Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold341
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: 1349338
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:303802 original size:39 final size:38
Alignment explanation
Indices: 303751--303829 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
303741 CCCACAACCG
*
303751 CCCACCCACCCCACACACCCCCCCCCCCC-CCCCCACCA
1 CCCAACCACCCCACAC-CCCCCCCCCCCCACCCCCACCA
*
303789 CCCAACCACCCCCACACCCCCCCCCCCCCACCCCCCCCA
1 CCCAACCA-CCCCACACCCCCCCCCCCCCACCCCCACCA
303828 CC
1 CC
303830 ACCCTCCCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 19 0.51
39 18 0.49
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (38 bp):
CCCAACCACCCCACACCCCCCCCCCCCCACCCCCACCA
Found at i:304681 original size:8 final size:7
Alignment explanation
Indices: 304647--304716 Score: 70
Period size: 7 Copynumber: 9.6 Consensus size: 7
304637 AAGCTAACCA
304647 CCCCACC
1 CCCCACC
304654 CCACACACC
1 CC-C-CACC
*
304663 ACCCACC
1 CCCCACC
*
304670 CCCAACC
1 CCCCACC
304677 CCCCACC
1 CCCCACC
*
304684 CCACCCCC
1 CC-CCACC
304692 CCCCACC
1 CCCCACC
304699 ACCCC-CC
1 -CCCCACC
304706 CCCCACC
1 CCCCACC
304713 CCCC
1 CCCC
304717 CCCACCCTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
6 4 0.08
7 31 0.60
8 12 0.23
9 5 0.10
ACGTcount: A:0.19, C:0.81, G:0.00, T:0.00
Consensus pattern (7 bp):
CCCCACC
Found at i:304695 original size:10 final size:10
Alignment explanation
Indices: 304675--304723 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
304665 CCACCCCCAA
304675 CCCCCCA-CC
1 CCCCCCACCC
*
304684 CCACCC-CCC
1 CCCCCCACCC
*
304693 CCCACCACCCC
1 CCCCCCA-CCC
304704 CCCCCCACCC
1 CCCCCCACCC
304714 CCCCCCACCC
1 CCCCCCACCC
304724 TCAAGGCGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 11 0.33
10 13 0.39
11 9 0.27
ACGTcount: A:0.12, C:0.88, G:0.00, T:0.00
Consensus pattern (10 bp):
CCCCCCACCC
Found at i:304720 original size:24 final size:25
Alignment explanation
Indices: 304649--304722 Score: 100
Period size: 23 Copynumber: 3.1 Consensus size: 25
304639 GCTAACCACC
* * *
304649 CCACCCCACACACCACCCACCCCCA
1 CCACCCCCCACCCCACCCCCCCCCA
304674 --ACCCCCCACCCCACCCCCCCCCA
1 CCACCCCCCACCCCACCCCCCCCCA
304697 CCACCCCCC-CCCCACCCCCCCCCA
1 CCACCCCCCACCCCACCCCCCCCCA
304721 CC
1 CC
304723 CTCAAGGCGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
23 20 0.45
24 17 0.39
25 7 0.16
ACGTcount: A:0.19, C:0.81, G:0.00, T:0.00
Consensus pattern (25 bp):
CCACCCCCCACCCCACCCCCCCCCA
Found at i:305035 original size:20 final size:19
Alignment explanation
Indices: 304943--305046 Score: 109
Period size: 19 Copynumber: 5.3 Consensus size: 19
304933 ACCCCAAATA
304943 AAAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAC
304962 AAAAAAAAAAAAAAAAAAACCC
1 -AAAAAAAAAAAAAAAAAA--C
* * *
304984 AAAACACACAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAC
* *
305003 AAAAAAACAAAAAAAAAAT
1 AAAAAAAAAAAAAAAAAAC
** *
305022 AAAAAAAAGGAAAAACAAC
1 AAAAAAAAAAAAAAAAAAC
305041 AAAAAA
1 AAAAAA
305047 CTAGCAAAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
19 35 0.51
20 18 0.26
21 15 0.22
22 1 0.01
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.01
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAAAC
Found at i:305046 original size:1 final size:1
Alignment explanation
Indices: 304942--305029 Score: 86
Period size: 1 Copynumber: 88.0 Consensus size: 1
304932 CACCCCAAAT
* *** * * * *
304942 AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAACCCAAAACACACAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
305007 AAACAAAAAAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
305030 GGAAAAACAA
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.89, C:0.10, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:305056 original size:27 final size:27
Alignment explanation
Indices: 304942--305046 Score: 82
Period size: 25 Copynumber: 4.2 Consensus size: 27
304932 CACCCCAAAT
304942 AAAAAA-AAAAAAAA--AAAAACAAAA
1 AAAAAATAAAAAAAAGGAAAAACAAAA
* *** *
304966 AAAAAAAAAAAAAAACCCAAAAC--AC
1 AAAAAATAAAAAAAAGGAAAAACAAAA
* *
304991 ACAAAA-AAAAACAA--AAAAACAAAA
1 AAAAAATAAAAAAAAGGAAAAACAAAA
*
305015 AAAAAATAAAAAAAAGGAAAAACAACA
1 AAAAAATAAAAAAAAGGAAAAACAAAA
305042 AAAAA
1 AAAAA
305047 CTAGCAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
22 5 0.08
24 19 0.30
25 21 0.33
27 19 0.30
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.01
Consensus pattern (27 bp):
AAAAAATAAAAAAAAGGAAAAACAAAA
Found at i:305056 original size:49 final size:49
Alignment explanation
Indices: 304944--305046 Score: 154
Period size: 49 Copynumber: 2.1 Consensus size: 49
304934 CCCCAAATAA
* *
304944 AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAACCCAAAACACAC
1 AAAAAAAAACAAAAAAACAAAAAAAAAAAAAAAAAAACCAAAAACACAC
* **
304993 AAAAAAAAACAAAAAAACAAAAAAAAAATAAAAAAAAGGAAAAACA-AC
1 AAAAAAAAACAAAAAAACAAAAAAAAAAAAAAAAAAACCAAAAACACAC
305041 AAAAAA
1 AAAAAA
305047 CTAGCAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 8 0.16
49 41 0.84
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.01
Consensus pattern (49 bp):
AAAAAAAAACAAAAAAACAAAAAAAAAAAAAAAAAAACCAAAAACACAC
Found at i:305474 original size:16 final size:17
Alignment explanation
Indices: 305444--305476 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
305434 TTTTGCCACC
305444 ACCCCACCACCCCCCCA
1 ACCCCACCACCCCCCCA
305461 ACCCCACC-CCCCCCCA
1 ACCCCACCACCCCCCCA
305477 CCACCCACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.21, C:0.79, G:0.00, T:0.00
Consensus pattern (17 bp):
ACCCCACCACCCCCCCA
Found at i:305483 original size:17 final size:18
Alignment explanation
Indices: 305439--305484 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
305429 TTTTTTTTTG
305439 CCACCACCCCACCACCCCC
1 CCACCA-CCCACCACCCCC
*
305458 CCAAC-CCCACC-CCCCC
1 CCACCACCCACCACCCCC
305474 CCACCACCCAC
1 CCACCACCCAC
305485 AAACCAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 9 0.38
17 11 0.46
19 4 0.17
ACGTcount: A:0.22, C:0.78, G:0.00, T:0.00
Consensus pattern (18 bp):
CCACCACCCACCACCCCC
Found at i:305515 original size:12 final size:13
Alignment explanation
Indices: 305480--305513 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
305470 CCCCCCACCA
305480 CCCACAAACCAACC
1 CCCACAAA-CAACC
*
305494 CACACAAACAACC
1 CCCACAAACAACC
305507 CCCACAA
1 CCCACAA
305514 CACCCCCCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (13 bp):
CCCACAAACAACC
Found at i:309729 original size:13 final size:13
Alignment explanation
Indices: 309711--309758 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
309701 CCTTTACACC
309711 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
*
309724 C-AAAAAAAAAAC
1 CAAAAAAAAAAAA
*
309736 CAAAACAAAAAAA
1 CAAAAAAAAAAAA
309749 CAAAAAAAAA
1 CAAAAAAAAA
309759 GAAAAAATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:309730 original size:10 final size:10
Alignment explanation
Indices: 309715--309775 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 10
309705 TACACCCAAA
309715 AAAAAAAAAC
1 AAAAAAAAAC
309725 AAAAAAAAAACC
1 -AAAAAAAAA-C
309737 AAAACAAAAAAAC
1 --AA-AAAAAAAC
*
309750 AAAAAAAAAG
1 AAAAAAAAAC
* *
309760 AAAAAATAGC
1 AAAAAAAAAC
309770 AAAAAA
1 AAAAAA
309776 TAGAAGGGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 20 0.47
11 11 0.26
12 1 0.02
13 4 0.09
14 7 0.16
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:309730 original size:12 final size:12
Alignment explanation
Indices: 309713--309758 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
309703 TTTACACCCA
309713 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
309725 AAAAAAAAAACC
1 AAAAAAAAAAAC
309737 AAAACAAAAAAAC
1 AAAA-AAAAAAAC
309750 AAAAAAAAA
1 AAAAAAAAA
309759 GAAAAAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 20 0.65
13 11 0.35
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:309734 original size:17 final size:17
Alignment explanation
Indices: 309712--309765 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
309702 CTTTACACCC
309712 AAAAAAAAAAAACAAAA
1 AAAAAAAAAAAACAAAA
**
309729 AAAAAACCAAAACAAAA
1 AAAAAAAAAAAACAAAA
*
309746 AAACAAAAAAAAAGAAAA
1 AAA-AAAAAAAAACAAAA
309764 AA
1 AA
309766 TAGCAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAACAAAA
Found at i:309738 original size:25 final size:25
Alignment explanation
Indices: 309710--309758 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
309700 TCCTTTACAC
309710 CCAAAAAAAAAAAACAAAAAAAAAA
1 CCAAAAAAAAAAAACAAAAAAAAAA
*
309735 CCAAAACAAAAAAACAAAAAAAAA
1 CCAAAAAAAAAAAACAAAAAAAAA
309759 GAAAAAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (25 bp):
CCAAAAAAAAAAAACAAAAAAAAAA
Found at i:309775 original size:1 final size:1
Alignment explanation
Indices: 309712--309765 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
309702 CTTTACACCC
