Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold481
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: 308087
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 12059 characters in sequence are not A, C, G, or T
Found at i:8350 original size:6 final size:6
Alignment explanation
Indices: 8339--8367 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
8329 TATCATCCCA
8339 TATTTT TATTTT TATTTT TATTTT TATTT
1 TATTTT TATTTT TATTTT TATTTT TATTT
8368 GCACAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:9783 original size:12 final size:12
Alignment explanation
Indices: 9768--9797 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
9758 TGATAATTGA
9768 TGTGATTATGAT
1 TGTGATTATGAT
9780 TGTGATTATGAT
1 TGTGATTATGAT
*
9792 TATGAT
1 TGTGAT
9798 AAATGTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (12 bp):
TGTGATTATGAT
Found at i:11602 original size:15 final size:14
Alignment explanation
Indices: 11552--11592 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 14
11542 TGACTAGCAG
11552 TAGGGATTTTGAGACT
1 TAGGGATTTT-AGA-T
11568 TAGGAGATTTTAGAT
1 TAGG-GATTTTAGAT
11583 TAGGGATTTT
1 TAGGGATTTT
11593 CAATTTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.25
15 5 0.21
16 7 0.29
17 6 0.25
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.41
Consensus pattern (14 bp):
TAGGGATTTTAGAT
Found at i:21237 original size:16 final size:16
Alignment explanation
Indices: 21216--21264 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
21206 TCTTTTAGTG
*
21216 AAGAAAGAATACGCCT
1 AAGAAAGAGTACGCCT
21232 AAGAAAGAGTACGCCT
1 AAGAAAGAGTACGCCT
21248 AAGGAAA-AGTACGCCT
1 AA-GAAAGAGTACGCCT
21264 A
1 A
21265 GAGTTTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.12
Consensus pattern (16 bp):
AAGAAAGAGTACGCCT
Found at i:22679 original size:25 final size:25
Alignment explanation
Indices: 22612--22722 Score: 107
Period size: 25 Copynumber: 4.4 Consensus size: 25
22602 AACCAAACCG
**
22612 AGCCTTTGTGGCAAGAAATTTGTAA
1 AGCCTTTGTGGCAAGTTATTTGTAA
22637 AGCCTTTGTGGCAAGTTATTTGTAA
1 AGCCTTTGTGGCAAGTTATTTGTAA
* ** *
22662 AGCCATTGTGGCGTGTTATCTGTAA
1 AGCCTTTGTGGCAAGTTATTTGTAA
* * * *
22687 AACCTTTGTGACGAA-TTATCTGAAA
1 AGCCTTTGTGGC-AAGTTATTTGTAA
*
22712 AGCCTATGTGG
1 AGCCTTTGTGG
22723 TGTCTTGCAG
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
25 70 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.34
Consensus pattern (25 bp):
AGCCTTTGTGGCAAGTTATTTGTAA
Found at i:42254 original size:17 final size:18
Alignment explanation
Indices: 42221--42257 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
42211 GCCACTTAGA
42221 TTAGTTTTAGGATTTTATT
1 TTAGTTTTA-GATTTTATT
42240 TTAGTTTTA-ATTTTATT
1 TTAGTTTTAGATTTTATT
42257 T
1 T
42258 CAATTTAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.68
Consensus pattern (18 bp):
TTAGTTTTAGATTTTATT
Found at i:43822 original size:22 final size:22
Alignment explanation
Indices: 43797--43845 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
43787 TGCACCAATA
43797 TATGAAAGCCCT-TAATGGGTAG
1 TATGAAAGCCCTGTAA-GGGTAG
*
43819 TATGAAATCCCTGTAAGGGTAG
1 TATGAAAGCCCTGTAAGGGTAG
43841 TATGA
1 TATGA
43846 GACTCTGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (22 bp):
TATGAAAGCCCTGTAAGGGTAG
Found at i:46404 original size:43 final size:42
Alignment explanation
Indices: 46356--46514 Score: 126
Period size: 42 Copynumber: 3.6 Consensus size: 42
46346 TATTGTACAA
* *
46356 ATGCCATGTCCTAGACATGGTCTTACATGGAAA-TCTCATATCG
1 ATGCCATGTCCCAGACATGGTCTTACA--CAAAGTCTCATATCG
46399 ATGCCAATAG-CCCAG-CTATGGTCTTACACAAAGTCTCATATCG
1 ATGCC-AT-GTCCCAGAC-ATGGTCTTACACAAAGTCTCATATCG
* * * *
46442 ATGCCATATCCCAGATATGGTCTTATACAAAATCTCAAATCAATGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACAAAGTCTC--AT--AT-C-G
* *
46490 ATGCCATATCCCAGATATGGTCTTA
1 ATGCCATGTCCCAGACATGGTCTTA
46515 TACGGGATCT
Statistics
Matches: 98, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
42 28 0.29
43 21 0.21
44 19 0.19
45 1 0.01
46 2 0.02
47 1 0.01
48 26 0.27
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (42 bp):
ATGCCATGTCCCAGACATGGTCTTACACAAAGTCTCATATCG
Found at i:46421 original size:44 final size:42
Alignment explanation
Indices: 46372--46514 Score: 144
Period size: 42 Copynumber: 3.2 Consensus size: 42
46362 TGTCCTAGAC
* *
46372 ATGGTCTTACATGGAAA-TCTCATATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA--CAAAGTCTCATATCGATGCC-ATAGCCCAGAT
*
46416 ATGGTCTTACACAAAGTCTCATATCGATGCCATATCCCAGAT
1 ATGGTCTTACACAAAGTCTCATATCGATGCCATAGCCCAGAT
* * *
46458 ATGGTCTTATACAAAATCTCAAATCAATGCTGATGCCATATCCCAGAT
1 ATGGTCTTACACAAAGTCTC--AT--AT-C-GATGCCATAGCCCAGAT
46506 ATGGTCTTA
1 ATGGTCTTA
46515 TACGGGATCT
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
42 30 0.34
43 15 0.17
44 13 0.15
46 2 0.02
47 1 0.01
48 26 0.30
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (42 bp):
ATGGTCTTACACAAAGTCTCATATCGATGCCATAGCCCAGAT
Found at i:46472 original size:42 final size:42
Alignment explanation
Indices: 46386--46565 Score: 171
Period size: 48 Copynumber: 4.0 Consensus size: 42
46376 TCTTACATGG
* * *
46386 AAATCTCATATCGATGCCAATAGCCCAGCTATGGTCTTACACA
1 AAATCTCATATCGATGCC-ATATCCCAGATATGGTCTTATACA
*
46429 AAGTCTCATATCGATGCCATATCCCAGATATGGTCTTATACA
1 AAATCTCATATCGATGCCATATCCCAGATATGGTCTTATACA
*
46471 AAATCTCAAATCAATGCTGATGCCATATCCCAGATATGGTCTTATACG
1 AAATCTC--AT--AT-C-GATGCCATATCCCAGATATGGTCTTATACA
** *
46519 GGATCTCAAATCGATGTCGATGCCATATCCCAGATATGGTTTTATAC
1 AAATCTC--AT--A--TCGATGCCATATCCCAGATATGGTCTTATAC
46566 GGGATCTCAA
Statistics
Matches: 119, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
42 27 0.23
43 17 0.14
44 2 0.02
46 2 0.02
47 1 0.01
48 68 0.57
49 1 0.01
50 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (42 bp):
AAATCTCATATCGATGCCATATCCCAGATATGGTCTTATACA
Found at i:46512 original size:48 final size:48
Alignment explanation
Indices: 46439--46581 Score: 225
Period size: 48 Copynumber: 3.0 Consensus size: 48
46429 AAGTCTCATA
***
46439 TCGATGCCATATCCCAGATATGGTCTTATACAAAATCTCAAATCAATG
1 TCGATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATCAATG
*
46487 -CTGATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATCGATG
1 TC-GATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATCAATG
*
46535 TCGATGCCATATCCCAGATATGGTTTTATACGGGATCTCAAATCAAT
1 TCGATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATCAAT
46582 TCGGTAATAC
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
47 1 0.01
48 85 0.98
49 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (48 bp):
TCGATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATCAATG
Found at i:46609 original size:32 final size:32
Alignment explanation
Indices: 46573--46669 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
46563 TACGGGATCT
* *
46573 CAAATCAATTCGGTAATACATATATACATATA
1 CAAATCAATTCGGCAATATATATATACATATA
* *
46605 CAAATCAATTCGACAATGTATATATCTACATAT-
1 CAAATCAATTCGGCAA--TATATATATACATATA
*
46638 -AAATCAATTCGGCAATATATA-AAACATATA
1 CAAATCAATTCGGCAATATATATATACATATA
46668 CA
1 CA
46670 TTTGAATTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
29 6 0.11
30 6 0.11
31 1 0.02
32 28 0.52
34 13 0.24
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.30
Consensus pattern (32 bp):
CAAATCAATTCGGCAATATATATATACATATA
Found at i:53650 original size:18 final size:18
Alignment explanation
Indices: 53624--53663 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
53614 GAAGAGGAGC
53624 AAGAGAGTGAGGAAC-AGG
1 AAGAGAGTGA-GAACGAGG
*
53642 AAGATAGTGAGAACGAGG
1 AAGAGAGTGAGAACGAGG
53660 AAGA
1 AAGA
53664 AGAATAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.47, C:0.05, G:0.40, T:0.07
