Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 5 of 292
Found at i:1352660 original size:20 final size:20
Alignment explanation
Indices: 1352621--1352661 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1352611 AATTGTCTAG
* *
1352621 TTTCTTAGAAAATTACTGAA
1 TTTCTTAAAAAAATACTGAA
*
1352641 TTTCTTAAAAAAATATTGAA
1 TTTCTTAAAAAAATACTGAA
1352661 T
1 T
1352662 ATCGACAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (20 bp):
TTTCTTAAAAAAATACTGAA
Found at i:1356324 original size:5 final size:5
Alignment explanation
Indices: 1356314--1356346 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1356304 TTGGGTTTTG
*
1356314 AAATA AAATA AAATA AAATA AAGTA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
1356347 AATAAATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1356358 original size:20 final size:20
Alignment explanation
Indices: 1356317--1356355 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1356307 GGTTTTGAAA
*
1356317 TAAAATAAAATAAAATAAAG
1 TAAAATAAAAAAAAATAAAG
1356337 TAAAATAAAAAATAAATAA
1 TAAAATAAAAAA-AAATAA
1356356 GTATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (20 bp):
TAAAATAAAAAAAAATAAAG
Found at i:1359764 original size:21 final size:21
Alignment explanation
Indices: 1359696--1359805 Score: 62
Period size: 21 Copynumber: 5.3 Consensus size: 21
1359686 AAGACCGAAG
* *
1359696 GCTGAACAGAAGCTCATGAGA
1 GCTGAATAGAAGCTCATAAGA
* * *
1359717 GCTAAATAGAAAC-CAATAAGG
1 GCTGAATAGAAGCTC-ATAAGA
* *
1359738 GTTGAATAGAAGCTCGTAAGA
1 GCTGAATAGAAGCTCATAAGA
* * * *
1359759 GCTGAA-CGAAACCCATAAGG
1 GCTGAATAGAAGCTCATAAGA
* * * *
1359779 GTTAAACAGAAGCTCAAAAGA
1 GCTGAATAGAAGCTCATAAGA
1359800 GCTGAA
1 GCTGAA
1359806 GGGAAACTCA
Statistics
Matches: 61, Mismatches: 25, Indels: 6
0.66 0.27 0.07
Matches are distributed among these distances:
20 14 0.23
21 46 0.75
22 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.15
Consensus pattern (21 bp):
GCTGAATAGAAGCTCATAAGA
Found at i:1359780 original size:41 final size:42
Alignment explanation
Indices: 1359698--1359805 Score: 137
Period size: 41 Copynumber: 2.6 Consensus size: 42
1359688 GACCGAAGGC
* *
1359698 TGAACAGAAGCTCATGAGAGCTAAATAGAAACCAATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAATAGAAACCAATAAGGGT
* * * *
1359740 TGAATAGAAGCTCGTAAGAGCTGAA-CGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAATAGAAACCAATAAGGGT
* *
1359781 TAAACAGAAGCTCAAAAGAGCTGAA
1 TGAACAGAAGCTCATAAGAGCTGAA
1359806 GGGAAACTCA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 35 0.62
42 21 0.38
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAATAGAAACCAATAAGGGT
Found at i:1359843 original size:42 final size:41
Alignment explanation
Indices: 1359725--1359853 Score: 114
Period size: 41 Copynumber: 3.1 Consensus size: 41
1359715 GAGCTAAATA
* * * *
1359725 GAAACCAATAAGGGTTGAATAGAAGCTCGTAAGAGCTGAAC
1 GAAACCCATAAGAGTTAAAAAGAAGCTCGTAAGAGCTGAAC
* * ** *
1359766 GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTGAAGG
1 GAAACCCATAAGAGTTAAAAAGAAGCTCGTAAGAGCTGAA-C
* ** * *
1359808 GAAACTCATATTAGTTAAAAAGAAGCTCGTGAGAGCTAAAC
1 GAAACCCATAAGAGTTAAAAAGAAGCTCGTAAGAGCTGAAC
1359849 AGAAA
1 -GAAA
1359854 GTAAACACAA
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
41 35 0.50
42 35 0.50
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16
Consensus pattern (41 bp):
GAAACCCATAAGAGTTAAAAAGAAGCTCGTAAGAGCTGAAC
Found at i:1366003 original size:37 final size:37
Alignment explanation
Indices: 1365962--1366034 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
1365952 ACATGTTCAA
* *
1365962 ATCCATTTGACATCTTTATAATCTATAAGAAAACAAC
1 ATCCATTTCACATCTTTACAATCTATAAGAAAACAAC
1365999 ATCCATTTCACATCTTTACAATCTATAAGAAAACAA
1 ATCCATTTCACATCTTTACAATCTATAAGAAAACAA
1366035 AGGTTAGATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.32
Consensus pattern (37 bp):
ATCCATTTCACATCTTTACAATCTATAAGAAAACAAC
Found at i:1366653 original size:73 final size:73
Alignment explanation
Indices: 1366534--1366723 Score: 292
Period size: 73 Copynumber: 2.6 Consensus size: 73
1366524 TCCCTGACTT
* * * * *
1366534 GGGTCACATGGCCAACCCAAACGCCCATGTGCTAGGCCGTGTGAGCATACTGACTTGTAAAATTA
1 GGGTCACAGGGCCAAGCCACATGCCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGTAAAATTA
1366599 AGGTGCAA
66 AGGTGCAA
1366607 GGGTCACAGGGCCAAGCCACATGCCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGTAAAATTA
1 GGGTCACAGGGCCAAGCCACATGCCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGTAAAATTA
*
1366672 AGGTGCAT
66 AGGTGCAA
* *
1366680 GGGTCAC-GCGGCCAAGTCACATGCTCGTGTGCTAGGCCGTGTGA
1 GGGTCACAG-GGCCAAGCCACATGCCCGTGTGCTAGGCCGTGTGA
1366724 AAATATTTGG
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
72 1 0.01
73 107 0.99
ACGTcount: A:0.24, C:0.25, G:0.30, T:0.21
Consensus pattern (73 bp):
GGGTCACAGGGCCAAGCCACATGCCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGTAAAATTA
AGGTGCAA
Found at i:1367606 original size:21 final size:21
Alignment explanation
Indices: 1367567--1367739 Score: 79
Period size: 21 Copynumber: 8.3 Consensus size: 21
1367557 ACATCGTTTT
*
1367567 CAAAAGCCCA-AAG-GCTAAA
1 CAAAAGCTCATAAGAGCTAAA
*
1367586 CAAAAGCTCATGAGAGCTAAA
1 CAAAAGCTCATAAGAGCTAAA
* * * *
1367607 CAGAAA-CCCATAAGGGTTGAA
1 CA-AAAGCTCATAAGAGCTAAA
* * *
1367628 CAGAAGCTCGTAAGAGCTGAA
1 CAAAAGCTCATAAGAGCTAAA
* * * *
1367649 CGAATA-CCCATAAGGGTTAAA
1 C-AAAAGCTCATAAGAGCTAAA
* *
1367670 CAAAAGCTCAAAAGAGCTGAA
1 CAAAAGCTCATAAGAGCTAAA
* *
1367691 CGAAAA-CTCATGTA-AGTTAAA
1 C-AAAAGCTCAT-AAGAGCTAAA
* * *
1367712 TAGAAGCTCATGAGAGCTAAA
1 CAAAAGCTCATAAGAGCTAAA
1367733 CAGAAAG
1 CA-AAAG
1367740 TAAACACGAA
Statistics
Matches: 108, Mismatches: 35, Indels: 19
0.67 0.22 0.12
Matches are distributed among these distances:
19 9 0.08
20 11 0.10
21 75 0.69
22 13 0.12
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (21 bp):
CAAAAGCTCATAAGAGCTAAA
Found at i:1367658 original size:42 final size:41
Alignment explanation
Indices: 1367582--1367695 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 41
1367572 GCCCAAAGGC
* *
1367582 TAAACAAAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGT
1 TAAACAAAAGCTCATAAGAGCTGAAC-GAAACCCATAAGGGT
* * *
1367624 TGAACAGAAGCTCGTAAGAGCTGAACGAATACCCATAAGGGT
1 TAAACAAAAGCTCATAAGAGCTGAACGAA-ACCCATAAGGGT
*
1367666 TAAACAAAAGCTCAAAAGAGCTGAACGAAA
1 TAAACAAAAGCTCATAAGAGCTGAACGAAA
1367696 ACTCATGTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 4 0.06
42 58 0.94
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (41 bp):
TAAACAAAAGCTCATAAGAGCTGAACGAAACCCATAAGGGT
Found at i:1367728 original size:42 final size:41
Alignment explanation
Indices: 1367568--1367738 Score: 141
Period size: 42 Copynumber: 4.1 Consensus size: 41
1367558 CATCGTTTTC
* * * *
1367568 AAAAGCCCA-AAGGCTAAACAAAAGCTCATGAGAGCTAAAC-
1 AAAA-CCCATAAGGTTAAACAGAAGCTCATAAGAGCTGAACG
* *
1367608 AGAAACCCATAAGGGTTGAACAGAAGCTCGTAAGAGCTGAACG
1 A-AAACCCATAA-GGTTAAACAGAAGCTCATAAGAGCTGAACG
* * *
1367651 AATACCCATAAGGGTTAAACAAAAGCTCAAAAGAGCTGAACG
1 AAAACCCATAA-GGTTAAACAGAAGCTCATAAGAGCTGAACG
* * * *
1367693 AAAACTCATGTAA-GTTAAATAGAAGCTCATGAGAGCTAAACAG
1 AAAACCCA--TAAGGTTAAACAGAAGCTCATAAGAGCTGAAC-G
1367736 AAA
1 AAA
1367739 GTAAACACGA
Statistics
Matches: 106, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
40 5 0.05
41 5 0.05
42 88 0.83
43 5 0.05
44 3 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (41 bp):
AAAACCCATAAGGTTAAACAGAAGCTCATAAGAGCTGAACG
Found at i:1370712 original size:30 final size:30
Alignment explanation
Indices: 1370626--1370723 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
1370616 TTAAACTAAA
* *
1370626 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
1370656 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
1370686 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
1370716 ATGAGCTA
1 ATGAGCTA
1370724 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:1373003 original size:30 final size:30
Alignment explanation