* ** * * *
309712 AAAAAAAAAAAACAAAAAAAAAACCAAAACAAAAAAACAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
309766 TAGCAAAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:311034 original size:29 final size:29
Alignment explanation
Indices: 310992--311962 Score: 1445
Period size: 29 Copynumber: 33.9 Consensus size: 29
310982 AATGTTCATC
310992 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
**
311021 CCTTTCAAAGCCCACAAACCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311050 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311079 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
311107 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
311136 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311165 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311193 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
311221 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
311250 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311279 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
311308 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
311337 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311365 CCTTTCAAAGCCCACAAGTCAGTGGCACC
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311394 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
311422 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
311451 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
311480 CTTTTTAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
311509 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
311537 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
311566 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
311595 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311624 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311652 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311680 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311708 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
311736 CCTTTCGAGGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
311764 CATTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
311793 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311820 CCTTTTAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
311849 -CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
311876 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
311904 TCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
311934 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
311963 ACCCTTTTCA
Statistics
Matches: 873, Mismatches: 57, Indels: 23
0.92 0.06 0.02
Matches are distributed among these distances:
27 1 0.00
28 400 0.46
29 436 0.50
30 36 0.04
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:311140 original size:86 final size:86
Alignment explanation
Indices: 310994--311974 Score: 1460
Period size: 86 Copynumber: 11.4 Consensus size: 86
310984 TGTTCATCCC
** *
310994 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAACCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAA
311059 GCCCACAAGTCAGTGGCACTCT
65 GCCCACAAGTCAGTGGCACTCT
*
311081 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
*
311146 CCCACAAATCAGTGGCACTCT
66 CCCACAAGTCAGTGGCACTCT
*
311167 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAACTCAGTGGCAC-CCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
*
311231 CCCACAAGTCAGTGGCACTCC
66 CCCACAAGTCAGTGGCACTCT
* *
311252 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAA
*
311317 GCCCACAAATCAGTGGCACTCT
65 GCCCACAAGTCAGTGGCACTCT
* *
311339 TTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
* *
311404 CCCACAACTCAGTGGCAC-CC
66 CCCACAAGTCAGTGGCACTCT
* *
311424 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAA
*
311489 GCCCACAAATCAGTGGCACTCT
65 GCCCACAAGTCAGTGGCACTCT
*
311511 TTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
311576 CCCACAAGTCAGTGGCACTCT
66 CCCACAAGTCAGTGGCACTCT
* *
311597 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAA
* *
311661 GCCCACAAGTTAGTGGCAC-CC
65 GCCCACAAGTCAGTGGCACTCT
* * * *
311682 TTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCAC-CCTTTCGAGG
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
*
311746 CCCACAAGTCAGTGGCAC-CA
66 CCCACAAGTCAGTGGCACTCT
* * * * *
311766 TTGCGAAGCCCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTTAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
311830 CCCACAAGTCAGTGGCACTC-
66 CCCACAAGTCAGTGGCACTCT
* * * *
311850 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTTAGTGGCA-TTCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
*
311914 CCCACGCAAGTCAGTGGCACCCT
66 CCCA--CAAGTCAGTGGCACTCT
*
311937 TTT-AAAGCCCATGCAAGTCAATGGCAACCCTTTTCAAA
1 TTTCAAAGCCCA--CAAGTCAGTGGC-ACCC-TTTCAAA
311975 TCACCACTGT
Statistics
Matches: 818, Mismatches: 62, Indels: 25
0.90 0.07 0.03
Matches are distributed among these distances:
84 183 0.22
85 106 0.13
86 373 0.46
87 135 0.17
88 11 0.01
89 3 0.00
90 7 0.01
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (86 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
CCCACAAGTCAGTGGCACTCT
Found at i:312516 original size:20 final size:20
Alignment explanation
Indices: 312488--312562 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
312478 TCATACCCTG
312488 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
312508 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
312528 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
312548 ATGTATCGATACATT
1 ATGTATCGATACATT
312563 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:312555 original size:40 final size:39
Alignment explanation
Indices: 312488--312565 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
312478 TCATACCCTG
* *
312488 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
312528 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
312566 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:313500 original size:23 final size:23
Alignment explanation
Indices: 313473--313524 Score: 97
Period size: 22 Copynumber: 2.3 Consensus size: 23
313463 AGCCTTTGAC
313473 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
313496 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
313518 CATGCAT
1 CATGCAT
313525 ATTTAACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:318748 original size:39 final size:39
Alignment explanation
Indices: 318696--318777 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
318686 TCCTATCAAG
* *
318696 AATCTATACATTAGACACATCATTTGG-ATTCTAATAAAA
1 AATCAATAAATTAGACACATC-TTTGGAATTCTAATAAAA
** * *
318735 AATCAATAAATTAGTTACATCTTTGGAATTCTTATAAAG
1 AATCAATAAATTAGACACATCTTTGGAATTCTAATAAAA
318774 AATC
1 AATC
318778 TATGTATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
38 5 0.14
39 31 0.86
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (39 bp):
AATCAATAAATTAGACACATCTTTGGAATTCTAATAAAA
Found at i:320337 original size:23 final size:23
Alignment explanation
Indices: 320287--320340 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
320277 TAATTGCTAT
***
320287 TTTTCTTATTTGAAAAAAAAATTG
1 TTTT-TTATTTGAAAAAAAAACCA
*
320311 TTTTTTATTTGAAAAAAATACCA
1 TTTTTTATTTGAAAAAAAAACCA
320334 TTTTTTA
1 TTTTTTA
320341 AAATTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTTTTATTTGAAAAAAAAACCA
Found at i:320943 original size:3 final size:3
Alignment explanation
Indices: 320885--320925 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
320875 CCTAAATTTA
320885 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
320926 GTAAATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:321136 original size:18 final size:20
Alignment explanation
Indices: 321108--321148 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
321098 AATTTAAATA
321108 AAAATATATTA-TTTTAATT
1 AAAATATATTATTTTTAATT
321127 AAAA-ATATTATTTTTAATT
1 AAAATATATTATTTTTAATT
321146 AAA
1 AAA
321149 TTAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATATATTATTTTTAATT
Found at i:327344 original size:16 final size:16
Alignment explanation
Indices: 327311--327354 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
327301 AATATTATGT
*
327311 TTTAAA-TAAGATTTAA
1 TTTAAATTAA-ATTAAA
327327 TTTAAATTAAATTAAA
1 TTTAAATTAAATTAAA
*
327343 TTCAAATTAAAT
1 TTTAAATTAAAT
327355 CTAATGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
TTTAAATTAAATTAAA
Found at i:327470 original size:4 final size:4
Alignment explanation
Indices: 327461--327487 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
327451 AGATAAAACT
327461 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
327488 TTAAAGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:328051 original size:3 final size:3
Alignment explanation
Indices: 328043--328083 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