Consensus pattern (18 bp):
AAGAGAGTGAGAACGAGG
Found at i:54446 original size:35 final size:35
Alignment explanation
Indices: 54400--54476 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
54390 TGTCGCTCCA
* * *
54400 AAGGACTTATATA-CAGTTTACATGGTGTTACCCCG
1 AAGGACCTATATACCA-TTTACATGATGTCACCCCG
* *
54435 AATGACCTATATACCATTTACATGATGTCACCCTG
1 AAGGACCTATATACCATTTACATGATGTCACCCCG
54470 AAGGACC
1 AAGGACC
54477 AGTCGATAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 33 0.94
36 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (35 bp):
AAGGACCTATATACCATTTACATGATGTCACCCCG
Found at i:54531 original size:35 final size:34
Alignment explanation
Indices: 54477--54547 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
54467 CTGAAGGACC
*
54477 AGTCGATAACCGTCATCACAGTGTCG-CTCTATAG
1 AGTCAATAACCGTCATCACAGTGTCGTC-CTATAG
*
54511 AGTCAATAGACCGTCGTCACAGTGTCGTCCTATAG
1 AGTCAATA-ACCGTCATCACAGTGTCGTCCTATAG
54546 AG
1 AG
54548 GCAGTAGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 7 0.21
35 25 0.76
36 1 0.03
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (34 bp):
AGTCAATAACCGTCATCACAGTGTCGTCCTATAG
Found at i:55575 original size:28 final size:28
Alignment explanation
Indices: 55515--55569 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
55505 AATATAATAT
*
55515 AATTA-TAAAATAATTAAATTTTACTTA
1 AATTATTAAAATAATTAAATTTTAATTA
*
55542 AATTATTAAAAT-ATTTAATTTTAATTA
1 AATTATTAAAATAATTAAATTTTAATTA
55569 A
1 A
55570 TTTTATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTATTAAAATAATTAAATTTTAATTA
Found at i:57905 original size:28 final size:28
Alignment explanation
Indices: 57865--57923 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
57855 AGATTCCTCA
57865 TAAAGTATTTCTTGCCTAGCAAGAATGC
1 TAAAGTATTTCTTGCCTAGCAAGAATGC
57893 TAAAGTATTTCTTGCCTAGCAAGAATGC
1 TAAAGTATTTCTTGCCTAGCAAGAATGC
57921 TAA
1 TAA
57924 GTTGAGGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (28 bp):
TAAAGTATTTCTTGCCTAGCAAGAATGC
Found at i:83706 original size:6 final size:6
Alignment explanation
Indices: 83685--83745 Score: 88
Period size: 6 Copynumber: 10.2 Consensus size: 6
83675 GTCGAAACCA
* *
83685 TTCC-T TTCCTT GTCCTT TTCCTT TTCCTTT TTCCTT TTCCTT TTTCTT
1 TTCCTT TTCCTT TTCCTT TTCCTT TTCC-TT TTCCTT TTCCTT TTCCTT
83733 TTCCTT TTCCTT T
1 TTCCTT TTCCTT T
83746 ACATAGATGC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
5 4 0.08
6 40 0.80
7 6 0.12
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (6 bp):
TTCCTT
Found at i:83720 original size:25 final size:24
Alignment explanation
Indices: 83685--83744 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 24
83675 GTCGAAACCA
83685 TTCC-TTTCCTTGTCCTTTTCCTT
1 TTCCTTTTCCTTGTCCTTTTCCTT
* *
83708 TTCCTTTTTCCTTTTCCTTTTTCTT
1 TTCC-TTTTCCTTGTCCTTTTCCTT
83733 TTCCTTTTCCTT
1 TTCCTTTTCCTT
83745 TACATAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 4 0.12
24 8 0.24
25 21 0.64
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (24 bp):
TTCCTTTTCCTTGTCCTTTTCCTT
Found at i:85845 original size:14 final size:14
Alignment explanation
Indices: 85826--85865 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
85816 TTGTTTGGCA
85826 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
85840 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
85854 GGAAAATGTTTT
1 GTAAAATGTTTT
85866 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:85874 original size:20 final size:20
Alignment explanation
Indices: 85849--85888 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
85839 CGTAAAATGA
*
85849 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
85869 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
85889 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:85878 original size:34 final size:35
Alignment explanation
Indices: 85834--85900 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
85824 CAGTAAAATG
*
85834 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
85868 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
85901 TTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:89341 original size:15 final size:16
Alignment explanation
Indices: 89321--89353 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
89311 AATACCACTT
89321 AAAATGAAAGCA-TGA
1 AAAATGAAAGCATTGA
89336 AAAATGAAAGCATTGA
1 AAAATGAAAGCATTGA
89352 AA
1 AA
89354 GTACCACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAATGAAAGCATTGA
Found at i:91586 original size:25 final size:26
Alignment explanation
Indices: 91531--91598 Score: 95
Period size: 25 Copynumber: 2.6 Consensus size: 26
91521 AAGCTTTGAG
91531 GAATGGAAAATGTCTGCTACTTAGAAGA
1 GAATGGAAAATGTCTG--ACTTAGAAGA
91559 GAATGGAAAATGTCTG-CTTAG-AGAA
1 GAATGGAAAATGTCTGACTTAGAAG-A
91584 GAATGGAAAATGTCT
1 GAATGGAAAATGTCT
91599 TACCAATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
24 2 0.05
25 21 0.54
28 16 0.41
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.25
Consensus pattern (26 bp):
GAATGGAAAATGTCTGACTTAGAAGA
Found at i:96344 original size:44 final size:44
Alignment explanation
Indices: 96283--96369 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
96273 CAGGTCAAAT
96283 AATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAACA
1 AATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAACA
* * *
96327 AATATTAAAATAACCTACACTATTTAGAGTTTAAGTGGGAAAC
1 AATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAC
96370 TAAAAATAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (44 bp):
AATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAACA
Found at i:97218 original size:158 final size:160
Alignment explanation
Indices: 96922--97243 Score: 431
Period size: 158 Copynumber: 2.0 Consensus size: 160
96912 ACATATTTCT
* * * *
96922 AACATCTGATAGTGTCTTGATTGTCTCGTCATGCATCCTGATCTGAACAGTAACAACATCGGTTA
1 AACATCTGACAGTGTCCTGATTGTCTCATCATGCATCCTGATCTGAACAGTAACAACATCAGTTA
*
96987 CTTTACTAGGTAAGTCATTCTCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAAC
66 CTTTACTAGGTAAGTCATTCCCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAAC
* * *
97052 TAGTCCCTGTT-GGA-ACACATGTGGAACG
131 CAGACCCTGTTGGGACACACATGTGGAAAG
* * * *
97080 AACATCTGACAGTGTCCTGATTGTC-CTATCGTGCATCCTGATTTGAATAGTACCAACA-CTAGT
1 AACATCTGACAGTGTCCTGATTGTCTC-ATCATGCATCCTGATCTGAACAGTAACAACATC-AGT
* *
97143 TACTTTACTAGGTAAGTCATTCCCTAGGCATACAACTCCACCTTCAA-TTGAATTGTATGT-GAA
64 TACTTTACTAGGTAAGTCATTCCCTAGGCACACAAATCCACCTTCAACTT-AATTGTATGTAG-A
*
97206 TAACCAGACCCTGTTGGGACACACATGTGGAAAG
127 GAACCAGACCCTGTTGGGACACACATGTGGAAAG
97240 AACA
1 AACA
97244 CCCCGAATCC
Statistics
Matches: 143, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
157 5 0.03
158 118 0.83
159 3 0.02
160 17 0.12
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (160 bp):
AACATCTGACAGTGTCCTGATTGTCTCATCATGCATCCTGATCTGAACAGTAACAACATCAGTTA
CTTTACTAGGTAAGTCATTCCCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAAC
CAGACCCTGTTGGGACACACATGTGGAAAG
Found at i:97739 original size:158 final size:160
Alignment explanation
Indices: 97443--97764 Score: 431
Period size: 158 Copynumber: 2.0 Consensus size: 160
97433 ACATATTTCT
* * * *
97443 AACATCTGATAGTGTCTTGATTGTCTCGTCATGCATCCTGATCTGAACAGTAACAACATCGGTTA
1 AACATCTGACAGTGTCCTGATTGTCTCATCATGCATCCTGATCTGAACAGTAACAACATCAGTTA
*
97508 CTTTACTAGGTAAGTCATTCTCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAAC
66 CTTTACTAGGTAAGTCATTCCCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAAC
* * *
97573 TAGTCCCTGTT-GGA-ACACATGTGGAACG
131 CAGACCCTGTTGGGACACACATGTGGAAAG
* * * *
97601 AACATCTGACAGTGTCCTGATTGTC-CTATCGTGCATCCTGATTTGAATAGTACCAACA-CTAGT