Indices: 1372932--1373014 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
1372922 CTTTTGTTTC
* *
1372932 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
1372963 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
1372992 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
1373015 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:1373014 original size:18 final size:18
Alignment explanation
Indices: 1372965--1373020 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
1372955 CACTCTCAAA
* *
1372965 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
1372982 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
1373000 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
1373019 TT
1 TT
1373021 CAAAGATTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:1373021 original size:12 final size:12
Alignment explanation
Indices: 1372990--1373014 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1372980 TTTTTCAATC
1372990 TCATTTTCTTTT
1 TCATTTTCTTTT
1373002 TCATTTTCTTTT
1 TCATTTTCTTTT
1373014 T
1 T
1373015 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:1373134 original size:15 final size:14
Alignment explanation
Indices: 1373094--1373139 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
1373084 CTCTTGCCTC
*
1373094 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
1373109 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
1373124 TCTTTTGCTTTTTCT
1 TCTTTT-CTTTTTCT
1373139 T
1 T
1373140 TTCTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 10 0.36
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:1373138 original size:12 final size:11
Alignment explanation
Indices: 1373094--1373147 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 11
1373084 CTCTTGCCTC
1373094 TCTTTTCTTTT
1 TCTTTTCTTTT
* *
1373105 T-ATTTCGTTT
1 TCTTTTCTTTT
*
1373115 TC-TTT-TTCT
1 TCTTTTCTTTT
1373124 TCTTTTGCTTTT
1 TCTTTT-CTTTT
1373136 TCTTTTCTTTT
1 TCTTTTCTTTT
1373147 T
1 T
1373148 TTGTTTTCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
9 4 0.12
10 14 0.41
11 7 0.21
12 9 0.26
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.78
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:1373141 original size:20 final size:19
Alignment explanation
Indices: 1373112--1373160 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
1373102 TTTTATTTCG
1373112 TTTTCTTTTTCTTCTTTTGCT
1 TTTTC-TTTTCTTCTTTTG-T
*
1373133 TTTTCTTTTCTTTTTTTGT
1 TTTTCTTTTCTTCTTTTGT
1373152 TTTCTCTTT
1 TTT-TCTTT
1373161 ACAAGAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 17 0.65
21 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTCTTCTTTTGT
Found at i:1374084 original size:11 final size:11
Alignment explanation
Indices: 1374070--1374123 Score: 81
Period size: 12 Copynumber: 4.7 Consensus size: 11
1374060 CTCTTTTCTT
1374070 TTTTTTTTTGA
1 TTTTTTTTTGA
1374081 TTTTTTTTTCGA
1 TTTTTTTTT-GA
*
1374093 ATTTTTTTTGAA
1 TTTTTTTTTG-A
1374105 TTTTTTTTTGA
1 TTTTTTTTTGA
1374116 TTTTTTTT
1 TTTTTTTT
1374124 AACTTGTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
11 19 0.49
12 20 0.51
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:1375855 original size:30 final size:30
Alignment explanation
Indices: 1375769--1375866 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 30
1375759 TTAAACTAAA
* * *
1375769 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
* * * * * *
1375799 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
* * *
1375829 CTGAGCTAAGGTTTAGCTCATGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
1375859 ATGAGCTA
1 ATGAGCTA
1375867 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCATGAGCTGAAG
Found at i:1378418 original size:48 final size:50
Alignment explanation
Indices: 1378366--1378472 Score: 121
Period size: 51 Copynumber: 2.2 Consensus size: 50
1378356 AATAGTATTG
* * *
1378366 AGTATTAAAAGTATATATAT-GAT-ATAGACAAAAATATATGCATAATGT
1 AGTATTAAAAGTATATACATGGATAATAGAAAAAAATATATGAATAATGT
* * *
1378414 AGTATTGAAAGTATTTACATGGGATAATATAAAAAAATATATGAATAATGT
1 AGTATTAAAAGTATATACAT-GGATAATAGAAAAAAATATATGAATAATGT
1378465 -GATATTAA
1 AG-TATTAA
1378473 TATACATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
48 17 0.35
50 4 0.08
51 27 0.56
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.34
Consensus pattern (50 bp):
AGTATTAAAAGTATATACATGGATAATAGAAAAAAATATATGAATAATGT
Found at i:1378488 original size:12 final size:11
Alignment explanation
Indices: 1378471--1378538 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
1378461 ATGTGATATT
1378471 AATATACATAAA
1 AATATA-ATAAA
1378483 AATATAATAAA
1 AATATAATAAA
*
1378494 AA-AAAATATAA
1 AATATAATA-AA
1378505 AATAT-ATATAA
1 AATATAATA-AA
* *
1378516 TATAGTATTAAA
1 AATA-TAATAAA
1378528 AATATATATAA
1 AATATA-ATAA
1378539 TACATACACA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
10 5 0.11
11 22 0.49
12 16 0.36
13 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (11 bp):
AATATAATAAA
Found at i:1378753 original size:18 final size:18
Alignment explanation
Indices: 1378705--1378746 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1378695 CATATAAGTG
*
1378705 TAATAATAGTAATTATAA
1 TAATAATACTAATTATAA
* *
1378723 TACTAATACTAATTCTAA
1 TAATAATACTAATTATAA
1378741 TAATAA
1 TAATAA
1378747 ATATAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (18 bp):
TAATAATACTAATTATAA
Found at i:1381589 original size:15 final size:14
Alignment explanation
Indices: 1381549--1381591 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1381539 ATTTGTTAAA
*
1381549 ATTTAATTATTTGT
1 ATTTAATTATTTTT
*
1381563 ATTTATTATATTTTT
1 ATTTAAT-TATTTTT
1381578 ATTTGAATTATTTT
1 ATTT-AATTATTTT
1381592 GAATATTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.25
15 16 0.67
16 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
ATTTAATTATTTTT
Found at i:1382304 original size:2 final size:2
Alignment explanation
Indices: 1382297--1382335 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1382287 TACTAAATTA
1382297 AT 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 AT A
1382336 ATTTAGATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1383384 original size:3 final size:3
Alignment explanation
Indices: 1383376--1383418 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
1383366 AGAATCAAAC
* * * *
1383376 CAT CAT CAT CAT CAC CAC CAC CAT CAT CAT CAC CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1383419 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (3 bp):
CAT
Found at i:1383400 original size:15 final size:15
Alignment explanation
Indices: 1383382--1383418 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1383372 AAACCATCAT
1383382 CATCATCACCACCAC
1 CATCATCACCACCAC
* *
1383397 CATCATCATCACCAT
1 CATCATCACCACCAC
1383412 CATCATC
1 CATCATC
1383419 CTCTCACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.46, G:0.00, T:0.22
Consensus pattern (15 bp):
CATCATCACCACCAC
Found at i:1383400 original size:18 final size:18
Alignment explanation
Indices: 1383374--1383410 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1383364 AAAGAATCAA
*
1383374 ACCATCATCATCATCACC
1 ACCACCATCATCATCACC
1383392 ACCACCATCATCATCACC
1 ACCACCATCATCATCACC
1383410 A
1 A
1383411 TCATCATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (18 bp):
ACCACCATCATCATCACC
Found at i:1383409 original size:12 final size:12
Alignment explanation
Indices: 1383376--1383418 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1383366 AGAATCAAAC
*
1383376 CATCATCATCAT
1 CATCATCACCAT
* *
1383388 CACCACCACCAT
1 CATCATCACCAT
1383400 CATCATCACCAT
1 CATCATCACCAT
1383412 CATCATC
1 CATCATC
1383419 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (12 bp):
CATCATCACCAT
Found at i:1384457 original size:20 final size:19
Alignment explanation
Indices: 1384432--1384469 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1384422 TACAAAATAA
*
1384432 TTCAAAATAATTTTTAAAAT
1 TTCAAAAT-ATTTATAAAAT
