Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 138 of 193
Found at i:43266498 original size:14 final size:14
Alignment explanation
Indices: 43266479--43266506 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43266469 GTTTAAAAAT
43266479 TTTAATTAATTAAA
1 TTTAATTAATTAAA
43266493 TTTAATTAATTAAA
1 TTTAATTAATTAAA
43266507 AATCTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:43272441 original size:13 final size:14
Alignment explanation
Indices: 43272423--43272451 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
43272413 ATTTCTTCGC
43272423 AAAAAAGAA-AAAA
1 AAAAAAGAAGAAAA
43272436 AAAAAAGAAGAAAA
1 AAAAAAGAAGAAAA
43272450 AA
1 AA
43272452 TGGATTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAGAAAA
Found at i:43279493 original size:15 final size:17
Alignment explanation
Indices: 43279473--43279506 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
43279463 AATTTTTTAA
43279473 AAATTA-TAAAAA-TAT
1 AAATTATTAAAAATTAT
43279488 AAATTATTAAAAATTAT
1 AAATTATTAAAAATTAT
43279505 AA
1 AA
43279507 TTTAATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTATTAAAAATTAT
Found at i:43284349 original size:16 final size:16
Alignment explanation
Indices: 43284324--43284358 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43284314 ACATAAACTC
*
43284324 AAATTAGAAATGATTT
1 AAATTAGAAATAATTT
*
43284340 AAATTTGAAATAATTT
1 AAATTAGAAATAATTT
43284356 AAA
1 AAA
43284359 ATGATTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (16 bp):
AAATTAGAAATAATTT
Found at i:43284940 original size:126 final size:126
Alignment explanation
Indices: 43284727--43284962 Score: 305
Period size: 126 Copynumber: 1.9 Consensus size: 126
43284717 TTAACTACAA
* * * *
43284727 GTGTCATCATCTTGTTTGGGCTAAAGATGATATGGTTTGAGATTAATCCTATTCATAATAACCTA
1 GTGTCATCATCTTGTTCGAGCTAAAGATGACATGGTTTGAGATCAATCCTATTCATAATAACCTA
* * * * *
43284792 AACACATAAGAACTCGAGCTTGAAATTGAAATTGACATAAAACCATCCTTTTTAAATATAG
66 AACACATAAGAACCCGAGCTTGAAACTAAAATTAACACAAAACCATCCTTTTTAAATATAG
* * * * * *
43284853 GTGTCCTCATCTTGTTCGAGCTAAGGATGGCATGGTTTGAGATCAATCCTGTTTATAATGACC-A
1 GTGTCATCATCTTGTTCGAGCTAAAGATGACATGGTTTGAGATCAATCCTATTCATAATAACCTA
43284917 GAACACA-AAGCAACCCGAGCTTGAAACTAAAATTAACACAAAACCA
66 -AACACATAAG-AACCCGAGCTTGAAACTAAAATTAACACAAAACCA
43284963 ATGATTTTTT
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
125 4 0.04
126 89 0.96
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (126 bp):
GTGTCATCATCTTGTTCGAGCTAAAGATGACATGGTTTGAGATCAATCCTATTCATAATAACCTA
AACACATAAGAACCCGAGCTTGAAACTAAAATTAACACAAAACCATCCTTTTTAAATATAG
Found at i:43285553 original size:60 final size:62
Alignment explanation
Indices: 43285488--43285659 Score: 186
Period size: 63 Copynumber: 2.8 Consensus size: 62
43285478 GCACCCACCA
* *
43285488 CCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCGCA-CC-CACCACAGCCAGAG
1 CCACAGCCACTGCTATTCACCATGCTTCCACAACCACCACCACAGCCACACCACAGCCAGAG
* * ** *
43285548 CCACAGCCGCTGCTATTCACTATGCTTCTGCAACCACCCCCACAGCCAGCACCACAGCCAGAG
1 CCACAGCCACTGCTATTCACCATGCTTCCACAACCACCACCACAGCCA-CACCACAGCCAGAG
** * * * * * *
43285611 CCACAGCCACCACTCTTCACCAAGTTTCCACATCCAGCACCACAACCAC
1 CCACAGCCACTGCTATTCACCATGCTTCCACAACCACCACCACAGCCAC
43285660 CGCAGCTGCC
Statistics
Matches: 89, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
60 37 0.42
61 2 0.02
62 1 0.01
63 49 0.55
ACGTcount: A:0.27, C:0.47, G:0.12, T:0.14
Consensus pattern (62 bp):
CCACAGCCACTGCTATTCACCATGCTTCCACAACCACCACCACAGCCACACCACAGCCAGAG
Found at i:43285604 original size:12 final size:12
Alignment explanation
Indices: 43285587--43285619 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43285577 GCAACCACCC
43285587 CCACAGCCAGCA-
1 CCACAGCCAG-AG
43285599 CCACAGCCAGAG
1 CCACAGCCAGAG
43285611 CCACAGCCA
1 CCACAGCCA
43285620 CCACTCTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 1 0.05
12 19 0.95
ACGTcount: A:0.33, C:0.48, G:0.18, T:0.00
Consensus pattern (12 bp):
CCACAGCCAGAG
Found at i:43285746 original size:108 final size:110
Alignment explanation
Indices: 43285551--43285815 Score: 426
Period size: 108 Copynumber: 2.4 Consensus size: 110
43285541 GCCAGAGCCA
* ** * * *
43285551 CAGCCGCTGCTATTCACTATGCTTCTGCAACCACCCCCACAGCCAGCACCACAGCCAGAGCCACA
1 CAGCCGCCGCTATTCACTATGCTTCCACAACCACCCCCACACCCACCACCACAACCA-AGCCACA
43285616 GCCACCACTCTTCACCAAGTTTCCACATCCAGCACCACAACCACCG
65 GCCACCACTCTTCACCAAGTTTCCACATCCAGCACCACAACCACCG
* *
43285662 CAGCTGCCGCTATTCACTATGCTTCCACAACCACCCCCGCACCCACCACCACAACC-A-CCACAG
1 CAGCCGCCGCTATTCACTATGCTTCCACAACCACCCCCACACCCACCACCACAACCAAGCCACAG
*
43285725 CCACCACTCTTCACCATGTTTCCACATCCAGCACCACAACCACCG
66 CCACCACTCTTCACCAAGTTTCCACATCCAGCACCACAACCACCG
43285770 CAGCCGCCGCTATTCACTATGCTTCCACAACCACCCCCACACCCAC
1 CAGCCGCCGCTATTCACTATGCTTCCACAACCACCCCCACACCCAC
43285816 TGCCGCAACC
Statistics
Matches: 143, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
108 94 0.66
109 1 0.01
111 48 0.34
ACGTcount: A:0.26, C:0.49, G:0.10, T:0.15
Consensus pattern (110 bp):
CAGCCGCCGCTATTCACTATGCTTCCACAACCACCCCCACACCCACCACCACAACCAAGCCACAG
CCACCACTCTTCACCAAGTTTCCACATCCAGCACCACAACCACCG
Found at i:43285768 original size:60 final size:60
Alignment explanation
Indices: 43285638--43285768 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 60
43285628 CACCAAGTTT
* * * ** * * *
43285638 CCACATCCAGCACCACAACCACCGCAGCTGCCGCTATTCACTATGCTTCCACAACCACCC
1 CCACAACCACCACCACAACCACCACAGCCACCACTATTCACCATGCTTCCACAACCACCA
* * * * * *
43285698 CCGCACCCACCACCACAACCACCACAGCCACCACTCTTCACCATGTTTCCACATCCAGCA
1 CCACAACCACCACCACAACCACCACAGCCACCACTATTCACCATGCTTCCACAACCACCA
43285758 CCACAACCACC
1 CCACAACCACC
43285769 GCAGCCGCCG
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.28, C:0.51, G:0.08, T:0.13
Consensus pattern (60 bp):
CCACAACCACCACCACAACCACCACAGCCACCACTATTCACCATGCTTCCACAACCACCA
Found at i:43285810 original size:48 final size:48
Alignment explanation
Indices: 43285704--43285815 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
43285694 ACCCCCGCAC
* * *
43285704 CCACCACCACAACCACCACAGCCACCACTCTTCACCATGTTTCCACAT
1 CCACCACCACAACCACCACAGCCACCACTATTCACCATGCTTCCACAA
* * * * *
43285752 CCAGCACCACAACCACCGCAGCCGCCGCTATTCACTATGCTTCCACAA
1 CCACCACCACAACCACCACAGCCACCACTATTCACCATGCTTCCACAA
* *
43285800 CCACCCCCACACCCAC
1 CCACCACCACAACCAC
43285816 TGCCGCAACC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.28, C:0.52, G:0.07, T:0.13
Consensus pattern (48 bp):
CCACCACCACAACCACCACAGCCACCACTATTCACCATGCTTCCACAA
Found at i:43285827 original size:12 final size:12
Alignment explanation
Indices: 43285812--43285836 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43285802 ACCCCCACAC
43285812 CCACTGCCGCAA
1 CCACTGCCGCAA
43285824 CCACTGCCGCAA
1 CCACTGCCGCAA
43285836 C
1 C
43285837 TACCACCACA
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:0.24, C:0.52, G:0.16, T:0.08
Consensus pattern (12 bp):
CCACTGCCGCAA
Found at i:43291373 original size:24 final size:25
Alignment explanation
Indices: 43291327--43291373 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
43291317 TAAAATTAAT
43291327 TAATCTAACTTTATTTTTTAATATG
1 TAATCTAACTTTATTTTTTAATATG
*
43291352 TAATTTAACTTTA-TTTTTAATA
1 TAATCTAACTTTATTTTTTAATA
43291374 ATATATTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.57
Consensus pattern (25 bp):
TAATCTAACTTTATTTTTTAATATG
Found at i:43297608 original size:26 final size:26
Alignment explanation
Indices: 43297577--43297656 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
43297567 TTAATTAAAT
*
43297577 TAATAATTAATATAGTTCAACTACTC
1 TAATAATTAATATAGTTCAACTAATC
* * *
43297603 TAATAA-AAATACA-TT-AATTAAAT-
1 TAATAATTAATATAGTTCAACT-AATC
*
43297626 TAATAATTAATATAGTTCAACTATTC
1 TAATAATTAATATAGTTCAACTAATC
43297652 TAATA
1 TAATA
43297657 GGCCATGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
23 9 0.22
24 9 0.22
25 9 0.22
26 14 0.34
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.39
Consensus pattern (26 bp):
TAATAATTAATATAGTTCAACTAATC
Found at i:43297625 original size:49 final size:49
Alignment explanation
Indices: 43297557--43297656 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
43297547 CCTAATCAAT
43297557 TAAAAATACATTAATTAAATTAATAATTAATATAGTTCAACTACTCTAA
1 TAAAAATACATTAATTAAATTAATAATTAATATAGTTCAACTACTCTAA
*
43297606 TAAAAATACATTAATTAAATTAATAATTAATATAGTTCAACTATTCTAA
1 TAAAAATACATTAATTAAATTAATAATTAATATAGTTCAACTACTCTAA
43297655 TA
1 TA
43297657 GGCCATGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (49 bp):
TAAAAATACATTAATTAAATTAATAATTAATATAGTTCAACTACTCTAA
Found at i:43297655 original size:23 final size:23
Alignment explanation
Indices: 43297580--43297655 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
43297570 ATTAAATTAA
*
43297580 TAATTAATATAGTTCAACTACTC
1 TAATTAATATAGTTCAACTATTC
* * * * *
43297603 TAATAAAAATACATT-AATTAAATTAA
1 TAATTAATATA-GTTCAACT--ATT-C
43297629 TAATTAATATAGTTCAACTATTC
1 TAATTAATATAGTTCAACTATTC
43297652 TAAT
1 TAAT
43297656 AGGCCATGAA
Statistics
Matches: 37, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
23 16 0.43
24 5 0.14
25 4 0.11
26 12 0.32
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (23 bp):
TAATTAATATAGTTCAACTATTC
Found at i:43300739 original size:28 final size:29
Alignment explanation
Indices: 43300708--43300783 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 29
43300698 AATCTTAGAT
*
43300708 TTTAAAATTAAGTTTAAATTGA-TTCAAA
1 TTTAAAATTAAATTTAAATTGATTTCAAA
*** * *
43300736 TTTATTTTTAAATTTAAATTTATTTTAAA
1 TTTAAAATTAAATTTAAATTGATTTCAAA
* *
43300765 TTT-AAATTTACTTTAAATT
1 TTTAAAATTAAATTTAAATT
