Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold23
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: 3824748
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 177433 characters in sequence are not A, C, G, or T
File 13 of 14
Found at i:3404093 original size:26 final size:26
Alignment explanation
Indices: 3404023--3404096 Score: 112
Period size: 27 Copynumber: 2.8 Consensus size: 26
3404013 TCTCATTCCT
*
3404023 ATTTTACCCCCAATAAAATTTTGACC
1 ATTTTACCCCCAATAAATTTTTGACC
3404049 ATTTTACCCCCAATAAAATTTTTGACC
1 ATTTTACCCCCAAT-AAATTTTTGACC
* *
3404076 ATTTTACCCCTAGTAAATTTT
1 ATTTTACCCCCAATAAATTTT
3404097 CGAGAAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 21 0.48
27 23 0.52
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCCAATAAATTTTTGACC
Found at i:3415698 original size:30 final size:30
Alignment explanation
Indices: 3415657--3415717 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
3415647 GTAGGAATGG
*
3415657 CCCAACGTTGTCTCATCTCTTCGCAGATAA
1 CCCAACATTGTCTCATCTCTTCGCAGATAA
3415687 CCCAACATTGTCTCATCTCTTCGCAGATAA
1 CCCAACATTGTCTCATCTCTTCGCAGATAA
3415717 C
1 C
3415718 TTAATTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.34, G:0.11, T:0.30
Consensus pattern (30 bp):
CCCAACATTGTCTCATCTCTTCGCAGATAA
Found at i:3421130 original size:27 final size:28
Alignment explanation
Indices: 3421075--3421146 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
3421065 CCAAAAAATT
** *
3421075 CAACGACCATATTGGAACAGTCAGATTC
1 CAACGACCATATTATAACAATCAGATTC
3421103 CAAC-ACCATATTATAACAATCAGATTC
1 CAACGACCATATTATAACAATCAGATTC
* *
3421130 CACCGGCCATATTATAA
1 CAACGACCATATTATAA
3421147 TGATTAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (28 bp):
CAACGACCATATTATAACAATCAGATTC
Found at i:3424509 original size:17 final size:17
Alignment explanation
Indices: 3424487--3424525 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3424477 AAAACATATT
* *
3424487 TTTTTTATATTTTTTAA
1 TTTTTTATAATTTTAAA
*
3424504 TTTTTTTTAATTTTAAA
1 TTTTTTATAATTTTAAA
3424521 TTTTT
1 TTTTT
3424526 AAAAAAATTA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTATAATTTTAAA
Found at i:3431126 original size:18 final size:18
Alignment explanation
Indices: 3431105--3431142 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3431095 TGTTTTAATT
*
3431105 AAATACAATTTTTTTTTA
1 AAATACAATGTTTTTTTA
*
3431123 AAATTCAATGTTTTTTTA
1 AAATACAATGTTTTTTTA
3431141 AA
1 AA
3431143 TTATGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (18 bp):
AAATACAATGTTTTTTTA
Found at i:3436815 original size:16 final size:15
Alignment explanation
Indices: 3436790--3436832 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
3436780 GATGGATTTC
3436790 AAAAATAAAAAAATA
1 AAAAATAAAAAAATA
*
3436805 AAAAATAAAAAAAATG
1 AAAAAT-AAAAAAATA
3436821 AAAAATGAAAAA
1 AAAAAT-AAAAA
3436833 TGAGAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:3436824 original size:7 final size:7
Alignment explanation
Indices: 3436814--3436863 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
3436804 AAAAAATAAA
3436814 AAAAATG
1 AAAAATG
3436821 AAAAATG
1 AAAAATG
3436828 AAAAATG
1 AAAAATG
*
3436835 -AGAATG
1 AAAAATG
3436841 AAAAATG
1 AAAAATG
3436848 -AAAATG
1 AAAAATG
3436854 -AAAATG
1 AAAAATG
3436860 AAAA
1 AAAA
3436864 TAGAGAGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 17 0.44
7 22 0.56
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:3436840 original size:13 final size:13
Alignment explanation
Indices: 3436814--3436864 Score: 77
Period size: 13 Copynumber: 3.9 Consensus size: 13
3436804 AAAAAATAAA
3436814 AAAAATGAAAAATG
1 AAAAATG-AAAATG
*
3436828 AAAAATGAGAATG
1 AAAAATGAAAATG
3436841 AAAAATGAAAATG
1 AAAAATGAAAATG
3436854 -AAAATGAAAAT
1 AAAAATGAAAAT
3436865 AGAGAGGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.31
13 17 0.49
14 7 0.20
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
AAAAATGAAAATG
Found at i:3438335 original size:131 final size:130
Alignment explanation
Indices: 3438091--3438646 Score: 715
Period size: 131 Copynumber: 4.2 Consensus size: 130
3438081 TCGGTGAAAT
* * *
3438091 CACAAGTCCTATGTCCCTGGTCAGTAGTGGAATAGGTTGGAAATTACAGATCTTGTTTCCCTG-A
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCC-GAA
*
3438155 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTACCTTCCCCAAGAGTAGGGAAACAGATTTAA
65 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTACCTT-CCCAGGAGTAGGGAAACAGATTTAA
3438220 GC
129 GC
* * * * *
3438222 CACACGTCCTATGTCCCTGGTCAGCAGTGGAGTTGGTTGGAAATTGCAGATCTTGTCTCCCGAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCGAAG
3438287 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTACCTTCCCTAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTACCTTCCC-AGGAGTAGGGAAACAGATTTAAG
3438352 C
130 C
* ** ** * *
3438353 CACAAGTCTTATGTCCCTGACCAGCAGTGGAATAGGTCAGAAATTGCAGATCTTATCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCGAAG
* * * *
3438418 CAGTAGCGGAGTAGATCCAATACGGCGAATCTTATCTTTCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTA-CCTTCCCAGGAGTAGGGAAACAGATTTAAG
3438483 C
130 C
** * * * *
3438484 CACAAGTCCTATGTCCCTGACCAGCAGAGGAATAGGTTGGAAATTACATATCTTATCTCTCTAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCGAAG
* * * *
3438549 CAGTAGTGGAGCAGATTGAAGACGGCGAATCTTATCTTCCCAAGGTAGTA-GGAAAGCAAATTTA
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTACCTTCCC-AGG-AGTAGGGAAA-CAGATTTA
3438613 AGC
128 AGC
* *
3438616 CACTAG-CCTTATCTCCCTGAGT-AGCAGTGGA
1 CACAAGTCC-TATGTCCCTG-GTCAGCAGTGGA
3438647 GTAAGTTGAA
Statistics
Matches: 376, Mismatches: 41, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
130 9 0.02
131 325 0.86
132 42 0.11
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (130 bp):
CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCGAAG
CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTACCTTCCCAGGAGTAGGGAAACAGATTTAAGC
Found at i:3438715 original size:44 final size:44
Alignment explanation
Indices: 3438622--3438738 Score: 144
Period size: 44 Copynumber: 2.7 Consensus size: 44
3438612 AAGCCACTAG
* * * * **
3438622 CCTTATCTCCCTGAGTAGCAGTGGAGTAAGTTGAAGATTGTAAA
1 CCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAAA
*
3438666 CCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGA
1 CCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAAA
* * *
3438710 TCTTATATCCCTAAGCAGTAGTGGAGTAG
1 CCTTATCTCCCTAAGCAGCAGTGGAGTAG
3438739 ATCGAATACG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
CCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAAA
Found at i:3438870 original size:44 final size:44
Alignment explanation
Indices: 3438802--3440032 Score: 474
Period size: 44 Copynumber: 26.1 Consensus size: 44
3438792 TAGATCGCAT
* * * *
3438802 CAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
*
3438846 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* ** * * *
3438890 CGGATT-AAAATAAAG-AATATTATCTCTCTGA-AGTTACAGTAGATTATATCGCAT
1 CAGATTGAAGCT--AGTAATCTTATCTCCCTGAGA-TTACAGT-G--------G-AG
* * * *
3438944 CAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
*
3438988 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* ** * * * **
3439032 CGGATT-AAAATAAATGATATTATCTTTCTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCT-AGTAATCTTATCTCCCTGAGA-TTACAGT---G--GA--G
* * * * *
3439083 CATCAGAATGAAGCCAGAAATCTTATCGCCCTGAGATTACAGCGGAG
1 ---CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
*
3439130 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* ** * **
3439174 CGGATT-AAAATAAAG-GATCTTATCTTTCTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCT--AGTAATCTTATCTCCCTGAGA-TTACAGT---G--GA--G
* * * *
3439225 CATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 ---CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
*
3439272 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* ** *
3439316 CGGATT-AAAATAAAG-AATCTTATCTCACTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCT--AGTAATCTTATCTCCCTGAGA-TTACAGT---G--GA--G
* * ***
3439367 CATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAAAG
1 ---CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* *
3439414 CAGATTGAAGCTAGTAATCATATCTCCTTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* ** *
3439458 CAAATT-AAAATAAAG-AATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCT--AGTAATCTTATCTCCCTGAGA-TTACAGT---G--GA--G
* ***
3439509 CATCAGATTGAAGCCAG-AAGTCTTATCTCCCTGAGATTACAGCAAAG
1 ---CAGATTGAAGCTAGTAA-TCTTATCTCCCTGAGATTACAGTGGAG
* *
3439556 CAGATTGAAGCTAGTAATCACTATCTCCTTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATC-TTATCTCCCTGAGATTACAGTGGAG
* ** * *
3439601 CGGATT-AAAATAAAG-GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCT--AGTAATCTTATCTCCCTGAGA-TTACAGT---G--GA--G
* * * *
3439652 TATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGTGAAG
1 ---CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * *
3439699 TAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAA
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* ** ** *
3439743 CGGATT-AAAATAAAAGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCTAGTA-ATCTTATCTCCCTGAGA-TTACAGT---G--GA--G
* * * * * *
3439794 CATCAGATTGAGGCCAGAAATATTATCTTCCTGAGATTACAGCGGAG
1 ---CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
*
3439841 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
** * * *
3439885 CAGATT-AAAATAAAG-GATCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCT--AGTAATCTTATCTCCCTGAGA-TTACAGT---G--GA--G
* * * * *
3439936 CATCAGAATGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAG
1 ---CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
*
3439983 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
*
3440027 CGGATT
1 CAGATT
3440033 AAAATAAATG
Statistics
Matches: 883, Mismatches: 178, Indels: 252
0.67 0.14 0.19
Matches are distributed among these distances:
43 32 0.04
44 517 0.59
45 42 0.05
46 2 0.00
47 14 0.02
49 25 0.03
51 11 0.01
53 16 0.02
54 194 0.22
55 30 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (44 bp):
CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAG
Found at i:3439012 original size:98 final size:97
Alignment explanation
Indices: 3438846--3439027 Score: 215
Period size: 98 Copynumber: 1.9 Consensus size: 97
3438836 TACAGCGGAG
* * * * * *
3438846 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGAATATT
1 CAGATTGAAACCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAT-AAGAATACT
*
3438911 ATCTCTCTGA-AGTTACAGTAGATTATATCGCAT
65 ATCTCCCTGAGA-TTACAGTAGATTATATCGCAT
* ** *
3438944 CAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCC
1 CAGATTGAAACCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATAAG-AATAC
3439008 TATCTCCCTGAGATTACAGT
64 TATCTCCCTGAGATTACAGT
3439028 GGAGCGGATT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
97 2 0.03
98 64 0.91
99 4 0.06
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (97 bp):
CAGATTGAAACCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAGAATACTA
TCTCCCTGAGATTACAGTAGATTATATCGCAT
Found at i:3439052 original size:142 final size:141
Alignment explanation
Indices: 3438789--3440083 Score: 2167
Period size: 142 Copynumber: 9.1 Consensus size: 141
3438779 NNNNNNNNNN
*
3438789 GAGTAGATCGCATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
1 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
*
3438854 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGAATATTATCTCTCT
66 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-ATCTTATCTCTCT
3438919 GAAGTTACAGTA
130 GAAGTTACAGTA
* * *
3438931 GATTATATCGCATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
1 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
* *
3438996 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATATTATCTTTCT
66 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA-GATCTTATCTCTCT
3439061 GAAGTTACAGTA
130 GAAGTTACAGTA
* *
3439073 GAGTAGATCGCATCAGAATGAAGCCAGAAATCTTATCGCCCTGAGATTACAGCGGAGCAGATTGA
1 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
*
3439138 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTTTCT
66 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA-GATCTTATCTCTCT
3439203 GAAGTTACAGTA
130 GAAGTTACAGTA
*
3439215 GAGTAGATCGCATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
1 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
*
3439280 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCACT
66 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-ATCTTATCTCTCT
3439345 GAAGTTACAGTA
130 GAAGTTACAGTA
**
3439357 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAAAGCAGATTGA
1 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
* * **
3439422 AGCTAGTAATCATATCTCCTTGAGATTACAGTGGAGCAAATTAAAATAAAGAATCTTATCTCTCT
66 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-ATCTTATCTCTCT
3439487 GAAGTTACAGTA
130 GAAGTTACAGTA
* **
3439499 GAGTAGATCGCATCAGATTGAAGCCAGAAGTCTTATCTCCCTGAGATTACAGCAAAGCAGATTGA
1 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
*
3439564 AGCTAGTAATCACTATCTCCTTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTC
66 AGCTAGTAATC-CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA-GATCTTATCTCTC
3439629 TGAAGTTACAGTA
129 TGAAGTTACAGTA
* * * * *
3439642 GAGTAGATCGTATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGTGAAGTAGATTGA
1 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
*
3439707 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAAAGATCTTATCTCTCT
66 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAAT-AAAGATCTTATCTCTCT
3439772 GAAGTTACAGTA
130 GAAGTTACAGTA
* * *
3439784 GAGTAGATCGCATCAGATTGAGGCCAGAAATATTATCTTCCTGAGATTACAGCGGAGCAGATTGA
1 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
*
3439849 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCT
66 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA-GATCTTATCTCTCT
*
3439914 AAAGTTACAGTA
130 GAAGTTACAGTA
* *
3439926 GAGTAGATCGCATCAGAATGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGA
1 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
* *
3439991 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATATTATCTTTCT
66 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA-GATCTTATCTCTCT
3440056 GAAGTTACAGTA
130 GAAGTTACAGTA
3440068 GAGTAGATCGCATCAG
1 GAGTAGATCGCATCAG
3440084 GTCTTATCTC
Statistics
Matches: 1091, Mismatches: 56, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
141 4 0.00
142 951 0.87
143 135 0.12
144 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (141 bp):
GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGATCTTATCTCTCTG
AAGTTACAGTA
Found at i:3440218 original size:50 final size:50
Alignment explanation
Indices: 3440159--3440339 Score: 175
Period size: 50 Copynumber: 3.6 Consensus size: 50
3440149 ACCGTGGAAC
* * * * *
3440159 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGATATTGCAGTTAAAG
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * * ** *
3440209 AGATTAAAGCTACAACAGCAAATCTTACTTCCCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGAC-ATTGCAGTTAAAA
* * *
3440259 AGATTAAAGTCACAACGGCGAATCATGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * *
3440309 AGATTAAAGCCAAAATGGTGAATCTTACTTC
1 AGATTAAAGCCACAACGGCGAATCTTACTTC
3440340 TAAAGTTACG
Statistics
Matches: 101, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
49 1 0.01
50 99 0.98
51 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:3440303 original size:100 final size:100
Alignment explanation
Indices: 3440130--3440318 Score: 288
Period size: 100 Copynumber: 1.9 Consensus size: 100
3440120 AGAATTATAG
* * * * *
3440130 ATCTTACCTCTCAGGCGATACCGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGA
1 ATCTTACCTCCCAGGCGATACAGTGGAACAGATTAAAGCCACAACGGCGAATCATGCTTCCCCGA
* *
3440195 TATTGCAGTTAAAGAGATTAAAGCTACAACAGCAA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCAA
* * *
3440230 ATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGTCACAACGGCGAATCATGCTTCCCCGA
1 ATCTTACCTCCCAGGCGATACAGTGGAACAGATTAAAGCCACAACGGCGAATCATGCTTCCCCGA
3440295 CATTGCAGTTAAAAAGATTAAAGC
66 CATTGCAGTTAAAAAGATTAAAGC
3440319 CAAAATGGTG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (100 bp):
ATCTTACCTCCCAGGCGATACAGTGGAACAGATTAAAGCCACAACGGCGAATCATGCTTCCCCGA
CATTGCAGTTAAAAAGATTAAAGCTACAACAGCAA
Found at i:3440348 original size:569 final size:559
Alignment explanation
Indices: 3438789--3440106 Score: 1624
Period size: 569 Copynumber: 2.3 Consensus size: 559
3438779 NNNNNNNNNN
* * * **
3438789 GAGTAGATCGCATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
1 GAGTAGATCGCATCAGAATGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCAAAGCAGATTGA
* **
3438854 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGAATATTATCTCTCT
66 AGCTAGTAATCATATCTCCCTGAGATTACAGTGGAGCAAATTAAAATAAAGAATATTATCTCTCT
* * * *
3438919 GAAGTTACAGTAGATTATATCGCATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACAGC
131 GAAGTTACAGTAGAGTAGATCG-A-CA-ATT---A-CAG-AGTCTTATCTCCCTAAGATTACAGC
** * * ** * * * *
3438984 GGAGCAGATTGAAGCTAGTAATC-CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATG
188 AAAGCAGATCGAAGCTAGTAATCACTACCTCCAGGAGATTACAGTGGAACAGATTAAAACAAAGG
* ** * * * * * *
3439048 ATATTATCTTTCTGAAGTTACAGTAGAGTAGATCGCATCAGAATGAAGCCAGAAATCTTATCGCC
253 ATCTTATCTCCCTGAAGTTACAGTAAAGTAGATC-TATAAGACTGAAACCAGAAATCTTATCTCC
* * * * * * * * * ***
3439113 CTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGA
317 CGGAGATTACAGTGAAGCAGATTAAAGCAAGGAATCCTATCTCCCCGACATTACAGTGAAAAAGA
* *
3439178 TTAAAATAAAGGATCTTATCTTTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGA
382 TTAAAACAAAAGATCTTATC-TTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGA
*
3439243 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
446 AATATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
* *
3439308 CAGTGGAGCGGATTAAAATAAAGAATCTTATCTCACTGAAGTTACAGTA
511 CAGTGGAGCAGATTAAAATAAAGAATCTTATCTCACTAAAGTTACAGTA
* *
3439357 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAAAGCAGATTGA
1 GAGTAGATCGCATCAGAATGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCAAAGCAGATTGA
* *
3439422 AGCTAGTAATCATATCTCCTTGAGATTACAGTGGAGCAAATTAAAATAAAGAATCTTATCTCTCT
66 AGCTAGTAATCATATCTCCCTGAGATTACAGTGGAGCAAATTAAAATAAAGAATATTATCTCTCT
*
3439487 GAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAGTCTTATCTCCCTGAGATTACAGC
131 GAAGTTACAGTAGAGTAGATCG-A-CA-ATT--A--CAG-AGTCTTATCTCCCTAAGATTACAGC
* * ** * * *
3439552 AAAGCAGATTGAAGCTAGTAATCACTATCTCCTTGAGATTACAGTGGAGCGGATTAAAATAAAGG
188 AAAGCAGATCGAAGCTAGTAATCACTACCTCCAGGAGATTACAGTGGAACAGATTAAAACAAAGG
* * * *
3439617 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGATTGAAACCAGAAATCTTATCTCC
253 ATCTTATCTCCCTGAAGTTACAGTAAAGTAGATC-TATAAGACTGAAACCAGAAATCTTATCTCC
* * * * * * * * **
3439682 CTGAGATTACAGTGAAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAACGGA
317 CGGAGATTACAGTGAAGCAGATTAAAGCAAGGAATCCTATCTCCCCGACATTACAGTGAAAAAGA
* **
3439747 TTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAGGCCAGA
382 TTAAAACAAAAGATCTTATCT-TCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGA
*
3439812 AATATTATCTTCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
446 AATATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
* *
3439877 CAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTA
511 CAGTGGAGCAGATTAAAATAAAGAATCTTATCTCACTAAAGTTACAGTA
**
3439926 GAGTAGATCGCATCAGAATGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGA
1 GAGTAGATCGCATCAGAATGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCAAAGCAGATTGA
* ** *
3439991 AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATG-ATATTATCTTTC
66 AGCTAGTAATCATATCTCCCTGAGATTACAGTGGAGCAAATTAAAATAAA-GAATATTATCTCTC
3440055 TGAAGTTACAGTAGAGTAGATCG-C-A-T-CAG-GTCTTATCTCCCTAAGATTACAG
130 TGAAGTTACAGTAGAGTAGATCGACAATTACAGAGTCTTATCTCCCTAAGATTACAG
3440107 TGGAATAGAT
Statistics
Matches: 700, Mismatches: 46, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
556 22 0.03
558 3 0.00
563 1 0.00
564 1 0.00
566 1 0.00
567 2 0.00
568 202 0.29
569 467 0.67
570 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (559 bp):
GAGTAGATCGCATCAGAATGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCAAAGCAGATTGA
AGCTAGTAATCATATCTCCCTGAGATTACAGTGGAGCAAATTAAAATAAAGAATATTATCTCTCT
GAAGTTACAGTAGAGTAGATCGACAATTACAGAGTCTTATCTCCCTAAGATTACAGCAAAGCAGA
TCGAAGCTAGTAATCACTACCTCCAGGAGATTACAGTGGAACAGATTAAAACAAAGGATCTTATC
TCCCTGAAGTTACAGTAAAGTAGATCTATAAGACTGAAACCAGAAATCTTATCTCCCGGAGATTA
CAGTGAAGCAGATTAAAGCAAGGAATCCTATCTCCCCGACATTACAGTGAAAAAGATTAAAACAA
AAGATCTTATCTTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGAAATATTATCT
CCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCA
GATTAAAATAAAGAATCTTATCTCACTAAAGTTACAGTA
Found at i:3441832 original size:18 final size:18
Alignment explanation
Indices: 3441811--3441848 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3441801 TGTTTTAATT
*
3441811 AAATACAATTTTTTTTTA
1 AAATACAATGTTTTTTTA
*
3441829 AAATTCAATGTTTTTTTA
1 AAATACAATGTTTTTTTA
3441847 AA
1 AA
3441849 TTATGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (18 bp):
AAATACAATGTTTTTTTA
Found at i:3443667 original size:18 final size:18
Alignment explanation
Indices: 3443644--3443682 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3443634 ATAATATTTA
3443644 CATTTTAATTATATTATG
1 CATTTTAATTATATTATG
3443662 CATTTTAATTATATTATG
1 CATTTTAATTATATTATG
3443680 CAT
1 CAT
3443683 ACTTTATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (18 bp):
CATTTTAATTATATTATG
Found at i:3444986 original size:22 final size:22
Alignment explanation
Indices: 3444958--3445002 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3444948 TTATGTTGAT
*
3444958 TCATAGAGCTGATTTGTAGGGA
1 TCATAGAACTGATTTGTAGGGA
*
3444980 TCATAGAACTGGTTTGTAGGGA
1 TCATAGAACTGATTTGTAGGGA
3445002 T
1 T
3445003 TTATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.31, T:0.33
Consensus pattern (22 bp):
TCATAGAACTGATTTGTAGGGA