1 AACATCTGACAGTGTCCTGATTGTCTC-ATCATGCATCCTGATCTGAACAGTAACAACATC-AGT
* *
97664 TACTTTACTAGGTAAGTCATTCCCTAGGCATACAACTCCACCTTCAA-TTGAATTGTATGT-GAA
64 TACTTTACTAGGTAAGTCATTCCCTAGGCACACAAATCCACCTTCAACTT-AATTGTATGTAG-A
*
97727 TAACCAGACCCTGTTGGGACACACATGTGGAAAG
127 GAACCAGACCCTGTTGGGACACACATGTGGAAAG
97761 AACA
1 AACA
97765 CCCCGAATCC
Statistics
Matches: 143, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
157 5 0.03
158 118 0.83
159 3 0.02
160 17 0.12
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (160 bp):
AACATCTGACAGTGTCCTGATTGTCTCATCATGCATCCTGATCTGAACAGTAACAACATCAGTTA
CTTTACTAGGTAAGTCATTCCCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAAC
CAGACCCTGTTGGGACACACATGTGGAAAG
Found at i:97775 original size:521 final size:521
Alignment explanation
Indices: 96794--97837 Score: 2088
Period size: 521 Copynumber: 2.0 Consensus size: 521
96784 GTCAATCTTT
96794 CTACCTTTCATCAAAAAGAGATCCTTATGAGATACCTTAATTCCGCTTGACTCGATGTTGATTTT
1 CTACCTTTCATCAAAAAGAGATCCTTATGAGATACCTTAATTCCGCTTGACTCGATGTTGATTTT
96859 ACAACCCTTCGAGTCCAAATTTCCCAAGGAGATGAGATTTTTCTTTAAGTCAGACATATTTCTAA
66 ACAACCCTTCGAGTCCAAATTTCCCAAGGAGATGAGATTTTTCTTTAAGTCAGACATATTTCTAA
96924 CATCTGATAGTGTCTTGATTGTCTCGTCATGCATCCTGATCTGAACAGTAACAACATCGGTTACT
131 CATCTGATAGTGTCTTGATTGTCTCGTCATGCATCCTGATCTGAACAGTAACAACATCGGTTACT
96989 TTACTAGGTAAGTCATTCTCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAACTA
196 TTACTAGGTAAGTCATTCTCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAACTA
97054 GTCCCTGTTGGAACACATGTGGAACGAACATCTGACAGTGTCCTGATTGTCCTATCGTGCATCCT
261 GTCCCTGTTGGAACACATGTGGAACGAACATCTGACAGTGTCCTGATTGTCCTATCGTGCATCCT
97119 GATTTGAATAGTACCAACACTAGTTACTTTACTAGGTAAGTCATTCCCTAGGCATACAACTCCAC
326 GATTTGAATAGTACCAACACTAGTTACTTTACTAGGTAAGTCATTCCCTAGGCATACAACTCCAC
97184 CTTCAATTGAATTGTATGTGAATAACCAGACCCTGTTGGGACACACATGTGGAAAGAACACCCCG
391 CTTCAATTGAATTGTATGTGAATAACCAGACCCTGTTGGGACACACATGTGGAAAGAACACCCCG
97249 AATCCAGGATCCACTCAGATGTAAGCTTGGAGCTTTCACTTGTTGACACCAACAAAAATCATCAC
456 AATCCAGGATCCACTCAGATGTAAGCTTGGAGCTTTCACTTGTTGACACCAACAAAAATCATCAC
97314 C
521 C
97315 CTACCTTTCATCAAAAAGAGATCCTTATGAGATACCTTAATTCCGCTTGACTCGATGTTGATTTT
1 CTACCTTTCATCAAAAAGAGATCCTTATGAGATACCTTAATTCCGCTTGACTCGATGTTGATTTT
97380 ACAACCCTTCGAGTCCAAATTTCCCAAGGAGATGAGATTTTTCTTTAAGTCAGACATATTTCTAA
66 ACAACCCTTCGAGTCCAAATTTCCCAAGGAGATGAGATTTTTCTTTAAGTCAGACATATTTCTAA
97445 CATCTGATAGTGTCTTGATTGTCTCGTCATGCATCCTGATCTGAACAGTAACAACATCGGTTACT
131 CATCTGATAGTGTCTTGATTGTCTCGTCATGCATCCTGATCTGAACAGTAACAACATCGGTTACT
97510 TTACTAGGTAAGTCATTCTCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAACTA
196 TTACTAGGTAAGTCATTCTCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAACTA
97575 GTCCCTGTTGGAACACATGTGGAACGAACATCTGACAGTGTCCTGATTGTCCTATCGTGCATCCT
261 GTCCCTGTTGGAACACATGTGGAACGAACATCTGACAGTGTCCTGATTGTCCTATCGTGCATCCT
97640 GATTTGAATAGTACCAACACTAGTTACTTTACTAGGTAAGTCATTCCCTAGGCATACAACTCCAC
326 GATTTGAATAGTACCAACACTAGTTACTTTACTAGGTAAGTCATTCCCTAGGCATACAACTCCAC
97705 CTTCAATTGAATTGTATGTGAATAACCAGACCCTGTTGGGACACACATGTGGAAAGAACACCCCG
391 CTTCAATTGAATTGTATGTGAATAACCAGACCCTGTTGGGACACACATGTGGAAAGAACACCCCG
97770 AATCCAGGATCCACTCAGATGTAAGCTTGGAGCTTTCACTTGTTGACACCAACAAAAATCATCAC
456 AATCCAGGATCCACTCAGATGTAAGCTTGGAGCTTTCACTTGTTGACACCAACAAAAATCATCAC
97835 C
521 C
97836 CT
1 CT
97838 TGTCATTGGC
Statistics
Matches: 523, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
521 523 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (521 bp):
CTACCTTTCATCAAAAAGAGATCCTTATGAGATACCTTAATTCCGCTTGACTCGATGTTGATTTT
ACAACCCTTCGAGTCCAAATTTCCCAAGGAGATGAGATTTTTCTTTAAGTCAGACATATTTCTAA
CATCTGATAGTGTCTTGATTGTCTCGTCATGCATCCTGATCTGAACAGTAACAACATCGGTTACT
TTACTAGGTAAGTCATTCTCTAGGCACACAAATCCACCTTCAACTTAATTGTATGTAGAGAACTA
GTCCCTGTTGGAACACATGTGGAACGAACATCTGACAGTGTCCTGATTGTCCTATCGTGCATCCT
GATTTGAATAGTACCAACACTAGTTACTTTACTAGGTAAGTCATTCCCTAGGCATACAACTCCAC
CTTCAATTGAATTGTATGTGAATAACCAGACCCTGTTGGGACACACATGTGGAAAGAACACCCCG
AATCCAGGATCCACTCAGATGTAAGCTTGGAGCTTTCACTTGTTGACACCAACAAAAATCATCAC
C
Found at i:99009 original size:44 final size:44
Alignment explanation
Indices: 98940--99030 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
98930 GTAGGTCAAA
* **
98940 TAATATTCAAATAACCTACACTAATCAAAGTTTAAGTTTGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAC
* * *
98984 TAATATTAAAATAACTTACATTAATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAC
99028 TAA
1 TAA
99031 AACTATAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAC
Found at i:101870 original size:51 final size:51
Alignment explanation
Indices: 101790--102128 Score: 302
Period size: 51 Copynumber: 6.7 Consensus size: 51
101780 TATCGATGAA
* * * *
101790 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATATTGGT
* * * * *
101841 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG-
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATATTG-GT
* * * * *
101892 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTA-TGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAA-TATTGGT
* * * * *
101943 TACATGTGTAGGACTAAGTGAAGGCTACTATG-GATACCGGA-AAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTG-TACC-GATAA-ATATTGGT
* *
101994 CACGTATGTAGTACTATGTGAAGGCTACTATGTG-AGCCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA-CCGATAAATA-TTGGT
* * * **
102044 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACTG-TAAA-ACTAAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATATTGGT
*
102093 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA
102129 TCGAATGATA
Statistics
Matches: 233, Mismatches: 42, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
49 37 0.16
50 50 0.21
51 142 0.61
52 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATATTGGT
Found at i:101966 original size:102 final size:101
Alignment explanation
Indices: 101790--102131 Score: 385
Period size: 102 Copynumber: 3.4 Consensus size: 101
101780 TATCGATGAA
* *
101790 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAGTA
101854 CTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG
65 CTAAGTGAAGGCTACTATGTGTACCGAGAAG-TTTGAG
* * * *
101892 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTATGGTTACATGTGTAGGAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
101957 TAAGTGAAGGCTACTATG-GATACCG-GAAAGCTTTG-G
66 TAAGTGAAGGCTACTATGTG-TACCGAG-AAG-TTTGAG
* * * * * *
101993 TCACGTATGTAGTACTATGTGAAGGCTACTATGTG-AGCCGTAAAACT-TGATCACGTGTGTAGT
1 -CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGT
* * * ** * *
102056 ACTATGTGAAGGCTACTATGTGAACTGTA-AA-ACTAAT
64 ACTAAGTGAAGGCTACTATGTGTACCG-AGAAGTTTGAG
102093 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
102132 AATGATAAAA
Statistics
Matches: 204, Mismatches: 26, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
99 33 0.16
100 2 0.01
101 43 0.21
102 125 0.61
103 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAGAAGTTTGAG
Found at i:105164 original size:16 final size:18
Alignment explanation
Indices: 105143--105175 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
105133 AATTTCTCTT
105143 TTCTCTT-TT-TTTTTTC
1 TTCTCTTATTATTTTTTC
105159 TTCTCTTATTATTTTTT
1 TTCTCTTATTATTTTTT
105176 AAAAATAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (18 bp):
TTCTCTTATTATTTTTTC
Found at i:105218 original size:29 final size:30
Alignment explanation
Indices: 105154--105218 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
105144 TCTCTTTTTT
*
105154 TTTTCTTCTCTTATTATTTTTTAAAAATAGG
1 TTTT-TTCTCTTATTATCTTTTAAAAATAGG
* * *
105185 -ATTTTCTTTTATTATCTTTT-AGAATAGG
1 TTTTTTCTCTTATTATCTTTTAAAAATAGG
105213 TTTTTT
1 TTTTTT
