Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 131 of 143
Found at i:38541426 original size:13 final size:13
Alignment explanation
Indices: 38541378--38541428 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
38541368 CTAAATCCAG
38541378 AACCCTAAACCTCA
1 AACCCTAAACCT-A
* *
38541392 AATCC-AAATCTA
1 AACCCTAAACCTA
* *
38541404 AACACTAAACCTG
1 AACCCTAAACCTA
38541417 AACCCTAAACCT
1 AACCCTAAACCT
38541429 TGAATATGAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
12 4 0.14
13 21 0.72
14 4 0.14
ACGTcount: A:0.45, C:0.35, G:0.02, T:0.18
Consensus pattern (13 bp):
AACCCTAAACCTA
Found at i:38541828 original size:18 final size:20
Alignment explanation
Indices: 38541805--38541846 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
38541795 TCTAACCCTG
38541805 AACCCAAAT-TCAAACTC-A
1 AACCCAAATCTCAAACTCTA
*
38541823 AACCCAAATCTTAAACTCTA
1 AACCCAAATCTCAAACTCTA
38541843 AACC
1 AACC
38541847 TCGAATCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 7 0.33
20 5 0.24
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (20 bp):
AACCCAAATCTCAAACTCTA
Found at i:38544583 original size:93 final size:93
Alignment explanation
Indices: 38544451--38544682 Score: 231
Period size: 93 Copynumber: 2.5 Consensus size: 93
38544441 TATTTCCGAT
* * * * * * *
38544451 AATGTTGAGTGTGATACTTGAAGTATCAATACGTATTTTATTATAATACT-TATACTTTCATAAA
1 AATGTTCAATGTGGTACTTGAACTATAAATATGTGTTTTATTATAATACTCTATACTTTCATAAA
* * *
38544515 ATGTCTAATGTAATAACTTAAACTTTGAA
66 ATGTCCAATATAAT-ACATAAACTTTGAA
** *
38544544 AATGTTCAATGTGGTACTTGAACTATAAATATGTGTTTTATTATGGTA-TCTATATTTTCATAAA
1 AATGTTCAATGTGGTACTTGAACTATAAATATGTGTTTTATTATAATACTCTATACTTTCATAAA
* ** * *
38544608 ATGTCCAATATGATACATGTATTTTGCA
66 ATGTCCAATATAATACATAAACTTTGAA
**
38544636 AATG-TCTAATGTGGTACTTGAACT-TTCA-ATGTGTTTTATTATAATAC
1 AATGTTC-AATGTGGTACTTGAACTATAAATATGTGTTTTATTATAATAC
38544683 ATGGTGCTAA
Statistics
Matches: 114, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
90 16 0.14
91 4 0.04
92 31 0.27
93 63 0.55
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (93 bp):
AATGTTCAATGTGGTACTTGAACTATAAATATGTGTTTTATTATAATACTCTATACTTTCATAAA
ATGTCCAATATAATACATAAACTTTGAA
Found at i:38545284 original size:13 final size:12
Alignment explanation
Indices: 38545266--38545295 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
38545256 TAGTTATTTG
38545266 TTTTTTAATTTAA
1 TTTTTT-ATTTAA
38545279 TTTTTTATTTAA
1 TTTTTTATTTAA
38545291 TTTTT
1 TTTTT
38545296 CACATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTATTTAA
Found at i:38552730 original size:219 final size:220
Alignment explanation
Indices: 38552363--38552793 Score: 711
Period size: 219 Copynumber: 2.0 Consensus size: 220
38552353 ATCGTATTCA
*
38552363 TCGACTTAAACGTTCGACGACTGGTCGCTGTTCTATATCGAAACCTAGGCAAGTCATTGGAATCC
1 TCGACTTAAACGTTCGACGACTGGTCGCTGTTCTATATCGAAACCTAGGCAAGTCACTGGAATCC
* *
38552428 TCTGTTTCAACTACATTGTGGACTTTCCCTTCGTCCAGTTCCATGTCTATCCTTTCGCTTCTGTA
66 TCTGTTTCAACCACATTGTCGACTTTCCCTTCGTCCAGTTCCATGTCTATCCTTTCGCTTCTGTA
* *
38552493 TGTCGGCCGTGAGTTTGGCCACTCA-TTGACTCTGGGTTTCGCCTCTTCTCCATTTTCAGACCCT
131 TGTCCGCCGTGAGTTTGGCCACTCATTTGACTCTGGGTTTCGCCTCTTCTCCATTTTCAAACCCT
* *
38552557 GTTGCAGTAGCAGCCATCGTCCTCG
196 GTTGCAGCAGCAACCATCGTCCTCG
* * *
38552582 TCGACTTAAACTTTCGACGGCTGGTCGCTGTTCTATATCGAAACCTAGTCAAGTCACTGGAATCC
1 TCGACTTAAACGTTCGACGACTGGTCGCTGTTCTATATCGAAACCTAGGCAAGTCACTGGAATCC
* * *
38552647 TCTGTTTCATCCACATTGTCGACTTTCCCTTTGTCCAGTTCCATGTCTATCCTTTTGCTTCTGTA
66 TCTGTTTCAACCACATTGTCGACTTTCCCTTCGTCCAGTTCCATGTCTATCCTTTCGCTTCTGTA
** *
38552712 TGTCCTTCGTGAGTTTGGCCACTCATTTGACTCTGGGTTTCGCCTTTTCTCCATTTTCAAACCCT
131 TGTCCGCCGTGAGTTTGGCCACTCATTTGACTCTGGGTTTCGCCTCTTCTCCATTTTCAAACCCT
38552777 GTTGCAGCAGCAACCAT
196 GTTGCAGCAGCAACCAT
38552794 TGGTCGAACC
Statistics
Matches: 195, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
219 143 0.73
220 52 0.27
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.36
Consensus pattern (220 bp):
TCGACTTAAACGTTCGACGACTGGTCGCTGTTCTATATCGAAACCTAGGCAAGTCACTGGAATCC
TCTGTTTCAACCACATTGTCGACTTTCCCTTCGTCCAGTTCCATGTCTATCCTTTCGCTTCTGTA
TGTCCGCCGTGAGTTTGGCCACTCATTTGACTCTGGGTTTCGCCTCTTCTCCATTTTCAAACCCT
GTTGCAGCAGCAACCATCGTCCTCG
Found at i:38553859 original size:2 final size:2
Alignment explanation
Indices: 38553852--38553882 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38553842 TGTAAAAAGA
38553852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38553883 ATGAGTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38556344 original size:19 final size:19
Alignment explanation
Indices: 38556320--38556358 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
38556310 TTAAAAAAAC
*
38556320 TTAAAAATAATATAAATTA
1 TTAAAAATAATAAAAATTA
*
38556339 TTAAAAATATTAAAAATTA
1 TTAAAAATAATAAAAATTA
38556358 T
1 T
38556359 GTTAAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAAATAATAAAAATTA
Found at i:38556988 original size:19 final size:19
Alignment explanation
Indices: 38556943--38557014 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
38556933 AATTACAAAA
*
38556943 AAAAATTCAAAATTATTTT
1 AAAAATTCAAAATAATTTT
38556962 AAAAAATTCAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
38556982 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
38557001 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
38557015 TTATATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
18 4 0.09
19 20 0.43
20 23 0.49
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:38558116 original size:21 final size:22
Alignment explanation
Indices: 38558087--38558132 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
38558077 AACCCGAAAG
38558087 TTTGATAAATATTTTAAG-ATTT
1 TTTGATAAA-ATTTTAAGAATTT
*
38558109 TTTG-TAAAATTTTTAGAATTT
1 TTTGATAAAATTTTAAGAATTT
38558130 TTT
1 TTT
38558133 ACATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 11 0.50
22 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (22 bp):
TTTGATAAAATTTTAAGAATTT
Found at i:38558130 original size:20 final size:22
Alignment explanation
Indices: 38558087--38558131 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
38558077 AACCCGAAAG
*
38558087 TTTGATAAATATTTTAAGATTT
1 TTTGATAAATATTTTAAGAATT
*
38558109 TTTG-TAAA-ATTTTTAGAATT
1 TTTGATAAATATTTTAAGAATT
38558129 TTT
1 TTT
38558132 TACATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 4 0.19
22 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (22 bp):
TTTGATAAATATTTTAAGAATT
Found at i:38570322 original size:3 final size:3
Alignment explanation
Indices: 38570316--38570345 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
38570306 GACGGTGCTG
*
38570316 GAT GAT GAT GAT GAT GAC GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
38570346 AAATGACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:38580581 original size:17 final size:17
Alignment explanation
Indices: 38580552--38580589 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
38580542 GGCATCAATT
*
38580552 TTTC-ACAAGAAAACTA
1 TTTCAACAAAAAAACTA
*
38580568 TTTCAACAAAAAAATTA
1 TTTCAACAAAAAAACTA
38580585 TTTCA
1 TTTCA
38580590 TCTTGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (17 bp):
TTTCAACAAAAAAACTA
Found at i:38583953 original size:19 final size:19
Alignment explanation
Indices: 38583929--38583996 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 19
38583919 AATATTCGAG
38583929 TATTTATATATAATATCAT
1 TATTTATATATAATATCAT
* * *
38583948 TATTTATAAGAAAATATTCGAG
