0.00
59 1 0.00
60 44 0.11
61 41 0.10
62 90 0.22
63 8 0.02
64 1 0.00
65 3 0.01
66 3 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (56 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:139218 original size:117 final size:117
Alignment explanation
Indices: 138792--139334 Score: 763
Period size: 117 Copynumber: 4.7 Consensus size: 117
138782 CTCCTTTCAC
* * **
138792 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCT-AGT
1 CCTTTCAGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTCAGT
138855 CCTCAAAGAGCAGGACG-C----C-TTTCAAAGCCCACACAAGTTGGTGGCA
66 CCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
138901 CC-TTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACGAGTTGGTGGCA-TTTTTCTAG
1 CCTTTCAGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTC-AG
*
138964 TCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGCTGGTGGCA
65 TCCTCAAAGAGCAGGACGCCTTTT-CTTTTCAAAGCCCACACAAGTTGGTGGCA
139017 CCTTT-AG-TCTTCAAAGAGCAGGACGCTTTTGCCTTTCAAAGCCCACACAAGTTGGTGGCACTT
1 CCTTTCAGTTC-TCAAAGAGCAGGA--C----GCCTTTCAAAGCCCACACAAGTTGGTGGCACTT
* *
139080 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTTTTTTCAAAGCCCACACGAGTTGGTGGCA
59 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
139139 CCTTTCAGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTCAAT
1 CCTTTCAGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTCAGT
* * *
139204 CCTCAAATAACAGGACGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
66 CCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
139256 CCTTTCAGTTCTCAAAGAGCAGGACGCCTTCCAAAGCCCACACGAGTTGGTGGCACTTTTT-AGT
1 CCTTTCAGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTCAGT
139320 CCTCAAAGAGCAGGA
66 CCTCAAAGAGCAGGA
139335 TACACTTTAT
Statistics
Matches: 391, Mismatches: 21, Indels: 37
0.87 0.05 0.08
Matches are distributed among these distances:
108 5 0.01
109 48 0.12
110 20 0.05
111 1 0.00
115 1 0.00
116 55 0.14
117 152 0.39
118 1 0.00
121 5 0.01
122 80 0.20
123 21 0.05
124 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (117 bp):
CCTTTCAGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTCAGT
CCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:139239 original size:239 final size:226
Alignment explanation
Indices: 138792--139334 Score: 763
Period size: 239 Copynumber: 2.3 Consensus size: 226
138782 CTCCTTTCAC
* * **
138792 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTC
1 CCTTTCAGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTC
138856 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
66 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
* * *
138921 GGACGCCTTTCAAAACCCACACGAGTTGGTGGCATTTTTCTAGTCCTCAAAGAGCAGGACGCCTT
131 GGACGCCTTTCAAAACCCACACAAGTTGGTGGCATTTTTCTAATCCTCAAAGAACAGGACGCCTT
138986 TTCCTTTTAAAGCCCACACAAGCTGGTGGCA
196 TTCCTTTTAAAGCCCACACAAGCTGGTGGCA
139017 CCTTT-AG-TCTTCAAAGAGCAGGACGCTTTTGCCTTTCAAAGCCCACACAAGTTGGTGGCACTT
1 CCTTTCAGTTC-TCAAAGAGCAGGA--C----GCCTTTCAAAGCCCACACAAGTTGGTGGCACTT
*
139080 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTTTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTC
59 TTT-AGTCCTCAAAGAGCAGGACGCC------TTTCAAAGCCCACACAAGTTGGTGGCACC-TTC
* *
139145 AGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTC-AATCCTCA
116 AGTCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACAAGTTGGTGGCA-TTTTTCTAATCCTCA
* * *
139209 AATAACAGGACGCCTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCA
180 AAGAACAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGCTGGTGGCA
* *
139256 CCTTTCAGTTCTCAAAGAGCAGGACGCCTTCCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTC
1 CCTTTCAGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTC
139321 CTCAAAGAGCAGGA
66 CTCAAAGAGCAGGA
139335 TACACTTTAT
Statistics
Matches: 284, Mismatches: 15, Indels: 30
0.86 0.05 0.09
Matches are distributed among these distances:
224 1 0.00
225 20 0.07
227 1 0.00
231 33 0.12
232 22 0.08
233 18 0.06
234 34 0.12
238 34 0.12
239 98 0.35
240 21 0.07
241 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (226 bp):
CCTTTCAGTTCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTC
CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
GGACGCCTTTCAAAACCCACACAAGTTGGTGGCATTTTTCTAATCCTCAAAGAACAGGACGCCTT
TTCCTTTTAAAGCCCACACAAGCTGGTGGCA
Found at i:140125 original size:26 final size:26
Alignment explanation
Indices: 140095--140213 Score: 193
Period size: 26 Copynumber: 4.6 Consensus size: 26
140085 TGAAAACTTA
* *
140095 CAGCATGGGAAAGGAAATAGAAAATG
1 CAGCATGGGAAAGCAAATAAAAAATG
* *
140121 CAGCATGGGAAAGGAAATAGAAAATG
1 CAGCATGGGAAAGCAAATAAAAAATG
*
140147 TAGCATGGGAAAGCAAATAAAAAATG
1 CAGCATGGGAAAGCAAATAAAAAATG
140173 CAGCATGGGAAAGCAAATAAAAAATG
1 CAGCATGGGAAAGCAAATAAAAAATG
140199 CAGCATGGGAAAGCA
1 CAGCATGGGAAAGCA
140214 TAAAAATTGC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 89 1.00
ACGTcount: A:0.50, C:0.10, G:0.28, T:0.12
Consensus pattern (26 bp):
CAGCATGGGAAAGCAAATAAAAAATG
Found at i:140257 original size:50 final size:50
Alignment explanation
Indices: 140201--140303 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
140191 AAAAAATGCA
140201 GCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATACAGAGGCAT
1 GCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATACAGAGGCAT
*
140251 GCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAGGCAT
1 GCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATACAGAGGCAT
140301 GCA
1 GCA
140304 AGAGAATGGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.16
Consensus pattern (50 bp):
GCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATACAGAGGCAT
Found at i:140609 original size:18 final size:18
Alignment explanation
Indices: 140584--140768 Score: 97
Period size: 18 Copynumber: 9.8 Consensus size: 18
140574 AACACGCAAA
140584 AGCAGCTCCAGCAGCAGC
1 AGCAGCTCCAGCAGCAGC
* * * *
140602 ACCAGCTCTAGCGGCGGC
1 AGCAGCTCCAGCAGCAGC
* * * *
140620 AACAGTTCTAGCACGCAAC
1 AGCAGCTCCAGCA-GCAGC
*
140639 AGCAGCTCCAACAGCAGC
1 AGCAGCTCCAGCAGCAGC
* *
140657 AGCAACTCCAGCAAC-GAC
1 AGCAGCTCCAGCAGCAG-C
*
140675 TGCAGCTCCAGCACGCAACAGC
1 AGCAGCTCCAGCA-G---CAGC
140697 AGCAGCAACTCCAGCAGC-GAC
1 AGCAG---CTCCAGCAGCAG-C
* * *
140718 TGTAGCTCCAGCACGCAAC
1 AGCAGCTCCAGCA-GCAGC
140737 AGCAGCTCCAGCGAG-AGC
1 AGCAGCTCCAGC-AGCAGC
*
140755 AGCAACTCCAGCAG
1 AGCAGCTCCAGCAG
140769 GTAGCAATTT
Statistics
Matches: 125, Mismatches: 28, Indels: 29
0.69 0.15 0.16
Matches are distributed among these distances:
17 3 0.02
18 73 0.58
19 26 0.21
20 2 0.02
21 5 0.04
22 6 0.05
23 1 0.01
24 1 0.01
25 8 0.06
ACGTcount: A:0.30, C:0.37, G:0.24, T:0.09
Consensus pattern (18 bp):
AGCAGCTCCAGCAGCAGC
Found at i:140688 original size:55 final size:55
Alignment explanation
Indices: 140570--140768 Score: 163
Period size: 55 Copynumber: 3.8 Consensus size: 55
140560 TAGCCAACGA
* * * * * * * * **
140570 CTCCAACACGCAAAAGCAGCTCCAGCAGCAGCACCAGCTCTAGCGGCGGCAACAG
1 CTCCAGCACGCAACAGCAGCTCCAACAGCAGCAGCAACTCCAGCAGCGACTGCAG
* * *
140625 TTCTAGCACGCAACAGCAGCTCCAACAGCAGCAGCAACTCCAGCAACGACTGCAG
1 CTCCAGCACGCAACAGCAGCTCCAACAGCAGCAGCAACTCCAGCAGCGACTGCAG
*
140680 CT-C--CA-G---CA-C-G---CAACAGCAGCAGCAACTCCAGCAGCGACTGTAG
1 CTCCAGCACGCAACAGCAGCTCCAACAGCAGCAGCAACTCCAGCAGCGACTGCAG