43300784 TAAATTCAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
28 28 0.78
29 8 0.22
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTAAAATTAAATTTAAATTGATTTCAAA
Found at i:43300751 original size:6 final size:6
Alignment explanation
Indices: 43300742--43300789 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
43300732 CAAATTTATT
* *
43300742 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
43300788 TT
1 TT
43300790 CAATCAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 8 0.22
6 28 0.78
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:43300763 original size:17 final size:17
Alignment explanation
Indices: 43300733--43300789 Score: 96
Period size: 17 Copynumber: 3.3 Consensus size: 17
43300723 AAATTGATTC
43300733 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAATTT
43300751 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
43300768 AAATTTACTTTAAATTT
1 AAATTTATTTTAAATTT
43300785 AAATT
1 AAATT
43300790 CAATCAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
17 31 0.82
18 7 0.18
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:43304146 original size:15 final size:17
Alignment explanation
Indices: 43304113--43304148 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
43304103 AACAAGAATA
43304113 AGAGGATAGATTGATTG
1 AGAGGATAGATTGATTG
43304130 AGAGGATA-ATT-ATTG
1 AGAGGATAGATTGATTG
43304145 AGAG
1 AGAG
43304149 TAACTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.28
Consensus pattern (17 bp):
AGAGGATAGATTGATTG
Found at i:43309300 original size:16 final size:17
Alignment explanation
Indices: 43309268--43309304 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
43309258 AACATGATTC
43309268 TTTTTATGTTTTCCATT
1 TTTTTATGTTTTCCATT
43309285 TTTTTATGTTTT-CATT
1 TTTTTATGTTTTCCATT
43309301 TTTT
1 TTTT
43309305 GAACAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTATGTTTTCCATT
Found at i:43314784 original size:15 final size:16
Alignment explanation
Indices: 43314759--43314788 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43314749 GATGGTTCTT
43314759 TTTTTCTTTTTAATTC
1 TTTTTCTTTTTAATTC
43314775 TTTTTC-TTTTAATT
1 TTTTTCTTTTTAATT
43314789 TTGATATGAT
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:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTCTTTTTAATTC
Found at i:43317421 original size:59 final size:59
Alignment explanation
Indices: 43317329--43317707 Score: 469
Period size: 59 Copynumber: 6.4 Consensus size: 59
43317319 CTAAACTATT
* **
43317329 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTGGATTTCAC
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
43317388 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* *
43317447 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCTC
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * * * * *
43317506 TAAAAATTACCCTTTTACCCTCAAACTTCCCAAAA-TCTCA-TTGTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTC-CATTTTTAACCCCGATTTCAC
* * * * * * *
43317564 CAAAAATTACCATTTTACCCCCAAACTTTTCAAAATCCCATCTTTAACCCCAAGTTCACC
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-C
* * * * * *
43317624 CAAAAATTACCATTTTATCCTTGAACTTTTCAAAATCCCATTTTTAACCTC-AATTCTAC
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTC-AC
*
43317683 CAAAAATTA-CATTTTTACCCCCGAA
1 CAAAAATTACCA-TTTTACCCTCGAA
43317708 AGTAAAAAAT
Statistics
Matches: 280, Mismatches: 34, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
58 50 0.18
59 183 0.65
60 47 0.17
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:43317510 original size:29 final size:29
Alignment explanation
Indices: 43317322--43317672 Score: 164
Period size: 29 Copynumber: 11.9 Consensus size: 29
43317312 TAGATCCCTA
* *
43317322 AACTATTCAAAAATTACCATTTTACCCCCG
1 AACT-TTCCAAAATTACCATTTTAACCCCG
*
43317352 AACTTTCCAAAATT-CCATTTTTAA-CCTG
1 AACTTTCCAAAATTACCA-TTTTAACCCCG
*
43317380 GA-TTTCACCAAAAATTACCATTTT-ACCCTCG
1 AACTTT--CC-AAAATTACCATTTTAACCC-CG
43317411 AACTTTCCAAAATT-CCATTTTTAACCCCG
1 AACTTTCCAAAATTACCA-TTTTAACCCCG
43317440 -A-TTTCACCAAAAATTACCATTTT-ACCCTCG
1 AACTTT--CC-AAAATTACCATTTTAACCC-CG
43317470 AACTTTCCAAAATT-CCATTTTTAACCCC-
1 AACTTTCCAAAATTACCA-TTTTAACCCCG
* *
43317498 AA-TTTCTCTAAAAATTACCCTTTT-ACCCTCA
1 AACTTTC-C--AAAATTACCATTTTAACCC-CG
* * *
43317529 AACTTCCCAAAA-T-CTCATTGTAACCTCG
1 AACTTTCCAAAATTAC-CATTTTAACCCCG
* *
43317557 -A-TTTCACCAAAAATTACCATTTTACCCCCA
1 AACTTT--CC-AAAATTACCATTTTAACCCCG
* *
43317587 AACTTTTCAAAA-TCCCATCTTTAACCCC-
1 AACTTTCCAAAATTACCAT-TTTAACCCCG
* * * **
43317615 AAGTTCACCCAAAAATTACCATTTTATCCTTG
1 AACTT--TCC-AAAATTACCATTTTAACCCCG
* *
43317647 AACTTTTCAAAA-TCCCATTTTTAACC
1 AACTTTCCAAAATTACCA-TTTTAACC
43317673 TCAATTCTAC
Statistics
Matches: 247, Mismatches: 32, Indels: 85
0.68 0.09 0.23
Matches are distributed among these distances:
26 2 0.01
27 12 0.05
28 38 0.15
29 84 0.34
30 64 0.26
31 26 0.11
32 21 0.09
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTTCCAAAATTACCATTTTAACCCCG
Found at i:43317634 original size:177 final size:177
Alignment explanation
Indices: 43317329--43317704 Score: 517
Period size: 177 Copynumber: 2.1 Consensus size: 177
43317319 CTAAACTATT
* * * *
43317329 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTGGATTTCACCAAAAA
1 CAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTCCATTTGTAACCTCGATTTCACCAAAAA
* * * * * *
43317394 TTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCA
66 TTACCATTTTACCCCCAAACTTTCCAAAATCCCATCTTTAACCCCAAGTTCACCAAAAATTACCA
*
43317459 TTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCT-C
131 TTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCCCAA-TTCTAC
* * *
43317506 TAAAAATTACCCTTTTACCCTCAAACTTCCCAAAA-TCTCA-TTGTAACCTCGATTTCACCAAAA
1 CAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTC-CATTTGTAACCTCGATTTCACCAAAA
*
43317569 ATTACCATTTTACCCCCAAACTTTTCAAAATCCCATCTTTAACCCCAAGTTCACCCAAAAATTAC
65 ATTACCATTTTACCCCCAAACTTTCCAAAATCCCATCTTTAACCCCAAGTTCA-CCAAAAATTAC
* * * *
43317634 CATTTTATCCTTGAACTTTTCAAAATCCCATTTTTAACCTCAATTCTAC
129 CATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCCCAATTCTAC
43317683 CAAAAATTA-CATTTTTACCCCC
1 CAAAAATTACCA-TTTTACCCCC
43317705 GAAAGTAAAA
Statistics
Matches: 173, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
176 74 0.43
177 99 0.57
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (177 bp):
CAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTCCATTTGTAACCTCGATTTCACCAAAAA
TTACCATTTTACCCCCAAACTTTCCAAAATCCCATCTTTAACCCCAAGTTCACCAAAAATTACCA
TTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCCCAATTCTAC
Found at i:43330190 original size:201 final size:201
Alignment explanation
Indices: 43329687--43330528 Score: 1241
Period size: 201 Copynumber: 4.2 Consensus size: 201
43329677 GGAGTAGTTC
* * * * ** * *
43329687 AACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTTAATGCTCAGACTC
1 AACAAGCGAGGCAGTCATCTTCCTGATGAGATACAAAGAAGAACACCAACTTAGCGCTCAAACAC
* * * *
43329752 GAGCAAATCTTCGAACCCGGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAAGT
66 GAGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
*
43329817 TAGCTTCTTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
131 TAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
43329882 -----A
196 AATCAA
* *
43329883 AACAAGCGAGGCTGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTTAGCGCTCAAACAC
1 AACAAGCGAGGCAGTCATCTTCCTGATGAGATACAAAGAAGAACACCAACTTAGCGCTCAAACAC
* * *
43329948 GAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGACGAAGCAATAAAAAGGT
66 GAGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
* * *
43330013 TAGCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTAAGGAGATCTAGAGAAGCG
131 TAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
43330078 AATCAA
196 AATCAA
*
43330084 AACAAGCGAGGCAGTCATCTTCTTGATGAGATACAAAGAAGAACACCAACTTAGCGCTCAAACAC
1 AACAAGCGAGGCAGTCATCTTCCTGATGAGATACAAAGAAGAACACCAACTTAGCGCTCAAACAC
*
43330149 GAGCAAATCTTAGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
66 GAGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
43330214 TAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
131 TAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
43330279 AATCAA
196 AATCAA
** *
43330285 AACAAGCGAGGCAGTCATCTTCCTGATGAGATACAGAA-AAGAACATTAACTCAGCG-TCAAACA
1 AACAAGCGAGGCAGTCATCTTCCTGATGAGATACA-AAGAAGAACACCAACTTAGCGCTCAAACA
* *
43330348 CCAGCAAATCTTCGAACCCAGCTTCCAGACGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGG
65 CGAGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGG
* * * * * *
43330413 TTAGCTTCCTGATGAGACATAGGGAAGTAGACTAGATTCGTCTTCCTGACGAGATCCAAAGAAGC
130 TTAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGC
*
43330478 GAATTAA
195 GAATCAA
* * * * *
43330485 AAC-AGATGATTGCAGTCATTTTCCTGATGAGACACAAGGAAGAA
1 AACAAG-CGA-GGCAGTCATCTTCCTGATGAGATACAAAGAAGAA
43330529 GATCAGGTCA
Statistics
Matches: 594, Mismatches: 43, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
196 181 0.30
199 2 0.00
200 140 0.24
201 269 0.45
202 2 0.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (201 bp):
AACAAGCGAGGCAGTCATCTTCCTGATGAGATACAAAGAAGAACACCAACTTAGCGCTCAAACAC
GAGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
TAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
AATCAA
Found at i:43332917 original size:30 final size:28
Alignment explanation
Indices: 43332860--43333088 Score: 139
Period size: 30 Copynumber: 7.8 Consensus size: 28
43332850 TAGGTCCTTA
* *
43332860 AACTATTCAAAAATTACCATTTTACCCCCG
1 AACT-TTCCAAAATT-CCATTTTACCCTCG
43332890 AACTTTCCAAAATTCCATTTTTAACCC-CG