1 TATTTAT-ATATAATA-TC-AT
38583970 TATTTATATATAATATCAT
1 TATTTATATATAATATCAT
38583989 TATTTATA
1 TATTTATA
38583997 ATTTAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 16 0.40
20 8 0.20
21 8 0.20
22 8 0.20
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (19 bp):
TATTTATATATAATATCAT
Found at i:38583971 original size:41 final size:41
Alignment explanation
Indices: 38583914--38583997 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
38583904 TGTCATATTA
38583914 AAGAAAATATTCGAGTATTTATATATAATATCATTATTTAT
1 AAGAAAATATTCGAGTATTTATATATAATATCATTATTTAT
38583955 AAGAAAATATTCGAGTATTTATATATAATATCATTATTTAT
1 AAGAAAATATTCGAGTATTTATATATAATATCATTATTTAT
38583996 AA
1 AA
38583998 TTTAATTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (41 bp):
AAGAAAATATTCGAGTATTTATATATAATATCATTATTTAT
Found at i:38585889 original size:12 final size:13
Alignment explanation
Indices: 38585863--38585895 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
38585853 AAATTTGATA
*
38585863 TTTAATTTATTAT
1 TTTAATTTATAAT
38585876 TTTAATTT-TAAT
1 TTTAATTTATAAT
38585888 TTTAATTT
1 TTTAATTT
38585896 GATCTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTAATTTATAAT
Found at i:38587253 original size:14 final size:14
Alignment explanation
Indices: 38587234--38587295 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
38587224 ATTAAATATT
38587234 GAATCTCAAACCTC
1 GAATCTCAAACCTC
38587248 GAATCTC-AA-CTC
1 GAATCTCAAACCTC
* *
38587260 TAAATCT-AAACCTT
1 -GAATCTCAAACCTC
*
38587274 GAACCTCAAACC-C
1 GAATCTCAAACCTC
38587287 -AATCTCAAA
1 GAATCTCAAA
38587296 ACATGAACCC
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
12 11 0.29
13 13 0.34
14 14 0.37
ACGTcount: A:0.40, C:0.32, G:0.05, T:0.23
Consensus pattern (14 bp):
GAATCTCAAACCTC
Found at i:38587802 original size:2 final size:2
Alignment explanation
Indices: 38587795--38587825 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38587785 TACTTTTATT
38587795 TA TA 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 TA TA T
38587826 GGAGATTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38587945 original size:7 final size:7
Alignment explanation
Indices: 38587901--38587926 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38587891 TAAGAGTTAA
38587901 GAAAAAT
1 GAAAAAT
38587908 GAAAAAT
1 GAAAAAT
38587915 GAAAAAT
1 GAAAAAT
38587922 GAAAA
1 GAAAA
38587927 GTTGTAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
GAAAAAT
Found at i:38594477 original size:72 final size:72
Alignment explanation
Indices: 38594401--38594548 Score: 296
Period size: 72 Copynumber: 2.1 Consensus size: 72
38594391 AACATATCAC
38594401 TTACTTCATCCACCACCCATTTTCATGACTTTCTATGATCCATCTTATTGGTTTTCATGTCTGAT
1 TTACTTCATCCACCACCCATTTTCATGACTTTCTATGATCCATCTTATTGGTTTTCATGTCTGAT
38594466 TCATTGA
66 TCATTGA
38594473 TTACTTCATCCACCACCCATTTTCATGACTTTCTATGATCCATCTTATTGGTTTTCATGTCTGAT
1 TTACTTCATCCACCACCCATTTTCATGACTTTCTATGATCCATCTTATTGGTTTTCATGTCTGAT
38594538 TCATTGA
66 TCATTGA
38594545 TTAC
1 TTAC
38594549 AGCTTCACGG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.21, C:0.25, G:0.09, T:0.45
Consensus pattern (72 bp):
TTACTTCATCCACCACCCATTTTCATGACTTTCTATGATCCATCTTATTGGTTTTCATGTCTGAT
TCATTGA
Found at i:38599996 original size:25 final size:24
Alignment explanation
Indices: 38599960--38600006 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
38599950 CAGGAACAAG
*
38599960 TATAATTTAAAATAAAACAAAATA
1 TATAATTCAAAATAAAACAAAATA
*
38599984 TATATATTCAAAATAAAATAAAA
1 TATA-ATTCAAAATAAAACAAAA
38600007 CAAAACATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
TATAATTCAAAATAAAACAAAATA
Found at i:38606934 original size:16 final size:16
Alignment explanation
Indices: 38606903--38606939 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
38606893 ATGTGAAGAA
38606903 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
38606919 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
38606935 TATTA
1 TATTA
38606940 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:38609013 original size:15 final size:14
Alignment explanation
Indices: 38608995--38609054 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 14
38608985 TATAATAAGA
38608995 TATTAAAAAATAAAT
1 TATTAAAAAA-AAAT
38609010 TATTCAAAAAAAAGA-
1 TATT-AAAAAAAA-AT
*
38609025 TATTAAAAATAAAT
1 TATTAAAAAAAAAT
*
38609039 TATTCAAAAAAAAT
1 TATTAAAAAAAAAT
38609053 TA
1 TA
38609055 AAAATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 1 0.03
14 21 0.54
15 10 0.26
16 7 0.18
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (14 bp):
TATTAAAAAAAAAT
Found at i:38609041 original size:29 final size:30
Alignment explanation
Indices: 38608991--38609051 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
38608981 TCAATATAAT
38608991 AAGATATTAAAAAATAAATTATTCAAAAAA
1 AAGATATTAAAAAATAAATTATTCAAAAAA
38609021 AAGATATT-AAAAATAAATTATTCAAAAAA
1 AAGATATTAAAAAATAAATTATTCAAAAAA
38609050 AA
1 AA
38609052 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (30 bp):
AAGATATTAAAAAATAAATTATTCAAAAAA
Found at i:38609052 original size:14 final size:15
Alignment explanation
Indices: 38608995--38609054 Score: 72
Period size: 15 Copynumber: 4.1 Consensus size: 15
38608985 TATAATAAGA
*
38608995 TATTAAAAAATAAAT
1 TATTCAAAAATAAAT
*
38609010 TATTCAAAAA-AAAGA
1 TATTCAAAAATAAA-T
38609025 TATT-AAAAATAAAT
1 TATTCAAAAATAAAT
38609039 TATTCAAAAA-AAAT
1 TATTCAAAAATAAAT
38609053 TA
1 TA
38609055 AAAATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 18 0.46
15 21 0.54
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (15 bp):
TATTCAAAAATAAAT
Found at i:38609069 original size:14 final size:14
Alignment explanation
Indices: 38608988--38609075 Score: 62
Period size: 14 Copynumber: 6.4 Consensus size: 14
38608978 TTGTCAATAT
*
38608988 AATAAGATATTAAAA
1 AATAA-ATATTTAAA
*
38609003 AATAAATTATTCAAA
1 AATAAA-TATTTAAA
*
38609018 AA-AAAGATATTAAA
1 AATAAATAT-TTAAA
*
38609032 AATAAAT-TATTCAA
1 AATAAATAT-TTAAA
38609046 AA-AAA-A-TTAAA
1 AATAAATATTTAAA
38609057 AATAAATATTT-AA
1 AATAAATATTTAAA
38609070 AATAAA
1 AATAAA
38609076 GCGACGCATA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
11 6 0.10
12 3 0.05
13 14 0.23
14 20 0.33
15 17 0.28
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (14 bp):
AATAAATATTTAAA
Found at i:38609543 original size:60 final size:59
Alignment explanation
Indices: 38609474--38609810 Score: 331
Period size: 60 Copynumber: 5.7 Consensus size: 59
38609464 AAATTTAATT
* * ***
38609474 TTTTTTGTGTTGGTCATTGCATAGTTAACACCACCTTTTTTATCTGATAAAAAAATCAAA
1 TTTTTTGTGTTGGCCATTGCATGGCCGACACCACC-TTTTTATCTGATAAAAAAATCAAA
** * *
38609534 TTTTTTGTGTTAACCATTGCATGGCCGACACC-CCTTTTT-TCAGATAAAAAATTCAAA
1 TTTTTTGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAAAAATCAAA
* *
38609591 TTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTATTTATCTAAT-AAAAAATCAAA
1 TTTTTT-GTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAAAAATCAAA
* * ** * * *
38609650 TTTTTTGGTGTTGGCGATTGCATGGCCGACACTACCTTTTTGCCAGATAAAAAATTTAAA
1 TTTTTT-GTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAAAAATCAAA
* * * * * *
38609710 TTTTTTTGTGTTGGACATTACATGACCGACACCACATTTTTTATCTGGTAAAAAACT-AAA
1 -TTTTTTGTGTTGGCCATTGCATGGCCGACACCAC-CTTTTTATCTGATAAAAAAATCAAA
* * * *
38609770 TTTTTTTGATGTTGACCATTGCATGACCGACATCAACTTTT
1 -TTTTTTG-TGTTGGCCATTGCATGGCCGACACCACCTTTT
38609811 CCTCCTTTCT
Statistics
Matches: 229, Mismatches: 41, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