328033 AATCCACTTA
328043 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
328084 ACTTTCTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:328373 original size:23 final size:22
Alignment explanation
Indices: 328335--328377 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
328325 GATTGCTAGT
*
328335 TTAAAAAACAAGAAGAAAAATA
1 TTAAAAAAAAAGAAGAAAAATA
328357 TTAAATAAAAAAGAAGAAAAA
1 TTAAA-AAAAAAGAAGAAAAA
328378 GCAAAGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.14
Consensus pattern (22 bp):
TTAAAAAAAAAGAAGAAAAATA
Found at i:340597 original size:23 final size:21
Alignment explanation
Indices: 340555--340597 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
340545 ATTAAAAATT
*
340555 TATTTTATATTAATATTGATA
1 TATTTTATATTAATAATGATA
340576 TATTTTATAATTAAATAATGAT
1 TATTTTAT-ATT-AATAATGAT
340598 TTAGATCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TATTTTATATTAATAATGATA
Found at i:341454 original size:3 final size:3
Alignment explanation
Indices: 341446--341502 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
341436 TAAAAAACTT
341446 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
341494 ATA ACA ATA
1 ATA ATA ATA
341503 TACATGGCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:347706 original size:12 final size:12
Alignment explanation
Indices: 347649--347687 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
347639 GTACAATGAT
347649 CAGCAACAACAG
1 CAGCAACAACAG
347661 CAGCAACAACAG
1 CAGCAACAACAG
347673 CAGCAACAACAG
1 CAGCAACAACAG
347685 CAG
1 CAG
347688 TCTCAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.49, C:0.33, G:0.18, T:0.00
Consensus pattern (12 bp):
CAGCAACAACAG
Found at i:353271 original size:5 final size:5
Alignment explanation
Indices: 353263--353385 Score: 56
Period size: 5 Copynumber: 23.6 Consensus size: 5
353253 AGTTAAAATC
* * *
353263 AATTA AATTTA ATATTCA AATT- AATCA AATTT AATTC AATTA AATTTA
1 AATTA AA-TTA A-ATT-A AATTA AATTA AATTA AATTA AATTA AA-TTA
* * **
353311 ATACTTA AATT- AATTA AATTT AATCA TTTTA AATTCA AATTTA AATT-
1 A-A-TTA AATTA AATTA AATTA AATTA AATTA AATT-A AA-TTA AATTA
* *
353358 AATT- ATTTA AATTA ATTTA AATTTA AAT
1 AATTA AATTA AATTA AATTA AA-TTA AAT
353386 CAATTTAATT
Statistics
Matches: 89, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
4 14 0.16
5 40 0.45
6 25 0.28
7 10 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (5 bp):
AATTA
Found at i:353311 original size:37 final size:35
Alignment explanation
Indices: 353259--353360 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 35
353249 TTTAAGTTAA
353259 AATCAATTAAATTTAATATTCAAATTAATCAAATTT
1 AATCAATTAAATTTAATATT-AAATTAATCAAATTT
*
353295 AATTCAATTAAATTTAATACTTAAATTAATTAAATTT
1 AA-TCAATTAAATTTAATA-TTAAATTAATCAAATTT
* *
353332 AATCATTTTAAATTCAA-ATTTAAATTAAT
1 AATCA-ATTAAATTTAATA-TTAAATTAAT
353361 TATTTAAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
36 16 0.27
37 41 0.69
38 2 0.03
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (35 bp):
AATCAATTAAATTTAATATTAAATTAATCAAATTT
Found at i:353318 original size:22 final size:22
Alignment explanation
Indices: 353295--353383 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 22
353285 AATCAAATTT
353295 AATTCAATTAAATTTAATACTTA
1 AATT-AATTAAATTTAATACTTA
*
353318 AATTAATTAAATTTAATCATTTTA
1 AATTAATTAAATTTAAT-A-CTTA
*
353342 AATTCAAATTTAAA-TTAATTATTTA
1 AATT--AA-TTAAATTTAA-TACTTA
353367 AATTAATTTAAATTTAA
1 AATTAA-TTAAATTTAA
353384 ATCAATTTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
22 13 0.22
23 13 0.22
24 11 0.19
25 8 0.14
26 7 0.12
27 6 0.10
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTAATTAAATTTAATACTTA
Found at i:353365 original size:13 final size:13
Alignment explanation
Indices: 353318--353374 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
353308 TTAATACTTA
*
353318 AATTAATTAAATTT
1 AATTATTTAAA-TT
*
353332 AATCATTTTAAATT
1 AATTA-TTTAAATT
353346 CAA--ATTTAAATT
1 -AATTATTTAAATT
353358 AATTATTTAAATT
1 AATTATTTAAATT
353371 AATT
1 AATT
353375 TAAATTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 2 0.05
12 8 0.22
13 14 0.38
14 6 0.16
15 7 0.19
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (13 bp):
AATTATTTAAATT
Found at i:353383 original size:16 final size:16
Alignment explanation
Indices: 353300--353400 Score: 80
Period size: 16 Copynumber: 6.1 Consensus size: 16
353290 AATTTAATTC
*
353300 AATTAAATTTAATACTTA
1 AATT-AATTTAA-ATTTA
353318 AATTAA-TTAAATTT-
1 AATTAATTTAAATTTA
* * *
353332 AATCATTTTAAATTCA
1 AATTAATTTAAATTTA
*
353348 AATTTAAATTAATTATTTA
1 AA-TTAATTTAA--ATTTA
353367 AATTAATTTAAATTTA
1 AATTAATTTAAATTTA
* *
353383 AATCAATTTAATTTTA
1 AATTAATTTAAATTTA
353399 AA
1 AA
353401 CTATTTCATA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
14 4 0.06
15 10 0.15
16 27 0.40
17 8 0.12
18 12 0.18
19 6 0.09
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAATTTAAATTTA
Found at i:353406 original size:15 final size:16
Alignment explanation
Indices: 353243--353400 Score: 73
Period size: 16 Copynumber: 10.1 Consensus size: 16
353233 TTTTATTTTT
* * *
353243 AATCACTTTAAGTTAA
1 AATCAATTTAAATTTA
353259 AATCAA-TTAAATTT-
1 AATCAATTTAAATTTA
*
353273 AAT--ATTCAAA-TT-
1 AATCAATTTAAATTTA
*
353285 AATCAAATTT-AATTCA
1 AATC-AATTTAAATTTA
* * *
353301 ATTAAATTTAATACTTA
1 AATCAATTTAA-ATTTA
*
353318 AATTAA-TTAAATTT-
1 AATCAATTTAAATTTA
* *
353332 AATCATTTTAAATTCA
1 AATCAATTTAAATTTA
* *
353348 AATTTAAATTAATTATTTA
1 AA-TCAATTTAA--ATTTA
*
353367 AATTAATTTAAATTTA
1 AATCAATTTAAATTTA
*
353383 AATCAATTTAATTTTA
1 AATCAATTTAAATTTA
353399 AA
1 AA
353401 CTATTTCATA
Statistics
Matches: 106, Mismatches: 23, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
12 6 0.06
13 4 0.04
14 9 0.08
15 25 0.24
16 35 0.33
17 13 0.12
18 8 0.08
19 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (16 bp):
AATCAATTTAAATTTA
Found at i:353714 original size:2 final size:2
Alignment explanation
Indices: 353707--353750 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
353697 GAAGTTAGTG
353707 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
353749 AT
1 AT
353751 TTTCATGGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360327 original size:20 final size:21
Alignment explanation
Indices: 360287--360327 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
360277 TCTTGTCTTC
* *
360287 TTTTAAACAAAATTTCATTTT
1 TTTTAAAAAAAATATCATTTT
360308 TTTTAAAAAAAATATC-TTTT
1 TTTTAAAAAAAATATCATTTT
360328 CTCTTTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAAAAAAATATCATTTT
Found at i:361005 original size:4 final size:4
Alignment explanation
Indices: 360996--361026 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
360986 AAGGCTCATA
360996 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
361027 CGTAACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:363152 original size:29 final size:29
Alignment explanation
Indices: 363119--363202 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
363109 ATTGAACTCG
*
363119 AATTATTATTTAGTAATAAAATATATTTA
1 AATTATTATTTAATAATAAAATATATTTA
* *
363148 AATTATTATTTATTAATAAAATATATTTT
1 AATTATTATTTAATAATAAAATATATTTA
* * *
363177 TATTTTTATTTAATTATAAAATATAT
1 AATTATTATTTAATAATAAAATATAT
363203 AAATATTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
AATTATTATTTAATAATAAAATATATTTA
Found at i:363244 original size:21 final size:21
Alignment explanation
Indices: 363218--363258 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
363208 TTGATAAAAA
*
363218 ATAATTTTTAAATATATATCT
1 ATAATTTATAAATATATATCT
*
363239 ATAATTTATAATTATATATC
1 ATAATTTATAAATATATATC
363259 AAAGGAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAATTTATAAATATATATCT
Found at i:363331 original size:13 final size:12
Alignment explanation
Indices: 363315--363360 Score: 65
Period size: 13 Copynumber: 3.6 Consensus size: 12
363305 GATGAAGGAG
363315 AAAGAAAAAAAA
1 AAAGAAAAAAAA
363327 GAAAGAAAAAAAA
1 -AAAGAAAAAAAA
363340 AAAGAAGGAAAAAA
1 AAAGAA--AAAAAA
363354 AAAGAAA
1 AAAGAAA
363361 GAGGGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.23
13 12 0.39
14 12 0.39
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:363340 original size:16 final size:16
Alignment explanation
Indices: 363313--363384 Score: 76
Period size: 16 Copynumber: 4.6 Consensus size: 16
363303 TTGATGAAGG
363313 AGAAAGAAAAAAAAGAA
1 AGAAA-AAAAAAAAGAA
363330 AGAAAAAAAAAAAG-A
1 AGAAAAAAAAAAAGAA
*
363345 AG-GAAAAAAAAAGAA
1 AGAAAAAAAAAAAGAA
****
363360 AGAGGGGAAAAAAGAA
1 AGAAAAAAAAAAAGAA
363376 AGAAAAAAA
1 AGAAAAAAA
363385 CTTTTATGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
14 10 0.22
15 6 0.13
16 24 0.53
17 5 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAAAGAA
Found at i:363370 original size:18 final size:17
Alignment explanation