1 AACTTTCCAAAATTCCA-TTTT-ACCCTCG
* **
43332919 -A-TTTCACCAAAAATTACCATTGTACCCTTA
1 AACTTT--CC-AAAATT-CCATTTTACCCTCG
*
43332949 AACTTTCCAAAATTCCATTTTAACCTCG
1 AACTTTCCAAAATTCCATTTTACCCTCG
*
43332977 -A-TTTCACCAAAAATTTACCATTTTACCCTCA
1 AACTTT--CC-AAAA-TT-CCATTTTACCCTCG
* *
43333008 AACTTTCCAAAATTTCATTTTTTAACCTCG
1 AACTTTCCAAAATTCCA--TTTTACCCTCG
* *
43333038 -A-TTTCACCAAAAATTACATTTTTACCCCCG
1 AACTTT--CC-AAAATTCCA-TTTTACCCTCG
43333068 AACTTTCCAAAATTCCATTTT
1 AACTTTCCAAAATTCCATTTT
43333089 TAACCCTAAT
Statistics
Matches: 159, Mismatches: 17, Indels: 48
0.71 0.08 0.21
Matches are distributed among these distances:
26 3 0.02
27 4 0.03
28 25 0.16
29 42 0.26
30 48 0.30
31 27 0.17
32 7 0.04
33 3 0.02
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (28 bp):
AACTTTCCAAAATTCCATTTTACCCTCG
Found at i:43332959 original size:59 final size:59
Alignment explanation
Indices: 43332867--43333299 Score: 502
Period size: 59 Copynumber: 7.3 Consensus size: 59
43332857 TTAAACTATT
*
43332867 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* ** *
43332926 CAAAAATTACCATTGTACCCTTAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * *
43332984 CAAAAATTTACCATTTTACCCTCAAACTTTCCAAAATTTCATTTTTTAACCTCGATTTCAC
1 CAAAAA-TTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTTAACCCCGATTTCAC
* ** *
43333045 CAAAAATTA-CATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTAATTTCTC
1 CAAAAATTACCA-TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * * * *
43333104 TAAAAATTACC-CTTTACCCCCAAACTTCCCAAAA-TCTCA-TTTTAAACCCGATTTTAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC-CATTTTTAACCCCGATTTCAC
* * * *
43333161 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATCTTTAACCCCAATTTCACC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-C
* * * * * * *
43333221 CAAAAATTACCATTTTATCTCTAAACTTTTCAAAATCCCATTTTAAACCCC-AATTCTAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTC-AC
43333280 CAAAAATTA-CATTTTTACCC
1 CAAAAATTACCA-TTTTACCC
43333300 TCGAAAGTCA
Statistics
Matches: 321, Mismatches: 41, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
57 25 0.08
58 69 0.21
59 126 0.39
60 77 0.24
61 24 0.07
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:43333060 original size:31 final size:31
Alignment explanation
Indices: 43332966--43333060 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
43332956 CAAAATTCCA
43332966 TTTTAACCTCGATTTCACCAAAAATTTACCA--
1 TTTTAACCTCGATTTCACCAAAAA-TTA-CATT
* * *
43332997 TTTTACCCTCAAACTTT--CC-AAAATTTCATT
1 TTTTAACCTC-GA-TTTCACCAAAAATTACATT
43333027 TTTTAACCTCGATTTCACCAAAAATTACATT
1 TTTTAACCTCGATTTCACCAAAAATTACATT
43333058 TTT
1 TTT
43333061 ACCCCCGAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
28 5 0.10
29 3 0.06
30 15 0.29
31 24 0.47
32 1 0.02
33 3 0.06
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (31 bp):
TTTTAACCTCGATTTCACCAAAAATTACATT
Found at i:43333194 original size:30 final size:30
Alignment explanation
Indices: 43332858--43333255 Score: 129
Period size: 30 Copynumber: 13.5 Consensus size: 30
43332848 TATAGGTCCT
43332858 TAAACTATT-CAAAAATTACCATTTTACCCC
1 TAAACT-TTCCAAAAATTACCATTTTACCCC
**
43332888 CGAACTTTCC-AAAATT-CCATTTTTAACCCC
1 TAAACTTTCCAAAAATTACCA-TTTT-ACCCC
* * *
43332918 --GA-TTTCACCAAAAATTACCATTGTACCCT
1 TAAACTTT--CCAAAAATTACCATTTTACCCC
*
43332947 TAAACTTTCC-AAAATT-CCATTTTA-ACC
1 TAAACTTTCCAAAAATTACCATTTTACCCC
**
43332974 TCGA-TTTCACCAAAAATTTACCATTTTA-CCC
1 TAAACTTT--CCAAAAA-TTACCATTTTACCCC
* *
43333005 TCAAACTTTCC-AAAATT-TCATTTTTTA-ACC
1 T-AAACTTTCCAAAAATTACCA--TTTTACCCC
**
43333035 TCGA-TTTCACCAAAAATTA-CATTTTTACCCC
1 TAAACTTT--CCAAAAATTACCA-TTTTACCCC
** *
43333066 CGAACTTTCC-AAAATT-CCATTTTTAACCC
1 TAAACTTTCCAAAAATTACCA-TTTTACCCC
*
43333095 T-AA-TTTCTCTAAAAATTACC-CTTTACCCC
1 TAAACTTTC-C-AAAAATTACCATTTTACCCC
* * *
43333124 CAAAC-TTCCCAAAA-T-CTCATTTTAAACCC
1 TAAACTTTCCAAAAATTAC-CATTTT-ACCCC
* *
43333153 --GATTTTACCAAAAATTACCATTTTACCCC
1 TAAACTTT-CCAAAAATTACCATTTTACCCC
*
43333182 TAAACTTTCC-AAAA-TCCCATCTTTAACCCC
1 TAAACTTTCCAAAAATTACCAT-TTT-ACCCC
* *
43333212 --AA-TTTCACCCAAAAATTACCATTTTATCTC
1 TAAACTTT---CCAAAAATTACCATTTTACCCC
*
43333242 TAAACTTTTCAAAA
1 TAAACTTTCCAAAA
43333256 TCCCATTTTA
Statistics
Matches: 276, Mismatches: 41, Indels: 102
0.66 0.10 0.24
Matches are distributed among these distances:
26 4 0.01
27 16 0.06
28 37 0.13
29 77 0.28
30 80 0.29
31 42 0.15
32 14 0.05
33 6 0.02
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.35
Consensus pattern (30 bp):
TAAACTTTCCAAAAATTACCATTTTACCCC
Found at i:43337537 original size:15 final size:15
Alignment explanation
Indices: 43337517--43337555 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
43337507 GCACATCAAA
*
43337517 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
43337532 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
43337546 CAAGAATTAA
1 CAAGAATTAA
43337556 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:43341017 original size:3 final size:3
Alignment explanation
Indices: 43341009--43341036 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43340999 TAGTTACCAC
43341009 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
43341037 GCAAATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:43343721 original size:24 final size:24
Alignment explanation
Indices: 43343670--43343724 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
43343660 TCTTTCAGTT
* *
43343670 AAACTCTATTTATTTGTTTCTATT
1 AAACTCTATTTATTTGTTTCGATC
*
43343694 AAACTCTGTTTATTTGTTT-GAGTC
1 AAACTCTATTTATTTGTTTCGA-TC
43343718 AAACTCT
1 AAACTCT
43343725 TATTACTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.51
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCGATC
Found at i:43349195 original size:25 final size:27
Alignment explanation
Indices: 43349160--43349210 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
43349150 TCTTTCGGTA
43349160 ATTTTATTTATAA-GCTTAACACAAAC
1 ATTTTATTTATAATGCTTAACACAAAC
*
43349186 ATTTT-TTTATAATGTTTAACACAAA
1 ATTTTATTTATAATGCTTAACACAAA
43349211 ATCGATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (27 bp):
ATTTTATTTATAATGCTTAACACAAAC
Found at i:43355283 original size:49 final size:48
Alignment explanation
Indices: 43355230--43355380 Score: 122
Period size: 49 Copynumber: 3.1 Consensus size: 48
43355220 GATTGAAAAC
*
43355230 CATCATTATCTGGCCATTCAGGATGGTAGAATATGCAAATTGTGAAAGT
1 CATCATTATCAGGCCA-TCAGGATGGTAGAATATGCAAATTGTGAAAGT
* * * * * ** * *
43355279 CATCATTTTCAAGCTACTCAAGATGGTAGAATGTGCAGGTAGTGAAAGC
1 CATCATTATCAGGCCA-TCAGGATGGTAGAATATGCAAATTGTGAAAGT
* * * * * * *
43355328 CAACGTTGTGAGGCCATCTGGGATGGTAGAATATGCAAATTCTAAAAGT
1 CATCATTATCAGGCCATC-AGGATGGTAGAATATGCAAATTGTGAAAGT
43355377 CATC
1 CATC
43355381 GTTCTCAAGC
Statistics
Matches: 74, Mismatches: 27, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
48 2 0.03
49 72 0.97
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (48 bp):
CATCATTATCAGGCCATCAGGATGGTAGAATATGCAAATTGTGAAAGT
Found at i:43356500 original size:6 final size:6
Alignment explanation
Indices: 43356475--43356517 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
43356465 ACAATTCATA
* * *
43356475 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT T
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT T
43356518 TGACCACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:43359771 original size:41 final size:41
Alignment explanation
Indices: 43359714--43359809 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
43359704 GAATTTTATT
*
43359714 TTAACAGGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
43359755 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
43359796 TTGACAAGAATTCT
1 TTAACAAGAATTCT
43359810 CTACAAACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.35, C:0.29, G:0.07, T:0.28
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:43359821 original size:17 final size:17
Alignment explanation
Indices: 43359799--43359837 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
43359789 CTCCACCTTG
* *
43359799 ACAAGAATTCTCTACAA
1 ACAAGAACTCTCAACAA
*
43359816 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACAA
43359833 ACAAG
1 ACAAG
43359838 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACAA
Found at i:43365650 original size:3 final size:3
Alignment explanation
Indices: 43365642--43365666 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43365632 TAGTTACCAC
43365642 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
43365667 GCAAATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:43377200 original size:24 final size:24
Alignment explanation
Indices: 43377184--43377282 Score: 162
Period size: 24 Copynumber: 4.1 Consensus size: 24
43377174 AGTTTGACTC
43377184 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
43377208 AAACAAATAAACAGAGTTTAAGTG
1 AAACAAATAAACAGAGTTTAATTG
*
43377232 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
43377256 AAACAAATAAATAAAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
43377280 AAA
1 AAA
43377283 GATTATTTCT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:43379057 original size:24 final size:24
Alignment explanation
Indices: 43379029--43379079 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
43379019 AATTTGACTC
43379029 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
43379053 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
43379077 AAA
1 AAA
43379080 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.06, G:0.12, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:43380708 original size:23 final size:22
