Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 4 of 126
Found at i:1020784 original size:176 final size:174
Alignment explanation
Indices: 1020466--1020824 Score: 540
Period size: 176 Copynumber: 2.1 Consensus size: 174
1020456 AGGGTAGTAC
* * *
1020466 GGTAATTTTGGTGAAATCGAGGTTTAAAATGGAATTTTGGAAAGTTCGGGGATAAAATGGTAATT
1 GGTAATTTTAGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGATAAAATGGTAATA
* * *
1020531 TTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTCGATG
66 TTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGTAAAATGGTAATTTTCGATG
* *
1020596 ATACCAGGGTTAAAAATGGAATTTTGGAAGGTTTAGGGGTAAAAT
131 ATAACAGGGTTAAAAATGGAATTTTGGAA-GTGTAGGGGTAAAAT
* * *
1020641 GGTAATTTTCAGTGAAATCGAGGTTAAAAATGGAATTTTGGATAGTTTGGGGGTAAAATGGTAAT
1 GGTAATTTT-AGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGATAAAATGGTAAT
* *
1020706 ATTCGGTGAAATTAGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTCGG
65 ATTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTT-GGGGTAAAATGGTAATTTTCGA
** *
1020771 TGA-AATTGGGTTAAAAATGGAATTTTGGAAGTGTGGGGGTAAAAT
129 TGATAACAGGGTTAAAAATGGAATTTTGGAAGTGTAGGGGTAAAAT
1020816 GGTAATTTT
1 GGTAATTTT
1020825 TAGAAGTTTC
Statistics
Matches: 166, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
175 31 0.19
176 111 0.67
177 24 0.14
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (174 bp):
GGTAATTTTAGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGATAAAATGGTAATA
TTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGTAAAATGGTAATTTTCGATG
ATAACAGGGTTAAAAATGGAATTTTGGAAGTGTAGGGGTAAAAT
Found at i:1020830 original size:29 final size:29
Alignment explanation
Indices: 1020606--1020852 Score: 87
Period size: 29 Copynumber: 8.5 Consensus size: 29
1020596 ATACCAGGGT
*
1020606 TAAAAATGG-AA-TTTTGGAAGGTTTAGGGG
1 TAAAAATGGTAATTTTTAGAA-GTTT-GGGG
* * * *
1020635 T-AAAATGGTAATTTTCAGTGAA-ATCGAGGT
1 TAAAAATGGTAATTTTTA--GAAGTTTG-GGG
*
1020665 TAAAAATGG-AA-TTTTGGATAGTTTGGGGG
1 TAAAAATGGTAATTTTTAGA-AGTTT-GGGG
* * * *
1020694 T-AAAATGGTAATATTCGGT-GAAATTAGGGT
1 TAAAAATGGTAAT-TT--TTAGAAGTTTGGGG
1020724 TAAAAATGG-AA-TTTTAGAAAGTTTAGGGG
1 TAAAAATGGTAATTTTTAG-AAGTTT-GGGG
* *
1020753 T-AAAATGGTAATTTTCGGT-GAA-ATTGGGT
1 TAAAAATGGTAATTTT---TAGAAGTTTGGGG
* *
1020782 TAAAAATGG-AA-TTTTGGAAGTGTGGGGG
1 TAAAAATGGTAATTTTTAGAAGT-TTGGGG
1020810 T-AAAATGGTAATTTTTAGAAGTTTCGGGG
1 TAAAAATGGTAATTTTTAGAAGTTT-GGGG
*
1020839 TCAAAAT-GTAATTT
1 TAAAAATGGTAATTT
1020853 CCTAAAATTT
Statistics
Matches: 162, Mismatches: 25, Indels: 62
0.65 0.10 0.25
Matches are distributed among these distances:
25 1 0.01
26 4 0.02
27 10 0.06
28 39 0.24
29 46 0.28
30 33 0.20
31 21 0.13
32 6 0.04
33 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAAAATGGTAATTTTTAGAAGTTTGGGG
Found at i:1021570 original size:12 final size:11
Alignment explanation
Indices: 1021553--1021597 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
1021543 CAAGGTAGTA
1021553 TTTCTTCTCTTT
1 TTTCTT-TCTTT
*
1021565 TTTCTTCCTTT
1 TTTCTTTCTTT
1021576 TTGT-TTTCTTT
1 TT-TCTTTCTTT
1021587 TTTCTTTCTTT
1 TTTCTTTCTTT
1021598 ATTGTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 1 0.03
11 21 0.72
12 7 0.24
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:1021587 original size:22 final size:23
Alignment explanation
Indices: 1021560--1021603 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1021550 GTATTTCTTC
1021560 TCTTTTTTCTTCCTTT-TTGTTT
1 TCTTTTTTCTTCCTTTATTGTTT
*
1021582 TCTTTTTTCTTTCTTTATTGTT
1 TCTTTTTTCTTCCTTTATTGTT
1021604 AAAACAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (23 bp):
TCTTTTTTCTTCCTTTATTGTTT
Found at i:1021863 original size:3 final size:3
Alignment explanation
Indices: 1021857--1021903 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
1021847 TTATCTTCTT
* *
1021857 TTA TTA TTA TTA TTA TTA TTTA TTA TTA ATA ATA TTA -TA TTTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA
1021903 T
1 T
1021904 AAAACCCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1022613 original size:13 final size:13
Alignment explanation
Indices: 1022583--1022668 Score: 58
Period size: 13 Copynumber: 6.8 Consensus size: 13
1022573 TTCTTGGACT
*
1022583 TTTAATATTTAATG
1 TTTAA-ATTTAATA
*
1022597 TTTAAATTTAGTA
1 TTTAAATTTAATA
1022610 TTTAAATTT-A-A
1 TTTAAATTTAATA
**
1022621 GGTAAATTTAAATA
1 TTTAAATTT-AATA
*
1022635 ATTAAATTTAA-A
1 TTTAAATTTAATA
1022647 TTTAAGA--TAA-A
1 TTTAA-ATTTAATA
1022658 TTTAAATTTAA
1 TTTAAATTTAA
1022669 ATAAACTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
10 1 0.02
11 17 0.29
12 8 0.14
13 19 0.33
14 13 0.22
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.48
Consensus pattern (13 bp):
TTTAAATTTAATA
Found at i:1022618 original size:6 final size:6
Alignment explanation
Indices: 1022583--1022670 Score: 65
Period size: 6 Copynumber: 14.2 Consensus size: 6
1022573 TTCTTGGACT
* * **
1022583 TTTAATA TTTAATG TTTAAA TTTAGTA TTTAAA TTT-AA GGTAAA TTTAAA
1 TTTAA-A TTTAA-A TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA
1022633 TAATTAAA TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA T
1 T--TTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA T
1022671 AAACTTAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
4 1 0.02
5 6 0.09
6 36 0.55
7 17 0.26
8 6 0.09
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:1022628 original size:11 final size:11
Alignment explanation
Indices: 1022612--1022662 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
1022602 ATTTAGTATT
*
1022612 TAAATTTAAGG
1 TAAATTTAAGA
1022623 TAAATTTAA-A
1 TAAATTTAAGA
* **
1022633 T-AATTAAATT
1 TAAATTTAAGA
1022643 TAAATTTAAGA
1 TAAATTTAAGA
1022654 TAAATTTAA
1 TAAATTTAA
1022663 ATTTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 24 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:1022631 original size:17 final size:17
Alignment explanation
Indices: 1022609--1022679 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
1022599 TAAATTTAGT
*
1022609 ATTTAAATTTAAGGTAA
1 ATTTAAATTTAAGATAA
*
1022626 ATTTAAA--TAA-TTAA
1 ATTTAAATTTAAGATAA
1022640 ATTTAAATTTAAGATAA
1 ATTTAAATTTAAGATAA
1022657 ATTTAAATTTAA-ATAA
1 ATTTAAATTTAAGATAA
*
1022673 ACTTAAA
1 ATTTAAA
1022680 ATCAATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
14 10 0.21
15 3 0.06
16 13 0.27
17 22 0.46
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAGATAA
Found at i:1023760 original size:87 final size:86
Alignment explanation
Indices: 1023612--1023869 Score: 333
Period size: 87 Copynumber: 3.0 Consensus size: 86
1023602 GTTGTAGGAC
* * * * * *
1023612 AAGAGGAGAATCCTTTTGATGAG-GTACCATCTCCAGAAGCCGAAAGGGTACTTTTGGGTTCAGG
1 AAGAGGAGAATCCTTTTGATG-GCATGCCACCTCGA-AAACCGAAAGGGTACTTTTGAGTTCAGG
*
1023676 TGAGGCAGCATCTCCAGAATCAG
64 GGAGGCAGCATCTCCAGAATCAG
1023699 AAGAGGAGAATCCTTTTGATGGCATGCCACCTCTGAAAACCGAAAGGGTACTTTTGAGTTCAGGG
1 AAGAGGAGAATCCTTTTGATGGCATGCCACCTC-GAAAACCGAAAGGGTACTTTTGAGTTCAGGG
* *
1023764 GAGGCGGCATCTCCAGAATCGG
65 GAGGCAGCATCTCCAGAATCAG
* * *
1023786 AAGAGGAGAGTCCTTTTGATGGCATGCTC-CCTCCGGAAACTGAAAGGGTACTTTTGAGTTCAGG
1 AAGAGGAGAATCCTTTTGATGGCATGC-CACCT-CGAAAACCGAAAGGGTACTTTTGAGTTCAGG
*
1023850 GGAGG-AGCATCCCCAGAATC
64 GGAGGCAGCATCTCCAGAATC
1023870 GAAAGTAGAA
Statistics
Matches: 153, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
86 14 0.09
87 136 0.89
88 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (86 bp):
AAGAGGAGAATCCTTTTGATGGCATGCCACCTCGAAAACCGAAAGGGTACTTTTGAGTTCAGGGG
AGGCAGCATCTCCAGAATCAG
Found at i:1026696 original size:49 final size:47
Alignment explanation
Indices: 1026641--1026783 Score: 115
Period size: 49 Copynumber: 3.1 Consensus size: 47
1026631 CGAAAGGGTA
1026641 CTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAGAATC
1 CTTTTGAGTT-AGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAG-ATC
* * * ** * * *
1026690 CTTTTGA--T--GGCATGC--CACCTCTGGAAACTGAA-AGG-G-TA
1 CTTTTGAGTTAGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAGATC
1026728 CTTTTGAGTTTAGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAGAGTC
1 CTTTTGAG-TTAGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAGA-TC
1026777 CTTTTGA
1 CTTTTGA
1026784 TGGCATGCCA
Statistics
Matches: 67, Mismatches: 16, Indels: 22
0.64 0.15 0.21
Matches are distributed among these distances:
38 8 0.12
40 1 0.01
41 4 0.06
42 12 0.18
43 5 0.07
44 5 0.07
45 12 0.18
46 3 0.04
47 2 0.03
49 15 0.22
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
CTTTTGAGTTAGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAGATC
Found at i:1026737 original size:87 final size:87
Alignment explanation
Indices: 1026591--1026854 Score: 413
Period size: 87 Copynumber: 3.0 Consensus size: 87
1026581 GTAGTAGGAC
* * * *
1026591 AAGAGGAGAATCCTTTTGATGAG-GTACCATCTCCGGAAGCCGAAAGGGTACTTTTGAGTTCAGG
1 AAGAGGAGAATCCTTTTGATG-GCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGG
1026655 GGAGGCAGCATCTCCAGAATCAG