1384452 TTCAAAATATTTATAAAA
1 TTCAAAATATTTATAAAA
1384470 ACTCCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCAAAATATTTATAAAAT
Found at i:1384470 original size:20 final size:20
Alignment explanation
Indices: 1384432--1384470 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1384422 TACAAAATAA
*
1384432 TTCAAAATAATTTTTAAAAT
1 TTCAAAATAATTTTAAAAAT
1384452 TTCAAAAT-ATTTATAAAAA
1 TTCAAAATAATTT-TAAAAA
1384471 CTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTCAAAATAATTTTAAAAAT
Found at i:1387185 original size:3 final size:3
Alignment explanation
Indices: 1387172--1387263 Score: 66
Period size: 3 Copynumber: 31.3 Consensus size: 3
1387162 TAATGGTAAA
* *
1387172 AAT AA- AAT AAT AAT AAT -AT AAT AGT AAT AAT AAT GAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
1387217 AGT AAT AAAT CAT AAT GAT AAT AGT GAT GAT AAT -AT AAGT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
1387263 A
1 A
1387264 TAAGTAAATA
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
2 7 0.10
3 56 0.81
4 6 0.09
ACGTcount: A:0.59, C:0.01, G:0.09, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1387378 original size:3 final size:3
Alignment explanation
Indices: 1387370--1387473 Score: 115
Period size: 3 Copynumber: 35.3 Consensus size: 3
1387360 AGGTGGAAAA
* * * * *
1387370 AAT AAT AAT AAT AAT -AT ATT AAT AAG AAT AA- AAA AAT -AT ATT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1387415 AAT AAC CAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1387461 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
1387474 GCATAATAGT
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
2 6 0.07
3 76 0.90
4 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1387739 original size:18 final size:19
Alignment explanation
Indices: 1387703--1387752 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1387693 AACAATAAAA
1387703 ATACA-ATATTAAAAGATGT
1 ATACATATA-TAAAAGATGT
*
1387722 ATATATATATAAAA-ATGT
1 ATACATATATAAAAGATGT
1387740 ATACATAATATAA
1 ATACAT-ATATAA
1387753 TATTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.33
19 15 0.56
20 3 0.11
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (19 bp):
ATACATATATAAAAGATGT
Found at i:1387760 original size:24 final size:24
Alignment explanation
Indices: 1387722--1387880 Score: 93
Period size: 24 Copynumber: 6.8 Consensus size: 24
1387712 TAAAAGATGT
*
1387722 ATATATATATAAAAATGTATACATA
1 ATATA-ATATAAAAATATATACATA
* *
1387747 ATATAATATTAAAATATTTACATA
1 ATATAATATAAAAATATATACATA
* *
1387771 GTATAATAATAATAATA-ATA-ATA
1 ATATAAT-ATAAAAATATATACATA
* *
1387794 ATAATAATAATAATAATA-ACTA-TTA
1 AT-ATAAT-ATAAAAATATA-TACATA
*
1387819 ATAT--TATATAAATATATACAT-
1 ATATAATATAAAAATATATACATA
* *
1387840 ATATCCAT-TAAAGATATATACATA
1 ATAT-AATATAAAAATATATACATA
* *
1387864 AGAT-ATATAAATATATA
1 ATATAATATAAAAATATA
1387881 AATATTAATT
Statistics
Matches: 108, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
21 13 0.12
22 5 0.05
23 26 0.24
24 46 0.43
25 18 0.17
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
ATATAATATAAAAATATATACATA
Found at i:1387781 original size:3 final size:3
Alignment explanation
Indices: 1387773--1387812 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1387763 TTTACATAGT
1387773 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1387813 CTATTAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1387843 original size:21 final size:21
Alignment explanation
Indices: 1387819--1387885 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1387809 ATAACTATTA
1387819 ATATTATATAAATATATACAT
1 ATATTATATAAATATATACAT
*
1387840 ATATCCAT-TAAAGATATATACAT
1 ATAT-TATAT-AA-ATATATACAT
* *
1387863 A-AGATATATAAATATATAAAT
1 ATA-TTATATAAATATATACAT
1387884 AT
1 AT
1387886 TAATTGAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
21 15 0.42
22 9 0.25
23 12 0.33
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (21 bp):
ATATTATATAAATATATACAT
Found at i:1388367 original size:53 final size:53
Alignment explanation
Indices: 1388300--1388405 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
1388290 CGCGGATCCC
* * *
1388300 ATGCCTGTCGGGTCGGGTCGGCCCCCTCCACCCCAAAATGGCATCGTTTTATG
1 ATGCCTGCCAGGTCGGGTCGGCCCCCTCCACCCCAAAACGGCATCGTTTTATG
* *
1388353 ATGCCTGCCAGGTCGGGTCGGCCCCCTCTACCCCAAAACGGCGTCGTTTTATG
1 ATGCCTGCCAGGTCGGGTCGGCCCCCTCCACCCCAAAACGGCATCGTTTTATG
1388406 CTTTGGGGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (53 bp):
ATGCCTGCCAGGTCGGGTCGGCCCCCTCCACCCCAAAACGGCATCGTTTTATG
Found at i:1389396 original size:20 final size:22
Alignment explanation
Indices: 1389363--1389411 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
1389353 AAGAATAGTA
* *
1389363 TAATAATGATAATAT-GT-TAG
1 TAATAATAACAATATAGTATAG
1389383 TAATAATAACAATATAGTAATAG
1 TAATAATAACAATATAGT-ATAG
1389406 TAATAA
1 TAATAA
1389412 AAATAGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.54
21 2 0.08
23 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (22 bp):
TAATAATAACAATATAGTATAG
Found at i:1389570 original size:3 final size:3
Alignment explanation
Indices: 1389548--1389669 Score: 147
Period size: 3 Copynumber: 39.3 Consensus size: 3
1389538 TTAATGCTAA
* *
1389548 AAT AAT GAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1389596 AAT AAT AAT AAT AAT AAT AAT AAT AATT CAAT AATT CAAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T -AAT AA-T -AAT AAT AAT AAT
* *
1389645 AAT GAC AAT AAT AGA- AAT AAT AAT A
1 AAT AAT AAT AAT A-AT AAT AAT AAT A
1389670 GTGTTTGAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
2 1 0.01
3 93 0.90
4 5 0.05
5 4 0.04
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1400094 original size:15 final size:15
Alignment explanation
Indices: 1400074--1400104 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1400064 TTGCATGTGG
*
1400074 AAAATAATATATTAA
1 AAAATAATACATTAA
1400089 AAAATAATACATTAA
1 AAAATAATACATTAA
1400104 A
1 A
1400105 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATAATACATTAA
Found at i:1403823 original size:25 final size:23
Alignment explanation
Indices: 1403770--1403828 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1403760 AAAAAGTTTT
*
1403770 AAAATATTATTTATTTTACTTTCA
1 AAAATATTATTTATTTTAC-TTAA
1403794 AAAATATTATTTTATTTTTA-TTAA
1 AAAATATTA-TTTA-TTTTACTTAA
*
1403818 ATAA-ATTATTT
1 AAAATATTATTT
1403829 TCATCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 3 0.10
23 4 0.13
24 15 0.48
25 4 0.13
26 5 0.16
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
AAAATATTATTTATTTTACTTAA
Found at i:1405101 original size:37 final size:37
Alignment explanation
Indices: 1405051--1405123 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1405041 AATTGCCCCT
*
1405051 TTCTGTTAAAAA-TTACATTCATTTCTACTATTAAAAC
1 TTCTGTTAAAAATTTA-ATTCACTTCTACTATTAAAAC
1405088 TTCTGTTAAAAATTTAATTCACTTCTACTATTAAAA
1 TTCTGTTAAAAATTTAATTCACTTCTACTATTAAAA
1405124 ACTGCCATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 31 0.91
38 3 0.09
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (37 bp):
TTCTGTTAAAAATTTAATTCACTTCTACTATTAAAAC
Found at i:1414619 original size:2 final size:2
Alignment explanation
Indices: 1414612--1414642 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1414602 TTGAAATTTA
1414612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1414643 AACTTTTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1417724 original size:13 final size:13
Alignment explanation
Indices: 1417706--1417733 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1417696 AAATTCACTT
1417706 GATAGACAAGCAA
1 GATAGACAAGCAA
1417719 GATAGACAAGCAA
1 GATAGACAAGCAA
1417732 GA
1 GA
1417734 GGTGGAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.25, T:0.07
Consensus pattern (13 bp):
GATAGACAAGCAA
Found at i:1419866 original size:24 final size:25
Alignment explanation
Indices: 1419839--1419890 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