*
140723 CTCCAGCACGCAACAGCAGCTCCAGCGAG-AGCAGCAACTCCAGCAG
1 CTCCAGCACGCAACAGCAGCTCCAAC-AGCAGCAGCAACTCCAGCAG
140769 GTAGCAATTT
Statistics
Matches: 113, Mismatches: 18, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
43 33 0.29
44 1 0.01
46 3 0.03
47 2 0.02
48 2 0.02
50 2 0.02
51 2 0.02
52 3 0.03
55 63 0.56
56 2 0.02
ACGTcount: A:0.31, C:0.38, G:0.23, T:0.09
Consensus pattern (55 bp):
CTCCAGCACGCAACAGCAGCTCCAACAGCAGCAGCAACTCCAGCAGCGACTGCAG
Found at i:140695 original size:43 final size:43
Alignment explanation
Indices: 140647--140742 Score: 174
Period size: 43 Copynumber: 2.2 Consensus size: 43
140637 ACAGCAGCTC
140647 CAACAGCAGCAGCAACTCCAGCAACGACTGCAGCTCCAGCACG
1 CAACAGCAGCAGCAACTCCAGCAACGACTGCAGCTCCAGCACG
* *
140690 CAACAGCAGCAGCAACTCCAGCAGCGACTGTAGCTCCAGCACG
1 CAACAGCAGCAGCAACTCCAGCAACGACTGCAGCTCCAGCACG
140733 CAACAGCAGC
1 CAACAGCAGC
140743 TCCAGCGAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.32, C:0.39, G:0.22, T:0.07
Consensus pattern (43 bp):
CAACAGCAGCAGCAACTCCAGCAACGACTGCAGCTCCAGCACG
Found at i:140756 original size:43 final size:43
Alignment explanation
Indices: 140647--140766 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 43
140637 ACAGCAGCTC
* ** *
140647 CAACAGCAGCAGCAACTCCAGCAACGACTGCAGCTCCAGCACG
1 CAACAGCAGCACCAACGACAGCAGCGACTGCAGCTCCAGCACG
* ** *
140690 CAACAGCAGCAGCAACTCCAGCAGCGACTGTAGCTCCAGCACG
1 CAACAGCAGCACCAACGACAGCAGCGACTGCAGCTCCAGCACG
* * * * *
140733 CAACAGCAGCTCCAGCGAGAGCAGCAACTCCAGC
1 CAACAGCAGCACCAACGACAGCAGCGACTGCAGC
140767 AGGTAGCAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.32, C:0.38, G:0.23, T:0.07
Consensus pattern (43 bp):
CAACAGCAGCACCAACGACAGCAGCGACTGCAGCTCCAGCACG
Found at i:141949 original size:79 final size:79
Alignment explanation
Indices: 141746--142291 Score: 797
Period size: 79 Copynumber: 6.9 Consensus size: 79
141736 TTTCCTTTAA
* * * * *
141746 CCGAGGAGATACTCCAACCCCGATTTTATCTCTAAAACATCAATTTTTCATAATCGGGGATACTC
1 CCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCACAATCGGGGATACTC
*
141811 CAACCCTGTTATTT
66 CAACCCCGTTATTT
* *
141825 TCGA-GGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTC
1 CCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCACAATCGGGGATACTC
*
141889 CAACCCCATTATTT
66 CAACCCCGTTATTT
* *
141903 CCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTC
1 CCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCACAATCGGGGATACTC
* *
141968 CAACCCCATTATTC
66 CAACCCCGTTATTT
* *
141982 CCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTC
1 CCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCACAATCGGGGATACTC
*
142047 TAACCCCGTTATTT
66 CAACCCCGTTATTT
* * * *
142061 TCGAGGGGATACTCCAACCTCGGTTTTATCTCTAAGACATTAATTTTTCACAATCGGGGATACTC
1 CCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCACAATCGGGGATACTC
142126 CAACCCCGTTATTT
66 CAACCCCGTTATTT
* ** *
142140 CCGAGGGGATACTCTAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTC
1 CCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCACAATCGGGGATACTC
*
142205 CAACCTCGTTATTT
66 CAACCCCGTTATTT
** * * **
142219 TTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGATGATACTC
1 CCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCACAATCGGGGATACTC
*
142284 TAACCCCG
66 CAACCCCG
142292 ATTTTATTTT
Statistics
Matches: 427, Mismatches: 39, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
78 69 0.16
79 358 0.84
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (79 bp):
CCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCACAATCGGGGATACTC
CAACCCCGTTATTT
Found at i:142317 original size:51 final size:52
Alignment explanation
Indices: 142224--142358 Score: 134
Period size: 51 Copynumber: 2.6 Consensus size: 52
142214 TATTTTTGAG
* *
142224 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTT-CATAATC-
1 GGGATACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTTCCATAATCA
* * * **
142274 GATGATACTCTAACCCCGATTTTATTTTTTAGAACA-CCGTTTTTCCATAATCA
1 G-GGATACTCTAACCCCGATTTTA-TTTCTAAAACATCAATTTTTCCATAATCA
* *
142327 GGGATACTCTAGCCCCG-TTGTTATCTCTAAAA
1 GGGATACTCTAACCCCGATT-TTATTTCTAAAA
142359 TACTAATTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
50 1 0.01
51 33 0.49
52 33 0.49
53 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (52 bp):
GGGATACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTTCCATAATCA
Found at i:144340 original size:2 final size:2
Alignment explanation
Indices: 144333--144369 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
144323 ACAAAAACAA
144333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144370 GCAACTAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:145018 original size:16 final size:15
Alignment explanation
Indices: 144997--145037 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
144987 AAATTTTGAT
144997 AATTTTTTAAATTCAA
1 AATTTTTTAAATT-AA
145013 AA-TTTTTACAATTAA
1 AATTTTTTA-AATTAA
145028 AATTTTTTAA
1 AATTTTTTAA
145038 TAAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTTTTAAATTAA
Found at i:145020 original size:15 final size:15
Alignment explanation
Indices: 145000--145034 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
144990 TTTTGATAAT
145000 TTTTTA-AATTCAAAA
1 TTTTTACAATT-AAAA
145015 TTTTTACAATTAAAA
1 TTTTTACAATTAAAA
145030 TTTTT
1 TTTTT
145035 TAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTTACAATTAAAA
Found at i:145255 original size:16 final size:16
Alignment explanation
Indices: 145223--145255 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
145213 TTTTCAATTA
*
145223 TTTTTTAAAATTATTT
1 TTTTTTAAAAATATTT
145239 TTTTTTAAAAA-ATTT
1 TTTTTTAAAAATATTT
145254 TT
1 TT
145256 GGAACAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTAAAAATATTT
Found at i:146847 original size:21 final size:21
Alignment explanation
Indices: 146821--146860 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
146811 TATATAAAAC
*
146821 ATATTT-TTTAGAATAAAAATT
1 ATATTTATTT-GAAAAAAAATT
146842 ATATTTATTTGAAAAAAAA
1 ATATTTATTTGAAAAAAAA
146861 AAGAGATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
ATATTTATTTGAAAAAAAATT
Found at i:147231 original size:31 final size:31
Alignment explanation
Indices: 147196--147255 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
147186 TATAGTTGGT
* **
147196 AAATATAAATTCTAAAAGTTATGAATAAATA
1 AAATACAAATTCTAAAAGCCATGAATAAATA
* *
147227 AAATACAACTTTTAAAAGCCATGAATAAA
1 AAATACAAATTCTAAAAGCCATGAATAAA
147256 GATAAAAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.28
Consensus pattern (31 bp):
AAATACAAATTCTAAAAGCCATGAATAAATA
Found at i:149210 original size:16 final size:14
Alignment explanation
Indices: 149177--149226 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
149167 TACTACGACA
*
149177 TTATAATTTTTATT
1 TTATTATTTTTATT
149191 TTATTATTTTTATT
1 TTATTATTTTTATT
*
149205 TT-TTATTATTAATAT
1 TTATTATT-TTTAT-T
149220 TTATTAT
1 TTATTAT
149227 AATTAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 5 0.16
14 19 0.61
15 3 0.10
16 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTATTTTTATT
Found at i:149231 original size:16 final size:16
Alignment explanation
Indices: 149201--149234 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