65 GGAGGCAGCATCTCCAGAATCAG
* * *
1026678 AAGAGGAGAATCCTTTTGATGGCATGCCACCTCTGGAAACTGAAAGGGTACTTTTGAGTTTAGGG
1 AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGGG
1026743 GAGGCAGCATCTCCAGAATCAG
66 GAGGCAGCATCTCCAGAATCAG
* *
1026765 AAGAGGAGAGTCCTTTTGATGGCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCATGG
1 AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGGG
* *
1026830 GAGGCAGCATCCCCAGAATTAG
66 GAGGCAGCATCTCCAGAATCAG
1026852 AAG
1 AAG
1026855 TAGAAGCTCC
Statistics
Matches: 162, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
86 1 0.01
87 161 0.99
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (87 bp):
AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGGG
GAGGCAGCATCTCCAGAATCAG
Found at i:1029088 original size:24 final size:24
Alignment explanation
Indices: 1029060--1029124 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
1029050 TGAGAAATAA
1029060 TCTTTCAGTTAAACTCTGCTTATT
1 TCTTTCAGTTAAACTCTGCTTATT
* *
1029084 TCTTTCAATTAAATTCTGCTTATT
1 TCTTTCAGTTAAACTCTGCTTATT
* * *
1029108 TGTTTAAGTCAAACTCT
1 TCTTTCAGTTAAACTCT
1029125 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (24 bp):
TCTTTCAGTTAAACTCTGCTTATT
Found at i:1032084 original size:87 final size:86
Alignment explanation
Indices: 1031938--1032201 Score: 388
Period size: 87 Copynumber: 3.0 Consensus size: 86
1031928 GTAGTAGGAC
* * * * *
1031938 AAGAGGAGAATCCTTTTGATGAG-GTACCATCTCCGGAAGCCGAAAGGATACTTTTGAGTTCAGG
1 AAGAGGAGAATCC-TTTGATG-GCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGG
1032002 GGAGGCAGCATCTCCAGAATCGG
64 GGAGGCAGCATCTCCAGAATCGG
* *
1032025 AAGAGGAGAATCCGTTTGATGGCATGCCACCTCCGGAAATCGAAAGGGTACTTTTGAGTTCAAGG
1 AAGAGGAGAATCC-TTTGATGGCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGGG
*
1032090 GAGGCAGCATCTCCAGAATTGG
65 GAGGCAGCATCTCCAGAATCGG
*
1032112 AAGAGGAGAATCCTTGTGATGGCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGAG
1 AAGAGGAGAATCCTT-TGATGGCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGGG
1032177 GAGGCAGCATC-CCTAGAATCGG
65 GAGGCAGCATCTCC-AGAATCGG
1032199 AAG
1 AAG
1032202 TAGAAGCTCC
Statistics
Matches: 161, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
86 5 0.03
87 156 0.97
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (86 bp):
AAGAGGAGAATCCTTTGATGGCATGCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGGGG
AGGCAGCATCTCCAGAATCGG
Found at i:1036508 original size:87 final size:87
Alignment explanation
Indices: 1036245--1036508 Score: 377
Period size: 87 Copynumber: 3.0 Consensus size: 87
1036235 GTAGTCGGAC
* * * * * *
1036245 AAGAGGAGAATCCTTTTGATGAG-GTACCATCTCCGGAAGCTGAAAGGGTACTTTTGAGTTCAGG
1 AAGAGGAGAATCCTTTTGATG-GCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGG
*
1036309 GGAGGCAGCATCTCCAGAATCAG
65 GGAGGCAGCATCTCCAGAATCGG
* * * * *
1036332 AAGAGGAGAATCCGTTTGATGGCTTGCCACCTCCTAAAAACAAAAGGGTACTTTTGAGTTCAGGG
1 AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGGG
1036397 GAGGCAGCATCTCCAGAATCGG
66 GAGGCAGCATCTCCAGAATCGG
1036419 AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGGG
1 AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGGG
* * *
1036484 GAGGCAACATCCCCAGAATTGG
66 GAGGCAGCATCTCCAGAATCGG
1036506 AAG
1 AAG
1036509 TAGAAGCTCC
Statistics
Matches: 157, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 1 0.01
87 156 0.99
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (87 bp):
AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGGG
GAGGCAGCATCTCCAGAATCGG
Found at i:1039340 original size:87 final size:87
Alignment explanation
Indices: 1039194--1039367 Score: 260
Period size: 87 Copynumber: 2.0 Consensus size: 87
1039184 GTAGTAGGAC
* * * * * *
1039194 AAGAGGAGAATCCTTTTGATGAGGTACCATCTCCAGAAGCTGAAAGGGTACTTTTGAGTTTAGGG
1 AAGAGGAAAATCCTTTTGATGAGATACCACCTCCAGAAACCGAAAGGGTACTTTTGAGTTCAGGG
1039259 GAGGCAGCATCTCCAGAATCAG
66 GAGGCAGCATCTCCAGAATCAG
* *
1039281 AAGAGGAAAATCCTTTTGATG-GCATTCCACCTCCGGAAACCGAAAGGGTACTTTTGAGTTCAGG
1 AAGAGGAAAATCCTTTTGATGAG-ATACCACCTCCAGAAACCGAAAGGGTACTTTTGAGTTCAGG
1039345 GGAGGCAGCATCTCCAGAATCAG
65 GGAGGCAGCATCTCCAGAATCAG
1039368 CATCTCCAGA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 1 0.01
87 77 0.99
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (87 bp):
AAGAGGAAAATCCTTTTGATGAGATACCACCTCCAGAAACCGAAAGGGTACTTTTGAGTTCAGGG
GAGGCAGCATCTCCAGAATCAG
Found at i:1039370 original size:15 final size:15
Alignment explanation
Indices: 1039350--1039380 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1039340 TCAGGGGAGG
1039350 CAGCATCTCCAGAAT
1 CAGCATCTCCAGAAT
1039365 CAGCATCTCCAGAAT
1 CAGCATCTCCAGAAT
1039380 C
1 C
1039381 GGAAGAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.35, G:0.13, T:0.19
Consensus pattern (15 bp):
CAGCATCTCCAGAAT
Found at i:1039439 original size:102 final size:102
Alignment explanation
Indices: 1039263--1039569 Score: 569
Period size: 102 Copynumber: 3.0 Consensus size: 102
1039253 TTAGGGGAGG
* * * **
1039263 CAGCATCTCCAGAATCAGAAGAGGAAAATCCTTTTGATGGCATTCCACCTCCGGAAACCGAAAGG
1 CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACCGAAAGG
1039328 GTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAAT
66 GTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAAT
1039365 CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACCGAAAGG
1 CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACCGAAAGG
1039430 GTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAAT
66 GTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAAT
1039467 CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACCGAAAGG
1 CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACCGAAAGG
1039532 GTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAAT
66 GTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAAT
1039569 C
1 C
1039570 GGAAGAGGAG
Statistics
Matches: 200, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 200 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (102 bp):
CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACCGAAAGG
GTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAAT
Found at i:1039472 original size:15 final size:15
Alignment explanation
Indices: 1039452--1039482 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1039442 TCAGGGGAGG
1039452 CAGCATCTCCAGAAT
1 CAGCATCTCCAGAAT
1039467 CAGCATCTCCAGAAT
1 CAGCATCTCCAGAAT
1039482 C
1 C
1039483 GGAAGAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.35, G:0.13, T:0.19
Consensus pattern (15 bp):
CAGCATCTCCAGAAT
Found at i:1041182 original size:87 final size:87
Alignment explanation
Indices: 1041036--1041293 Score: 403
Period size: 87 Copynumber: 3.0 Consensus size: 87
1041026 GTAGTAGGAC
* * * * *
1041036 AAGAGGAGAATCCTTTTGATGAG-GTACCATCTCCGGAAGCCGAAAGGGTACTTTTGAGTTCAGG
1 AAGAGGAGAATCCTTTTGATG-GCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGG
1041100 GGAGGCAGCATCTCCAGAATCAG
65 GGAGGCAGCATCTCCAGAATCAG
*
1041123 AAGAGGAAAATCCTTTTGATGGCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGGG
1 AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGGG
*
1041188 GAGGCAGCATCTCCAGAATCGG
66 GAGGCAGCATCTCCAGAATCAG
* *
1041210 AAGAGGAGAATCCTTTCGATGGCATGCCACCTCCGAAAACTGAAAGGGTACTTTTGAGTTCAGGG
1 AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGGG
1041275 GAGGCAGCATC-CCTAGAAT
66 GAGGCAGCATCTCC-AGAAT
1041294 AGGAAGTAGA
Statistics
Matches: 159, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
86 3 0.02
87 156 0.98
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.21
Consensus pattern (87 bp):
AAGAGGAGAATCCTTTTGATGGCATGCCACCTCCGAAAACCGAAAGGGTACTTTTGAGTTCAGGG
GAGGCAGCATCTCCAGAATCAG
Found at i:1044139 original size:87 final size:87
Alignment explanation
Indices: 1044027--1044246 Score: 368
Period size: 87 Copynumber: 2.5 Consensus size: 87
1044017 TCCAGAAGCT
*
1044027 GAAAGGGTACTTTTGAGTTTAGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAAAATCCTTTTGA
1 GAAAGGGTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAAAATCCTTTTGA
* * *
1044092 TGGCATTCCACCTCCGGAAATC
66 TGGCATGCCACCTCAGGAAACC
* * *
1044114 GAAAGGGTACTTTTGAGTTCCGGGGAGGCAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGA
1 GAAAGGGTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAAAATCCTTTTGA
*
1044179 TGGCATGCCACCTCATGAAACC
66 TGGCATGCCACCTCAGGAAACC
1044201 GAAAGGGTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAATCAG
1 GAAAGGGTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAATCAG
1044247 CATCTCCAGA
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 123 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (87 bp):
GAAAGGGTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAATCAGAAGAGGAAAATCCTTTTGA
TGGCATGCCACCTCAGGAAACC
Found at i:1044249 original size:15 final size:15
Alignment explanation
Indices: 1044229--1044259 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1044219 TCAGGGGAGG
1044229 CAGCATCTCCAGAAT