1419829 AATATTTTCA
*
1419839 AAAATTAAATAT-TTAATTAATAAT
1 AAAATTAAATATGATAATTAATAAT
1419863 AAAATTAAATATGATAATTAATAAT
1 AAAATTAAATATGATAATTAATAAT
1419888 AAA
1 AAA
1419891 TATAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
AAAATTAAATATGATAATTAATAAT
Found at i:1419872 original size:29 final size:29
Alignment explanation
Indices: 1419839--1419908 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1419829 AATATTTTCA
1419839 AAAATTAAATATTTAATTAAT-AATAAAAT
1 AAAATTAAATATTTAA-TAATAAATAAAAT
* * * *
1419868 TAAA-TATGATAATTAATAATAAATATAAT
1 AAAATTA-AATATTTAATAATAAATAAAAT
1419897 AAAATTAAATAT
1 AAAATTAAATAT
1419909 GTTTAAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
28 6 0.19
29 23 0.74
30 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAATTAAATATTTAATAATAAATAAAAT
Found at i:1419905 original size:15 final size:15
Alignment explanation
Indices: 1419858--1419908 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 15
1419848 TATTTAATTA
1419858 ATAATAAAATTAAAT
1 ATAATAAAATTAAAT
*
1419873 ATGATAATTAATAATAAAT
1 ATAATAA--AAT--TAAAT
1419892 ATAATAAAATTAAAT
1 ATAATAAAATTAAAT
1419907 AT
1 AT
1419909 GTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 13 0.43
17 6 0.20
19 11 0.37
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
ATAATAAAATTAAAT
Found at i:1423435 original size:40 final size:40
Alignment explanation
Indices: 1423390--1423470 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
1423380 AGAATGCTAA
1423390 TACTTCAAGCCATTATCTGTCTGTGTAGACACAAGTGATG
1 TACTTCAAGCCATTATCTGTCTGTGTAGACACAAGTGATG
1423430 TACTTCAAGCCATTATCTGTCTGTGTAGACACAAGTGATG
1 TACTTCAAGCCATTATCTGTCTGTGTAGACACAAGTGATG
1423470 T
1 T
1423471 CCTCCAACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (40 bp):
TACTTCAAGCCATTATCTGTCTGTGTAGACACAAGTGATG
Found at i:1427572 original size:20 final size:20
Alignment explanation
Indices: 1427476--1427585 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
1427466 CAGGAACACT
* *
1427476 GAAGTGCAGACAGGGGCA-C
1 GAAGTGCAAACAGAGGCACC
* *
1427495 AAATGTGCAAACAGGGGCACC
1 GAA-GTGCAAACAGAGGCACC
* * *
1427516 GTAGTGCGAACA-AGGAACCC
1 GAAGTGCAAACAGAGGCA-CC
* ** *
1427536 GAAGTGTATGCAAAGGCACC
1 GAAGTGCAAACAGAGGCACC
* *
1427556 GGAGTGCAAACAGAGGCAAC
1 GAAGTGCAAACAGAGGCACC
1427576 GAAGTGCAAA
1 GAAGTGCAAA
1427586 TCCCGTACAA
Statistics
Matches: 67, Mismatches: 20, Indels: 7
0.71 0.21 0.07
Matches are distributed among these distances:
19 5 0.07
20 56 0.84
21 6 0.09
ACGTcount: A:0.37, C:0.21, G:0.33, T:0.09
Consensus pattern (20 bp):
GAAGTGCAAACAGAGGCACC
Found at i:1427993 original size:13 final size:14
Alignment explanation
Indices: 1427969--1428006 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1427959 AGTTTCACTG
1427969 AAAATGACTTTC-GA
1 AAAATGA-TTTCTGA
*
1427983 AAAATGATTTCTGG
1 AAAATGATTTCTGA
1427997 AAAATGATTT
1 AAAATGATTT
1428007 ACTTTTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (14 bp):
AAAATGATTTCTGA
Found at i:1428489 original size:15 final size:15
Alignment explanation
Indices: 1428469--1428534 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
1428459 ACTACAAAAC
1428469 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
1428484 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
1428503 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
1428518 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
1428531 ATTT
1 ATTT
1428535 TCAATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:1428584 original size:16 final size:16
Alignment explanation
Indices: 1428553--1428589 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1428543 ATGTGAATAA
1428553 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
1428569 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
1428585 TATTA
1 TATTA
1428590 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:1428641 original size:22 final size:22
Alignment explanation
Indices: 1428597--1428656 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
1428587 TTAAAATAAA
* *
1428597 ATTAAAAT-ATTAAGTA-ATTT
1 ATTAAAATAATAAATTATATTT
1428617 ATTAAAATAATAAATTATATTT
1 ATTAAAATAATAAATTATATTT
* * *
1428639 ATTATATTAATAAGTTAT
1 ATTAAAATAATAAATTAT
1428657 TAGAAGACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 8 0.24
21 6 0.18
22 19 0.58
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
ATTAAAATAATAAATTATATTT
Found at i:1434993 original size:6 final size:6
Alignment explanation
Indices: 1434984--1435008 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1434974 AATTCTGCTC
1434984 CTTTTA CTTTTA CTTTTA CTTTTA C
1 CTTTTA CTTTTA CTTTTA CTTTTA C
1435009 ACACTGTGCC
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:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (6 bp):
CTTTTA
Found at i:1435426 original size:20 final size:20
Alignment explanation
Indices: 1435401--1435439 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1435391 GATCAACAAT
1435401 AATTAAAAATTTATAAAATA
1 AATTAAAAATTTATAAAATA
* *
1435421 AATTAAAATTTTATTAAAT
1 AATTAAAAATTTATAAAAT
1435440 TTGTTCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTAAAAATTTATAAAATA
Found at i:1436290 original size:2 final size:2
Alignment explanation
Indices: 1436283--1436313 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1436273 AAATGAGTTA
1436283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1436314 CACTAACTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1437362 original size:10 final size:10
Alignment explanation
Indices: 1437321--1437380 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
1437311 ATATTTAAAT
1437321 AATTTAATAA
1 AATTTAATAA
* *
1437331 TATTTTATAA
1 AATTTAATAA
** *
1437341 CTTTTTA-AA
1 AATTTAATAA
*
1437350 AATTTAATGA
1 AATTTAATAA
1437360 AATTTAATAA
1 AATTTAATAA
1437370 TAATTTAATAA
1 -AATTTAATAA
1437381 GGTTACATGT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
9 6 0.15
10 23 0.59
11 10 0.26
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (10 bp):
AATTTAATAA
Found at i:1437376 original size:29 final size:30
Alignment explanation
Indices: 1437312--1437377 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
1437302 GACTAAAAAA
*
1437312 TATTTAAATAATTTAATAATATTTTATAAC
1 TATTTAAATAATTTAATAATATTTAATAAC
*
1437342 TTTTTAAA-AATTTAATGAA-ATTTAATAA-
1 TATTTAAATAATTTAAT-AATATTTAATAAC
1437370 TAATTTAA
1 T-ATTTAA
1437378 TAAGGTTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 21 0.68
30 9 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TATTTAAATAATTTAATAATATTTAATAAC
Found at i:1438690 original size:3 final size:3
Alignment explanation
Indices: 1438682--1438734 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
1438672 TGAGAAGCCA
* *
1438682 AAG AAG AAG ATG AAG AAA AAG AAG AAG AAG AAG AAG AAG AA- AACG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G
1438727 AAG AAG AA
1 AAG AAG AA
1438735 AGTGGAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:1447497 original size:132 final size:132
Alignment explanation
Indices: 1447259--1447498 Score: 329
Period size: 132 Copynumber: 1.8 Consensus size: 132
1447249 TCTCGCTTTG
* * * * * *
1447259 GAAAACGTGAATGAAATTTCAAAGGGATATTCGATTATTTTGCACAAACGAGAAATTGCAACCCA
1 GAAAACATGAACGAAATTTCAAAGAGACATCCGATTATTTTGCACAAACAAGAAATTGCAACCCA
* * * *
1447324 GCACGATGGGGCACGATTCCCTGAATTGCCGAACGTCGAACATTTCCTTCGTTTTAAAATTTTTT
66 GCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTTAAAATTTTTT
1447389 TA
131 TA
***
1447391 GAAAACATGAACGAAA-TTCTAAAGAGACATCCGATTATTTTGGGTAAACAAGAAATTGCAACCC
1 GAAAACATGAACGAAATTTC-AAAGAGACATCCGATTATTTTGCACAAACAAGAAATTGCAACCC
* *
1447455 AGCACGATAGGGCACGATTCCCCGAATTGCTAAACATTGAACAT
65 AGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACAT
1447499 CGTCTCCGTT
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
131 3 0.03
132 89 0.97
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (132 bp):
GAAAACATGAACGAAATTTCAAAGAGACATCCGATTATTTTGCACAAACAAGAAATTGCAACCCA
GCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTTAAAATTTTTT
TA
Found at i:1447813 original size:3 final size:3
Alignment explanation
Indices: 1447800--1447867 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
1447790 ACAAACAATG
* *
1447800 ATA AAA ATA ATA ATA ATA ACA 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
1447848 ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
1447868 GCAATGATAG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1448508 original size:3 final size:3
Alignment explanation
Indices: 1448500--1448561 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
1448490 AAATATATAT
1448500 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1448548 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
1448562 GTAAAATCGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1448713 original size:18 final size:18
Alignment explanation
Indices: 1448690--1448731 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1448680 TATAAACAGA
*
1448690 AAATAAAATAAATAGAAC
1 AAATAAAATAAAAAGAAC
* *
1448708 AAATAAGATAAAAATAAC
1 AAATAAAATAAAAAGAAC
1448726 AAATAA
1 AAATAA
1448732 TATTGATGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.17
Consensus pattern (18 bp):
AAATAAAATAAAAAGAAC
Found at i:1449538 original size:28 final size:27
Alignment explanation
Indices: 1449471--1449543 Score: 121
Period size: 26 Copynumber: 2.7 Consensus size: 27
1449461 CCAAAAAAAA
1449471 AACTTTCCTTTTTTTTATTCCATTACC
1 AACTTTCCTTTTTTTTATTCCATTACC
*
1449498 AACTTTCC-CTTTTTTATTCCATTACC
1 AACTTTCCTTTTTTTTATTCCATTACC
1449524 AACTTTCTCTTTTTTTTATT
1 AACTTTC-CTTTTTTTTATT
1449544 TTTTTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
26 24 0.57
27 9 0.21
28 9 0.21
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.58
Consensus pattern (27 bp):
AACTTTCCTTTTTTTTATTCCATTACC
Found at i:1453969 original size:7 final size:7
Alignment explanation
Indices: 1453957--1453987 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1453947 TGTTAAAAGA
1453957 TATTTTG
1 TATTTTG
1453964 TATTTTG
1 TATTTTG
1453971 TATTTTG
1 TATTTTG
1453978 TATTTT-
1 TATTTTG
1453984 TATT
1 TATT
1453988 AAAAAAATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (7 bp):
TATTTTG
Found at i:1459488 original size:38 final size:38
Alignment explanation
Indices: 1459434--1459598 Score: 172
Period size: 38 Copynumber: 4.3 Consensus size: 38
1459424 GCAGGCTATA
*
1459434 TGCTGGAATTATATCCGGGTTAAATCCTGCAAGCTTCG
1 TGCTGGTATTATATCCGGGTTAAATCCTGCAAGCTTCG
* *
1459472 TGCTAGTAATATATCCGGGTT-AAT-CTCGCAAGCTTCG
1 TGCTGGTATTATATCCGGGTTAAATCCT-GCAAGCTTCG
* * * * *
1459509 TGCTGGTATTATATCCGGTTTAAATCCCGCAGGCCTAG
1 TGCTGGTATTATATCCGGGTTAAATCCTGCAAGCTTCG
* * * *
1459547 TGCTGGTATTATATCTGAGTTTAAAGTCCTGTAGGCTTCG
1 TGCTGGTATTATATCCG-GGTTAAA-TCCTGCAAGCTTCG
*
1459587 TGCTGGTGTTAT
1 TGCTGGTATTAT
1459599 GTTTGGGTTT
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
36 2 0.02
37 31 0.29
38 44 0.42
39 8 0.08
40 21 0.20
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (38 bp):
TGCTGGTATTATATCCGGGTTAAATCCTGCAAGCTTCG
Found at i:1459512 original size:37 final size:37
Alignment explanation
Indices: 1459443--1459531 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
1459433 ATGCTGGAAT
1459443 TATATCCGGGTTAAATCCTGCAAGCTTCGTGCTAGTAA
1 TATATCCGGGTT-AATCCTGCAAGCTTCGTGCTAGTAA
* *
1459481 TATATCCGGGTTAAT-CTCGCAAGCTTCGTGCTGGTAT
1 TATATCCGGGTTAATCCT-GCAAGCTTCGTGCTAGTAA
*
1459518 TATATCCGGTTTAA
1 TATATCCGGGTTAA
1459532 ATCCCGCAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
36 2 0.04
37 33 0.70
38 12 0.26
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (37 bp):
TATATCCGGGTTAATCCTGCAAGCTTCGTGCTAGTAA
Found at i:1471559 original size:33 final size:29
Alignment explanation
Indices: 1471522--1471586 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
1471512 TATTATATAA
*
1471522 TTATATTAAAATTTTAAAATTAATAATAAATAT
1 TTATA-TAAAATTAT-AAATTAA-AATAAAT-T
*
1471555 TTATATGAAATTATAAATTAAAATAAATT
1 TTATATAAAATTATAAATTAAAATAAATT
1471584 TTA
1 TTA
1471587 AAACATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.13
30 7 0.23
31 7 0.23
32 7 0.23
33 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATATAAAATTATAAATTAAAATAAATT
Found at i:1472721 original size:16 final size:14
Alignment explanation
Indices: 1472690--1472728 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1472680 TTATTTATTA
1472690 AATTAATTTTAATT
1 AATTAATTTTAATT
1472704 AATTAAATTTTCAATT
1 AATT-AATTTT-AATT
*
1472720 AAATAATTT
1 AATTAATTT
1472729 CTTAACCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 11 0.50
16 7 0.32
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTAATTTTAATT
Found at i:1474913 original size:18 final size:17
Alignment explanation
Indices: 1474892--1474930 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1474882 TAATAATTTG
1474892 ATTTAAAATTTTAATAAA
1 ATTT-AAATTTTAATAAA
* *
1474910 ATTTAGATTTTAATATA
1 ATTTAAATTTTAATAAA
1474927 ATTT
1 ATTT
1474931 TTTTAGCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTTAATAAA
Found at i:1478877 original size:49 final size:49
Alignment explanation
Indices: 1478800--1478902 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 49
1478790 TCCTACAGGC
* *
1478800 AAAGTTGGGAAGCTTACCCTCATTTACTTGGAAGAGCATTTGGGCAGTG
1 AAAGGTGGGAAGCTTACCCTCATTTACTTGGAAGAGCATTTGGGCAGCG
1478849 AAAGGTGGGAAGCTTACCCTCATTTACTTGGAAGAGCATTTGGGCAGCG
1 AAAGGTGGGAAGCTTACCCTCATTTACTTGGAAGAGCATTTGGGCAGCG
1478898 AAAGG
1 AAAGG
1478903 ACTTCCTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (49 bp):
AAAGGTGGGAAGCTTACCCTCATTTACTTGGAAGAGCATTTGGGCAGCG
Found at i:1483205 original size:38 final size:38
Alignment explanation
Indices: 1483163--1483238 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1483153 ATTTGATTTA
1483163 ATATATTTTCTAAACCTATTAAAAAGGTTTTAATTTTT
1 ATATATTTTCTAAACCTATTAAAAAGGTTTTAATTTTT
1483201 ATATATTTTCTAAACCTATTAAAAAGGTTTTAATTTTT
1 ATATATTTTCTAAACCTATTAAAAAGGTTTTAATTTTT
1483239 TTTTACTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (38 bp):
ATATATTTTCTAAACCTATTAAAAAGGTTTTAATTTTT
Found at i:1485377 original size:21 final size:24
Alignment explanation
Indices: 1485333--1485384 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
1485323 TATGTACATA
*
1485333 ACATATACTTAGTAATAATGTTGG
1 ACATATACTTAGTAATAATATTGG
1485357 ACATATAC-TA-T-ATAATATTGG
1 ACATATACTTAGTAATAATATTGG
*
1485378 AAATATA
1 ACATATA
1485385 TACACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.58
22 1 0.04
23 2 0.08
24 8 0.31
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (24 bp):
ACATATACTTAGTAATAATATTGG
Found at i:1485684 original size:24 final size:24
Alignment explanation
Indices: 1485634--1485685 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1485624 AAATATTTAC
**
1485634 ATAATATATACATATAAAATACTA
1 ATAATATATACATATAAAATAAAA
* **
1485658 ATAATATATATATATCTAATAAAA
1 ATAATATATACATATAAAATAAAA
1485682 ATAA
1 ATAA
1485686 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAATATATACATATAAAATAAAA
Found at i:1485745 original size:2 final size:2
Alignment explanation
Indices: 1485738--1485763 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1485728 AACCTAAATG
1485738 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
1485764 TAGAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1487572 original size:12 final size:12
Alignment explanation
Indices: 1487555--1487593 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1487545 ACTAACAATC
1487555 ATTTATTAATAT
1 ATTTATTAATAT
1487567 ATTTATATAAATAT
1 ATTTAT-T-AATAT
*
1487581 ATTTTTTAATAT
1 ATTTATTAATAT
1487593 A
1 A
1487594 AAATATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.50
13 2 0.08
14 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATTAATAT
Found at i:1489879 original size:40 final size:39
Alignment explanation
Indices: 1489714--1489897 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