Found at i:3448113 original size:22 final size:23
Alignment explanation
Indices: 3448077--3448122 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3448067 TTATGTTGAT
*
3448077 TCATAGGAGTTGATTTGTAAGGA
1 TCATAGGAATTGATTTGTAAGGA
*
3448100 TCATA-GAATTGATTTGTAGGGA
1 TCATAGGAATTGATTTGTAAGGA
3448122 T
1 T
3448123 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.37
Consensus pattern (23 bp):
TCATAGGAATTGATTTGTAAGGA
Found at i:3448364 original size:60 final size:60
Alignment explanation
Indices: 3448290--3448404 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
3448280 AATTTTTAAC
* *
3448290 TAATAATTTTAAATTAAATTATAATTATATTTTATCATAAATTTT-TTATATTTTCCAAT
1 TAATAATTTTAAATTAAATTATAATCATAATTTATCATAAATTTTCTTATATTTTCCAAT
*
3448349 TAATAATATTTAAATTAAATTATAATCATAATTTATCATAATTTTTCTTATATTTT
1 TAATAAT-TTTAAATTAAATTATAATCATAATTTATCATAAATTTTCTTATATTTT
3448405 AGGGTAAACT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 7 0.14
60 35 0.69
61 9 0.18
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (60 bp):
TAATAATTTTAAATTAAATTATAATCATAATTTATCATAAATTTTCTTATATTTTCCAAT
Found at i:3450265 original size:222 final size:220
Alignment explanation
Indices: 3449854--3450269 Score: 535
Period size: 222 Copynumber: 1.9 Consensus size: 220
3449844 GTGCCTGGCC
* * * *
3449854 GTGTGGTTGGCCGTGTGCGAGACACGACTGTGTGGTTGACGAGGGCATGGTTGTACATAAGACAC
1 GTGTGGTTGGCCATGTGCGAGACACGACTGTATGGTTGACGAGGGCATGGTCGTACACAAGACAC
* * * *
3449919 GACCATGTGGTGGTATGAGTGTGGCCACGTGAGCTACACGGGTTAAGCCAAGTTGGACGTGTGGA
66 GACCATATGGTGGTATGAGTGTGGCCACATGAGCCACACGGGCTAAGCCAAGTTGGACGTGTGGA
* * * *
3449984 TTTTGGGCTAGGCCGTGTGGGCCACACGGGCAAGACCAATCTAGATGTATGGGCCACACGGGCAT
131 CTTTAGGCTAGGCCGTGTGGGCCACACGGGCAAGACCAATCTAGACGTATGGACCACACGGGCAT
3450049 GTGGGACAATAATTCTGTAACACGG
196 GTGGGACAATAATTCTGTAACACGG
* * *
3450074 GTGTGTGTCTGGCCATGTGTGAGACACGATTGTATGGTTGACGAGGGCATGGTCGTACGCAAGAC
1 GTGTG-GT-TGGCCATGTGCGAGACACGACTGTATGGTTGACGAGGGCATGGTCGTACACAAGAC
** * * * * * **
3450139 ACGGTCATATGGTGGTGTGAGTGTGGCCGCATGGGCCACATGGGCTAGGCCAAGTTGGGTGTGTG
64 ACGACCATATGGTGGTATGAGTGTGGCCACATGAGCCACACGGGCTAAGCCAAGTTGGACGTGTG
* * * * * * *
3450204 GGCTTTAGGTTAGGTCGTGTGGGCCATACGGGCAAGACCAATCTGGGCGTGTGGACCACACGGGC
129 GACTTTAGGCTAGGCCGTGTGGGCCACACGGGCAAGACCAATCTAGACGTATGGACCACACGGGC
3450269 A
194 A
3450270 CAGGTCGTTC
Statistics
Matches: 163, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
220 5 0.03
221 2 0.01
222 156 0.96
ACGTcount: A:0.20, C:0.19, G:0.38, T:0.23
Consensus pattern (220 bp):
GTGTGGTTGGCCATGTGCGAGACACGACTGTATGGTTGACGAGGGCATGGTCGTACACAAGACAC
GACCATATGGTGGTATGAGTGTGGCCACATGAGCCACACGGGCTAAGCCAAGTTGGACGTGTGGA
CTTTAGGCTAGGCCGTGTGGGCCACACGGGCAAGACCAATCTAGACGTATGGACCACACGGGCAT
GTGGGACAATAATTCTGTAACACGG
Found at i:3454051 original size:2 final size:2
Alignment explanation
Indices: 3454044--3454191 Score: 296
Period size: 2 Copynumber: 74.0 Consensus size: 2
3454034 TACCTCTTTG
3454044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3454086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3454128 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3454170 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3454192 TGAGATGGTC
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 146 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3455572 original size:12 final size:12
Alignment explanation
Indices: 3455550--3455595 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
3455540 GGAAAGGTAT
3455550 ATAAA-ATATTC
1 ATAAATATATTC
*
3455561 CTAAATATATTC
1 ATAAATATATTC
3455573 ATAAATATATTC
1 ATAAATATATTC
*
3455585 TTAAAATATAT
1 AT-AAATATAT
3455596 ACAATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 4 0.13
12 18 0.60
13 8 0.27
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAAATATATTC
Found at i:3455584 original size:24 final size:24
Alignment explanation
Indices: 3455550--3455595 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3455540 GGAAAGGTAT
3455550 ATAAAATATTCCT-AAATATATTC
1 ATAAAATATTCCTAAAATATATTC
*
3455573 ATAAATATATTCTTAAAATATAT
1 ATAAA-ATATTCCTAAAATATAT
3455596 ACAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAAAATATTCCTAAAATATATTC
Found at i:3455604 original size:25 final size:23
Alignment explanation
Indices: 3455550--3455606 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
3455540 GGAAAGGTAT
* *
3455550 ATAAAATATTCCTAAATATATTC
1 ATAATATATTCCTAAATATATAC
*
3455573 ATAAATATATTCTTAAAATATATAC
1 AT-AATATATTCCT-AAATATATAC
3455598 AATAATATA
1 -ATAATATA
3455607 CAATATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 2 0.07
24 9 0.32
25 15 0.54
26 2 0.07
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAATATATTCCTAAATATATAC
Found at i:3476580 original size:44 final size:42
Alignment explanation
Indices: 3476430--3476592 Score: 229
Period size: 42 Copynumber: 3.8 Consensus size: 42
3476420 CAAACAAAAA
* * *
3476430 CGCCGCTGAAGACCATGTTCTTCAGCGGCG-TTTTTTCATAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTC-TAAG
3476472 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
* *
3476514 CGCCTCTAAAGAATATGTTCTTTAGCGGCGTTTTTATGTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT-T-TCTAAG
* *
3476558 CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
3476593 ATACAAAAAC
Statistics
Matches: 109, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
42 64 0.59
43 8 0.07
44 37 0.34
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:3476934 original size:21 final size:21
Alignment explanation
Indices: 3476908--3476950 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3476898 TTTTGCTCTG
* *
3476908 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTGCCCTCGCTGCAGC
3476929 CTCTGCTGCCCTCGCTGCAGC
1 CTCTGCTGCCCTCGCTGCAGC
3476950 C
1 C
3476951 NNNNNNNNNN
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.47, G:0.21, T:0.28
Consensus pattern (21 bp):
CTCTGCTGCCCTCGCTGCAGC
Found at i:3480503 original size:9 final size:9
Alignment explanation
Indices: 3480489--3480841 Score: 103
Period size: 9 Copynumber: 41.8 Consensus size: 9
3480479 NNNNTATACA
3480489 TTATGTAAG
1 TTATGTAAG
3480498 TTATGTAAG
1 TTATGTAAG
3480507 TTATGTAAG
1 TTATGTAAG
*
3480516 TTGTGTAAG
1 TTATGTAAG
**
3480525 TTGCGTAAG
1 TTATGTAAG
* *
3480534 ATGTGT-A-
1 TTATGTAAG
* *
3480541 TTATGAAAC
1 TTATGTAAG
3480550 TTATGTAAG
1 TTATGTAAG
*
3480559 TTATGT--C
1 TTATGTAAG
3480566 TTATGTAAG
1 TTATGTAAG
*
3480575 TTATGTAAA
1 TTATGTAAG
*
3480584 ATATGT-A-
1 TTATGTAAG
*
3480591 TTATTTACA-
1 TTATGTA-AG
*
3480600 -CATGTAAG
1 TTATGTAAG
*
3480608 TTATGT--C
1 TTATGTAAG
3480615 TTATGTAAG
1 TTATGTAAG
**
3480624 TTGCGTAAG
1 TTATGTAAG
*
3480633 TTGTGT-A-
1 TTATGTAAG
*
3480640 TTATGAAAG
1 TTATGTAAG
* *
3480649 TTTTGT--C
1 TTATGTAAG
3480656 TTATGTAAG
1 TTATGTAAG
*
3480665 TTATGTAAT
1 TTATGTAAG
3480674 TTATGT-A-
1 TTATGTAAG
*
3480681 TTATTTACA-
1 TTATGTA-AG
*
3480690 -CATGTAAG
1 TTATGTAAG
* *
3480698 TTGTGT--C
1 TTATGTAAG
3480705 TTATGTAAG
1 TTATGTAAG
* **
3480714 ATGCGTAAG
1 TTATGTAAG
3480723 -T-TGT--G
1 TTATGTAAG
3480728 TTATGTAAG
1 TTATGTAAG
**
3480737 TTGCGTAAG
1 TTATGTAAG
*
3480746 TTGTGT-A-
1 TTATGTAAG
*
3480753 TTATGTAAC
1 TTATGTAAG
* *
3480762 TTATTTAAT
1 TTATGTAAG
*
3480771 TTATGTAGG
1 TTATGTAAG
*
3480780 GTATGTATTA-
1 TTATGTA--AG
*
3480790 TTATGTAAC
1 TTATGTAAG
* *
3480799 TTATTTAAT
1 TTATGTAAG
*
3480808 TTATGTAGG
1 TTATGTAAG
* *
3480817 GTATGCAAG
1 TTATGTAAG
3480826 TTATGTAAG
1 TTATGTAAG
*
3480835 TTCTGTA
1 TTATGTA
3480842 TTATTTACAC
Statistics
Matches: 249, Mismatches: 66, Indels: 58
0.67 0.18 0.16
Matches are distributed among these distances:
5 1 0.00
6 1 0.00
7 50 0.20
8 18 0.07
9 173 0.69
10 6 0.02
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3480557 original size:25 final size:25
Alignment explanation
Indices: 3480529--3480594 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
3480519 TGTAAGTTGC
*
3480529 GTAAGATGTGTATTATGAAACTTAT
1 GTAAGATATGTATTATGAAACTTAT
* * * *
3480554 GTAAGTTATGTCTTATGTAAGTTAT
1 GTAAGATATGTATTATGAAACTTAT
*
3480579 GTAAAATATGTATTAT
1 GTAAGATATGTATTAT
3480595 TTACACATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.44
Consensus pattern (25 bp):
GTAAGATATGTATTATGAAACTTAT
Found at i:3480568 original size:16 final size:16
Alignment explanation
Indices: 3480549--3480670 Score: 73
Period size: 16 Copynumber: 8.0 Consensus size: 16
3480539 TATTATGAAA
3480549 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
3480565 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
** *
3480581 AAAATATGT-A-TTATTT
1 --CTTATGTAAGTTATGT
**
3480597 ACACATGTAAGTTATGT
1 -CTTATGTAAGTTATGT
3480614 CTTATGTAAG-T-TG-
1 CTTATGTAAGTTATGT
*
3480627 C----GTAAGTTGTGT
1 CTTATGTAAGTTATGT
* * *
3480639 ATTATGAAAGTTTTGT
1 CTTATGTAAGTTATGT
3480655 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
3480671 AATTTATGTA
Statistics
Matches: 81, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 2 0.02
13 1 0.01
14 2 0.02
15 7 0.09
16 52 0.64
17 6 0.07
18 5 0.06
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.47
Consensus pattern (16 bp):
CTTATGTAAGTTATGT
Found at i:3480616 original size:49 final size:49
Alignment explanation
Indices: 3480552--3480713 Score: 187
Period size: 49 Copynumber: 3.5 Consensus size: 49
3480542 TATGAAACTT
3480552 ATGTAAGTTATGTCTTATGTAAGTTATGTAAAATATGTATTATTTACAC
1 ATGTAAGTTATGTCTTATGTAAGTTATGTAAAATATGTATTATTTACAC
** * *
3480601 ATGTAAGTTATGTCTTATGTAAGTTGCGT-AAGT-TGT-GTA-TT----
1 ATGTAAGTTATGTCTTATGTAAGTTATGTAAAATATGTATTATTTACAC
* * **
3480642 ATGAAAGTTTTGTCTTATGTAAGTTATGTAATTTATGTATTATTTACAC
1 ATGTAAGTTATGTCTTATGTAAGTTATGTAAAATATGTATTATTTACAC
*
3480691 ATGTAAGTTGTGTCTTATGTAAG
1 ATGTAAGTTATGTCTTATGTAAG
3480714 ATGCGTAAGT
Statistics
Matches: 92, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
41 25 0.27
42 2 0.02
43 3 0.03
44 2 0.02
45 4 0.04
46 2 0.02
47 3 0.03
48 3 0.03
49 48 0.52
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.46
Consensus pattern (49 bp):
ATGTAAGTTATGTCTTATGTAAGTTATGTAAAATATGTATTATTTACAC
Found at i:3480650 original size:90 final size:90
Alignment explanation
Indices: 3480550--3480728 Score: 304
Period size: 90 Copynumber: 2.0 Consensus size: 90
3480540 ATTATGAAAC
*
3480550 TTATGTAAGTTATGTCTTATGTAAGTTATGTAAAATATGTATTATTTACACATGTAAGTTATGTC
1 TTATGAAAGTTATGTCTTATGTAAGTTATGTAAAATATGTATTATTTACACATGTAAGTTATGTC
*
3480615 TTATGTAAGTTGCGTAAGTTGTGTA
66 TTATGTAAGATGCGTAAGTTGTGTA
* ** *
3480640 TTATGAAAGTTTTGTCTTATGTAAGTTATGTAATTTATGTATTATTTACACATGTAAGTTGTGTC
1 TTATGAAAGTTATGTCTTATGTAAGTTATGTAAAATATGTATTATTTACACATGTAAGTTATGTC
3480705 TTATGTAAGATGCGTAAGTTGTGT
66 TTATGTAAGATGCGTAAGTTGTGT
3480729 TATGTAAGTT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (90 bp):
TTATGAAAGTTATGTCTTATGTAAGTTATGTAAAATATGTATTATTTACACATGTAAGTTATGTC
TTATGTAAGATGCGTAAGTTGTGTA
Found at i:3480656 original size:41 final size:41
Alignment explanation
Indices: 3480605--3480684 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
3480595 TTACACATGT