1 CAGCATCTCCAGAAT
1044244 CAGCATCTCCAGAAT
1 CAGCATCTCCAGAAT
1044259 C
1 C
1044260 GGAAGAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.35, G:0.13, T:0.19
Consensus pattern (15 bp):
CAGCATCTCCAGAAT
Found at i:1044318 original size:102 final size:102
Alignment explanation
Indices: 1044142--1044345 Score: 390
Period size: 102 Copynumber: 2.0 Consensus size: 102
1044132 TCCGGGGAGG
*
1044142 CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACCGAAAGG
1 CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACAGAAAGG
*
1044207 GTACTTTTGAGTTCAGGGGAGGCAGCATCTCCAGAAT
66 GTACTTTTGAGTTCAGGGGAGGCAGCATCCCCAGAAT
1044244 CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACAGAAAGG
1 CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACAGAAAGG
1044309 GTACTTTTGAGTTCAGGGGAGGCAGCATCCCCAGAAT
66 GTACTTTTGAGTTCAGGGGAGGCAGCATCCCCAGAAT
1044346 TGGAAGTAGA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (102 bp):
CAGCATCTCCAGAATCGGAAGAGGAGAATCCTTTTGATGGCATGCCACCTCATGAAACAGAAAGG
GTACTTTTGAGTTCAGGGGAGGCAGCATCCCCAGAAT
Found at i:1047743 original size:14 final size:15
Alignment explanation
Indices: 1047712--1047760 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
1047702 TATTATAATT
1047712 TTAATTAAGTTTTAA
1 TTAATTAAGTTTTAA
* *
1047727 TTAGTTAA-TTTTTA
1 TTAATTAAGTTTTAA
*
1047741 TTAATTAAAGGTTTAA
1 TTAATT-AAGTTTTAA
1047757 TTAA
1 TTAA
1047761 ATTATAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 10 0.37
15 9 0.33
16 8 0.30
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (15 bp):
TTAATTAAGTTTTAA
Found at i:1048110 original size:14 final size:14
Alignment explanation
Indices: 1048087--1048117 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1048077 CCAATCACAC
*
1048087 ACATGTTTTATCAA
1 ACATGCTTTATCAA
1048101 ACATGCTTTATCAA
1 ACATGCTTTATCAA
1048115 ACA
1 ACA
1048118 ATTTTAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (14 bp):
ACATGCTTTATCAA
Found at i:1055247 original size:23 final size:23
Alignment explanation
Indices: 1055218--1055271 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1055208 TGTCCATCCT
*
1055218 TGCTGACTAGACCTTCTGGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
* * **
1055241 TGTTGACTGGGTCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
1055264 TGCTGACT
1 TGCTGACT
1055272 GGATGCCACG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAGAAGC
Found at i:1055272 original size:23 final size:23
Alignment explanation
Indices: 1055230--1055273 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1055220 CTGACTAGAC
* *
1055230 CTTCTGGAAGCTGTTGACTGGGT
1 CTTCTAGAAGCTGCTGACTGGGT
1055253 CTTCTAGAAGCTGCTGACTGG
1 CTTCTAGAAGCTGCTGACTGG
1055274 ATGCCACGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (23 bp):
CTTCTAGAAGCTGCTGACTGGGT
Found at i:1064229 original size:14 final size:15
Alignment explanation
Indices: 1064193--1064241 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
1064183 TATTATTATG
1064193 TTAATTAAGGTTTAA
1 TTAATTAAGGTTTAA
* * *
1064208 TTAGTTAA-TTTTGA
1 TTAATTAAGGTTTAA
1064222 TTAATTAAAGGTTTAA
1 TTAATT-AAGGTTTAA
1064238 TTAA
1 TTAA
1064242 ATTATAAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 9 0.35
15 9 0.35
16 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (15 bp):
TTAATTAAGGTTTAA
Found at i:1065203 original size:5 final size:5
Alignment explanation
Indices: 1065193--1065221 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1065183 AGATATAAAT
1065193 TGATA TGATA TGATA TGATA TGATA TGAT
1 TGATA TGATA TGATA TGATA TGATA TGAT
1065222 CTAATACGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (5 bp):
TGATA
Found at i:1071549 original size:51 final size:51
Alignment explanation
Indices: 1071422--1071662 Score: 284
Period size: 51 Copynumber: 4.6 Consensus size: 51
1071412 CTCGCATTTG
* ** ** * *
1071422 TTACTCATGATGACACAAAGTCATCGGACCCCTTTGTTCCGTATAGAAATTCAT
1 TTACTCACGATGACACTTAGTCATCGGA--CCTTTAATCCGTAAAG-GATTCAT
* * * * *
1071476 ATACTCACGATGACACTGAGTCATCGGACCTTTAATTCGTCATGGATTCAT
1 TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
* * *
1071527 TTACTCAAGACGACATTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
1 TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
* * *
1071578 TTACTCATGATGACACTTAGTCATCAGACCTTTAATCCGTTAAGGATTCAT
1 TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
1071629 TTACTCACGATGACACTTAGTCATCGGACTCTTT
1 TTACTCACGATGACACTTAGTCATCGGAC-CTTT
1071663 CATTTATAGC
Statistics
Matches: 160, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
51 122 0.76
52 14 0.09
54 24 0.15
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
Found at i:1075164 original size:23 final size:23
Alignment explanation
Indices: 1075138--1075262 Score: 155
Period size: 23 Copynumber: 5.3 Consensus size: 23
1075128 ACACTAGCGC
*
1075138 GCTCTCTGATTAGCACTGTATGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
1075161 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
1075184 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
1075209 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
1075232 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
1075255 GCTCTCTG
1 GCTCTCTG
1075263 TTGCCCAGCA
Statistics
Matches: 90, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
22 4 0.04
23 66 0.73
24 1 0.01
25 16 0.18
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:1075210 original size:48 final size:46
Alignment explanation
Indices: 1075138--1075264 Score: 175
Period size: 48 Copynumber: 2.7 Consensus size: 46
1075128 ACACTAGCGC
*
1075138 GCTCTCTGATTAGCACTGTATGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCGT-GT
* * *
1075184 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCGTGT
*
1075232 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTT
1075265 GCCCAGCACT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
46 30 0.42
48 40 0.56
49 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCGTGT
Found at i:1075281 original size:48 final size:44
Alignment explanation
Indices: 1075138--1075287 Score: 156
Period size: 48 Copynumber: 3.2 Consensus size: 44
1075128 ACACTAGCGC
* * *
1075138 GCTCTCTGATTAGCACTGTATGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTG-TTAGCACTTAT-GT
* *
1075184 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTG-TTAGCACTT-ATGT
*
1075232 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTT----AGCACTTATGT
1075280 GCTCTCTG
1 GCTCTCTG
1075288 TTCAGTACTT
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
45 2 0.02
46 29 0.33
48 50 0.56
49 8 0.09
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (44 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTAGCACTTATGT
Found at i:1075299 original size:71 final size:71
Alignment explanation
Indices: 1075138--1075285 Score: 167
Period size: 71 Copynumber: 2.1 Consensus size: 71
1075128 ACACTAGCGC
* * * **
1075138 GCTCTCTGATTAGCACTGT-ATGTGCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCAC
1 GCTCTCCGATTAGCACT-TCGTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTGTTACCAGCAC
*
1075202 TGTGTGT
65 TGTATGT
* * *
1075209 GCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCAC-TTTGTGTGCTCTCTGTTGCCCAGCA
1 GCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACGTCT-CGTGCTCTCTGTT-ACCAGCA
1075273 CT-TATGT
64 CTGTATGT
1075280 GCTCTC
1 GCTCTC
1075286 TGTTCAGTAC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
70 3 0.05
71 56 0.86
72 6 0.09
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (71 bp):
GCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTGTTACCAGCACT
GTATGT
Found at i:1077375 original size:6 final size:6
Alignment explanation
Indices: 1077364--1077392 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1077354 TAGTATATTT
1077364 ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
1077393 TAGTTTTAGT
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:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTC
Found at i:1078001 original size:91 final size:91
Alignment explanation
Indices: 1077845--1078012 Score: 327
Period size: 91 Copynumber: 1.8 Consensus size: 91
1077835 TGAATGATTT
1077845 AATTTTTAAGCTATGAGAGAGTCAAGCATGATGAGTTGTCTTCAAAATTAAATATTTTAGATTGT
1 AATTTTTAAGCTATGAGAGAGTCAAGCATGATGAGTTGTCTTCAAAATTAAATATTTTAGATTGT
1077910 CTTCCTTAATTGAATTATTATCTTCA
66 CTTCCTTAATTGAATTATTATCTTCA
*
1077936 AATTTTTAAGCTATGAGAGAGTCAAGCATGATGAGTTGTCTTCAAAATTAAATATTTTAGGTTGT
1 AATTTTTAAGCTATGAGAGAGTCAAGCATGATGAGTTGTCTTCAAAATTAAATATTTTAGATTGT
1078001 CTTCCTTAATTG
66 CTTCCTTAATTG
1078013 TCTTCAAATT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (91 bp):
AATTTTTAAGCTATGAGAGAGTCAAGCATGATGAGTTGTCTTCAAAATTAAATATTTTAGATTGT
CTTCCTTAATTGAATTATTATCTTCA
Found at i:1078471 original size:20 final size:20
Alignment explanation
Indices: 1078443--1078506 Score: 73
Period size: 19 Copynumber: 3.3 Consensus size: 20
1078433 TATTATTTAG