57 22 0.10
58 29 0.13
59 59 0.26
60 76 0.33
61 43 0.19
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (59 bp):
TTTTTTGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAAAAATCAAA
Found at i:38609763 original size:119 final size:118
Alignment explanation
Indices: 38609450--38609810 Score: 424
Period size: 119 Copynumber: 3.0 Consensus size: 118
38609440 TCTGTCATGC
* * ***
38609450 TTTTGTCAGATAAAAAATTTAATTTTTTTTGTGTTGGTCATTGCAT-AGTTAACACCACCTTTTT
1 TTTTGTCAGATAAAAAATTTAAATTTTTTTGTGTTGGACATTGCATGA-CCGACACCA-CTTTTT
* *
38609514 TATCTGATAAAAAAATCAAATTTTTT-GTGTTAACCATTGCATGGCCGACACCCCT
64 TATCTGAT-AAAAAATCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACACCT
* * * * * *
38609569 TTTT-TCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTATTTA
1 TTTTGTCAGATAAAAAATTTAAATTTTTTTGTGTTGGACATTGCATGACCGACACCACTTTTTTA
* * *
38609633 TCTAATAAAAAATCAAATTTTTTGGTGTTGGCGATTGCATGGCCGACACTACCT
66 TCTGATAAAAAATCAAATTTTTTGGTGTTGACCATTGCATGGCCGACAC-ACCT
* *
38609687 TTTTGCCAGATAAAAAATTTAAATTTTTTTGTGTTGGACATTACATGACCGACACCACATTTTTT
1 TTTTGTCAGATAAAAAATTTAAATTTTTTTGTGTTGGACATTGCATGACCGACACCAC-TTTTTT
* * * *
38609752 ATCTGGTAAAAAA-CTAAATTTTTTTGATGTTGACCATTGCATGACCGACATCAACT
65 ATCTGATAAAAAATC-AAA-TTTTTTGGTGTTGACCATTGCATGGCCGACA-CACCT
38609808 TTT
1 TTT
38609811 CCTCCTTTCT
Statistics
Matches: 204, Mismatches: 30, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
116 17 0.08
117 33 0.16
118 50 0.25
119 52 0.25
120 18 0.09
121 33 0.16
122 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (118 bp):
TTTTGTCAGATAAAAAATTTAAATTTTTTTGTGTTGGACATTGCATGACCGACACCACTTTTTTA
TCTGATAAAAAATCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACACCT
Found at i:38612259 original size:24 final size:24
Alignment explanation
Indices: 38612207--38612259 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
38612197 TAATTATACA
**
38612207 AATTTGAATTTAAAATTCTACTTT
1 AATTTGAATTTAAAATTCTAAATT
*
38612231 AATTTGAATTTGAAATT-TAAATT
1 AATTTGAATTTAAAATTCTAAATT
38612254 ACATTT
1 A-ATTT
38612260 AAAATTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (24 bp):
AATTTGAATTTAAAATTCTAAATT
Found at i:38612368 original size:94 final size:94
Alignment explanation
Indices: 38612269--38612602 Score: 560
Period size: 94 Copynumber: 3.5 Consensus size: 94
38612259 TAAAATTATG
* * *
38612269 TTAAAATTATTTAAATCAAAAACTATTATTATTTTATAATCTTTATCAAATAATATGTTGATTTA
1 TTAAAATTATTTAAATCAAAAACTATTATTATTTTACAATTTTTATCAAATAATGTGTTGATTTA
*
38612334 ACAATACATTATTTATCAATTTTTAATAT
66 ACAATACATTATTTACCAATTTTTAATAT
*
38612363 TTAAAATTATTTAAATCAAAAACTATTATTATTTTACAATTTTTATCAAATAATGTGTTGATTTT
1 TTAAAATTATTTAAATCAAAAACTATTATTATTTTACAATTTTTATCAAATAATGTGTTGATTTA
* *
38612428 ATAATATATTATTTACCAATTTTTAATAT
66 ACAATACATTATTTACCAATTTTTAATAT
*
38612457 TTAAAATTATTTAAATAAAAAACTATTATTATTTTACAATTTTTTATCAAATAATGTGTTGATTT
1 TTAAAATTATTTAAATCAAAAACTATTATTATTTTACAA-TTTTTATCAAATAATGTGTTGATTT
* * *
38612522 GACAATACATTATTTGCTAATTTTTAATAT
65 AACAATACATTATTTACCAATTTTTAATAT
38612552 TTAAAATTATTTAAATCAAAAACTATTATTATTTTACAATTTTTATCAAAT
1 TTAAAATTATTTAAATCAAAAACTATTATTATTTTACAATTTTTATCAAAT
38612603 TTTATATTTA
Statistics
Matches: 225, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
94 137 0.61
95 88 0.39
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.49
Consensus pattern (94 bp):
TTAAAATTATTTAAATCAAAAACTATTATTATTTTACAATTTTTATCAAATAATGTGTTGATTTA
ACAATACATTATTTACCAATTTTTAATAT
Found at i:38612720 original size:22 final size:22
Alignment explanation
Indices: 38612691--38612754 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
38612681 GCATTGGACC
*
38612691 AACC-AAATTCTAGCTCACCTA
1 AACCGAAATTCTAGCTCACCAA
38612712 AACCGAAATT-TCAGCTCACCAA
1 AACCGAAATTCT-AGCTCACCAA
* *
38612734 AACTGAAATTCCAGCTCACCA
1 AACCGAAATTCTAGCTCACCA
38612755 CCACCCAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.14
22 32 0.86
ACGTcount: A:0.39, C:0.33, G:0.08, T:0.20
Consensus pattern (22 bp):
AACCGAAATTCTAGCTCACCAA
Found at i:38613991 original size:19 final size:18
Alignment explanation
Indices: 38613969--38614021 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
38613959 TTTTCAAATT
*
38613969 TTTTATAATATTTTTTCTA
1 TTTT-TAATATTTTTTATA
38613988 TTTTTGAAATATTTTTTATA
1 TTTTT--AATATTTTTTATA
38614008 TTTTCTAAT-TTTTT
1 TTTT-TAATATTTTT
38614022 AAGAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 16 0.53
21 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTAATATTTTTTATA
Found at i:38614683 original size:12 final size:12
Alignment explanation
Indices: 38614665--38614736 Score: 72
Period size: 12 Copynumber: 6.0 Consensus size: 12
38614655 ATTCAGATTT
38614665 CGAGCCCGAGGA
1 CGAGCCCGAGGA
* * *
38614677 TGAGCCCAATGA
1 CGAGCCCGAGGA
* *
38614689 TGAGCCCGAGTA
1 CGAGCCCGAGGA
*
38614701 CGAGCCCGCGGA
1 CGAGCCCGAGGA
**
38614713 CGAGCCCGATTA
1 CGAGCCCGAGGA
38614725 CGAGCCCGAGGA
1 CGAGCCCGAGGA
38614737 TCAACCCTAG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.25, C:0.32, G:0.35, T:0.08
Consensus pattern (12 bp):
CGAGCCCGAGGA
Found at i:38614718 original size:36 final size:36
Alignment explanation
Indices: 38614665--38614734 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
38614655 ATTCAGATTT
* *
38614665 CGAGCCCGAGGATGAGCCCAATGATGAGCCCGAGTA
1 CGAGCCCGAGGACGAGCCCAATGACGAGCCCGAGTA
* * *
38614701 CGAGCCCGCGGACGAGCCCGATTACGAGCCCGAG
1 CGAGCCCGAGGACGAGCCCAATGACGAGCCCGAG
38614735 GATCAACCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.24, C:0.33, G:0.34, T:0.09
Consensus pattern (36 bp):
CGAGCCCGAGGACGAGCCCAATGACGAGCCCGAGTA
Found at i:38615228 original size:30 final size:30
Alignment explanation
Indices: 38615194--38615315 Score: 154
Period size: 30 Copynumber: 4.1 Consensus size: 30
38615184 TTTTGATTTT
* *
38615194 TTTCGTTTATTTTTTTAATTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTGTAA
*
38615224 TTTCGTTTATATTTTAAATTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTGTAA
* * *
38615254 TTTCCTATATATTTTAATTTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTGTAA
** * *
38615284 TTTATTTTATATTTTAAATTTCATTTTTAA
1 TTTCGTTTATATTTTAAATTTAATTTGTAA
38615314 TT
1 TT
38615316 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTGTAA
Found at i:38615297 original size:18 final size:18
Alignment explanation
Indices: 38615270--38615315 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
38615260 ATATATTTTA
38615270 ATTTTAATTTGT-AATTT-
1 ATTTTAATTT-TAAATTTC
38615287 ATTTTATATTTTAAATTTC
1 ATTTTA-ATTTTAAATTTC
38615306 ATTTTTAATT
1 A-TTTTAATT
38615316 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 4 0.16
20 5 0.20
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTAATTTTAAATTTC
Found at i:38616322 original size:60 final size:60
Alignment explanation
Indices: 38616153--38616512 Score: 262
Period size: 59 Copynumber: 6.0 Consensus size: 60
38616143 GAAATGAGGG
* * * *
38616153 AAAGTTGGTGTCGGCCAAGCAACGGTCAACACCAAAAAAA-TTGATTTTTTT-TCAGATAA
1 AAAGGTGGTGTCGACCATGCAATGGTCAACA-CAAAAAAATTTGATTTTTTTATCAGATAA
* * *
38616212 AAAGGTAGTGTC-AGCCAATGC-ATGG-CTAACACTAAAAAAATTTAAATTTTTTTATCAGATAG
1 AAAGGTGGTGTCGA-CC-ATGCAATGGTC-AACAC-AAAAAAATTT-GATTTTTTTATCAGATAA
** *
38616274 AAAGGTGGTGTCGACCATGCAATGACCAACACAAAAAAATTTGATTTTTTTATCAAAT-A
1 AAAGGTGGTGTCGACCATGCAATGGTCAACACAAAAAAATTTGATTTTTTTATCAGATAA
* * * * * * *
38616333 ATAGGTGGTGTGGACTAATGC-ATGATCAACACCAAAAAATTTGAATTTTTTTATCTGACAA
1 AAAGGTGGTGTCGAC-CATGCAATGGTCAACACAAAAAAATTTG-ATTTTTTTATCAGATAA
