Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 55
Found at i:3786718 original size:44 final size:44
Alignment explanation
Indices: 3786670--3787025 Score: 198
Period size: 43 Copynumber: 8.4 Consensus size: 44
3786660 TTATAATCAT
* * * *
3786670 ACTTTTTATCTTTGTAATTGAGGCCTTTAATTTTTTTCTATCCC
1 ACTTTTTACCTTTATAATTGAGGCCTTTAATTTTTTTCAATCTC
** * * * * *
3786714 ACTTTCTTATATTTATAATTGACGACTCTAA-GTTTTTCGATCTC
1 ACTTT-TTACCTTTATAATTGAGGCCTTTAATTTTTTTCAATCTC
* *
3786758 ACTTTGTACCTTTATAATTGA-G-CTCTTAATTTTTTTCAAACTC
1 ACTTTTTACCTTTATAATTGAGGCCT-TTAATTTTTTTCAATCTC
* * * *
3786801 ACTTTCTACCTTTATAATTAAGGCCATTGA-TTTTTT-AATCTC
1 ACTTTTTACCTTTATAATTGAGGCCTTTAATTTTTTTCAATCTC
* * **
3786843 AC-----A-TTTTATAATTGAGACCCCTAA-TTTTTTCAATCTC
1 ACTTTTTACCTTTATAATTGAGGCCTTTAATTTTTTTCAATCTC
* *
3786880 ACTTTTGA-CTTATATAATTTAGGCCCTTT-A--TTTTTCAATCTC
1 ACTTTTTACCTT-TATAATTGAGG-CCTTTAATTTTTTTCAATCTC
* * ** *
3786922 ACTTTTTA-CTTTAAAACTGAGGCCCAT-A-TTTTTT-AATTTTC
1 ACTTTTTACCTTTATAATTGAGGCCTTTAATTTTTTTCAA-TCTC
* * * *
3786963 ACTTGTTACTTTTATAGTTGAGGTCC-CTAATTTTTTTCAATCAT-
1 ACTTTTTACCTTTATAATTGAGG-CCTTTAATTTTTTTCAATC-TC
*
3787007 ACTTTTTACTTTTATAATT
1 ACTTTTTACCTTTATAATT
3787026 TAATCCCCTA
Statistics
Matches: 244, Mismatches: 47, Indels: 42
0.73 0.14 0.13
Matches are distributed among these distances:
36 21 0.09
37 9 0.04
40 6 0.02
41 25 0.10
42 47 0.19
43 61 0.25
44 51 0.21
45 24 0.10
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.50
Consensus pattern (44 bp):
ACTTTTTACCTTTATAATTGAGGCCTTTAATTTTTTTCAATCTC
Found at i:3786871 original size:79 final size:79
Alignment explanation
Indices: 3786768--3786929 Score: 204
Period size: 79 Copynumber: 2.1 Consensus size: 79
3786758 ACTTTGTACC
* *
3786768 TTTATAATTGAGCTCTTAATTTTTTTCAAACTCACTTTCT-ACCTT-TATAATTAAGGCCATTGA
1 TTTATAATTGAGCCCCTAATTTTTTTCAAACTCACTTT-TGA-CTTATATAATTAAGGCCATTGA
*
3786831 TTTTTTAATCTCACAT
64 TTTTTCAATCTCACAT
* * * *
3786847 TTTATAATTGAGACCCCTAA-TTTTTTCAATCTCACTTTTGACTTATATAATTTAGGCCCTTTAT
1 TTTATAATTGAG-CCCCTAATTTTTTTCAAACTCACTTTTGACTTATATAATTAAGGCCATTGAT
*
3786911 TTTTCAATCTCACTT
65 TTTTCAATCTCACAT
3786926 TTTA
1 TTTA
3786930 CTTTAAAACT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 4 0.06
79 63 0.88
80 5 0.07
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.49
Consensus pattern (79 bp):
TTTATAATTGAGCCCCTAATTTTTTTCAAACTCACTTTTGACTTATATAATTAAGGCCATTGATT
TTTCAATCTCACAT
Found at i:3787315 original size:60 final size:57
Alignment explanation
Indices: 3787210--3787334 Score: 196
Period size: 60 Copynumber: 2.1 Consensus size: 57
3787200 AGGCAGCGAT
*
3787210 GTTGGTGGTTTCGATCGAGTTTTAATTTTCTCCCTATCGTGCTTGTTGTCATGCAAC
1 GTTGGTGGATTCGATCGAGTTTTAATTTTCTCCCTATCGTGCTTGTTGTCATGCAAC
*
3787267 GTTGGTGGATTCGATCGGGTTTTAATAATTTTCTCCCTATCGTGCTTGTTGTCATGCAAC
1 GTTGGTGGATTCGATCGAG-TTT--TAATTTTCTCCCTATCGTGCTTGTTGTCATGCAAC
*
3787327 ATTGGTGG
1 GTTGGTGG
3787335 CAGAAGTCGG
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
57 17 0.27
58 3 0.05
60 42 0.68
ACGTcount: A:0.15, C:0.18, G:0.25, T:0.42
Consensus pattern (57 bp):
GTTGGTGGATTCGATCGAGTTTTAATTTTCTCCCTATCGTGCTTGTTGTCATGCAAC
Found at i:3788940 original size:19 final size:19
Alignment explanation
Indices: 3788925--3788962 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3788915 TTGAACTTTC
3788925 TAGATTAAGGTGAACTCAT
1 TAGATTAAGGTGAACTCAT
3788944 TAGATTAAGGTGAACTCAT
1 TAGATTAAGGTGAACTCAT
3788963 AACACACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
TAGATTAAGGTGAACTCAT
Found at i:3791197 original size:27 final size:27
Alignment explanation
Indices: 3791143--3791197 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3791133 CAATAATAAA
* *
3791143 TAATTGATAATAAGGAAATCTTTTTTT
1 TAATTGATAATAAGGAAATCTATCTTT
*
3791170 TAATTGATAATGA-GAAATCTCATCTTT
1 TAATTGATAATAAGGAAATCT-ATCTTT
3791197 T
1 T
3791198 CAATCATGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (27 bp):
TAATTGATAATAAGGAAATCTATCTTT
Found at i:3791480 original size:11 final size:11
Alignment explanation
Indices: 3791464--3791494 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3791454 ACCCGTCACT
3791464 GGTAGTGGGCG
1 GGTAGTGGGCG
3791475 GGTAGTGGGCG
1 GGTAGTGGGCG
*
3791486 GGTAATGGG
1 GGTAGTGGG
3791495 TTTGAGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.06, G:0.61, T:0.19
Consensus pattern (11 bp):
GGTAGTGGGCG
Found at i:3804503 original size:2 final size:2
Alignment explanation
Indices: 3804496--3804520 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3804486 TGATTGAACT
3804496 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 T
3804521 TTGGTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3813710 original size:17 final size:17
Alignment explanation
Indices: 3813688--3813740 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
3813678 TGAATAAAGT
3813688 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
3813705 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
3813722 TAATTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
3813739 TA
1 TA
3813741 ACTATTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:3813741 original size:17 final size:17
Alignment explanation
Indices: 3813691--3813750 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
3813681 ATAAAGTTAG
*
3813691 TTCATTAATTAAACTAG
1 TTCATTAATTAAACTAA
* *
3813708 TTCATTCATCAAACTAA
1 TTCATTAATTAAACTAA
*
3813725 TTCATTTATTAAACTAA
1 TTCATTAATTAAACTAA
*
3813742 CT-ATTAATT
1 TTCATTAATT
3813751 GTTTCATGCA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
16 6 0.17
17 30 0.83
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (17 bp):
TTCATTAATTAAACTAA
Found at i:3816510 original size:36 final size:35
Alignment explanation
Indices: 3816452--3816554 Score: 116
Period size: 36 Copynumber: 2.9 Consensus size: 35
3816442 TAGTGCACCA
* *
3816452 ACGATGCAATCATAAGGCACTAAATGTGTCAAACCT
1 ACGATACAATCATAAGGTACTAAATGTGTCAAA-CT
* * * *
3816488 ATGGTACAATCATAGGGTACTAAATGTGTCGCAACT
1 ACGATACAATCATAAGGTACTAAATGTGTC-AAACT
* *
3816524 ACGATGCAATCACAAGGTACTAAATGTGTCA
1 ACGATACAATCATAAGGTACTAAATGTGTCA
3816555 CACAGATATA
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
36 52 0.96
37 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (35 bp):
ACGATACAATCATAAGGTACTAAATGTGTCAAACT
Found at i:3816725 original size:17 final size:17
Alignment explanation
Indices: 3816702--3816793 Score: 78
Period size: 17 Copynumber: 5.4 Consensus size: 17
3816692 AAAATAAAAG
*
3816702 TAAAAGATATAGTACAA
1 TAAAAGATATAATACAA
* *
3816719 CAAAAGATACAATACAA
1 TAAAAGATATAATACAA
* *
3816736 TAAAAAATATAGA-ACAG
1 TAAAAGATATA-ATACAA
*
3816753 TAAAAGATATAATACAG
1 TAAAAGATATAATACAA
* * * *
3816770 TAAGAGAAATAGTATAA
1 TAAAAGATATAATACAA
3816787 TAAAAGA
1 TAAAAGA
3816794 AATGATGCAG
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
16 1 0.02
17 57 0.97
18 1 0.02
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.20
Consensus pattern (17 bp):
TAAAAGATATAATACAA
Found at i:3816791 original size:34 final size:33
Alignment explanation
Indices: 3816704--3816813 Score: 94
Period size: 34 Copynumber: 3.3 Consensus size: 33
3816694 AATAAAAGTA
* * * *
3816704 AAAGATATAGTACAACAAAAGATACAATACAAT
1 AAAGAAATAGTACAATAAAAGATATAATACAGT
* * *
3816737 AAAAAATATAGAACAGTAAAAGATATAATACAGT
1 AAAGAA-ATAGTACAATAAAAGATATAATACAGT
* * * *
3816771 AAGAGAAATAGTATAATAAAAGAAATGATGCAGT
1 AA-AGAAATAGTACAATAAAAGATATAATACAGT
*
3816805 AAAGGAATA
1 AAAGAAATA
3816814 AGTATAGAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
33 10 0.17
34 47 0.78
35 3 0.05
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (33 bp):
AAAGAAATAGTACAATAAAAGATATAATACAGT
Found at i:3816818 original size:34 final size:35
Alignment explanation
Indices: 3816753--3816829 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 35
3816743 TATAGAACAG
*
3816753 TAAAAGATATAATACAGTAAGAGAAATAGTATA-A
1 TAAAAGAAATAATACAGTAAGAGAAATAGTATAGA
* * *
3816787 TAAAAGAAATGATGCAGTAA-AGGAATAAGTATAGA
1 TAAAAGAAATAATACAGTAAGAGAAAT-AGTATAGA
*
3816822 AAAAAGAA
1 TAAAAGAA
3816830 CAGTACATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 5 0.14
34 23 0.64
35 8 0.22
ACGTcount: A:0.60, C:0.03, G:0.18, T:0.19
Consensus pattern (35 bp):
TAAAAGAAATAATACAGTAAGAGAAATAGTATAGA
Found at i:3816874 original size:17 final size:17
Alignment explanation
Indices: 3816828--3816877 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
3816818 TAGAAAAAAG
* *
3816828 AACAGTACATGAAGTATA
1 AACAGTACAAGAAG-AGA
* *
3816846 AATAGTATAAGAAGAGA
1 AACAGTACAAGAAGAGA
3816863 AACAGTACAAGAAGA
1 AACAGTACAAGAAGA
3816878 AAAGATAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (17 bp):
AACAGTACAAGAAGAGA
Found at i:3819858 original size:56 final size:56
Alignment explanation
Indices: 3819774--3819883 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 56
3819764 TTAAAGGGTT
* *
3819774 AGTATCGATACCGAAGTGATTTTGAAAATATCGAAGCCAAATTTAGTATCAATAAG
1 AGTATCGATACCCAAGTGATTTTCAAAATATCGAAGCCAAATTTAGTATCAATAAG
* * * * *
3819830 AGTATTGATACCCAAGT-ATTTTTCAAAATATCGAATCTAATTTTGGTATCAATA
1 AGTATCGATACCCAAGTGA-TTTTCAAAATATCGAAGCCAAATTTAGTATCAATA
3819884 CTCACATGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
55 1 0.02
56 45 0.98
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (56 bp):
AGTATCGATACCCAAGTGATTTTCAAAATATCGAAGCCAAATTTAGTATCAATAAG
Found at i:3834113 original size:35 final size:35
Alignment explanation
Indices: 3834067--3834142 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
3834057 AAAACATTCC
* * *
3834067 TCAATTTCATTCTAAACCCCAAATTCTAAAGTAAT
1 TCAATTACATTCTAAAACCCAAATTCTAAAATAAT
*