1078443 AAAAA-GAAAAAAAAGTCG-A
1 AAAAATGAAAAAAAA-TCGAA
1078462 AAAAATG-AAAAAAATCGAA
1 AAAAATGAAAAAAAATCGAA
*
1078481 AAAAATCGAAAAAAAA-AGAA
1 AAAAAT-GAAAAAAAATCGAA
1078501 AAAAAT
1 AAAAAT
1078507 TGGAAAAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 3 0.08
19 19 0.47
20 11 0.28
21 7 0.17
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.08
Consensus pattern (20 bp):
AAAAATGAAAAAAAATCGAA
Found at i:1078484 original size:30 final size:31
Alignment explanation
Indices: 1078448--1078534 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
1078438 TTTAGAAAAA
1078448 GAAAAAAAAGTCGAAAAAATGAAAAAAA-TC
1 GAAAAAAAAGTCGAAAAAATGAAAAAAATTC
* *
1078478 G-AAAAAAA-TCGAAAAAAAAAGAAAAAAATTG
1 GAAAAAAAAGTCG--AAAAAATGAAAAAAATTC
* *
1078509 GAAAAAAGAAGACGAAAAGAT-AAAAA
1 GAAAAAA-AAGTCGAAAAAATGAAAAA
1078535 TGTGTTTGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
28 3 0.07
29 7 0.15
30 15 0.33
31 7 0.15
32 10 0.22
33 2 0.04
34 2 0.04
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.08
Consensus pattern (31 bp):
GAAAAAAAAGTCGAAAAAATGAAAAAAATTC
Found at i:1078503 original size:21 final size:20
Alignment explanation
Indices: 1078461--1078520 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
1078451 AAAAAAGTCG
**
1078461 AAAAAATGAAAAAAATCG-A
1 AAAAAATGAAAAAAAAAGAA
1078480 AAAAAATCGAAAAAAAAAGAA
1 AAAAAAT-GAAAAAAAAAGAA
* *
1078501 AAAAATTGGAAAAAAGAAGA
1 AAAAAAT-GAAAAAAAAAGA
1078521 CGAAAAGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 7 0.21
20 9 0.26
21 18 0.53
ACGTcount: A:0.75, C:0.03, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAAAGAA
Found at i:1078513 original size:20 final size:20
Alignment explanation
Indices: 1078468--1078520 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1078458 TCGAAAAAAT
*
1078468 GAAAAAAATCGAAAAAAATCG
1 GAAAAAAA-AGAAAAAAATCG
* *
1078489 AAAAAAAAAGAAAAAAATTG
1 GAAAAAAAAGAAAAAAATCG
1078509 GAAAAAAGAAGA
1 GAAAAAA-AAGA
1078521 CGAAAAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.74, C:0.04, G:0.15, T:0.08
Consensus pattern (20 bp):
GAAAAAAAAGAAAAAAATCG
Found at i:1078515 original size:10 final size:10
Alignment explanation
Indices: 1078450--1078506 Score: 73
Period size: 10 Copynumber: 5.8 Consensus size: 10
1078440 TAGAAAAAGA
1078450 AAAAAAAGTCG
1 AAAAAAA-TCG
1078461 -AAAAAAT-G
1 AAAAAAATCG
1078469 AAAAAAATCG
1 AAAAAAATCG
1078479 AAAAAAATCG
1 AAAAAAATCG
**
1078489 AAAAAAAAAG
1 AAAAAAATCG
1078499 AAAAAAAT
1 AAAAAAAT
1078507 TGGAAAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
8 1 0.02
9 8 0.20
10 32 0.78
ACGTcount: A:0.75, C:0.05, G:0.11, T:0.09
Consensus pattern (10 bp):
AAAAAAATCG
Found at i:1087499 original size:12 final size:12
Alignment explanation
Indices: 1087482--1087509 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1087472 AATGTACATG
1087482 TAAAAGATAAGC
1 TAAAAGATAAGC
1087494 TAAAAGATAAGC
1 TAAAAGATAAGC
1087506 TAAA
1 TAAA
1087510 GCATTGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.07, G:0.14, T:0.18
Consensus pattern (12 bp):
TAAAAGATAAGC
Found at i:1090498 original size:30 final size:30
Alignment explanation
Indices: 1090464--1090566 Score: 143
Period size: 30 Copynumber: 3.3 Consensus size: 30
1090454 CATGTATTAT
1090464 TCATTAAAAATTCAATCAACTCAATACAAA
1 TCATTAAAAATTCAATCAACTCAATACAAA
*
1090494 TCATTAAAAATTCAATCAATTCAACTCAACACAAA
1 TCATTAAAAA-T---TCAA-TCAACTCAATACAAA
*
1090529 TCATTAAAAATTCAATCAATTCAATACAAA
1 TCATTAAAAATTCAATCAACTCAATACAAA
1090559 TCATTAAA
1 TCATTAAA
1090567 TTATGCCCAT
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
30 31 0.48
31 5 0.08
34 5 0.08
35 24 0.37
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.28
Consensus pattern (30 bp):
TCATTAAAAATTCAATCAACTCAATACAAA
Found at i:1090520 original size:35 final size:35
Alignment explanation
Indices: 1090475--1090552 Score: 140
Period size: 35 Copynumber: 2.3 Consensus size: 35
1090465 CATTAAAAAT
*
1090475 TCAA-TCAACTCAATACAAATCATTAAAAATTCAA
1 TCAATTCAACTCAACACAAATCATTAAAAATTCAA
1090509 TCAATTCAACTCAACACAAATCATTAAAAATTCAA
1 TCAATTCAACTCAACACAAATCATTAAAAATTCAA
1090544 TCAATTCAA
1 TCAATTCAA
1090553 TACAAATCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 4 0.10
35 38 0.90
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (35 bp):
TCAATTCAACTCAACACAAATCATTAAAAATTCAA
Found at i:1090766 original size:20 final size:20
Alignment explanation
Indices: 1090741--1090796 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
1090731 TAATTTAATT
1090741 TCCATATTAATTAAATCCAA
1 TCCATATTAATTAAATCCAA
* *
1090761 TCCATA-TAATTTAAT---T
1 TCCATATTAATTAAATCCAA
*
1090777 TCCATATTGATTAAATCCAA
1 TCCATATTAATTAAATCCAA
1090797 ATCAGAACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
16 6 0.22
17 7 0.26
19 8 0.30
20 6 0.22
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (20 bp):
TCCATATTAATTAAATCCAA
Found at i:1090775 original size:36 final size:36
Alignment explanation
Indices: 1090728--1090796 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
1090718 AATTAAAAAA
1090728 ATATAATTTAATTTCCATATTAATTAAATCCAATCC
1 ATATAATTTAATTTCCATATTAATTAAATCCAATCC
*
1090764 ATATAATTTAATTTCCATATTGATTAAATCCAA
1 ATATAATTTAATTTCCATATTAATTAAATCCAA
1090797 ATCAGAACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.42
Consensus pattern (36 bp):
ATATAATTTAATTTCCATATTAATTAAATCCAATCC
Found at i:1097551 original size:19 final size:18
Alignment explanation
Indices: 1097527--1097575 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
1097517 TTAATATCAA
1097527 TGTAATAAAAAATTAATAT
1 TGTAATAAAAAATTAA-AT
*
1097546 TGTAAT-GAAAA-TAAAT
1 TGTAATAAAAAATTAAAT
1097562 T-TAATAGAAAAATT
1 TGTAATA-AAAAATT
1097576 TTATCGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
15 4 0.16
16 3 0.12
17 7 0.28
18 5 0.20
19 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (18 bp):
TGTAATAAAAAATTAAAT
Found at i:1097918 original size:16 final size:16
Alignment explanation
Indices: 1097910--1097941 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1097900 TTTGAATTTT
1097910 CATTTTTTTAAATATC
1 CATTTTTTTAAATATC
1097926 CATTTTTATTAAATAT
1 CATTTTT-TTAAATAT
1097942 TTGGAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
CATTTTTTTAAATATC
Found at i:1102629 original size:16 final size:16
Alignment explanation
Indices: 1102610--1102646 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1102600 TTAATAATCT
* *
1102610 AAAATTTTAAAATTTG
1 AAAATTATAAAATTTA
1102626 AAAATTATAAAATTTA
1 AAAATTATAAAATTTA
1102642 AAAAT
1 AAAAT
1102647 AACCAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAATTATAAAATTTA
Found at i:1109114 original size:19 final size:19
Alignment explanation
Indices: 1109090--1109133 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
1109080 TTCTAACATA
1109090 AAAAAAT-ATTAATTTTTT
1 AAAAAATAATTAATTTTTT
*
1109108 CAAAAAATCAATTTATTTTTT
1 -AAAAAAT-AATTAATTTTTT
1109129 AAAAA
1 AAAAA
1109134 TCATTTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 5 0.23
21 10 0.45
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAAATAATTAATTTTTT
Found at i:1109126 original size:20 final size:19
Alignment explanation
Indices: 1109103--1109142 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1109093 AAATATTAAT
1109103 TTTTTCAAAAAATCAATTTA
1 TTTTT-AAAAAATCAATTTA
* *
1109123 TTTTTTAAAAATCATTTTA
1 TTTTTAAAAAATCAATTTA
1109142 T
1 T
1109143 GTAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTAAAAAATCAATTTA
Found at i:1123885 original size:27 final size:27
Alignment explanation
Indices: 1123855--1123911 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
1123845 AAAAGGATCA
1123855 ATTTACTCTTTGATCCAAAGTACAGGG
1 ATTTACTCTTTGATCCAAAGTACAGGG
*
1123882 ATTTACTCTTTGATCCCAAGTACAGGG
1 ATTTACTCTTTGATCCAAAGTACAGGG
1123909 ATT
1 ATT
1123912 AATTTGCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (27 bp):
ATTTACTCTTTGATCCAAAGTACAGGG
Found at i:1130879 original size:32 final size:31
Alignment explanation
Indices: 1130834--1130904 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 31
1130824 ATCTGGTGTG
*
1130834 AAATATATTTAAAACACGTTAATCAAATTGT
1 AAATATATTTAAAACACGTTAATCAAACTGT
* * **
1130865 AAATATGTGTTAAAACACTTTAATTGAACTGT
1 AAATATAT-TTAAAACACGTTAATCAAACTGT
1130897 AAATATAT
1 AAATATAT
1130905 GTATACTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 7 0.21
32 26 0.79
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (31 bp):
AAATATATTTAAAACACGTTAATCAAACTGT
Found at i:1140792 original size:14 final size:14
Alignment explanation
Indices: 1140757--1140785 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1140747 AGAAATCCGA
1140757 TTAAATTCAATTTC
1 TTAAATTCAATTTC
1140771 TTAAATTCAATTTC
1 TTAAATTCAATTTC
1140785 T
1 T
1140786 ATCATTCCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAATTCAATTTC
Found at i:1147362 original size:18 final size:18
Alignment explanation