Indices: 363308--363372 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 17
363298 TAGGCTTGAT
363308 GAAGGAGAAAGAAAAAAAA
1 GAAGG-GAAA-AAAAAAAA
*
363327 GAA-AGAAAAAAAAAAA
1 GAAGGGAAAAAAAAAAA
*
363343 GAAGGAAAAAAAAAGAAA
1 GAAGGGAAAAAAAA-AAA
*
363361 GAGGGGAAAAAA
1 GAAGGGAAAAAA
363373 GAAAGAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 11 0.28
17 12 0.31
18 13 0.33
19 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
GAAGGGAAAAAAAAAAA
Found at i:363371 original size:30 final size:30
Alignment explanation
Indices: 363313--363384 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
363303 TTGATGAAGG
363313 AGAAAG-AAAAAAAAGAAAGAAAAAAAAAA
1 AGAAAGAAAAAAAAAGAAAGAAAAAAAAAA
* ****
363342 AGAAGGAAAAAAAAAGAAAGAGGGGAAAAA
1 AGAAAGAAAAAAAAAGAAAGAAAAAAAAAA
363372 AGAAAGAAAAAAA
1 AGAAAGAAAAAAA
363385 CTTTTATGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (30 bp):
AGAAAGAAAAAAAAAGAAAGAAAAAAAAAA
Found at i:363412 original size:12 final size:12
Alignment explanation
Indices: 363386--363424 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
363376 AGAAAAAAAC
363386 TTTTATGTT-TGT
1 TTTTATGTTAT-T
363398 TTTTATGTTATT
1 TTTTATGTTATT
*
363410 TTTTGTGTTATT
1 TTTTATGTTATT
363422 TTT
1 TTT
363425 GTGTATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 24 0.96
13 1 0.04
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (12 bp):
TTTTATGTTATT
Found at i:363503 original size:17 final size:18
Alignment explanation
Indices: 363481--363527 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
363471 AGATCAAATA
363481 TTATGTTTATTTAATT-T
1 TTATGTTTATTTAATTAT
363498 TTATGTTATATTTTAATTAT
1 TTATGTT-TA-TTTAATTAT
363518 TT-T-TTTATTT
1 TTATGTTTATTT
363528 TTAATTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.11
17 9 0.33
18 4 0.15
19 8 0.30
20 3 0.11
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TTATGTTTATTTAATTAT
Found at i:371273 original size:6 final size:6
Alignment explanation
Indices: 371262--371286 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
371252 TAGGAAAATG
371262 CTAATA CTAATA CTAATA CTAATA C
1 CTAATA CTAATA CTAATA CTAATA C
371287 AAGTTTATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (6 bp):
CTAATA
Found at i:373265 original size:14 final size:14
Alignment explanation
Indices: 373246--373274 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
373236 AAAAAGAATA
373246 AGGAAGAATTAGCT
1 AGGAAGAATTAGCT
373260 AGGAAGAATTAGCT
1 AGGAAGAATTAGCT
373274 A
1 A
373275 TATTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.21
Consensus pattern (14 bp):
AGGAAGAATTAGCT
Found at i:373965 original size:28 final size:27
Alignment explanation
Indices: 373910--373992 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 27
373900 AACCCAACTC
** *
373910 AAAAAATATATAA-AATTTAAATAATA
1 AAAAAATATATAATAATTTATTTATTA
373936 AAAAAATATAATAATAATTTATTTATTA
1 AAAAAATAT-ATAATAATTTATTTATTA
* *
373964 AAAATATAATTATATTAATTTATTTATTA
1 AAAAAAT-A-TATAATAATTTATTTATTA
373993 CAATTTTTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
26 9 0.19
27 4 0.08
28 16 0.33
29 18 0.38
30 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAAAATATATAATAATTTATTTATTA
Found at i:373966 original size:26 final size:29
Alignment explanation
Indices: 373937--373992 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
373927 TAAATAATAA
373937 AAAAATATAA-TA-A-TAATTTATTTATT
1 AAAAATATAATTATATTAATTTATTTATT
373963 AAAAATATAATTATATTAATTTATTTATT
1 AAAAATATAATTATATTAATTTATTTATT
373992 A
1 A
373993 CAATTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 10 0.37
27 2 0.07
28 1 0.04
29 14 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AAAAATATAATTATATTAATTTATTTATT
Found at i:373984 original size:25 final size:26
Alignment explanation
Indices: 373937--373987 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
373927 TAAATAATAA
*
373937 AAAAATATAATAATAATTTATTTATT
1 AAAAATATAATAATAATTAATTTATT
*
373963 AAAAATATAATTAT-ATTAATTTATT
1 AAAAATATAATAATAATTAATTTATT
373988 TATTACAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAAATATAATAATAATTAATTTATT
Found at i:378939 original size:47 final size:46
Alignment explanation
Indices: 378798--378947 Score: 147
Period size: 47 Copynumber: 3.2 Consensus size: 46
378788 GGAAGGTCTA
* * * *
378798 TAACTTTATCTGTGTAAAAGTTACAAGTTGTTTGTGAGAAAAGTTTA
1 TAACTTTATCTGTGTAAAAGTTACAAGTTATTTGTAAGAAGA-TTTG
* * ** * * *
378845 TAACTTAATCTATACAAAAGTTGCAAGTTATTTATAAAGAAGGTTTG
1 TAACTTTATCTGTGTAAAAGTTACAAGTTATTTGT-AAGAAGATTTG
* *
378892 TAACTTTATCTGTGTAAAAGTTACAAGTTACTTGTCAGGAAGATTTG
1 TAACTTTATCTGTGTAAAAGTTACAAGTTATTTGT-AAGAAGATTTG
*
378939 TAGCTTTAT
1 TAACTTTAT
378948 TAGTGCAAAA
Statistics
Matches: 80, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
47 76 0.95
48 4 0.05
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (46 bp):
TAACTTTATCTGTGTAAAAGTTACAAGTTATTTGTAAGAAGATTTG
Found at i:378958 original size:47 final size:47
Alignment explanation
Indices: 378798--378967 Score: 130
Period size: 47 Copynumber: 3.6 Consensus size: 47
378788 GGAAGGTCTA
* ** * *
378798 TAACTTTATCTGTGTAAAAGTTACAAGTTGTTTGTGAGAA-AAG-TTTA
1 TAACTTTATCTGTGCAAAAGTTACAAGTTACTTAT-A-AAGAAGATTTG
* * * * * *
378845 TAACTTAATCTATACAAAAGTTGCAAGTTATTTATAAAGAAGGTTTG
1 TAACTTTATCTGTGCAAAAGTTACAAGTTACTTATAAAGAAGATTTG
* * * *
378892 TAACTTTATCTGTGTAAAAGTTACAAGTTACTTGTCAGGAAGATTTG
1 TAACTTTATCTGTGCAAAAGTTACAAGTTACTTATAAAGAAGATTTG
* * *
378939 TAGCTTTAT-TAGTGCAAAAGCTATAAGTT
1 TAACTTTATCT-GTGCAAAAGTTACAAGTT
378968 TGGTTGTGAC
Statistics
Matches: 98, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
45 2 0.02
46 5 0.05
47 91 0.93
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (47 bp):
TAACTTTATCTGTGCAAAAGTTACAAGTTACTTATAAAGAAGATTTG
Found at i:379204 original size:33 final size:33
Alignment explanation
Indices: 379144--379206 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
379134 AAATAAAATA
*
379144 AAACTTTATTCTAAATAGAGATCTAAATGAGCT
1 AAACTTTATTCTAAATAGAGATATAAATGAGCT
*
379177 AAACTTTATTTTAAATAGA-ATTATAAATGA
1 AAACTTTATTCTAAATAGAGA-TATAAATGA
379207 AATAGAACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.37
Consensus pattern (33 bp):
AAACTTTATTCTAAATAGAGATATAAATGAGCT
Found at i:389861 original size:39 final size:39
Alignment explanation
Indices: 389813--389981 Score: 155
Period size: 39 Copynumber: 4.2 Consensus size: 39
389803 CAAAAAAAAG
* * * *
389813 TAAATAACAAGAATGAAAGTAAAGCAAATAACTTGATTT
1 TAAATAACAATAATAAAAGTAAAGTAAATAACTTGAATT
* *
389852 TAAATAACAATAATAAAAATTCAA-TAAATAA-TATGAATT
1 TAAATAACAATAAT-AAAAGTAAAGTAAATAACT-TGAATT
* * *
389891 TAAATAAAAATAATAAAAGTAAAGTAAATAACATGAACT
1 TAAATAACAATAATAAAAGTAAAGTAAATAACTTGAATT
* *
389930 TAAATAACAAAAATAATAACAAGTAACGTAAATGAACGT-AATT
1 TAAATAAC---AATAATAA-AAGTAAAGTAAAT-AACTTGAATT
389973 TAAATAACA
1 TAAATAACA
389982 TTAGATGTAA
Statistics
Matches: 106, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
38 8 0.08
39 56 0.53
40 7 0.07
42 8 0.08
43 23 0.22
44 4 0.04
ACGTcount: A:0.60, C:0.07, G:0.08, T:0.25
Consensus pattern (39 bp):
TAAATAACAATAATAAAAGTAAAGTAAATAACTTGAATT
Found at i:390690 original size:33 final size:33
Alignment explanation
Indices: 390653--390718 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
390643 GCTCATGCTT
*
390653 GGCTACCAAAAAAACTTTGAAACCTTTAAGCTC
1 GGCTACAAAAAAAACTTTGAAACCTTTAAGCTC
*
390686 GGCTATAAAAAAAACTTTGAAACCTTTAAGCTC
1 GGCTACAAAAAAAACTTTGAAACCTTTAAGCTC
390719 AATCGAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (33 bp):
GGCTACAAAAAAAACTTTGAAACCTTTAAGCTC
Found at i:391235 original size:11 final size:11
Alignment explanation
Indices: 391219--391254 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
391209 ATTTCTTATC
391219 TTTCTTTTTTT
1 TTTCTTTTTTT
391230 TTTC-TTTTTT
1 TTTCTTTTTTT
391240 TTTCTTTTTCTT
1 TTTCTTTTT-TT
391252 TTT
1 TTT
391255 TCTCTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.43
11 8 0.35
12 5 0.22
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:391237 original size:6 final size:6
Alignment explanation
Indices: 391219--391254 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
391209 ATTTCTTATC
391219 TTTCTT TTT-TT TTTC-T TTT-TT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
391255 TCTCTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 13 0.48
6 14 0.52
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (6 bp):
TTTCTT
Found at i:391247 original size:16 final size:15
Alignment explanation
Indices: 391217--391255 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
391207 AAATTTCTTA
*
391217 TCTTTCTTTTTTTTT
1 TCTTTTTTTTTTTTT
391232 TCTTTTTTTTTCTTTT
1 TCTTTTTTTTT-TTTT
391248 TCTTTTTT
1 TCTTTTTT
391256 CTCTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TCTTTTTTTTTTTTT
Found at i:393115 original size:28 final size:29