3834102 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTACATTCTAAAACCCAAATTCTAAAATAAT
3834137 TCAATT
1 TCAATT
3834143 TAAGGAGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTACATTCTAAAACCCAAATTCTAAAATAAT
Found at i:3835137 original size:27 final size:27
Alignment explanation
Indices: 3835063--3835146 Score: 64
Period size: 27 Copynumber: 3.0 Consensus size: 27
3835053 TAAATGAATT
* *
3835063 ATTATCATATATTCTTACTATTGAAAAA
1 ATTATCATATATTTTTAATATT-AAAAA
* *
3835091 ATT-TCATGTCTTTAAATTAATATTAAAAA
1 ATTATCATATATTT---TTAATATTAAAAA
*
3835120 ATTATCATATGTTTTTAA-ATATAAAAA
1 ATTATCATATATTTTTAATAT-TAAAAA
3835147 GTAAATTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
26 2 0.04
27 17 0.38
28 3 0.07
29 8 0.18
30 15 0.33
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (27 bp):
ATTATCATATATTTTTAATATTAAAAA
Found at i:3835249 original size:35 final size:34
Alignment explanation
Indices: 3835200--3835313 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 34
3835190 AAAAAAGACA
* *
3835200 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
3835235 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
* *
3835270 AAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
3835305 GAAATTGAA
1 GAAATTGAA
3835314 GATTGTTTTG
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 66 0.94
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:3839087 original size:20 final size:20
Alignment explanation
Indices: 3839062--3839138 Score: 154
Period size: 20 Copynumber: 3.9 Consensus size: 20
3839052 GAATGTCATG
3839062 AGGGTATCGATACCCCCAGT
1 AGGGTATCGATACCCCCAGT
3839082 AGGGTATCGATACCCCCAGT
1 AGGGTATCGATACCCCCAGT
3839102 AGGGTATCGATACCCCCAGT
1 AGGGTATCGATACCCCCAGT
3839122 AGGGTATCGATACCCCC
1 AGGGTATCGATACCCCC
3839139 CTAAAGGAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (20 bp):
AGGGTATCGATACCCCCAGT
Found at i:3840685 original size:24 final size:24
Alignment explanation
Indices: 3840655--3840713 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
3840645 CTTAAGGAAT
*
3840655 TTCTATGTGGTCCTTCGAGACAAA
1 TTCTATGCGGTCCTTCGAGACAAA
*
3840679 TTCTATGCGGTCCTTCGGGACAAA
1 TTCTATGCGGTCCTTCGAGACAAA
*
3840703 TTTCTACGCGG
1 -TTCTATGCGG
3840714 CACTTCGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (24 bp):
TTCTATGCGGTCCTTCGAGACAAA
Found at i:3840713 original size:25 final size:25
Alignment explanation
Indices: 3840652--3840735 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
3840642 ATTCTTAAGG
* * *
3840652 AATTTCTATGTGGTCCTTCGAGACA
1 AATTTCTACGCGGTCCTTCGGGACA
*
3840677 AA-TTCTATGCGGTCCTTCGGGACA
1 AATTTCTACGCGGTCCTTCGGGACA
3840701 AATTTCTACGCGG-CACTTCGGTG-CA
1 AATTTCTACGCGGTC-CTTCGG-GACA
*
3840726 AAATTCTACG
1 AATTTCTACG
3840736 TGGCATTACG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
24 23 0.44
25 28 0.54
26 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (25 bp):
AATTTCTACGCGGTCCTTCGGGACA
Found at i:3849469 original size:2 final size:2
Alignment explanation
Indices: 3849462--3849530 Score: 69
Period size: 2 Copynumber: 37.5 Consensus size: 2
3849452 CCGCCCTGAT
*
3849462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3849502 TT TT TA TA T- TA -A T- TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3849531 TTTATACTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
1 6 0.10
2 52 0.90
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:3849510 original size:36 final size:34
Alignment explanation
Indices: 3849466--3849567 Score: 116
Period size: 34 Copynumber: 2.8 Consensus size: 34
3849456 CCTGATTATA
3849466 TATATATATATATATATATATATATAATATTTTATATTTT
1 TATAT-TA-ATATATATATATA-AT-AT-TTT-ATATTTT
3849506 TATATTAATTATATATATATAATATTTTATACTTTT
1 TATATTAA-TATATATATATAATATTTTATA-TTTT
*
3849542 TATATTAAT-TATATATAAAATATTTT
1 TATATTAATATATATATATAATATTTT
3849568 TGGGTTCGGA
Statistics
Matches: 59, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
34 16 0.27
35 4 0.07
36 15 0.25
37 2 0.03
38 3 0.05
39 14 0.24
40 5 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATTAATATATATATATAATATTTTATATTTT
Found at i:3849525 original size:35 final size:36
Alignment explanation
Indices: 3849480--3849567 Score: 155
Period size: 35 Copynumber: 2.5 Consensus size: 36
3849470 TATATATATA
3849480 TATATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATATAATATTTTATACTTTTTATATTAAT
3849515 TATATATATATAATATTTTATACTTTTTATATTAAT
1 TATATATATATAATATTTTATACTTTTTATATTAAT
3849551 TATATATA-A-AATATTTT
1 TATATATATATAATATTTT
3849568 TGGGTTCGGA
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
34 8 0.15
35 23 0.44
36 21 0.40
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (36 bp):
TATATATATATAATATTTTATACTTTTTATATTAAT
Found at i:3850241 original size:23 final size:23
Alignment explanation
Indices: 3850191--3850248 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3850181 TTGTGATATG
3850191 TTCTCTGCCTTTCTGGCACATTT
1 TTCTCTGCCTTTCTGGCACATTT
* * **
3850214 ATCTCTGCCTTTGTGGCATGTTT
1 TTCTCTGCCTTTCTGGCACATTT
*
3850237 TTCTCTGTCTTT
1 TTCTCTGCCTTT
3850249 TGGTAGTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.07, C:0.26, G:0.16, T:0.52
Consensus pattern (23 bp):
TTCTCTGCCTTTCTGGCACATTT
Found at i:3851864 original size:16 final size:17
Alignment explanation
Indices: 3851845--3851878 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3851835 CATAAATTTT
*
3851845 AAAATTATA-TAATTAA
1 AAAATTAAATTAATTAA
3851861 AAAATTAAATTAATTAA
1 AAAATTAAATTAATTAA
3851878 A
1 A
3851879 TATAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATTAAATTAATTAA
Found at i:3851870 original size:21 final size:21
Alignment explanation
Indices: 3851846--3851902 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
3851836 ATAAATTTTA
3851846 AAATTATATAATTAAAAAATT
1 AAATTATATAATTAAAAAATT
* *
3851867 AAATTA-ATTAAATATAAAATT
1 AAATTATA-TAATTAAAAAATT
*
3851888 AAATAAATATAATTA
1 AAAT-TATATAATTA
3851903 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 1 0.03
21 21 0.72
22 6 0.21
23 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATTATATAATTAAAAAATT
Found at i:3851886 original size:16 final size:16
Alignment explanation
Indices: 3851850--3851899 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
3851840 ATTTTAAAAT
*
3851850 TATATAATTAAA-AAA
1 TATAAAATTAAATAAA
*
3851865 T-T-AAATTAATTAAA
1 TATAAAATTAAATAAA
3851879 TATAAAATTAAATAAA
1 TATAAAATTAAATAAA
3851895 TATAA
1 TATAA
3851900 TTATATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 6 0.21
14 5 0.17
15 2 0.07
16 16 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TATAAAATTAAATAAA
Found at i:3852006 original size:5 final size:5
Alignment explanation
Indices: 3851996--3852142 Score: 294
Period size: 5 Copynumber: 29.4 Consensus size: 5
3851986 AATGTTAGGG
3851996 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
3852046 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
3852096 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TG
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TG
3852143 TGTTAAAAAC
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 142 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TGATA
Found at i:3852497 original size:45 final size:46
Alignment explanation
Indices: 3852448--3852538 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
3852438 GAACATCGAA
* * *
3852448 TGCATTTTATGCATCGATGCA-TATACCATGCACCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCACCGATGCACTCAG
*
3852493 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCACCGATGCACTCAG
3852539 GCTTTTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 20 0.49
46 21 0.51
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCACCGATGCACTCAG
Found at i:3858388 original size:22 final size:22
Alignment explanation
Indices: 3858360--3858453 Score: 136
Period size: 22 Copynumber: 4.3 Consensus size: 22
3858350 ACACCTAACA
3858360 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
3858382 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
* * *
3858404 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
3858425 GTGCATCGATGCACGCCTTGAAT
1 GTGCATCGATGCA-TCCTTGAAT
3858448 GTGCAT
1 GTGCAT
3858454 GCATCGATGC
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.28
22 34 0.53
23 12 0.19
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:3861342 original size:160 final size:160
Alignment explanation
Indices: 3861164--3861488 Score: 614
Period size: 160 Copynumber: 2.0 Consensus size: 160
3861154 ACTCAGGCTT
*
3861164 TTTCAAAACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTAAGTGTTC
1 TTTCAAAACATCGAATGCATTTTATGCATCGATACACACTTGGTGCACCGATGCACTAAGTGTTC
*
3861229 CAACGGTCAAAATATTTGAATTTTACACTGATGCACCGATGCACCATGGGTATGCATCGATGCAC
66 CAAAGGTCAAAATATTTGAATTTTACACTGATGCACCGATGCACCATGGGTATGCATCGATGCAC
*
3861294 TGACGTTCCTAACTGAATTTAATTAATTGG
131 TGACGTTCCCAACTGAATTTAATTAATTGG
3861324 TTTCAAAACATCGAATGCATTTTATGCATCGATACACACTTGGTGCACCGATGCACTAAGTGTTC
1 TTTCAAAACATCGAATGCATTTTATGCATCGATACACACTTGGTGCACCGATGCACTAAGTGTTC
3861389 CAAAGGTCAAAATATTTGAATTTTACACTGATGCACCGATGCACCATGGGTATGCATCGATGCAC
66 CAAAGGTCAAAATATTTGAATTTTACACTGATGCACCGATGCACCATGGGTATGCATCGATGCAC
*
3861454 TGACGTTCCCAACTGAATTTAATTAATTGT
131 TGACGTTCCCAACTGAATTTAATTAATTGG
3861484 TTTCA
1 TTTCA
3861489 CACTTAAACG
Statistics
Matches: 161, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (160 bp):
TTTCAAAACATCGAATGCATTTTATGCATCGATACACACTTGGTGCACCGATGCACTAAGTGTTC
CAAAGGTCAAAATATTTGAATTTTACACTGATGCACCGATGCACCATGGGTATGCATCGATGCAC
TGACGTTCCCAACTGAATTTAATTAATTGG
Found at i:3866471 original size:2 final size:2