* *
3480605 AAGTTATGTCTTATGTAAGTTGCGTAAGTTGTGTATTATGA
1 AAGTTATGTCTTATGTAAGTTACGTAAGTTATGTATTATGA
* * *
3480646 AAGTTTTGTCTTATGTAAGTTATGTAATTTATGTATTAT
1 AAGTTATGTCTTATGTAAGTTACGTAAGTTATGTATTAT
3480685 TTACACATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.49
Consensus pattern (41 bp):
AAGTTATGTCTTATGTAAGTTACGTAAGTTATGTATTATGA
Found at i:3480684 original size:25 final size:25
Alignment explanation
Indices: 3480640--3480777 Score: 77
Period size: 25 Copynumber: 5.6 Consensus size: 25
3480630 AAGTTGTGTA
* * *
3480640 TTATGAAAGTTTTGTCTTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
* *
3480665 TTATGTAATTTATGTATTATTTACA-
1 TTATGTAAGTTATGTATTATGTA-AG
* * *
3480690 -CATGTAAGTTGTGTCTTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
* ** *
3480714 ATGCGTAAG-T-TGTGTTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
** * *
3480737 TTGCGTAAGTTGTGTATTATGTAAC
1 TTATGTAAGTTATGTATTATGTAAG
* *
3480762 TTATTTAATTTATGTA
1 TTATGTAAGTTATGTA
3480778 GGGTATGTAT
Statistics
Matches: 86, Mismatches: 22, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
23 21 0.24
24 19 0.22
25 45 0.52
26 1 0.01
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.48
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTAAG
Found at i:3480735 original size:23 final size:24
Alignment explanation
Indices: 3480693--3480760 Score: 102
Period size: 23 Copynumber: 2.8 Consensus size: 24
3480683 ATTTACACAT
3480693 GTAAGTTGTGTCTTATGTAAGATGC
1 GTAAGTTGTGT-TTATGTAAGATGC
*
3480718 GTAAGTTGTG-TTATGTAAGTTGC
1 GTAAGTTGTGTTTATGTAAGATGC
3480741 GTAAGTTGTGTATTATGTAA
1 GTAAGTTGTGT-TTATGTAA
3480761 CTTATTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 22 0.55
25 18 0.45
ACGTcount: A:0.25, C:0.04, G:0.28, T:0.43
Consensus pattern (24 bp):
GTAAGTTGTGTTTATGTAAGATGC
Found at i:3480796 original size:37 final size:37
Alignment explanation
Indices: 3480751--3480821 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
3480741 GTAAGTTGTG
3480751 TATTATGTAACTTATTTAATTTATGTAGGGTATGTAT
1 TATTATGTAACTTATTTAATTTATGTAGGGTATGTAT
3480788 TATTATGTAACTTATTTAATTTATGTAGGGTATG
1 TATTATGTAACTTATTTAATTTATGTAGGGTATG
3480822 CAAGTTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.51
Consensus pattern (37 bp):
TATTATGTAACTTATTTAATTTATGTAGGGTATGTAT
Found at i:3481022 original size:22 final size:22
Alignment explanation
Indices: 3480994--3481040 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3480984 AATCCAAAAA
*
3480994 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
3481016 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
3481038 TAA
1 TAA
3481041 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:3481115 original size:140 final size:140
Alignment explanation
Indices: 3480863--3482278 Score: 2832
Period size: 140 Copynumber: 10.1 Consensus size: 140
3480853 TGTAAGTTGC
3480863 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3480928 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3480993 ATAACAGAAA
131 ATAACAGAAA
3481003 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3481068 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3481133 ATAACAGAAA
131 ATAACAGAAA
3481143 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3481208 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3481273 ATAACAGAAA
131 ATAACAGAAA
3481283 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3481348 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3481413 ATAACAGAAA
131 ATAACAGAAA
3481423 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3481488 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3481553 ATAACAGAAA
131 ATAACAGAAA
3481563 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3481628 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3481693 ATAACAGAAA
131 ATAACAGAAA
3481703 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3481768 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3481833 ATAACAGAAA
131 ATAACAGAAA
3481843 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3481908 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3481973 ATAACAGAAA
131 ATAACAGAAA
3481983 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3482048 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3482113 ATAACAGAAA
131 ATAACAGAAA
3482123 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
1 CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
3482188 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
66 TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
3482253 ATAACAGAAA
131 ATAACAGAAA
3482263 CGCCTTACCTATTTAA
1 CGCCTTACCTATTTAA
3482279 TCGAAAAATC
Statistics
Matches: 1276, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 1276 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.26
Consensus pattern (140 bp):
CGCCTTACCTATTTAACAGAAACGCCTTACATATTTAATCGGAATAGTACATTGTTGAAGTTGTT
TAATCGAAACCCTAAAACCCCAAATAACTAGGACTGACCTAAAACCCTAAAAATTTAATCCAAAA
ATAACAGAAA
Found at i:3481162 original size:22 final size:22
Alignment explanation
Indices: 3481134--3481180 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3481124 AATCCAAAAA
*
3481134 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
3481156 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
3481178 TAA
1 TAA
3481181 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:3481302 original size:22 final size:22
Alignment explanation
Indices: 3481274--3481320 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3481264 AATCCAAAAA
*
3481274 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
3481296 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
3481318 TAA
1 TAA
3481321 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:3481442 original size:22 final size:22
Alignment explanation
Indices: 3481414--3481460 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3481404 AATCCAAAAA
*
3481414 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
3481436 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
3481458 TAA
1 TAA
3481461 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:3481582 original size:22 final size:22
Alignment explanation
Indices: 3481554--3481600 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3481544 AATCCAAAAA
*
3481554 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
3481576 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
3481598 TAA
1 TAA
3481601 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:3481722 original size:22 final size:22
Alignment explanation
Indices: 3481694--3481740 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3481684 AATCCAAAAA
*
3481694 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
3481716 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
3481738 TAA
1 TAA
3481741 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:3481862 original size:22 final size:22
Alignment explanation
Indices: 3481834--3481880 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3481824 AATCCAAAAA
*
3481834 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
3481856 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
3481878 TAA
1 TAA
3481881 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:3482002 original size:22 final size:22
Alignment explanation
Indices: 3481974--3482020 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3481964 AATCCAAAAA
*
3481974 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
3481996 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
3482018 TAA
1 TAA
3482021 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:3482142 original size:22 final size:22
Alignment explanation
Indices: 3482114--3482160 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3482104 AATCCAAAAA
*
3482114 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
3482136 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
3482158 TAA
1 TAA
3482161 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:3483161 original size:7 final size:7
Alignment explanation
Indices: 3483149--3483179 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
3483139 TTTGGGATTT
3483149 AACCCTA
1 AACCCTA
3483156 AACCCTA
1 AACCCTA
3483163 AACCTCTA
1 AACC-CTA
3483171 AACCCTA
1 AACCCTA
3483178 AA
1 AA
3483180 ATCCTAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (7 bp):
AACCCTA
Found at i:3483186 original size:15 final size:14
Alignment explanation
Indices: 3483149--3483179 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3483139 TTTGGGATTT
3483149 AACCCTAAACCCTA
1 AACCCTAAACCCTA
3483163 AACCTCTAAACCCTA
1 AACC-CTAAACCCTA
3483178 AA
1 AA
3483180 ATCCTAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (14 bp):
AACCCTAAACCCTA
Found at i:3483330 original size:8 final size:7
Alignment explanation
Indices: 3483282--3483392 Score: 84
Period size: 7 Copynumber: 15.1 Consensus size: 7
3483272 ACTAAAGTAG
3483282 CCTAAAC
1 CCTAAAC
*
3483289 CCCAAAC
1 CCTAAAC
*
3483296 CTTAAAC
1 CCTAAAC
*
3483303 CTTAAAC
1 CCTAAAC
*
3483310 CTTAAAC
1 CCTAAAC
3483317 CCTAAAC
1 CCTAAAC
3483324 TCCTAAAC
1 -CCTAAAC
*
3483332 CTTAAA-
1 CCTAAAC
3483338 CCTAAAACAC
1 CCT--AA-AC
3483348 CCTAATAC
1 CCTAA-AC
3483356 CCT-AAC
1 CCTAAAC
3483362 CCTAAATGC
1 CCTAAA--C
3483371 CCTAATAC
1 CCTAA-AC
3483379 CCT-AAC
1 CCTAAAC
3483385 CCTAAAC
1 CCTAAAC
3483392 C
1 C
3483393 TACATCGTAA
Statistics
Matches: 87, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
6 12 0.14
7 44 0.51
8 20 0.23
9 7 0.08
10 4 0.05
ACGTcount: A:0.41, C:0.39, G:0.01, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:3483337 original size:29 final size:28
Alignment explanation
Indices: 3483284--3483360 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 28
3483274 TAAAGTAGCC
*
3483284 TAAACCCCAAACCTTAAACCTTAAACCT
1 TAAACCCCAAACCCTAAACCTTAAACCT
*
3483312 TAAACCCTAAACTCCTAAACCTTAAACCT
1 TAAACCCCAAAC-CCTAAACCTTAAACCT
*
3483341 AAAACACCCTAATACCCTAA
1 TAAAC-CCC-AA-ACCCTAA
3483361 CCCTAAATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 11 0.27
29 19 0.46
30 2 0.05
31 7 0.17
32 2 0.05
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (28 bp):
TAAACCCCAAACCCTAAACCTTAAACCT
Found at i:3483362 original size:23 final size:24
Alignment explanation
Indices: 3483325--3483390 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
3483315 ACCCTAAACT
* *
3483325 CCTAA-ACCTTAAACCTAAAACAC
1 CCTAATACCCTAACCCTAAAACAC
**
3483348 CCTAATACCCTAACCCT-AAATGC
1 CCTAATACCCTAACCCTAAAACAC
3483371 CCTAATACCCTAACCCTAAA
1 CCTAATACCCTAACCCTAAA
3483391 CCTACATCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 26 0.70
24 11 0.30
ACGTcount: A:0.41, C:0.38, G:0.02, T:0.20
Consensus pattern (24 bp):
CCTAATACCCTAACCCTAAAACAC
Found at i:3483873 original size:112 final size:113
Alignment explanation
Indices: 3483658--3484058 Score: 461
Period size: 112 Copynumber: 3.5 Consensus size: 113
3483648 TACAAAAAAT
* * * * * * *
3483658 CGCCGCTAATACTATGCTTTAGCGGCGTTTTACCGTAATCGCCACTAAATCAAGTATACATCAAG