Alignment explanation
Indices: 393083--393138 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
393073 GCCTAAATGA
393083 TAAAT-CAAGAACTTGAATA-GGTGATATT
1 TAAATCCAA-AACTTGAATATGGTGATATT
* *
393111 TAAATCCAAAACTTTAATATGGTTATAT
1 TAAATCCAAAACTTGAATATGGTGATAT
393139 GTTACCTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (29 bp):
TAAATCCAAAACTTGAATATGGTGATATT
Found at i:393559 original size:2 final size:2
Alignment explanation
Indices: 393552--393578 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
393542 TAAGGAACTT
393552 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
393579 TTGCATGCTG
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:398427 original size:33 final size:33
Alignment explanation
Indices: 398390--398453 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
398380 TGAGAAAATA
* * *
398390 TAAGGGAAATATCTATATAGTATCAATACTTCT
1 TAAGGAAAATATCAATAGAGTATCAATACTTCT
*
398423 TAAGGAAAATATCAATAGGGTATCAATACTT
1 TAAGGAAAATATCAATAGAGTATCAATACTT
398454 ACTTTCCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (33 bp):
TAAGGAAAATATCAATAGAGTATCAATACTTCT
Found at i:398516 original size:21 final size:22
Alignment explanation
Indices: 398492--398559 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
398482 GGCAAGAAAT
*
398492 TATTGATACTCT-ACTTA-AAAG
1 TATTGATACT-TAACCTATAAAG
398513 TATTGATACTTAACCTATAAAG
1 TATTGATACTTAACCTATAAAG
* *
398535 TATTGATACTTCACAT-TAAAG
1 TATTGATACTTAACCTATAAAG
398556 TATT
1 TATT
398560 CATATCTGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 1 0.02
21 23 0.55
22 18 0.43
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (22 bp):
TATTGATACTTAACCTATAAAG
Found at i:399813 original size:142 final size:133
Alignment explanation
Indices: 399533--399972 Score: 554
Period size: 132 Copynumber: 3.2 Consensus size: 133
399523 TAGGTTCAAC
* * *
399533 AACAACCCACCAAATTGAACTCCTATATTTATTTTTTTTATTATCAATAGTTGTCCACTAATAGA
1 AACAACCCACCAAATTGAACTCTTATATATATTTTTTTTATTATCAATAGTTGT-CACT-ATAAA
* * *
399598 AACAC-CATGGACAAGATTTCAAAAT-AAAAAGGATTAATAACATGAATAGGTATTTTTTAATTA
64 AACACACATGGACAAGATTTCAAAATAAAAAAAGACTAATAACATGAATAGATA-TTTTTAATTA
399661 ATGCAT
128 ATGCAT
* * *
399667 AACAACCCATCAAATTGAACTCTTATATATATTTTTTCTATTATCAATAGTTATCTACTGATAAA
1 AACAACCCACCAAATTGAACTCTTATATATATTTTTTTTATTATCAATAGTTGTC-ACT-AT-AA
399732 AATACCACTGCACATGGACTAAGATTTCAAAATAAAAAAAGACTAATAACATGAATAGATATTTT
63 AA-A-CA---CACATGGAC-AAGATTTCAAAATAAAAAAAGACTAATAACATGAATAGATATTTT
399797 TAATTAATGCAT
122 TAATTAATGCAT
* *
399809 AACAACCTACCAAATTGAACTCTTATATATAATTTTTTTTATTATCAATAGTTGTC-C-AT-AGA
1 AACAACCCACCAAATTGAACTCTTATATAT-ATTTTTTTTATTATCAATAGTTGTCACTATAAAA
*
399871 A-ACACA--GACCAAGATTTCAAAATTTTAAAAAAAAACTAATAACATGAATAGATATTTTTAAT
65 ACACACATGGA-CAAGATTTCAAAA---TAAAAAAAGACTAATAACATGAATAGATATTTTTAAT
*
399933 TACTGCAT
126 TAATGCAT
399941 AACAACCCACCAAATTGAACTCTTATATATAT
1 AACAACCCACCAAATTGAACTCTTATATATAT
399973 ATATATATAT
Statistics
Matches: 273, Mismatches: 18, Indels: 33
0.84 0.06 0.10
Matches are distributed among these distances:
129 14 0.05
130 1 0.00
131 6 0.02
132 72 0.26
133 1 0.00
134 55 0.20
135 3 0.01
136 2 0.01
137 4 0.01
139 2 0.01
140 1 0.00
141 8 0.03
142 57 0.21
143 47 0.17
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (133 bp):
AACAACCCACCAAATTGAACTCTTATATATATTTTTTTTATTATCAATAGTTGTCACTATAAAAA
CACACATGGACAAGATTTCAAAATAAAAAAAGACTAATAACATGAATAGATATTTTTAATTAATG
CAT
Found at i:399971 original size:2 final size:2
Alignment explanation
Indices: 399964--399988 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
399954 ATTGAACTCT
399964 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 T
399989 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:400460 original size:21 final size:21
Alignment explanation
Indices: 400436--400482 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
400426 TTTTAATACG
*
400436 AATATATCATAAAAA-ATAATT
1 AATATATAATAAAAATAT-ATT
*
400457 AATATATAATATAAATATATT
1 AATATATAATAAAAATATATT
400478 AATAT
1 AATAT
400483 TTGAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATATAATAAAAATATATT
Found at i:400570 original size:23 final size:23
Alignment explanation
Indices: 400513--400575 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
400503 AATTATTAAC
*
400513 ATATTAAAAATTATATATAAAAAAT
1 ATATTAAATA-TA-ATATAAAAAAT
*
400538 ATATTAAATATAATATAATAAGAT
1 ATATTAAATATAATATAA-AAAAT
*
400562 ATA-TGAATATAATA
1 ATATTAAATATAATA
400576 CGATAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 16 0.47
24 9 0.26
25 9 0.26
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (23 bp):
ATATTAAATATAATATAAAAAAT
Found at i:400572 original size:18 final size:17
Alignment explanation
Indices: 400545--400590 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
400535 AATATATTAA
400545 ATATAATATAATAAGAT
1 ATATAATATAATAAGAT
*
400562 ATATGAATATAATACGAT
1 ATAT-AATATAATAAGAT
400580 A-ATATATATAA
1 ATATA-ATATAA
400591 ATTTTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 12 0.46
18 13 0.50
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (17 bp):
ATATAATATAATAAGAT
Found at i:400581 original size:23 final size:23
Alignment explanation
Indices: 400544--400588 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
400534 AAATATATTA
*
400544 AATATAATATAATAAGATATATG
1 AATATAATACAATAAGATATATG
* *
400567 AATATAATACGATAATATATAT
1 AATATAATACAATAAGATATAT
400589 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
AATATAATACAATAAGATATATG
Found at i:400893 original size:17 final size:16
Alignment explanation
Indices: 400860--400905 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
400850 AAAATTTTTA
400860 TAATTT-TAATTTATT
1 TAATTTATAATTTATT
400875 TAATTTATAATTTATTT
1 TAATTTATAATTTA-TT
* *
400892 TAAATTATTATTTA
1 TAATTTATAATTTA
400906 AATAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 6 0.22
16 7 0.26
17 14 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTATAATTTATT
Found at i:401768 original size:19 final size:19
Alignment explanation
Indices: 401744--401786 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
401734 GAACAATAAT
401744 TAAATATA-TAAAAATAGCA
1 TAAATATACTAAAAATA-CA
*
401763 TAAATATACTACAAATACA
1 TAAATATACTAAAAATACA
401782 TAAAT
1 TAAAT
401787 TTGTCAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (19 bp):
TAAATATACTAAAAATACA
Found at i:402128 original size:9 final size:11
Alignment explanation
Indices: 402092--402268 Score: 74
Period size: 11 Copynumber: 16.1 Consensus size: 11
402082 TATGATACAG
402092 ATATAT-AAAT
1 ATATATAAAAT
*
402102 ATGT-TAAAAT
1 ATATATAAAAT
402112 ATATATAAAAT
1 ATATATAAAAT
* *
402123 AAATAATTAAAT
1 ATAT-ATAAAAT
402135 -TAATTATAAAAAT
1 AT-A-TAT-AAAAT
*
402148 TTATATAAATTTAT
1 ATATATAAA---AT
* *
402162 AATATTTTAAAT
1 -ATATATAAAAT
402174 ATATA-AAAGAT
1 ATATATAAA-AT
402185 A-ATAT-AAAT
1 ATATATAAAAT
402194 ATAATATAAAA-
1 AT-ATATAAAAT
*
402205 ATAAATTAAAAT
1 ATATA-TAAAAT
402217 ATA-ATATAAAT
1 ATATATA-AAAT
402228 AT-TAT-AAAT
1 ATATATAAAAT
402237 ATA-A-AATAA-
1 ATATATAA-AAT
402246 ATATATAAAAT
1 ATATATAAAAT
*
402257 ATATATATAAT
1 ATATATAAAAT
402268 A
1 A
402269 CAATATAAAT
Statistics
Matches: 128, Mismatches: 13, Indels: 51
0.67 0.07 0.27
Matches are distributed among these distances:
9 15 0.12
10 26 0.20
11 52 0.41
12 20 0.16
13 6 0.05
14 3 0.02
15 6 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
ATATATAAAAT
Found at i:402192 original size:72 final size:73
Alignment explanation
Indices: 402068--402277 Score: 200
Period size: 72 Copynumber: 2.9 Consensus size: 73
402058 AACATAATAT
* * * * * *
402068 AAAAATAATATAAATATGATACAGATATATAAATATGTTAAAATATATATAAA-ATAA-ATAATT
1 AAAAATAATATAAATATTATAAATATAAATAAATATATAAAAATATATATAAATATAATATAA--
*
402131 AAATTAATTA
64 AAATAAATTA
* **
402141 TAAAAATTTATATAAAT-TTAT-AATAT-TTTAAATATATAAAAGATA-ATATAAATATAATATA
1 -AAAAA-TAATATAAATATTATAAATATAAATAAATATATAAAA-ATATATATAAATATAATATA
402202 AAAATAAATTA
63 AAAATAAATTA
* *
402213 AAATATAATATAAATATTATAAATATAAAATAAATATAT-AAAATATATATATAATACAATATAA
1 AAAAATAATATAAATATTATAAATAT-AAATAAATATATAAAAATATATATA-AATATAATATAA
402277 A
64 A
402278 TTTATAATAT
Statistics
Matches: 113, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
70 9 0.08
71 8 0.07
72 36 0.32
73 18 0.16
74 33 0.29
75 9 0.08
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (73 bp):
AAAAATAATATAAATATTATAAATATAAATAAATATATAAAAATATATATAAATATAATATAAAA
ATAAATTA
Found at i:402196 original size:6 final size:6
Alignment explanation
Indices: 402185--402313 Score: 78
Period size: 6 Copynumber: 22.3 Consensus size: 6
402175 TATAAAAGAT
*
402185 AATATA AATAT- AATATA AAAATA AAT-TA AA-ATA TAATATA AATAT-
1 AATATA AATATA AATATA AATATA AATATA AATATA -AATATA AATATA
* * *
402230 --TATA AATATA AA-ATA AATATA TAAAATA TATATA TAATA-C AATATA