Alignment explanation
Indices: 43380682--43380755 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 22
43380672 AAACAGTAAA
43380682 CACACACAGCGCAATCCAGTAGG
1 CACACACAGCGCAAT-CAGTAGG
**
43380705 CACACACAGTACAATCAGTAGG
1 CACACACAGCGCAATCAGTAGG
* * *
43380727 CGCACATAACGCAAATCAGTAGG
1 CACACACAGCGC-AATCAGTAGG
43380750 CACACA
1 CACACA
43380756 AGGTGAGAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 14 0.33
23 28 0.67
ACGTcount: A:0.39, C:0.31, G:0.19, T:0.11
Consensus pattern (22 bp):
CACACACAGCGCAATCAGTAGG
Found at i:43380769 original size:23 final size:23
Alignment explanation
Indices: 43380743--43380796 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
43380733 TAACGCAAAT
* *
43380743 CAGTAGGCACACAAGGTGAGAAA
1 CAGTAAGCACACAAAGTGAGAAA
*
43380766 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAAGCACACAAAGTGAGAAA
43380789 CAGTAAGC
1 CAGTAAGC
43380797 GCGCTAGCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.44, C:0.20, G:0.26, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACAAAGTGAGAAA
Found at i:43381276 original size:11 final size:11
Alignment explanation
Indices: 43381250--43381279 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
43381240 TTAGACTCTA
43381250 ATGATTTTTCT
1 ATGATTTTTCT
43381261 A-GATTTTTCT
1 ATGATTTTTCT
43381271 ATGATTTTT
1 ATGATTTTT
43381280 TAAAGTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (11 bp):
ATGATTTTTCT
Found at i:43384496 original size:49 final size:52
Alignment explanation
Indices: 43384436--43384536 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
43384426 TTGTTAGTGT
*
43384436 TATTTGAGGTTAATATTT-T-T-ATTGAATTTAATGCT-ATTAAATTAATTGC
1 TATTGGAGGTTAATATTTATATCATTGAATTTAATGCTCATTAAA-TAATTGC
*
43384485 TATTGGAGGTTAATATTTATATCTTTGAATTTAATGCTCATTAAATAATTGC
1 TATTGGAGGTTAATATTTATATCATTGAATTTAATGCTCATTAAATAATTGC
43384537 AGATTCTCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
49 17 0.37
50 1 0.02
51 1 0.02
52 21 0.46
53 6 0.13
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.49
Consensus pattern (52 bp):
TATTGGAGGTTAATATTTATATCATTGAATTTAATGCTCATTAAATAATTGC
Found at i:43385446 original size:49 final size:50
Alignment explanation
Indices: 43385393--43385525 Score: 155
Period size: 49 Copynumber: 2.7 Consensus size: 50
43385383 GGCCATTCAG
* *
43385393 GATGGTAGAATATGCAAATTGTGAAAGTCATCATTTTTG-GGCCA-CTCGA
1 GATGGTAGAATATGCAAATTGTGAAAGTCATC-GTTGTGAGGCCACCTCGA
* * * * *
43385442 GATGGTAGAATATGCAAGTAGTGAAAGCCAACGTTGTGAGGCCACCTGGA
1 GATGGTAGAATATGCAAATTGTGAAAGTCATCGTTGTGAGGCCACCTCGA
* *
43385492 -ATGGTAGAATATGCAAATTCTAAAAGTCATCGTT
1 GATGGTAGAATATGCAAATTGTGAAAGTCATCGTT
43385526 CTCAGGCAAC
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 4 0.06
49 61 0.88
50 4 0.06
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (50 bp):
GATGGTAGAATATGCAAATTGTGAAAGTCATCGTTGTGAGGCCACCTCGA
Found at i:43386415 original size:18 final size:18
Alignment explanation
Indices: 43386394--43386434 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
43386384 ATTTTAAAAA
*
43386394 TAAATAAATTA-TGATATT
1 TAAATAAAATATTGAT-TT
43386412 TAAA-AAAATATTGATTT
1 TAAATAAAATATTGATTT
43386429 TAAATA
1 TAAATA
43386435 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TAAATAAAATATTGATTT
Found at i:43389133 original size:6 final size:6
Alignment explanation
Indices: 43389122--43389148 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43389112 CAAACCCATA
43389122 TCTTTC TCTTTC TCTTTC TCTTTC TCT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCT
43389149 ATCTATCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TCTTTC
Found at i:43390363 original size:15 final size:14
Alignment explanation
Indices: 43390343--43390378 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
43390333 AGAGAGATTG
43390343 TTTTCTTTTTCTTTT
1 TTTTCTTTTT-TTTT
43390358 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
*
43390372 TGTTCTT
1 TTTTCTT
43390379 CTTTGAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:43391159 original size:39 final size:39
Alignment explanation
Indices: 43391105--43391192 Score: 167
Period size: 39 Copynumber: 2.3 Consensus size: 39
43391095 ATCATAGAAG
43391105 AAAGTTGTTTGGATTTTGACTAATAGATTCGTGATATAC
1 AAAGTTGTTTGGATTTTGACTAATAGATTCGTGATATAC
*
43391144 AAAGTTGTTTGGATTTTGACTAATAGATTCGTGATATGC
1 AAAGTTGTTTGGATTTTGACTAATAGATTCGTGATATAC
43391183 AAAGTTGTTT
1 AAAGTTGTTT
43391193 CGTGAAACAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.42
Consensus pattern (39 bp):
AAAGTTGTTTGGATTTTGACTAATAGATTCGTGATATAC
Found at i:43392802 original size:17 final size:16
Alignment explanation
Indices: 43392775--43392806 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
43392765 AAAATTAAAT
43392775 AAATAAAAAGAAAAGA
1 AAATAAAAAGAAAAGA
43392791 AAATAGAAAAGAAAAG
1 AAATA-AAAAGAAAAG
43392807 TTTTGTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
AAATAAAAAGAAAAGA
Found at i:43397574 original size:14 final size:14
Alignment explanation
Indices: 43397550--43397587 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
43397540 CAGTCCACCA
43397550 AAAAGGGAAATAGAG
1 AAAA-GGAAATAGAG
43397565 AAAAGGAAATAGAG
1 AAAAGGAAATAGAG
43397579 AAAAGGAAA
1 AAAAGGAAA
43397588 GTATTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (14 bp):
AAAAGGAAATAGAG
Found at i:43398445 original size:70 final size:69
Alignment explanation
Indices: 43398308--43398445 Score: 179
Period size: 69 Copynumber: 2.0 Consensus size: 69
43398298 ATACATGATT
* * *
43398308 ACTTAAATTTAATTTAGTTAGAAATATGGGTTTAAAAAATTTAAAAATATATTTATATTTATAAA
1 ACTTAAATTTAATATAGTTAGAAATATGGATTTAAAAAATTTAAAAACATATTTATATTTATAAA
43398373 GGCC
66 GGCC
* * * * *
43398377 ACTTAAATTTAGTATAGTTTGAAATATGGATCTT-AAAATTTCTCAAAACATATTTATATTTGTA
1 ACTTAAATTTAATATAGTTAGAAATATGGAT-TTAAAAAATT-TAAAAACATATTTATATTTATA
43398441 AAGGC
64 AAGGC
43398446 TAATTTAAGC
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
69 33 0.56
70 26 0.44
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.41
Consensus pattern (69 bp):
ACTTAAATTTAATATAGTTAGAAATATGGATTTAAAAAATTTAAAAACATATTTATATTTATAAA
GGCC
Found at i:43400215 original size:59 final size:57
Alignment explanation
Indices: 43400018--43400215 Score: 191
Period size: 59 Copynumber: 3.4 Consensus size: 57
43400008 TGGGTTTTTA
**
43400018 GGGGTAAAATGGTAATTTTT-GTGAAATCGGGACTAAAAATGGAATTTGGAAAGTTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTGGAAAGTTT
* * ** * * * * *
43400074 GGGGGATAAAGTGGTAAATTTTGGCAAAAAACGAGGTCAAAAATGAAATTTTGGAAAGTTC
1 -GGGG-TAAAATGGTAATTTTTGG-TGAAATCGGGGTTAAAAATGGAA-TTTGGAAAGTTT
* * * *
43400135 GGAGGTAAAACGGTAAGTTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTT
1 GG-GGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTT-GGAAAGTTT
43400194 GAGGGTAAAATGGTAATTTTTG
1 G-GGGTAAAATGGTAATTTTTG
43400216 AAATTTTTGG
Statistics
Matches: 109, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
57 4 0.04
58 17 0.16
59 42 0.39
60 33 0.30
61 13 0.12
ACGTcount: A:0.36, C:0.04, G:0.31, T:0.29
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTGGAAAGTTT
Found at i:43400254 original size:30 final size:30
Alignment explanation
Indices: 43400191--43400392 Score: 300
Period size: 30 Copynumber: 6.7 Consensus size: 30
43400181 TTTAGGGAAG
* *
43400191 TTTGAGGGT-AAAATGGTAATTTTTG-AAATT
1 TTTG-GGGTCAAAAT-GTAATTTTGGAAAAGT
43400221 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
43400251 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
43400281 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* * *
43400311 TTTAGGGTTAAAATGTAATTTAGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* *
43400341 TTTGGGGTTAAAATATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
*
43400371 TTTAGGGTCAAAATGTAATTTT
1 TTTGGGGTCAAAATGTAATTTT
43400393 TGGACAATTT
Statistics
Matches: 159, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
29 13 0.08
30 146 0.92
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (30 bp):
TTTGGGGTCAAAATGTAATTTTGGAAAAGT
Found at i:43402368 original size:17 final size:16
Alignment explanation
Indices: 43402314--43402374 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
43402304 TTAAAACCAT
*
43402314 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
* *
43402330 TTTAAATTCAAAACAAA
1 TTTAAATT-TAAATAAA
43402347 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
*
43402363 TCTTAAAATTAA
1 T-TTAAATTTAA
43402375 TTCAAACTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 15 0.41
17 22 0.59
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:43402384 original size:17 final size:17
Alignment explanation
Indices: 43402364--43402397 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43402354 TTAAATAAAT
*
43402364 CTTAAAATTAATTCAAA
1 CTTAAAATAAATTCAAA
*
43402381 CTTAATATAAATTCAAA
1 CTTAAAATAAATTCAAA
43402398 AATCTCAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (17 bp):
CTTAAAATAAATTCAAA
Found at i:43403023 original size:68 final size:68
Alignment explanation
Indices: 43402881--43403511 Score: 803
Period size: 68 Copynumber: 8.9 Consensus size: 68
43402871 AACGATGTTA
*
43402881 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC
43402946 GTTG
65 GTTG
* *
43402950 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
43403015 TTG
66 TTG
* * * *
43403018 CTCTTACTTCAATTTTAGAGACGAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGAT--G
*
43403083 AAACGATGTTA
63 --AC---GTTG
* *
43403094 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGAT--G
*