Alignment explanation
Indices: 3866460--3866490 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3866450 TAGATTCTAA
3866460 AT AT -T 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
3866491 CAACTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3866698 original size:20 final size:20
Alignment explanation
Indices: 3866673--3866841 Score: 135
Period size: 20 Copynumber: 8.3 Consensus size: 20
3866663 GATCCGTATC
*
3866673 GCGATTCTGACTATCGCATT
1 GCGATTCTGACTATCGCAAT
** * **
3866693 GCGATT-TTCCAAATTCGCGTT
1 GCGATTCTGAC-TA-TCGCAAT
3866714 GCGATTTTCTGACTATCGCAAT
1 GCGA-TT-CTGACTATCGCAAT
* * *
3866736 GCGAATATGTA-AATCGCAAT
1 GCGATTCTG-ACTATCGCAAT
* * *
3866756 GCAATTATGACTATCGCAAC
1 GCGATTCTGACTATCGCAAT
*
3866776 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAT
* *
3866796 GAGATTCTGACAATCGCAAT
1 GCGATTCTGACTATCGCAAT
*
3866816 GCGATTCTGAATATCGCAAT
1 GCGATTCTGACTATCGCAAT
3866836 GCGATT
1 GCGATT
3866842 TTCAAAGCGC
Statistics
Matches: 118, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.03
20 89 0.75
21 12 0.10
22 11 0.09
23 1 0.01
24 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAT
Found at i:3866785 original size:60 final size:60
Alignment explanation
Indices: 3866720--3866841 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
3866710 CGTTGCGATT
* * *
3866720 TTCTGACTATCGCAATGCGAATATGTA-AATCGCAATGCAATTATGACTATCGCAACGCGA
1 TTCTGACTATCGCAACGAGAATATG-ACAATCGCAATGCAATTATGAATATCGCAACGCGA
* * * * *
3866780 TTCTGACTATCGCAACGAGATTCTGACAATCGCAATGCGATTCTGAATATCGCAATGCGA
1 TTCTGACTATCGCAACGAGAATATGACAATCGCAATGCAATTATGAATATCGCAACGCGA
3866840 TT
1 TT
3866842 TTCAAAGCGC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.02
60 52 0.98
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (60 bp):
TTCTGACTATCGCAACGAGAATATGACAATCGCAATGCAATTATGAATATCGCAACGCGA
Found at i:3867529 original size:20 final size:20
Alignment explanation
Indices: 3867445--3867531 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
3867435 AGAATCGCAA
*
3867445 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
*
3867464 TGCGATTTTTA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
3867483 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
3867503 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
3867523 TGCGATTTT
1 TGCGATTTT
3867532 AAGTTTCAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 25 0.42
20 35 0.58
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.51
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:3869462 original size:20 final size:20
Alignment explanation
Indices: 3869437--3869484 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3869427 TAGTTTACTT
3869437 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
3869457 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
3869477 TCGCAACG
1 TCGCAACG
3869485 AAATAATCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:3869555 original size:20 final size:20
Alignment explanation
Indices: 3869527--3869570 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3869517 GCGATTCTCT
*
3869527 CGTTGCGATAGTCAAATTCG
1 CGTTACGATAGTCAAATTCG
**
3869547 CGTTACGATAGTCATTTTCG
1 CGTTACGATAGTCAAATTCG
3869567 CGTT
1 CGTT
3869571 GTGAAAGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTACGATAGTCAAATTCG
Found at i:3870174 original size:21 final size:21
Alignment explanation
Indices: 3870083--3870187 Score: 104
Period size: 21 Copynumber: 5.0 Consensus size: 21
3870073 GACTCACCTA
*
3870083 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
3870105 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
3870125 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
3870146 TCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
3870167 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
3870188 CCAACATTCT
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 3 0.05
21 61 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:3871621 original size:14 final size:14
Alignment explanation
Indices: 3871584--3871645 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
3871574 TTTCTTGTTT
*
3871584 AATTGATTTATAAA
1 AATTGATTTGTAAA
3871598 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
3871612 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
3871627 TATTGATGTGTAAA
1 AATTGATTTGTAAA
3871641 TAATT
1 -AATT
3871646 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3871797 original size:20 final size:20
Alignment explanation
Indices: 3871744--3871797 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
3871734 AGGTAAACTT
* **
3871744 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
3871764 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
3871784 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
3871798 TCAATTCGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:3871813 original size:19 final size:20
Alignment explanation
Indices: 3871791--3871833 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3871781 AAATCGCAAC
*
3871791 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
3871810 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
3871830 GCGA
1 GCGA
3871834 TTTTCTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:3871874 original size:20 final size:20
Alignment explanation
Indices: 3871842--3872084 Score: 181
Period size: 20 Copynumber: 12.8 Consensus size: 20
3871832 GATTTTCTCA
* * *
3871842 TTGCGATAGTCAAATACCCG
1 TTGCGATAATCAAATTCGCG
*
3871862 TTGTGATAATCAAATTCGCG
1 TTGCGATAATCAAATTCGCG
* *
3871882 TTGCGATACTCAAATTCGTG
1 TTGCGATAATCAAATTCGCG
* *
3871902 TTGCGATAGTGAAATTCGCG
1 TTGCGATAATCAAATTCGCG
*
3871922 TTGCGATAATCAAA-TAGTCG
1 TTGCGATAATCAAATTCG-CG
**
3871942 TTGCGATAATCAAATTTACG
1 TTGCGATAATCAAATTCGCG
3871962 TTGCGATAGA-CAAATTCGCG
1 TTGCGATA-ATCAAATTCGCG
*
3871982 TTGCGAT--T----TTTGCG
1 TTGCGATAATCAAATTCGCG
* * * *
3871996 TTACGATAGTCATATTCGTG
1 TTGCGATAATCAAATTCGCG
* *
3872016 TTGCGATAGTCAAATTTGCG
1 TTGCGATAATCAAATTCGCG
* *
3872036 TTGCGAT--T----TTTGAG
1 TTGCGATAATCAAATTCGCG
3872050 TTGCGATAATCAAATTCGCG
1 TTGCGATAATCAAATTCGCG
*
3872070 TTGCGATATTCAAAT
1 TTGCGATAATCAAAT
3872085 GAATGTGTAA
Statistics
Matches: 178, Mismatches: 29, Indels: 32
0.74 0.12 0.13
Matches are distributed among these distances:
14 23 0.13
16 2 0.01
18 1 0.01
19 2 0.01
20 148 0.83
21 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (20 bp):
TTGCGATAATCAAATTCGCG
Found at i:3871935 original size:60 final size:60
Alignment explanation
Indices: 3871842--3872084 Score: 215
Period size: 54 Copynumber: 4.2 Consensus size: 60
3871832 GATTTTCTCA
* * * * *
3871842 TTGCGATAGTCAAATACCCGTTGTGATAATCAAATTCGCGTTGCGATACTCAAATTCGTG
1 TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTAGCGTTGCGATAATCAAATTCGTG
* ***
3871902 TTGCGATAGTGAAATTCGCGTTGCGATAATCAAA-TAGTCGTTGCGATAATCAAATTTACG
1 TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTAG-CGTTGCGATAATCAAATTCGTG
* * * * *
3871962 TTGCGATAGACAAATTCGCGTTGCGAT--T----TTTGCGTTACGATAGTCATATTCGTG
1 TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTAGCGTTGCGATAATCAAATTCGTG
* * * *
3872016 TTGCGATAGTCAAATTTGCGTTGCGAT--T----TTTGAGTTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTAGCGTTGCGATAATCAAATTCGTG
*
3872070 TTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
3872085 GAATGTGTAA
Statistics
Matches: 155, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
54 77 0.50
55 2 0.01
58 1 0.01
59 2 0.01
60 73 0.47
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (60 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTAGCGTTGCGATAATCAAATTCGTG
Found at i:3872224 original size:140 final size:140
Alignment explanation
Indices: 3872059--3872324 Score: 505
Period size: 140 Copynumber: 1.9 Consensus size: 140
3872049 GTTGCGATAA
*
3872059 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
*
3872124 AATGTTCAAACTCAAGTTACTAATACATATCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATACCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
3872189 CACATAATAG
131 CACATAATAG
3872199 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
*
3872264 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 AATGTTCAAACTCAAGTTACTAATACATACCTAACTGAAAATGTTAAAAGTTTACACATAA
3872325 TACAACGTTT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 123 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
AATGTTCAAACTCAAGTTACTAATACATACCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
CACATAATAG
Found at i:3872399 original size:12 final size:12
Alignment explanation
Indices: 3872384--3872414 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3872374 AAGCCGGTTG
*
3872384 TGATTGGGATTT
1 TGATTGCGATTT
3872396 TGATTGCGATTT
1 TGATTGCGATTT
3872408 TGATTGC
1 TGATTGC
3872415 CTTTTTCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.06, G:0.29, T:0.48
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:3874074 original size:30 final size:31
Alignment explanation
Indices: 3874017--3874074 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3874007 TTAAGTTTTG
3874017 AAAAAATTGAAGTTTAGGTACTGAAACATAT
1 AAAAAATTGAAGTTTAGGTACTGAAACATAT
3874048 AAAAAA-TGATAGTTTAGGTACT-AAACA
1 AAAAAATTGA-AGTTTAGGTACTGAAACA
3874075 CTTTAAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.28
Consensus pattern (31 bp):
AAAAAATTGAAGTTTAGGTACTGAAACATAT
Found at i:3875168 original size:226 final size:225
Alignment explanation
Indices: 3874618--3875303 Score: 919
Period size: 226 Copynumber: 3.0 Consensus size: 225
3874608 TAATATAACT
* *
3874618 GGTTAATT-ACTGAAAACATTATCAACCATAATAACATAACATGTATCGCTTATGTAATGTAATA