1 CGCCGCTAATACTATGCTTTAACGGCG-TTTACCCTAAGCGCCACTAATTCTACTATACATC-GG
* ** * *
3483723 ACCAAAACGATGCATTTTGGTTCAGATATTTGGTGGCGCTTTTACCCAAG
64 GCCAAAATTATGCGTTTTGGTTAAGATATTTGGTGGCGCTTTTACCCAAG
3483773 CGCCGCTAATACTATGCTTTAACGGCGTTT-CCCTAAGCGCCACTAATTCTACTATACATCGGGC
1 CGCCGCTAATACTATGCTTTAACGGCGTTTACCCTAAGCGCCACTAATTCTACTATACATCGGGC
* *
3483837 CAAAGTTATGCGTTTTGGTTAAGATATTTGGTGGCGCTTTTATCCATA-
66 CAAAATTATGCGTTTTGGTTAAGATATTTGGTGGCGCTTTTACCCA-AG
*
3483885 CGCCGCTAATACTATGCTTTAACGGCGTTT-CCCTAAGCGCCACTAATTTTACTATACATCGAGG
1 CGCCGCTAATACTATGCTTTAACGGCGTTTACCCTAAGCGCCACTAATTCTACTATACATCG-GG
* * * * *
3483949 TCAAAATTATGCGTTTTGGTTAAGATATTTTGCGGCGCTTGT-CACAAAG
65 CCAAAATTATGCGTTTTGGTTAAGATATTTGGTGGCGCTTTTAC-CCAAG
* * * * * * *
3483998 TGCCGCTATTAAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTA-TATACAT
1 CGCCGCTAAT-ACTATGCTTTAACGGC-GTTTACCCTAAGCGCCACTAATTCTACTATACAT
3484059 TAAGATCAAA
Statistics
Matches: 251, Mismatches: 28, Indels: 14
0.86 0.10 0.05
Matches are distributed among these distances:
112 103 0.41
113 75 0.30
114 16 0.06
115 37 0.15
116 20 0.08
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (113 bp):
CGCCGCTAATACTATGCTTTAACGGCGTTTACCCTAAGCGCCACTAATTCTACTATACATCGGGC
CAAAATTATGCGTTTTGGTTAAGATATTTGGTGGCGCTTTTACCCAAG
Found at i:3484078 original size:113 final size:113
Alignment explanation
Indices: 3483580--3484445 Score: 549
Period size: 113 Copynumber: 7.6 Consensus size: 113
3483570 GCTTTCAACA
* * * * * * *
3483580 AAGCGCCACTAATTTTAGTATAAATCAAGACCAAAACGTTGCGTTTTGTTTATGGTATGTCGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAAC--AGCGTTTTGGTTAAGATATTTTGCGG
* * * * * *
3483645 CGC-T-ACAAAAAATCGCCGCTAATACTATGCTTTAGCGGCGTTTTACCGT
64 CGCTTGTC-AAAAAGCGCCGCTATTACTATCCTTTAACGGCGGTTTACCGT
* * ** * * * *
3483694 AATCGCCACTAAATCAAGTATACATCAAGACCAAAACGATGCATTTTGGTTCAGATATTTGGTGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAAC-A-GCGTTTTGGTTAAGATATTTTGCGG
* ** * * *
3483759 CGCTT-TTACCCAAGCGCCGCTAATACTATGCTTTAACGGC-GTTT-CCCT
64 CGCTTGTCA-AAAAGCGCCGCTATTACTATCCTTTAACGGCGGTTTACCGT
* * * * ** * *
3483807 AAGCGCCACTAATTCTACTATACATC-GGGCCAAAGTTATGCGTTTTGGTTAAGATATTTGGTGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAA-ACA-GCGTTTTGGTTAAGATATTTTGCGG
* * * * * *
3483871 CGCTT-TTATCCATA-CGCCGCTAATACTATGCTTTAACGGC-GTTT-CCCT
64 CGCTTGTCA--AAAAGCGCCGCTATTACTATCCTTTAACGGCGGTTTACCGT
* * ** *
3483919 AAGCGCCACTAATTTTACTATACATCGAGGTCAAAATTATGCGTTTTGGTTAAGATATTTTGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAA-CA-GCGTTTTGGTTAAGATATTTTGCGG
* * * * *
3483984 CGCTTGTCACAAAGTGCCGCTATTAAATATTCTTTAGCGGCGGTTTACCGT
64 CGCTTGTCAAAAAGCGCCGCTATT-ACTATCCTTTAACGGCGGTTTACCGT
* * * *
3484035 AAGCGCCACTAATTTTA-TATACATTAAGATCAAAACAGTGTTTTGGTTAAGATATTTTGTGGCG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACAGCGTTTTGGTTAAGATATTTTGCGGCG
* * ** * * * * * * *
3484099 CTAGCCAGGAATCGCAGCTAATACTATTCTTTAGCGGCGTTTTACCGC
66 CTTGTCAAAAAGCGCCGCTATTACTATCCTTTAACGGCGGTTTACCGT
* * * * * * * *
3484147 ATGCGCCACTAGTTCTAGTATACATCAAGACCAAAACGATGTGTTTCGGTTCAGAGAGTTTGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAAC-A-GCGTTTTGGTTAAGATATTTTGCGG
* * * * * * * *
3484212 TGC-T-TCAGTATAGCGCCACTATTACTGTCCTTTAACGGCGTTTTCCCAT
64 CGCTTGTCA-AAAAGCGCCGCTATTACTATCCTTTAACGGCGGTTTACCGT
* * * * * *
3484261 AAACGCCACTAATTCTAAG-ATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGCTATTTTGCGG
1 AAGCGCCACTAATT-TTAGTATACATCAAGACCAAA-ACAGCGTTTTGGTTAAGATATTTTGCGG
* * **
3484325 CG-TTGCCAAAAAGCGCCGCTATTACTGTCCTTTAACGGC-GTTTTGCGT
64 CGCTTGTCAAAAAGCGCCGCTATTACTATCCTTTAACGGCGGTTTACCGT
* * * * * *
3484373 AAACGCCACTACTTTTAGGATACATCAAGACGAAAACACAGCGTTTTGGTTGAGAGATTTTGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGAC-CAAA-ACAGCGTTTTGGTTAAGATATTTTGCGG
3484438 CGCATTGT
64 CGC-TTGT
3484446 GGTAAACGCC
Statistics
Matches: 603, Mismatches: 125, Indels: 47
0.78 0.16 0.06
Matches are distributed among these distances:
111 3 0.00
112 167 0.28
113 209 0.35
114 129 0.21
115 75 0.12
116 20 0.03
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (113 bp):
AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACAGCGTTTTGGTTAAGATATTTTGCGGCG
CTTGTCAAAAAGCGCCGCTATTACTATCCTTTAACGGCGGTTTACCGT
Found at i:3489876 original size:19 final size:19
Alignment explanation
Indices: 3489831--3489891 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
3489821 ATCTAATTAC
3489831 AAATATTTAATTATTATATTT
1 AAATATTTAATTA-TA-ATTT
*
3489852 AAATATTTAAATATAATTT
1 AAATATTTAATTATAATTT
*
3489871 ATATATTCTAATTA-AATTT
1 AAATATT-TAATTATAATTT
3489890 AA
1 AA
3489892 TAAATAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 7 0.20
21 12 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAATTATAATTT
Found at i:3497980 original size:20 final size:20
Alignment explanation
Indices: 3497935--3498006 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
3497925 ATCGTACATT
* * *
3497935 ATTATTTAAAGTTTT-TTTC
1 ATTATTTTAAGTTTTCATGC
3497954 ATATATTTTAAGTTTTCATGC
1 AT-TATTTTAAGTTTTCATGC
* *
3497975 ATTATTATTCAAATTCATCATGC
1 ATTATT-TT-AAGTT-TTCATGC
3497998 ATTATTTTA
1 ATTATTTTA
3498007 TATATTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.05
20 16 0.37
21 7 0.16
22 6 0.14
23 12 0.28
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.54
Consensus pattern (20 bp):
ATTATTTTAAGTTTTCATGC
Found at i:3498485 original size:19 final size:20
Alignment explanation
Indices: 3498442--3498478 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3498432 TGGTTTACGA
3498442 ATTATCACTTCTCGTTGCAC
1 ATTATCACTTCTCGTTGCAC
*
3498462 ATTATCATTTC-CGTTGC
1 ATTATCACTTCTCGTTGC
3498479 GCTTTATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (20 bp):
ATTATCACTTCTCGTTGCAC
Found at i:3500303 original size:24 final size:24
Alignment explanation
Indices: 3500259--3500306 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3500249 CACATTTTTG
* *
3500259 CATTCATTTCATGCATTTGCATTA
1 CATTCATTACATGCATATGCATTA
3500283 CATTACATTACAT-CATATGCATTA
1 CATT-CATTACATGCATATGCATTA
3500307 AAGTCTACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (24 bp):
CATTCATTACATGCATATGCATTA
Found at i:3505065 original size:51 final size:51
Alignment explanation
Indices: 3505003--3505404 Score: 606
Period size: 51 Copynumber: 7.9 Consensus size: 51
3504993 AAGTCATTAT
*
3505003 AGCGAATCTTATTTCCCTGGTGTTGCAGTGGAACAGATTAAAGCTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* *
3505054 AGTGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGTTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * *
3505105 AGCGAATCTTATTTCCCTGGCGTTGTAGTGGAATAGATTAAAGTTGAAGGT
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * *
3505156 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAGCAGATTAAAGTTGAAGGT
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* *
3505207 AGCGAATTTTATTTCTCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* ** *
3505258 AGCGAATCTTATTTCCCTGGCGTTGTAGTGGAGTAGATTAAAACTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* *
3505309 AACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * *
3505360 AGCGAATCTTATTTCCCTGACGTTACAGCGGAATAGATTAAAGCT
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCT
3505405 ACAAATTATG
Statistics
Matches: 320, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 320 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (51 bp):
AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
Found at i:3507627 original size:23 final size:24
Alignment explanation
Indices: 3507577--3507627 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
3507567 TTTTTCATTC
* *
3507577 CATATGTATTATTTATTTAGATTA
1 CATATATATTATTTATGTAGATTA
*
3507601 -ATATATATTATTT-TGTATATTA
1 CATATATATTATTTATGTAGATTA
3507623 CATAT
1 CATAT
3507628 TTTGATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (24 bp):
CATATATATTATTTATGTAGATTA
Found at i:3507732 original size:185 final size:184
Alignment explanation
Indices: 3507462--3507879 Score: 820
Period size: 185 Copynumber: 2.3 Consensus size: 184
3507452 TTTTATATAC
3507462 ATTTACTTTGAAAATTCATTTTGATATTATCATTTCATATAGTATTTATTTTTATCTTCATTTTT
1 ATTTACTTTGAAAATTCATTTTGATATTATCATTTCATATAGTATTTATTTTTATCTTCATTTTT
3507527 TATCTATTTCAAACTCGTATATATATTTATTTATTTCGAATTTTTCATTCCATATGTATTATTTA
66 TATCTATTTCAAACTCGTATATATATTTATTTATTTCGAATTTTTCATTCCATATGTATTATTTA
3507592 TTTAGATTAATATATATTATTTTGTATATTACATATTTTGATTTTTTTATACAAT
131 TTTAGATTAATATATATTATTTTGTATATTACATATTTTGA-TTTTTTATACAAT
3507647 ATTTACTTTGAAAATTCATTTTGATATTATCATTTCATATAGTATTTATTTTTATCTTCATTTTT
1 ATTTACTTTGAAAATTCATTTTGATATTATCATTTCATATAGTATTTATTTTTATCTTCATTTTT
3507712 TATCTATTTCAAACTCGTATATATATTTATTTATTTCGAATTTTTCATTCCATATGTATTATTTA
66 TATCTATTTCAAACTCGTATATATATTTATTTATTTCGAATTTTTCATTCCATATGTATTATTTA
3507777 TTTAGATTAATATATATTATTTTGTATATTACATATTTTGATTTTTTATACAAT
131 TTTAGATTAATATATATTATTTTGTATATTACATATTTTGATTTTTTATACAAT
3507831 ATTTACTTTG-AAATTCATTTTGATATTATCATTTCATATAGTATTTATT
1 ATTTACTTTGAAAATTCATTTTGATATTATCATTTCATATAGTATTTATT
3507880 GATTATTTGT
Statistics
Matches: 233, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
183 39 0.17
184 23 0.10
185 171 0.73
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (184 bp):
ATTTACTTTGAAAATTCATTTTGATATTATCATTTCATATAGTATTTATTTTTATCTTCATTTTT
TATCTATTTCAAACTCGTATATATATTTATTTATTTCGAATTTTTCATTCCATATGTATTATTTA
TTTAGATTAATATATATTATTTTGTATATTACATATTTTGATTTTTTATACAAT
Found at i:3507812 original size:23 final size:24
Alignment explanation
Indices: 3507762--3507812 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
3507752 TTTTTCATTC
* *
3507762 CATATGTATTATTTATTTAGATTA
1 CATATATATTATTTATGTAGATTA
*
3507786 -ATATATATTATTT-TGTATATTA
1 CATATATATTATTTATGTAGATTA
3507808 CATAT
1 CATAT
3507813 TTTGATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (24 bp):
CATATATATTATTTATGTAGATTA
Found at i:3508760 original size:9 final size:9
Alignment explanation
Indices: 3508746--3508776 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3508736 GTTAAACGAA
3508746 TCGAGTTAT
1 TCGAGTTAT
*
3508755 TCGAGTTAA
1 TCGAGTTAT
3508764 TCGAGTTAT
1 TCGAGTTAT
3508773 TCGA
1 TCGA
3508777 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:3509578 original size:21 final size:21
Alignment explanation
Indices: 3509537--3509583 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3509527 GAACAAATAT
*
3509537 ATTCG-ATTCCATTCGATTCG
1 ATTCGAATTCCATTCGACTCG
3509557 ATTCGAATTCCATCTC-ACTCG
1 ATTCGAATTCCAT-TCGACTCG
*
3509578 ACTCGA
1 ATTCGA
3509584 TTCGAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 16 0.70
22 2 0.09
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (21 bp):
ATTCGAATTCCATTCGACTCG
Found at i:3512897 original size:13 final size:13
Alignment explanation
Indices: 3512879--3512903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3512869 TTCGACTGGA
3512879 GAGAAGAAAGAAG
1 GAGAAGAAAGAAG
3512892 GAGAAGAAAGAA
1 GAGAAGAAAGAA
3512904 AAAGAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