149191 TTATTATTTT
* *
149201 TATTTTTTATTATTAA
1 TATTTATTATAATTAA
149217 TATTTATTATAATTAA
1 TATTTATTATAATTAA
149233 TA
1 TA
149235 ATAATAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTATTATAATTAA
Found at i:149242 original size:25 final size:24
Alignment explanation
Indices: 149214--149260 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
149204 TTTTTATTAT
149214 TAATATTTATTATAATTAATAATAA
1 TAATATTTATTAT-ATTAATAATAA
*
149239 TAATATTTATTATATTTATAAT
1 TAATATTTATTATATTAATAAT
149261 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATATTTATTATATTAATAATAA
Found at i:149965 original size:21 final size:21
Alignment explanation
Indices: 149935--149978 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
149925 TTTGATTTTT
*
149935 AAATAATTGAT-CTTTTTAAA
1 AAATAATTGATCCTTTATAAA
149955 AAATATATTGATCCTTTATAAA
1 AAATA-ATTGATCCTTTATAAA
149977 AA
1 AA
149979 GACGATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (21 bp):
AAATAATTGATCCTTTATAAA
Found at i:149972 original size:20 final size:21
Alignment explanation
Indices: 149935--149978 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
149925 TTTGATTTTT
*
149935 AAATAATTGATCTTTTTA-AA
1 AAATAATTGATCTCTTTATAA
149955 AAATATATTGATC-CTTTATAA
1 AAATA-ATTGATCTCTTTATAA
149976 AAA
1 AAA
149979 GACGATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (21 bp):
AAATAATTGATCTCTTTATAA
Found at i:150136 original size:21 final size:21
Alignment explanation
Indices: 150112--150151 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
150102 AATTAAAAAT
*
150112 TATTTT-TAATTAATATTTATA
1 TATTTTATAAATAA-ATTTATA
150133 TATTTTATAAATAAATTTA
1 TATTTTATAAATAAATTTA
150152 AATAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATAAATAAATTTATA
Found at i:150206 original size:20 final size:20
Alignment explanation
Indices: 150181--150230 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
150171 AAAAAATTTA
150181 AAATTAAAATAATC-TAACTT
1 AAATTAAAATAATCTTAA-TT
*
150201 AAATTAAAAAAATCTTAATT
1 AAATTAAAATAATCTTAATT
150221 AAATTAAAAT
1 AAATTAAAAT
150231 TAAATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTAAAATAATCTTAATT
Found at i:150238 original size:20 final size:19
Alignment explanation
Indices: 150181--150240 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 19
150171 AAAAAATTTA
150181 AAATTAAAAT-AATCTAACTT
1 AAATTAAAATAAAT-TAA-TT
150201 AAATTAAAA-AAATCTTAATT
1 AAATTAAAATAAA--TTAATT
150221 AAATTAAAATTAAATTAATT
1 AAATTAAAA-TAAATTAATT
150241 GAATAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
20 28 0.80
21 3 0.09
22 4 0.11
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTAAAATAAATTAATT
Found at i:155253 original size:2 final size:2
Alignment explanation
Indices: 155246--155272 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
155236 ATGGGAGCTT
155246 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
155273 TTTGCCTCAA
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:155616 original size:16 final size:16
Alignment explanation
Indices: 155595--155627 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
155585 TTCCTGTCCT
*
155595 TTGGCTGCCTATGCGG
1 TTGGCTGCCAATGCGG
155611 TTGGCTGCCAATGCGG
1 TTGGCTGCCAATGCGG
155627 T
1 T
155628 CGCCAGCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.24, G:0.36, T:0.30
Consensus pattern (16 bp):
TTGGCTGCCAATGCGG
Found at i:156110 original size:17 final size:17
Alignment explanation
Indices: 156077--156110 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
156067 TCTTCTCTCT
**
156077 TCTCTCCTCTCTTATTC
1 TCTCTCCTCTCACATTC
156094 TCTCTCCTCTCACATTC
1 TCTCTCCTCTCACATTC
156111 ATTTTTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.44, G:0.00, T:0.47
Consensus pattern (17 bp):
TCTCTCCTCTCACATTC
Found at i:157987 original size:55 final size:55
Alignment explanation
Indices: 157903--158014 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
157893 AGCACAACTT
157903 AATCTCACTCTGAATCTGTCCACTGAATCTCTTTGTTGGGTTTTAAAGAGGGTTA
1 AATCTCACTCTGAATCTGTCCACTGAATCTCTTTGTTGGGTTTTAAAGAGGGTTA
*
157958 AATCTTACTCTGAATCTGTCCACTGAATCTCTTTGTTGGGTTTTAAAGAGGGTTA
1 AATCTCACTCTGAATCTGTCCACTGAATCTCTTTGTTGGGTTTTAAAGAGGGTTA
158013 AA
1 AA
158015 CCAAGATGAG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (55 bp):
AATCTCACTCTGAATCTGTCCACTGAATCTCTTTGTTGGGTTTTAAAGAGGGTTA
Found at i:160195 original size:20 final size:19
Alignment explanation
Indices: 160171--160227 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
160161 ATTTGATATT
160171 ATTTTTATTATAAAAATTA
1 ATTTTTATTATAAAAATTA
*
160190 CTTTTTATTATAAAAATTA
1 ATTTTTATTATAAAAATTA
160209 ATTTTTGATCT-TAAAAATT
1 ATTTTT-AT-TATAAAAATT
160228 GTATCAATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 23 0.68
20 10 0.29
21 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTTTTATTATAAAAATTA
Found at i:162098 original size:24 final size:23
Alignment explanation
Indices: 162052--162098 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
162042 ATTTTCAACA
* *
162052 TTTTTTTTTATATTGTTGTTTTT
1 TTTTTTTTTAGATTGTTGCTTTT
*
162075 TTTTTTTTTCAGATTTTTGCTTTT
1 TTTTTTTTT-AGATTGTTGCTTTT
162099 CCCTTTTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.09, C:0.04, G:0.09, T:0.79
Consensus pattern (23 bp):
TTTTTTTTTAGATTGTTGCTTTT
Found at i:162454 original size:3 final size:3
Alignment explanation
Indices: 162446--162484 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
162436 TACTTTCTGA
* *
162446 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATA ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
162485 TGAGATATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:163612 original size:12 final size:13
Alignment explanation
Indices: 163584--163621 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
163574 GCATTAAAAA
*
163584 AATTTTATTATTT
1 AATTTTATTATTG
163597 AATTTT-TTATTG
1 AATTTTATTATTG
*
163609 AATTGTATTATTG
1 AATTTTATTATTG
163622 TTATTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (13 bp):
AATTTTATTATTG
Found at i:164398 original size:23 final size:22
Alignment explanation
Indices: 164370--164451 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
164360 ATTATATATA
164370 TTTTTAGTTTATTTAAAAATAAT
1 TTTTTA-TTTATTTAAAAATAAT
* *
164393 TTTTTATTAATTTTTAAAAT-AT
1 TTTTTATTTA-TTTAAAAATAAT
*
164415 ATTTTAATTTATTTAAAAAATAAT
1 -TTTTTATTTATTT-AAAAATAAT
*
164439 TTTTTATTAATTT
1 TTTTTATTTATTT
164452 TTAAAATATA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
22 8 0.17
23 38 0.79
24 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (22 bp):
TTTTTATTTATTTAAAAATAAT
Found at i:164415 original size:46 final size:46
Alignment explanation
Indices: 164365--164461 Score: 169
Period size: 46 Copynumber: 2.1 Consensus size: 46
164355 TTCAAATTAT
*
164365 ATATATTTTTAGTTTATTT-AAAAATAATTTTTTATTAATTTTTAAA
1 ATATA-TTTTAATTTATTTAAAAAATAATTTTTTATTAATTTTTAAA
164411 ATATATTTTAATTTATTTAAAAAATAATTTTTTATTAATTTTTAAA
1 ATATATTTTAATTTATTTAAAAAATAATTTTTTATTAATTTTTAAA
164457 ATATA
1 ATATA
164462 AATAACTTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 12 0.24
46 37 0.76
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (46 bp):
ATATATTTTAATTTATTTAAAAAATAATTTTTTATTAATTTTTAAA