1 GGTTAATTAACTG-AAACATTATCAACCATAATAACATAACAAGTATCGCTTATTTAATGTAATA
* * * * *
3874682 GGTAACATATTTTTAAAGCTAATGGGGCCTTAGAAATTTGACGATAACAAAATATGTTAATTACT
65 GGTAGCGTCTATTTAAAGCTGATGGGGCCTTAGAAATTTGACGATAACAAAATATGTTAATTACT
* * *
3874747 TGATTTTTTATCAATATTATAAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGA
130 TAATTTGTTATCAATATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGA
* * *
3874812 TGGAGCCTTA-AAATATGAGGATAACAAAATA
195 -GGAACCTTAGAAATCTGACGATAACAAAATA
* * * * *
3874843 TGTTAATTATCGGAAACATTATCAACCATAATAACATAACCAGTAGCGCTTATTTAATGTAATAG
1 GGTTAATTAACTGAAACATTATCAACCATAATAACATAACAAGTATCGCTTATTTAATGTAATAG
* * * * **
3874908 GTAGCG-CTTATTTAAAGTTGATAGAGTCTTAGAAATCCGACGATAACAAAATATGTTAATTACT
66 GTAGCGTC-TATTTAAAGCTGATGGGGCCTTAGAAATTTGACGATAACAAAATATGTTAATTACT
* *
3874972 TAATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTAACCAAAGTTTAAGCTGA
130 TAATTTGTTATCAATATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGA
* *
3875037 CGGAACCTTAGAAATCGGATGATAACAAAATA
195 -GGAACCTTAGAAATCTGACGATAACAAAATA
* * *
3875069 GGTTAATTAAATGAAACATTATCAACAATAATAACATAACAAGTATTGCTTATTTAATGTAATAG
1 GGTTAATTAACTGAAACATTATCAACCATAATAACATAACAAGTATCGCTTATTTAATGTAATAG
* * * * *
3875134 GTAGCGTCTGTTTAAAGCTGATGGGGCCTTAGAAATTTGAAGATAAAAAAATAGGTTAATTAGTT
66 GTAGCGTCTATTTAAAGCTGATGGGGCCTTAGAAATTTGACGATAACAAAATATGTTAATTACTT
* * * *
3875199 AATTTGTTATCAATATTATCAACATATTAGGTAACACATAAAATATTACCAAAGTTTAAGCTGAT
131 AATTTGTTATCAATATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGAG
* *
3875264 GAGACCTTAGAAATCTAACAATAACAAAATA
196 GA-ACCTTAGAAATCTGACGATAACAAAATA
*
3875295 GATTAATTA
1 GGTTAATTA
3875304 TTTATTTTAT
Statistics
Matches: 398, Mismatches: 58, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
225 177 0.44
226 220 0.55
227 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (225 bp):
GGTTAATTAACTGAAACATTATCAACCATAATAACATAACAAGTATCGCTTATTTAATGTAATAG
GTAGCGTCTATTTAAAGCTGATGGGGCCTTAGAAATTTGACGATAACAAAATATGTTAATTACTT
AATTTGTTATCAATATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGAG
GAACCTTAGAAATCTGACGATAACAAAATA
Found at i:3875349 original size:108 final size:108
Alignment explanation
Indices: 3875143--3875372 Score: 264
Period size: 108 Copynumber: 2.1 Consensus size: 108
3875133 GGTAGCGTCT
* * * * * *
3875143 GTTTAAAGCTGATGGGGCCTTAGAAATTTGAAGATAAAAAAATAGGTTAATTAGTTAATTTGTTA
1 GTTT-AAGCTGATGAGACCTTAGAAATCTGAAAATAAAAAAATAGATTAATTAGTTAATTTATTA
*
3875208 TCAATATTATCAACATATTAGGTAACACATAAAATATTACCAAA
65 TCAATATGATCAACATATTAGGTAACACATAAAATATTACCAAA
* * *
3875252 GTTTAAGCTGATGAGACCTTAGAAATCT-AACAATAACAAAATAGATTAATTATTTATTTTATTA
1 GTTTAAGCTGATGAGACCTTAGAAATCTGAA-AATAAAAAAATAGATTAATTAGTTAATTTATTA
* * * * * * * *
3875316 TTAATATGATTAACATATTATGTAGCCCCTAAAATGTTATCAAA
65 TCAATATGATCAACATATTAGGTAACACATAAAATATTACCAAA
*
3875360 ATTTAAGCTGATG
1 GTTTAAGCTGATG
3875373 GGACATTCGA
Statistics
Matches: 101, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
107 2 0.02
108 95 0.94
109 4 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (108 bp):
GTTTAAGCTGATGAGACCTTAGAAATCTGAAAATAAAAAAATAGATTAATTAGTTAATTTATTAT
CAATATGATCAACATATTAGGTAACACATAAAATATTACCAAA
Found at i:3875436 original size:108 final size:105
Alignment explanation
Indices: 3875179--3875440 Score: 240
Period size: 108 Copynumber: 2.4 Consensus size: 105
3875169 TTTGAAGATA
* * * * *
3875179 AAAAAATAGGTTAATTAGTTAATTTGTTATCAATATTATCAACATATTAGGTAACACATAAAATA
1 AAAAAATA-GTTAATT-TTTATTTTGTTATAAATAATATTAACATATTAGGTAACACATAAAATA
* * *
3875244 TTACCAAAGTTTAAGCTGATGAGACCTTAGAAATCTAACAAT
64 TTACCAAAATTTAAGCTGATGAGACATTAGAAATCTAACAAC
* * * * * *
3875286 AACAAAATAGATTAATTATTTATTTTATTATTAAT-ATGATTAACATATTATGTAGCCCCTAAAA
1 AA-AAAATAG-TTAATT-TTTATTTTGTTATAAATAAT-ATTAACATATTAGGTAACACATAAAA
* * * * * *
3875350 TGTTATCAAAATTTAAGCTGATGGGACATTCGAAAT-TCCACGAC
62 TATTACCAAAATTTAAGCTGATGAGACATTAGAAATCT-AACAAC
3875394 AAAAAATATGTTAATTTCTTATTTTGTTATAAATAAATATTAACATA
1 AAAAAATA-GTTAATTT-TTATTTTGTTATAAAT-AATATTAACATA
3875441 CTAAGTTAAG
Statistics
Matches: 126, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
106 1 0.01
107 31 0.25
108 92 0.73
109 2 0.02
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (105 bp):
AAAAAATAGTTAATTTTTATTTTGTTATAAATAATATTAACATATTAGGTAACACATAAAATATT
ACCAAAATTTAAGCTGATGAGACATTAGAAATCTAACAAC
Found at i:3875981 original size:23 final size:23
Alignment explanation
Indices: 3875953--3876016 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
3875943 CGGTAGCTAG
3875953 TTTAATGTTAA-AGGTAGCG-CTTA
1 TTTAATG-TAATAGGTAGCGTC-TA
3875976 TTTAATGTAATAGGTAGCGTCTA
1 TTTAATGTAATAGGTAGCGTCTA
**
3875999 TTTAACATAATAGGTAGC
1 TTTAATGTAATAGGTAGC
3876017 CCCTATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.08
23 33 0.89
24 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (23 bp):
TTTAATGTAATAGGTAGCGTCTA
Found at i:3876022 original size:23 final size:23
Alignment explanation
Indices: 3875964--3876024 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
3875954 TTAATGTTAA
* **
3875964 AGGTAGCGCTTATTTAATGTAAT
1 AGGTAGCGCCTATTTAACATAAT
*
3875987 AGGTAGCGTCTATTTAACATAAT
1 AGGTAGCGCCTATTTAACATAAT
*
3876010 AGGTAGCCCCTATTT
1 AGGTAGCGCCTATTT
3876025 TATTTTGCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (23 bp):
AGGTAGCGCCTATTTAACATAAT
Found at i:3876220 original size:75 final size:75
Alignment explanation
Indices: 3875998--3876256 Score: 275
Period size: 75 Copynumber: 3.5 Consensus size: 75
3875988 GGTAGCGTCT
** * * *
3875998 ATTTAACATAATAGGTAGCCCCTATTTTATTTTGCGATTTACATTATTATTAACCTTTAAACAAA
1 ATTTAACATAATAGGTAGTGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAACAAA
* **
3876063 CCGATAACTA
66 CCGGTAGGTA
* * * * ** * * *
3876073 GTTTGACGTAATAGGCAGAACCTATTTTATTTTACCGTTTACATTATTAGTAACTTTTAAACAAA
1 ATTTAACATAATAGGTAGTGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAACAAA
*
3876138 CCAGTAGGTA
66 CCGGTAGGTA
* * * * * *
3876148 ATTTAACGTAGTAGGTAGTGCCTATTTTATTTTATCATATACATTATTAATAACCTTCAAATAAA
1 ATTTAACATAATAGGTAGTGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAACAAA
3876213 CCGGTAGGTA
66 CCGGTAGGTA
* * *
3876223 GTTTAACATAATAGATAGTGCATATTTTATTTTA
1 ATTTAACATAATAGGTAGTGCCTATTTTATTTTA
3876257 ACATGTTAAG
Statistics
Matches: 150, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
75 150 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (75 bp):
ATTTAACATAATAGGTAGTGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAACAAA
CCGGTAGGTA
Found at i:3876781 original size:20 final size:21
Alignment explanation
Indices: 3876758--3876801 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3876748 TTTCAACATT
*
3876758 TTTAATAA-TATTTTATCAAA
1 TTTAATAATTATCTTATCAAA
* *
3876778 TTTATTAATTATCTTATTAAA
1 TTTAATAATTATCTTATCAAA
3876799 TTT
1 TTT
3876802 TCGTACAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAATAATTATCTTATCAAA
Found at i:3887281 original size:125 final size:129
Alignment explanation
Indices: 3887122--3887383 Score: 345
Period size: 125 Copynumber: 2.0 Consensus size: 129
3887112 ACATTTGTCG
*
3887122 TCATAATTAGCAATTTTTAATTGTTTGGAGAAGTTTATAATGGGACTTTCTCACATAATTAG-CT
1 TCATAATTAGCAATTTTTAATTGTTTGGAGAAGTTTATAATAGGACTTTCTCACATAATTAGACT
*
3887186 ATTTTTAATTATTTGGAAAAGTTTA-T-GGTAGGAATGTTTGGAACATCATTGCTTAATGTCAT
66 ATTTTTAATTATTTGGAAAAGTTTAGTAGGTAGGAATGTTTGGAAAATCATTGCTTAATGTCAT
*
3887248 TCATAATTAGCAA-TTTTAATTGTTTGG-GTAAGTTTATAGTAGGACTTTCTCACATAATTAGCT
1 TCATAATTAGCAATTTTTAATTGTTTGGAG-AAGTTTATAATAGGACTTTCTCACATAATTAG--
* * ** ** **
3887311 ACTATTTTTTATTCTTTGGGGAAGTTTACGGTAGGTAGGAATGTTTGGAAAATTTTTGCTTCGTG
63 ACTATTTTTAATTATTTGGAAAAGTTTA--GTAGGTAGGAATGTTTGGAAAATCATTGCTTAATG
3887376 TCAT
126 TCAT
3887380 TCAT
1 TCAT
3887384 TTAAACAAAG
Statistics
Matches: 117, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
124 1 0.01
125 44 0.38
126 13 0.11
128 23 0.20
131 1 0.01
132 35 0.30
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.44
Consensus pattern (129 bp):
TCATAATTAGCAATTTTTAATTGTTTGGAGAAGTTTATAATAGGACTTTCTCACATAATTAGACT
ATTTTTAATTATTTGGAAAAGTTTAGTAGGTAGGAATGTTTGGAAAATCATTGCTTAATGTCAT
Found at i:3898159 original size:23 final size:21
Alignment explanation
Indices: 3898133--3898185 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
3898123 CAAGTAATTA
3898133 AAATTAAATTAAAATATAATAAT
1 AAATTAAATTAAAA-ATAAT-AT
*
3898156 AAATATAATTTAAAAATAATAT
1 AAAT-TAAATTAAAAATAATAT
3898178 -AATTAAAT
1 AAATTAAAT
3898186 ATGTAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 3 0.11
22 2 0.07
23 9 0.33
24 9 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTAAATTAAAAATAATAT
Found at i:3900835 original size:15 final size:15
Alignment explanation
Indices: 3900817--3900846 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3900807 ACCACGGTGC
3900817 TCCCGGAATCCTGCG
1 TCCCGGAATCCTGCG
3900832 TCCCGGAATCCTGCG
1 TCCCGGAATCCTGCG
3900847 CGATTGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.40, G:0.27, T:0.20
Consensus pattern (15 bp):
TCCCGGAATCCTGCG
Found at i:3905782 original size:15 final size:15
Alignment explanation
Indices: 3905764--3905793 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3905754 ACCACGGTGC
3905764 TCCCGGAATCCTGCG
1 TCCCGGAATCCTGCG
3905779 TCCCGGAATCCTGCG
1 TCCCGGAATCCTGCG
3905794 CGATTGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.40, G:0.27, T:0.20
Consensus pattern (15 bp):
TCCCGGAATCCTGCG
Found at i:3908550 original size:31 final size:31
Alignment explanation
Indices: 3908506--3908573 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
3908496 ACTCATATAT
*
3908506 TTAAAATTCAATAAAAATACAATAAAAAA-AA