* * ** *
38616394 AAAGGAT--TGTCGGCAATGCAATGGTCAACACAAAAAAATTT-AAATTTTTATCTGA-AA
1 AAAGG-TGGTGTCGACCATGCAATGGTCAACACAAAAAAATTTGATTTTTTTATCAGATAA
* ** * * * *
38616451 AAAGG-GGTGTC-AGTCATTTAATGGTCAATACAAAAACAAATT-AATTTTTTACCAGATAA
1 AAAGGTGGTGTCGA-CCATGCAATGGTCAACACAAAAA-AATTTGATTTTTTTATCAGATAA
38616510 AAA
1 AAA
38616513 AGGAGATTTA
Statistics
Matches: 244, Mismatches: 37, Indels: 40
0.76 0.12 0.12
Matches are distributed among these distances:
57 29 0.12
58 29 0.12
59 69 0.28
60 59 0.24
61 27 0.11
62 29 0.12
63 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (60 bp):
AAAGGTGGTGTCGACCATGCAATGGTCAACACAAAAAAATTTGATTTTTTTATCAGATAA
Found at i:38616342 original size:59 final size:58
Alignment explanation
Indices: 38616179--38616461 Score: 220
Period size: 60 Copynumber: 4.8 Consensus size: 58
38616169 AAGCAACGGT
* *
38616179 CAACACCAAAAAAA-TTGATTTTTTT-TCAGATAAAAAGGTAGTGTC-AGCCAATGCATGGC
1 CAACA-CAAAAAAATTTGATTTTTTTATCAGAT-AAAAGGTGGTGTCGA-CC-ATGCATGAC
* *
38616238 TAACACTAAAAAAATTTAAATTTTTTTATCAGATAGAAAGGTGGTGTCGACCATGCAATGAC
1 CAACAC-AAAAAAATTT-GATTTTTTTATCAGATA-AAAGGTGGTGTCGACCATGC-ATGAC
* * * * *
38616300 CAACACAAAAAAATTTGATTTTTTTATCAAATAATAGGTGGTGTGGACTAATGCATGAT
1 CAACACAAAAAAATTTGATTTTTTTATCAGATAAAAGGTGGTGTCGAC-CATGCATGAC
* * * * * **
38616359 CAACACCAAAAAATTTGAATTTTTTTATCTGACAAAAAGGAT--TGTCGGCAATGCAATGGT
1 CAACACAAAAAAATTTG-ATTTTTTTATCAGA-TAAAAGG-TGGTGTCGACCATGC-ATGAC
** * *
38616419 CAACACAAAAAAATTT-AAATTTTTATCTGAAAAAAGG-GGTGTC
1 CAACACAAAAAAATTTGATTTTTTTATCAGATAAAAGGTGGTGTC
38616462 AGTCATTTAA
Statistics
Matches: 188, Mismatches: 22, Indels: 30
0.78 0.09 0.12
Matches are distributed among these distances:
57 11 0.06
58 13 0.07
59 49 0.26
60 57 0.30
61 28 0.15
62 29 0.15
63 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (58 bp):
CAACACAAAAAAATTTGATTTTTTTATCAGATAAAAGGTGGTGTCGACCATGCATGAC
Found at i:38616353 original size:121 final size:120
Alignment explanation
Indices: 38616152--38616434 Score: 308
Period size: 121 Copynumber: 2.4 Consensus size: 120
38616142 AGAAATGAGG
* * * *
38616152 GAAAGTTGGTGTCGGCCAAGCAACGGTCAACACCAAAAAAA-TTGATTTTTTTTCAGATAAAAAG
1 GAAAGGTGGTGTCGGCCATGCAATGGTCAACA-CAAAAAAATTTGATTTTTTTTCAAATAAAAAG
* *
38616216 GTAGTGTCAGCCAATGCATG-GCTAACACTAAAAAAATTTAAATTTTTTTATCAGATA
65 GTAGTGTCAGCCAATGCATGATC-AACAC-AAAAAAATTTAAATTTTTTTATCAGACA
* ** *
38616273 GAAAGGTGGTGTCGACCATGCAATGACCAACACAAAAAAATTTGATTTTTTTATCAAAT-AATAG
1 GAAAGGTGGTGTCGGCCATGCAATGGTCAACACAAAAAAATTTGATTTTTTT-TCAAATAAAAAG
* * * * * *
38616337 GTGGTGT-GGACTAATGCATGATCAACACCAAAAAATTTGAATTTTTTTATCTGACA
65 GTAGTGTCAG-CCAATGCATGATCAACACAAAAAAATTTAAATTTTTTTATCAGACA
* *
38616393 AAAAGGAT--TGTCGGCAATGCAATGGTCAACACAAAAAAATTT
1 GAAAGG-TGGTGTCGGCCATGCAATGGTCAACACAAAAAAATTT
38616435 AAATTTTTAT
Statistics
Matches: 136, Mismatches: 21, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
119 30 0.22
120 38 0.28
121 62 0.46
122 6 0.04
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (120 bp):
GAAAGGTGGTGTCGGCCATGCAATGGTCAACACAAAAAAATTTGATTTTTTTTCAAATAAAAAGG
TAGTGTCAGCCAATGCATGATCAACACAAAAAAATTTAAATTTTTTTATCAGACA
Found at i:38621081 original size:30 final size:30
Alignment explanation
Indices: 38621045--38621258 Score: 103
Period size: 30 Copynumber: 7.2 Consensus size: 30
38621035 ACCCGGGGGC
38621045 AAAATGGTAATTTTGGTAAAATCGGGGTTA
1 AAAATGGTAATTTTGGTAAAATCGGGGTTA
*
38621075 AAAATGG-AA-TTT--TAAAAGTTTCGGGGGT-
1 AAAATGGTAATTTTGGTAAAA---TCGGGGTTA
* * **
38621103 AAAATGGTAATTTTTGATGAAATCGAAGTTA
1 AAAATGGTAA-TTTTGGTAAAATCGGGGTTA
* * ** *
38621134 AAAACGG-AATTTTAG-AAGCTTCGGGGGT-
1 AAAATGGTAATTTTGGTAA-AATCGGGGTTA
** *
38621162 AAAATGGTAACTTCCGGTGAAATCGGGGTTA
1 AAAATGGTAA-TTTTGGTAAAATCGGGGTTA
*
38621193 AAAATGG-AATTTT--AAAAGATTCAGGGG-T-
1 AAAATGGTAATTTTGGTAAA-A-TC-GGGGTTA
*
38621221 AAAATGGTAAATTTTGGTGAAATCGGGGTTA
1 AAAATGGT-AATTTTGGTAAAATCGGGGTTA
*
38621252 AACATGG
1 AAAATGG
38621259 GATTTTTAAA
Statistics
Matches: 132, Mismatches: 29, Indels: 45
0.64 0.14 0.22
Matches are distributed among these distances:
26 5 0.04
27 2 0.02
28 25 0.19
29 31 0.23
30 39 0.30
31 24 0.18
32 2 0.02
33 4 0.03
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTAAAATCGGGGTTA
Found at i:38621143 original size:59 final size:59
Alignment explanation
Indices: 38621038--38621294 Score: 354
Period size: 59 Copynumber: 4.4 Consensus size: 59
38621028 TATGGATACC
* * *
38621038 CGGGGGCAAAATGGTAA-TTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAAAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* ** * * *
38621096 CGGGGGTAAAATGGTAATTTTTGATGAAATCGAAGTTAAAAACGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* **
38621155 CGGGGGTAAAATGGTAACTTCCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * * *
38621214 CAGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAACATGGGATTTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GGAATTTTAAAAGATT
38621274 CGGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
38621295 CGAAAGTTTC
Statistics
Matches: 172, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
58 16 0.09
59 122 0.71
60 34 0.20
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.30
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:38621294 original size:30 final size:30
Alignment explanation
Indices: 38621038--38621308 Score: 101
Period size: 30 Copynumber: 9.2 Consensus size: 30
38621028 TATGGATACC
*
38621038 CGGGGGCAAAATGGTAATTTTGGT-AAA-A-T
1 CGGGGGTAAAATGGTAATTTT--TAAAAGATT
* *
38621067 CGGGGTTAAAAATGG-AA-TTTTAAAAGTTT
1 CGGGGGT-AAAATGGTAATTTTTAAAAGATT
*
38621096 CGGGGGTAAAATGGTAATTTTTGATGAA-A-T
1 CGGGGGTAAAATGGTAATTTTT-A-AAAGATT
** * * * *
38621126 CGAAGTTAAAAACGG-AA-TTTTAGAAGCTT
1 CGGGGGT-AAAATGGTAATTTTTAAAAGATT
** *
38621155 CGGGGGTAAAATGGTAACTTCCGGT-GAA-A-T
1 CGGGGGTAAAATGGTAA-TT--TTTAAAAGATT
*
38621185 CGGGGTTAAAAATGG-AA-TTTTAAAAGATT
1 CGGGGGT-AAAATGGTAATTTTTAAAAGATT
* *
38621214 CAGGGGTAAAATGGTAAATTTTGGT-GAA-A-T
1 CGGGGGTAAAATGGT-AATTTT--TAAAAGATT
* *
38621244 CGGGGTTAAACATGG-GATTTTTAAAAGATT
1 CGGGGGTAAA-ATGGTAATTTTTAAAAGATT
** *
38621274 CGGGGGTAAAATGGTAATTTTCGAAAGTTT
1 CGGGGGTAAAATGGTAATTTTTAAAAGATT
38621304 CGGGG
1 CGGGG
38621309 TCGAAATGCA
Statistics
Matches: 178, Mismatches: 34, Indels: 59
0.66 0.13 0.22
Matches are distributed among these distances:
26 2 0.01
27 9 0.05
28 28 0.16
29 43 0.24
30 64 0.36
31 23 0.13
32 7 0.04
33 2 0.01
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.30
Consensus pattern (30 bp):
CGGGGGTAAAATGGTAATTTTTAAAAGATT
Found at i:38621682 original size:162 final size:163
Alignment explanation
Indices: 38621415--38621736 Score: 540
Period size: 162 Copynumber: 2.0 Consensus size: 163
38621405 GATCAAATTG
38621415 TAAATCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAGTAAAAGTTGATTTAGGGATTAAATCA
1 TAAATCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAGTAAAAGTTGATTTAGGGATTAAATCA
* *
38621480 AAACAAATTAAAAATGTCAAGGACTAAATGCATAAATAAGCC-AAAAAGTGACACGTGGCAGTCC
66 AAACAAATTAAAAATATCAAGGACTAAATGCATAAATAAGCCAAAAAAGTGACACGTGACAG-CC
*
38621544 -CTGGTACAGCCACACAGTCAAAGGACTAATTTA
130 TCTGGTACAGCCAAACAGTCAAAGGACTAATTTA
* *
38621577 TAAATCTTGAAAATTTGTTGGGCCAATTTCGTAATTAAGTAAAAGTTGATTTAGGGATTAAATCA
1 TAAATCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAGTAAAAGTTGATTTAGGGATTAAATCA
*
38621642 AAACAAATTAAAAATATCAGGGACTAAATGCATAAATAAGCCAAAAAAAGTGACACGTGACAGCC
66 AAACAAATTAAAAATATCAAGGACTAAATGCATAAATAAGCC-AAAAAAGTGACACGTGACAGCC
* *