GAGAAGAAAGAAG
Found at i:3512908 original size:10 final size:10
Alignment explanation
Indices: 3512895--3512992 Score: 52
Period size: 10 Copynumber: 9.2 Consensus size: 10
3512885 AAAGAAGGAG
3512895 AAGAAAGAAA
1 AAGAAAGAAA
3512905 AAGAAAGAAAA
1 AAGAAAG-AAA
* *
3512916 GGGAAGGAAAGGAG
1 ---AA-GAAAGAAA
*
3512930 AAGAAAGGAA
1 AAGAAAGAAA
3512940 AAGAAAGAAA
1 AAGAAAGAAA
* * *
3512950 AGGAAAGGAG
1 AAGAAAGAAA
**
3512960 AAGAAGAGGGA
1 AAGAA-AGAAA
* *
3512971 GAGAAGGAAA
1 AAGAAAGAAA
3512981 AAGAAAGAAA
1 AAGAAAGAAA
3512991 AA
1 AA
3512993 AATAAGTAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
10 46 0.70
11 12 0.18
14 3 0.05
15 5 0.08
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:3512933 original size:35 final size:36
Alignment explanation
Indices: 3512887--3512991 Score: 131
Period size: 35 Copynumber: 2.8 Consensus size: 36
3512877 GAGAGAAGAA
*
3512887 AGAAGGAGAAGAAAGAAAAAGAAAGAAAAGGGAAGG
1 AGAAGGAGAAGAAAGAAAAAGAAAGAAAAGGAAAGG
*
3512923 A-AAGGAGAAGAAAGGAAAAGAAAGAAAAGGAAAGG
1 AGAAGGAGAAGAAAGAAAAAGAAAGAAAAGGAAAGG
*
3512958 AGAAGAAGAGGGAGAGAAGGAAAAAGAAAGAAAA
1 AGAAG--GA--GA-AGAAAGAAAAAGAAAGAAAA
3512992 AAATAAGTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
35 33 0.56
36 4 0.07
38 2 0.03
40 2 0.03
41 18 0.31
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (36 bp):
AGAAGGAGAAGAAAGAAAAAGAAAGAAAAGGAAAGG
Found at i:3512940 original size:5 final size:5
Alignment explanation
Indices: 3512897--3512958 Score: 54
Period size: 5 Copynumber: 12.4 Consensus size: 5
3512887 AGAAGGAGAA
* * * * *
3512897 GAAAG AAAAA GAAAG AAAAG GGAAG GAAAG GAGAA- GAAAG GAAAA GAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GA-AAG GAAAG GAAAG GAAAG
*
3512947 AAAAG GAAAG GA
1 GAAAG GAAAG GA
3512959 GAAGAAGAGG
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
4 2 0.05
5 39 0.91
6 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:3512943 original size:41 final size:41
Alignment explanation
Indices: 3512898--3512994 Score: 98
Period size: 40 Copynumber: 2.4 Consensus size: 41
3512888 GAAGGAGAAG
3512898 AAAGAAAAAGAAAGAAAAGG-GAAGGAA-A-GGAGAAGAAAGGA
1 AAAGAAAAAGAAAGAAAAGGAGAA-GAAGAGGGAG-AG-AAGGA
* *
3512939 AAAGAAAGA-AAAGGAAAGGAGAAGAAGAGGGAGAGAAGGA
1 AAAGAAAAAGAAAGAAAAGGAGAAGAAGAGGGAGAGAAGGA
*
3512979 AAA-AGAAAGAAA-AAAA
1 AAAGAAAAAGAAAGAAAA
3512995 TAAGTAAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
39 6 0.13
40 23 0.49
41 14 0.30
42 4 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (41 bp):
AAAGAAAAAGAAAGAAAAGGAGAAGAAGAGGGAGAGAAGGA
Found at i:3513029 original size:19 final size:19
Alignment explanation
Indices: 3513005--3513042 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3512995 TAAGTAAAGA
*
3513005 TAATTTTTTTGTATTATTT
1 TAATTTTTTTGTAATATTT
3513024 TAATTTTTTTGTAATATTT
1 TAATTTTTTTGTAATATTT
3513043 ATGTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TAATTTTTTTGTAATATTT
Found at i:3513696 original size:156 final size:157
Alignment explanation
Indices: 3513369--3513877 Score: 716
Period size: 156 Copynumber: 3.3 Consensus size: 157
3513359 AGGGTTTTTT
* ** * *
3513369 ACTAAATTAATGCATTTCAAACATAATGTACTAAAATAGCGTAAAATGATAAAATAC-GAAAATA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAAATA
* *** * * *
3513433 ATATA-TTTT-TTGAAA-CAATGAGGCTTCGGTAAAAAAATACGAATAAATGGCCGAAATAAGAG
66 ATATATTTTTATTGAAAGTAAT-AAAATTCGG-AAAAAAATACGAACAAAGGGCCGAAATAAGGG
3513495 -T--TTTTTACTAAATTTATTTAAAAAACAC
129 TTAATTTTTA--AAATTTATTTAAAAAACAC
*
3513523 ACTAAATTAATACATTTCAAACATAATGTACTGAAATAATGTAAAATAATAAAATACAAAAAATA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAAATA
*
3513588 ATATATTTTTATTGAAAGTAATAAAATTC-GAGAAAAAATACAAACAAAGGGCCGAAATAAGGGT
66 ATATATTTTTATTGAAAGTAATAAAATTCGGA-AAAAAATACGAACAAAGGGCCGAAATAAGGGT
3513652 TAATTTTTAAAATTTATTTAAAAAA-AC
130 TAATTTTTAAAATTTATTTAAAAAACAC
*
3513679 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGT-AAATAATAAAATA-ATAAAATA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAAATA
**
3513742 ATATATTTTTATTGAAAGTAATAAAATTCGCGAAGAAAAATGTGAACAAAGGGCCGAAATAAGGG
66 ATATATTTTTATTGAAAGTAATAAAATTCG-GAA-AAAAATACGAACAAAGGGCCGAAATAAGGG
*
3513807 TTAATTTTTGAAATTTATTTAAAAAACAC
129 TTAATTTTTAAAATTTATTTAAAAAACAC
3513836 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGT
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGT
3513878 TGTAACAGCC
Statistics
Matches: 323, Mismatches: 20, Indels: 21
0.89 0.05 0.06
Matches are distributed among these distances:
154 88 0.27
155 26 0.08
156 129 0.40
157 71 0.22
158 3 0.01
159 6 0.02
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (157 bp):
ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAAATA
ATATATTTTTATTGAAAGTAATAAAATTCGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTT
AATTTTTAAAATTTATTTAAAAAACAC
Found at i:3513734 original size:8 final size:8
Alignment explanation
Indices: 3513710--3513744 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
3513700 CATAATGTAC
3513710 TAAAATAA
1 TAAAATAA
*
3513718 TGTAAATAA
1 T-AAAATAA
3513727 TAAAATAA
1 TAAAATAA
3513735 TAAAATAA
1 TAAAATAA
3513743 TA
1 TA
3513745 TATTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (8 bp):
TAAAATAA
Found at i:3522160 original size:37 final size:37
Alignment explanation
Indices: 3522083--3522169 Score: 113
Period size: 37 Copynumber: 2.3 Consensus size: 37
3522073 ACTAACACAA
** *
3522083 TAACAATAATAATAGTTTTTTACTCAAAAAAATACTAAC
1 TAACAATAATAATAGGGTTTTACT--AAAAAATAATAAC
3522122 TAACAATAATAATTAGGGTTTTACT-AAAAATAATAAC
1 TAACAATAATAA-TAGGGTTTTACTAAAAAATAATAAC
3522159 TAACAATAATA
1 TAACAATAATA
3522170 TAATGTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 22 0.50
39 12 0.27
40 10 0.23
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (37 bp):
TAACAATAATAATAGGGTTTTACTAAAAAATAATAAC
Found at i:3522201 original size:23 final size:23
Alignment explanation
Indices: 3522156--3522202 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3522146 TAAAAATAAT
*
3522156 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
3522179 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
3522202 A
1 A
3522203 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:3522524 original size:3 final size:3
Alignment explanation
Indices: 3522518--3522565 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
3522508 TCCGCACCAC
* *
3522518 CTT CTT CTT CTT CTT CTT CTT CTC CTT CAT CTCT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT
3522564 CT
1 CT
3522566 CCTTTAGCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:3523131 original size:17 final size:18
Alignment explanation
Indices: 3523101--3523136 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3523091 GGGTAATGAT
*
3523101 TAAAATATAATTATTTTA
1 TAAAATATAATTATATTA
3523119 TAAAATA-AATTATATTA
1 TAAAATATAATTATATTA
3523136 T
1 T
3523137 TTTGAGGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAATATAATTATATTA
Found at i:3524528 original size:20 final size:20
Alignment explanation
Indices: 3524478--3524528 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
3524468 GTTTAGTTTT
* *
3524478 TTATTTAT-TATTTAAATTC
1 TTATTTATAAATTAAAATTC
*
3524497 TT-TTAATAAAATTAAAATTC
1 TTATTTAT-AAATTAAAATTC
3524517 TTATTTATAAAT
1 TTATTTATAAAT
3524529 ATAATAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 4 0.16
19 2 0.08
20 15 0.60
21 4 0.16
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTTATAAATTAAAATTC
Found at i:3524907 original size:12 final size:12
Alignment explanation
Indices: 3524890--3524914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3524880 TAAATCTAAA
3524890 ATTACATAGAAT
1 ATTACATAGAAT
3524902 ATTACATAGAAT
1 ATTACATAGAAT
3524914 A
1 A
3524915 GGTTAGAGGT
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACATAGAAT
Found at i:3525148 original size:30 final size:30
Alignment explanation
Indices: 3525104--3525166 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
3525094 ACTTAACAAG
3525104 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
3525134 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
3525164 CAA
1 CAA
3525167 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:3532264 original size:17 final size:17
Alignment explanation
Indices: 3532242--3532274 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3532232 GCCCTAGTTT
3532242 CAAATTTTATTTTTTGG
1 CAAATTTTATTTTTTGG
3532259 CAAATTTTATTTTTTG
1 CAAATTTTATTTTTTG
3532275 ATGACCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (17 bp):
CAAATTTTATTTTTTGG
Found at i:3532596 original size:108 final size:108
Alignment explanation
Indices: 3532407--3532725 Score: 503
Period size: 108 Copynumber: 3.0 Consensus size: 108
3532397 TACTTTTTAA
* * *
3532407 AAAATGCAAAAATTGTCTCCGGTAGTGATTATGACCACCAAGCTCTATCATGCCAATCATCAATT
1 AAAATGCAAAAATTGTCTCCGGTAGTGATTATGACCACCATGCTCTGTCATGCCAATCATCAACT
*
3532472 CAAGTTCAAGTTTCGTCTATTTAAAGTTCTCATGGTTCTAGGG
66 CAAGTTCAAGCTTCGTCTATTTAAAGTTCTCATGGTTCTAGGG
* * * *
3532515 AAAATGCAAAAATTGTCTCCGGTAGTGAGTATGACCACCGTGCTTTGTCACGCCAATCATCAACT
1 AAAATGCAAAAATTGTCTCCGGTAGTGATTATGACCACCATGCTCTGTCATGCCAATCATCAACT
* *
3532580 CAAGTTCAAGCTTCGTCCATTTAAAGCTCTCATGGTTCTAGGG
66 CAAGTTCAAGCTTCGTCTATTTAAAGTTCTCATGGTTCTAGGG
* * *
3532623 AAAATGCAAAAATTGTCTCCGATAGTGATTATGACCACTATGCTCTGTTATGCCAATCATCAACT
1 AAAATGCAAAAATTGTCTCCGGTAGTGATTATGACCACCATGCTCTGTCATGCCAATCATCAACT
* *
3532688 CAAGTTCATGCTTCATCTATTTAAAGTTCTCATGGTTC
66 CAAGTTCAAGCTTCGTCTATTTAAAGTTCTCATGGTTC
3532726 CACAACCAAT
Statistics
Matches: 190, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 190 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (108 bp):
AAAATGCAAAAATTGTCTCCGGTAGTGATTATGACCACCATGCTCTGTCATGCCAATCATCAACT
CAAGTTCAAGCTTCGTCTATTTAAAGTTCTCATGGTTCTAGGG
Found at i:3544390 original size:26 final size:26
Alignment explanation
Indices: 3544341--3544390 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3544331 ATAAAAACCT
* *
3544341 AGAAAAGAAGCTAACTAACCTCCAAA
1 AGAAAAGAAGCTAACAAACATCCAAA
3544367 AGAAAAGAAGCTAGA-AAACATCCA
1 AGAAAAGAAGCTA-ACAAACATCCA
3544391 TTGGAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.56, C:0.20, G:0.14, T:0.10
Consensus pattern (26 bp):
AGAAAAGAAGCTAACAAACATCCAAA
Found at i:3546128 original size:41 final size:41
Alignment explanation
Indices: 3546071--3546306 Score: 375
Period size: 41 Copynumber: 5.8 Consensus size: 41
3546061 AAATGCTTTT
* * * ***
3546071 GCGGCGCTTTTTCAAAAAAGCCGCTAAAGCATTGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
*
3546112 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
3546153 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
3546194 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
* *
3546235 GCGGCGCTTCTCCAAAAACACCGCTAAAGCGCGGAG-ATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
*
3546275 GCGGCACTTCTCCAAAAACGCCGCTAAAGCCC
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCC
3546307 CAAAAGGTCA
Statistics