43403159 AAATGATCTTG
63 --ACG---TTG
* *
43403170 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
43403235 TTG
66 TTG
* * * *
43403238 CTCTTACTTCAATTTCAGAGACGAAGACGTGATATCCAGTTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGAT--G
*
43403303 AAACGATGTTA
63 --AC---GTTG
* * *
43403314 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATGGC
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC
43403379 GTTG
65 GTTG
* * *
43403383 CTCTTACTTCAATTTCAGAGATAAAAACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
43403448 TTG
66 TTG
*
43403451 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGCGGAT
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
43403512 TGGAAATGAT
Statistics
Matches: 494, Mismatches: 47, Indels: 43
0.85 0.08 0.07
Matches are distributed among these distances:
68 189 0.38
69 112 0.23
71 4 0.01
72 1 0.00
73 6 0.01
74 1 0.00
75 23 0.05
76 156 0.32
77 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (68 bp):
CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
TTG
Found at i:43403101 original size:213 final size:213
Alignment explanation
Indices: 43402733--43403517 Score: 1338
Period size: 213 Copynumber: 3.7 Consensus size: 213
43402723 GGAAATGATC
* *
43402733 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
** * *
43402798 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGTTTTACTTCAATTTCAAGA
65 GACGTTGCTCTTACTTCAATTTCAGAGACGAAGACGTGATATCCAGCTTTACTTCAATTTCAAGA
*
43402863 GGATAGGAAACGATGTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTT
130 GGATAGGAAACGATGTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTGTCCAACTCTACTT
43402928 CAATTTCAAGAGGATGACG
195 CAATTTCAAGAGGATGACG
43402947 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
43403012 ACGTTGCTCTTACTTCAATTTTAGAGACGAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAG
66 ACGTTGCTCTTACTTCAATTTCAGAGACGAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAG
43403077 GATAGGAAACGATGTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTGTCCAACTCTACTTC
131 GATAGGAAACGATGTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTGTCCAACTCTACTTC
*
43403142 AATTTCAAGAGGATAGGAAATG
196 AATTTCAAGAGGAT--G--ACG
43403164 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
1 ---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
*
43403229 ATGACGTTGCTCTTACTTCAATTTCAGAGACGAAGACGTGATATCCAGTTTTACTTCAATTTCAA
63 ATGACGTTGCTCTTACTTCAATTTCAGAGACGAAGACGTGATATCCAGCTTTACTTCAATTTCAA
43403294 GAGGATAGGAAACGATGTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTGTCCAACTCTAC
128 GAGGATAGGAAACGATGTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTGTCCAACTCTAC
*
43403359 TTCAATTTCAAGAGGATGGCG
193 TTCAATTTCAAGAGGATGACG
*
43403380 TTGCTCTTACTTCAATTTCAGAGATAAAAACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* * * *
43403445 ACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGCG
66 ACGTTGCTCTTACTTCAATTTCAGAGACGAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAG
*
43403509 GATTGGAAA
131 GATAGGAAA
43403518 TGATCTTGTT
Statistics
Matches: 544, Mismatches: 20, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
212 25 0.05
213 268 0.49
214 39 0.07
215 1 0.00
216 1 0.00
217 2 0.00
218 1 0.00
220 207 0.38
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (213 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
ACGTTGCTCTTACTTCAATTTCAGAGACGAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAG
GATAGGAAACGATGTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTGTCCAACTCTACTTC
AATTTCAAGAGGATGACG
Found at i:43415462 original size:30 final size:30
Alignment explanation
Indices: 43415430--43415509 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
43415420 GGGAAGTTCG
43415430 GGGGT-AAAATGGTAATTTTTG-AAAGTTTC
1 GGGGTCAAAAT-GTAATTTTTGAAAAGTTTC
* *
43415459 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTTGAAAAGTTTC
*
43415489 GGTGTCAAAATGTAATTTTTG
1 GGGGTCAAAATGTAATTTTTG
43415510 GACAATTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 14 0.31
30 31 0.69
ACGTcount: A:0.31, C:0.04, G:0.26, T:0.39
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTTGAAAAGTTTC
Found at i:43416616 original size:3 final size:3
Alignment explanation
Indices: 43416608--43416641 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
43416598 TTTCTTTTTG
*
43416608 TTA TTA TTA GTA TTAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
43416642 AAATCATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:43416629 original size:16 final size:16
Alignment explanation
Indices: 43416608--43416638 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43416598 TTTCTTTTTG
43416608 TTATTATTAGTATTAA
1 TTATTATTAGTATTAA
*
43416624 TTATTATTATTATTA
1 TTATTATTAGTATTA
43416639 TTAAAATCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTATTATTAGTATTAA
Found at i:43417481 original size:17 final size:16
Alignment explanation
Indices: 43417427--43417487 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
43417417 TTAAAACCAT
*
43417427 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
* *
43417443 TTTAAATTCAAAACAAA
1 TTTAAATT-TAAATAAA
43417460 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
*
43417476 TCTTAAAATTAA
1 T-TTAAATTTAA
43417488 TTCAAACTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 15 0.41
17 22 0.59
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:43417497 original size:17 final size:17
Alignment explanation
Indices: 43417477--43417510 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43417467 TTAAATAAAT
*
43417477 CTTAAAATTAATTCAAA
1 CTTAAAATAAATTCAAA
*
43417494 CTTAATATAAATTCAAA
1 CTTAAAATAAATTCAAA
43417511 AATCTCAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (17 bp):
CTTAAAATAAATTCAAA
Found at i:43420085 original size:6 final size:6
Alignment explanation
Indices: 43420074--43420191 Score: 50
Period size: 6 Copynumber: 19.5 Consensus size: 6
43420064 TATTATTTTT
* *
43420074 TATTAA TATTAA GTAATTAA TAATCTTTA TATTAA GTAATTAA TAAT-A
1 TATTAA TATTAA -T-ATTAA T-A--TTAA TATTAA -T-ATTAA TATTAA
* * * *
43420122 T-TTA- TATTAA TATT-A TATTTA TATTAA TA-T-A TTTTTA TATTTA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
* * *
43420165 TATTTA TATTTA TATTTA TATTAA TAT
1 TATTAA TATTAA TATTAA TATTAA TAT
43420192 ATTTCGATTT
Statistics
Matches: 92, Mismatches: 8, Indels: 24
0.74 0.06 0.19
Matches are distributed among these distances:
4 4 0.04
5 12 0.13
6 55 0.60
7 6 0.07
8 11 0.12
9 4 0.04
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.56
Consensus pattern (6 bp):
TATTAA
Found at i:43420107 original size:23 final size:23
Alignment explanation
Indices: 43420074--43420131 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
43420064 TATTATTTTT
*
43420074 TATTAATATTAAGTAATTAATAA
1 TATTTATATTAAGTAATTAATAA
*
43420097 TCTTTATATTAAGTAATTAATAA
1 TATTTATATTAAGTAATTAATAA
43420120 TATTTATATTAA
1 TATTTATATTAA
43420132 TATTATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (23 bp):
TATTTATATTAAGTAATTAATAA
Found at i:43420134 original size:12 final size:12
Alignment explanation
Indices: 43420059--43420191 Score: 91
Period size: 12 Copynumber: 11.2 Consensus size: 12
43420049 ATTATTATTA
43420059 ATTTATATT-AT
1 ATTTATATTAAT
*
43420070 -TTTTTATTAAT
1 ATTTATATTAAT
*
43420081 ATTAAGTAATTAAT
1 ATTTA-T-ATTAAT
43420095 AATCTTTATATTAAGT
1 -A--TTTATATTAA-T
*
43420111 AATTA-A-TAAT
1 ATTTATATTAAT
43420121 ATTTATATTAAT
1 ATTTATATTAAT
*
43420133 A-TTATATTTAT
1 ATTTATATTAAT
*
43420144 ATTAATA-T-AT
1 ATTTATATTAAT
* *
43420154 TTTTATATTTAT
1 ATTTATATTAAT
*
43420166 ATTTATATTTAT
1 ATTTATATTAAT
43420178 ATTTATATTAAT
1 ATTTATATTAAT
43420190 AT
1 AT
43420192 ATTTCGATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
10 19 0.20
11 18 0.19
12 38 0.39
13 4 0.04
14 6 0.06
15 7 0.07
16 2 0.02
17 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (12 bp):
ATTTATATTAAT
Found at i:43420177 original size:34 final size:33
Alignment explanation
Indices: 43420112--43420185 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 33
43420102 ATATTAAGTA
43420112 ATTAATA-ATATTTATATTAATATTATATTTAT
1 ATTAATATATATTTATATTAATATTATATTTAT
* *
43420144 ATTAATATATTTTTATATTTATATTTATATTTAT
1 ATTAATATATATTTATATTAATA-TTATATTTAT
*
43420178 ATTTATAT
1 ATTAATAT
43420186 TAATATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 7 0.19
33 13 0.35
34 17 0.46
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
ATTAATATATATTTATATTAATATTATATTTAT
Found at i:43420178 original size:40 final size:39
Alignment explanation
Indices: 43420119--43420195 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 39
43420109 GTAATTAATA
43420119 ATATTTATATTAATATTATATTTATATTAATATATTTTT
1 ATATTTATATTAATATTATATTTATATTAATATATTTTT
*
43420158 ATATTTATATTTATATTTATATTTATATTAATATATTT
1 ATATTTATATTAATA-TTATATTTATATTAATATATTT
43420196 CGATTTAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 14 0.39
40 22 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (39 bp):
ATATTTATATTAATATTATATTTATATTAATATATTTTT
Found at i:43420213 original size:40 final size:40
Alignment explanation
Indices: 43420134--43420224 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
43420124 TATATTAATA
** * * *
43420134 TTATATTTATATTAATATATTTTTATATTTATATTTATAT
1 TTATATTTATATTAATATATTTCGATATTGAAATCTATAT
43420174 TTATATTTATATTAATATATTTCGAT-TTAGAAATCTATAT
1 TTATATTTATATTAATATATTTCGATATT-GAAATCTATAT
*
43420214 TTCTATATTAT
1 TTATAT-TTAT
43420225 TTATTTTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
39 2 0.05
40 37 0.86