1489704 AAATTGAATG
* * *
1489714 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
1489754 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
1489794 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
1489834 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
1489873 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
1489898 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:1489922 original size:80 final size:81
Alignment explanation
Indices: 1489754--1489942 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
1489744 GCTGGAAATT
* * * *
1489754 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
1489819 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
1489835 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
1489898 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
1489914 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
1489943 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:1497987 original size:40 final size:39
Alignment explanation
Indices: 1497823--1498005 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
1497813 AAATTGAATG
* *
1497823 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
1497862 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
1497902 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
1497942 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
1497981 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
1498006 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 15 0.13
40 92 0.81
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:1498030 original size:80 final size:81
Alignment explanation
Indices: 1497862--1498050 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
1497852 GCTGGAAATT
* * * *
1497862 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
1497927 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
1497943 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
1498006 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
1498022 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
1498051 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:1501120 original size:429 final size:429
Alignment explanation
Indices: 1500318--1501180 Score: 1414
Period size: 429 Copynumber: 2.0 Consensus size: 429
1500308 GTGACAGCCC
*
1500318 AAAATTGACCCTAGTCGGAAGGTGGTCTCGGGACCACAAAACCGAGGCATAAAAATAATTTAAAA
1 AAAATTGACCCTAGTCGGAAGGTGGTCTCGGGACCACAAAACCGAGGCATAAAAATAATTAAAAA
*
1500383 TTTATTTCGATGCCTATAATATGTGTATTCATGTATGACATTTTTTGATGATTGATTTAGTGTTA
66 TTTATTTCGATGCCTATAATATGTGTATTCATGTATGACATTTTATGATGATTGATTTAGTGTTA
* * * *
1500448 TAAAGGTGAATTTCACTAGAAAGGACCTAGTAGTGAACTTTGAAAGTATGATGGGGAAATGTGTG
131 TAAAGGTGAATTCCACAAGAAAGGACCTAGTAATGAACTTTGAAAGTATGATAGGGAAATGTGTG
1500513 ATGACTAATTAAAGCATGCATGCAAAATAATGGACTTGCATGTCAAATTCCCCTTTGTACAAGTG
196 ATGACTAATTAAAGCATGCATGCAAAATAATGGACTTGCATGTCAAATTCCCCTTTGTACAAGTG
*
1500578 ATGGCCGGCCATGACAAAGAGATATGGGCTAAACATGTCATGAAACATGTTTTGTTGGGCATTAG
261 ATGGCCGGCCATGACAAAGAGAGATGGGCTAAACATGTCATGAAACATGTTTTGTTGGGCATTAG
* *
1500643 GGAGAAATAATAAACAAATAAGCATGGGTAAGAAAAGAATGAAAAAAAAATGTGTGTGAGTGTGG
326 GGAGAAATAATAAACAAAGAAGCATGGGTAAGAAAAAAATGAAAAAAAAATGTGTGTGAGTGTGG
1500708 TAAT-CCCCCCC-TTGCCGTGAGTTG-AGAAAGAAGG-AAG
391 TAATCCCCCCCCATTGCCGTGAGTTGTAG--AGAAGGAAAG
1500745 AAAATTGACCCTAGTCGGAAGGTGGTCTCGGGACCACAAAACCGAGGCATAAAAATAATTAAAAA
1 AAAATTGACCCTAGTCGGAAGGTGGTCTCGGGACCACAAAACCGAGGCATAAAAATAATTAAAAA
* *
1500810 TTTATTTTGATGCCTATAATATGTGTGTGCTCATGTATGACATTTTATGATGATTGATTTAGTGT
66 TTTATTTCGATGCCTATAATATGTGTAT--TCATGTATGACATTTTATGATGATTGATTTAGTGT
* *
1500875 TATAAGGGTGAATTCCACAAGAAAGGACTTAGTAATGAACTTTGAAAGTATGATAGGGAAATGTG
129 TATAAAGGTGAATTCCACAAGAAAGGACCTAGTAATGAACTTTGAAAGTATGATAGGGAAATGTG
* *
1500940 TGATGACTAATTAAAGCATGCATGCAAAATAATGGACTTGCATGTCAAATTCCCCCTTT-TATAG
194 TGATGACTAATTAAAGCATGCATGCAAAATAATGGACTTGCATGTCAAATT-CCCCTTTGTACAA
* *
1501004 GTGGTGGCCGGCCATGAC-AAGGGAGGATGGGCTAAACATGTCATGAAACATGTTTTGTTGGTGC
258 GTGATGGCCGGCCATGACAAAGAGA-GATGGGCTAAACATGTCATGAAACATGTTTTGTTGG-GC
* ** * * *
1501068 ATTAGGGTGAAATAATAAACAAAGGTGTATGGGTGATAAAAAAATGAAAAAAAAATGTGTGTGAG
321 ATTAGGGAGAAATAATAAACAAAGAAGCATGGGTAAGAAAAAAATGAAAAAAAAATGTGTGTGAG
1501133 TGTGGTAATCCCCCCCCATTGCCGTGAGTTGTAGAGAAGGAAAG
386 TGTGGTAATCCCCCCCCATTGCCGTGAGTTGTAGAGAAGGAAAG
1501177 AAAA
1 AAAA
1501181 AAATTTTGTT
Statistics
Matches: 404, Mismatches: 23, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
427 90 0.22
428 5 0.01
429 199 0.49
430 75 0.19
431 13 0.03
432 20 0.05
433 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (429 bp):
AAAATTGACCCTAGTCGGAAGGTGGTCTCGGGACCACAAAACCGAGGCATAAAAATAATTAAAAA
TTTATTTCGATGCCTATAATATGTGTATTCATGTATGACATTTTATGATGATTGATTTAGTGTTA
TAAAGGTGAATTCCACAAGAAAGGACCTAGTAATGAACTTTGAAAGTATGATAGGGAAATGTGTG
ATGACTAATTAAAGCATGCATGCAAAATAATGGACTTGCATGTCAAATTCCCCTTTGTACAAGTG
ATGGCCGGCCATGACAAAGAGAGATGGGCTAAACATGTCATGAAACATGTTTTGTTGGGCATTAG
GGAGAAATAATAAACAAAGAAGCATGGGTAAGAAAAAAATGAAAAAAAAATGTGTGTGAGTGTGG
TAATCCCCCCCCATTGCCGTGAGTTGTAGAGAAGGAAAG
Found at i:1502572 original size:40 final size:39
Alignment explanation
Indices: 1502407--1502590 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
1502397 AAATTGAATG
* * *
1502407 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
1502447 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
1502487 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
1502527 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
1502566 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
1502591 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:1502615 original size:80 final size:81
Alignment explanation
Indices: 1502447--1502635 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
1502437 GCTGGAAATT
* * * *
1502447 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
1502512 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
1502528 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
1502591 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
1502607 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
1502636 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:1510686 original size:40 final size:39
Alignment explanation
Indices: 1510521--1510704 Score: 131
Period size: 40 Copynumber: 4.6 Consensus size: 39
1510511 AAATTGAATG
* * *
1510521 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * *
1510561 ATAAT-CGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 AT-ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
1510601 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
1510641 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
1510680 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
1510705 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 24, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 5 0.04
40 100 0.88
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:1510687 original size:80 final size:80
Alignment explanation
Indices: 1510566--1510713 Score: 181
Period size: 80 Copynumber: 1.9 Consensus size: 80
1510556 AAATTATAAT
* * * *
1510566 CGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCATTCGT
1 CGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCGT
1510631 GCGAGTCATTCTATC
66 GCGAGTCATTCTATC
* * * * * * *
1510646 CGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGCCTTGG
1 CGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGCATTCG
1510710 TGCG
65 TGCG
1510714 GGTTACCATA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 55 0.98
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.23
Consensus pattern (80 bp):
CGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCGT
GCGAGTCATTCTATC
Found at i:1523135 original size:27 final size:27
Alignment explanation
Indices: 1523094--1523147 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1523084 TTGCTGTTAG
* *
1523094 CCCAATACCCAGAGGGTCGTGGGCAAT