105219 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
28 7 0.25
29 19 0.68
30 2 0.07
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (30 bp):
TTTTTTCTCTTATTATCTTTTAAAAATAGG
Found at i:122525 original size:33 final size:33
Alignment explanation
Indices: 122477--122584 Score: 153
Period size: 33 Copynumber: 3.3 Consensus size: 33
122467 TACTCTCTTT
* * *
122477 TTGGTGTGCTAGTTGGATTAGCTTTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
* *
122510 TTAGTGTGATGGTTGGTTTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
**
122543 TTGGTGTGATGGTCAGATTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
122576 TTGGTGTGA
1 TTGGTGTGA
122585 ATTGACTCGA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.19, C:0.09, G:0.31, T:0.41
Consensus pattern (33 bp):
TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
Found at i:125070 original size:43 final size:44
Alignment explanation
Indices: 124994--125085 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
124984 TTCCACATAA
*
124994 CTTCC-TTTTTGTCGTTTCTTGATAGTGATTTTTTCCTACGTAG
1 CTTCCTTTTTTGTCGTTTCCTGATAGTGATTTTTTCCTACGTAG
* * * *
125037 TTTCCTTTTTTGTTGTTTCCTGGTAGTGATTTTTT-TTACGTAG
1 CTTCCTTTTTTGTCGTTTCCTGATAGTGATTTTTTCCTACGTAG
125080 CTTCCT
1 CTTCCT
125086 CTATTTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 16 0.38
44 26 0.62
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (44 bp):
CTTCCTTTTTTGTCGTTTCCTGATAGTGATTTTTTCCTACGTAG
Found at i:132226 original size:42 final size:44
Alignment explanation
Indices: 132178--132311 Score: 143
Period size: 42 Copynumber: 3.1 Consensus size: 44
132168 GTAATCAACT
* * *
132178 ATCGATGCCACTATCCCAGACAGGATCTTACACGAAATCAT-AT
1 ATCGATGCCAATGTCCCAGACAGGATCTTACACGAAATCATCAA
**
132221 A-CGATGCCAATGTCTTAGACATGG-TCTTACACGTAAATC-TCAA
1 ATCGATGCCAATGTCCCAGACA-GGATCTTACACG-AAATCATCAA
* * *
132264 ATCGATGCCAATGTACCAGACATGATCTTACACGAAATCA-CAT
1 ATCGATGCCAATGTCCCAGACAGGATCTTACACGAAATCATCAA
132307 ATCGA
1 ATCGA
132312 AGTCCTATGT
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
42 26 0.35
43 23 0.31
44 26 0.35
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (44 bp):
ATCGATGCCAATGTCCCAGACAGGATCTTACACGAAATCATCAA
Found at i:132285 original size:44 final size:42
Alignment explanation
Indices: 132177--132311 Score: 141
Period size: 44 Copynumber: 3.1 Consensus size: 42
132167 TGTAATCAAC
* *
132177 TATCGATGCCACTATCCCAGACA-GGATCTTACACGAAA--TCA
1 TATCGATGCCAATGT-CCAGACATGG-TCTTACACGAAATCTCA
*
132218 TATACGATGCCAATGTCTTAGACATGGTCTTACACGTAAATCTCA
1 TAT-CGATGCCAATGTC-CAGACATGGTCTTACACG-AAATCTCA
* * *
132263 AATCGATGCCAATGTACCAGACATGATCTTACACGAAATCACA
1 TATCGATGCCAATGT-CCAGACATGGTCTTACACGAAATCTCA
132306 TATCGA
1 TATCGA
132312 AGTCCTATGT
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
41 4 0.05
42 24 0.30
43 17 0.22
44 28 0.35
45 6 0.08
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (42 bp):
TATCGATGCCAATGTCCAGACATGGTCTTACACGAAATCTCA
Found at i:132624 original size:21 final size:22
Alignment explanation
Indices: 132600--132654 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
132590 TCCTCTTTTC
132600 TTAATCTAATTTAAT-ACAAAT
1 TTAATCTAATTTAATCACAAAT
* *
132621 TTAA-CTTATTTAATCACATAT
1 TTAATCTAATTTAATCACAAAT
* *
132642 TTACTCAAATTTA
1 TTAATCTAATTTA
132655 TCCAAAAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 9 0.33
21 12 0.44
22 6 0.22
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATCTAATTTAATCACAAAT
Found at i:134814 original size:20 final size:20
Alignment explanation
Indices: 134791--134829 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
134781 TTAGTATTGT
134791 TTTTAAGACAT-TTTTATTTA
1 TTTTAAGA-ATATTTTATTTA
*
134811 TTTTAGGAATATTTTATTT
1 TTTTAAGAATATTTTATTT
134830 TATACACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTAAGAATATTTTATTTA
Found at i:139039 original size:16 final size:16
Alignment explanation
Indices: 139006--139044 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
138996 TGAAATTTGG
*
139006 TTTATTTAATTTTGTT
1 TTTATTTAATTATGTT
139022 TTTATTTAATTAAT-TT
1 TTTATTTAATT-ATGTT
139038 TTTATTT
1 TTTATTT
139045 TTTGTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTATTTAATTATGTT
Found at i:139675 original size:12 final size:12
Alignment explanation
Indices: 139658--139682 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
139648 ATATATAAAA
139658 TTGAATTAATCT
1 TTGAATTAATCT
139670 TTGAATTAATCT
1 TTGAATTAATCT
139682 T
1 T
139683 CTCACCATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TTGAATTAATCT
Found at i:147153 original size:13 final size:11
Alignment explanation
Indices: 147110--147155 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
147100 CAGAAAATTT
*
147110 AATTTCTCTCC
1 AATTTCTCTCA
147121 AATATTCTCTCA
1 AAT-TTCTCTCA
147133 AATTTCTCTCA
1 AATTTCTCTCA
*
147144 AATTCCTCTCA
1 AATTTCTCTCA
147155 A
1 A
147156 GAAAGCTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.41
Consensus pattern (11 bp):
AATTTCTCTCA
Found at i:149668 original size:20 final size:22
Alignment explanation
Indices: 149643--149751 Score: 95
Period size: 23 Copynumber: 5.0 Consensus size: 22
149633 TGCCACACTG
149643 ATATGTAGCCGAT-GCTACCA-
1 ATATGTAGCCGATAGCTACCAC
149663 ATATGTAGCCG-TAGCTACCAC
1 ATATGTAGCCGATAGCTACCAC
*
149684 TGAAATGTAGCCGA-AGCTACCAC
1 --ATATGTAGCCGATAGCTACCAC
149707 TGATATGTAGCC-ATAGCTACCAC
1 --ATATGTAGCCGATAGCTACCAC
* *
149730 TGAAATGTAGCC-AAAGCTACCA
1 --ATATGTAGCCGATAGCTACCA
149752 TTGATCAATA
Statistics
Matches: 79, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
19 1 0.01
20 18 0.23
22 1 0.01
23 59 0.75
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (22 bp):
ATATGTAGCCGATAGCTACCAC
Found at i:149694 original size:23 final size:23
Alignment explanation
Indices: 149665--149751 Score: 129
Period size: 23 Copynumber: 3.8 Consensus size: 23
149655 TGCTACCAAT
**
149665 ATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCAAAGCTACCACTGAA
* *
149688 ATGTAGCCGAAGCTACCACTGAT
1 ATGTAGCCAAAGCTACCACTGAA
*
149711 ATGTAGCCATAGCTACCACTGAA
1 ATGTAGCCAAAGCTACCACTGAA
149734 ATGTAGCCAAAGCTACCA
1 ATGTAGCCAAAGCTACCA
149752 TTGATCAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
ATGTAGCCAAAGCTACCACTGAA
Found at i:149729 original size:46 final size:45
Alignment explanation
Indices: 149638--149752 Score: 171
Period size: 46 Copynumber: 2.6 Consensus size: 45
149628 ATAAGTGCCA
* * *
149638 CACTGATATGTAGCCGATGCTACCA--ATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCATGATATGTAGCCATAGCTAC
149681 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCA-TGATATGTAGCCATAGCTAC
*
149727 CACTGAAATGTAGCCAAAGCTACCAT
1 CACTGAAATGTAGCCGAAGCTACCAT
149753 TGATCAATAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
43 23 0.35
45 1 0.02
46 41 0.63
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (45 bp):
CACTGAAATGTAGCCGAAGCTACCATGATATGTAGCCATAGCTAC
Found at i:150019 original size:18 final size:17
Alignment explanation
Indices: 149993--150031 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
149983 ATTTTCCTTC
149993 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
150010 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
150028 CACA
1 CACA
150032 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:152609 original size:18 final size:18
Alignment explanation
Indices: 152578--152620 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
152568 TGCCAGGTGC
*
152578 GTATCCTAGACCTTTTAT
1 GTATCCTAGACCTTATAT
152596 GTATCCTA-ACCCTTATAT
1 GTATCCTAGA-CCTTATAT
*
152614 GTTTCCT
1 GTATCCT
152621 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAGACCTTATAT
Found at i:152886 original size:21 final size:21
Alignment explanation
Indices: 152861--152908 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
152851 CCAACATCGA
152861 CAACCAG-ATCCCCTACCGGAG
1 CAACCAGAATCCCC-ACCGGAG
* *
152882 GAACCAGAATCTCCACCGGAG
1 CAACCAGAATCCCCACCGGAG
152903 CAACCA
1 CAACCA
152909 CAACCCCCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.33, C:0.40, G:0.19, T:0.08
Consensus pattern (21 bp):
CAACCAGAATCCCCACCGGAG
Found at i:156086 original size:37 final size:37
Alignment explanation
Indices: 156045--156119 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
156035 TTCCTAATCC
156045 TTGTATGTTTCCTTTTTCCTTCTCTCCTATACTCTTT
1 TTGTATGTTTCCTTTTTCCTTCTCTCCTATACTCTTT
156082 TTGTATGTTTCCTTTTTCCTTCTCTCCTATACTCTTT
1 TTGTATGTTTCCTTTTTCCTTCTCTCCTATACTCTTT
156119 T
1 T
156120 AATAAATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.08, C:0.27, G:0.05, T:0.60
Consensus pattern (37 bp):
TTGTATGTTTCCTTTTTCCTTCTCTCCTATACTCTTT
Found at i:183197 original size:28 final size:27
Alignment explanation
Indices: 183142--183199 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
183132 CTAACATAAA
*
183142 ATAAAATCCCAAATAGTAATAAAGTCC
1 ATAAAATCCCAAATAGTAATAAAATCC
*
183169 ATAAAAGTCCCAAGT-GTAATAAAAATCC
1 ATAAAA-TCCCAAATAGTAAT-AAAATCC
183197 ATA
1 ATA
183200 TTTATGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (27 bp):
ATAAAATCCCAAATAGTAATAAAATCC
Found at i:203970 original size:27 final size:26
Alignment explanation
Indices: 203933--203986 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
203923 GTTACATTTT
203933 AGTCTTTTGGCA-TCATTGGTGCCGCC
1 AGTCTTTTGGCACT-ATTGGTGCCGCC
*
203959 AGTCTCTTTGGCACTTTTGGTGCCGCC
1 AGTCT-TTTGGCACTATTGGTGCCGCC
203986 A
1 A
203987 ATGTGATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 5 0.20
27 19 0.76
28 1 0.04
ACGTcount: A:0.11, C:0.28, G:0.26, T:0.35
Consensus pattern (26 bp):
AGTCTTTTGGCACTATTGGTGCCGCC
Found at i:204087 original size:28 final size:28
Alignment explanation
Indices: 204051--204116 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
204041 TTTTTGTGGT
204051 ATATTTTGGTAAATAAAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAAATTATA
*
204079 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAATTATA
204107 ATATTTTGGT
1 ATATTTTGGT
204117 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAATTATA
Found at i:204487 original size:25 final size:23
Alignment explanation
Indices: 204450--204498 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
204440 AGCGCAAGTA
204450 ATTTTTATCAATATATTCTTTTCTT
1 ATTTTTAT-AA-ATATTCTTTTCTT
*
204475 ATTTTTGTAAATATTCTTTTCTT
1 ATTTTTATAAATATTCTTTTCTT
204498 A
1 A
204499 GTTTCCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.61
24 2 0.09
25 7 0.30
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (23 bp):
ATTTTTATAAATATTCTTTTCTT
Found at i:219942 original size:28 final size:29
Alignment explanation
Indices: 219910--219966 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
219900 TTCCCCCTAA
* *
219910 TTTTTAT-GGCTTAACTTAAACCTTTTAG
1 TTTTTATAGGCTTAACTAAAACCCTTTAG
219938 TTTTTATGAGGCTTAACTAAAACCCTTTA
1 TTTTTAT-AGGCTTAACTAAAACCCTTTA
219967 CAAATTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
30 18 0.72
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.46
Consensus pattern (29 bp):
TTTTTATAGGCTTAACTAAAACCCTTTAG
Found at i:220460 original size:22 final size:21
Alignment explanation
Indices: 220418--220476 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
220408 ACCCCAGTTG
* * *
220418 GAAAGGTGTTGTACTTTTTGA
1 GAAAAGTGTTGTACCTCTTGA
220439 GTAAAAGTGTTGTACCTCTTGA
1 G-AAAAGTGTTGTACCTCTTGA
**
220461 GAAGGGTGTTGTACCT
1 GAAAAGTGTTGTACCT
220477 AGACGGAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.37
Consensus pattern (21 bp):
GAAAAGTGTTGTACCTCTTGA
Found at i:220471 original size:21 final size:21
Alignment explanation
Indices: 220418--220518 Score: 82
Period size: 21 Copynumber: 4.8 Consensus size: 21
220408 ACCCCAGTTG
* *
220418 GAAAGGTGTTGTACTTTTTGA
1 GAAAGGTGTTGTACCTCTTGA
*
220439 GTAAAAGTGTTGTACCTCTTGA
1 G-AAAGGTGTTGTACCTCTTGA
* *
220461 GAAGGGTGTTGTA-C-CTAGA
1 GAAAGGTGTTGTACCTCTTGA
*
220480 CGGAAAGGTGTTGTACCACTTGA
1 --GAAAGGTGTTGTACCTCTTGA
*
220503 G-AAGTGTGATGTACCT
1 GAAAG-GTGTTGTACCT
220519 TTCAGTAGGG
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.06
20 4 0.06
21 33 0.52
22 19 0.30
23 4 0.06
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (21 bp):
GAAAGGTGTTGTACCTCTTGA
Found at i:234975 original size:24 final size:25
Alignment explanation
Indices: 234943--234995 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
234933 CGAAAGAGCA
*
234943 TCCCGTTAT-TAGCTATTGTGAGTT
1 TCCCATTATATAGCTATTGTGAGTT
* * *
234967 TCCCATTATATGGTTCTTGTGAGTT
1 TCCCATTATATAGCTATTGTGAGTT
234992 TCCC
1 TCCC
234996 GTTAAAGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (25 bp):
TCCCATTATATAGCTATTGTGAGTT
Found at i:239126 original size:45 final size:44
Alignment explanation
Indices: 239075--239265 Score: 239
Period size: 45 Copynumber: 4.4 Consensus size: 44
239065 ATATGCCGAC
* *
239075 TACTGTTACTGTTACTATTACTGATTCGGCACTCTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTAC-GATTCGGCACTTTGTGTGTCGAA
*
239120 TACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTA-CGATTCGGCACTTTGTGTGTCGAA
239165 TACTGTTACTGTTAC-----CGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACGATTCGGCACTTTGTGTGTCGAA
** * ** *
239204 TACTGTTACCATTATTGTTACAGATTCATCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTAC-GATTCGGCACTTTGTGTGTCGAA
239249 TACTGTTACTGTTACTG
1 TACTGTTACTGTTACTG
239266 CTACCGTTAC
Statistics
Matches: 126, Mismatches: 13, Indels: 14
0.82 0.08 0.09
Matches are distributed among these distances:
39 35 0.28
44 1 0.01
45 89 0.71
46 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (44 bp):
TACTGTTACTGTTACTGTTACGATTCGGCACTTTGTGTGTCGAA
Found at i:239213 original size:33 final size:36
Alignment explanation
Indices: 239131--239205 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 36
239121 ACTGTTACTG
239131 TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
1 TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
*
239167 CTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATA
1 ---TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
239206 CTGTTACCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (36 bp):
TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
Found at i:239223 original size:84 final size:84
Alignment explanation
Indices: 239081--239263 Score: 278
Period size: 84 Copynumber: 2.2 Consensus size: 84
239071 CGACTACTGT
* * ** *
239081 TACTGTTACTATTACTGATTCGGCACTCTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATT
1 TACTGTTACTGTTACCGATTCGGCACTCTGTGTGTCGAATACTGTTACCATTACTGTTACAGATT
239146 CGA-CACTTTGTGTGTCGAA
66 C-ATCACTTTGTGTGTCGAA
* *
239165 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACCATTATTGTTACAGATT
1 TACTGTTACTGTTACCGATTCGGCACTCTGTGTGTCGAATACTGTTACCATTACTGTTACAGATT
*
239230 CATCACTTTGTGTGTTGAA
66 CATCACTTTGTGTGTCGAA
239249 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
239264 TGCTACCGTT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
83 1 0.01
84 89 0.99
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (84 bp):
TACTGTTACTGTTACCGATTCGGCACTCTGTGTGTCGAATACTGTTACCATTACTGTTACAGATT
CATCACTTTGTGTGTCGAA
Found at i:243677 original size:180 final size:180
Alignment explanation
Indices: 243375--243738 Score: 728
Period size: 180 Copynumber: 2.0 Consensus size: 180
243365 TTTTTAGACC
243375 ATATCTGGATAGATTTGTTGTGGTGTTTACTGATAATATTCTGGTATACTCCCAAGATGAAAATG