Matches: 184, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
40 33 0.18
41 151 0.82
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (41 bp):
GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
Found at i:3546476 original size:40 final size:39
Alignment explanation
Indices: 3546383--3546478 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 39
3546373 AATTCTTATT
** *
3546383 TTTAGCGGCGCTTTCCTTAAAGCGCTGCTAATGCTCGATC
1 TTTAGCGGCG-TTTTTTTAAAGCGCCGCTAATGCTCGATC
3546423 TTTAGCGGCGTTTTTTGTAAAGCGCCGCTAATGCTCGATC
1 TTTAGCGGCGTTTTTT-TAAAGCGCCGCTAATGCTCGATC
3546463 TTTAGCGGCGTTTTTT
1 TTTAGCGGCGTTTTTT
3546479 ATCCAAACGC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 4 0.08
40 48 0.92
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.38
Consensus pattern (39 bp):
TTTAGCGGCGTTTTTTTAAAGCGCCGCTAATGCTCGATC
Found at i:3558680 original size:15 final size:15
Alignment explanation
Indices: 3558660--3558700 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3558650 CGTACAGGTT
3558660 GATGAAGAAGACGAA
1 GATGAAGAAGACGAA
* *
3558675 GATGAAGATGACGAT
1 GATGAAGAAGACGAA
*
3558690 GAAGAAGAAGA
1 GATGAAGAAGA
3558701 AAAAGAAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.05, G:0.34, T:0.10
Consensus pattern (15 bp):
GATGAAGAAGACGAA
Found at i:3560766 original size:18 final size:18
Alignment explanation
Indices: 3560725--3560767 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
3560715 TTCTTAATAA
*
3560725 ATATGTAGTTTATATAGT
1 ATATGTTGTTTATATAGT
* * *
3560743 AAATGTTGTTTATTTATT
1 ATATGTTGTTTATATAGT
3560761 ATATGTT
1 ATATGTT
3560768 TGAGTTAACA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (18 bp):
ATATGTTGTTTATATAGT
Found at i:3562789 original size:18 final size:19
Alignment explanation
Indices: 3562760--3562795 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3562750 GTTTAAGAAC
3562760 ATATAGTATGTAAATTATT
1 ATATAGTATGTAAATTATT
3562779 ATATA-TATGTAAATTAT
1 ATATAGTATGTAAATTAT
3562796 GAATGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (19 bp):
ATATAGTATGTAAATTATT
Found at i:3567641 original size:15 final size:15
Alignment explanation
Indices: 3567621--3567653 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3567611 CATTGGTAAA
3567621 AGCATTTTTTTTATT
1 AGCATTTTTTTTATT
3567636 AGCATTTTTTTTATT
1 AGCATTTTTTTTATT
3567651 AGC
1 AGC
3567654 GGTGAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (15 bp):
AGCATTTTTTTTATT
Found at i:3570010 original size:31 final size:32
Alignment explanation
Indices: 3569972--3570035 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3569962 ATAGTTATAT
* *
3569972 TAAGCAT-AAAAAACATGGGATATACCTGGGA
1 TAAGCATAAAAAAACAAGGGATATACATGGGA
3570003 TAAGCATAAAAAAACAAGGGATATACATGGGA
1 TAAGCATAAAAAAACAAGGGATATACATGGGA
3570035 T
1 T
3570036 CTCTATCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.23
32 23 0.77
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (32 bp):
TAAGCATAAAAAAACAAGGGATATACATGGGA
Found at i:3572191 original size:95 final size:92
Alignment explanation
Indices: 3572053--3572223 Score: 227
Period size: 95 Copynumber: 1.8 Consensus size: 92
3572043 TAACAAAGGT
* *
3572053 GAATAAAATATGTTTCGGATTTATCCCCGCCGTTCAACGGATTTTATT-CTAATTTTGATTTTTA
1 GAATAAAATATGTTTCGGATTTATCCCCGCCGTGCAACAGATTTTATTCCT-ATTTTGA-TTTTA
3572117 TTTCCAAAAACGAGTTTCTTTTTAAATATA
64 TTTCC-AAAACGAGTTTCTTTTTAAATATA
* * * * * *
3572147 GAATAAAATCTGTTTTGGGATTTATTCCCGCCGTGCAGCAGATTTTATTCCTTTTTTTATTTTAT
1 GAATAAAATATG-TTTCGGATTTATCCCCGCCGTGCAACAGATTTTATTCCTATTTTGATTTTAT
3572212 TTCCAAAACGAG
65 TTCCAAAACGAG
3572224 AAATTAAATT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 8 0.12
94 21 0.31
95 36 0.54
96 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (92 bp):
GAATAAAATATGTTTCGGATTTATCCCCGCCGTGCAACAGATTTTATTCCTATTTTGATTTTATT
TCCAAAACGAGTTTCTTTTTAAATATA
Found at i:3574416 original size:49 final size:49
Alignment explanation
Indices: 3574344--3574437 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
3574334 CATATGTAAG
* **
3574344 AACCTTATTTCTGGGACACTCCTTAGTGTACATGGCTTTAAAATGCAAA
1 AACCTTATTTCTAGGACACTCCTTAGTGTACATAACTTTAAAATGCAAA
*
3574393 AACCTTGTTTCTAGGACACTCCTTAGTGTACATAACTTTAAAATG
1 AACCTTATTTCTAGGACACTCCTTAGTGTACATAACTTTAAAATG
3574438 GTGTTTGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (49 bp):
AACCTTATTTCTAGGACACTCCTTAGTGTACATAACTTTAAAATGCAAA
Found at i:3585009 original size:33 final size:32
Alignment explanation
Indices: 3584966--3585030 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
3584956 GTCCCACATA
*
3584966 CTCTATCTGTGGTTACTGTCCCAGTGGACTAT
1 CTCTATCTGTGGTTACTATCCCAGTGGACTAT
*
3584998 CTCTATTCTGTGTTTACTATCCCAGTGGACTAT
1 CTCTA-TCTGTGGTTACTATCCCAGTGGACTAT
3585031 TTATGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 5 0.17
33 25 0.83
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (32 bp):
CTCTATCTGTGGTTACTATCCCAGTGGACTAT
Found at i:3585047 original size:33 final size:33
Alignment explanation
Indices: 3584978--3585048 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
3584968 CTATCTGTGG
* * * *
3584978 TTACTGTCCCAGTGGACTATCTCTATTCTGTGT
1 TTACTATCCCAGTGGACTATCTATATTATGTAT
* * *
3585011 TTACTATCCCAGTGGACTATTTATGTTATTTAT
1 TTACTATCCCAGTGGACTATCTATATTATGTAT
3585044 TTACT
1 TTACT
3585049 GTCCTAACAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (33 bp):
TTACTATCCCAGTGGACTATCTATATTATGTAT
Found at i:3586355 original size:129 final size:129
Alignment explanation
Indices: 3586125--3586384 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 129
3586115 AATATGATGC
3586125 TTGTGTGATAATGCGTACATGTTATATGTCTTTGGGTGGAAATCATGTTTGGATGATTTAAAATG
1 TTGTGTGATAATGCGTACATGTTATATGTCTTTGGGTGGAAATCATGTTTGGATGATTTAAAATG
*
3586190 AAGCTAAAAATTAGATGTGAAATCTGCCAGAAAAAATTATTACATGAACAGTAAGTTTAAAAAT
66 AAGCTAAAAATTAGATGTGAAATCTGCCAGAAAAAATTATTACATGAACAGTAAGTTAAAAAAT
3586254 TTGTGTGATAATGCGTACATGTTATATGTCTTTGGGTGGAAATCATGTTTGGATGATTTAAAATG
1 TTGTGTGATAATGCGTACATGTTATATGTCTTTGGGTGGAAATCATGTTTGGATGATTTAAAATG
3586319 AAGCTAAAAATTAGATGTGAAATCTGCCAGAAAAAATTATTACATGAACAGTAAGTTAAAAAAT
66 AAGCTAAAAATTAGATGTGAAATCTGCCAGAAAAAATTATTACATGAACAGTAAGTTAAAAAAT
3586383 TT
1 TT
3586385 TCCATAAATT
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (129 bp):
TTGTGTGATAATGCGTACATGTTATATGTCTTTGGGTGGAAATCATGTTTGGATGATTTAAAATG
AAGCTAAAAATTAGATGTGAAATCTGCCAGAAAAAATTATTACATGAACAGTAAGTTAAAAAAT
Found at i:3590136 original size:71 final size:71
Alignment explanation
Indices: 3590013--3590146 Score: 189
Period size: 71 Copynumber: 1.9 Consensus size: 71
3590003 TTTATTCGAT
*
3590013 GTTGCTCACTCAAGCTGTCGAACATCCGCAATATATGTTGGATCCCAACCATCGATAAAGAATAA
1 GTTGCTCACTCAAGCTGTCGAACATCCGCAACATATGTTGGATCCCAACCATCGATAAAGAATAA
3590078 TTTGAC
66 TTTGAC
* * * ** *
3590084 GTTGTTCACTCAAGCTGTCGCGA-ATCCGCAACATATGTTGGGTCTTAGCCATCGATAAAGAAT
1 GTTGCTCACTCAAGCTGTCG-AACATCCGCAACATATGTTGGATCCCAACCATCGATAAAGAAT
3590147 GATTCGTACT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 54 0.98
72 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (71 bp):
GTTGCTCACTCAAGCTGTCGAACATCCGCAACATATGTTGGATCCCAACCATCGATAAAGAATAA
TTTGAC
Found at i:3592412 original size:20 final size:19
Alignment explanation
Indices: 3592362--3592413 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
3592352 AAAAATCTTT
*
3592362 AAAA-TTTAAAAAATAAAA
1 AAAATTTTAAAATATAAAA
**
3592380 ATGATTTTGAAAATATAAACA
1 AAAATTTT-AAAATATAAA-A
3592401 AAAATTTTAAAAT
1 AAAATTTTAAAAT
3592414 TCAATGTGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 14 0.54
21 7 0.27
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAATTTTAAAATATAAAA
Found at i:3593139 original size:23 final size:23
Alignment explanation
Indices: 3593105--3593154 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
3593095 AGTTGGACCG
3593105 ATTTTTATATGTTTTAATAATTCT
1 ATTTTTATATGTTTTAATAATT-T
3593129 ATTTTTA-ATGTTTTAATAATTT
1 ATTTTTATATGTTTTAATAATTT
3593151 ATTT
1 ATTT
3593155 GCTTTGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.19
23 14 0.54
24 7 0.27
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
ATTTTTATATGTTTTAATAATTT
Found at i:3593362 original size:17 final size:17
Alignment explanation
Indices: 3593342--3593389 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
3593332 ATGACATTGA
3593342 ATTTTGAAATTTTTTAT
1 ATTTTGAAATTTTTTAT
* *
3593359 ATTTTAAAACCATTTTTAT
1 ATTTTGAAA--TTTTTTAT
*
3593378 TTTTTGAAATTT
1 ATTTTGAAATTT
3593390 AAAGAGTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
17 10 0.42
19 14 0.58
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTTGAAATTTTTTAT
Found at i:3597838 original size:6 final size:6
Alignment explanation
Indices: 3597827--3597856 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3597817 GCAATTGAAT
3597827 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
3597857 TTTTTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:3598260 original size:18 final size:18
Alignment explanation
Indices: 3598237--3598276 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3598227 GTTATCAAAT
*
3598237 TTTAATTTTTATTTCTAA
1 TTTAATTTTTAATTCTAA
*
3598255 TTTAATTTTTAATTCTGA
1 TTTAATTTTTAATTCTAA
3598273 TTTA
1 TTTA
3598277 CTCAAGTATT
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:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTAATTTTTAATTCTAA
Found at i:3610007 original size:22 final size:22
Alignment explanation
Indices: 3609962--3610003 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
3609952 AACATGATCT
3609962 AAGCTTAATTTCTATCAATTTC
1 AAGCTTAATTTCTATCAATTTC
3609984 AAGCTTAA-TTC-ATCAATTTC
1 AAGCTTAATTTCTATCAATTTC
3610004 TCAATAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (22 bp):
AAGCTTAATTTCTATCAATTTC
Found at i:3610306 original size:21 final size:21
Alignment explanation
Indices: 3610266--3610306 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3610256 TGGTGAATTA
* *
3610266 ATTTAGTTAATCATATTTTAC
1 ATTTAATTAATCATAATTTAC
*
3610287 ATTTAATTAATCTTAATTTA
1 ATTTAATTAATCATAATTTA
3610307 ATTGTTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTAATTAATCATAATTTAC
Found at i:3611339 original size:24 final size:24
Alignment explanation
Indices: 3611307--3611357 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3611297 GCCAACTATT
3611307 CAAATTTATCTTTTTTTCGATCAC
1 CAAATTTATCTTTTTTTCGATCAC
3611331 CAAATTTATCTTTTTTTCGATCAC
1 CAAATTTATCTTTTTTTCGATCAC
3611355 CAA
1 CAA
3611358 CTGAGGTAGC
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:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (24 bp):
CAAATTTATCTTTTTTTCGATCAC
Found at i:3611370 original size:27 final size:24
Alignment explanation
Indices: 3611316--3611371 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
3611306 TCAAATTTAT
** *
3611316 CTTTTTTTCGATCACCAAATTTAT
1 CTTTTTTTCGATCACCAAAGGTAG
3611340 CTTTTTTTCGATCACCAACTGAGGTAG
1 CTTTTTTTCGATCACCAA---AGGTAG
3611367 CTTTT
1 CTTTT
3611372 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 18 0.69