Indices: 1147321--1147372 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1147311 TTTTTAGTTG
*
1147321 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
1147339 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
*
1147357 TTATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
1147373 CTCATCCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 9 0.29
17 7 0.23
18 15 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:1149016 original size:27 final size:27
Alignment explanation
Indices: 1148978--1149034 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1148968 AACACTTTTC
*
1148978 ATCGTAGTTCCTCCATAGATGAAACGT
1 ATCGTAATTCCTCCATAGATGAAACGT
*
1149005 ATCGTAATTCCTCCATAGATGAATCGT
1 ATCGTAATTCCTCCATAGATGAAACGT
1149032 ATC
1 ATC
1149035 TGATAACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (27 bp):
ATCGTAATTCCTCCATAGATGAAACGT
Found at i:1149477 original size:231 final size:231
Alignment explanation
Indices: 1149063--1149520 Score: 727
Period size: 231 Copynumber: 2.0 Consensus size: 231
1149053 GTTACCCAAG
*
1149063 TTCATCCCTGAGTTCATCACCCAGAAATGAGTGGCGATATAACATTCATTCATCTACAACTTCAA
1 TTCATCCCTGAGTTCATCACCCAGAAATGAATGGCGATATAACATTCATTCATCTACAACTTCAA
* * *
1149128 CCAAACCACCTCAGTCCTCGTTTAAGCCGGATCTATATCCTCCTACTCCACTGCCATCATTTAAA
66 CCAAACCACCTCAGTCCTCGGTTAAGCCGGATCAATATCCTCCGACTCCACTGCCATCATTTAAA
* * *
1149193 ACGTCATTCACAGCCCAAAAACCATCTCCATCACCTAAAGGCCTGACACCACCTAAACCAACCAC
131 AAGTCATTCACAGCCCAAAAACCATCTCCATCACCTAAAGGACTGAAACCACCTAAACCAACCAC
* * *
1149258 ACCGTCTTTGAAACCCTCTTCATCGTCTTCTACAAC
196 ACCGCCTCTGAAACCCTCTTCATCGTCCTCTACAAC
** *
1149294 TTCATCCCTGAGTTCATCACCTGGAAATGAATGGCTATATAACATTCATTCATCTACAACTTCAA
1 TTCATCCCTGAGTTCATCACCCAGAAATGAATGGCGATATAACATTCATTCATCTACAACTTCAA
* * * **
1149359 CCAAACCACCTCAGTCCTTGGTTAAGCCGGATCAATTTCCTCCGAGTCTGCTGCCATCATTTAAA
66 CCAAACCACCTCAGTCCTCGGTTAAGCCGGATCAATATCCTCCGACTCCACTGCCATCATTTAAA
* *
1149424 AAGTCATTCACGGCCCAAAAACCATCTCCATCACCTGAAGGACTGAAACCACCTAAACCAACCAC
131 AAGTCATTCACAGCCCAAAAACCATCTCCATCACCTAAAGGACTGAAACCACCTAAACCAACCAC
*
1149489 ACTGCCTCTGAAACCCTCTTCATCGTCCTCTA
196 ACCGCCTCTGAAACCCTCTTCATCGTCCTCTA
1149521 AGCCAAGTCT
Statistics
Matches: 206, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
231 206 1.00
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (231 bp):
TTCATCCCTGAGTTCATCACCCAGAAATGAATGGCGATATAACATTCATTCATCTACAACTTCAA
CCAAACCACCTCAGTCCTCGGTTAAGCCGGATCAATATCCTCCGACTCCACTGCCATCATTTAAA
AAGTCATTCACAGCCCAAAAACCATCTCCATCACCTAAAGGACTGAAACCACCTAAACCAACCAC
ACCGCCTCTGAAACCCTCTTCATCGTCCTCTACAAC
Found at i:1151031 original size:29 final size:28
Alignment explanation
Indices: 1150993--1151062 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 28
1150983 TAGAAACTTT
*
1150993 ATCAAATTAGTCCTTCTATTATTAAATGG
1 ATCAAATTAGTCCTT-TACTATTAAATGG
*
1151022 ATCAATTTAGTCCCTTTACTATTAAATGG
1 ATCAAATTAGT-CCTTTACTATTAAATGG
1151051 ATCAAATTAGTC
1 ATCAAATTAGTC
1151063 TCTCCTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 32 0.86
30 4 0.11
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (28 bp):
ATCAAATTAGTCCTTTACTATTAAATGG
Found at i:1153605 original size:58 final size:56
Alignment explanation
Indices: 1153509--1153677 Score: 144
Period size: 60 Copynumber: 2.9 Consensus size: 56
1153499 GGGGCCTGGT
* *
1153509 CTTGGCAACTT-TT-CTCACATTAGAGCCTGAACTTTTTTTGTCCAAGTTAGACCCTGAA
1 CTTGGCAA-TTGTTCCT-ACATT-GAGCTTGAA-TTTTTTTGTCCAAGTTAGACCCTAAA
* * * **
1153567 CTTGGCAATTGTTCCTACATTGGAGCTTGAATTATTTTTTTATTCAAGTTAGGCTTTAAA
1 CTTGGCAATTGTTCCTACATT-GAGCTTG-A--ATTTTTTTGTCCAAGTTAGACCCTAAA
* *
1153627 CTTGGCAATTGTTCCCACATTGAGGCTTAAAATTTCTTTTGTCCAAGTTAG
1 CTTGGCAATTGTTCCTACATTGA-GCTT-GAATTT-TTTTGTCCAAGTTAG
1153678 TCCTTGAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
57 2 0.02
58 25 0.27
59 18 0.20
60 45 0.49
61 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (56 bp):
CTTGGCAATTGTTCCTACATTGAGCTTGAATTTTTTTGTCCAAGTTAGACCCTAAA
Found at i:1156613 original size:10 final size:10
Alignment explanation
Indices: 1156582--1156625 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
1156572 CAATAAGTAC
1156582 GATTTAATTT
1 GATTTAATTT
*
1156592 -ATTTAATAT
1 GATTTAATTT
*
1156601 GATTTGATTT
1 GATTTAATTT
1156611 GATTTAATTT
1 GATTTAATTT
*
1156621 AATTT
1 GATTT
1156626 TAACATGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (10 bp):
GATTTAATTT
Found at i:1158278 original size:132 final size:132
Alignment explanation
Indices: 1158036--1158301 Score: 325
Period size: 132 Copynumber: 2.0 Consensus size: 132
1158026 GAAGCTTTAA
* * * ** * * *
1158036 AGCAATCAAATCTGGGGAACAACTAACAAACAAGTATCAATGAATCTGGACTTGGTCTAATTAGT
1 AGCAATCAAATCTAGGGAACAACTAACAAACAAGTACCAATGAACCCAGACTTAGACCAATTAGT
* * * * * * * *
1158101 TCATGCTTCCACCTATACGAGGTGATATGTAGCAAGTCTAGGATTCGAATGCGAAAGAACCTTAA
66 TCATACATCCACCTATAAGAGGTGATATCTAACAAGTCTAAGATTCGAATGCCAAAGAAACTTAA
1158166 TT
131 TT
* * * *
1158168 AGCAATCAAATCTAGGTAACAAGTAACAAACAAGTACCAATGAGCCCAGACTTAGACCAGTTAGT
1 AGCAATCAAATCTAGGGAACAACTAACAAACAAGTACCAATGAACCCAGACTTAGACCAATTAGT
* * *
1158233 TCATACATCCACCTTTAAGAGGTGATATCTAACACGTCTAAGATTCGAATGCCAGAGAAACTTAA
66 TCATACATCCACCTATAAGAGGTGATATCTAACAAGTCTAAGATTCGAATGCCAAAGAAACTTAA
1158298 TT
131 TT
1158300 AG
1 AG
1158302 TACCATCCTG
Statistics
Matches: 111, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
132 111 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (132 bp):
AGCAATCAAATCTAGGGAACAACTAACAAACAAGTACCAATGAACCCAGACTTAGACCAATTAGT
TCATACATCCACCTATAAGAGGTGATATCTAACAAGTCTAAGATTCGAATGCCAAAGAAACTTAA
TT
Found at i:1165100 original size:20 final size:18
Alignment explanation
Indices: 1165054--1165093 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1165044 CGTTTAAAAA
*
1165054 AATTGAAATATACTTGAC
1 AATTAAAATATACTTGAC
*
1165072 AATTAAAATATATTTGAC
1 AATTAAAATATACTTGAC
1165090 AATT
1 AATT
1165094 TTAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (18 bp):
AATTAAAATATACTTGAC
Found at i:1165120 original size:23 final size:23
Alignment explanation
Indices: 1165090--1165138 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1165080 TATATTTGAC
1165090 AATTTTAAAATTAAAATATGGAA
1 AATTTTAAAATTAAAATATGGAA
1165113 AATTTTAAAATTAAAATATGGAA
1 AATTTTAAAATTAAAATATGGAA
1165136 AAT
1 AAT
1165139 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (23 bp):
AATTTTAAAATTAAAATATGGAA
Found at i:1166889 original size:15 final size:16
Alignment explanation
Indices: 1166864--1166895 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1166854 AAATTTGAAT
1166864 TTGAGCTTGAATAAGC
1 TTGAGCTTGAATAAGC
1166880 TTGA-CTTGAATAAGC
1 TTGAGCTTGAATAAGC
1166895 T
1 T
1166896 CAAGCTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGAGCTTGAATAAGC
Found at i:1167356 original size:21 final size:21
Alignment explanation
Indices: 1167318--1167361 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1167308 TAATCATTTG
* * *
1167318 ATTGAATTCGAGTTTTTTCAA
1 ATTGAACTCGAATATTTTCAA
*
1167339 ATTGAACTCGAATATTTTTAA
1 ATTGAACTCGAATATTTTCAA
1167360 AT
1 AT
1167362 CCAAACATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (21 bp):
ATTGAACTCGAATATTTTCAA
Found at i:1169488 original size:16 final size:15
Alignment explanation
Indices: 1169467--1169497 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
1169457 TTGGTGATTA
1169467 TTAAAATTTTAAAAAT
1 TTAAAA-TTTAAAAAT
1169483 TTAAAATTTAAAAAT
1 TTAAAATTTAAAAAT
1169498 AATAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAATTTAAAAAT
Found at i:1173899 original size:11 final size:11
Alignment explanation
Indices: 1173883--1173920 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1173873 GATGATGATT
1173883 ATAATTTTAAA
1 ATAATTTTAAA
1173894 ATAATTTT--A
1 ATAATTTTAAA
1173903 ATAATTTTAAA
1 ATAATTTTAAA
*
1173914 ATCATTT
1 ATAATTT
1173921 GCTAACGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:1173908 original size:20 final size:20
Alignment explanation
Indices: 1173883--1173920 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1173873 GATGATGATT
1173883 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
*
1173903 ATAATTTTAAAATCATTT
1 ATAATTTTAAAATAATTT
1173921 GCTAACGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:1175174 original size:81 final size:81
Alignment explanation
Indices: 1175087--1175300 Score: 232
Period size: 81 Copynumber: 2.6 Consensus size: 81
1175077 AAATTAATTT
*** * * * * * *
1175087 TTATACGTTAAATCTGGGAGCAAATTGGATCTATCAAGAATTTCATCAATTTTTACTGTTAAAAA
1 TTATACGTTAAATCAAAGAGCAAATTAGTTCTATAAAAAATTTCATCAATTTCTACTATTAAAAA
* *
1175152 TTGGTTCTATTAA-TCC
66 TTGATTCTATTAACT-A
* * * * * *
1175168 TTATACGCTATATGAAAGAGCAAATTAGTTCTATAAAAAAATTCATTAATTTCTACTATTGAAAA
1 TTATACGTTAAATCAAAGAGCAAATTAGTTCTATAAAAAATTTCATCAATTTCTACTATTAAAAA
1175233 TTGATTCTATTAACTA
66 TTGATTCTATTAACTA
* * *
1175249 TTATACGTTAGATCAAAGAACAAATTAGTTCTATTAAAAATTTCATCAATTT
1 TTATACGTTAAATCAAAGAGCAAATTAGTTCTATAAAAAATTTCATCAATTT
1175301 GCTCGTTTAT