1 ATATCTGGATAGATTTGTTGTGGTGTTTACTGATAATATTCTGGTATACTCCCAAGATGAAAATG
243440 AACATGTTGATCATTTGAGAATTGTGATGTAAACTCTACGTGAGAAACAACTGTATGCCAAATTC
66 AACATGTTGATCATTTGAGAATTGTGATGTAAACTCTACGTGAGAAACAACTGTATGCCAAATTC
243505 AGTAAATGTGAATTTTGGCTTCAGGAAGTTGGATTCCTTGGACATATAGT
131 AGTAAATGTGAATTTTGGCTTCAGGAAGTTGGATTCCTTGGACATATAGT
243555 ATATCTGGATAGATTTGTTGTGGTGTTTACTGATAATATTCTGGTATACTCCCAAGATGAAAATG
1 ATATCTGGATAGATTTGTTGTGGTGTTTACTGATAATATTCTGGTATACTCCCAAGATGAAAATG
243620 AACATGTTGATCATTTGAGAATTGTGATGTAAACTCTACGTGAGAAACAACTGTATGCCAAATTC
66 AACATGTTGATCATTTGAGAATTGTGATGTAAACTCTACGTGAGAAACAACTGTATGCCAAATTC
243685 AGTAAATGTGAATTTTGGCTTCAGGAAGTTGGATTCCTTGGACATATAGT
131 AGTAAATGTGAATTTTGGCTTCAGGAAGTTGGATTCCTTGGACATATAGT
243735 ATAT
1 ATAT
243739 GCTGAAGGCA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 184 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (180 bp):
ATATCTGGATAGATTTGTTGTGGTGTTTACTGATAATATTCTGGTATACTCCCAAGATGAAAATG
AACATGTTGATCATTTGAGAATTGTGATGTAAACTCTACGTGAGAAACAACTGTATGCCAAATTC
AGTAAATGTGAATTTTGGCTTCAGGAAGTTGGATTCCTTGGACATATAGT
Found at i:246556 original size:24 final size:25
Alignment explanation
Indices: 246524--246580 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
246514 CGAAAGAGAG
246524 TCCCGTTAT-TAGATCTTGTGAGCT
1 TCCCGTTATATAGATCTTGTGAGCT
* *
246548 TCCCGTTATATGGTTCTTGTGAGCT
1 TCCCGTTATATAGATCTTGTGAGCT
*
246573 TCCTGTTA
1 TCCCGTTA
246581 AAACTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (25 bp):
TCCCGTTATATAGATCTTGTGAGCT
Found at i:246752 original size:25 final size:24
Alignment explanation
Indices: 246724--246779 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
246714 CTCGTTTGAA
246724 CTTCCCGATATATGGCTATCCGGAG
1 CTTCCCGATA-ATGGCTATCCGGAG
* * * *
246749 CTTCCTGTTAATGGCTCTTCGGAG
1 CTTCCCGATAATGGCTATCCGGAG
*
246773 CTACCCG
1 CTTCCCG
246780 TTATTGTCTC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.16, C:0.30, G:0.23, T:0.30
Consensus pattern (24 bp):
CTTCCCGATAATGGCTATCCGGAG
Found at i:246782 original size:24 final size:24
Alignment explanation
Indices: 246735--246782 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
246725 TTCCCGATAT
* *
246735 ATGGCTATCCGGAGCTTCCTGTTA
1 ATGGCTATCCGGAGCTACCCGTTA
* *
246759 ATGGCTCTTCGGAGCTACCCGTTA
1 ATGGCTATCCGGAGCTACCCGTTA
246783 TTGTCTCGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (24 bp):
ATGGCTATCCGGAGCTACCCGTTA
Found at i:246822 original size:72 final size:73
Alignment explanation
Indices: 246647--246823 Score: 164
Period size: 72 Copynumber: 2.4 Consensus size: 73
246637 AGCTCTTATT
* * *
246647 AGCTTCCTG-ATCATAGGCTCTGTGTGAGCTTCTCGTTAATTGACTCTTTGTGAGCTTCCCGATA
1 AGCTTCCTGAAT-AT-GGCTCT-TCTGAGCTTCTCGTTAATTGACTCTTCGTGAGCTACCCGATA
*
246711 TGGCTCGTTTG
63 TGGCTCGCTTG
* * * * * * *
246722 AACTTCCCGATATATGGCTATCCGGAGCTTC-CTGTTAA-TGGCTCTTCG-GAGCTACCCGTTAT
1 AGCTTCCTGA-ATATGGCTCTTCTGAGCTTCTC-GTTAATTGACTCTTCGTGAGCTACCCGATA-
*
246784 TGTCTCGCTTG
63 TGGCTCGCTTG
246795 AGCTTCCTGAATATGGCTCTTCTGAGCTT
1 AGCTTCCTGAATATGGCTCTTCTGAGCTT
246824 TTTGTTTCAG
Statistics
Matches: 81, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
72 27 0.33
73 26 0.32
74 12 0.15
75 12 0.15
76 2 0.02
77 2 0.02
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.37
Consensus pattern (73 bp):
AGCTTCCTGAATATGGCTCTTCTGAGCTTCTCGTTAATTGACTCTTCGTGAGCTACCCGATATGG
CTCGCTTG
Found at i:247402 original size:38 final size:38
Alignment explanation
Indices: 247347--247422 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
247337 AGATACATCT
*
247347 CATTATCCCTCAGACTTCTCGGTATATAAAGCAAACTA
1 CATTATCCCTCAAACTTCTCGGTATATAAAGCAAACTA
247385 CATTATCCCTCAAACTTCTCGGTATATAAAGCAAACTA
1 CATTATCCCTCAAACTTCTCGGTATATAAAGCAAACTA
247423 ACTTTTGGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.29
Consensus pattern (38 bp):
CATTATCCCTCAAACTTCTCGGTATATAAAGCAAACTA
Found at i:250276 original size:30 final size:29
Alignment explanation
Indices: 250222--250281 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
250212 GTTTTGTGAC
* ** *
250222 CACACGAGTAGCCACACGGGCGTGTGCCG
1 CACACGAGCAGCCACACGACCGTGTACCG
250251 CACACGAGCAGTCCACACGACCGTGTACCG
1 CACACGAGCAG-CCACACGACCGTGTACCG
250281 C
1 C
250282 TGTGGAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.10
Consensus pattern (29 bp):
CACACGAGCAGCCACACGACCGTGTACCG
Found at i:250584 original size:21 final size:21
Alignment explanation
Indices: 250560--250629 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
250550 GTGTCTCCGC
250560 CACATGGTCGTGTGCCTCTTT
1 CACATGGTCGTGTGCCTCTTT
**
250581 CACATAGG-CGTGCCCCTCTTT
1 CACAT-GGTCGTGTGCCTCTTT
* * *
250602 CACACGGTCATGTAGACTC-TT
1 CACATGGTCGTGT-GCCTCTTT
250623 CACATGG
1 CACATGG
250630 CCTAGACTCT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.05
21 31 0.82
22 5 0.13
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.30
Consensus pattern (21 bp):
CACATGGTCGTGTGCCTCTTT
Found at i:253203 original size:32 final size:31
Alignment explanation
Indices: 253159--253222 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 31
253149 ATTTTTTCTA
*
253159 AAATTAAATATTTTAAT-TAATGTTAAAATT
1 AAATTAAATATTTAAATATAATGTTAAAATT
* *
253189 AAATATAATATATTTAAATATATTTTTAAAATT
1 AAAT-TAA-ATATTTAAATATAATGTTAAAATT
253222 A
1 A
253223 TCATAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 4 0.14
31 3 0.11
32 9 0.32
33 12 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
AAATTAAATATTTAAATATAATGTTAAAATT
Found at i:254845 original size:14 final size:14
Alignment explanation
Indices: 254822--254855 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
254812 TACAAAAAAT
* *
254822 AATATATTTATTAA
1 AATATTTTTAATAA
254836 AATATTTTTAATAA
1 AATATTTTTAATAA
254850 AATATT
1 AATATT
254856 ATGAATACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTTTTAATAA
Found at i:260472 original size:33 final size:33
Alignment explanation
Indices: 260430--260496 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
260420 TATCAAGATT
260430 TGTTTGGATAGTGAATAGAGTTTTGGTCTACCA
1 TGTTTGGATAGTGAATAGAGTTTTGGTCTACCA
260463 TGTTTGGATAGTGAATAGAGTTTTGGTCTACCA
1 TGTTTGGATAGTGAATAGAGTTTTGGTCTACCA
260496 T
1 T
260497 TTATATGCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (33 bp):
TGTTTGGATAGTGAATAGAGTTTTGGTCTACCA
Found at i:261216 original size:14 final size:14
Alignment explanation
Indices: 261197--261234 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
261187 GTTTGCCAGT
* *
261197 AAAATGTTTTCTGG
1 AAAATGATTTCTAG
261211 AAAATGATTTCTAG
1 AAAATGATTTCTAG
261225 AAAATGATTT
1 AAAATGATTT
261235 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (14 bp):
AAAATGATTTCTAG
Found at i:261895 original size:43 final size:43
Alignment explanation
Indices: 261817--262108 Score: 363
Period size: 43 Copynumber: 6.8 Consensus size: 43
261807 TAAAGACATT
* * *
261817 GACCTTTAGCGGCGC-TTTCCCAAAAACGCTGCTATATCTCGA
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCGA
* *
261859 GACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGCTCAA
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCGA
* * *
261902 GACATTTAGCGGCGCTTTTCTCACAAACGCCGCTATAGCTCAA
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCGA
* * *
261945 GAGCTTTAGCGGCGCTTTTCCCACAAATGCCGCTATAGGTC-A
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCGA
* *
261987 CGACCTTTAGCGGCGCTTTTTCCACAAACGTCGCTATAGCTCGA
1 -GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCGA
* * *
262031 TACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAACTCGA
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCGA
* * * * * *
262074 TACCTTTAGCGGTGCTTCTCACAAAAACCCCGCTA