38621707 TCTGGTTCAGTCAAACAGTCAAAGGACTAA
130 TCTGGTACAGCCAAACAGTCAAAGGACTAA
38621737 ATTGAAAAGC
Statistics
Matches: 149, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
162 103 0.69
163 2 0.01
164 44 0.30
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (163 bp):
TAAATCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAGTAAAAGTTGATTTAGGGATTAAATCA
AAACAAATTAAAAATATCAAGGACTAAATGCATAAATAAGCCAAAAAAGTGACACGTGACAGCCT
CTGGTACAGCCAAACAGTCAAAGGACTAATTTA
Found at i:38623488 original size:27 final size:27
Alignment explanation
Indices: 38623458--38623509 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
38623448 GACATTGGAC
38623458 TTTTAA-TTCTTAATGTTAAATTTAATG
1 TTTTAATTTCTTAAT-TTAAATTTAATG
* *
38623485 TTTTAATTTTTTTATTTAAATTTAA
1 TTTTAATTTCTTAATTTAAATTTAA
38623510 ATTCAAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTTAATTTCTTAATTTAAATTTAATG
Found at i:38623507 original size:6 final size:6
Alignment explanation
Indices: 38623498--38623565 Score: 68
Period size: 6 Copynumber: 11.3 Consensus size: 6
38623488 TAATTTTTTT
* **
38623498 ATTTAA ATTTAA ATTCAA A-GCAA ATTTAA ATAATTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
*
38623547 A-ATAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
38623566 AAAATTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 8 0.15
6 38 0.73
8 6 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:38623535 original size:31 final size:31
Alignment explanation
Indices: 38623500--38623559 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
38623490 ATTTTTTTAT
*
38623500 TTAAATTTAAATTCAAAGCAAATTTAAATAA
1 TTAAATTTAAATTCAAAACAAATTTAAATAA
* *
38623531 TTAAATTTAAATTTAAAATAAATTTAAAT
1 TTAAATTTAAATTCAAAACAAATTTAAAT
38623560 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (31 bp):
TTAAATTTAAATTCAAAACAAATTTAAATAA
Found at i:38623554 original size:17 final size:16
Alignment explanation
Indices: 38623501--38623574 Score: 80
Period size: 17 Copynumber: 4.6 Consensus size: 16
38623491 TTTTTTTATT
*
38623501 TAAATTTAAATTCAAA
1 TAAATTTAAATTTAAA
* *
38623517 GCAAATTTAAA--TAAT
1 -TAAATTTAAATTTAAA
38623532 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
38623549 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
38623565 TAAAATTAAA
1 TAAATTTAAA
38623575 AATCAATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
14 9 0.19
15 2 0.04
16 13 0.27
17 24 0.50
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:38623592 original size:28 final size:28
Alignment explanation
Indices: 38623539--38623593 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
38623529 AATTAAATTT
* *
38623539 AAATTTAAAATAAATTTAAATTTAAATA
1 AAATTAAAAATAAATTTAAATCTAAATA
* *
38623567 AAATTAAAAATCAATTTAACTCTAAAT
1 AAATTAAAAATAAATTTAAATCTAAAT
38623594 TAAACGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATTAAAAATAAATTTAAATCTAAATA
Found at i:38623603 original size:28 final size:28
Alignment explanation
Indices: 38623545--38623603 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
38623535 ATTTAAATTT
* **
38623545 AAAATAAATTTAAATTTAAATAAAATTA
1 AAAATAAATTTAAATCTAAATAAAACGA
* * *
38623573 AAAATCAATTTAACTCTAAATTAAACGA
1 AAAATAAATTTAAATCTAAATAAAACGA
38623601 AAA
1 AAA
38623604 GTCTAAGCCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAATAAATTTAAATCTAAATAAAACGA
Found at i:38625018 original size:18 final size:18
Alignment explanation
Indices: 38624995--38625034 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
38624985 ATTACTTTTT
38624995 AAAAATAATTTTG-GAATA
1 AAAAATAATTTTGAG-ATA
*
38625013 AAAAATACTTTTGAGATA
1 AAAAATAATTTTGAGATA
38625031 AAAA
1 AAAA
38625035 CATTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (18 bp):
AAAAATAATTTTGAGATA
Found at i:38627428 original size:19 final size:19
Alignment explanation
Indices: 38627406--38627443 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38627396 TTTTACATAA
* *
38627406 AATATTTTTTTTTATTTTC
1 AATATATTTTTTTAGTTTC
38627425 AATATATTTTTTTAGTTTC
1 AATATATTTTTTTAGTTTC
38627444 TAAAAAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (19 bp):
AATATATTTTTTTAGTTTC
Found at i:38631648 original size:31 final size:31
Alignment explanation
Indices: 38631610--38631677 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
38631600 TACAATTTGA
38631610 TCACTGAACTATT-TGAAAATTTTCATTTAAG
1 TCACTGAACTATTCT-AAAATTTTCATTTAAG
* *
38631641 TCACTGAACTATTCTAAAGTTTTTATTTAAG
1 TCACTGAACTATTCTAAAATTTTCATTTAAG
38631672 TCACTG
1 TCACTG
38631678 GGTTGTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (31 bp):
TCACTGAACTATTCTAAAATTTTCATTTAAG
Found at i:38637482 original size:15 final size:16
Alignment explanation
Indices: 38637450--38637487 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38637440 ATTTACTAAT
*
38637450 ATATTTTTATAAACAA
1 ATATTTTAATAAACAA
*
38637466 ATATTTTAATATA-AA
1 ATATTTTAATAAACAA
38637481 ATATTTT
1 ATATTTT
38637488 CAATTCACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTTAATAAACAA
Found at i:38637568 original size:3 final size:3
Alignment explanation
Indices: 38637560--38637587 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38637550 ATAAACTTAA
38637560 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
38637588 TGTGATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38645124 original size:6 final size:6
Alignment explanation
Indices: 38645113--38645141 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
38645103 AAGCATTACA
38645113 TATATC TATATC TATATC TATATC TATAT
1 TATATC TATATC TATATC TATATC TATAT
38645142 ATTATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (6 bp):
TATATC
Found at i:38655789 original size:31 final size:31
Alignment explanation
Indices: 38655747--38655818 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
38655737 AAAATTACAA
* *
38655747 AAATCATTAAATTATTTAAAAATTTTCATTT
1 AAATCACTAAATTATTTAAAAATTTTCATCT
* ** *
38655778 AAATCACTAAATTATTTAGAGGTTTTTATCT
1 AAATCACTAAATTATTTAAAAATTTTCATCT
38655809 AAATCACTAA
1 AAATCACTAA
38655819 GATGTTAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (31 bp):
AAATCACTAAATTATTTAAAAATTTTCATCT
Found at i:38662436 original size:24 final size:24
Alignment explanation
Indices: 38662384--38662429 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38662374 CTTGTTGAAA
*
38662384 TTAATATGATATTTTTATATTATG
1 TTAATATGATATTTTTATATAATG
38662408 TTAATATGATA-TTTTATATAAT
1 TTAATATGATATTTTTATATAAT
38662430 TTATAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (24 bp):
TTAATATGATATTTTTATATAATG
Found at i:38662939 original size:11 final size:11
Alignment explanation
Indices: 38662923--38662949 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
38662913 CAAACCCAAC
38662923 TCAATATAAAA
1 TCAATATAAAA
38662934 TCAATATAAAA
1 TCAATATAAAA
38662945 TCAAT
1 TCAAT
38662950 CCAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (11 bp):
TCAATATAAAA
Found at i:38665507 original size:18 final size:18
Alignment explanation
Indices: 38665480--38665522 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
38665470 ATGTAGGATG
* *
38665480 ATATAAACACATACATAC
1 ATATATACACACACATAC
*
38665498 ATATATACACACACATAT
1 ATATATACACACACATAC
38665516 ATATATA
1 ATATATA
38665523 GAAAGAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (18 bp):
ATATATACACACACATAC
Found at i:38674539 original size:33 final size:30
Alignment explanation
Indices: 38674501--38674568 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 30
38674491 TTTAAATTCG