Statistics
Matches: 108, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
81 107 0.99
82 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (81 bp):
TTATACGTTAAATCAAAGAGCAAATTAGTTCTATAAAAAATTTCATCAATTTCTACTATTAAAAA
TTGATTCTATTAACTA
Found at i:1176720 original size:15 final size:16
Alignment explanation
Indices: 1176693--1176722 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1176683 ACAGTTAATA
1176693 TAAAATATATAATTAT
1 TAAAATATATAATTAT
1176709 TAAAAT-TATAATTA
1 TAAAATATATAATTA
1176723 CACTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATATATAATTAT
Found at i:1180324 original size:12 final size:12
Alignment explanation
Indices: 1180307--1180339 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1180297 ACCAAACCGA
1180307 CCACCACCAC-G
1 CCACCACCACGG
1180318 CCTACCACCACGG
1 CC-ACCACCACGG
1180331 CCACCACCA
1 CCACCACCA
1180340 TCCCTTCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.10
12 15 0.75
13 3 0.15
ACGTcount: A:0.27, C:0.61, G:0.09, T:0.03
Consensus pattern (12 bp):
CCACCACCACGG
Found at i:1180358 original size:24 final size:24
Alignment explanation
Indices: 1180303--1180361 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1180293 CACCACCAAA
1180303 CCGACCACCACCACGCCTACCACC
1 CCGACCACCACCACGCCTACCACC
* * * *
1180327 ACGGCCACCACCATC-CCTTCCTCC
1 CCGACCACCACCA-CGCCTACCACC
1180351 CCGACCACCAC
1 CCGACCACCAC
1180362 GACCACCACG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.22, C:0.61, G:0.08, T:0.08
Consensus pattern (24 bp):
CCGACCACCACCACGCCTACCACC
Found at i:1189764 original size:19 final size:19
Alignment explanation
Indices: 1189740--1189785 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1189730 CTACAATGTC
1189740 TTTTTTTTT--TCTTTGGT
1 TTTTTTTTTAATCTTTGGT
*
1189757 TTTTTTTTTAATCTTTTGT
1 TTTTTTTTTAATCTTTGGT
*
1189776 TTTTATTTTA
1 TTTTTTTTTA
1189786 TTCGATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
19 16 0.64
ACGTcount: A:0.09, C:0.04, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTAATCTTTGGT
Found at i:1190221 original size:59 final size:59
Alignment explanation
Indices: 1190105--1190228 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 59
1190095 GATCAAGTTT
* * * **
1190105 AAGTACTTAACTGGACAAAAAAAACTTTAAGTACCAATTTGAACTATTAAGTTAAATTC
1 AAGTACTTAACTGGACAAAAAAAACCTAAAGTACCAATTTAAACTATTAAGCCAAATTC
* *
1190164 AAGTACTTGATTGGACAAAAAAAACCTAAAGTACCAATTTAAACT-TTGAAGCCAAATTC
1 AAGTACTTAACTGGACAAAAAAAACCTAAAGTACCAATTTAAACTATT-AAGCCAAATTC
*
1190223 AGGTAC
1 AAGTAC
1190229 CGATATATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 2 0.04
59 54 0.96
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (59 bp):
AAGTACTTAACTGGACAAAAAAAACCTAAAGTACCAATTTAAACTATTAAGCCAAATTC
Found at i:1192738 original size:27 final size:26
Alignment explanation
Indices: 1192703--1192754 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1192693 AAATTTGCCA
* *
1192703 AATAGAAGTACCATATTGGACAAAAAT
1 AATAGAAGTAACATATTAGA-AAAAAT
*
1192730 AATATAAGTAACATATTAGAAAAAA
1 AATAGAAGTAACATATTAGAAAAAA
1192755 CGTCAAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (26 bp):
AATAGAAGTAACATATTAGAAAAAAT
Found at i:1207262 original size:21 final size:23
Alignment explanation
Indices: 1207233--1207274 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1207223 TAATACGAAT
*
1207233 ACATACAAAACC-ATTTAATTTG
1 ACATACAAAACCTATTAAATTTG
1207255 ACAT-CAAAACCTATTAAATT
1 ACATACAAAACCTATTAAATT
1207275 GAACAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (23 bp):
ACATACAAAACCTATTAAATTTG
Found at i:1207276 original size:21 final size:22
Alignment explanation
Indices: 1207233--1207276 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1207223 TAATACGAAT
*
1207233 ACATACAAAACCATTTAATTTG
1 ACATACAAAACCATTTAAATTG
1207255 ACAT-CAAAACC-TATTAAATTG
1 ACATACAAAACCAT-TTAAATTG
1207276 A
1 A
1207277 ACAAACCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 15 0.75
22 4 0.20
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (22 bp):
ACATACAAAACCATTTAAATTG
Found at i:1244172 original size:23 final size:24
Alignment explanation
Indices: 1244125--1244172 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1244115 GGTTGAAAAT
* *
1244125 AAATTGTAATTTTTATAATAGTAA
1 AAATTGTAATTTTTAAAAGAGTAA
*
1244149 AAATT-TAATTTTTAAAAGATTAA
1 AAATTGTAATTTTTAAAAGAGTAA
1244172 A
1 A
1244173 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (24 bp):
AAATTGTAATTTTTAAAAGAGTAA
Found at i:1244728 original size:30 final size:30
Alignment explanation
Indices: 1244694--1244766 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 30
1244684 CATTTAATAC
1244694 AACAGTCACTCAAC-T-TTGAAAATGCGACAA
1 AACAGTCACT-AACGTATTGAAAA-GCGACAA
*
1244724 AACAGTCACTAACGTTATTGAAAAGTGACAA
1 AACAGTCACTAACG-TATTGAAAAGCGACAA
1244755 AACAGTCACTAA
1 AACAGTCACTAA
1244767 TTAACAGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 3 0.08
30 10 0.26
31 19 0.49
32 7 0.18
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (30 bp):
AACAGTCACTAACGTATTGAAAAGCGACAA
Found at i:1244971 original size:47 final size:46
Alignment explanation
Indices: 1244902--1245024 Score: 124
Period size: 47 Copynumber: 2.6 Consensus size: 46
1244892 AAACAGTAAC
*
1244902 AATCAGAACCCAATCAAAATCGAA-ACAACCCTAAAGT-AAAAATAAA
1 AATCAGAACCAAATCAAAATCGAATA-AACCCTAAA-TCAAAAATAAA
* * *
1244948 AATCAGAATCCAAATCAAGATCGAATAAACCCTAAATCAAAAATCAC
1 AATCAGAA-CCAAATCAAAATCGAATAAACCCTAAATCAAAAATAAA
* * * *
1244995 AATCAGTATCGACATCAAATTCGAATAAAC
1 AATCAG-AACCAAATCAAAATCGAATAAAC
1245025 ACAAAATAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
46 9 0.14
47 53 0.83
48 2 0.03
ACGTcount: A:0.54, C:0.22, G:0.07, T:0.17
Consensus pattern (46 bp):
AATCAGAACCAAATCAAAATCGAATAAACCCTAAATCAAAAATAAA
Found at i:1260206 original size:22 final size:22
Alignment explanation
Indices: 1260181--1260223 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1260171 CAAAAAAAAA
* *
1260181 ACTATTTTTTTAATGTTTTGCC
1 ACTATTTGTTCAATGTTTTGCC
*
1260203 ACTATTTGTTCATTGTTTTGC
1 ACTATTTGTTCAATGTTTTGC
1260224 TATTATTTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (22 bp):
ACTATTTGTTCAATGTTTTGCC
Found at i:1262827 original size:6 final size:6
Alignment explanation
Indices: 1262816--1262841 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1262806 ATTTCTATTA
1262816 ATTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT AT
1262842 AAACTTGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTAT
Found at i:1263015 original size:18 final size:18
Alignment explanation
Indices: 1262992--1263026 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1262982 TAAAATTATA
* *
1262992 ATTTTTTTATTTTTAAAT
1 ATTTTTTAAATTTTAAAT
1263010 ATTTTTTAAATTTTAAA
1 ATTTTTTAAATTTTAAA
1263027 AGGGATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTAAATTTTAAAT
Found at i:1265274 original size:15 final size:16
Alignment explanation
Indices: 1265244--1265282 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1265234 TGGCAAAAAT
1265244 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
1265261 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
1265276 ATAATTT
1 ATAATTT
1265283 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:1265359 original size:29 final size:30
Alignment explanation
Indices: 1265291--1265353 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
1265281 TTTTAAAAAA
* *
1265291 TTAAATTA-AATTATTATTATTTTTAGATG
1 TTAAAATATAATTATTATTATTATTAGATG
1265320 TTAAAATATAATT-TTATTATTATTA-AT-
1 TTAAAATATAATTATTATTATTATTAGATG
1265347 TTAAAAT
1 TTAAAAT
1265354 TTATAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 7 0.23
28 2 0.06
29 18 0.58
30 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TTAAAATATAATTATTATTATTATTAGATG
Found at i:1266785 original size:20 final size:22
Alignment explanation
Indices: 1266760--1266817 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
1266750 AAAAACGCAT
1266760 AAAAATAACATCTAAACA-A-C
1 AAAAATAACATCTAAACACAGC
* *
1266780 AAAAATAACAACCAAACAGCAGC
1 AAAAATAACATCTAAACA-CAGC
1266803 AAAAATAACAT-TAAA
1 AAAAATAACATCTAAA
1266818 AAAAACAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 16 0.52
22 4 0.13
23 11 0.35
ACGTcount: A:0.66, C:0.19, G:0.03, T:0.12
Consensus pattern (22 bp):
AAAAATAACATCTAAACACAGC
Found at i:1266791 original size:12 final size:12
Alignment explanation
Indices: 1266774--1266875 Score: 63
Period size: 12 Copynumber: 8.8 Consensus size: 12
1266764 ATAACATCTA
1266774 AACAACAAAAAT
1 AACAACAAAAAT
* *
1266786 AACAAC-CAAAC
1 AACAACAAAAAT
* *
1266797 AGCAGCAAAAAT
1 AACAACAAAAAT
**
1266809 AAC-ATTAAAA-
1 AACAACAAAAAT
1266819 AA-AACAAAAAT
1 AACAACAAAAAT
*
1266830 AGGC-ACAAAAAT
1 A-ACAACAAAAAT
* *
1266842 AACAGCAAAAAC
1 AACAACAAAAAT
1266854 AAC-ACAAAAAT
1 AACAACAAAAAT
1266865 AACAATCAAAA
1 AACAA-CAAAA
1266876 CAATAAAAAA
Statistics
Matches: 64, Mismatches: 18, Indels: 15