Found at i:164457 original size:23 final size:23
Alignment explanation
Indices: 164385--164459 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
164375 AGTTTATTTA
164385 AAAATAATTTTTTATTAATTTTT
1 AAAATAATTTTTTATTAATTTTT
* * **
164408 AAAAT-ATATTTTAATTTATTTAA
1 AAAATAAT-TTTTTATTAATTTTT
164431 AAAATAATTTTTTATTAATTTTT
1 AAAATAATTTTTTATTAATTTTT
164454 AAAATA
1 AAAATA
164460 TAAATAACTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 2 0.05
23 38 0.90
24 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAAATAATTTTTTATTAATTTTT
Found at i:164492 original size:15 final size:15
Alignment explanation
Indices: 164472--164506 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
164462 AATAACTTAA
164472 TATATTTTAA-ATATT
1 TATATTTTAATAT-TT
164487 TATATTTTAATATTT
1 TATATTTTAATATTT
164502 TATAT
1 TATAT
164507 ATGTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATTTTAATATTT
Found at i:164503 original size:23 final size:23
Alignment explanation
Indices: 164473--164522 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
164463 ATAACTTAAT
164473 ATATTTTAAATAT-TTATATTTTA
1 ATATTTTAAATATGTT-TATTTTA
* *
164496 ATATTTTATATATGTTTATTTTT
1 ATATTTTAAATATGTTTATTTTA
164519 ATAT
1 ATAT
164523 GATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATATTTTAAATATGTTTATTTTA
Found at i:164911 original size:10 final size:11
Alignment explanation
Indices: 164896--164927 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
164886 ATTTGAATTG
164896 TATTATAT-TA
1 TATTATATATA
164906 TATTATATATA
1 TATTATATATA
164917 TA-TATATATA
1 TATTATATATA
164927 T
1 T
164928 CTTTCTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTATATATA
Found at i:166084 original size:16 final size:16
Alignment explanation
Indices: 166065--166099 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
166055 TAATTAAAAT
*
166065 AAATTGATATTTTTTA
1 AAATTAATATTTTTTA
*
166081 AAATTAATGTTTTTTA
1 AAATTAATATTTTTTA
166097 AAA
1 AAA
166100 CTATTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
AAATTAATATTTTTTA
Found at i:166698 original size:19 final size:19
Alignment explanation
Indices: 166670--166708 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
166660 TTTTACATAT
166670 TATTAACAATTCAT-TACTA
1 TATTAACAA-TCATATACTA
*
166689 TATTATCAATCATATACTA
1 TATTAACAATCATATACTA
166708 T
1 T
166709 TATGTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTAACAATCATATACTA
Found at i:166748 original size:22 final size:22
Alignment explanation
Indices: 166696--166749 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
166686 CTATATTATC
* *
166696 AATCATATACTATTATGTAATT
1 AATCATTTACTACTATGTAATT
*
166718 AATCTTTTACTACTAT-TATATT
1 AATCATTTACTACTATGTA-ATT
*
166740 CATCATTTAC
1 AATCATTTAC
166750 AAAATTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (22 bp):
AATCATTTACTACTATGTAATT
Found at i:167890 original size:30 final size:26
Alignment explanation
Indices: 167830--167880 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
167820 TTTTCATAAC
*
167830 ATTTATCTAATATTTAGTAGTCTCAT
1 ATTTATCTAATATTTAGTAGTCACAT
167856 ATTTATCTAATATTTAGTAGTCACA
1 ATTTATCTAATATTTAGTAGTCACA
167881 AACATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (26 bp):
ATTTATCTAATATTTAGTAGTCACAT
Found at i:169400 original size:105 final size:104
Alignment explanation
Indices: 169246--169487 Score: 270
Period size: 105 Copynumber: 2.3 Consensus size: 104
169236 TTATGTAGAT
* * ** *
169246 TTTTTAAATATTTAGTTGATTTAAATCTGAATAAATTAATAAAACTACATATTTAAATAGGAAAA
1 TTTTTAAATATTTA-TTAATTTAAATTTGAATAAAACAATAAAACTACATATTTAAATAGAAAAA
* * * * * * ***
169311 TTTTATTAATTTTAAATTTA-TTTAATATCATGTGCTCTCTA
65 ATTTATTAA-TTCAAA-GTAGATTAAAATCACGTAAACTCTA
* * *
169352 TTTTTAAATATTTATTAATTTAAATTTGAATAAAACGATGAAATTACATATTTAAATAGAAAAAA
1 TTTTTAAATATTTATTAATTTAAATTTGAATAAAACAATAAAACTACATATTTAAATAGAAAAAA
169417 TTTATTAATTCAAAGTAGATTAAAATCACGTAAACTCTA
66 TTTATTAATTCAAAGTAGATTAAAATCACGTAAACTCTA
* * *
169456 TTTTCAAATATTTATCAATTTAAATTTAAATA
1 TTTTTAAATATTTATTAATTTAAATTTGAATA
169488 GATTAGTAAA
Statistics
Matches: 115, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
103 2 0.02
104 49 0.43
105 50 0.43
106 14 0.12
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (104 bp):
TTTTTAAATATTTATTAATTTAAATTTGAATAAAACAATAAAACTACATATTTAAATAGAAAAAA
TTTATTAATTCAAAGTAGATTAAAATCACGTAAACTCTA
Found at i:169500 original size:104 final size:104
Alignment explanation
Indices: 169246--169513 Score: 281
Period size: 104 Copynumber: 2.5 Consensus size: 104
169236 TTATGTAGAT
* * * * *
169246 TTTTTAAATATTTAGTTGATTTAAATCTGAATAAATTAATAAAACTACATATTTAAATAGGAAAA
1 TTTTTAAATATTTA-TTAATTTAAATTTGAAT-AATTAGTAAAATTACATATTTAAATAGAAAAA
* * * * * * ***
169311 TTTTATTAATTTTAAATTTATTTAATATCATGTGCTCTCTA
64 ATTTATTAATTTCAAATGTAATTAAAATCACGTAAACTCTA
* *
169352 TTTTTAAATATTTATTAATTTAAATTTGAATAA-AACGATGAAATTACATATTTAAATAGAAAAA
1 TTTTTAAATATTTATTAATTTAAATTTGAATAATTA-G-TAAAATTACATATTTAAATAGAAAAA
169416 ATTTATTAA-TTCAAA-GTAGATTAAAATCACGTAAACTCTA
64 ATTTATTAATTTCAAATGTA-ATTAAAATCACGTAAACTCTA
* * * *
169456 TTTTCAAATATTTATCAATTTAAATTTAAATAGATTAGTAAAATTACATAATTAAATA
1 TTTTTAAATATTTATTAATTTAAATTTGAATA-ATTAGTAAAATTACATATTTAAATA
169514 AGATACTTTT
Statistics
Matches: 135, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
103 3 0.02
104 69 0.51
105 48 0.36
106 15 0.11
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (104 bp):
TTTTTAAATATTTATTAATTTAAATTTGAATAATTAGTAAAATTACATATTTAAATAGAAAAAAT
TTATTAATTTCAAATGTAATTAAAATCACGTAAACTCTA
Found at i:171307 original size:2 final size:2
Alignment explanation
Indices: 171300--171330 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
171290 CTTTCTAAAA
171300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
171331 AAACGATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:173979 original size:11 final size:10
Alignment explanation
Indices: 173959--173983 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
173949 AGCTTACGTA
173959 TTTTTGTTTT
1 TTTTTGTTTT
173969 TTTTTGTTTT
1 TTTTTGTTTT
173979 TTTTT
1 TTTTT
173984 AACAGAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:176153 original size:25 final size:26
Alignment explanation
Indices: 176092--176194 Score: 83
Period size: 25 Copynumber: 4.0 Consensus size: 26
176082 TTTTATTCGA
176092 TAAATATTTAAATATA-AATATAAAT
1 TAAATATTTAAATATATAATATAAAT
* *
176117 TATATTTTTTAAATATATAA-A-AAAT
1 TA-AATATTTAAATATATAATATAAAT
**
176142 TAAATATATTAAATATAT--T-TGTAT
1 TAAATAT-TTAAATATATAATATAAAT
*
176166 TAAATATGTTATATACTATAATATAAAT
1 TAAATAT-TTAAATA-TATAATATAAAT
176194 T
1 T
176195 CAGATAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
24 18 0.31
25 21 0.36
26 13 0.22
27 3 0.05
28 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (26 bp):
TAAATATTTAAATATATAATATAAAT
Found at i:176711 original size:14 final size:14
Alignment explanation
Indices: 176692--176766 Score: 70
Period size: 12 Copynumber: 5.5 Consensus size: 14
176682 ATACTTAAAA
176692 TTTTTAAATCATAT
1 TTTTTAAATCATAT
176706 TTTTT--ATCATAT
1 TTTTTAAATCATAT
*
176718 TTTTT--ATTATAT
1 TTTTTAAATCATAT
176730 TTTTTAAAT-ATATTT
1 TTTTTAAATCATA--T
*
176745 TTTTTCAAATCATTT
1 TTTTT-AAATCATAT
176760 TTTTTAA
1 TTTTTAA