41 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.59
Consensus pattern (40 bp):
TTATATTTATATTAATATATTTCGATATTGAAATCTATAT
Found at i:43420269 original size:34 final size:31
Alignment explanation
Indices: 43420231--43420336 Score: 87
Period size: 34 Copynumber: 3.4 Consensus size: 31
43420221 TTATTTATTT
* *
43420231 TATTATTCTATCTATTATT-TTATTATTCTTATAA
1 TATTATTATATATATTATTATT-TTA-T-TTA-AA
43420265 TATTATTATATATATTATTATTTTATTTAAA
1 TATTATTATATATATTATTATTTTATTTAAA
* **
43420296 TATTATT-TA-A-ATTATTGTTTTTATTTAGT
1 TATTATTATATATATTATT-ATTTTATTTAAA
43420325 TATTATT-TATAT
1 TATTATTATATAT
43420337 TTAGTCTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
28 6 0.10
29 19 0.30
30 3 0.05
31 9 0.14
32 3 0.05
33 1 0.02
34 20 0.32
35 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (31 bp):
TATTATTATATATATTATTATTTTATTTAAA
Found at i:43420273 original size:20 final size:20
Alignment explanation
Indices: 43420226--43420273 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
43420216 CTATATTATT
* *
43420226 TATTTTATTATTCTATCTAT
1 TATTTTATTATTCTATATAA
43420246 TATTTTATTATTCT-TATAA
1 TATTTTATTATTCTATATAA
43420265 TATTATTAT
1 TATT-TTAT
43420274 ATATATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTATTATTCTATATAA
Found at i:43420302 original size:3 final size:3
Alignment explanation
Indices: 43420219--43420291 Score: 50
Period size: 3 Copynumber: 25.3 Consensus size: 3
43420209 TATATTTCTA
* *
43420219 TAT TATT TAT T-T TAT TAT T-C TAT CTAT TAT T-T TAT TAT TCT TA-
1 TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
*
43420262 TAA TAT TAT TA- TAT ATAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT T
43420292 TAAATATTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
2 11 0.20
3 36 0.64
4 9 0.16
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:43420328 original size:29 final size:28
Alignment explanation
Indices: 43420266--43420366 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 28
43420256 TTCTTATAAT
* *
43420266 ATTATTATATATATTATTATTTTATTTA
1 ATTATTATTTAAATTATTATTTTATTTA
* *
43420294 AATATTATTTAAATTATTGTTTTTATTTA
1 ATTATTATTTAAATTATT-ATTTTATTTA
* *
43420323 GTTATTATTTATATTTAGTCTATTTATAATTT-
1 ATTATTATTTA-AATTA-T-TATTT-T-ATTTA
43420355 ATTATTATTTAA
1 ATTATTATTTAA
43420367 TTTAACATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
28 15 0.26
29 18 0.31
30 4 0.07
31 5 0.09
32 12 0.21
33 4 0.07
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (28 bp):
ATTATTATTTAAATTATTATTTTATTTA
Found at i:43420376 original size:29 final size:30
Alignment explanation
Indices: 43420318--43420400 Score: 114
Period size: 29 Copynumber: 2.7 Consensus size: 30
43420308 TATTGTTTTT
* *
43420318 ATTTAGTTATTATTTATATTTAGTCTATTTATA
1 ATTTA-TTATTATTTA-ATTTA-ACTATTTAGA
43420351 ATTTATTATTATTTAATTTAAC-ATTTAGA
1 ATTTATTATTATTTAATTTAACTATTTAGA
43420380 ATTTATTATTATTTAATTTAA
1 ATTTATTATTATTTAATTTAA
43420401 GTTAAATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
29 27 0.56
30 1 0.02
31 5 0.10
32 10 0.21
33 5 0.10
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (30 bp):
ATTTATTATTATTTAATTTAACTATTTAGA
Found at i:43420499 original size:19 final size:20
Alignment explanation
Indices: 43420472--43420512 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
43420462 ATTTAATAAT
*
43420472 TTATAATTTC-ATTTTTTTA
1 TTATAATTTCGATTTTATTA
*
43420491 TTATGATTTCGATTTTATTA
1 TTATAATTTCGATTTTATTA
43420511 TT
1 TT
43420513 TTCTTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (20 bp):
TTATAATTTCGATTTTATTA
Found at i:43425455 original size:25 final size:24
Alignment explanation
Indices: 43425412--43425479 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 24
43425402 ACTTCTCGAC
43425412 TTATAATA-TTTTATAAATAAATATA
1 TTATAATATTTTTAT-AATAAATA-A
**
43425437 TTATAATATTTTTATAATATGTAA
1 TTATAATATTTTTATAATAAATAA
*
43425461 AT-TAAT-TTTTTATAATAAA
1 TTATAATATTTTTATAATAAA
43425480 CTTTTTAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 11 0.30
23 4 0.11
24 2 0.05
25 14 0.38
26 6 0.16
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
TTATAATATTTTTATAATAAATAA
Found at i:43430596 original size:31 final size:31
Alignment explanation
Indices: 43430561--43430634 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
43430551 AAAATAAAAA
*
43430561 TCAAAATTTAAAAATAT-TCCATGCAATTAAC
1 TCAAAATTTAAAAATGTCT-CATGCAATTAAC
43430592 TCAAAATTTAAAAATGTCTCATGCAATTAAC
1 TCAAAATTTAAAAATGTCTCATGCAATTAAC
*
43430623 TCAAAATCTAAA
1 TCAAAATTTAAA
43430635 GACATAACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (31 bp):
TCAAAATTTAAAAATGTCTCATGCAATTAAC
Found at i:43431877 original size:15 final size:17
Alignment explanation
Indices: 43431847--43431878 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
43431837 TTGTTTTGAA
43431847 GTTTTGAAATTTTAAAT
1 GTTTTGAAATTTTAAAT
43431864 GTTTT-AAA-TTTAAAT
1 GTTTTGAAATTTTAAAT
43431879 ATTACTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
GTTTTGAAATTTTAAAT
Found at i:43432501 original size:22 final size:23
Alignment explanation
Indices: 43432468--43432523 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
43432458 AACAAGAAGC
* *
43432468 AAATTGAT-ATTTTTATTAAAAA
1 AAATTAATCATTTTTAATAAAAA
**
43432490 AAATT-ATCATTTTTAATATTAA
1 AAATTAATCATTTTTAATAAAAA
43432512 AAATTAATCATT
1 AAATTAATCATT
43432524 AATCACGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 21 0.72
23 6 0.21
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTAATCATTTTTAATAAAAA
Found at i:43433319 original size:21 final size:21
Alignment explanation
Indices: 43433293--43433337 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43433283 AGGAATTGAA
*
43433293 AAAAAAAAAAATCAAAAACCC
1 AAAAAAAAAAATAAAAAACCC
**
43433314 AAAAAAAATTATAAAAAACCC
1 AAAAAAAAAAATAAAAAACCC
43433335 AAA
1 AAA
43433338 CTTTTTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.09
Consensus pattern (21 bp):
AAAAAAAAAAATAAAAAACCC
Found at i:43441687 original size:10 final size:10
Alignment explanation
Indices: 43441672--43441700 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
43441662 TTATATATTT
43441672 TAATTAATTA
1 TAATTAATTA
43441682 TAATTAATT-
1 TAATTAATTA
43441691 TAATTAATTA
1 TAATTAATTA
43441701 AAGGGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATTAATTA
Found at i:43450947 original size:258 final size:257
Alignment explanation
Indices: 43450630--43451148 Score: 804
Period size: 258 Copynumber: 2.0 Consensus size: 257
43450620 AACTATAACT
* *
43450630 AAAATATCAATTTGCTACTTTTAAATTTTTTCTTAATAGTAATTTTAAAAAATTTAAAAGATAAA
1 AAAATATCAATTTGATACTTTTAAATTTTTTCTTAATAATAATTTTAAAAAATTTAAAAGATAAA
* *
43450695 TTACAAAAGTCACCCAAGTTTTAAATTTAGTCACTTCCAATAGATTAATTGTCATTTTTAATCAC
66 TTACAAAAGTCACCCAAGTTTTAAATTTAGTCACTTCCAATAAATTAATTATCATTTTTAATCAC
* * * * * *
43450760 TCCACTGCTAAAATGCCTTGGTCACTGAACAAAATGTTAATGTGTCAATCTTTTGATTGGTATAA
131 TCCACCGCTAAAATGCCTTGATCACTAAACAAAATGTTAATGTATCAATATTTTAATTGGTATAA
* * * *
43450825 TTTTCTTAACAATTAAGACAAGTTCGTTAGTTGGGCTTGTTTGAGAGCCCACAAAACCAATA
196 TTTTCTTAACAATTAAGACAAATTCATTAGTTGGACTTGTTTGAGAGCCCACAAAAACAATA
*
43450887 AAAATATCAATTTGATACTTTTAAATTTTTTTCTTAATAATAATTTTAAAAAATTTAAAAGATAT
1 AAAATATCAATTTGATACTTTTAAA-TTTTTTCTTAATAATAATTTTAAAAAATTTAAAAGATAA
* * * *
43450952 ATTACTAAAGTCACCCAAGTTTTAAATTTAGTCACTTTCGATAAATTAATTATCATTTTTAGTCA
65 ATTACAAAAGTCACCCAAGTTTTAAATTTAGTCACTTCCAATAAATTAATTATCATTTTTAATCA
* * *
43451017 CTCCACCGTTAAAATGCCTTGATCACTAAACAAAATGTTGATGTATTAATATTTTAATTGGTATA
130 CTCCACCGCTAAAATGCCTTGATCACTAAACAAAATGTTAATGTATCAATATTTTAATTGGTATA
* * *
43451082 ATTTTCTTAACAATTCAGACAAATTCATTAGTTGGACTTGTTTGAGGGCCCATAAAAACAATA
195 ATTTTCTTAACAATTAAGACAAATTCATTAGTTGGACTTGTTTGAGAGCCCACAAAAACAATA
43451145 AAAA
1 AAAA
43451149 AACTCTAAAT
Statistics
Matches: 236, Mismatches: 25, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
257 24 0.10
258 212 0.90
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (257 bp):
AAAATATCAATTTGATACTTTTAAATTTTTTCTTAATAATAATTTTAAAAAATTTAAAAGATAAA
TTACAAAAGTCACCCAAGTTTTAAATTTAGTCACTTCCAATAAATTAATTATCATTTTTAATCAC
TCCACCGCTAAAATGCCTTGATCACTAAACAAAATGTTAATGTATCAATATTTTAATTGGTATAA
TTTTCTTAACAATTAAGACAAATTCATTAGTTGGACTTGTTTGAGAGCCCACAAAAACAATA
Found at i:43451324 original size:15 final size:17
Alignment explanation
Indices: 43451305--43451347 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
43451295 AAAGCTACAA
43451305 AATATTATTATTT-TTT
1 AATATTATTATTTATTT
43451321 -ATATTATT-TTTATTT
1 AATATTATTATTTATTT
*
43451336 AATATCATTATT
1 AATATTATTATT
43451348 CTTCTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 3 0.13
15 11 0.48
16 7 0.30
17 2 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
AATATTATTATTTATTT
Found at i:43459460 original size:14 final size:14
Alignment explanation
Indices: 43459441--43459471 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43459431 AGAAATTCAT
*
43459441 ATAAATTTGTAATA
1 ATAAATTTATAATA
43459455 ATAAATTTATAATA
1 ATAAATTTATAATA
43459469 ATA
1 ATA
43459472 CTTTAAATGT
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
ATAAATTTATAATA
Found at i:43469939 original size:6 final size:6
Alignment explanation
Indices: 43469928--43469972 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
43469918 TTTTTACAGA
43469928 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATA
43469973 CATACATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:43469955 original size:24 final size:24
Alignment explanation
Indices: 43469930--43470008 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 24
43469920 TTTACAGAAT
* *