* *
38674501 TTTATATTAATTTTTATTTTTAAAAATATTTA
1 TTTATATT-ATTTTAATATTTAAAAAT-TTTA
*
38674533 TATTATATTATTTTAATATTTAATAATTTTA
1 T-TTATATTATTTTAATATTTAAAAATTTTA
38674564 TTTAT
1 TTTAT
38674569 TGAAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 4 0.12
31 5 0.16
32 16 0.50
33 7 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTATATTATTTTAATATTTAAAAATTTTA
Found at i:38677044 original size:20 final size:21
Alignment explanation
Indices: 38677003--38677054 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
38676993 AATATTATAA
38677003 ATATAATTTTATATTAATATTT
1 ATAT-ATTTTATATTAATATTT
38677025 ATATATTTT-TACTTAA-ATTT
1 ATATATTTTATA-TTAATATTT
38677045 -TATTATTTTA
1 ATA-TATTTTA
38677055 ATAATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.07
20 12 0.44
21 9 0.33
22 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATATTTTATATTAATATTT
Found at i:38682510 original size:86 final size:84
Alignment explanation
Indices: 38682367--38682525 Score: 228
Period size: 86 Copynumber: 1.9 Consensus size: 84
38682357 TGGCATCAGG
*
38682367 AGATGTAACTTATGATTATTCTATGCTAATGATGAAATGGAATCGGCAAAAGATAGTCCATAAGC
1 AGATGTAACTTATGATTATTCTATACTAATGATGAAATGGAATCGGCAAAAGATAGTCCATAAGC
38682432 ACATCCAAGTGACATTAGT
66 ACATCCAAGTGACATTAGT
* * * * * *
38682451 AGATGTAGCTTATGGTTATGTCCTATACTGATGATGAAATTGAATCTGCATAAGATAGTCCATAA
1 AGATGTAACTTATGATTAT-T-CTATACTAATGATGAAATGGAATCGGCAAAAGATAGTCCATAA
*
38682516 GCCCATCCAA
64 GCACATCCAA
38682526 CAGTTATAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
84 17 0.26
85 1 0.02
86 47 0.72
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (84 bp):
AGATGTAACTTATGATTATTCTATACTAATGATGAAATGGAATCGGCAAAAGATAGTCCATAAGC
ACATCCAAGTGACATTAGT
Found at i:38693470 original size:17 final size:17
Alignment explanation
Indices: 38693448--38693481 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38693438 TTAAATTAAC
38693448 TAAATTAATTTCTCAAT
1 TAAATTAATTTCTCAAT
*
38693465 TAAATTATTTTCTCAAT
1 TAAATTAATTTCTCAAT
38693482 CCAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTAATTTCTCAAT
Found at i:38693487 original size:17 final size:17
Alignment explanation
Indices: 38693449--38693487 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
38693439 TAAATTAACT
*
38693449 AAATTAATTTCTCAATT
1 AAATTAATTTCTCAATC
*
38693466 AAATTATTTTCTCAATC
1 AAATTAATTTCTCAATC
*
38693483 CAATT
1 AAATT
38693488 TTAATTCTAT
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:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATTAATTTCTCAATC
Found at i:38703965 original size:22 final size:22
Alignment explanation
Indices: 38703937--38703978 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
38703927 TCTGTGTTTT
*
38703937 TTTTTTTAATTTTGAAATTTAA
1 TTTTTTTAATTTTCAAATTTAA
38703959 TTTTTTTAATTTTCAAATTT
1 TTTTTTTAATTTTCAAATTT
38703979 TAAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTTAATTTTCAAATTTAA
Found at i:38704666 original size:29 final size:29
Alignment explanation
Indices: 38704634--38704697 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
38704624 TAGGTATCTG
*
38704634 ATTAAACTAATATTTT-TATTATTAAATAA
1 ATTAAACTAAT-TTTTATATTATTAAAAAA
**
38704663 ATTAATTTAATTTTTATATTATTAAAAAA
1 ATTAAACTAATTTTTATATTATTAAAAAA
38704692 ATTAAA
1 ATTAAA
38704698 TAAGGTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTAAACTAATTTTTATATTATTAAAAAA
Found at i:38707051 original size:24 final size:24
Alignment explanation
Indices: 38707008--38707070 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
38706998 TAAACTAATA
* *
38707008 AGAGTTTGATTCAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
* *
38707032 AGAGTTTAATTGAAATAAATAAAT
1 AGAGTTTAATTGAAACAAATAAAC
*
38707056 AGAGTTTAACTGAAA
1 AGAGTTTAATTGAAA
38707071 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:38709035 original size:24 final size:24
Alignment explanation
Indices: 38708971--38709042 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
38708961 AAAATAATCT
* * *
38708971 AAATTAATAAGAGTTTGATTCAAAC
1 AAATAAATAA-AGTTTAATTGAAAC
*
38708996 AAATAAACAGAA-TTTAATTGAAAC
1 AAATAAATA-AAGTTTAATTGAAAC
*
38709020 AAATAAATAAAGTTTAACTGAAA
1 AAATAAATAAAGTTTAATTGAAA
38709043 GATTATTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.05
24 28 0.72
25 8 0.21
26 1 0.03
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.28
Consensus pattern (24 bp):
AAATAAATAAAGTTTAATTGAAAC
Found at i:38709075 original size:16 final size:16
Alignment explanation
Indices: 38709054--38709085 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38709044 ATTATTTATC
38709054 AAATTTGACTTGAAAT
1 AAATTTGACTTGAAAT
38709070 AAATTTGACTTGAAAT
1 AAATTTGACTTGAAAT
38709086 GAGAGTCGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
AAATTTGACTTGAAAT
Found at i:38719938 original size:6 final size:6
Alignment explanation
Indices: 38719927--38719992 Score: 66
Period size: 6 Copynumber: 10.8 Consensus size: 6
38719917 AAAATCTAAA
*
38719927 AAAAAG AAAAAG AAAAAG AAAACA- ATCCAAAA- AAAAA- AAAAAA AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAA-AG A---AAAAG AAAAAG AAAAAG AAAAAG
38719976 AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAA
38719993 AGAATTGACC
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.17
6 39 0.72
7 1 0.02
8 2 0.04
9 3 0.06
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:38719959 original size:1 final size:1
Alignment explanation
Indices: 38719955--38719993 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
38719945 AAAACAATCC
* * *
38719955 AAAAAAAAAAAAAAAAAAAAGAAAAAGAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38719994 GAATTGACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:38719962 original size:31 final size:31
Alignment explanation
Indices: 38719914--38719980 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
38719904 TTCATTAAAT
* * *
38719914 AAAAAAATCTAAAAAAAAGAAAAAGAAAAAG
1 AAAAAAATCCAAAAAAAAAAAAAAAAAAAAG
*
38719945 AAAACAATCCAAAAAAAAAAAAAAAAAAAAG
1 AAAAAAATCCAAAAAAAAAAAAAAAAAAAAG
38719976 AAAAA
1 AAAAA
38719981 GAAAAAGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.84, C:0.06, G:0.06, T:0.04
Consensus pattern (31 bp):
AAAAAAATCCAAAAAAAAAAAAAAAAAAAAG
Found at i:38720877 original size:2 final size:2
Alignment explanation
Indices: 38720870--38720900 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
38720860 CCACCATTGA
38720870 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
38720901 CAACAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38721086 original size:43 final size:42
Alignment explanation
Indices: 38721038--38721165 Score: 170
Period size: 43 Copynumber: 3.0 Consensus size: 42
38721028 TTTTTCTATC
38721038 CACGAGATTTGAACTCGAGATTTTAGTAGAGGTATATTAAACT
1 CACGAGATTTGAACTCGAGATTTTAGTAGAGG-ATATTAAACT
* *
38721081 CACGAGATTTGAACTCGAGATTTTAGTA-AAGAGATTAAACT
1 CACGAGATTTGAACTCGAGATTTTAGTAGAGGATATTAAACT
* * *
38721122 CATGTGATTTGAACCCGAGATTTTAGT-GAAGGGATATTAAACT
1 CACGAGATTTGAACTCGAGATTTTAGTAG-A-GGATATTAAACT
38721165 C
1 C
38721166 CTTACCGCTT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 33 0.44
42 3 0.04
43 39 0.52
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (42 bp):
CACGAGATTTGAACTCGAGATTTTAGTAGAGGATATTAAACT
Found at i:38721131 original size:41 final size:43
Alignment explanation
Indices: 38721038--38721152 Score: 164
Period size: 41 Copynumber: 2.7 Consensus size: 43
38721028 TTTTTCTATC
* *
38721038 CACGAGATTTGAACTCGAGATTTTAGTAGAGGTATATTAAACT