176767 CTCAACTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
12 23 0.43
13 3 0.06
14 9 0.17
15 12 0.23
16 4 0.08
17 2 0.04
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTAAATCATAT
Found at i:177091 original size:22 final size:22
Alignment explanation
Indices: 177066--177107 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
177056 TTTAAAAAAT
177066 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
177088 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
177108 AAAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:177116 original size:34 final size:34
Alignment explanation
Indices: 177078--177148 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
177068 TTTTTATATT
* *
177078 AATATTTATATATTTTTATAATTA-AATTTAAA-AA
1 AATATTTATA-ATTATTA-AATAATAATTTAAATAA
*
177112 AATATTTTTAATTATTAAATAATAATTTAAATAA
1 AATATTTATAATTATTAAATAATAATTTAAATAA
177146 AAT
1 AAT
177149 CAATTCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 4 0.12
33 14 0.44
34 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
AATATTTATAATTATTAAATAATAATTTAAATAA
Found at i:177497 original size:18 final size:18
Alignment explanation
Indices: 177476--177519 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
177466 AAATGAGTAA
177476 AATTTAAAT-ATAATATTT
1 AATTTAAATGATAA-ATTT
*
177494 AATTTAATTGATAAATTT
1 AATTTAAATGATAAATTT
177512 AA-TTAAAT
1 AATTTAAAT
177520 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 14 0.61
19 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AATTTAAATGATAAATTT
Found at i:180324 original size:2 final size:2
Alignment explanation
Indices: 180317--180343 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
180307 ATGCGTGAAA
180317 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
180344 TATGTATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:183286 original size:5 final size:5
Alignment explanation
Indices: 183276--183301 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
183266 ATAATATACA
183276 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
183302 CATCAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:183561 original size:21 final size:21
Alignment explanation
Indices: 183532--183571 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
183522 AAAAATTATT
183532 ATTAATTTATTTTATAAATTG
1 ATTAATTTATTTTATAAATTG
*
183553 ATTATTTTATTTTATAAAT
1 ATTAATTTATTTTATAAAT
183572 ATATTTTAAG
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:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTAATTTATTTTATAAATTG
Found at i:183887 original size:19 final size:20
Alignment explanation
Indices: 183834--183888 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
183824 GAAATAAAAC
*
183834 ATTTGATAGTATTTATTATATT
1 ATTT-ATAGT-TTTTTTATATT
*
183856 TTTTATAAGTTTTTTTATA-T
1 ATTTAT-AGTTTTTTTATATT
183876 ATTTATAGTTTTT
1 ATTTATAGTTTTT
183889 AATTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.24
20 6 0.21
21 10 0.34
22 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.65
Consensus pattern (20 bp):
ATTTATAGTTTTTTTATATT
Found at i:184224 original size:2 final size:2
Alignment explanation
Indices: 184217--184284 Score: 84
Period size: 2 Copynumber: 34.5 Consensus size: 2
184207 TGTATGTGAA
* * * **
184217 AT AT AT AT AT AT AT AT AT AT AC CT TT CC A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
184258 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
184285 CACCTTTCCA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:184920 original size:2 final size:2
Alignment explanation
Indices: 184913--184987 Score: 64
Period size: 2 Copynumber: 38.5 Consensus size: 2
184903 GAGAGCATAC
* * *
184913 AT AT AT AT AT AT AT AT AT AC A- AC AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
184954 AT A- AC AT AC AT AC AT AC AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
184988 AATAGTATTT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (2 bp):
AT
Found at i:184938 original size:23 final size:23
Alignment explanation
Indices: 184911--184965 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
184901 GGGAGAGCAT
*
184911 ACATATATATATATATATATACA
1 ACATACATATATATATATATACA
*
184934 ACATACATATATATATATATATA
1 ACATACATATATATATATATACA
184957 ACATACATA
1 ACATACATA
184966 CATACATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (23 bp):
ACATACATATATATATATATACA
Found at i:184946 original size:27 final size:28
Alignment explanation
Indices: 184908--184985 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 28
184898 AAAGGGAGAG
184908 CATACATATATATATATATATATACA-A
1 CATACATATATATATATATATATACATA
184935 CATACATATATATATATATATA-ACATA
1 CATACATATATATATATATATATACATA
* *
184962 CATACATACATACATATATATATA
1 CATACATATATATATATATATATA
184986 TAAATAGTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 3 0.06
27 43 0.91
28 1 0.02
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (28 bp):
CATACATATATATATATATATATACATA
Found at i:184951 original size:31 final size:31
Alignment explanation
Indices: 184908--184988 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
184898 AAAGGGAGAG
*
184908 CATACATATATATATATATATATACA-ACATA
1 CATACATATATATATATA-ACATACATACATA
*
184939 CATATATATATATATATAACATACATACATA
1 CATACATATATATATATAACATACATACATA
184970 CATACATATATATATATAA
1 CATACATATATATATATAA
184989 ATAGTATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 6 0.13
31 40 0.87
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (31 bp):
CATACATATATATATATAACATACATACATA
Found at i:184978 original size:23 final size:23
Alignment explanation
Indices: 184933--184979 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
184923 ATATATATAC
* * *
184933 AACATACATATATATATATATAT
1 AACATACATACATACATACATAT
184956 AACATACATACATACATACATAT
1 AACATACATACATACATACATAT
184979 A
1 A
184980 TATATATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (23 bp):
AACATACATACATACATACATAT
Found at i:186726 original size:3 final size:3
Alignment explanation
Indices: 186720--186765 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
186710 TTTTTAAATG
186720 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
186766 AGAAGCAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:187690 original size:21 final size:22
Alignment explanation
Indices: 187652--187694 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
187642 ATTTGAATCG
**
187652 ATTTAATATAATTTAAATTATT
1 ATTTAATATAATAAAAATTATT
187674 ATTTAA-ATAATAAAAATTATT
1 ATTTAATATAATAAAAATTATT
187695 TTATCTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAATATAATAAAAATTATT
Found at i:187725 original size:22 final size:22
Alignment explanation
Indices: 187695--187744 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
187685 AAAAATTATT
*
187695 TTATCTAAAT-TTAATTATAAAA
1 TTATATAAATATTAA-TATAAAA
187717 TTATATAAATATTAATATAAAA
1 TTATATAAATATTAATATAAAA
*
187739 TAATAT
1 TTATAT
187745 TTAATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATATAAATATTAATATAAAA
Found at i:188606 original size:19 final size:19
Alignment explanation
Indices: 188578--188615 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
188568 TTAATTTATC
*
188578 ATAAATTATTATTTAAATA
1 ATAAAATATTATTTAAATA