43469930 ATACATATACATATACATATACAT
1 ATACATATACATATACATACACAC
*
43469954 ATACATATACATATACATACATAC
1 ATACATATACATATACATACACAC
* * *
43469978 ATACATACATACATACATACACAC
1 ATACATATACATATACATACACAC
43470002 ATACATA
1 ATACATA
43470009 CATATGTTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.28
Consensus pattern (24 bp):
ATACATATACATATACATACACAC
Found at i:43469975 original size:4 final size:4
Alignment explanation
Indices: 43469966--43470012 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
43469956 ACATATACAT
*
43469966 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ACAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
43470013 TGTTCATAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:43479617 original size:15 final size:16
Alignment explanation
Indices: 43479578--43479619 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
43479568 ACAAATTGAC
* *
43479578 ATGACATTATAAATTG
1 ATGAAATTAAAAATTG
*
43479594 ATTAAATTAAAAATT-
1 ATGAAATTAAAAATTG
43479609 ATGAAATTAAA
1 ATGAAATTAAA
43479620 GTACAAGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (16 bp):
ATGAAATTAAAAATTG
Found at i:43481934 original size:27 final size:27
Alignment explanation
Indices: 43481896--43481969 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
43481886 GGGTGATGCT
* * *
43481896 TACCTGACAGGCGGCACTAGTGGTGCC
1 TACCTGTCAGGCGGCACCAATGGTGCC
43481923 TACCTGTCAGGCGGCACCAATGGTGCC
1 TACCTGTCAGGCGGCACCAATGGTGCC
**
43481950 TTTCTGTCAGGCGGCACCAA
1 TACCTGTCAGGCGGCACCAA
43481970 CCCGTATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (27 bp):
TACCTGTCAGGCGGCACCAATGGTGCC
Found at i:43483176 original size:13 final size:14
Alignment explanation
Indices: 43483158--43483203 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
43483148 AATTTTTTTA
43483158 ATTTTATATT-ATT
1 ATTTTATATTAATT
43483171 ATTTTAGTATTAATT
1 ATTTTA-TATTAATT
43483186 -TTTTATATATATATT
1 ATTTTATAT-TA-ATT
43483201 ATT
1 ATT
43483204 ATTGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 9 0.32
14 11 0.39
15 6 0.21
16 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
ATTTTATATTAATT
Found at i:43483206 original size:25 final size:25
Alignment explanation
Indices: 43483155--43483206 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
43483145 GCTAATTTTT
*
43483155 TTAATTTTATATTATTATTTTAGTA
1 TTAATTTTATATTATTATATTAGTA
* *
43483180 TTAATTTTTTA-TATATATATTATTA
1 TTAATTTTATATTAT-TATATTAGTA
43483205 TT
1 TT
43483207 GTAAAAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTAATTTTATATTATTATATTAGTA
Found at i:43483352 original size:27 final size:26
Alignment explanation
Indices: 43483322--43483386 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
43483312 ATTTGACAAG
*
43483322 TGGTGCCTTTAGGGTAGGCGGCACCAA
1 TGGTGCCTTT-GGGTAGACGGCACCAA
* * *
43483349 TGGTGCCTACTGGGTAGACGGCACTAG
1 TGGTGCCT-TTGGGTAGACGGCACCAA
43483376 TGGTGCCTTTG
1 TGGTGCCTTTG
43483387 TCAAAACTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.06
27 29 0.91
28 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.37, T:0.26
Consensus pattern (26 bp):
TGGTGCCTTTGGGTAGACGGCACCAA
Found at i:43484036 original size:24 final size:24
Alignment explanation
Indices: 43484004--43484054 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
43483994 AGTGGGATTA
43484004 ATATCAATCTTAATGTTGCACCCG
1 ATATCAATCTTAATGTTGCACCCG
43484028 ATATCAATCTTAATGTTGCACCCG
1 ATATCAATCTTAATGTTGCACCCG
43484052 ATA
1 ATA
43484055 ATGATACGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (24 bp):
ATATCAATCTTAATGTTGCACCCG
Found at i:43486358 original size:26 final size:26
Alignment explanation
Indices: 43486309--43486358 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
43486299 TCTATTTAAA
**
43486309 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
43486335 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
43486359 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:43488913 original size:17 final size:17
Alignment explanation
Indices: 43488884--43488931 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
43488874 GTCATTTTAA
43488884 AAAATATTT-AATATAT
1 AAAATATTTAAATATAT
43488900 AAAATATTTAAATATAT
1 AAAATATTTAAATATAT
* *
43488917 CAAATGAATTAAATA
1 AAAAT-ATTTAAATA
43488932 AAATATTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 11 0.39
18 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATATTTAAATATAT
Found at i:43505132 original size:19 final size:19
Alignment explanation
Indices: 43505092--43505135 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
43505082 GAATTCCCTC
**
43505092 TTCTTTTTCTGCTCTTTTT
1 TTCTTTTTCTGCTCTTACT
43505111 TTCTTTTTCT-CTCTTAACT
1 TTCTTTTTCTGCTCTT-ACT
43505130 TTCTTT
1 TTCTTT
43505136 CATTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.70
Consensus pattern (19 bp):
TTCTTTTTCTGCTCTTACT
Found at i:43506643 original size:17 final size:18
Alignment explanation
Indices: 43506623--43506658 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
43506613 ATCATAACTT
43506623 TTGTTAAAT-TATAATTA
1 TTGTTAAATGTATAATTA
43506640 TTGTTAAATGTATAATTA
1 TTGTTAAATGTATAATTA
43506658 T
1 T
43506659 AACAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
TTGTTAAATGTATAATTA
Found at i:43511220 original size:24 final size:25
Alignment explanation
Indices: 43511188--43511237 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
43511178 GTCTCTGAAC
*
43511188 ATAACTCATCAGCACCATCTGCAGA
1 ATAACTCATCAACACCATCTGCAGA
* *
43511213 ATAA-TCATCAACACTATTTGCAGA
1 ATAACTCATCAACACCATCTGCAGA
43511237 A
1 A
43511238 ACACCAGCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (25 bp):
ATAACTCATCAACACCATCTGCAGA
Found at i:43513860 original size:6 final size:6
Alignment explanation
Indices: 43513849--43513878 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
43513839 CACAATGAAA
*
43513849 TGCTTT TGCTTT TGCTTT TGCTTT TACTTT
1 TGCTTT TGCTTT TGCTTT TGCTTT TGCTTT
43513879 CAATTTCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.17, G:0.13, T:0.67
Consensus pattern (6 bp):
TGCTTT
Found at i:43515746 original size:5 final size:5
Alignment explanation
Indices: 43515724--43515762 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
43515714 TGGAAAATAA
*
43515724 TTATT CTATT ATTA-T TTATT TTATT TTATT TTATT TTAT
1 TTATT TTATT -TTATT TTATT TTATT TTATT TTATT TTAT
43515763 CATGAAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 3 0.10
5 25 0.83
6 2 0.07
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:43520471 original size:2 final size:2
Alignment explanation
Indices: 43520464--43520488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43520454 ACTCAAAATC
43520464 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 A
43520489 AATTGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43520852 original size:22 final size:24
Alignment explanation
Indices: 43520813--43520860 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
43520803 ATTTTTAAGA
*
43520813 TAATAAATTTATAATTTTATTATTT
1 TAATAAATTTAT-ATTTTATAATTT
43520838 TAAT-AATTTAT-TTTTATAATTT
1 TAATAAATTTATATTTTATAATTT
43520860 T
1 T
43520861 TAAAGGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 11 0.50
24 7 0.32
25 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TAATAAATTTATATTTTATAATTT
Found at i:43523325 original size:31 final size:31
Alignment explanation
Indices: 43523290--43523386 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
43523280 AACAATCGAG
* *
43523290 TGACTTAAATAAAAACTTTCGAATAATTCAA
1 TGACTTAAATGAAAACTTTTGAATAATTCAA
* * * *
43523321 TGACTCAAACGAAAACTTTTGAATAGTTTAA
1 TGACTTAAATGAAAACTTTTGAATAATTCAA
*
43523352 TGACTTAAATGAAATCTTTTGAATAATTCAA
1 TGACTTAAATGAAAACTTTTGAATAATTCAA
43523383 TGAC
1 TGAC
43523387 CATTTTATAA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTTGAATAATTCAA
Found at i:43530351 original size:34 final size:34
Alignment explanation
Indices: 43530304--43530372 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
43530294 AATTTTTAAA
*
43530304 TAAGTTTGAATTTA-TTTTAAATTCAAATTCATTT
1 TAAGTTTGAATTTACTTTAAAATT-AAATTCATTT
* *
43530338 TAAGTTTGGATTTACTTTAAAATTAAATTTATTT
1 TAAGTTTGAATTTACTTTAAAATTAAATTCATTT
43530372 T
1 T
43530373 TAAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 23 0.74
35 8 0.26
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (34 bp):
TAAGTTTGAATTTACTTTAAAATTAAATTCATTT
Found at i:43530367 original size:17 final size:17
Alignment explanation
Indices: 43530347--43530381 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43530337 TTAAGTTTGG
43530347 ATTTACTTTAAAATTAA
1 ATTTACTTTAAAATTAA
* *
43530364 ATTTATTTTTAAATTAA
1 ATTTACTTTAAAATTAA
43530381 A
1 A
43530382 ATTAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTACTTTAAAATTAA
Found at i:43530422 original size:19 final size:19
Alignment explanation
Indices: 43530380--43530422 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
43530370 TTTTAAATTA
43530380 AAATTAAATTAAAGAAGTCC
1 AAATTAAA-TAAAGAAGTCC
43530400 -AATTAAA-AAAGACAGTCC
1 AAATTAAATAAAGA-AGTCC
43530418 AAATT
1 AAATT
43530423 CAAAGTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 11 0.52
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (19 bp):
AAATTAAATAAAGAAGTCC
Found at i:43532304 original size:29 final size:29
Alignment explanation
Indices: 43532278--43532418 Score: 146
Period size: 29 Copynumber: 4.9 Consensus size: 29
43532268 TTGAAATTAT
43532278 ATTTTGACCCTAAAACTTTCAAAAATTCC
1 ATTTTGACCCTAAAACTTTCAAAAATTCC
* *
43532307 ATTTTTACCCCT-AAACTTCCAAAAATTCC
1 ATTTTGA-CCCTAAAACTTTCAAAAATTCC
*