27 8 0.31
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (24 bp):
CTTTTTTTCGATCACCAAAGGTAG
Found at i:3613298 original size:39 final size:40
Alignment explanation
Indices: 3613238--3613316 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
3613228 TTATTTTTTA
* *
3613238 AAATACGTTTTTTTAGTATTATCACCGTATGTACGAGTGT
1 AAATACGTTTTTTTAGGATTATCACCGTATATACGAGTGT
*
3613278 AAATACG-TTTTTTAGGATTATCACGGTATATACGAGTGT
1 AAATACGTTTTTTTAGGATTATCACCGTATATACGAGTGT
3613317 CAAGTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 29 0.81
40 7 0.19
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (40 bp):
AAATACGTTTTTTTAGGATTATCACCGTATATACGAGTGT
Found at i:3614464 original size:27 final size:25
Alignment explanation
Indices: 3614434--3614507 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 25
3614424 CTCGACAGAT
3614434 TATCCCATGTTTAACGTCCTGTCGGAC
1 TATCCCATGTTTAACGTCCT-T-GGAC
* *
3614461 TATCTCGTGTTTAACGTCTCATTGGAC
1 TATCCCATGTTTAACGTC-C-TTGGAC
*
3614488 TATCCCATATTTAACGTCCT
1 TATCCCATGTTTAACGTCCT
3614508 ACCAAACTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 35 0.88
28 2 0.05
29 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.38
Consensus pattern (25 bp):
TATCCCATGTTTAACGTCCTTGGAC
Found at i:3614813 original size:45 final size:47
Alignment explanation
Indices: 3614764--3614891 Score: 138
Period size: 45 Copynumber: 2.8 Consensus size: 47
3614754 TCTTGTTTAC
*
3614764 CATGATGTCATGGCGTCTTTCAGCCATGATCTTACTCAATT-ATA-T
1 CATGATGTCATGGCGTCTTTCAGCCATGGTCTTACTCAATTGATAGT
** * ** * *
3614809 CATGATGTCATAACATCTTTCAGTTATGGTCTTATTC-ATTGTTAGT
1 CATGATGTCATGGCGTCTTTCAGCCATGGTCTTACTCAATTGATAGT
* *
3614855 -GTGATGCCATGGCGTCTTTCAGCCATGGTCTTACTCA
1 CATGATGTCATGGCGTCTTTCAGCCATGGTCTTACTCA
3614892 TCTTTAGGCG
Statistics
Matches: 64, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
44 3 0.05
45 60 0.94
46 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (47 bp):
CATGATGTCATGGCGTCTTTCAGCCATGGTCTTACTCAATTGATAGT
Found at i:3617425 original size:43 final size:43
Alignment explanation
Indices: 3617367--3617480 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
3617357 AGTGTTTCTT
* * * *
3617367 TGTAAGACCACGTCTGGGACGTTGGCATCGA-CTTGTGTTTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATC-AGTGATTACA
*
3617410 TGTAAGACC-CTGTCTGGGATAG-TGGCATCGATCAGTGATTACA
1 TGTAAGACCAC-GTCTGGGA-CGTTGGCATCGATCAGTGATTACA
3617453 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
3617481 TGTACGAGCC
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.03
43 55 0.92
44 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATCAGTGATTACA
Found at i:3618698 original size:2 final size:2
Alignment explanation
Indices: 3618691--3618717 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3618681 ATTTATAAAC
3618691 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
3618718 TTACATGTAT
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:3626648 original size:23 final size:20
Alignment explanation
Indices: 3626589--3626657 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
3626579 AACAAAATTA
3626589 ATTTTTATAATAAAATATTT
1 ATTTTTATAATAAAATATTT
* *
3626609 ATGTTTATAATATAATATTT
1 ATTTTTATAATAAAATATTT
* *
3626629 ATAACTTTTATAAAAAAATATAT
1 AT---TTTTATAATAAAATATTT
3626652 ATTTTT
1 ATTTTT
3626658 TAAATTTAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 24 0.60
23 16 0.40
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (20 bp):
ATTTTTATAATAAAATATTT
Found at i:3635190 original size:43 final size:43
Alignment explanation
Indices: 3635134--3635402 Score: 285
Period size: 43 Copynumber: 6.3 Consensus size: 43
3635124 TTTTTGAAAT
* *
3635134 AAACGCCGTTATAGATCATGACCTTTAGCGGCGCTTTTTCCGA-
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCC-AC
* * *
3635177 AAACGCCGCTATAGATCAAGACCTTTAACGACACTTTTT-CAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * * * *
3635219 AAATGCAGCTATAGATCAGGACCTTTAGCGACGGTTTTTCAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * *
3635262 AAAACGCTGCTATAGATCAGGACTTTTAGCGGCGCTTGTTCCAC
1 -AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * *
3635306 AAACGCTGCTATAGATAAAGACTTTTAGCGGCGCTTTTTCCTAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCC-AC
*
3635350 AAACGCCGCTATAGAAC-AGACCTTTAGCGGCGC-TTTTCACAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTC-CAC
*
3635392 AAACTCCGCTA
1 AAACGCCGCTA
3635403 AAAACATATC
Statistics
Matches: 192, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 50 0.26
43 90 0.47
44 51 0.27
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:3635290 original size:129 final size:130
Alignment explanation
Indices: 3635112--3635378 Score: 317
Period size: 129 Copynumber: 2.1 Consensus size: 130
3635102 GCGTCGCTAA
* * * * * *
3635112 CTTTAGCAACGTTTTTTGAAATAAACGCCGTTATAGATCATGACCTTTAGCGGCGCTTTTTCCGA
1 CTTTAGCGACGGTTTTTCAAATAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTGTTCC-A
* * *
3635177 -AAACGCCGCTATAGATCAAGACCTTTAACGACACTTTTT-C-ACAAATGCAGCTATAGATCAGG
65 CAAACGCCGCTATAGATAAAGACCTTTAACGACACTTTTTCCTACAAACGCAGCTATAGAACA-G
3635239 AC
129 AC
* *
3635241 CTTTAGCGACGGTTTTTCAACA-AAACGCTGCTATAGATCAGGACTTTTAGCGGCGCTTGTTCCA
1 CTTTAGCGACGGTTTTTCAA-ATAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTGTTCCA
* * * * * * *
3635305 CAAACGCTGCTATAGATAAAGACTTTTAGCGGCGCTTTTTCCTATAAACGCCGCTATAGAACAGA
65 CAAACGCCGCTATAGATAAAGACCTTTAACGACACTTTTTCCTACAAACGCAGCTATAGAACAGA
3635370 C
130 C
3635371 CTTTAGCG
1 CTTTAGCG
3635379 GCGCTTTTCA
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
128 1 0.01
129 86 0.74
130 13 0.11
131 16 0.14
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (130 bp):
CTTTAGCGACGGTTTTTCAAATAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTGTTCCAC
AAACGCCGCTATAGATAAAGACCTTTAACGACACTTTTTCCTACAAACGCAGCTATAGAACAGAC
Found at i:3640474 original size:7 final size:7
Alignment explanation
Indices: 3640462--3640504 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
3640452 TACCTATCCA
3640462 TAACCCC
1 TAACCCC
3640469 TAACCCC
1 TAACCCC
* *
3640476 TAATCCT
1 TAACCCC
*
3640483 TAACCTC
1 TAACCCC
3640490 TAACCCC
1 TAACCCC
3640497 TAACCCC
1 TAACCCC
3640504 T
1 T
3640505 CTTTTACAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.28, C:0.49, G:0.00, T:0.23
Consensus pattern (7 bp):
TAACCCC
Found at i:3640481 original size:21 final size:21
Alignment explanation
Indices: 3640457--3640499 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3640447 ATAGTTACCT
3640457 ATCCATAACCCCTAACCCCTA
1 ATCCATAACCCCTAACCCCTA
* *
3640478 ATCCTTAACCTCTAACCCCTA
1 ATCCATAACCCCTAACCCCTA
3640499 A
1 A
3640500 CCCCTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (21 bp):
ATCCATAACCCCTAACCCCTA
Found at i:3641007 original size:20 final size:20
Alignment explanation
Indices: 3640982--3641019 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3640972 TAAAGTTATA
* *
3640982 TATTTTATATTGGATGGATG
1 TATTTTACATTAGATGGATG
3641002 TATTTTACATTAGATGGA
1 TATTTTACATTAGATGGA
3641020 GATGGAGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (20 bp):
TATTTTACATTAGATGGATG
Found at i:3641353 original size:41 final size:40
Alignment explanation
Indices: 3641158--3641435 Score: 152
Period size: 41 Copynumber: 6.8 Consensus size: 40
3641148 CGTTTGTACA
*** * *
3641158 AAAAACGCCGCTAAAAATC-GAGCATTAGCGGCGCTTTCTA
1 AAAAACGCCGCTAATGCTCTGAGCATTAGCGGCG-TTTTTG
* * * *
3641198 AAAAACACCGCTAA-GACCTTTCGAGGCTTTAGCAGCGTTTTTG
1 AAAAACGCCGCTAATG--CTCT-GA-GCATTAGCGGCGTTTTTG
* * *
3641241 AAAAAGCGCCGCTAATGCCCT-AGTCTTTAGTGGCGTTTTTGG
1 AAAAA-CGCCGCTAATGCTCTGAG-CATTAGCGGCGTTTTT-G
* * ** * *
3641283 ATAAGCGAAGCTATTGCTCAGAG-ATTTAGCGGCGTTTTTG
1 AAAAACGCCGCTAATGCTCTGAGCA-TTAGCGGCGTTTTTG
* * * **
3641323 AAAAATCGCCGCTAATGCTCTGAGCATTAGCAGCGCCTCTCC
1 AAAAA-CGCCGCTAATGCTCTGAGCATTAGCGGCG-TTTTTG
* * * *
3641365 AAAAACGCCGCTAAAGCTTTGAGCATTAACGGCGATTTTTC
1 AAAAACGCCGCTAATGCTCTGAGCATTAGCGGCG-TTTTTG
*
3641406 AAAAACGCCGCTAAAT-CTCTGAGCAATAGC
1 AAAAACGCCGCT-AATGCTCTGAGCATTAGC
3641436 TTCGCTTATC
Statistics
Matches: 178, Mismatches: 45, Indels: 29
0.71 0.18 0.12
Matches are distributed among these distances:
40 18 0.10
41 112 0.63
42 16 0.09
43 13 0.07
44 18 0.10
45 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (40 bp):
AAAAACGCCGCTAATGCTCTGAGCATTAGCGGCGTTTTTG
Found at i:3641502 original size:82 final size:82
Alignment explanation
Indices: 3641308--3641502 Score: 234
Period size: 82 Copynumber: 2.4 Consensus size: 82
3641298 GCTCAGAGAT
* * *
3641308 TTAGCGGCGTTTTTGAAAAATCGCCGCT-AATGCTCTGAGCATTAGCAGCGCCTCTCCAAAAACG
1 TTAGCGGCGTTTTTCAAAAA-CGCCGCTAAATGCTCTGAGCAATAGCAGCGCCTATCCAAAAACG
* *
3641372 CCGCTAAAGCTTTGAGCA
65 CCACTAAAGCTTAGAGCA
* ** *
3641390 TTAACGGCGATTTTTCAAAAACGCCGCTAAAT-CTCTGAGCAATAGCTTCGCTTATCCAAAAACG
1 TTAGCGGCG-TTTTTCAAAAACGCCGCTAAATGCTCTGAGCAATAGCAGCGCCTATCCAAAAACG
*
3641454 CCACTAAAGAC-TAGGGCA
65 CCACTAAAG-CTTAGAGCA
*
3641472 TTAGCGGCGCTTTTTCAAAAACGCTGCTAAA
1 TTAGCGGCG-TTTTTCAAAAACGCCGCTAAA
3641503 GCCTCGAAAG
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
82 83 0.86
83 14 0.14
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (82 bp):
TTAGCGGCGTTTTTCAAAAACGCCGCTAAATGCTCTGAGCAATAGCAGCGCCTATCCAAAAACGC
CACTAAAGCTTAGAGCA
Found at i:3641503 original size:41 final size:40
Alignment explanation
Indices: 3641308--3641504 Score: 171
Period size: 41 Copynumber: 4.8 Consensus size: 40
3641298 GCTCAGAGAT
** *
3641308 TTAGCGGCG-TTTTTGAAAAATCGCCGCTAATGCTCTGAGCA
1 TTAGCGGCGCTTTTCCAAAAA-CGCCGCTAAAGCT-TGAGCA
* * *
3641349 TTAGCAGCGCCTCTCCAAAAACGCCGCTAAAGCTTTGAGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGC-TTGAGCA
* * * *
3641390 TTAACGGCGATTTTTCAAAAACGCCGCTAAATCTCTGAGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCT-TGAGCA
* ** * * * *
3641431 ATAGCTTCGCTTATCCAAAAACGCCACTAAAGACTAGGGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG-CTTGAGCA
* *
3641472 TTAGCGGCGCTTTTTCAAAAACGCTGCTAAAGC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGC
3641505 CTCGAAAGGT
Statistics
Matches: 121, Mismatches: 31, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
40 2 0.02
41 109 0.90
42 10 0.08
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCTTGAGCA
Found at i:3641733 original size:20 final size:20
Alignment explanation
Indices: 3641708--3641745 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3641698 ATTCTCCATC
* *
3641708 TCCATCTAATGTAAAATACA
1 TCCATCCAATATAAAATACA
3641728 TCCATCCAATATAAAATA
1 TCCATCCAATATAAAATA
3641746 TATAACTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (20 bp):
TCCATCCAATATAAAATACA
Found at i:3654323 original size:13 final size:13
Alignment explanation
Indices: 3654307--3654345 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3654297 ATTTTTTTAA
*
3654307 TTTAAAAAATTTT
1 TTTAAAAAATATT
3654320 TTTAAAAAATATT
1 TTTAAAAAATATT
3654333 TTTAAAAAATATT
1 TTTAAAAAATATT
3654346 AAAAAGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTAAAAAATATT
Done.