1 CACGAGATTTGAACTCGAGATTTTAGTAGAAGTAGATTAAACT
38721081 CACGAGATTTGAACTCGAGATTTTAGTA-AAG-AGATTAAACT
1 CACGAGATTTGAACTCGAGATTTTAGTAGAAGTAGATTAAACT
* * *
38721122 CATGTGATTTGAACCCGAGATTTTAGT-GAAG
1 CACGAGATTTGAACTCGAGATTTTAGTAGAAG
38721153 GGATATTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 36 0.55
42 2 0.03
43 28 0.42
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (43 bp):
CACGAGATTTGAACTCGAGATTTTAGTAGAAGTAGATTAAACT
Found at i:38730563 original size:92 final size:92
Alignment explanation
Indices: 38730421--38730596 Score: 343
Period size: 92 Copynumber: 1.9 Consensus size: 92
38730411 CACATATACG
38730421 ACGATGGTCCCGGAGAGGCTCGAACTCGCGACCTTCGGCTCATAAGACCAACGCTCTAACCGACT
1 ACGATGGTCCCGGAGAGGCTCGAACTCGCGACCTTCGGCTCATAAGACCAACGCTCTAACCGACT
38730486 GAGCTACGGGACCAACCAAACACATAT
66 GAGCTACGGGACCAACCAAACACATAT
*
38730513 ACGATGGTCCCGGCGAGGCTCGAACTCGCGACCTTCGGCTCATAAGACCAACGCTCTAACCGACT
1 ACGATGGTCCCGGAGAGGCTCGAACTCGCGACCTTCGGCTCATAAGACCAACGCTCTAACCGACT
38730578 GAGCTACGGGACCAACCAA
66 GAGCTACGGGACCAACCAA
38730597 TAATATCTTG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 83 1.00
ACGTcount: A:0.28, C:0.34, G:0.24, T:0.15
Consensus pattern (92 bp):
ACGATGGTCCCGGAGAGGCTCGAACTCGCGACCTTCGGCTCATAAGACCAACGCTCTAACCGACT
GAGCTACGGGACCAACCAAACACATAT
Found at i:38743426 original size:2 final size:2
Alignment explanation
Indices: 38743419--38743444 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38743409 ACAAAATGAA
38743419 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
38743445 GACGTCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38746833 original size:17 final size:18
Alignment explanation
Indices: 38746807--38746857 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
38746797 TTGTTGACAT
38746807 GTCCTGCGACACCAGTGA
1 GTCCTGCGACACCAGTGA
*
38746825 -TCCTACGACACCAGT-A
1 GTCCTGCGACACCAGTGA
*
38746841 GTCCTGCGACTCCAGTG
1 GTCCTGCGACACCAGTG
38746858 GTCTTGCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCTGCGACACCAGTGA
Found at i:38749486 original size:463 final size:463
Alignment explanation
Indices: 38748621--38749528 Score: 1710
Period size: 463 Copynumber: 2.0 Consensus size: 463
38748611 ACCAACTAGT
38748621 AAGATAAAATGATTACCAATGTATTATTTTTATAGGGTTGATAATCGGGCATAGAGAGCTATAAA
1 AAGATAAAATGATTACCAATGTATTATTTTTATAGGGTTGATAATCGGGCATAGAGAGCTATAAA
* * *
38748686 TAGTAAGGAAATAATTTTCGAGGTGAATTCTTCTCGATCATGTTTTGTCCTTTCTATCATCAAGA
66 TAGTAAGGAAATAATTCTCGAGGTGAATTCTTCTCAATCATGTTTTGTCCTCTCTATCATCAAGA
*
38748751 AGAAGAAGAAGAAGATAAGAGAGCTCTGCATGGAGCAATATTCTTGAAGATTGAGTCAAGAGAAT
131 AAAAGAAGAAGAAGATAAGAGAGCTCTGCATGGAGCAATATTCTTGAAGATTGAGTCAAGAGAAT
38748816 AGATAAGCAAGGAGACAGGTAGCCTTCTAAGTCTTTCGGTGATCGTAAATTTGAGAAAATGGAGT
196 AGATAAGCAAGGAGACAGGTAGCCTTCTAAGTCTTTCGGTGATCGTAAATTTGAGAAAATGGAGT
*
38748881 TAAGAATTTTTAGAACCTTTGAGGGGGTTCTGCATGTTTCTAGAAACAGGGTTATTCGGCTGGAA
261 TAAGAATTTTTAGAACCTTTGAGGGGGTTCTGCATGTTTCTAAAAACAGGGTTATTCGGCTGGAA
38748946 TGATGAGTTTAACTTATGACTTTGGTTGTGATGCTTAGCTGCTAGGAGAATGGACGTACTGACAT
326 TGATGAGTTTAACTTATGACTTTGGTTGTGATGCTTAGCTGCTAGGAGAATGGACGTACTGACAT
38749011 TCAGAAAAGCTAAGTTGAGGAGGCAAAGAAGCATCAGGTGAATTTTTATACTTTACAACTAGTTC
391 TCAGAAAAGCTAAGTTGAGGAGGCAAAGAAGCATCAGGTGAATTTTTATACTTTACAACTAGTTC
38749076 CTTAGTGA
456 CTTAGTGA
38749084 AAGATAAAATGATTACCAATGTATTATTTTTATAGGGTTGATAATCGGGCATAGA-AGGCTATAA
1 AAGATAAAATGATTACCAATGTATTATTTTTATAGGGTTGATAATCGGGCATAGAGA-GCTATAA
*
38749148 ATAGTAAGGAAATAATTCTCGAGGTGAATTCTTCTCAATCTTGTTTTGTCCTCTCTATCATCAAG
65 ATAGTAAGGAAATAATTCTCGAGGTGAATTCTTCTCAATCATGTTTTGTCCTCTCTATCATCAAG
*
38749213 AAAAAGAAGAAGAAGTTAAGAGAGCTCTGCATGGAGCAATATTCTTGAAGATTGAGTCAAGAGAA
130 AAAAAGAAGAAGAAGATAAGAGAGCTCTGCATGGAGCAATATTCTTGAAGATTGAGTCAAGAGAA
*
38749278 TAGATAAGCAAGGAGACTGGTAGCCTTCTAAGTCTTTCGGTGATCGTAAATTTGAGAAAATGGAG
195 TAGATAAGCAAGGAGACAGGTAGCCTTCTAAGTCTTTCGGTGATCGTAAATTTGAGAAAATGGAG
*
38749343 TTCAGAATTTTTAGAACCTTTGAGGGGGTTCTGCATGTTTCTAAAAACAGGGTTATTCGGCTGGA
260 TTAAGAATTTTTAGAACCTTTGAGGGGGTTCTGCATGTTTCTAAAAACAGGGTTATTCGGCTGGA
38749408 ATGATGAGTTTAACTTATGACTTTGGTTGTGATGCTTAGCTGCTAGGAGAATGGACGTACTGACA
325 ATGATGAGTTTAACTTATGACTTTGGTTGTGATGCTTAGCTGCTAGGAGAATGGACGTACTGACA
*
38749473 TTCAGAAAAGCTAAGTTGAGGAGGCGAAGAAGCATCAGGTGAATTTTTATACTTTA
390 TTCAGAAAAGCTAAGTTGAGGAGGCAAAGAAGCATCAGGTGAATTTTTATACTTTA
38749529 TTCCTAGGTT
Statistics
Matches: 434, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
462 1 0.00
463 433 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (463 bp):
AAGATAAAATGATTACCAATGTATTATTTTTATAGGGTTGATAATCGGGCATAGAGAGCTATAAA
TAGTAAGGAAATAATTCTCGAGGTGAATTCTTCTCAATCATGTTTTGTCCTCTCTATCATCAAGA
AAAAGAAGAAGAAGATAAGAGAGCTCTGCATGGAGCAATATTCTTGAAGATTGAGTCAAGAGAAT
AGATAAGCAAGGAGACAGGTAGCCTTCTAAGTCTTTCGGTGATCGTAAATTTGAGAAAATGGAGT
TAAGAATTTTTAGAACCTTTGAGGGGGTTCTGCATGTTTCTAAAAACAGGGTTATTCGGCTGGAA
TGATGAGTTTAACTTATGACTTTGGTTGTGATGCTTAGCTGCTAGGAGAATGGACGTACTGACAT
TCAGAAAAGCTAAGTTGAGGAGGCAAAGAAGCATCAGGTGAATTTTTATACTTTACAACTAGTTC
CTTAGTGA
Found at i:38750081 original size:67 final size:67
Alignment explanation
Indices: 38749973--38750331 Score: 363
Period size: 67 Copynumber: 5.4 Consensus size: 67
38749963 ATACGCTGTA
* *
38749973 ATGGGGTAT-ATAGTGTAAGATCATAGCTCGACTATTG-CAACATAGAGAGTTCGTCAGGACATT
1 ATGGGGTATGAT-GTGTAAGACCATAGTTCGACTA-TGACAACATAGAGAGTTCGTCAGGACATT
38750036 AAAC
64 AAAC
* * * *
38750040 ATGGGGTATGACGTGTAAAACTATAGTTCGACTATGACAACATAGAGAG-TCTGTCAGGATATTA
1 ATGGGGTATGATGTGTAAGACCATAGTTCGACTATGACAACATAGAGAGTTC-GTCAGGACATTA
38750104 AAC
65 AAC
* * * * *
38750107 ATGGGGTATGATGTGTAAGACCATAACTT-GACTATGACAACATAAAGAGTTTGCCCGGACATTA
1 ATGGGGTATGATGTGTAAGACCAT-AGTTCGACTATGACAACATAGAGAGTTCGTCAGGACATTA
38750171 AAC
65 AAC
** * * * * *
38750174 ATATGGTATGATGTGTAAGACCATAATTTGATTATGACAACATAGAGAGTCCGTCAAGACATTAA
1 ATGGGGTATGATGTGTAAGACCATAGTTCGACTATGACAACATAGAGAGTTCGTCAGGACATTAA
*
38750239 AT
66 AC
* * * * * *
38750241 ATGGGGTATGATATGTAAGATCATA-TCTCGGCTATGGCAACATAGAGAG-TCAG-CTGAAACAT
1 ATGGGGTATGATGTGTAAGACCATAGT-TCGACTATGACAACATAGAGAGTTC-GTCAG-GACAT
*
38750303 TAAAA
63 TAAAC
*
38750308 ATAGGGTATGATGTGTAAGACCAT
1 ATGGGGTATGATGTGTAAGACCAT
38750332 GGCTCGGTTT
Statistics
Matches: 241, Mismatches: 42, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
66 10 0.04
67 226 0.94
68 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (67 bp):
ATGGGGTATGATGTGTAAGACCATAGTTCGACTATGACAACATAGAGAGTTCGTCAGGACATTAA
AC
Found at i:38750213 original size:134 final size:132
Alignment explanation
Indices: 38749973--38750331 Score: 414
Period size: 134 Copynumber: 2.7 Consensus size: 132
38749963 ATACGCTGTA
* *
38749973 ATGGGGTAT-ATAGTGTAAGATCATAGCTCGACTATTGCAACATAGAGAGTTCGTCAGGACATTA
1 ATGGGGTATGAT-GTGTAAGATCATAACTCGACTA-TGCAACATAGAGAGTTAG-CAGGACATTA
* * * * * * * *
38750037 AACATGGGGTATGACGTGTAAAACTATAGTTCGACTATGACAACATAGAGAGTCTGTCAGGATAT
63 AACATAGGGTATGATGTGTAAGACCATAATTCGACTATGACAACATAGAGAGTCCGTCAAGACAT
38750102 TAAAC
128 TAAAC
* * * * *
38750107 ATGGGGTATGATGTGTAAGACCATAACTTGACTATGACAACATAAAGAGTTTGCCCGGACATTAA
1 ATGGGGTATGATGTGTAAGATCATAACTCGACTATG-CAACATAGAGAGTTAG-CAGGACATTAA
* * *
38750172 ACATATGGTATGATGTGTAAGACCATAATTTGATTATGACAACATAGAGAGTCCGTCAAGACATT
64 ACATAGGGTATGATGTGTAAGACCATAATTCGACTATGACAACATAGAGAGTCCGTCAAGACATT
*
38750237 AAAT
129 AAAC
* * * * * *
38750241 ATGGGGTATGATATGTAAGATCATATCTCGGCTATGGCAACATAGAGAGTCAGCTGAAACATTAA
1 ATGGGGTATGATGTGTAAGATCATAACTCGACTAT-GCAACATAGAGAGTTAGCAG-GACATTAA
*