188597 ATAAAATATTATTTAAATA
1 ATAAAATATTATTTAAATA
188616 TTAATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAAATATTATTTAAATA
Found at i:188628 original size:13 final size:13
Alignment explanation
Indices: 188600--188638 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
188590 TTAAATAATA
188600 AAATATT-ATT-T
1 AAATATTAATTAT
188611 AAATATTAATTAT
1 AAATATTAATTAT
188624 AAATATTAA-TAT
1 AAATATTAATTAT
188636 AAA
1 AAA
188639 ATAAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.27
12 9 0.35
13 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATATTAATTAT
Found at i:188640 original size:13 final size:12
Alignment explanation
Indices: 188598--188641 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
188588 ATTTAAATAA
188598 TAAAATATT-AT
1 TAAAATATTAAT
*
188609 TTAAATATTAAT
1 TAAAATATTAAT
188621 TATAAATATTAAT
1 TA-AAATATTAAT
188634 ATAAAATA
1 -TAAAATA
188642 AATTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 8 0.29
12 3 0.11
13 15 0.54
14 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAAATATTAAT
Found at i:190740 original size:17 final size:17
Alignment explanation
Indices: 190714--190757 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
190704 AATTATTTAA
190714 TAAATTATTTAA-AATT
1 TAAATTATTTAATAATT
190730 TAAATTTATTTAATAA-T
1 TAAA-TTATTTAATAATT
*
190747 TAAGTTATTTA
1 TAAATTATTTA
190758 TTTTTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 11 0.44
17 12 0.48
18 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TAAATTATTTAATAATT
Found at i:190880 original size:21 final size:21
Alignment explanation
Indices: 190851--190893 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
190841 AAATATATTT
*
190851 TTATTTAAAT-TTAATTATAAA
1 TTATATAAATATT-ATTATAAA
190872 TTATATAAATATTATTATAAA
1 TTATATAAATATTATTATAAA
190893 T
1 T
190894 AACTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATATAAATATTATTATAAA
Found at i:192052 original size:23 final size:22
Alignment explanation
Indices: 192020--192083 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
192010 GTACGTCAAT
*
192020 TATTTGTATTTGAAAAATTACAT-
1 TATTTTTATTTGAAAAA-TA-ATA
* *
192043 TTTTTTTATTTGAATAA-AATA
1 TATTTTTATTTGAAAAATAATA
192064 TATTTTTATTTGAAAAATAA
1 TATTTTTATTTGAAAAATAA
192084 AAAGATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.06
21 16 0.47
22 2 0.06
23 14 0.41
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (22 bp):
TATTTTTATTTGAAAAATAATA
Found at i:192620 original size:29 final size:30
Alignment explanation
Indices: 192576--192650 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
192566 GAACAATAAA
192576 ATTTTTTAAATA-TTATTA-ATGATAAAC-AT
1 ATTTTTTAAA-AGTTATTATATGAT-AACTAT
* *
192605 ATTTTTTAAAGGTTA-TATATGATAGCTAT
1 ATTTTTTAAAAGTTATTATATGATAACTAT
*
192634 AATTTTTAAAAGTTATT
1 ATTTTTTAAAAGTTATT
192651 GATAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 4 0.11
29 33 0.87
30 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (30 bp):
ATTTTTTAAAAGTTATTATATGATAACTAT
Found at i:192870 original size:19 final size:20
Alignment explanation
Indices: 192838--192885 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
192828 TGTCTCATAT
*
192838 TTAA-ATATTTTTAAA-TCA
1 TTAATATATTATTAAACTCA
*
192856 TTAATATATTATTAAACGTTA
1 TTAATATATTATTAAAC-TCA
192877 TTAATATAT
1 TTAATATAT
192886 CAATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 10 0.40
21 11 0.44
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAATATATTATTAAACTCA
Found at i:193242 original size:16 final size:15
Alignment explanation
Indices: 193221--193265 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
193211 TCAAAACTTA
193221 AAAATAATTCAAATCT
1 AAAATAATTCAAA-CT
*
193237 AAAATAATTCGAACT
1 AAAATAATTCAAACT
* *
193252 TAAATTATTCAAAC
1 AAAATAATTCAAAC
193266 AGTTAATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAATAATTCAAACT
Found at i:193484 original size:16 final size:18
Alignment explanation
Indices: 193459--193497 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
193449 ATTTAAATTC
*
193459 AAAATAAATCGAA-TTAA
1 AAAATAAATCAAACTTAA
193476 AAAAT-AATCAAACTTAA
1 AAAATAAATCAAACTTAA
193493 AAAAT
1 AAAAT
193498 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATAAATCAAACTTAA
Found at i:194685 original size:16 final size:13
Alignment explanation
Indices: 194653--194682 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
194643 ATATTTTTAT
194653 AAAATATAATAAC
1 AAAATATAATAAC
194666 AAAATATAATAAC
1 AAAATATAATAAC
194679 AAAA
1 AAAA
194683 AAAATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATATAATAAC
Found at i:194876 original size:13 final size:13
Alignment explanation
Indices: 194858--194884 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
194848 AAATTTAATT
194858 TAATTAATTTATA
1 TAATTAATTTATA
194871 TAATTAATTTATA
1 TAATTAATTTATA
194884 T
1 T
194885 TTAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTAATTTATA
Found at i:200434 original size:2 final size:2
Alignment explanation
Indices: 200421--200450 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
200411 AGGCCTACTG
*
200421 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
200451 TGCAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:200851 original size:2 final size:2
Alignment explanation
Indices: 200844--200871 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
200834 AACCTTATCA
200844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
200872 CATCAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:206450 original size:32 final size:33
Alignment explanation
Indices: 206405--206469 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
206395 ATATTTAGAT
*
206405 AAAAATGATAAAATAAAAAAAAAAGATAAAAGG
1 AAAAAGGATAAAATAAAAAAAAAAGATAAAAGG
* * *
206438 AAAAAGGA-AAAATGAAAAAAGAAGCTAAAAGG
1 AAAAAGGATAAAATAAAAAAAAAAGATAAAAGG
206470 GGGTTCATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (33 bp):
AAAAAGGATAAAATAAAAAAAAAAGATAAAAGG
Found at i:210481 original size:18 final size:18
Alignment explanation
Indices: 210460--210507 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
210450 ATAATTTTAT
* **
210460 TAATTAAATTAATATTAC
1 TAATTTAATTAATAACAC
*
210478 TAATTTAATTCATAACAC
1 TAATTTAATTAATAACAC
210496 TAATTTAATTAA
1 TAATTTAATTAA
210508 AAACTTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTTAATTAATAACAC
Found at i:211966 original size:17 final size:15
Alignment explanation
Indices: 211941--211986 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
211931 TATTTTCTAT
211941 TTTTC-ATTTTTTTCC
1 TTTTCAATTTTTTT-C
211956 TCTTTCAATTTTTTATC
1 T-TTTCAATTTTTT-TC
211973 TTTTCAATTTTTTT
1 TTTTCAATTTTTTT
211987 TTCTCCCGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.07
16 16 0.57
17 9 0.32
18 1 0.04
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTCAATTTTTTTC
Found at i:215459 original size:9 final size:9
Alignment explanation
Indices: 215445--215574 Score: 51
Period size: 8 Copynumber: 14.9 Consensus size: 9
215435 ATTTATGTAT
215445 TTTTATATA
1 TTTTATATA
215454 TTTTATATCA
1 TTTTATAT-A
**
215464 TAAT-TATA
1 TTTTATATA
* **
215472 TTTAACGTA
1 TTTTATATA
215481 TTTTATATAAA
1 TTTTATAT--A
215492 TTTT-TATA
1 TTTTATATA
215500 TTTTA-ATA