1 AATATA AATATA AATATA AATATA -AATATA AATATA -AATATA AATATA
* * * * *
402276 AATTTA TAATAT- ATTAAA AATAAA AATATA AAGATA AA
1 AATATA -AATATA AATATA AATATA AATATA AATATA AA
402314 ATTATTTTTT
Statistics
Matches: 95, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
3 3 0.03
5 23 0.24
6 54 0.57
7 15 0.16
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:402199 original size:5 final size:5
Alignment explanation
Indices: 402183--402288 Score: 64
Period size: 5 Copynumber: 21.6 Consensus size: 5
402173 TATATAAAAG
* *
402183 ATAAT ATAAAT ATAAT ATAA- A-AAT A-AATT AAAAT ATAAT ATAA- ATATT
1 ATAAT AT-AAT ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT
* * *
402231 ATAAAT ATAAA ATAA- ATATAT AAAAT ATATAT ATAAT ACAAT ATAA-
1 AT-AAT ATAAT ATAAT ATA-AT ATAAT ATA-AT ATAAT ATAAT ATAAT
*
402277 AT-TT ATAAT ATA
1 ATAAT ATAAT ATA
402289 TTAAAAATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
3 2 0.03
4 14 0.17
5 46 0.57
6 18 0.22
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:402277 original size:31 final size:29
Alignment explanation
Indices: 402230--402303 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 29
402220 ATATAAATAT
*
402230 TATAAATATAAAATAAATATATAAAATAT
1 TATAAATACAAAATAAATATATAAAATAT
* * *
402259 ATATATAATACAATATAAATTTATAATATAT
1 -TATA-AATACAAAATAAATATATAAAATAT
*
402290 TAAAAATA-AAAATA
1 TATAAATACAAAATA
402304 TAAAGATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 5 0.14
29 4 0.11
30 7 0.19
31 21 0.57
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (29 bp):
TATAAATACAAAATAAATATATAAAATAT
Found at i:402637 original size:27 final size:27
Alignment explanation
Indices: 402607--402659 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
402597 CCACAATTAG
*
402607 AAAATTTTAATTAAATTATAATTTAAAA
1 AAAATTTAAATTAAATT-TAATTTAAAA
*
402635 AAAATTTAAATTATATTTAATTTAA
1 AAAATTTAAATTAAATTTAATTTAA
402660 TTAATTGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATTTAAATTAAATTTAATTTAAAA
Found at i:402769 original size:20 final size:18
Alignment explanation
Indices: 402740--402781 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
402730 TATAATTACA
402740 TTTAAATAAAAATATATTAT
1 TTTAAAT-AAAATA-ATTAT
*
402760 TTTAATTAAAATAATTAT
1 TTTAAATAAAATAATTAT
402778 TTTA
1 TTTA
402782 CAATTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAAATAATTAT
Found at i:402811 original size:25 final size:24
Alignment explanation
Indices: 402761--402811 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
402751 ATATATTATT
* ** *
402761 TTAATTAAAATAATTATTTTACAA
1 TTAATTAAAATAATAAAATTAAAA
402785 TTAATTTAAAATAATAAAATTAAAA
1 TTAA-TTAAAATAATAAAATTAAAA
402810 TT
1 TT
402812 TAACTCAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAATTAAAATAATAAAATTAAAA
Found at i:403009 original size:2 final size:2
Alignment explanation
Indices: 403004--403043 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
402994 TCTGTGAACA
403004 AT AT AT AT AT AT 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 AT AT AT AT AT AT
403044 CTCTGCTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:404589 original size:29 final size:29
Alignment explanation
Indices: 404544--404600 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
404534 TTTAGAAGAA
*
404544 TTTATATTATATATTTTCTTAAATGTTTAT
1 TTTATATTATATATTTTATTAAAT-TTTAT
404574 TTTATATT-TA-ATTTTTATTAAATTTTA
1 TTTATATTATATA-TTTTATTAAATTTTA
404601 AAATATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 12 0.48
30 8 0.32
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTATATTATATATTTTATTAAATTTTAT
Found at i:405132 original size:18 final size:18
Alignment explanation
Indices: 405104--405151 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
405094 ATGCACTTGT
405104 AATTATTATTTATTAATAA
1 AATT-TTATTTATTAATAA
* * *
405123 AATTTTATTTTTTATTTA
1 AATTTTATTTATTAATAA
405141 AA-TTTATTTAT
1 AATTTTATTTAT
405152 AAAAATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 8 0.32
18 13 0.52
19 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTTATTTATTAATAA
Found at i:405506 original size:2 final size:2
Alignment explanation
Indices: 405499--405535 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
405489 AATCAATGAC
*
405499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
405536 AACTTGTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:406049 original size:60 final size:60
Alignment explanation
Indices: 405964--406132 Score: 202
Period size: 59 Copynumber: 2.8 Consensus size: 60
405954 TTTGGGGCGG
* * *
405964 AGCAAAGACAAAGAAACCTTGAGCAAATCAAGCATTAGCACATTAGGACAAGATTGGGGA
1 AGCAAAGACAAAGAAACCTTAAGCAAATCAAGCATTAGGACATTAGGACAAGATTGGAGA
* * * *
406024 AGCAAAGACAAAGAGAA-CTTAAGCAAATC-TGACATTAGGGC-TTAGGACAGGATTTGAGA
1 AGCAAAGACAAAGA-AACCTTAAGCAAATCAAG-CATTAGGACATTAGGACAAGATTGGAGA
* *
406083 AACAAAGACAAAGAAACCTTAAGCAAATCAAACAGTT-GGACATTAGGACA
1 AGCAAAGACAAAGAAACCTTAAGCAAATCAAGCA-TTAGGACATTAGGACA
406133 GGCACAACTA
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
58 2 0.02
59 46 0.50
60 42 0.46
61 2 0.02
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (60 bp):
AGCAAAGACAAAGAAACCTTAAGCAAATCAAGCATTAGGACATTAGGACAAGATTGGAGA
Found at i:406730 original size:14 final size:14
Alignment explanation
Indices: 406711--406738 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
406701 TGATAGAGCA
406711 AACAATAAGATAGG
1 AACAATAAGATAGG
406725 AACAATAAGATAGG
1 AACAATAAGATAGG
406739 GCCTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
AACAATAAGATAGG
Found at i:409722 original size:46 final size:45
Alignment explanation
Indices: 409656--409752 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 45
409646 TTTAAAATAG
* *
409656 TTAGTGGTATTGCTAGGATCCCACAATTTAA-AGGAATCTCTTTGT
1 TTAGTGGTATTGCTAGGATCCCACAATTTAAGA-GAATCTCCTTAT
*
409701 TTAGTGGATATTGTTAGGATCCCACAATTTAAGAGAATCTCCTTAT
1 TTAGTGG-TATTGCTAGGATCCCACAATTTAAGAGAATCTCCTTAT
409747 TTAGTG
1 TTAGTG
409753 AGATTAGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
45 7 0.15
46 39 0.83
47 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (45 bp):
TTAGTGGTATTGCTAGGATCCCACAATTTAAGAGAATCTCCTTAT
Found at i:410228 original size:30 final size:30
Alignment explanation
Indices: 410189--410247 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
410179 ACTAATTTAA
*
410189 ATCTTTTAAATTAAAGACTAGTGCACCACT
1 ATCTCTTAAATTAAAGACTAGTGCACCACT
* *
410219 ATCTCTTAAATTAAGGATTAGTGCACCAC
1 ATCTCTTAAATTAAAGACTAGTGCACCAC
410248 ATAATGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (30 bp):
ATCTCTTAAATTAAAGACTAGTGCACCACT
Found at i:410263 original size:2 final size:2
Alignment explanation
Indices: 410256--410292 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
410246 ACATAATGAA
410256 AT AT AT 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 AT AT AT A
410293 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:410824 original size:105 final size:105
Alignment explanation
Indices: 410642--410845 Score: 372
Period size: 105 Copynumber: 1.9 Consensus size: 105
410632 TCTATCTACC
*
410642 TCGATGTGCTTCGTCCTATCATGCTGAATTAGGTTGTAGGCTATGCTTATTACTGATTTATTATC
1 TCGATGTGCTTCGTCCTATCATGCTGAATTAGGTTGTAGGCTATGCTTATTACTGATTTACTATC
*
410707 ACAGTAGAGTCTCATAGGACCATCCCACTTAATTTTTACT
66 ACAGGAGAGTCTCATAGGACCATCCCACTTAATTTTTACT
*
410747 TCGATGTGCTTCGTCCTATCATGCTGAATTGGGTTGTAGGCTATGCTTATTACTGATTTACTATC
1 TCGATGTGCTTCGTCCTATCATGCTGAATTAGGTTGTAGGCTATGCTTATTACTGATTTACTATC
*
410812 ATAGGAGAGTCTCATAGGACCATCCCACTTAATT
66 ACAGGAGAGTCTCATAGGACCATCCCACTTAATT
410846 CTTAAGTCTT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (105 bp):
TCGATGTGCTTCGTCCTATCATGCTGAATTAGGTTGTAGGCTATGCTTATTACTGATTTACTATC
ACAGGAGAGTCTCATAGGACCATCCCACTTAATTTTTACT
Found at i:414012 original size:21 final size:21
Alignment explanation
Indices: 413982--414021 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
413972 GTACATGTAC
*
413982 CTGCAGGTTTCTCTAGGTTTG
1 CTGCAAGTTTCTCTAGGTTTG
414003 CTGCAAGTTTCTCTAGGTT
1 CTGCAAGTTTCTCTAGGTT
414022 GCTAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.42
Consensus pattern (21 bp):
CTGCAAGTTTCTCTAGGTTTG
Found at i:416862 original size:14 final size:14
Alignment explanation
Indices: 416843--416871 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
416833 CTCACACCTT
416843 CCATTCTTCAATTA
1 CCATTCTTCAATTA
416857 CCATTCTTCAATTA
1 CCATTCTTCAATTA
416871 C
1 C
416872 ATTGGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (14 bp):
CCATTCTTCAATTA
Found at i:420820 original size:15 final size:15
Alignment explanation
Indices: 420785--420822 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
420775 TACATTTATG
420785 TATTTTAA-TATCTT
1 TATTTTAATTATCTT
* *
420799 AATTTTAATTATTTT
1 TATTTTAATTATCTT
420814 TATTTTAAT
1 TATTTTAAT
420823 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTAATTATCTT
Found at i:421600 original size:16 final size:16
Alignment explanation
Indices: 421590--421621 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
421580 AATTAATTTT
*
421590 AATTATTATTAAATTA
1 AATTATGATTAAATTA
421606 AATTATGATTAAATTA
1 AATTATGATTAAATTA
421622 TATCATAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AATTATGATTAAATTA
Found at i:421965 original size:14 final size:14
Alignment explanation
Indices: 421939--421973 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
421929 AAAAATAAAA
421939 TTTATTT-TTTATT
1 TTTATTTATTTATT
421952 TTTATTTATTTATT
1 TTTATTTATTTATT
*
421966 TTTCTTTA
1 TTTATTTA
421974 ATCAATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:424951 original size:23 final size:23
Alignment explanation
Indices: 424923--424967 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
424913 TACATTAATC
424923 ATTACTGTAATAAAATATTTTGT
1 ATTACTGTAATAAAATATTTTGT
424946 ATTACTGTAATAAAATATTTTG
1 ATTACTGTAATAAAATATTTTG
424968 GTATCTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (23 bp):
ATTACTGTAATAAAATATTTTGT
Found at i:429645 original size:166 final size:166
Alignment explanation
Indices: 429371--429693 Score: 540
Period size: 166 Copynumber: 1.9 Consensus size: 166
429361 CATAACCCTC
* * *
429371 TTAAGATCATCATGCATTATTGTGGCCATGGATGTGGTAGCTTATGAATGTTTTGATGTTTTCAT
1 TTAAGATCATCATGCATTATTGTAGCCATGGATGTGGTAGCATAGGAATGTTTTGATGTTTTCAT
* * *
429436 GTTATTTATGTGCTTAAAATGTCATGTTTATCTCCATCATCTTAGCAGCTCATATTCATGCATTT
66 GTCATTTATGTGCTTAAAATGTCATGTTCATCTCCATCATCTTAGCAGCCCATATTCATGCATTT
429501 TATGCCATGTTCCATGCATTCCATCATCTTTACCTT
131 TATGCCATGTTCCATGCATTCCATCATCTTTACCTT
* * *
429537 TTAAGATCATCATGCTTTATTGTAGCCTTGGATGTGGTAGCATAGGATTGTTTTGATGTTTTCAT
1 TTAAGATCATCATGCATTATTGTAGCCATGGATGTGGTAGCATAGGAATGTTTTGATGTTTTCAT
*
429602 GTCATTTATGTGCTTAAAATG-CTATGTTCATCTCCATCATCTTAGCAGCCCCTATTCATGCATT
66 GTCATTTATGTGCTTAAAATGTC-ATGTTCATCTCCATCATCTTAGCAGCCCATATTCATGCATT
429666 TTATGCCATGTTCCATGCATTCCATCAT
130 TTATGCCATGTTCCATGCATTCCATCAT
429694 GTCCAATCTA
Statistics
Matches: 146, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
165 1 0.01
166 145 0.99
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (166 bp):
TTAAGATCATCATGCATTATTGTAGCCATGGATGTGGTAGCATAGGAATGTTTTGATGTTTTCAT
GTCATTTATGTGCTTAAAATGTCATGTTCATCTCCATCATCTTAGCAGCCCATATTCATGCATTT
TATGCCATGTTCCATGCATTCCATCATCTTTACCTT
Found at i:433649 original size:17 final size:17
Alignment explanation
Indices: 433612--433649 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
433602 GGGTCGTGGA
*
433612 AAAATGATGGAATTACT
1 AAAATGATGGAATAACT
433629 AAAATGATGAGAATAAC-
1 AAAATGATG-GAATAACT
433646 AAAA
1 AAAA
433650 ACAGTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (17 bp):
AAAATGATGGAATAACT
Found at i:433650 original size:18 final size:17
Alignment explanation
Indices: 433611--433650 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
433601 AGGGTCGTGG
*
433611 AAAAATGATGGAATTAC
1 AAAAATGATGGAATAAC
*
433628 TAAAATGATGAGAATAAC
1 AAAAATGATG-GAATAAC
433646 AAAAA
1 AAAAA
433651 CAGTAAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.60, C:0.05, G:0.15, T:0.20
Consensus pattern (17 bp):
AAAAATGATGGAATAAC
Found at i:435251 original size:52 final size:52
Alignment explanation
Indices: 435194--435979 Score: 404
Period size: 52 Copynumber: 15.1 Consensus size: 52
435184 GACGACACTA
* * *
435194 GACTTAATGATGATAAAGGTGAC-AATGTACTGATTCAAGGCCAATGACATTG
1 GACTTAAAGATGATAAAGGTG-CTAATATGCTGATTCAAGGCCAATGACATTG
* * ** * *
435246 GACTTAAAGATGATAAAGGTGCTAATATGCTGATTTAAGACCAGCGATATTT
1 GACTTAAAGATGATAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * *
435298 GA-TGACAG--G----A-GTGCTAATATGCTGATTCAAGGCCAATGACATTA
1 GACTTAAAGATGATAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * * * * * *
435342 GACTTGAAGACGA-GAAGAGTGCTAATGTACTGATTCAAGGCTAGA-GAAATTG
1 GACTTAAAGATGATAAAG-GTGCTAATATGCTGATTCAAGGCCA-ATGACATTG
** * * ** *
435394 GACTTAAAGAT-AGTAAATATGCGAATATGCTGATTCAAGGCTAGCGATATTG
1 GACTTAAAGATGA-TAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * * * * * *
435446 GACTTAAAGATGAGAAAGGTGCCAATATGCTGATTCACGGTCGATGATATCG
1 GACTTAAAGATGATAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * * * * * *
435498 GACTTAAAGATGAGAAAAGTGCCAATATGCTAATTCAAGGCTAGTTACATTG
1 GACTTAAAGATGATAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * * *
435550 GACTTAAAGATGATAAAGGTG-TCAATATGTTGATTTAAGGCC-ATCGATATCG
1 GACTTAAAGATGATAAAGGTGCT-AATATGCTGATTCAAGGCCAAT-GACATTG
* * * * *
435602 GACTTAAAGATGAT-AGGAGTGCTAATATGCTGATTCAAGACCAACGATATTA
1 GACTTAAAGATGATAAAG-GTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * * * * * *
435654 GACTTAAAGACGA-GAAGAGTGTTAATGTACTTATTCAAGGCTAGA-GACATTG
1 GACTTAAAGATGATAAAG-GTGCTAATATGCTGATTCAAGGCCA-ATGACATTG
* * * * ** *
435706 AACTTAAAGATAATAAAGATAATAAAGATGCCAATATGCTGATTCAAGGCTAGCGATATTG
1 GACTTAAAG---AT---G---ATAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * * ** ** * **
435767 GACTTAAAGATGAGAAATGTGCTAATATGCT-ATTCACGATCGGTGATATCA
1 GACTTAAAGATGATAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * * * * * * *
435818 GACTTAAAGATGAGAAAAGCGCCAATATGCTAATTCAAGGCCAGTCACATTA
1 GACTTAAAGATGATAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * * ** * * *
435870 GTCTTAAAGATGATAAAGATGCCAATATTTTGATTTAAGGCCAACGACATTA
1 GACTTAAAGATGATAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
* * * * * * *
435922 GACTTAAATATGA-AAAGAGTGCCAATGTGCTGATTTAAGGCCAACGACGTTA
1 GACTTAAAGATGATAAAG-GTGCTAATATGCTGATTCAAGGCCAATGACATTG
435974 GACTTA
1 GACTTA
435980 GAAAGAGATA
Statistics
Matches: 563, Mismatches: 137, Indels: 68
0.73 0.18 0.09
Matches are distributed among these distances:
44 30 0.05
45 4 0.01
47 1 0.00
49 1 0.00
50 1 0.00
51 53 0.09
52 424 0.75
53 7 0.01
55 2 0.00
58 3 0.01
61 34 0.06
62 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (52 bp):
GACTTAAAGATGATAAAGGTGCTAATATGCTGATTCAAGGCCAATGACATTG
Found at i:435534 original size:156 final size:156
Alignment explanation
Indices: 435193--435965 Score: 645
Period size: 156 Copynumber: 5.0 Consensus size: 156
435183 CGACGACACT
* * * * * * * *
435193 AGACTTAATGATGATAAAGGTGACAATGTACTGATTCAAGGCCA-ATGACATTGGACTTAAAGAT
1 AGACTTAAAGACGAGAAAAGTGCCAATATACTAATTCAAGGCTAGA-GACATTGGACTTAAAGAT
* * * * * *
435257 GATAAAGGTGCTAATATGCTGATTTAAGACCAGCGATA-T----TT---GATGACAGGAGTGCTA
65 GATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGAGTGCTA
* * *
435314 ATATGCTGATTCAAGGCCAATGACATT
130 ATATGCTGATTCAAGACCAATGATATC
* * * * * *
435341 AGACTTGAAGACGAGAAGAGTGCTAATGTACTGATTCAAGGCTAGAGAAATTGGACTTAAAGAT-
1 AGACTTAAAGACGAGAAAAGTGCCAATATACTAATTCAAGGCTAGAGACATTGGACTTAAAGATG
* * * *
435405 AGTAAATATGCGAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGATGAGAAAG-GTGCC
66 A-TAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAAGAGTGCT
* ** *
435469 AATATGCTGATTCACGGTCGATGATATC
129 AATATGCTGATTCAAGACCAATGATATC
* * * **
435497 GGACTTAAAGATGAGAAAAGTGCCAATATGCTAATTCAAGGCTAGTTACATTGGACTTAAAGATG
1 AGACTTAAAGACGAGAAAAGTGCCAATATACTAATTCAAGGCTAGAGACATTGGACTTAAAGATG
* * * * * * * *
435562 ATAAAGGTGTCAATATGTTGATTTAAGGCCATCGATATCGGACTTAAAGATGATAGGAGTGCTAA
66 ATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGAGTGCTAA
* *
435627 TATGCTGATTCAAGACCAACGATATT
131 TATGCTGATTCAAGACCAATGATATC
* ** * * *
435653 AGACTTAAAGACGAGAAGAGTGTTAATGTACTTATTCAAGGCTAGAGACATTGAACTTAAAGATA
1 AGACTTAAAGACGAGAAAAGTGCCAATATACTAATTCAAGGCTAGAGACATTGGACTTAAAG---
*
435718 ATAAAGATAATAAAGATGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGATGAGAA
63 AT---G---ATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AA
* * * **
435783 A-TGTGCTAATATGCT-ATTCACGATCGGTGATATC
121 AGAGTGCTAATATGCTGATTCAAGACCAATGATATC
* * * * ** * *
435817 AGACTTAAAGATGAGAAAAGCGCCAATATGCTAATTCAAGGCCAGTCACATTAGTCTTAAAGATG
1 AGACTTAAAGACGAGAAAAGTGCCAATATACTAATTCAAGGCTAGAGACATTGGACTTAAAGATG
** * * * * * *
435882 ATAAAGATGCCAATATTTTGATTTAAGGCCAACGACATTAGACTTAAATATGAAAAGAGTGCCAA
66 ATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGAGTGCTAA
* * *
435947 TGTGCTGATTTAAGGCCAA
131 TATGCTGATTCAAGACCAA
435966 CGACGTTAGA
Statistics
Matches: 489, Mismatches: 111, Indels: 42
0.76 0.17 0.07
Matches are distributed among these distances:
147 1 0.00
148 82 0.17
149 2 0.00
153 2 0.00
154 3 0.01
155 58 0.12
156 211 0.43
157 3 0.01
158 1 0.00
159 2 0.00
161 2 0.00
162 1 0.00
164 61 0.12
165 59 0.12
166 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (156 bp):
AGACTTAAAGACGAGAAAAGTGCCAATATACTAATTCAAGGCTAGAGACATTGGACTTAAAGATG
ATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGAGTGCTAA
TATGCTGATTCAAGACCAATGATATC
Found at i:435724 original size:9 final size:9
Alignment explanation
Indices: 435710--435734 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
435700 ACATTGAACT