1 TTAAAAGTCAAT-AAAATACAATAAAAAATAA
* *
3908537 TTAAAAGTGAATAAAATTCAATAAAAAATAA
1 TTAAAAGTCAATAAAATACAATAAAAAATAA
3908568 TGTAAA
1 T-TAAA
3908574 GCTAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 15 0.47
31 13 0.41
32 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.25
Consensus pattern (31 bp):
TTAAAAGTCAATAAAATACAATAAAAAATAA
Found at i:3911035 original size:19 final size:19
Alignment explanation
Indices: 3911011--3911055 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
3911001 TATTATAGAT
3911011 ATAATTCCATAATCAAAAC
1 ATAATTCCATAATCAAAAC
3911030 ATAATTCCATAATCAAAAC
1 ATAATTCCATAATCAAAAC
3911049 ATAATTC
1 ATAATTC
3911056 ATATCTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAATTCCATAATCAAAAC
Found at i:3913173 original size:31 final size:30
Alignment explanation
Indices: 3913137--3913199 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
3913127 AATATATAAC
3913137 TTTAAAAATTATAATTTCAGTCC-CTAAACTT
1 TTTAAAAATTATAATTT-AG-CCACTAAACTT
** *
3913168 TTTAAAGTTTATACTTTAGCCACTAAACTT
1 TTTAAAAATTATAATTTAGCCACTAAACTT
3913198 TT
1 TT
3913200 AGAACTTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.07
30 12 0.43
31 14 0.50
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTAAAAATTATAATTTAGCCACTAAACTT
Found at i:3924996 original size:3 final size:3
Alignment explanation
Indices: 3924990--3925097 Score: 153
Period size: 3 Copynumber: 35.0 Consensus size: 3
3924980 TTCATTTAAA
* * *
3924990 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT ATA ATT ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
3925038 ATTT ATT ATT ATT ATT ATT ATT AAT ATT ATAT ATT ATT ATT ATT ATAT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT AT-T
3925086 ATT ATT ATT ATT
1 ATT ATT ATT ATT
3925098 TAATAAATAA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
3 85 0.90
4 9 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3925542 original size:15 final size:14
Alignment explanation
Indices: 3925515--3925541 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3925505 CAGACGGCAG
3925515 AGAACGAAAAAAAC
1 AGAACGAAAAAAAC
3925529 AGAACGAAAAAAA
1 AGAACGAAAAAAA
3925542 AAACAGAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.11, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAACGAAAAAAAC
Found at i:3925828 original size:13 final size:13
Alignment explanation
Indices: 3925810--3925838 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3925800 ACCACCGTTA
3925810 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
3925823 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
3925836 CGG
1 CGG
3925839 AATACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:3926442 original size:53 final size:53
Alignment explanation
Indices: 3926382--3926482 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 53
3926372 GATGATTCAG
* * * *
3926382 GTTATGTTCATAATTTTACATTTATTATTTT-ATTTATTTTTAATCATTGTTTA
1 GTTATGTT-ATAACTTAACATTTATTATTTTAATATATTTTCAATCATTGTTTA
* **
3926435 GTTATGTTTTAACTTAATTTTTATTATTTTAATATATTTTCAATCATT
1 GTTATGTTATAACTTAACATTTATTATTTTAATATATTTTCAATCATT
3926483 ACTTTAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 17 0.43
53 23 0.57
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.61
Consensus pattern (53 bp):
GTTATGTTATAACTTAACATTTATTATTTTAATATATTTTCAATCATTGTTTA
Found at i:3926529 original size:35 final size:35
Alignment explanation
Indices: 3926454--3926529 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
3926444 TAACTTAATT
* * *
3926454 TTTATTATTTTAATATATTTTCAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACATTA
* * *
3926489 ATTATTGTTTTACTATATTATAAAT-ATATACATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACATTA
3926524 TTTATT
1 TTTATT
3926530 TAACAATGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACATTA
Found at i:3933906 original size:83 final size:83
Alignment explanation
Indices: 3933764--3934194 Score: 729
Period size: 83 Copynumber: 5.2 Consensus size: 83
3933754 AATGGAACAA
* *
3933764 ATGAATTTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAAAACC
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
3933829 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
*
3933847 ATTAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
3933912 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
*
3933930 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACA
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
3933995 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
* * *
3934013 ATTAATGTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
3934078 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* *
3934096 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
*
3934160 CAGTCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
3934179 ATGAATTTGCTCATAG
1 ATGAATTTGTTCATAG
3934195 TAGAAATAAG
Statistics
Matches: 327, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
82 4 0.01
83 323 0.99
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (83 bp):
ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTGGAAG
Found at i:3936418 original size:22 final size:22
Alignment explanation
Indices: 3936392--3936443 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
3936382 TACACTCTTC
*
3936392 AAAGATGATAGATTCTCTTTTT
1 AAAGATGACAGATTCTCTTTTT
3936414 AAAGATGACAGATTCTCTTTTT
1 AAAGATGACAGATTCTCTTTTT
3936436 AAAGATGA
1 AAAGATGA
3936444 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
AAAGATGACAGATTCTCTTTTT
Found at i:3937362 original size:76 final size:76
Alignment explanation
Indices: 3937111--3938132 Score: 1899
Period size: 76 Copynumber: 13.5 Consensus size: 76
3937101 CTATTTCCCA
3937111 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3937175 AGCCTTCGGGT
66 AGCCTTCGGGT
*
3937186 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
3937251 AAGCCTTCGGGT
65 AAGCCTTCGGGT
3937263 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3937328 AGCCTTCGGGT
66 AGCCTTCGGGT
3937339 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3937403 AGCCTTCGGGT
66 AGCCTTCGGGT
*
3937414 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3937479 AGCCTTAGGGT
66 AGCCTTCGGGT
3937490 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3937554 AGCCTTCGGGT
66 AGCCTTCGGGT
*
3937565 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
3937630 AAGCCTTCGGGT
65 AAGCCTTCGGGT
3937642 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3937707 AGCCTTCGGGT
66 AGCCTTCGGGT
3937718 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3937782 AGCCTTCGGGT
66 AGCCTTCGGGT
*
3937793 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
3937858 AAGCCTTCGGGT
65 AAGCCTTCGGGT
3937870 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3937935 AGCTTTCGGGT
66 AGCCTTCGGGT
3937946 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3938011 AGCTTTCGGGT
66 AGCCTTCGGGT
*
3938022 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3938087 AACCTTCGGGT
66 AGCCTTCGGGT
*
3938098 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
3938133 CATTTCCATC
Statistics
Matches: 926, Mismatches: 14, Indels: 13
0.97 0.01 0.01
Matches are distributed among these distances:
75 251 0.27
76 480 0.52
77 195 0.21
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:3938264 original size:3 final size:3
Alignment explanation
Indices: 3938258--3938368 Score: 159
Period size: 3 Copynumber: 36.0 Consensus size: 3
3938248 TTCATTTAAA
* * *
3938258 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT ATA ATT ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
3938306 ATTT ATT ATT ATT ATT ATT ATT ATT AAT ATT ATAT ATT ATT ATT ATT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
3938353 ATAT ATT ATT ATT ATT
1 AT-T ATT ATT ATT ATT
3938369 TAATAAATAA
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
3 88 0.91
4 9 0.09
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3938827 original size:17 final size:15
Alignment explanation
Indices: 3938786--3938818 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3938776 CAGACGGCAG
3938786 AGAACGAAAAAAAAC
1 AGAACGAAAAAAAAC
3938801 AGAACGAAAAAAAAC
1 AGAACGAAAAAAAAC
3938816 AGA
1 AGA
3938819 GGAGGAAAAG
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:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (15 bp):
AGAACGAAAAAAAAC
Found at i:3939703 original size:53 final size:53
Alignment explanation
Indices: 3939643--3939743 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 53
3939633 GATGATTCAG
* * * *
3939643 GTTATGTTCATAATTTTACATTTATTATTTT-ATTTATTTTTAATCATTGTTTA
1 GTTATGTT-ATAACTTAACATTTATTATTTTAATATATTTTCAATCATTGTTTA
* **
3939696 GTTATGTTTTAACTTAATTTTTATTATTTTAATATATTTTCAATCATT
1 GTTATGTTATAACTTAACATTTATTATTTTAATATATTTTCAATCATT
3939744 ACTTTAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 17 0.43
53 23 0.57
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.61
Consensus pattern (53 bp):
GTTATGTTATAACTTAACATTTATTATTTTAATATATTTTCAATCATTGTTTA
Found at i:3939790 original size:35 final size:35
Alignment explanation
Indices: 3939715--3939790 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
3939705 TAACTTAATT
* * *
3939715 TTTATTATTTTAATATATTTTCAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACATTA
* * *
3939750 ATTATTGTTTTACTATATTATAAAT-ATATACATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACATTA
3939785 TTTATT
1 TTTATT
3939791 TAACAATGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACATTA
Found at i:3942707 original size:22 final size:21
Alignment explanation