1 TTTTATATA
* *
215508 ATTCATAATA
1 TTTTAT-ATA
*
215518 TATTA-AT-
1 TTTTATATA
*
215525 TTTTAGATA
1 TTTTATATA
*
215534 -TTTATGTA
1 TTTTATATA
215542 TTTTATAT-
1 TTTTATATA
*
215550 TTTAAT-TA
1 TTTTATATA
*
215558 TTTTATTTA
1 TTTTATATA
*
215567 TATTATAT
1 TTTTATAT
215575 TCGTATAAAT
Statistics
Matches: 86, Mismatches: 23, Indels: 24
0.65 0.17 0.18
Matches are distributed among these distances:
7 5 0.06
8 33 0.38
9 32 0.37
10 11 0.13
11 5 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTATATA
Found at i:216150 original size:2 final size:2
Alignment explanation
Indices: 216137--216171 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
216127 AATTTTGAAC
*
216137 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
216172 GTAAAAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:218865 original size:10 final size:9
Alignment explanation
Indices: 218852--218886 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
218842 AAATAACATA
218852 AAAATAAAAG
1 AAAA-AAAAG
218862 AAAAAAAA-
1 AAAAAAAAG
218870 AAAAAAAAG
1 AAAAAAAAG
218879 AAAAAAAA
1 AAAAAAAA
218887 TTCAATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 12 0.50
10 4 0.17
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:218877 original size:17 final size:17
Alignment explanation
Indices: 218851--218886 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
218841 AAAATAACAT
*
218851 AAAAATAAAAGAAAAAA
1 AAAAAAAAAAGAAAAAA
218868 AAAAAAAAAAGAAAAAA
1 AAAAAAAAAAGAAAAAA
218885 AA
1 AA
218887 TTCAATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.92, C:0.00, G:0.06, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAA
Found at i:219343 original size:18 final size:17
Alignment explanation
Indices: 219317--219356 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
219307 ATAATTTTTT
*
219317 ATATTTTATTATATTTAA
1 ATATATTATTAT-TTTAA
*
219335 ATATATTATTATTTTTA
1 ATATATTATTATTTTAA
219352 ATATA
1 ATATA
219357 AAATTAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATATTATTATTTTAA
Found at i:219408 original size:30 final size:30
Alignment explanation
Indices: 219347--219417 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
219337 ATATTATTAT
*
219347 TTTTAATATAAAATTAAAGTTCAAATGTTA
1 TTTTAATATAAAATTAAAGTTAAAATGTTA
*
219377 TTTTGATAT-AAATTAAAGATTAAAAAT-TTA
1 TTTTAATATAAAATTAAAG-TT-AAAATGTTA
*
219407 TTTAAATATAA
1 TTTTAATATAA
219418 TAAAAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 9 0.26
30 20 0.59
31 5 0.15
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (30 bp):
TTTTAATATAAAATTAAAGTTAAAATGTTA
Found at i:222246 original size:3 final size:3
Alignment explanation
Indices: 222240--222286 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
222230 TTCATTTTTT
222240 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
222287 CTTTATTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:222664 original size:19 final size:19
Alignment explanation
Indices: 222640--222678 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
222630 ATGATTATTT
222640 TAAT-AAATTATTTAATTAA
1 TAATAAAATT-TTTAATTAA
*
222659 TAATAAAATTTTTATTTAA
1 TAATAAAATTTTTAATTAA
222678 T
1 T
222679 TTTAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAAAATTTTTAATTAA
Found at i:225538 original size:22 final size:23
Alignment explanation
Indices: 225513--225556 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
225503 TCCAAAGTAA
225513 AAATAAAAAATTA-TAAATATTT
1 AAATAAAAAATTATTAAATATTT
** *
225535 AAATTTAAATTTATTAAATATT
1 AAATAAAAAATTATTAAATATT
225557 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATAAAAAATTATTAAATATTT
Found at i:225556 original size:23 final size:23
Alignment explanation
Indices: 225526--225570 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
225516 TAAAAAATTA
225526 TAAATATT-TAAATTTAAATTTAT
1 TAAATATTAT-AATTTAAATTTAT
*
225549 TAAATATTATATTTTAAATTTA
1 TAAATATTATAATTTAAATTTA
225571 ATATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATATTATAATTTAAATTTAT
Found at i:225575 original size:16 final size:15
Alignment explanation
Indices: 225520--225581 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 15
225510 TAAAAATAAA
225520 AAATTATAAATA-TTT
1 AAATT-TAAATATTTT
225535 AAATTTAAAT-TTATT
1 AAATTTAAATATT-TT
225550 AAATATT--ATATTTT
1 AAAT-TTAAATATTTT
225564 AAATTTAATATATTTT
1 AAATTTAA-ATATTTT
225580 AA
1 AA
225582 TTATTAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 2 0.05
14 14 0.35
15 13 0.32
16 11 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATTTAAATATTTT
Found at i:229359 original size:2 final size:2
Alignment explanation
Indices: 229352--229394 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
229342 GACAGTGAAC
*
229352 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
229394 A
1 A
229395 AACACTAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:238685 original size:21 final size:20
Alignment explanation
Indices: 238661--238713 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
238651 TATTATTTGA
* *
238661 TTTAAATTTAAAATAATTTTT
1 TTTAATTTTAAAATAA-TTAT
*
238682 TTTATTTTTTAAAATAATTAT
1 TTTA-ATTTTAAAATAATTAT
238703 TTTAATTTTAA
1 TTTAATTTTAA
238714 GTAAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.22
21 11 0.41
22 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAATTTTAAAATAATTAT
Found at i:238695 original size:22 final size:22
Alignment explanation
Indices: 238667--238711 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
238657 TTGATTTAAA
* *
238667 TTTAAAATAATTTTTTTTATTT
1 TTTAAAATAATTATTTTAATTT
238689 TTTAAAATAATTATTTTAATTT
1 TTTAAAATAATTATTTTAATTT
238711 T
1 T
238712 AAGTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTAAAATAATTATTTTAATTT
Found at i:238964 original size:19 final size:18
Alignment explanation
Indices: 238940--238989 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
238930 AGTTTTAATA
238940 ATTTATATATTTATATTGT
1 ATTTATATATTT-TATTGT
*
238959 ATTTATTTATTTTA-TGT
1 ATTTATATATTTTATTGT
238976 A-TTATA-ATTTTATT
1 ATTTATATATTTTATT
238990 TAAATTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 6 0.21
16 5 0.18
17 4 0.14
18 2 0.07
19 11 0.39
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (18 bp):
ATTTATATATTTTATTGT
Found at i:238972 original size:28 final size:26
Alignment explanation
Indices: 238941--239010 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
238931 GTTTTAATAA
*
238941 TTTATATATTTATATTGTATTTATTTAT
1 TTTATATATTTATATTGTATTTA--AAT
* *
238969 TTTATGTA-TTATAATTTTATTTAAAT
1 TTTATATATTTAT-ATTGTATTTAAAT
238995 TATTATATATTTATAT
1 T-TTATATATTTATAT
239011 AAATTTCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
26 3 0.09
27 12 0.34
28 20 0.57
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTATATATTTATATTGTATTTAAAT
Found at i:238998 original size:20 final size:20
Alignment explanation
Indices: 238975--239015 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
238965 TTATTTTATG
*
238975 TATTATA-ATTTTATTTAAAT
1 TATTATATA-TTTATATAAAT
238995 TATTATATATTTATATAAAT
1 TATTATATATTTATATAAAT
239015 T
1 T
239016 TCAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTATATATTTATATAAAT
Found at i:239209 original size:7 final size:8
Alignment explanation