1 CCCAATACCCAGAGGGTCATGGACAAT
*
1523121 CCCAATACCCTGAGGGTCATGGACAAT
1 CCCAATACCCAGAGGGTCATGGACAAT
1523148 TATTTTACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.17
Consensus pattern (27 bp):
CCCAATACCCAGAGGGTCATGGACAAT
Found at i:1531154 original size:28 final size:28
Alignment explanation
Indices: 1531089--1531189 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
1531079 ATAGTGAATC
*
1531089 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
1531118 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
1531146 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
1531176 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1531190 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:1534702 original size:27 final size:27
Alignment explanation
Indices: 1534664--1534719 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1534654 TATATACTGC
1534664 TTCGACTCTTCATTTTTCTTTTTCTTT
1 TTCGACTCTTCATTTTTCTTTTTCTTT
1534691 TTCGACTCTTCATTTTTCTTTTTCTTT
1 TTCGACTCTTCATTTTTCTTTTTCTTT
1534718 TT
1 TT
1534720 AACATTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.07, C:0.21, G:0.04, T:0.68
Consensus pattern (27 bp):
TTCGACTCTTCATTTTTCTTTTTCTTT
Found at i:1534708 original size:15 final size:15
Alignment explanation
Indices: 1534664--1534708 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1534654 TATATACTGC
1534664 TTCGACTCTTCATTT
1 TTCGACTCTTCATTT
* *
1534679 TTC--TTTTTC-TTT
1 TTCGACTCTTCATTT
1534691 TTCGACTCTTCATTT
1 TTCGACTCTTCATTT
1534706 TTC
1 TTC
1534709 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
12 6 0.26
13 4 0.17
14 4 0.17
15 9 0.39
ACGTcount: A:0.09, C:0.24, G:0.04, T:0.62
Consensus pattern (15 bp):
TTCGACTCTTCATTT
Found at i:1548255 original size:2 final size:2
Alignment explanation
Indices: 1548248--1548280 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1548238 ATAGTCTTTC
1548248 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 A
1548281 ACACATGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1548854 original size:7 final size:7
Alignment explanation
Indices: 1548842--1548874 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1548832 CTTGTTTTTA
1548842 TTTCTTT
1 TTTCTTT
1548849 TTTCTTT
1 TTTCTTT
1548856 TTTCTTT
1 TTTCTTT
1548863 TTTCTTT
1 TTTCTTT
1548870 TTTCT
1 TTTCT
1548875 AATAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTCTTT
Found at i:1549363 original size:24 final size:24
Alignment explanation
Indices: 1549331--1549377 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1549321 CGATTGTATC
1549331 TCGAGTCAACTTTGAGCTTAAAAT
1 TCGAGTCAACTTTGAGCTTAAAAT
1549355 TCGAGTCAACTTTGAGCTTAAAA
1 TCGAGTCAACTTTGAGCTTAAAA
1549378 ATTGATGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (24 bp):
TCGAGTCAACTTTGAGCTTAAAAT
Found at i:1553394 original size:23 final size:23
Alignment explanation
Indices: 1553368--1553412 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1553358 TATATACTAA
*
1553368 ATATATATTTTTTATTTTTAATC
1 ATATATATATTTTATTTTTAATC
*
1553391 ATATTTATATTTTATTTTTAAT
1 ATATATATATTTTATTTTTAAT
1553413 TTTAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATATATATTTTATTTTTAATC
Found at i:1553529 original size:20 final size:19
Alignment explanation
Indices: 1553487--1553530 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1553477 ACTTTTTATT
*
1553487 TATTTTTTGTTTTAATATT
1 TATTTTTTGTTTTAATATG
1553506 TATTTTTATGTTTTTAA-ATG
1 TATTTTT-TG-TTTTAATATG
1553526 TATTT
1 TATTT
1553531 GATTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 9 0.41
21 6 0.27
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (19 bp):
TATTTTTTGTTTTAATATG
Found at i:1553535 original size:25 final size:24
Alignment explanation
Indices: 1553502--1553559 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
1553492 TTTGTTTTAA
*
1553502 TATTTATTT-TTATGTTTTTAAATG
1 TATTTATTTATTAT-ATTTTAAATG
1553526 TATTTGATTTATTATATTTTAAAT-
1 TATTT-ATTTATTATATTTTAAATG
*
1553550 TTTTTATTTA
1 TATTTATTTA
1553560 ATGAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 5 0.17
24 9 0.30
25 12 0.40
26 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (24 bp):
TATTTATTTATTATATTTTAAATG
Found at i:1557776 original size:18 final size:17
Alignment explanation
Indices: 1557755--1557791 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1557745 AATTTCATTT
1557755 ATTTTAAATATTTTATAA
1 ATTTTAAATATTTT-TAA
*
1557773 ATTTTTAATATTTTTAA
1 ATTTTAAATATTTTTAA
1557790 AT
1 AT
1557792 ATATAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTAAATATTTTTAA
Found at i:1559339 original size:2 final size:2
Alignment explanation
Indices: 1559328--1559362 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1559318 CCACCAAAGT
1559328 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1559363 AATACTGCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1560360 original size:59 final size:58
Alignment explanation
Indices: 1560227--1560363 Score: 132
Period size: 59 Copynumber: 2.3 Consensus size: 58
1560217 CTTGGTAAAA
* * * *
1560227 ATTCTCATATTAAGGTC-TAAATTTTTTTTACCCAAGTTAATCTCTAAACTTAATAATT
1 ATTCTCACA-TAAGGGCTTAAATTTTATTTACCCAAGTTAATCCCTAAACTTAATAATT
* *** * *
1560285 ATTTTTGTATAAGGGCTTAAACTTTTATTTATCCAAGTTAATCCCTAAACTTGATAATT
1 ATTCTCACATAAGGGCTTAAA-TTTTATTTACCCAAGTTAATCCCTAAACTTAATAATT
* **
1560344 GTTCTCACATTGGGGCTTAA
1 ATTCTCACATAAGGGCTTAA
1560364 GCTTAATAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
57 6 0.10
58 10 0.16
59 46 0.74
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.43
Consensus pattern (58 bp):
ATTCTCACATAAGGGCTTAAATTTTATTTACCCAAGTTAATCCCTAAACTTAATAATT
Found at i:1564339 original size:21 final size:20
Alignment explanation
Indices: 1564315--1564361 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1564305 TCATTTTTAT
1564315 ACTTAAATTATAGCTTAATTA
1 ACTTAAATTA-AGCTTAATTA
* * *
1564336 ACTTTAATTAATCTTAATTT
1 ACTTAAATTAAGCTTAATTA
1564356 ACTTAA
1 ACTTAA
1564362 TAAATTTACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (20 bp):
ACTTAAATTAAGCTTAATTA
Found at i:1572134 original size:22 final size:22
Alignment explanation
Indices: 1572106--1572156 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1572096 AGCACACGGT
1572106 CGTGTGGTGGCTCGAGTGAGGC
1 CGTGTGGTGGCTCGAGTGAGGC
*
1572128 CGTGTGGTGGCTCGATTGAGGC
1 CGTGTGGTGGCTCGAGTGAGGC
1572150 CGTGTGG
1 CGTGTGG
1572157 GCTACACGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.18, G:0.49, T:0.25
Consensus pattern (22 bp):
CGTGTGGTGGCTCGAGTGAGGC
Found at i:1573788 original size:14 final size:14
Alignment explanation
Indices: 1573765--1573803 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1573755 GTTAAGTTTG
1573765 TTTTAAAAAATAAT
1 TTTTAAAAAATAAT
* *
1573779 TTTTAGAAAATAAG
1 TTTTAAAAAATAAT
*
1573793 TTTAAAAAAAT
1 TTTTAAAAAAT
1573804 TTGCCAATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (14 bp):
TTTTAAAAAATAAT
Found at i:1573862 original size:26 final size:26
Alignment explanation
Indices: 1573832--1573885 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1573822 ACCAGAAAAT
1573832 TTCATATTTTTTAGAAAATCAATTTA
1 TTCATATTTTTTAGAAAATCAATTTA
1573858 TTCATATTTTTTAGAAAATCAATTTA
1 TTCATATTTTTTAGAAAATCAATTTA
1573884 TT
1 TT
1573886 TTCCAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (26 bp):
TTCATATTTTTTAGAAAATCAATTTA
Found at i:1575687 original size:9 final size:10
Alignment explanation
Indices: 1575659--1575720 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 10
1575649 ATTCATTCTG
*
1575659 AAATTATAAA
1 AAATTATTAA
1575669 AAATTATTAA
1 AAATTATTAA
1575679 AAATT-TT--
1 AAATTATTAA
**
1575686 AAATTAGAAA
1 AAATTATTAA
1575696 AAATTA-TAA
1 AAATTATTAA
1575705 AAA-TATTAA
1 AAATTATTAA
*
1575714 AAGTTAT
1 AAATTAT
1575721 AAATGAGATA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
7 5 0.12
8 2 0.05
9 12 0.29
10 23 0.55
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (10 bp):
AAATTATTAA