Indices: 3942682--3942722 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3942672 TATAAAAAAT
3942682 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
3942704 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
3942723 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:3944933 original size:24 final size:22
Alignment explanation
Indices: 3944898--3944952 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
3944888 TTTTAGTGTA
3944898 ATAA-TTAATTAACAATTTAAAT
1 ATAATTTAATTAA-AATTTAAAT
* *
3944920 ATAATTTAACTTAATATTTTAAT
1 ATAATTTAA-TTAAAATTTAAAT
3944943 ATATATTTAA
1 ATA-ATTTAA
3944953 ACATGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.14
23 14 0.50
24 10 0.36
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATTTAATTAAAATTTAAAT
Found at i:3945224 original size:26 final size:26
Alignment explanation
Indices: 3945195--3945248 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3945185 CGTATAATGT
3945195 ATGTATCTAT-ATATAATTAATGTATA
1 ATGTATCTATAAT-TAATTAATGTATA
* *
3945221 ATGTATGTATAATTAGTTAATGTATA
1 ATGTATCTATAATTAATTAATGTATA
3945247 AT
1 AT
3945249 TTATGAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (26 bp):
ATGTATCTATAATTAATTAATGTATA
Found at i:3948700 original size:31 final size:31
Alignment explanation
Indices: 3948616--3948721 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
3948606 TTCGAGGGTT
*
3948616 TACCTATGTTCTACGGAATATATGGAC-ATAA
1 TACCTATGTTCTACGGAACATATGGACAAT-A
* *
3948647 TTACCTATG-TCTTTCGGGACATATGGACAATA
1 -TACCTATGTTC-TACGGAACATATGGACAATA
* * *
3948679 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAATA
*
3948710 TACCTAGGTTCT
1 TACCTATGTTCT
3948722 TCGGGATTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
31 36 0.58
32 24 0.39
33 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAATA
Found at i:3952558 original size:31 final size:31
Alignment explanation
Indices: 3952488--3952607 Score: 100
Period size: 31 Copynumber: 3.8 Consensus size: 31
3952478 GTTGAGGGTT
* *
3952488 TACCTATGTT-TTACAGAACATATGGACAGAA
1 TACCTATGTTATT-CGGAACATATGGACAGTA
*
3952519 TTACCTATGTCT-TTCGGGACATATGGACAGTA
1 -TACCTATGT-TATTCGGAACATATGGACAGTA
** * *
3952551 TACCTATGTTATAAGGAACATATAGACAGTT
1 TACCTATGTTATTCGGAACATATGGACAGTA
* * * *
3952582 TACCTAGGTTCTTCGGGACCTATGGA
1 TACCTATGTTATTCGGAACATATGGA
3952608 TAGTTGCCGA
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
30 1 0.01
31 43 0.61
32 24 0.34
33 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (31 bp):
TACCTATGTTATTCGGAACATATGGACAGTA
Found at i:3952571 original size:63 final size:62
Alignment explanation
Indices: 3952488--3952607 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 62
3952478 GTTGAGGGTT
* * *
3952488 TACCTATGTTTTACAGAACATATGGACAGAATTACCTATG-TCTTTCGGGACATATGGACAGTA
1 TACCTATGTTATACAGAACATATAGACAG-ATTACCTAGGTTC-TTCGGGACATATGGACAGTA
* *
3952551 TACCTATGTTATA-AGGAACATATAGACAGTTTACCTAGGTTCTTCGGGACCTATGGA
1 TACCTATGTTATACA-GAACATATAGACAGATTACCTAGGTTCTTCGGGACATATGGA
3952608 TAGTTGCCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
62 23 0.46
63 27 0.54
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (62 bp):
TACCTATGTTATACAGAACATATAGACAGATTACCTAGGTTCTTCGGGACATATGGACAGTA
Found at i:3954283 original size:31 final size:31
Alignment explanation
Indices: 3954243--3954338 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 31
3954233 GTCTCGAAGG
*
3954243 ACCTATCCATATGTTCTGAAGAACATAGGTA
1 ACCTGTCCATATGTTCTGAAGAACATAGGTA
* *
3954274 ACCTGTCCATATGTCCCGAAGAACATAGGTA
1 ACCTGTCCATATGTTCTGAAGAACATAGGTA
* *
3954305 AACTGTCCATAAG-TCTCGAA-AGACATAGGTA
1 ACCTGTCCATATGTTCT-GAAGA-ACATAGGTA
3954336 ACC
1 ACC
3954339 CTCGACTCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.04
31 53 0.96
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (31 bp):
ACCTGTCCATATGTTCTGAAGAACATAGGTA
Found at i:3956298 original size:18 final size:17
Alignment explanation
Indices: 3956275--3956321 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
3956265 CTTGTCATTT
*
3956275 TTTTTCTTTTAAATTCCC
1 TTTTTCATTT-AATTCCC
3956293 TTTTTCATTTAATT-CC
1 TTTTTCATTTAATTCCC
* *
3956309 TTATCCATTTAAT
1 TTTTTCATTTAAT
3956322 CCTTCATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 13 0.50
17 4 0.15
18 9 0.35
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTCATTTAATTCCC
Found at i:3959256 original size:31 final size:30
Alignment explanation
Indices: 3959170--3959257 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
3959160 GAAGGACCTA
** *
3959170 TCCATATGTTCTTAAGAACATAGGTAACCTG
1 TCCATATGTTCCAAAGAA-ATAGGTAAACTG
* *
3959201 TCTATAT-TTCCAAAGGACATAGGTAAACTG
1 TCCATATGTTCCAAA-GAAATAGGTAAACTG
*
3959231 TCCATATGTCTCGAAAGAAATAGGTAA
1 TCCATATGT-TCCAAAGAAATAGGTAA
3959258 CCCTTGACTC
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
30 22 0.48
31 19 0.41
32 5 0.11
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (30 bp):
TCCATATGTTCCAAAGAAATAGGTAAACTG
Found at i:3959519 original size:2 final size:2
Alignment explanation
Indices: 3959512--3959590 Score: 133
Period size: 2 Copynumber: 39.0 Consensus size: 2
3959502 TCTATTGTCG
3959512 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3959553 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA
3959591 GATTTAACAC
Statistics
Matches: 74, Mismatches: 0, Indels: 6
0.93 0.00 0.08
Matches are distributed among these distances:
1 1 0.01
2 69 0.93
3 4 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3963649 original size:33 final size:33
Alignment explanation
Indices: 3963579--3963642 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
3963569 TCGAGTATTA
*
3963579 TTTTTGAGGCTACATGTATAATGAATTCGATTC
1 TTTTTGAGGCTACATGTATAATAAATTCGATTC
* *
3963612 TTTTTGAGGTTATATGTATAATAAATTCGAT
1 TTTTTGAGGCTACATGTATAATAAATTCGAT
3963643 GTTTTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (33 bp):
TTTTTGAGGCTACATGTATAATAAATTCGATTC
Found at i:3965051 original size:25 final size:25
Alignment explanation
Indices: 3964989--3965060 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 25
3964979 GAAACAATTC
3964989 TTTC-TTGTTATTTCTTTCTTTTTAG
1 TTTCTTTGTTATTTCTTTC-TTTTAG
* ***
3965014 TTT-TATAAAATTTCTTTCTTTTAG
1 TTTCTTTGTTATTTCTTTCTTTTAG
*
3965038 TTTCTTTGTTATTT-TTACTTTTA
1 TTTCTTTGTTATTTCTTTCTTTTA
3965061 AGCTTTTTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
24 17 0.47
25 19 0.53
ACGTcount: A:0.15, C:0.10, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTCTTTGTTATTTCTTTCTTTTAG
Found at i:3972149 original size:21 final size:21
Alignment explanation
Indices: 3972125--3972164 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3972115 TTTGCATCTT
3972125 TACATT-CACATATATACATCA
1 TACATTGCACA-ATATACATCA
3972146 TACATTGCACAATATACAT
1 TACATTGCACAATATACAT
3972165 TGCATCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.33
Consensus pattern (21 bp):
TACATTGCACAATATACATCA
Found at i:3973646 original size:13 final size:13
Alignment explanation
Indices: 3973612--3973702 Score: 58
Period size: 13 Copynumber: 7.5 Consensus size: 13
3973602 AAAAATATAT
**
3973612 AAAAGAAGGGAGA
1 AAAAGAAGATAGA
3973625 AAGAA-AAGATAGA
1 AA-AAGAAGATAGA
3973638 AAAAGAAGA-AGGA
1 AAAAGAAGATA-GA
3973651 AAAAG-AG-T--A
1 AAAAGAAGATAGA
3973660 AAAAGAA-A-AG-
1 AAAAGAAGATAGA
3973670 AAAA-AAGATAGA
1 AAAAGAAGATAGA
*
3973682 AAAAGAAGAAAGA
1 AAAAGAAGATAGA
3973695 AAAGAGAA
1 AAA-AGAA
3973703 AAGATATAAG
Statistics
Matches: 62, Mismatches: 3, Indels: 25
0.69 0.03 0.28
Matches are distributed among these distances:
9 8 0.13
10 6 0.10
11 2 0.03
12 9 0.15
13 31 0.50
14 6 0.10
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.03
Consensus pattern (13 bp):
AAAAGAAGATAGA
Found at i:3973652 original size:22 final size:22
Alignment explanation
Indices: 3973622--3973752 Score: 94
Period size: 22 Copynumber: 6.0 Consensus size: 22
3973612 AAAAGAAGGG
*
3973622 AGAAAGAAAAGATAGAAAAAGA
1 AGAAGGAAAAGATAGAAAAAGA
*
3973644 AGAAGGAAAA-AGAGTAAAAAGA
1 AGAAGGAAAAGATAG-AAAAAGA
*
3973666 A-AAGAAAAAAGATAGAAAAAGA
1 AGAAG-GAAAAGATAGAAAAAGA
* * *
3973688 AGAAAGAAAAGAGA-AAAGATATA
1 AGAAGGAAAAGATAGAAA-A-AGA
* *
3973711 AGAA-GAAAAGATATAAGAAGA
1 AGAAGGAAAAGATAGAAAAAGA
* *
3973732 A-AAGAAAAAGA-GGAAAAAGA
1 AGAAGGAAAAGATAGAAAAAGA
3973752 A
1 A
3973753 AAATGAGAAG
Statistics
Matches: 86, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
20 9 0.10
21 18 0.21
22 46 0.53
23 13 0.15
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (22 bp):
AGAAGGAAAAGATAGAAAAAGA
Found at i:3973683 original size:44 final size:43
Alignment explanation
Indices: 3973625--3973754 Score: 160
Period size: 44 Copynumber: 3.0 Consensus size: 43
3973615 AGAAGGGAGA
3973625 AAGAAAAGATAGAAAAAGAAGAAGGAAAAAGAGTAAAAAGAAAAG
1 AAGAAAAGATAGAAAAAGAAGAA-GAAAAAGAG-AAAAAGAAAAG
3973670 AA-AAAAGATAGAAAAAGAAGAA-AGAAAAGAG-AAAAGATATAAG
1 AAGAAAAGATAGAAAAAGAAGAAGA-AAAAGAGAAAAAGA-A-AAG
* *
3973713 AAGAAAAGATATAAGAAGAA-AAGAAAAAGAGGAAAAAGAAAA
1 AAGAAAAGATAGAAAAAGAAGAAGAAAAAGA-GAAAAAGAAAA
3973755 ATGAGAAGGA
Statistics
Matches: 76, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
41 6 0.08
42 2 0.03
43 22 0.29
44 38 0.50
45 8 0.11
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.05
Consensus pattern (43 bp):
AAGAAAAGATAGAAAAAGAAGAAGAAAAAGAGAAAAAGAAAAG
Found at i:3973748 original size:8 final size:7
Alignment explanation
Indices: 3973651--3973754 Score: 65
Period size: 7 Copynumber: 14.6 Consensus size: 7
3973641 AGAAGAAGGA
3973651 AAAAGAG
1 AAAAGAG
3973658 TAAAA-AG
1 -AAAAGAG
*
3973665 AAAAGAA
1 AAAAGAG
3973672 AAAAGATAG
1 AAAAG--AG
3973681 AAAA-AG
1 AAAAGAG
3973687 AAGAA-AG
1 AA-AAGAG
3973694 AAAAGAG
1 AAAAGAG
*