Indices: 239187--239244 Score: 50
Period size: 7 Copynumber: 7.2 Consensus size: 8
239177 AAATTTTAAC
239187 ATATTTAT
1 ATATTTAT
239195 ATATTTAT
1 ATATTTAT
239203 A-ATTTAT
1 ATATTTAT
*
239210 TTATATTAT
1 ATAT-TTAT
*
239219 -TATTTTT
1 ATATTTAT
239226 ATTATATTAT
1 A-TAT-TTAT
239236 AT-TTTAT
1 ATATTTAT
239243 AT
1 AT
239245 CGTATAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
7 15 0.36
8 15 0.36
9 8 0.19
10 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATATTTAT
Found at i:239214 original size:17 final size:17
Alignment explanation
Indices: 239189--239263 Score: 65
Period size: 16 Copynumber: 4.8 Consensus size: 17
239179 ATTTTAACAT
239189 ATTTATA-TAT-TTATA
1 ATTTATATTATATTATA
*
239204 ATTTAT-TTATATTATT
1 ATTTATATTATATTATA
*
239220 ATTTTTATTATATTAT-
1 ATTTATATTATATTATA
**
239236 ATTT-TA-TATCGTATA
1 ATTTATATTATATTATA
239251 A-TTATATTATATT
1 ATTTATATTATATT
239264 TAAAATTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 8 0.17
15 14 0.29
16 17 0.35
17 9 0.19
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (17 bp):
ATTTATATTATATTATA
Found at i:239215 original size:25 final size:25
Alignment explanation
Indices: 239187--239265 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 25
239177 AAATTTTAAC
239187 ATATTTATATATTTATAATT-TATT
1 ATATTTATATATTTATAATTATATT
*
239211 -TATATTAT-TATTT-TTATTATATT
1 ATAT-TTATATATTTATAATTATATT
*
239234 ATATTT-TATATCGTATAATTATATT
1 ATATTTATATAT-TTATAATTATATT
239259 ATATTTA
1 ATATTTA
239266 AAATTATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
22 5 0.11
23 17 0.38
24 8 0.18
25 15 0.33
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (25 bp):
ATATTTATATATTTATAATTATATT
Found at i:239221 original size:19 final size:18
Alignment explanation
Indices: 239188--239265 Score: 56
Period size: 19 Copynumber: 4.3 Consensus size: 18
239178 AATTTTAACA
239188 TATTTATA-TATTTATAATT
1 TATTTATATTA-TTAT-ATT
*
239207 TATTTATATTATTATTTT
1 TATTTATATTATTATATT
239225 TA-TTATATTA-TAT-TT
1 TATTTATATTATTATATT
** *
239240 TATATCGTATAATTATATT
1 TAT-TTATATTATTATATT
239259 ATATTTA
1 -TATTTA
239266 AAATTATTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
15 4 0.09
16 3 0.06
17 13 0.28
18 7 0.15
19 15 0.32
20 5 0.11
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (18 bp):
TATTTATATTATTATATT
Found at i:239853 original size:22 final size:22
Alignment explanation
Indices: 239827--239870 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
239817 AAAAATTTAT
*
239827 TTTTAT-ATTAATATTTACATAA
1 TTTTATAATTAA-ATTTAAATAA
239849 TTTTATAATTAAATTTAAATAA
1 TTTTATAATTAAATTTAAATAA
239871 AAATATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAA
Found at i:240057 original size:6 final size:6
Alignment explanation
Indices: 240048--240075 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
240038 TTAATATGAA
240048 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
240076 TTTGACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:240438 original size:3 final size:3
Alignment explanation
Indices: 240430--240462 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
240420 AATTTTAAGG
240430 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
240463 TGTGTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:240787 original size:21 final size:20
Alignment explanation
Indices: 240750--240800 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
240740 ATTTTTAATT
240750 TAAAT-TTAATTATAATTATA
1 TAAATATTAATTATAATT-TA
*
240770 TAAATATTAA-TATAAATTTT
1 TAAATATTAATTAT-AATTTA
240790 TATAATATTAA
1 TA-AATATTAA
240801 CATATTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATATTAATTATAATTTA
Found at i:241083 original size:22 final size:22
Alignment explanation
Indices: 241057--241124 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
241047 ATTATAACAA
241057 ATAAAAAATAATTAATAATATT
1 ATAAAAAATAATTAATAATATT
* * * *
241079 ATAAAATATTATAAAAAATATTT
1 ATAAAAAATAATTAATAATA-TT
241102 ATAAAGAAAATAATTAATAATAT
1 AT-AA-AAAATAATTAATAATAT
241125 AAATTTTTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 16 0.46
23 4 0.11
24 3 0.09
25 12 0.34
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (22 bp):
ATAAAAAATAATTAATAATATT
Found at i:241310 original size:14 final size:14
Alignment explanation
Indices: 241293--241343 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
241283 TTCATAATAT
*
241293 TTAAGATATAAAAA
1 TTAAAATATAAAAA
* *
241307 TTAAAATATTAAAT
1 TTAAAATATAAAAA
241321 TTAATAATATAAAAA
1 TTAA-AATATAAAAA
241336 -TAAAATAT
1 TTAAAATAT
241344 TTTCTTCCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 5 0.16
14 18 0.58
15 8 0.26
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:243578 original size:15 final size:16
Alignment explanation
Indices: 243558--243591 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
243548 TGGTGGGTAG
243558 TAGGCTAAA-TTTAAA
1 TAGGCTAAACTTTAAA
243573 TAGGCTAAACTTTTAAA
1 TAGGCTAAAC-TTTAAA
243590 TA
1 TA
243592 TGAAGTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (16 bp):
TAGGCTAAACTTTAAA
Found at i:244765 original size:70 final size:70
Alignment explanation
Indices: 244598--244742 Score: 290
Period size: 70 Copynumber: 2.1 Consensus size: 70
244588 TATTTTTATT
244598 ATATTAAATTATGGCATACCCATTATATGGTGGTTAAGAAAAAATAATTAAAATAATATATTTTT
1 ATATTAAATTATGGCATACCCATTATATGGTGGTTAAGAAAAAATAATTAAAATAATATATTTTT
244663 AATAA
66 AATAA
244668 ATATTAAATTATGGCATACCCATTATATGGTGGTTAAGAAAAAATAATTAAAATAATATATTTTT
1 ATATTAAATTATGGCATACCCATTATATGGTGGTTAAGAAAAAATAATTAAAATAATATATTTTT
244733 AATAA
66 AATAA
244738 ATATT
1 ATATT
244743 GATTAGTTAG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.38
Consensus pattern (70 bp):
ATATTAAATTATGGCATACCCATTATATGGTGGTTAAGAAAAAATAATTAAAATAATATATTTTT
AATAA
Found at i:247729 original size:16 final size:15
Alignment explanation
Indices: 247692--247739 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
247682 ACATATATTT
247692 ATTAAAATTTAAATAA
1 ATTAAAATTT-AATAA
*
247708 A-AAAAATATTAATAA
1 ATTAAAAT-TTAATAA
247723 ATTAAAATTTATATAA
1 ATTAAAATTTA-ATAA
247739 A
1 A
247740 AATATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAAAATTTAATAA
Found at i:247758 original size:28 final size:31
Alignment explanation
Indices: 247709--247777 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 31
247699 TTTAAATAAA
247709 AAAAATAT-TAATAAATTAAAAT-TTAT-AT
1 AAAAATATATAATAAATTAAAATATTATGAT
* *
247737 AAAAATATATAAT-ATTTTAAATATTATGAT
1 AAAAATATATAATAAATTAAAATATTATGAT
*
247767 AAATATATATA
1 AAAAATATATA
247778 TAATTATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 15 0.43
29 8 0.23
30 12 0.34
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
AAAAATATATAATAAATTAAAATATTATGAT
Found at i:253864 original size:11 final size:11
Alignment explanation
Indices: 253832--253870 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 11
253822 TATAAACAGC
253832 AAAAAATAACAT
1 AAAAAATAA-AT
253844 AAGTAAAATAAAT
1 AA--AAAATAAAT
253857 AAAAAATAAAT
1 AAAAAATAAAT
253868 AAA
1 AAA
253871 TTTGATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 12 0.48
12 2 0.08
13 4 0.16
14 7 0.28
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAAATAAAT
Done.