435710 TAAAGATAA
1 TAAAGATAA
435719 TAAAGATAA
1 TAAAGATAA
435728 TAAAGAT
1 TAAAGAT
435735 GCCAATATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (9 bp):
TAAAGATAA
Found at i:436102 original size:33 final size:33
Alignment explanation
Indices: 435992--436107 Score: 121
Period size: 32 Copynumber: 3.6 Consensus size: 33
435982 AAGAGATACC
* * *
435992 ACCGACTTATGTGGGCTTTTG-AAAAGGTTGCT
1 ACCGACTTGTGTGAGCTTTTGCAAAAGGTTGCA
* * * *
436024 A-CGAACTTGTGTGGGC-TTTACAAAAGGTTACC
1 ACCG-ACTTGTGTGAGCTTTTGCAAAAGGTTGCA
* *
436056 ACCAACTTGTGTGAGCTTTTGCAAAGGGTTGCA
1 ACCGACTTGTGTGAGCTTTTGCAAAAGGTTGCA
436089 ACCGACTTGTGTGAGCTTT
1 ACCGACTTGTGTGAGCTTT
436108 GAAAAAGAGT
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
31 5 0.07
32 33 0.48
33 31 0.45
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (33 bp):
ACCGACTTGTGTGAGCTTTTGCAAAAGGTTGCA
Found at i:436140 original size:30 final size:30
Alignment explanation
Indices: 436098--436235 Score: 136
Period size: 30 Copynumber: 4.6 Consensus size: 30
436088 AACCGACTTG
* *
436098 TGTGAGCTTTGAAAAAGAGTGCCACGAAAT
1 TGTGAACTTTGAAAAAGGGTGCCACGAAAT
* *
436128 TTTGAACTTTGAAAAA-GGTGCCACGAAGT
1 TGTGAACTTTGAAAAAGGGTGCCACGAAAT
* * *
436157 TGTGGACTTTAAAAAAAGGGCGCCAC-AAAGT
1 TGTGAACTTT-GAAAAAGGGTGCCACGAAA-T
* * *
436188 TGTGGACTTTGAAAAAGGGTGCTACGAATT
1 TGTGAACTTTGAAAAAGGGTGCCACGAAAT
* *
436218 TATGAACTTTAAAAAAGG
1 TGTGAACTTTGAAAAAGG
436236 TTAATCGACT
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
29 19 0.22
30 49 0.56
31 20 0.23
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (30 bp):
TGTGAACTTTGAAAAAGGGTGCCACGAAAT
Found at i:436173 original size:60 final size:61
Alignment explanation
Indices: 436109--436233 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 61
436099 GTGAGCTTTG
* * * *
436109 AAAAAGAGTGCCACGAAA-TTTTGAACTTTGAAAAA-GGTGCCACGAAGTTGTGGACTTTAA
1 AAAAAGAGCGCCAC-AAAGTTGTGAACTTTGAAAAAGGGTGCCACGAAGTTATGAACTTTAA
* * * *
436169 AAAAAGGGCGCCACAAAGTTGTGGACTTTGAAAAAGGGTGCTACGAATTTATGAACTTTAA
1 AAAAAGAGCGCCACAAAGTTGTGAACTTTGAAAAAGGGTGCCACGAAGTTATGAACTTTAA
436230 AAAA
1 AAAA
436234 GGTTAATCGA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.05
60 27 0.49
61 25 0.45
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (61 bp):
AAAAAGAGCGCCACAAAGTTGTGAACTTTGAAAAAGGGTGCCACGAAGTTATGAACTTTAA
Found at i:436188 original size:31 final size:30
Alignment explanation
Indices: 436139--436203 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
436129 TTGAACTTTG
* *
436139 AAAAAGGTGCCACGAAGTTGTGGACTTTAA
1 AAAAAGGCGCCACAAAGTTGTGGACTTTAA
*
436169 AAAAAGGGCGCCACAAAGTTGTGGACTTTGA
1 AAAAA-GGCGCCACAAAGTTGTGGACTTTAA
436200 AAAA
1 AAAA
436204 GGGTGCTACG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.20
Consensus pattern (30 bp):
AAAAAGGCGCCACAAAGTTGTGGACTTTAA
Found at i:437132 original size:33 final size:33
Alignment explanation
Indices: 437067--437132 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
437057 AAGGCTAGCT
* *
437067 TGACAAGAAAGGTGATATAGTTTGATTTATTTC
1 TGACAAGAAAGGTGATATAGTTCGATTCATTTC
* *
437100 TGACAATAAAGGTGATAT-GATTCGGTTCATTTC
1 TGACAAGAAAGGTGATATAG-TTCGATTCATTTC
437133 AACAAAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (33 bp):
TGACAAGAAAGGTGATATAGTTCGATTCATTTC
Found at i:437725 original size:56 final size:55
Alignment explanation
Indices: 437637--437746 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 55
437627 TGCTTTTCAA
* *
437637 TTTTTTATTGTTCCCTTTTTTATCATGCCTTTGCTCTTTTCACTTTTTTCATTTG
1 TTTTTTATTGTTCCCATTTTGATCATGCCTTTGCTCTTTTCACTTTTTTCATTTG
* * *
437692 TTTTTTGTTGTTCCTCATTTTGATCTTGCCTTTGCTCTTTTCTCTTTTTTCATTT
1 TTTTTTATTGTTCC-CATTTTGATCATGCCTTTGCTCTTTTCACTTTTTTCATTT
437747 TTTCTATTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 13 0.27
56 36 0.73
ACGTcount: A:0.07, C:0.20, G:0.08, T:0.65
Consensus pattern (55 bp):
TTTTTTATTGTTCCCATTTTGATCATGCCTTTGCTCTTTTCACTTTTTTCATTTG
Found at i:445092 original size:52 final size:52
Alignment explanation
Indices: 445035--445154 Score: 152
Period size: 52 Copynumber: 2.3 Consensus size: 52
445025 AGTTAACTGG
* * *
445035 ATGTATCGATACATTTAGGTCAAAAA-CTTAGAATGTATTAATACAATGAAAA
1 ATGTATCGATACATTTAGGTAAAAAATC-TAGAATGTATCAATACAATAAAAA
* * *
445087 ATGTATCGATAGATTTAGGTAAAAAATCTAGAATGTATCGATAGAATAAAAA
1 ATGTATCGATACATTTAGGTAAAAAATCTAGAATGTATCAATACAATAAAAA
* *
445139 ATTTATTGATACATTT
1 ATGTATCGATACATTT
445155 TCACTCCAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 57 0.98
53 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACATTTAGGTAAAAAATCTAGAATGTATCAATACAATAAAAA
Found at i:445224 original size:20 final size:20
Alignment explanation
Indices: 445194--445251 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
445184 AAGGTCCAGT
*
445194 ATCGTTACATTCACTTATGC
1 ATCGATACATTCACTTATGC
* * *
445214 ATCGATGCATTCACTTAGGT
1 ATCGATACATTCACTTATGC
*
445234 ATCGATACATTAACTTAT
1 ATCGATACATTCACTTAT
445252 TATATCGATA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (20 bp):
ATCGATACATTCACTTATGC
Found at i:447805 original size:13 final size:13
Alignment explanation
Indices: 447787--447813 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
447777 ACATTATTCT
447787 TTGTATTGATACA
1 TTGTATTGATACA
447800 TTGTATTGATACA
1 TTGTATTGATACA
447813 T
1 T
447814 GAAACTGGCA
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:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:448690 original size:35 final size:35
Alignment explanation
Indices: 448651--448717 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
448641 AACTTATATT
*
448651 AATATT-TATGTATT-TTATAATTAGATTTAAATAAA
1 AATATTAT-TGTATTATTAAAATTA-ATTTAAATAAA
*
448686 AATATTATTTTATTATTAAAATTAATTTAAAT
1 AATATTATTGTATTATTAAAATTAATTTAAAT
448718 TTATAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
35 19 0.68
36 9 0.32
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (35 bp):
AATATTATTGTATTATTAAAATTAATTTAAATAAA
Found at i:450431 original size:15 final size:15
Alignment explanation
Indices: 450408--450437 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
450398 TTAGTTAAAA
*
450408 GAGACGAAGGAGAAG
1 GAGAAGAAGGAGAAG
450423 GAGAAGAAGGAGAAG
1 GAGAAGAAGGAGAAG
450438 TTATTGATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (15 bp):
GAGAAGAAGGAGAAG
Found at i:457831 original size:2 final size:2
Alignment explanation
Indices: 457826--457854 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
457816 ATGTGTGTGT
457826 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
457855 CAAACAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:478137 original size:162 final size:164
Alignment explanation
Indices: 477848--478179 Score: 422
Period size: 162 Copynumber: 2.0 Consensus size: 164
477838 TAAATAGCAA
* *
477848 TGTAACAAAATCAAAAAATAAATCAAAACCTAGAGATTATATGGTTAAAAGGTACCGATTTAGGG
1 TGTAACAAAATCAAAAAATAAATCAAAACCTAGAGATTATATGGTAAAAAGGTACCGATTTAGAG
** * *
477913 CGCTGTAGGGGTGTTAATCATTCCTCACACATAACCGACTCCAAAGTTCTCTTATCGAACTCTGG
66 CGCTGTAGGAATGTTAATCATTCCTCACACATAACCAACTCCAAAGTTCTCTTATCGAACTCTGA
* *
477978 TGCACATAGACCATAAAATTAAATCTACGAGTTT
131 TGCACATAGACCATAAAATCAAATCTACGAATTT
* * * * *
478012 TGTAAGAAAATC-GAAAA-AAATCAAAACTTAGATATTATATGGTAAAAAGGTACTGATTTAGAG
1 TGTAACAAAATCAAAAAATAAATCAAAACCTAGAGATTATATGGTAAAAAGGTACCGATTTAGAG
* * * * *
478075 C-ATCGT-GGAAATGTTAATCCTTCCTCACACGTAACCAACTCCAAGGTTCT-TCTATTGAACTC
66 CGCT-GTAGG-AATGTTAATCATTCCTCACACATAACCAACTCCAAAGTTCTCT-TATCGAACTC
* *
478137 TGATGCACGTAGACCATAAAATCAAATCTATGAATTT
128 TGATGCACATAGACCATAAAATCAAATCTACGAATTT
478174 TGTAAC
1 TGTAAC
478180 TTGAGATATT
Statistics
Matches: 144, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
161 4 0.03
162 125 0.87
163 4 0.03
164 11 0.08
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (164 bp):
TGTAACAAAATCAAAAAATAAATCAAAACCTAGAGATTATATGGTAAAAAGGTACCGATTTAGAG
CGCTGTAGGAATGTTAATCATTCCTCACACATAACCAACTCCAAAGTTCTCTTATCGAACTCTGA
TGCACATAGACCATAAAATCAAATCTACGAATTT
Found at i:479912 original size:14 final size:15
Alignment explanation
Indices: 479895--479929 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
479885 TATATATTTG
479895 AATATAA-ATATTAA
1 AATATAATATATTAA
*
479909 AATATAATATTTTAA
1 AATATAATATATTAA
479924 AATATA
1 AATATA
479930 TAATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATAATATATTAA
Found at i:483005 original size:19 final size:20
Alignment explanation
Indices: 482977--483030 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
482967 ATCGATACAT
*
482977 TGTATTGATACAAAACT-TA
1 TGTATCGATACAAAACTATA
* *
482996 TGTATCGATACATATACTATT
1 TGTATCGATACA-AAACTATA
483017 TGTATCGATACAAA
1 TGTATCGATACAAA
483031 CTGTAGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 11 0.38
20 5 0.17
21 13 0.45
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAAACTATA
Done.