3973701 AAAAGAT
1 AAAAGAG
*
3973708 ATAAGAAG
1 AAAAG-AG
*
3973716 AAAAGAT
1 AAAAGAG
*
3973723 ATAAGAAG
1 AAAAG-AG
3973731 AAAAGA-
1 AAAAGAG
3973737 AAAAGAGG
1 AAAAGA-G
3973745 AAAA-AG
1 AAAAGAG
3973751 AAAA
1 AAAA
3973755 ATGAGAAGGA
Statistics
Matches: 77, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
6 21 0.27
7 33 0.43
8 18 0.23
9 5 0.06
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (7 bp):
AAAAGAG
Found at i:3973749 original size:15 final size:15
Alignment explanation
Indices: 3973624--3973755 Score: 80
Period size: 15 Copynumber: 8.6 Consensus size: 15
3973614 AAGAAGGGAG
3973624 AAAG-AAAAGATAGAA
1 AAAGAAAAAGA-AGAA
*
3973639 AAAGAAGAAG--GAA
1 AAAGAAAAAGAAGAA
*
3973652 AAAGAGTAAA-AAG-A
1 AAAGA-AAAAGAAGAA
3973666 AAAGAAAAAAGATAGAA
1 AAAG-AAAAAGA-AGAA
3973683 AAAGAAGAAAGAAAAGAGA
1 AAAGAA-AAAG--AAGA-A
*
3973702 AAAGATATAAGAAG-A
1 AAAGA-AAAAGAAGAA
*
3973717 AAAGATATAAGAAG-A
1 AAAGA-AAAAGAAGAA
*
3973732 AAAGAAAAAGAGGAA
1 AAAGAAAAAGAAGAA
3973747 AAAGAAAAA
1 AAAGAAAAA
3973756 TGAGAAGGAA
Statistics
Matches: 96, Mismatches: 7, Indels: 28
0.73 0.05 0.21
Matches are distributed among these distances:
13 8 0.08
14 16 0.17
15 38 0.40
16 8 0.08
17 12 0.12
18 3 0.03
19 10 0.10
20 1 0.01
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (15 bp):
AAAGAAAAAGAAGAA
Found at i:3973761 original size:29 final size:28
Alignment explanation
Indices: 3973635--3973754 Score: 99
Period size: 29 Copynumber: 4.2 Consensus size: 28
3973625 AAGAAAAGAT
3973635 AGAAAA-AGAAGAAGGA-AAAAG-AGTAAAA
1 AGAAAAGAGAA-AA-GATAAAAGAAG-AAAA
*
3973663 AGAAAAGAAAAAAGATAGAAA-AAGAAGAA
1 AGAAAAGAGAAAAGATA-AAAGAAGAA-AA
*
3973692 AGAAAAGAGAAAAGATATAAGAAG-AAA
1 AGAAAAGAGAAAAGATAAAAGAAGAAAA
*
3973719 AGATATAAGAAGAAAAGA-AAAAGAGGAAAA
1 AGA-A-AAG-AGAAAAGATAAAAGAAGAAAA
3973749 AGAAAA
1 AGAAAA
3973755 ATGAGAAGGA
Statistics
Matches: 77, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
27 7 0.09
28 17 0.22
29 39 0.51
30 14 0.18
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (28 bp):
AGAAAAGAGAAAAGATAAAAGAAGAAAA
Found at i:3976201 original size:2 final size:2
Alignment explanation
Indices: 3976194--3976244 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
3976184 ATACATACAT
* *
3976194 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AT AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3976236 AC AC AC AC A
1 AC AC AC AC A
3976245 ATTCTTACAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.45, G:0.00, T:0.04
Consensus pattern (2 bp):
AC
Found at i:3976845 original size:41 final size:42
Alignment explanation
Indices: 3976739--3976861 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 42
3976729 CCAAAATTGG
* * * *
3976739 TAAGTCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCGGGTCATCCA-TAAGCCTTTCGAGCAAGATGCA
* * * *
3976781 TAAATCATTTGGGTCATCTATAAGCCTTTCGAGCAAGATG-A
1 TAAGTCCTTCGGGTCATCCATAAGCCTTTCGAGCAAGATGCA
*
3976822 TAAGTCCTTCGGGTCATCCATAAGTCC-TTCGGGCAAGATG
1 TAAGTCCTTCGGGTCATCCATAAG-CCTTTCGAGCAAGATG
3976862 TTTTCGCATG
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
41 32 0.48
42 33 0.50
43 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (42 bp):
TAAGTCCTTCGGGTCATCCATAAGCCTTTCGAGCAAGATGCA
Found at i:3977489 original size:134 final size:133
Alignment explanation
Indices: 3977087--3977518 Score: 539
Period size: 134 Copynumber: 3.2 Consensus size: 133
3977077 GTTAATGTTT
* * * *
3977087 AATCTTCCCTGGGTAACAGTGGAATGAATCAACGTCCACAAATATGATATTCCCTCAAGAAGAAG
1 AATCTTCCCTGAG-AACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTCAAGAAGAAG
* * * * *
3977152 CGGAACATAT-CCGTCTCTTTCAAGATTTGATATTTCCTGAGTAATAGTGGAACAAATCTGTCTC
65 CGGAACATATACC-TCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGACTT
3977216 AATTC
129 AATTC
* * * * *
3977221 AATATTTCCTAAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAAAAG
1 AATCTTCCCT-GAGAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTCAAGAAGAAG
* *
3977286 TGGAACA-A-ATCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGACTTA
65 CGGAACATATACCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGACTTA
*
3977349 AGTC
130 ATTC
* * * * *
3977353 AATCTTCCCTGAGTAATAGTGGAATGAATCAACGTCCCCACATCTGATTTTTCGTCAAGAAGTAG
1 AATCTTCCCTGAG-AACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTCAAGAAGAAG
** * *
3977418 CATAACATATACCTCTATTTCAAGATTTGATATTCCCTGGGTAACAGTGGAACAAGTCT-ACATT
65 CGGAACATATACCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGAC-TT
*
3977482 GATTC
129 AATTC
3977487 AATCTTCCCTGAAGAACAGTGGAATGAATCAA
1 AATCTTCCCTG-AGAACAGTGGAATGAATCAA
3977519 TGTTTCTAAA
Statistics
Matches: 256, Mismatches: 35, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
131 2 0.01
132 107 0.42
133 5 0.02
134 139 0.54
135 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (133 bp):
AATCTTCCCTGAGAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTCAAGAAGAAGC
GGAACATATACCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGACTTAA
TTC
Found at i:3977699 original size:3 final size:3
Alignment explanation
Indices: 3977691--3977723 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3977681 TGCCCGGACC
*
3977691 ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3977724 TATTTCTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:3979588 original size:31 final size:30
Alignment explanation
Indices: 3979550--3979609 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
3979540 TTATATAAGC
3979550 TATGTGATAAA-GTGATGGAAAATGATATGTT
1 TATGTGATAAAGGT-ATGG-AAATGATATGTT
*
3979581 TATGTGATAAAGGTATGGAAATTATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
3979610 CTATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.37
31 15 0.56
32 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTT
Found at i:3979873 original size:23 final size:23
Alignment explanation
Indices: 3979833--3979892 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
3979823 AATCTTATAT
*
3979833 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
3979856 GGCTCTTCGGTGCGATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
3979879 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3979893 TTTATACGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:3988686 original size:19 final size:17
Alignment explanation
Indices: 3988652--3988703 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
3988642 AGATTATCAA
* *
3988652 TAAAATATAAAAAAATAT
1 TAAAATATATAGAAAT-T
3988670 CTAAAATATATAGAAATT
1 -TAAAATATATAGAAATT
*
3988688 TAAAATTTTATAGAAA
1 TAAAA-TATATAGAAA
3988704 GGGCGAACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 5 0.17
18 10 0.34
19 14 0.48
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
TAAAATATATAGAAATT
Found at i:3994724 original size:30 final size:30
Alignment explanation
Indices: 3994690--3994749 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
3994680 AAATAATAAC
* *
3994690 ATTTACCGAATTTTATTTAATAAGGATGAT
1 ATTTACCGAATTTTACTTAATAAGAATGAT
*
3994720 ATTTACCGTATTTTACTTAATAAGAATGAT
1 ATTTACCGAATTTTACTTAATAAGAATGAT
3994750 TTTGAGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (30 bp):
ATTTACCGAATTTTACTTAATAAGAATGAT
Found at i:3996472 original size:18 final size:18
Alignment explanation
Indices: 3996437--3996472 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3996427 TTAATCAATC
**
3996437 TAAATAGTCCGTTTAAAT
1 TAAATAGTCCGTAAAAAT
3996455 TAAATAGTCCGTAAAAAT
1 TAAATAGTCCGTAAAAAT
3996473 CAAAGTGGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
TAAATAGTCCGTAAAAAT
Found at i:3997062 original size:31 final size:32
Alignment explanation
Indices: 3997005--3997066 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
3996995 TAAAGCATAA
3997005 GGAATATATTTTTTAATTTAATTATAATTTTG
1 GGAATATATTTTTTAATTTAATTATAATTTTG
**
3997037 GGAATAT-TTTTTTTGTTTCAA-TATAATTTT
1 GGAATATATTTTTTAATTT-AATTATAATTTT
3997067 AAAATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (32 bp):
GGAATATATTTTTTAATTTAATTATAATTTTG
Found at i:4000170 original size:3 final size:3
Alignment explanation
Indices: 4000164--4000253 Score: 105
Period size: 3 Copynumber: 31.0 Consensus size: 3
4000154 AGTTATTATT
* * *
4000164 TAA TAA TGA TAA TAA TAA TAA TAA TAT TAA TAA -AA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
4000211 TAA TAT TAA TAA -AA TAA TAA TAT TAA TAA TAA TAT TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4000254 AATGGGAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
2 6 0.08
3 66 0.92
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4000180 original size:26 final size:25
Alignment explanation
Indices: 4000163--4000253 Score: 110
Period size: 26 Copynumber: 3.5 Consensus size: 25
4000153 TAGTTATTAT
* *
4000163 TTAATAATGATAATAATAATAATAATA
1 TTAATAA-AATAATAAT-ATTATAATA
4000190 TTAATAAAATAATAATATTAATAATA
1 TTAATAAAATAATAATATT-ATAATA
4000216 TTAATAAAATAATAATATTAATAATA
1 TTAATAAAATAATAATATT-ATAATA
* *
4000242 ATATTAAAATAA
1 TTAATAAAATAA
4000254 AATGGGAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
25 2 0.03
26 50 0.85
27 7 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (25 bp):
TTAATAAAATAATAATATTATAATA
Found at i:4000663 original size:20 final size:20
Alignment explanation
Indices: 4000638--4000692 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
4000628 AAAACATTCT
* *
4000638 GCCCGAAGGTCTTATGAATG
1 GCCCGAAGGACTTATAAATG
4000658 GCCCGAAGGACTTATAAATG
1 GCCCGAAGGACTTATAAATG
4000678 GCCCGAAGGACTTAT
1 GCCCGAAGGACTTAT
4000693 CATCTTGCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (20 bp):
GCCCGAAGGACTTATAAATG
Found at i:4001207 original size:20 final size:20