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
262109 AAAATATAAC
Statistics
Matches: 220, Mismatches: 27, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
42 16 0.07
43 203 0.92
44 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (43 bp):
GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCGA
Found at i:266440 original size:19 final size:20
Alignment explanation
Indices: 266412--266454 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
266402 AATTTATAAA
*
266412 TTTTAGTTTTTTTATTTCAT
1 TTTTAGTTTTTGTATTTCAT
*
266432 TTTTA-TTTTTGTATTTTAT
1 TTTTAGTTTTTGTATTTCAT
266451 TTTT
1 TTTT
266455 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTAGTTTTTGTATTTCAT
Found at i:266822 original size:7 final size:7
Alignment explanation
Indices: 266812--266849 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
266802 CTCTAACTCT
266812 TAACCCC
1 TAACCCC
266819 TAACCCC
1 TAACCCC
*
266826 TAACCCT
1 TAACCCC
*
266833 TTACCCC
1 TAACCCC
266840 TAACCCC
1 TAACCCC
266847 TAA
1 TAA
266850 ATCTCAAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (7 bp):
TAACCCC
Found at i:266828 original size:21 final size:21
Alignment explanation
Indices: 266804--266849 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
266794 CCCTAAATCT
*
266804 CTAACTCTTAACCCCTAACCC
1 CTAACCCTTAACCCCTAACCC
*
266825 CTAACCCTTTACCCCTAACCC
1 CTAACCCTTAACCCCTAACCC
266846 CTAA
1 CTAA
266850 ATCTCAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.48, G:0.00, T:0.24
Consensus pattern (21 bp):
CTAACCCTTAACCCCTAACCC
Found at i:267087 original size:25 final size:24
Alignment explanation
Indices: 267035--267089 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
267025 ATTATATATG
* * *
267035 AAATTATTTAATATATAAATTTAT
1 AAATTATTTAAAATATAAATTAAA
267059 AAATATATTTAAAATATAAATTAAA
1 AAAT-TATTTAAAATATAAATTAAA
267084 AAATTA
1 AAATTA
267090 ATCTAAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTATTTAAAATATAAATTAAA
Found at i:267310 original size:41 final size:41
Alignment explanation
Indices: 267251--267597 Score: 462
Period size: 41 Copynumber: 8.5 Consensus size: 41
267241 ATTTGAAATT
* * * **
267251 AAAAACGCTGCTATAGCCCCAAGCATTAGCGGCGCTTTCCC
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTTTC
* * **
267292 AAAAACGCCGCTAGAGCCCCAAGCATTAGCGGCGCTTTCCC
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTTTC
*
267333 AAAAACGCCGCTAATGCCCC-AGCATTAGCGGCGCTTTTTC
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTTTC
* ** * *
267373 AAAAACGCCGCTAAAGCCCCCAGCATTAATGTCACTTTTTC
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTTTC
* *
267414 AAAAACGCCGCTAAAGCACCGAGCATTAGCGACGCTTTTTC
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTTTC
* *
267455 AAAAACGCCGCTAAAGCACCGAGCATTAGCGACGCTTTTTC
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTTTC
* * *
267496 AAAAACGCCGCTAAAGCACCGAGCATTAGCGGCGTTTTTTT
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTTTC
* * *
267537 AGAAACGCCGCTAAAGCACCGAGCATTAGAGGCGCTTTTTC
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTTTC
267578 AAAAACGCCGCTAAAGCCCC
1 AAAAACGCCGCTAAAGCCCC
267598 AAATTTGTTA
Statistics
Matches: 279, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 37 0.13
41 242 0.87
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTTTC
Found at i:268813 original size:27 final size:27
Alignment explanation
Indices: 268762--268816 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
268752 ATCAATCATT
*
268762 TCAATATCTAACAAGCTTAAAACATAA
1 TCAATATCTAACAAGATTAAAACATAA
*
268789 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
268816 T
1 T
268817 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:272190 original size:4 final size:4
Alignment explanation
Indices: 272181--272243 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
272171 ATATATGTGA
272181 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
272229 ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATG
272244 CTGCCCTTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:279306 original size:48 final size:48
Alignment explanation
Indices: 279230--279327 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
279220 CATTTAGCCT
*
279230 TAGTCTGGTTATCATTCCTATCGAGAATCATGAGATATGAACCCACGC
1 TAGTCTGGTTATCATTCCTATCGAGAATCATAAGATATGAACCCACGC
* *
279278 TAGTTTGGTTATCATTCCTATCGAGAATCATAAGATATGAACCCATGC
1 TAGTCTGGTTATCATTCCTATCGAGAATCATAAGATATGAACCCACGC
279326 TA
1 TA
279328 AAACCTTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (48 bp):
TAGTCTGGTTATCATTCCTATCGAGAATCATAAGATATGAACCCACGC
Found at i:280677 original size:17 final size:17
Alignment explanation
Indices: 280644--280677 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
280634 ATATGATTTA
*
280644 TAAAATTTTAAAAATAT
1 TAAAATTTCAAAAATAT
*
280661 TAAAATTTCAAATATAT
1 TAAAATTTCAAAAATAT
280678 ATTTTTAAAA
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:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATTTCAAAAATAT
Found at i:280737 original size:17 final size:17
Alignment explanation
Indices: 280686--280757 Score: 65
Period size: 18 Copynumber: 4.0 Consensus size: 17
280676 ATATTTTTAA
*
280686 AATTTTTAGTAAATTTT-
1 AATTTTTA-TAATTTTTG
280703 AACTTTTTATATAGTTTTTG
1 AA-TTTTTATA-A-TTTTTG
*
280723 AATTTTTATAATTTTTC
1 AATTTTTATAATTTTTG
*
280740 TATTTTTAATAATTTTTG
1 AATTTTT-ATAATTTTTG
280758 TAAAATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
17 15 0.33
18 17 0.37
19 12 0.26
20 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (17 bp):
AATTTTTATAATTTTTG
Found at i:283016 original size:16 final size:16
Alignment explanation
Indices: 282995--283025 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
282985 TAGAGCAAAT
282995 ACGCTAGTAAATAAAC
1 ACGCTAGTAAATAAAC
283011 ACGCTAGTAAATAAA
1 ACGCTAGTAAATAAA
283026 ATACTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.19
Consensus pattern (16 bp):
ACGCTAGTAAATAAAC
Found at i:287748 original size:43 final size:43
Alignment explanation
Indices: 287675--287799 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 43
287665 TGTAATCTCG
*
287675 TATCGATGCCAATAG-CCCA-ACCATGATCTTACACGAAATCACA
1 TATCGATGCCAAT-GTCCCAGA-CATGGTCTTACACGAAATCACA
* *
287718 TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAGTCTCA
1 TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCACA
* * * * *
287761 TATCGATGCC-ATATCCTAGATAGGGTCTTACACGTAATC
1 TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATC
287800 TCGGTAACCA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
42 24 0.34
43 46 0.65
44 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCACA
Found at i:297449 original size:125 final size:121
Alignment explanation
Indices: 297219--297540 Score: 457
Period size: 121 Copynumber: 2.6 Consensus size: 121
297209 AAATCATTAT
* * * *
297219 ATATATGATCAATAGTAAAGATCTTAAATTTTATAGATAAATAAAGCAGTAATAAAAAAACAATT
1 ATATATGATAAATAGTGAAGATCTAAAATTTTATAGATAAATAAAGCAGTAAT-AAAAAATAATT
* *
297284 GAAATAGGGAAGTAATAAAGATATTTTGAAAAATAATATTAACTATTAATACAATAAATCA
65 GAAATAGGAAAGTAATAAAAATATTTTGAAAAATAATATTAACTATTAATACAAT--A--A
*
297345 ATATATGATAAATAGTGAACATCTAAAATTTTATAGATAAATAAAGCAGTAATAAAAAATAATTG
1 ATATATGATAAATAGTGAAGATCTAAAATTTTATAGATAAATAAAGCAGTAATAAAAAATAATTG
*
297410 AAATAGGAAAGTAATAAAAATATTTTGAAAAATAATATTAACTATTAATAGAATAA
66 AAATAGGAAAGTAATAAAAATATTTTGAAAAATAATATTAACTATTAATACAATAA
* * * * **
297466 ATATATGATAAATAGTGAAGATATTAAAA-TTTATAAATAAACAAAGCAATAATAAAAGTTAATT
1 ATATATGATAAATAGTGAAGAT-CTAAAATTTTATAGATAAATAAAGCAGTAATAAAAAATAATT
297530 GAAATAGGAAA
65 GAAATAGGAAA
297541 ATATAGCCCT
Statistics