0.66 0.19 0.15
Matches are distributed among these distances:
10 7 0.11
11 22 0.34
12 30 0.47
13 5 0.08
ACGTcount: A:0.69, C:0.19, G:0.05, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:1266861 original size:11 final size:11
Alignment explanation
Indices: 1266802--1266868 Score: 66
Period size: 12 Copynumber: 6.0 Consensus size: 11
1266792 CAAACAGCAG
1266802 CAAAAATAACA
1 CAAAAATAACA
*
1266813 TTAAAAA-AA-A
1 -CAAAAATAACA
*
1266823 CAAAAATAGGCA
1 CAAAAATA-ACA
1266835 CAAAAATAACA
1 CAAAAATAACA
*
1266846 GCAAAAACAACA
1 -CAAAAATAACA
1266858 CAAAAATAACA
1 CAAAAATAACA
1266869 ATCAAAACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 5 0.11
10 2 0.04
11 14 0.31
12 24 0.53
ACGTcount: A:0.70, C:0.16, G:0.04, T:0.09
Consensus pattern (11 bp):
CAAAAATAACA
Found at i:1266884 original size:56 final size:56
Alignment explanation
Indices: 1266778--1266884 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 56
1266768 CATCTAAACA
* * *
1266778 ACAAAAATAACAACCAAACAGCAGCAAAAATAACATTAAAAAAAACAAAAATAGGC
1 ACAAAAATAACAACAAAACAACAGCAAAAATAACAATAAAAAAAACAAAAATAGGC
* * * *
1266834 ACAAAAATAACAGCAAAAACAACA-CAAAAATAACAATCAAAACAATAAAAA
1 ACAAAAATAACAAC-AAAACAACAGCAAAAATAACAATAAAAAAAACAAAAA
1266885 AAGCACCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 36 0.84
57 7 0.16
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (56 bp):
ACAAAAATAACAACAAAACAACAGCAAAAATAACAATAAAAAAAACAAAAATAGGC
Found at i:1266885 original size:23 final size:23
Alignment explanation
Indices: 1266836--1266886 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1266826 AAATAGGCAC
*
1266836 AAAAATAACAGCAAAAACAACAC
1 AAAAATAACAGCAAAAACAACAA
* *
1266859 AAAAATAACAATC-AAAACAATAA
1 AAAAATAAC-AGCAAAAACAACAA
1266882 AAAAA
1 AAAAA
1266887 GCACCAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.75, C:0.16, G:0.02, T:0.08
Consensus pattern (23 bp):
AAAAATAACAGCAAAAACAACAA
Found at i:1266913 original size:18 final size:18
Alignment explanation
Indices: 1266881--1266947 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 18
1266871 CAAAACAATA
*
1266881 AAAAAAGCACCAAAACAGT
1 AAAAAA-CACAAAAACAGT
1266900 AAAAAACACAAAAACAGT
1 AAAAAACACAAAAACAGT
*
1266918 AAAAAATAGCAACCAAAGCAGT
1 AAAAAACA-CAA--AAA-CAGT
1266940 AAAAAACA
1 AAAAAACA
1266948 ACATCAAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 18 0.44
19 9 0.22
21 3 0.07
22 11 0.27
ACGTcount: A:0.67, C:0.18, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAAACACAAAAACAGT
Found at i:1266914 original size:38 final size:42
Alignment explanation
Indices: 1266871--1266962 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 42
1266861 AAATAACAAT
1266871 CAAAACAATAAAAAA-AGC-ACCAAAACAGTAAAAAAC-ACA
1 CAAAACAATAAAAAATAGCAACCAAAACAGTAAAAAACAACA
* *
1266910 -AAAACAGTAAAAAATAGCAACCAAAGCAGTAAAAAACAACA
1 CAAAACAATAAAAAATAGCAACCAAAACAGTAAAAAACAACA
1266951 TCAAAACAATAA
1 -CAAAACAATAA
1266963 TATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 13 0.29
39 3 0.07
40 17 0.38
41 3 0.07
43 9 0.20
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.08
Consensus pattern (42 bp):
CAAAACAATAAAAAATAGCAACCAAAACAGTAAAAAACAACA
Found at i:1267344 original size:18 final size:18
Alignment explanation
Indices: 1267321--1267362 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1267311 ATTTGAAATG
1267321 TAATTTTTATTATTT-TAA
1 TAATTTTTATT-TTTATAA
*
1267339 TAATTTATATTTTTATAA
1 TAATTTTTATTTTTATAA
1267357 -AATTTT
1 TAATTTT
1267363 AAAAAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TAATTTTTATTTTTATAA
Found at i:1271551 original size:27 final size:27
Alignment explanation
Indices: 1271521--1271572 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1271511 CCCTAAATAT
*
1271521 AAACCTTAAACCTCAAATCCAAAACTA
1 AAACCCTAAACCTCAAATCCAAAACTA
* *
1271548 AAACCCTAAACCTTAAATCCCAAAC
1 AAACCCTAAACCTCAAATCCAAAAC
1271573 CCAAACTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (27 bp):
AAACCCTAAACCTCAAATCCAAAACTA
Found at i:1271578 original size:27 final size:27
Alignment explanation
Indices: 1271521--1271578 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1271511 CCCTAAATAT
* *
1271521 AAACCTTAAACCTCAAATCCAAAACTA
1 AAACCCTAAACCTCAAATCCAAAACCA
* * *
1271548 AAACCCTAAACCTTAAATCCCAAACCC
1 AAACCCTAAACCTCAAATCCAAAACCA
1271575 AAAC
1 AAAC
1271579 TTTGAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (27 bp):
AAACCCTAAACCTCAAATCCAAAACCA
Found at i:1274427 original size:2 final size:2
Alignment explanation
Indices: 1274420--1274456 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1274410 TCAATCTTTT
*
1274420 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1274457 TATATTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:1274461 original size:2 final size:2
Alignment explanation
Indices: 1274456--1274515 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
1274446 ACACATACAC
*
1274456 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1274498 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1274516 TATTTATTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1278244 original size:20 final size:21
Alignment explanation
Indices: 1278206--1278244 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1278196 CATTAATCTG
1278206 TTTTTATTATTGGGCTTTAAT
1 TTTTTATTATTGGGCTTTAAT
1278227 TTTTTAATT-TTGGG-TTTA
1 TTTTT-ATTATTGGGCTTTA
1278245 TATGATGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 10 0.59
22 3 0.18
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (21 bp):
TTTTTATTATTGGGCTTTAAT
Found at i:1282766 original size:2 final size:2
Alignment explanation
Indices: 1282759--1282785 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1282749 ATTAATTAAT
1282759 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1282786 TATTGTACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1285600 original size:29 final size:29
Alignment explanation
Indices: 1285568--1285628 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1285558 ATATCTATGA
1285568 AAACGTGTTAAGATTGAAATATCCTAGCC
1 AAACGTGTTAAGATTGAAATATCCTAGCC
1285597 AAACGTGTTAAGATTGAAATATCCTAGCC
1 AAACGTGTTAAGATTGAAATATCCTAGCC
1285626 AAA
1 AAA
1285629 TTCTGAAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (29 bp):
AAACGTGTTAAGATTGAAATATCCTAGCC
Found at i:1295974 original size:142 final size:141
Alignment explanation
Indices: 1295756--1296036 Score: 438
Period size: 142 Copynumber: 2.0 Consensus size: 141
1295746 TTTTGATACC
* ** * *
1295756 TTAAGCTAAGTTCATTAGAACTAGCCTAGAATTTCAAAATTTAGGCACGACGTAGCCAACAAATC
1 TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAAAAAATC
**
1295821 AGTTCTTAACCTCTCACTTGCCATGACTCAA-TTAGATACCTTAAGCTAAGTTCAATCAGTTCAA
66 AGTTCTTAACCTCTCACGCGCCATGACTCAATTTA-ATACCTTAAGCTAAGTTCAATCAGTTCAA
*
1295885 GTTCAATTAACT
130 CTTCAATTAACT
* *
1295897 TTAAGCTAAGTTCAGTTAAAACTAGCCTAGAGTTTCAAAAAATAGGCACTACATAGCCAAAAAAT
1 TTAAGCTAAGTTCA-TTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAAAAAAT
*
1295962 CAGTTCTTAACCTCTCACGCGCCATGATTCAATTTAATACCTTAAGCTAAGTTCAATCAGTTCAA
65 CAGTTCTTAACCTCTCACGCGCCATGACTCAATTTAATACCTTAAGCTAAGTTCAATCAGTTCAA
1296027 CTTCAATTAA
130 CTTCAATTAA
1296037 AGCTAGCTTA
Statistics
Matches: 127, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
141 14 0.11
142 110 0.87
143 3 0.02
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (141 bp):
TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAAAAAATC
AGTTCTTAACCTCTCACGCGCCATGACTCAATTTAATACCTTAAGCTAAGTTCAATCAGTTCAAC
TTCAATTAACT
Found at i:1303041 original size:110 final size:110
Alignment explanation
Indices: 1302840--1303048 Score: 310
Period size: 110 Copynumber: 1.9 Consensus size: 110
1302830 ACTCTTGATA
* *
1302840 TTATAACTTCTCCTATAGAATCCGGAAAGAAGCATGCATAATCAACCTTAATGATATTCAAACTG
1 TTATAACTTCTCCTATAGAATCCGGAAACAAGCATGCATAATCAACCTTAATGATATTCAAACTA
*
1302905 CTCTAAACGATACACATTCATATACACGAAGGCATTGATGTCGTG
66 CTCTAAACGATACACATACATATACACGAAGGCATTGATGTCGTG
* * * *
1302950 TTATAACTTCTTCTATAGAATCTGGAAACAGGCATGCATAATCAACCTTATTGATATTCAAACTA
1 TTATAACTTCTCCTATAGAATCCGGAAACAAGCATGCATAATCAACCTTAATGATATTCAAACTA
* ** * *
1303015 CTCTGAATTATACATATACATGTACACGAAGGCA
66 CTCTAAACGATACACATACATATACACGAAGGCA
1303049 AAGTTCTCAA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (110 bp):
TTATAACTTCTCCTATAGAATCCGGAAACAAGCATGCATAATCAACCTTAATGATATTCAAACTA
CTCTAAACGATACACATACATATACACGAAGGCATTGATGTCGTG
Found at i:1305860 original size:26 final size:26
Alignment explanation
Indices: 1305822--1305873 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1305812 TTACTATGAA
1305822 AATAATAAAGGTTAAAATACAAACACT
1 AATAATAAAGGTTAAAAT-CAAACACT
* *
1305849 AATAA-AAAGGTTGAAATCTAACACT
1 AATAATAAAGGTTAAAATCAAACACT
1305874 TGATAGTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.23
Consensus pattern (26 bp):
AATAATAAAGGTTAAAATCAAACACT
Found at i:1309035 original size:15 final size:16
Alignment explanation