Alignment explanation
Indices: 4001182--4001257 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
4001172 TATCATCTTT
4001182 CTCGAAAGACTTATAGATGA
1 CTCGAAAGACTTATAGATGA
* * * *
4001202 CTCGAAAGATTTAAACATCA
1 CTCGAAAGACTTATAGATGA
* *
4001222 TGCTCGAAAGACTTACAGATGG
1 --CTCGAAAGACTTATAGATGA
* *
4001244 CCCGAAGGACTTAT
1 CTCGAAAGACTTAT
4001258 GAATCAAGAA
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 27 0.64
22 15 0.36
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
CTCGAAAGACTTATAGATGA
Found at i:4001286 original size:260 final size:260
Alignment explanation
Indices: 4000661--4001516 Score: 1288
Period size: 260 Copynumber: 3.3 Consensus size: 260
4000651 ATGAATGGCC
* * * * * * *
4000661 CGAAGGACTTATAAATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGGCTTACAGATGGCCCGA
1 CGAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGA
* * *
4000725 AGGACTGACGAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTTTGTTA
66 AGGACTTATGAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTA
* * **
4000790 GGCTTAGCTTCCTTTAACCACTCTTTTGAGATAATTAGGAAACCCCTTAAAATTAAACTTAGTTT
131 GGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCC-CAAAGGT----TTAGTTT
* * * *
4000855 -TAAAAACCTCATTTGAAAACATCCTA-CACTGAAGGTCTTATGGATGGCCCTAA-GTCTTATCA
191 CT-AAAATCTCATTTGAAAACATCC-AGCACTGAAGGTCTTATGGATGACCCAAAGGTTTTATCA
4000917 TCTTGCT
254 TCTTGCT
* * *
4000924 CGAAAGGCTTATAGATGACCCGAAGGATTTAAACATCACGCTCGAAAGACTTATAGATGGCCCGA
1 CGAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGA
*
4000989 AGGACTTATGAATCAAGAAACCCTCGAAAGATTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTA
66 AGGACTTATGAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTA
*
4001054 GGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCCAAAGGTTTAGTTTCTAAA
131 GGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCCAAAGGTTTAGTTTCTAAA
* *
4001119 ATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTATCATCTTTCT
196 ATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGACCCAAAGGTTTTATCATCTTGCT
* *
4001184 CGAAAGACTTATAGATGACTCGAAAGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGA
1 CGAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGA
* *
4001249 AGGACTTATGAATCAAGAAACACTTGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTA
66 AGGACTTATGAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTA
* *
4001314 GGCTTAGCTTCCTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCAAAGGCTTAGTTTCTAAA
131 GGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCCAAAGGTTTAGTTTCTAAA
* *
4001379 ATCTCATTTGAAAACATCCAGCACTAAAGGTCTTATGGATGACCCAAAGGTTTTATCAACTTGCT
196 ATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGACCCAAAGGTTTTATCATCTTGCT
* **
4001444 CGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTAGTGATGGCCCGA
1 CGAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGA
*
4001509 AGAACTTA
66 AGGACTTA
4001517 CAAATTCGAG
Statistics
Matches: 544, Mismatches: 45, Indels: 11
0.91 0.08 0.02
Matches are distributed among these distances:
258 1 0.00
259 53 0.10
260 327 0.60
263 29 0.05
264 134 0.25
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (260 bp):
CGAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGA
AGGACTTATGAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTA
GGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCCAAAGGTTTAGTTTCTAAA
ATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGACCCAAAGGTTTTATCATCTTGCT
Found at i:4004121 original size:7 final size:7
Alignment explanation
Indices: 4004109--4004157 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
4004099 TTGATTCAAT
4004109 TTTTTTC
1 TTTTTTC
4004116 TTTTTT-
1 TTTTTTC
*
4004122 TCTTTTC
1 TTTTTTC
4004129 TTTTTTC
1 TTTTTTC
4004136 ATTTTTTTC
1 --TTTTTTC
*
4004145 TTTTCTC
1 TTTTTTC
4004152 TTTTTT
1 TTTTTT
4004158 TTTCCTGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 5 0.14
7 23 0.66
9 7 0.20
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:4004129 original size:13 final size:12
Alignment explanation
Indices: 4004111--4004161 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
4004101 GATTCAATTT
4004111 TTTTCTTTTTTTC
1 TTTT-TTTTTTTC
*
4004124 TTTTCTTTTTTC
1 TTTTTTTTTTTC
4004136 ATTTTTTTCTTTTC
1 -TTTTTTT-TTTTC
*
4004150 TCTTTTTTTTTC
1 TTTTTTTTTTTC
4004162 CTGATAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 12 0.36
13 16 0.48
14 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:4004134 original size:21 final size:22
Alignment explanation
Indices: 4004108--4004157 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 22
4004098 CTTGATTCAA
4004108 TTTTTTTC-TTTTTTTCTTTTC
1 TTTTTTTCATTTTTTTCTTTTC
4004129 -TTTTTTCATTTTTTTCTTTTC
1 TTTTTTTCATTTTTTTCTTTTC
4004150 TCTTTTTT
1 T-TTTTTT
4004158 TTTCCTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.27
21 13 0.50
23 6 0.23
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTTCATTTTTTTCTTTTC
Found at i:4004140 original size:26 final size:26
Alignment explanation
Indices: 4004110--4004161 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
4004100 TGATTCAATT
*
4004110 TTTTTCTTTTTTTCT-TTTCTTTTTTCA
1 TTTTT-TTCTTTTCTCTTT-TTTTTTCA
4004137 TTTTTTTCTTTTCTCTTTTTTTTTC
1 TTTTTTTCTTTTCTCTTTTTTTTTC
4004162 CTGATAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (26 bp):
TTTTTTTCTTTTCTCTTTTTTTTTCA
Found at i:4004159 original size:16 final size:15
Alignment explanation
Indices: 4004108--4004159 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
4004098 CTTGATTCAA
4004108 TTTTTTTC-TTTT-T
1 TTTTTTTCTTTTTCT
* *
4004121 TTCTTTTCTTTTTTCA
1 TTTTTTTC-TTTTTCT
4004137 TTTTTTTCTTTTCTCT
1 TTTTTTTCTTTT-TCT
4004153 TTTTTTT
1 TTTTTTT
4004160 TCCTGATAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 7 0.23
15 8 0.26
16 16 0.52
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTCTTTTTCT
Found at i:4009739 original size:2 final size:2
Alignment explanation
Indices: 4009732--4009756 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4009722 ACTAATGAAG
4009732 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 T
4009757 GTAAGCAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4011267 original size:3 final size:3
Alignment explanation
Indices: 4011261--4011333 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
4011251 ATTTATTATT
* * * * *
4011261 TAA TAA TAG TGA TAA TAA TAA TAA TAT TGA TAA TAT TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4011308 TAA TAA TAA TAT TAA TAT TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
4011334 AATGGGAAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4011333 original size:23 final size:23
Alignment explanation
Indices: 4011273--4011324 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
4011263 ATAATAGTGA
* *
4011273 TAATAATAATAATATTGATAATAT
1 TAATAA-AATAATAATAATAATAT
4011297 TAATAAAATAATAATAATAATAT
1 TAATAAAATAATAATAATAATAT
4011320 TAATA
1 TAATA
4011325 TTAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TAATAAAATAATAATAATAATAT
Found at i:4011662 original size:20 final size:20
Alignment explanation
Indices: 4011637--4011677 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4011627 CTTCTCGTAT
4011637 AAGATAAAATACGAATTTGA
1 AAGATAAAATACGAATTTGA
4011657 AAGATAAAATACGAATTTGA
1 AAGATAAAATACGAATTTGA
4011677 A
1 A
4011678 GAGTCGCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.24
Consensus pattern (20 bp):
AAGATAAAATACGAATTTGA
Found at i:4013302 original size:26 final size:25
Alignment explanation
Indices: 4013273--4013321 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
4013263 TGGGTTGGAC
4013273 TTGTAAAATGGGCTTTCGGGTTTTTG
1 TTGT-AAATGGGCTTTCGGGTTTTTG
* *
4013299 TTGTAATTGGGCTTTTGGGTTTT
1 TTGTAAATGGGCTTTCGGGTTTT
4013322 GTAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.12, C:0.06, G:0.31, T:0.51
Consensus pattern (25 bp):
TTGTAAATGGGCTTTCGGGTTTTTG
Found at i:4013329 original size:24 final size:25
Alignment explanation
Indices: 4013273--4013329 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
4013263 TGGGTTGGAC
4013273 TTGTAA-AA-TGGGCTTTCGGGTTT
1 TTGTAATAATTGGGCTTTCGGGTTT
** *
4013296 TTGTTGTAATTGGGCTTTTGGG-TT
1 TTGTAATAATTGGGCTTTCGGGTTT
4013320 TTGTAATAAT
1 TTGTAATAAT
4013330 AATAATAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 4 0.15
24 12 0.44
25 11 0.41
ACGTcount: A:0.18, C:0.05, G:0.28, T:0.49
Consensus pattern (25 bp):
TTGTAATAATTGGGCTTTCGGGTTT
Found at i:4013337 original size:9 final size:8
Alignment explanation
Indices: 4013323--4013392 Score: 61
Period size: 8 Copynumber: 8.4 Consensus size: 8
4013313 TTGGGTTTTG
4013323 TAATAATAA
1 TAATAAT-A
4013332 TAATAAT-
1 TAATAATA
* *
4013339 TATTATTA
1 TAATAATA
4013347 TTATATAATA
1 -TA-ATAATA
4013357 TAATGAATA
1 TAAT-AATA
4013366 TAATAATA
1 TAATAATA
4013374 TAATAATA
1 TAATAATA
* *
4013382 TTATTATA
1 TAATAATA
4013390 TAA
1 TAA
4013393 GTCCATATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
7 5 0.10
8 22 0.44
9 19 0.38
10 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (8 bp):
TAATAATA
Found at i:4013389 original size:22 final size:23
Alignment explanation
Indices: 4013323--4013389 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
4013313 TTGGGTTTTG
*
4013323 TAATAATAATAATAATTATTATTA
1 TAAT-ATAATAATAATTATTATAA
* * *
4013347 TTATATAAT-ATAATGAATATAA
1 TAATATAATAATAATTATTATAA
4013369 TAATATAATAAT-ATTATTATA
1 TAATATAATAATAATTATTATA
4013390 TAAGTCCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 25 0.71
23 7 0.20
24 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (23 bp):
TAATATAATAATAATTATTATAA
Done.