Matches: 180, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
121 63 0.35
122 5 0.03
123 1 0.01
125 62 0.34
126 49 0.27
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.30
Consensus pattern (121 bp):
ATATATGATAAATAGTGAAGATCTAAAATTTTATAGATAAATAAAGCAGTAATAAAAAATAATTG
AAATAGGAAAGTAATAAAAATATTTTGAAAAATAATATTAACTATTAATACAATAA
Found at i:297539 original size:121 final size:122
Alignment explanation
Indices: 297219--297540 Score: 450
Period size: 125 Copynumber: 2.6 Consensus size: 122
297209 AAATCATTAT
* * * *
297219 ATATATGATCAATAGTAAAGATCTTAAATTTTATAGATAAATAAAGCAGTAATAAAAAAACAATT
1 ATATATGATAAATAGTGAAGAT-TTAAAATTTATAGATAAATAAAGCAGTAAT-AAAAAATAATT
* *
297284 GAAATAGGGAAGTAATAAAGATATTTTGAAAAATAATATTAACTATTAATACAATAAATCA
64 GAAATAGGAAAGTAATAAAAATATTTTGAAAAATAATATTAACTATTAATACAAT-AA-CA
* *
297345 ATATATGATAAATAGTGAACATCTAAAATTTTATAGATAAATAAAGCAGTAATAAAAAATAATTG
1 ATATATGATAAATAGTGAAGATTTAAAA-TTTATAGATAAATAAAGCAGTAATAAAAAATAATTG
*
297410 AAATAGGAAAGTAATAAAAATATTTTGAAAAATAATATTAACTATTAATAGAAT-A-A
65 AAATAGGAAAGTAATAAAAATATTTTGAAAAATAATATTAACTATTAATACAATAACA
* * * **
297466 ATATATGATAAATAGTGAAGATATTAAAATTTATAAATAAACAAAGCAATAATAAAAGTTAATTG
1 ATATATGATAAATAGTGAAGAT-TTAAAATTTATAGATAAATAAAGCAGTAATAAAAAATAATTG
297531 AAATAGGAAA
65 AAATAGGAAA
297541 ATATAGCCCT
Statistics
Matches: 178, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
121 63 0.35
122 5 0.03
123 1 0.01
125 66 0.37
126 43 0.24
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.30
Consensus pattern (122 bp):
ATATATGATAAATAGTGAAGATTTAAAATTTATAGATAAATAAAGCAGTAATAAAAAATAATTGA
AATAGGAAAGTAATAAAAATATTTTGAAAAATAATATTAACTATTAATACAATAACA
Found at i:299822 original size:26 final size:24
Alignment explanation
Indices: 299777--299845 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
299767 CAATTTATAA
*
299777 TAAAATATTAATAAAATATCTTAT
1 TAAAATATTAATAAAATATCTAAT
* *
299801 TAAAATTTTATTAAAATTTATCTAAT
1 TAAAATATTAATAAAA--TATCTAAT
299827 T-AAATAATT-ATAAAATATC
1 TAAAAT-ATTAATAAAATATC
299846 ATCAAATATC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 4 0.11
24 14 0.38
25 9 0.24
26 10 0.27
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAATATTAATAAAATATCTAAT
Found at i:301042 original size:17 final size:17
Alignment explanation
Indices: 301020--301055 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
301010 TCATAATATT
* *
301020 ATTATAAACTATCAAAA
1 ATTATAAAATACCAAAA
301037 ATTATAAAATACCAAAA
1 ATTATAAAATACCAAAA
301054 AT
1 AT
301056 ATGGGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (17 bp):
ATTATAAAATACCAAAA
Found at i:302953 original size:23 final size:22
Alignment explanation
Indices: 302914--302957 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
302904 TTTTGATTTC
*
302914 AATTAACATTATAAATTAAAAA
1 AATTAACAATATAAATTAAAAA
*
302936 AATTAAACAATATCAATTAAAA
1 AATT-AACAATATAAATTAAAA
302958 TTTATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTAACAATATAAATTAAAAA
Found at i:303205 original size:22 final size:23
Alignment explanation
Indices: 303170--303212 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
303160 GTAAAATAAT
*
303170 TTTCTCAATAATTACATTCCACA
1 TTTCTCAAAAATTACATTCCACA
303193 TTTCT-AAAAATTACATTCCA
1 TTTCTCAAAAATTACATTCCA
303213 TTAAAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTCTCAAAAATTACATTCCACA
Found at i:303652 original size:21 final size:23
Alignment explanation
Indices: 303623--303674 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
303613 AACGTTAACA
*
303623 TTTTCTTTTCTC-C-AATGGTTAC
1 TTTT-TTTTCTCTCTAATGATTAC
*
303645 TTTTTTTTCTCTCTAGTGATTAC
1 TTTTTTTTCTCTCTAATGATTAC
303668 TTTTTTT
1 TTTTTTT
303675 CCCTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 7 0.27
22 5 0.19
23 14 0.54
ACGTcount: A:0.12, C:0.17, G:0.08, T:0.63
Consensus pattern (23 bp):
TTTTTTTTCTCTCTAATGATTAC
Found at i:303751 original size:33 final size:33
Alignment explanation
Indices: 303714--303778 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
303704 TTTTTTCCAT
*
303714 TCAATCCTATTCTCTCAATTCTTTTAATCTCAG
1 TCAATCCTATTCTCTCAATTATTTTAATCTCAG
*
303747 TCAATCCTATTCTCTCAATTATTTTATTCTCA
1 TCAATCCTATTCTCTCAATTATTTTAATCTCA
303779 ATATTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.02, T:0.48
Consensus pattern (33 bp):
TCAATCCTATTCTCTCAATTATTTTAATCTCAG
Found at i:303817 original size:23 final size:24
Alignment explanation
Indices: 303774--303818 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
303764 ATTATTTTAT
*
303774 TCTCAATATTTTTCATTCAATTCA
1 TCTCAATATTCTTCATTCAATTCA
*
303798 TCTCAA-ATTCTTCTTTCAATT
1 TCTCAATATTCTTCATTCAATT
303819 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (24 bp):
TCTCAATATTCTTCATTCAATTCA
Found at i:305916 original size:24 final size:24
Alignment explanation
Indices: 305868--305917 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
305858 TGGAAGAATA
* *
305868 AGATGAAGATGAAGATAATGTTGG
1 AGATAAAGATGAAGATAATGATGG
305892 AGATAAAGATGAAGATCAA-GATGG
1 AGATAAAGATGAAGAT-AATGATGG
305916 AG
1 AG
305918 GTGGAGGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.46, C:0.02, G:0.32, T:0.20
Consensus pattern (24 bp):
AGATAAAGATGAAGATAATGATGG
Found at i:305928 original size:12 final size:12
Alignment explanation
Indices: 305910--305949 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
305900 ATGAAGATCA
305910 AGATGGAGGTGG
1 AGATGGAGGTGG
* *
305922 AGGTGGAGATGG
1 AGATGGAGGTGG
*
305934 AGATGGAGGTGA
1 AGATGGAGGTGG
305946 AGAT
1 AGAT
305950 AAAGGGCTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.53, T:0.17
Consensus pattern (12 bp):
AGATGGAGGTGG
Found at i:305931 original size:18 final size:18
Alignment explanation
Indices: 305909--305949 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
305899 GATGAAGATC
*
305909 AAGATGGAGGTGGAGGTG
1 AAGATGGAGATGGAGGTG
*
305927 GAGATGGAGATGGAGGTG
1 AAGATGGAGATGGAGGTG
305945 AAGAT
1 AAGAT
305950 AAAGGGCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.51, T:0.17
Consensus pattern (18 bp):
AAGATGGAGATGGAGGTG
Found at i:306020 original size:13 final size:13
Alignment explanation
Indices: 305968--306020 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
305958 AGTTTGGCAA
305968 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
***
305981 TGCTGCGGAAAAG
1 TGCTTTTGAAAAG
305994 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
306007 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
306020 T
1 T
306021 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:307024 original size:75 final size:74
Alignment explanation
Indices: 306756--307031 Score: 403
Period size: 75 Copynumber: 3.7 Consensus size: 74
306746 ATTGTATTCA
* * * *
306756 ATTTTTACATCCATAATATATTTATTTACAATTTA-CAAAAAAAT-AAAAAATTATTTGTATTAT
1 ATTTTTACATCAATAATATACTTATTTACAATTTACCAAAAAAATGAAAAAATTGTTTGTA-TGT
*
306819 ATTCTATGGT
65 ATTCTATTGT
* * * *
306829 ATTTTTACATAAATAATATACTTATTTACAATTTATCAAAAAAATTTAAAAAATTGTTTGTATGA
1 ATTTTTACATCAATAATATACTTATTTACAATTTACCAAAAAAA-TGAAAAAATTGTTTGTATGT
306894 ATTCTATTGT
65 ATTCTATTGT
*
306904 ATTTTTACATCAATAATATACTTGTTTACAATTTACCAAAAAAATGAAAAAATTGTTTGTATGTA
1 ATTTTTACATCAATAATATACTTATTTACAATTTACCAAAAAAATGAAAAAATTGTTTGTATGTA
306969 TTCTATTGT
66 TTCTATTGT
*
306978 ATGTTTTACATCAATAATATACTTATTTACAATTTACCTAAAAAATGACAAAAA
1 AT-TTTTACATCAATAATATACTTATTTACAATTTACCAAAAAAATGA-AAAAA
307032 ATGAATTCTA
Statistics
Matches: 184, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
73 32 0.17
74 38 0.21
75 95 0.52
76 19 0.10
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (74 bp):
ATTTTTACATCAATAATATACTTATTTACAATTTACCAAAAAAATGAAAAAATTGTTTGTATGTA
TTCTATTGT
Done.