Indices: 1309017--1309049 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1309007 AAAGTACATT
*
1309017 AATTAAAA-ACAATAA
1 AATTAAAATACAAGAA
1309032 AATTAAAATACAAGAA
1 AATTAAAATACAAGAA
1309048 AA
1 AA
1309050 AAAGCCACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (16 bp):
AATTAAAATACAAGAA
Found at i:1319714 original size:25 final size:25
Alignment explanation
Indices: 1319694--1319742 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1319684 CCATTTTCTA
1319694 TATTTATA-ATATAATATATTTTAT
1 TATTTATATATATAATATATTTTAT
* *
1319718 TATTTTTATATATTATATATTTTAT
1 TATTTATATATATAATATATTTTAT
1319743 AACACATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTTATATATATAATATATTTTAT
Found at i:1319743 original size:16 final size:18
Alignment explanation
Indices: 1319707--1319740 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1319697 TTATAATATA
*
1319707 ATATATTTTATTATTTTT
1 ATATATTATATTATTTTT
1319725 ATATATTATA-TATTTT
1 ATATATTATATTATTTT
1319741 ATAACACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATATATTATATTATTTTT
Found at i:1323358 original size:35 final size:35
Alignment explanation
Indices: 1323319--1323390 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1323309 ATAAAAGATA
* *
1323319 TTCCATTTTTATAATTAATCTATTTCCCGTACAAT
1 TTCCATTTTTACAATTAATCTATTTCCCGTAAAAT
1323354 TTCCATTTTTACAATTAATCTATTTCCCGTAAAAT
1 TTCCATTTTTACAATTAATCTATTTCCCGTAAAAT
1323389 TT
1 TT
1323391 TCATAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.49
Consensus pattern (35 bp):
TTCCATTTTTACAATTAATCTATTTCCCGTAAAAT
Found at i:1324912 original size:29 final size:29
Alignment explanation
Indices: 1324879--1324947 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
1324869 CATTTAAAAA
*
1324879 TTGAGTAATTATTTTATAATTTTTTATAG
1 TTGAGTAATCATTTTATAATTTTTTATAG
*
1324908 TTGAGTGATCATTTTATAATTTTTTATAG
1 TTGAGTAATCATTTTATAATTTTTTATAG
*
1324937 TTGAGTGATCA
1 TTGAGTAATCA
1324948 AAAAAGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.54
Consensus pattern (29 bp):
TTGAGTAATCATTTTATAATTTTTTATAG
Found at i:1326101 original size:16 final size:16
Alignment explanation
Indices: 1326072--1326122 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
1326062 ATTTATTCAG
* *
1326072 ATCATTTCATGTTTAA
1 ATCATTTTAGGTTTAA
*
1326088 CTCATTTTAGGTTTAA
1 ATCATTTTAGGTTTAA
* *
1326104 ATTATTTTAGGTTTCA
1 ATCATTTTAGGTTTAA
1326120 ATC
1 ATC
1326123 GTCTTAATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (16 bp):
ATCATTTTAGGTTTAA
Found at i:1339505 original size:29 final size:29
Alignment explanation
Indices: 1339462--1339539 Score: 147
Period size: 29 Copynumber: 2.7 Consensus size: 29
1339452 TTTTATTCAC
1339462 AAAAAAGAGAAAATAATAAAATATTTGAAT
1 AAAAAAGA-AAAATAATAAAATATTTGAAT
1339492 AAAAAAGAAAAATAATAAAATATTTGAAT
1 AAAAAAGAAAAATAATAAAATATTTGAAT
1339521 AAAAAAGAAAAATAATAAA
1 AAAAAAGAAAAATAATAAA
1339540 TAAAATAACC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 40 0.83
30 8 0.17
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (29 bp):
AAAAAAGAAAAATAATAAAATATTTGAAT
Found at i:1339563 original size:38 final size:38
Alignment explanation
Indices: 1339521--1339634 Score: 228
Period size: 38 Copynumber: 3.0 Consensus size: 38
1339511 ATATTTGAAT
1339521 AAAAAAGAAAAATAATAAATAAAATAACCCCACCAGTA
1 AAAAAAGAAAAATAATAAATAAAATAACCCCACCAGTA
1339559 AAAAAAGAAAAATAATAAATAAAATAACCCCACCAGTA
1 AAAAAAGAAAAATAATAAATAAAATAACCCCACCAGTA
1339597 AAAAAAGAAAAATAATAAATAAAATAACCCCACCAGTA
1 AAAAAAGAAAAATAATAAATAAAATAACCCCACCAGTA
1339635 CATTAGATAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.66, C:0.16, G:0.05, T:0.13
Consensus pattern (38 bp):
AAAAAAGAAAAATAATAAATAAAATAACCCCACCAGTA
Found at i:1340301 original size:21 final size:19
Alignment explanation
Indices: 1340272--1340320 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
1340262 TTTTTATTTA
*
1340272 AAAAATATTTTTAAAAAAATT
1 AAAATTATTTTT-AAAAAA-T
* *
1340293 AAAATTATTTTTTAAATAT
1 AAAATTATTTTTAAAAAAT
1340312 AAAATTATT
1 AAAATTATT
1340321 AAAATCATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.40
20 4 0.16
21 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATTATTTTTAAAAAAT
Found at i:1341128 original size:38 final size:37
Alignment explanation
Indices: 1341049--1341140 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 37
1341039 ATGATGATGA
* * *
1341049 TTTAATAATTTTATATTTTAAATTAATTTTAAGTTAGT
1 TTTAATAATTTTTTATTTTAAAATAATTTTAAG-TAAT
1341087 TTTAATAATTTTTTATTTTAAAAAATAATTTTAA-TAAT
1 TTTAATAATTTTTTATTTT--AAAATAATTTTAAGTAAT
*
1341125 TTTAA-AATTATTTATT
1 TTTAATAATTTTTTATT
1341141 GACGTGGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 10 0.21
38 26 0.54
40 12 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (37 bp):
TTTAATAATTTTTTATTTTAAAATAATTTTAAGTAAT
Found at i:1341131 original size:20 final size:19
Alignment explanation
Indices: 1341052--1341137 Score: 54
Period size: 20 Copynumber: 4.4 Consensus size: 19
1341042 ATGATGATTT
1341052 AATAATTTTAT-ATTTTAA
1 AATAATTTTATAATTTTAA
* *
1341070 ATTAATTTTAAGTTAGTTTT--
1 AATAATTTT-A--TAATTTTAA
*
1341090 AATAATTTT-TTATTTTAAAA
1 AATAATTTTATAATTTT--AA
1341110 AATAATTTTAATAATTTTAA
1 AATAATTTT-ATAATTTTAA
*
1341130 AATTATTT
1 AATAATTT
1341138 ATTGACGTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
16 5 0.10
18 8 0.16
19 1 0.02
20 26 0.51
21 1 0.02
22 10 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATAATTTTATAATTTTAA
Found at i:1341846 original size:29 final size:29
Alignment explanation
Indices: 1341783--1341855 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
1341773 TACCTTTTAA
*
1341783 TAAA-TTTGAAAATTAATCTTTGTACTTT
1 TAAATTTTGAAATTTAATCTTTGTACTTT
**
1341811 TGTATTTT-AGAATTTAATCTCTT-TACTTT
1 TAAATTTTGA-AATTTAATCT-TTGTACTTT
1341840 TAAATTTTGAAATTTA
1 TAAATTTTGAAATTTA
1341856 GTCTAATTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
28 3 0.08
29 30 0.83
30 3 0.08
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (29 bp):
TAAATTTTGAAATTTAATCTTTGTACTTT
Found at i:1343352 original size:6 final size:6
Alignment explanation
Indices: 1343341--1343375 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1343331 AAAATAAATT
*
1343341 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1343376 AATGTCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:1343360 original size:17 final size:17
Alignment explanation
Indices: 1343340--1343373 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1343330 CAAAATAAAT
1343340 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
1343357 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
1343374 AAAATGTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:1343960 original size:29 final size:31
Alignment explanation
Indices: 1343894--1344060 Score: 152
Period size: 30 Copynumber: 5.6 Consensus size: 31
1343884 ACCCCCAAAA
* * * *
1343894 TTTTCTAAAATTACATTTT-AGCACATAAAC
1 TTTTCCAAAATTATATTTTGACCTCATAAAC
* *
1343924 GTTT-CAAAATTATATTTTAACCTCAT-AAC
1 TTTTCCAAAATTATATTTTGACCTCATAAAC
* * *
1343953 -TTTCCAAAAATACATTTTGACC-C-CAAAC
1 TTTTCCAAAATTATATTTTGACCTCATAAAC
* *
1343981 TTTTCCAAAAATTACATTTTGACCGC-TAAAC
1 TTTTCC-AAAATTATATTTTGACCTCATAAAC
*
1344012 TTTTCCAAAATTATATTTTGACCT-TTAAAC
1 TTTTCCAAAATTATATTTTGACCTCATAAAC
*
1344042 TTTCCCAAAATTATATTTT
1 TTTTCCAAAATTATATTTT
1344061 AACCCAAAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.06
29 35 0.30
30 63 0.54
31 11 0.09
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.40
Consensus pattern (31 bp):
TTTTCCAAAATTATATTTTGACCTCATAAAC
Found at i:1344080 original size:89 final size:87
Alignment explanation
Indices: 1343881--1344089 Score: 210
Period size: 89 Copynumber: 2.4 Consensus size: 87
1343871 AAATCATATA
* * *
1343881 TTAACCCCCAAAATTTTCTAAAATTACATTTTAGCACATAAACGTTTCAAAATTATATTTTAACC
1 TTAA-CCCAAAAATTTTCAAAAATTACATTTTACCACATAAACGTTTCAAAATTATATTTTAACC
1343946 TCATAACTTTCCAAAAATACATT
65 TCATAACTTTCCAAAAATACATT
* * * * * *
1343969 TTGACCCCAAACTTTTCCAAAAATTACATTTTGACCGC-TAAACTTTTCCAAAATTATATTTTGA
1 TTAACCCAAAAATTTT-CAAAAATTACATTTT-ACCACATAAACGTTT-CAAAATTATATTTTAA
* * *
1344033 CCT-TTAAACTTTCCCAAAATTATATT
63 CCTCAT-AACTTT-CCAAAAATACATT
1344059 TTAACCCAAAAATTCTT-AAAAACTT-CATTTT
1 TTAACCCAAAAATT-TTCAAAAA-TTACATTTT
1344090 TTCGACCCCA
Statistics
Matches: 101, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
87 11 0.11
88 26 0.26
89 38 0.38
90 24 0.24
91 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (87 bp):
TTAACCCAAAAATTTTCAAAAATTACATTTTACCACATAAACGTTTCAAAATTATATTTTAACCT
CATAACTTTCCAAAAATACATT
Found at i:1347249 original size:14 final size:15
Alignment explanation
Indices: 1347232--1347261 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1347222 ATAAGTATTT
1347232 TTATATAAAT-TTAA
1 TTATATAAATATTAA
1347246 TTATATAAATATTAA
1 TTATATAAATATTAA
1347261 T
1 T
1347262 ATAAAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATAAATATTAA
Done.