Found at i:1575691 original size:17 final size:18
Alignment explanation
Indices: 1575668--1575723 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
1575658 GAAATTATAA
1575668 AAAATTATTAAAAATT-T
1 AAAATTATTAAAAATTAT
* **
1575685 TAAATTAGAAAAAATTAT
1 AAAATTATTAAAAATTAT
* *
1575703 AAAAATATTAAAAGTTAT
1 AAAATTATTAAAAATTAT
1575721 AAA
1 AAA
1575724 TGAGATAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (18 bp):
AAAATTATTAAAAATTAT
Found at i:1575691 original size:27 final size:27
Alignment explanation
Indices: 1575659--1575723 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1575649 ATTCATTCTG
*
1575659 AAATTATAAAAAATTATTAAAAAT-TTT
1 AAATTATAAAAAATTA-TAAAAATATTA
*
1575686 AAATTAGAAAAAATTATAAAAATATTA
1 AAATTATAAAAAATTATAAAAATATTA
1575713 AAAGTTATAAA
1 AAA-TTATAAA
1575724 TGAGATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.21
27 20 0.61
28 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (27 bp):
AAATTATAAAAAATTATAAAAATATTA
Found at i:1575961 original size:26 final size:26
Alignment explanation
Indices: 1575932--1576014 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
1575922 AAATCTATGT
*
1575932 TTTTATAGATATTTTATAATTATTTA
1 TTTTATAAATATTTTATAATTATTTA
* * *
1575958 TTTTTTATAAT-TTTAATATTTATTGTAA
1 TTTTATA-AATATTTTATAATTATT-T-A
*
1575986 TTTT-TAAATATTTT-TAATGATTT-
1 TTTTATAAATATTTTATAATTATTTA
1576009 TTTTAT
1 TTTTAT
1576015 TTTTTATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
23 4 0.09
24 1 0.02
25 1 0.02
26 26 0.58
27 8 0.18
28 5 0.11
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTATAAATATTTTATAATTATTTA
Found at i:1576018 original size:29 final size:28
Alignment explanation
Indices: 1575942--1576026 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
1575932 TTTTATAGAT
*
1575942 ATTTT-ATAATTA-TTTATTTTTT-ATA
1 ATTTTAATATTTATTTTATTTTTTAATA
* *
1575967 ATTTTAATATTTATTGTAATTTTTAAATA
1 ATTTTAATATTTATT-TTATTTTTTAATA
*
1575996 TTTTTAATGATTT-TTTTATTTTTT-ATA
1 ATTTTAAT-ATTTATTTTATTTTTTAATA
1576023 ATTT
1 ATTT
1576027 CAAAATGAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
25 5 0.10
26 6 0.12
27 7 0.15
28 14 0.29
29 12 0.25
30 4 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (28 bp):
ATTTTAATATTTATTTTATTTTTTAATA
Found at i:1576026 original size:18 final size:18
Alignment explanation
Indices: 1575943--1576026 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 18
1575933 TTTATAGATA
*
1575943 TTTTATAATTATT-TATT
1 TTTTATAATTTTTATATT
*
1575960 TTTTATAATTTTAATATT
1 TTTTATAATTTTTATATT
* *
1575978 TATTGTAATTTTTAAATATT
1 TTTTATAATTTTT--ATATT
* * *
1575998 TTTAATGATTTTTTTATT
1 TTTTATAATTTTTATATT
1576016 TTTTATAATTT
1 TTTTATAATTT
1576027 CAAAATGAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
17 11 0.21
18 27 0.52
20 14 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTATAATTTTTATATT
Found at i:1577988 original size:13 final size:13
Alignment explanation
Indices: 1577970--1578008 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1577960 AGTTGAATTC
*
1577970 TTAAAAATATTAA
1 TTAAAAATAATAA
1577983 TTAAAAATAATAA
1 TTAAAAATAATAA
*
1577996 -TAATAATAATAA
1 TTAAAAATAATAA
1578008 T
1 T
1578009 AAGAGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAATAATAA
Found at i:1578569 original size:22 final size:22
Alignment explanation
Indices: 1578528--1578586 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
1578518 GTTTTAAGAA
* *
1578528 TTGTTTTAGTA-TCATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
1578549 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
1578571 AT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
1578587 GATTTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.48
22 10 0.30
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:1578584 original size:24 final size:24
Alignment explanation
Indices: 1578557--1578615 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
1578547 ATTTGTTTTA
1578557 ATATTTATTT-TTATATTTTTAAAT
1 ATATTTATTTATTATA-TTTTAAAT
1578581 ATATTTGATTTATTATATTTTAAAT
1 ATATTT-ATTTATTATATTTTAAAT
*
1578606 -TTTTTATTTA
1 ATATTTATTTA
1578616 ATGAAATAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.16
24 10 0.31
25 12 0.38
26 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
ATATTTATTTATTATATTTTAAAT
Found at i:1578874 original size:25 final size:25
Alignment explanation
Indices: 1578845--1578894 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1578835 TACTCAACCA
1578845 AAACTTTATTTAATTTTATTATTTT
1 AAACTTTATTTAATTTTATTATTTT
1578870 AAACTTTATTTAATTTTATTATTTT
1 AAACTTTATTTAATTTTATTATTTT
1578895 CCGTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
AAACTTTATTTAATTTTATTATTTT
Found at i:1589097 original size:32 final size:30
Alignment explanation
Indices: 1589045--1589103 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
1589035 TAACCAAGTA
1589045 AATTAATTGATTTTTTAATTAAATAAATTT
1 AATTAATTGATTTTTTAATTAAATAAATTT
* *
1589075 AATTAGTTGAATTTTTTAAATTAATTAAA
1 AATTAATTG-ATTTTTT-AATTAAATAAA
1589104 GGAAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.32
31 7 0.28
32 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (30 bp):
AATTAATTGATTTTTTAATTAAATAAATTT
Found at i:1592247 original size:34 final size:34
Alignment explanation
Indices: 1592204--1592272 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1592194 TAGCACACGG
1592204 GCGTGTGGCTTGGCCATGTGGCACAAGTCAGTGA
1 GCGTGTGGCTTGGCCATGTGGCACAAGTCAGTGA
*
1592238 GCGTGTGGCTTGGCCGTGTGGCACAAGTCAGTGA
1 GCGTGTGGCTTGGCCATGTGGCACAAGTCAGTGA
1592272 G
1 G
1592273 TTACACGGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.16, C:0.20, G:0.41, T:0.23
Consensus pattern (34 bp):
GCGTGTGGCTTGGCCATGTGGCACAAGTCAGTGA
Found at i:1593314 original size:22 final size:23
Alignment explanation
Indices: 1593289--1593334 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1593279 ATTTAAATAT
*
1593289 AAAAAATAAA-TAAATATACTTA
1 AAAAAATAAAGAAAATATACTTA
*
1593311 AAAAAATAAAGAAAATATATTTA
1 AAAAAATAAAGAAAATATACTTA
1593334 A
1 A
1593335 TGCATTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
AAAAAATAAAGAAAATATACTTA
Found at i:1593448 original size:20 final size:19
Alignment explanation
Indices: 1593396--1593449 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1593386 AGTGAAAGAT
1593396 TTATAAATAAATACTAATAA
1 TTATAAATAAATA-TAATAA
* ** *
1593416 TTTTATTTCAATATAATTAA
1 TTATAAATAAATATAA-TAA
1593436 TTATAAATAAATAT
1 TTATAAATAAATAT
1593450 TAAAACTCCG
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TTATAAATAAATATAATAA
Found at i:1597066 original size:15 final size:15
Alignment explanation
Indices: 1597048--1597102 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1597038 AAAAAGTATA
*
1597048 TAATTTTAGTTTCAT
1 TAATTGTAGTTTCAT
*
1597063 TAATTGTA-TAT-A-
1 TAATTGTAGTTTCAT
*
1597075 TAATTTTAGTTTCAT
1 TAATTGTAGTTTCAT
1597090 TAATTGTAGTTTC
1 TAATTGTAGTTTC
1597103 TTATTCCACA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 7 0.22
13 3 0.09
14 3 0.09
15 19 0.59
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.56
Consensus pattern (15 bp):
TAATTGTAGTTTCAT
Found at i:1597081 original size:27 final size:27
Alignment explanation
Indices: 1597044--1597097 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1597034 AATTAAAAAG
1597044 TATATAATTTTAGTTTCATTAATTGTA
1 TATATAATTTTAGTTTCATTAATTGTA
1597071 TATATAATTTTAGTTTCATTAATTGTA
1 TATATAATTTTAGTTTCATTAATTGTA
1597098 GTTTCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (27 bp):
TATATAATTTTAGTTTCATTAATTGTA
Found at i:1597139 original size:26 final size:26
Alignment explanation
Indices: 1597089--1597140 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1597079 TTTAGTTTCA
*
1597089 TTAATTGTAGTTTCTTATTCCACAAG
1 TTAATTGTAGTTTCTTATGCCACAAG
*
1597115 TTAATTTTAGTTTCTTA-GCCTACAAG
1 TTAATTGTAGTTTCTTATGCC-ACAAG
1597141 AATAAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (26 bp):
TTAATTGTAGTTTCTTATGCCACAAG
Done.