43532336 ATTTTAACCCTAAAACTTTCAAAAATTACC
1 ATTTTGACCCTAAAACTTTCAAAAATT-CC
** * * *
43532366 ATTTT-ACCCCCCAAA-TGTCAAAAAACTCT
1 ATTTTGA-CCCTAAAACTTTC-AAAAATTCC
43532395 ATTTTGACCC-AAAACTTTCAAAAA
1 ATTTTGACCCTAAAACTTTCAAAAA
43532419 ATACCAAATT
Statistics
Matches: 94, Mismatches: 11, Indels: 15
0.78 0.09 0.12
Matches are distributed among these distances:
28 12 0.13
29 58 0.62
30 24 0.26
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.32
Consensus pattern (29 bp):
ATTTTGACCCTAAAACTTTCAAAAATTCC
Found at i:43532419 original size:59 final size:59
Alignment explanation
Indices: 43532277--43532434 Score: 198
Period size: 58 Copynumber: 2.7 Consensus size: 59
43532267 CTTGAAATTA
* * *
43532277 TATTTTGACCCTAAAACTTTCAAAAATT-CCATTTTTA-CCCCTAAACTTCCAAAAATTC
1 TATTTTGACCCTAAAACTTTCAAAAATTACCA-TTTTACCCCCCAAACTTCAAAAAACTC
* *
43532335 CATTTTAACCCTAAAACTTTCAAAAATTACCATTTTACCCCCCAAA-TGTCAAAAAACTC
1 TATTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCCCCAAACT-TCAAAAAACTC
* **
43532394 TATTTTGACCC-AAAACTTTCAAAAAATACCAAATTACCCCC
1 TATTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCCC
43532435 GAGTGTCCAA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 59 0.68
59 28 0.32
ACGTcount: A:0.39, C:0.28, G:0.02, T:0.31
Consensus pattern (59 bp):
TATTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCCCCAAACTTCAAAAAACTC
Found at i:43532458 original size:58 final size:58
Alignment explanation
Indices: 43532279--43532459 Score: 156
Period size: 58 Copynumber: 3.1 Consensus size: 58
43532269 TGAAATTATA
* ** * *
43532279 TTTTGACCCTAAAACTTTC-AAAAATTCCATTTTTA-CCCCTAAACT-TCCAAAAATTCCA
1 TTTTGACCCTAAAACTTTCAAAAAATACCA-AATTACCCCCCAAA-TGTCCAAAAATT-CT
* * ** * *
43532337 TTTTAACCCTAAAACTTTCAAAAATTACCATTTTACCCCCCAAATGTCAAAAAACTCT
1 TTTTGACCCTAAAACTTTCAAAAAATACCAAATTACCCCCCAAATGTCCAAAAATTCT
* *
43532395 ATTTTGACCC-AAAACTTTCAAAAAATACCAAATTA-CCCCCGAGTGTCCAAAAATTTCGT
1 -TTTTGACCCTAAAACTTTCAAAAAATACCAAATTACCCCCCAAATGTCCAAAAA-TTC-T
43532454 TTTTGA
1 TTTTGA
43532460 TCCCGATTTT
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
57 15 0.15
58 55 0.54
59 32 0.31
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (58 bp):
TTTTGACCCTAAAACTTTCAAAAAATACCAAATTACCCCCCAAATGTCCAAAAATTCT
Found at i:43546449 original size:50 final size:50
Alignment explanation
Indices: 43546365--43546462 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
43546355 ACCATGCTGT
** *
43546365 ACAAGTAGAATCCGTATAGAATTACGATTTTTCTATTTGACATTGATTGC
1 ACAAGTAGAATCCGTATAGAACCACGATTCTTCTATTTGACATTGATTGC
* *
43546415 ACAAGTAGAATCCTTATAGAACCACGCTTCTTCTATTTGACATTGATT
1 ACAAGTAGAATCCGTATAGAACCACGATTCTTCTATTTGACATTGATT
43546463 AGAATAAGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (50 bp):
ACAAGTAGAATCCGTATAGAACCACGATTCTTCTATTTGACATTGATTGC
Found at i:43548095 original size:39 final size:39
Alignment explanation
Indices: 43548051--43548309 Score: 262
Period size: 39 Copynumber: 6.7 Consensus size: 39
43548041 GTATTTGGTA
* * *
43548051 TTTACAGTGTTACTGATTGTATTAGTATTGTATTGT-GTG
1 TTTACAGTGTCACTGATAGT-TCAGTATTGTATTGTAGTG
* *
43548090 TTTACAGTGTCACTG-TCGGTTCAGTATTGTATTGTAATG
1 TTTACAGTGTCACTGAT-AGTTCAGTATTGTATTGTAGTG
* *
43548129 TTTACAGTGTCACT-ACCAGTTCAGTATTGTACTGTAGTG
1 TTTACAGTGTCACTGA-TAGTTCAGTATTGTATTGTAGTG
** *
43548168 TTTACAGTGTCACTGCCAGTTCAGTATTGTATTATAGTG
1 TTTACAGTGTCACTGATAGTTCAGTATTGTATTGTAGTG
* * *
43548207 TTTACACTGTCACAG-TCAGTTCAATATTGTATTGTAGTG
1 TTTACAGTGTCACTGAT-AGTTCAGTATTGTATTGTAGTG
* * * *
43548246 TTTACAATGTCACTG-TCAGATCAGTATTATA-TGCAGTG
1 TTTACAGTGTCACTGAT-AGTTCAGTATTGTATTGTAGTG
43548284 TTTACAGTGTCACTG-TCAGTTCAGTA
1 TTTACAGTGTCACTGAT-AGTTCAGTA
43548310 ATTTGATAAC
Statistics
Matches: 190, Mismatches: 24, Indels: 13
0.84 0.11 0.06
Matches are distributed among these distances:
38 45 0.24
39 145 0.76
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (39 bp):
TTTACAGTGTCACTGATAGTTCAGTATTGTATTGTAGTG
Found at i:43548170 original size:78 final size:78
Alignment explanation
Indices: 43548074--43548309 Score: 325
Period size: 78 Copynumber: 3.1 Consensus size: 78
43548064 TGATTGTATT
* *
43548074 AGTATTGTATTGT-GTGTTTACAGTGTCACTGTCGGTTCAGTATTGTATTGTAATGTTTACAGTG
1 AGTATTGTATTGTAGTGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTGTTTACAGTG
*
43548138 TCACTACCAGTTC
66 TCACTATCAGTTC
* * * *
43548151 AGTATTGTACTGTAGTGTTTACAGTGTCACTGCCAGTTCAGTATTGTATTATAGTGTTTACACTG
1 AGTATTGTATTGTAGTGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTGTTTACAGTG
43548216 TCAC-AGTCAGTTC
66 TCACTA-TCAGTTC
* * * * *
43548229 AATATTGTATTGTAGTGTTTACAATGTCACTGTCAGATCAGTATTATA-TGCAGTGTTTACAGTG
1 AGTATTGTATTGTAGTGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTGTTTACAGTG
*
43548293 TCACTGTCAGTTC
66 TCACTATCAGTTC
43548306 AGTA
1 AGTA
43548310 ATTTGATAAC
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
77 40 0.29
78 98 0.71
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.41
Consensus pattern (78 bp):
AGTATTGTATTGTAGTGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTGTTTACAGTG
TCACTATCAGTTC
Found at i:43548218 original size:117 final size:115
Alignment explanation
Indices: 43548074--43548309 Score: 337
Period size: 117 Copynumber: 2.0 Consensus size: 115
43548064 TGATTGTATT
* * * * * *
43548074 AGTATTGTATTGTGTGTTTACAGTGTCACTGTCGGTTCAGTATTGTATTGTAATGTTTACAGTGT
1 AGTATTGTATTATGTGTTTACACTGTCACAGTCAGTTCAATATTGTATTGTAATGTTTACAATGT
* * *
43548139 CACTACCAGTTCAGTATTGTACTGTAGTGTTTACAGTGTCACTGCCAGTTC
66 CACTACCAGATCAGTATTATA-TGCAGTGTTTACAGTGTCACTGCCAGTTC
*
43548190 AGTATTGTATTATAGTGTTTACACTGTCACAGTCAGTTCAATATTGTATTGTAGTGTTTACAATG
1 AGTATTGTATTAT-GTGTTTACACTGTCACAGTCAGTTCAATATTGTATTGTAATGTTTACAATG
** *
43548255 TCACTGTCAGATCAGTATTATATGCAGTGTTTACAGTGTCACTGTCAGTTC
65 TCACTACCAGATCAGTATTATATGCAGTGTTTACAGTGTCACTGCCAGTTC
43548306 AGTA
1 AGTA
43548310 ATTTGATAAC
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
116 43 0.41
117 63 0.59
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.41
Consensus pattern (115 bp):
AGTATTGTATTATGTGTTTACACTGTCACAGTCAGTTCAATATTGTATTGTAATGTTTACAATGT
CACTACCAGATCAGTATTATATGCAGTGTTTACAGTGTCACTGCCAGTTC
Found at i:43553446 original size:4 final size:4
Alignment explanation
Indices: 43553428--43553461 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
43553418 AATTGTCATA
*
43553428 AAAG AAA- AAAA AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
43553462 AAGTTTTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:43553456 original size:12 final size:12
Alignment explanation
Indices: 43553427--43553463 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
43553417 TAATTGTCAT
43553427 AAAAGAAA-AAA
1 AAAAGAAAGAAA
43553438 AAAAGAAAGAAA
1 AAAAGAAAGAAA
*
43553450 GAAAGAAAGAAA
1 AAAAGAAAGAAA
43553462 AA
1 AA
43553464 GTTTTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:43556739 original size:22 final size:22
Alignment explanation
Indices: 43556714--43556795 Score: 67
Period size: 23 Copynumber: 3.7 Consensus size: 22
43556704 TTAAATTAAT
* *
43556714 TAAATTATAATTTTTACGATAG
1 TAAAATATAATTTTTACGATAA
** * *
43556736 TAAAAATATAATTTTTAAAAGAT
1 T-AAAATATAATTTTTACGATAA
* *
43556759 TAAATTA-AAATTTTACGATAA
1 TAAAATATAATTTTTACGATAA
*
43556780 TAAAATGTAATTTTTA
1 TAAAATATAATTTTTA
43556796 TTAATTTAAA
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
21 14 0.32
22 13 0.30
23 17 0.39
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (22 bp):
TAAAATATAATTTTTACGATAA
Found at i:43556805 original size:43 final size:44
Alignment explanation
Indices: 43556708--43556812 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
43556698 TAAAAATTAA
* *
43556708 ATTAATTAAATTATAATTTTTACGATAGTAAAAATATAATTTTT
1 ATTAATTAAATTATAAATTTTACGATAATAAAAATATAATTTTT
** *
43556752 AAAAGATTAAATTA-AAATTTTACGATAAT-AAAATGTAATTTTT
1 ATTA-ATTAAATTATAAATTTTACGATAATAAAAATATAATTTTT
*
43556795 ATTAATTTAAATTTTAAA
1 ATTAA-TTAAATTATAAA
43556813 AAATTTTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
42 1 0.02
43 22 0.44
44 18 0.36
45 9 0.18
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (44 bp):
ATTAATTAAATTATAAATTTTACGATAATAAAAATATAATTTTT
Found at i:43562442 original size:24 final size:24
Alignment explanation
Indices: 43562414--43562472 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
43562404 TAGACTAATA
* *
43562414 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAAAAAATAAAC
* *
43562438 AGAGTTTAATTGAAAAAAATAAAC
1 AGAGTTTAACTCAAAAAAATAAAC
*
43562462 AGAGATTAACT
1 AGAGTTTAACT
43562473 GAAAGATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTCAAAAAAATAAAC
Found at i:43562475 original size:24 final size:24
Alignment explanation
Indices: 43562430--43562476 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
43562420 TGACTCAAAC
* *
43562430 AAATAAACAGAGTTTAATTGAAAA
1 AAATAAACAGAGATTAACTGAAAA
43562454 AAATAAACAGAGATTAACTGAAA
1 AAATAAACAGAGATTAACTGAAA
43562477 GATTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.21
Consensus pattern (24 bp):
AAATAAACAGAGATTAACTGAAAA
Found at i:43566170 original size:50 final size:50
Alignment explanation
Indices: 43566086--43566183 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
43566076 ACCATGCTGT
** *
43566086 ACAAGTAGAATCCGTATAGAATTACGATTTTTCTATTTGACATTGATTGC
1 ACAAGTAGAATCCGTATAGAACCACGATTCTTCTATTTGACATTGATTGC
* *
43566136 ACAAGTAGAATCCTTATAGAACCACGCTTCTTCTATTTGACATTGATT
1 ACAAGTAGAATCCGTATAGAACCACGATTCTTCTATTTGACATTGATT
43566184 AGAATAAGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (50 bp):
ACAAGTAGAATCCGTATAGAACCACGATTCTTCTATTTGACATTGATTGC
Done.