38750306 AAATAGGGTATGATGTGTAAGACCAT
64 ACATAGGGTATGATGTGTAAGACCAT
38750332 GGCTCGGTTT
Statistics
Matches: 190, Mismatches: 31, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
133 4 0.02
134 183 0.96
135 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (132 bp):
ATGGGGTATGATGTGTAAGATCATAACTCGACTATGCAACATAGAGAGTTAGCAGGACATTAAAC
ATAGGGTATGATGTGTAAGACCATAATTCGACTATGACAACATAGAGAGTCCGTCAAGACATTAA
AC
Found at i:38752894 original size:19 final size:19
Alignment explanation
Indices: 38752868--38752905 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
38752858 TTTTCATATA
38752868 TATTTAATTT-TTCAAAAT
1 TATTTAATTTATTCAAAAT
38752886 TATTATAATTTATTCAAAAT
1 TATT-TAATTTATTCAAAAT
38752906 ACAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTAATTTATTCAAAAT
Found at i:38752903 original size:20 final size:18
Alignment explanation
Indices: 38752833--38752905 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
38752823 CACATTTTTT
* *
38752833 TTTAATCTTTTGAATATT-
1 TTTAAT-TTTTCAAAATTA
*
38752851 TTTATATTTTTC-ATATATA
1 TTTA-ATTTTTCAAAAT-TA
38752870 TTTAATTTTTCAAAATTA
1 TTTAATTTTTCAAAATTA
38752888 TTATAATTTATTCAAAAT
1 TT-TAATTT-TTCAAAAT
38752906 ACAAAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
17 4 0.09
18 20 0.43
19 15 0.32
20 8 0.17
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (18 bp):
TTTAATTTTTCAAAATTA
Found at i:38753071 original size:21 final size:24
Alignment explanation
Indices: 38753018--38753064 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
38753008 CTTAAAAATT
38753018 AAAATAAATTTAAAAATTTTCAAAA
1 AAAATAAATTT-AAAATTTTCAAAA
38753043 AAAATAAATTT-AAA-TTTCAAAA
1 AAAATAAATTTAAAATTTTCAAAA
38753065 GAATAAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 3 0.14
25 11 0.50
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAATAAATTTAAAATTTTCAAAA
Found at i:38762597 original size:10 final size:10
Alignment explanation
Indices: 38762582--38762637 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
38762572 ATAATTATTT
38762582 TTATATTAAA
1 TTATATTAAA
38762592 TTATATTAAA
1 TTATATTAAA
*
38762602 ATAT-TTAAA
1 TTATATTAAA
38762611 --ATATT---
1 TTATATTAAA
38762616 TTATATTAAA
1 TTATATTAAA
38762626 TTATATTTAAA
1 TTATA-TTAAA
38762637 T
1 T
38762638 CTTTCAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
7 7 0.18
8 2 0.05
9 5 0.13
10 18 0.47
11 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTATATTAAA
Found at i:38762619 original size:34 final size:34
Alignment explanation
Indices: 38762580--38762653 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
38762570 ATATAATTAT
38762580 TTTTATATTAAATTATATTAAAATATTTAAAATA
1 TTTTATATTAAATTATATTAAAATATTTAAAATA
* * *
38762614 TTTTATATTAAATTATATTTAAATCTTTCAAATA
1 TTTTATATTAAATTATATTAAAATATTTAAAATA
38762648 TTTTAT
1 TTTTAT
38762654 TTTTATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (34 bp):
TTTTATATTAAATTATATTAAAATATTTAAAATA
Found at i:38763689 original size:24 final size:24
Alignment explanation
Indices: 38763661--38763723 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
38763651 AGAAATAATC
38763661 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
38763685 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
38763709 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
38763724 CTGGATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:38766250 original size:29 final size:29
Alignment explanation
Indices: 38766176--38766260 Score: 98
Period size: 31 Copynumber: 2.8 Consensus size: 29
38766166 GATTAAATCA
* *
38766176 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAG-TTCATGTATACAATTGAACC
* * *
38766206 ACAATTAGAAATTCATGTATATAATTGTACC
1 A-AATTA-AAGTTCATGTATACAATTGAACC
38766237 AAATTAAAGTTCATGTATACAATT
1 AAATTAAAGTTCATGTATACAATT
38766261 ACACATTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 16 0.35
30 6 0.13
31 22 0.48
32 2 0.04
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (29 bp):
AAATTAAAGTTCATGTATACAATTGAACC
Found at i:38768273 original size:42 final size:41
Alignment explanation
Indices: 38768227--38768338 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 41
38768217 CATGTCAGCA
* *
38768227 AAAGCTCGTCCAACTGGACGTA-CTTTCCTGCCAATTGTGCAG
1 AAAGCTCG-CCAACTGGACG-AGCTTTCCAGACAATTGTGCAG
* * *
38768269 AAAGCTCGCCCAATTGGACGAGTTTTTCAGACAATTGTGCAG
1 AAAGCTCG-CCAACTGGACGAGCTTTCCAGACAATTGTGCAG
*
38768311 AAAACTCGCCTAACTGGACGAGCATTTC
1 AAAGCTCGCC-AACTGGACGAGC-TTTC
38768339 TATAACTGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 3 0.05
42 51 0.89
43 3 0.05
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (41 bp):
AAAGCTCGCCAACTGGACGAGCTTTCCAGACAATTGTGCAG
Found at i:38768370 original size:41 final size:41
Alignment explanation
Indices: 38768262--38768370 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 41
38768252 TCCTGCCAAT
* ** *
38768262 TGTGCAGAAAGCTCGCCCAATTGGACGAGTTTTTCAGACAAT
1 TGTGCAGAAAACTCG-CCAATTGGACGAGCATTTCAGACAAC
* * *
38768304 TGTGCAGAAAACTCGCCTAACTGGACGAGCATTTC-TATAAC
1 TGTGCAGAAAACTCGCC-AATTGGACGAGCATTTCAGACAAC
* *
38768345 TGTGCAGAAATCGCGTCCAATTGGAC
1 TGTGCAGAAAACTCG-CCAATTGGAC
38768371 ACTCTTTTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 25 0.45
42 30 0.55
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (41 bp):
TGTGCAGAAAACTCGCCAATTGGACGAGCATTTCAGACAAC
Found at i:38768854 original size:26 final size:27
Alignment explanation
Indices: 38768809--38768860 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
38768799 ATTTTTTTAA
38768809 AAAAATAAAAAAATATTTTTAAAAATT
1 AAAAATAAAAAAATATTTTTAAAAATT
* *
38768836 AAAAGTAATAAAATA-TTTTAAAAAT
1 AAAAATAAAAAAATATTTTTAAAAAT
38768861 ATTTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
AAAAATAAAAAAATATTTTTAAAAATT
Found at i:38769117 original size:71 final size:72
Alignment explanation
Indices: 38769012--38769153 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 72
38769002 ATTCTTTATT
*
38769012 TAGACATTAAAATATATAATAAACCTTTATGTTTGACTGGTTTTGGAGATATATTAAATGTTCTT
1 TAGACATTAAAATATATAATAAACCTTTATGTTTGACTGGTTTTGGAGATATATTAAACGTTCTT
38769077 TATCATA
66 TATCATA
* * ** *
38769084 TAGACATT-AAATTTATAATAAATCTTTATGTTTGGTTGGTTTTGGAGATATATTAAACGTTTTT
1 TAGACATTAAAATATATAATAAACCTTTATGTTTGACTGGTTTTGGAGATATATTAAACGTTCTT
38769148 TATCAT
66 TATCAT
38769154 TTGCCAAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 56 0.88
72 8 0.12
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (72 bp):
TAGACATTAAAATATATAATAAACCTTTATGTTTGACTGGTTTTGGAGATATATTAAACGTTCTT
TATCATA
Found at i:38772508 original size:9 final size:9
Alignment explanation
Indices: 38772494--38772520 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
38772484 TTAGGTTTAA
38772494 TATAATTAT
1 TATAATTAT
38772503 TATAATTAT
1 TATAATTAT
38772512 TATAATTAT
1 TATAATTAT
38772521 AGACAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATAATTAT
Found at i:38778889 original size:6 final size:6
Alignment explanation
Indices: 38778878--38778922 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
38778868 TGAGCAAAAT
* * * *
38778878 TGAAAG TGAAAG TGAAAG TGAAAA TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
38778923 TATGAATTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:38781057 original size:16 final size:16
Alignment explanation
Indices: 38781036--38781084 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
38781026 TACGAATATG
38781036 AACATGTATTTGTTTT
1 AACATGTATTTGTTTT
38781052 AACATGATATTT-TTTT
1 AACATG-TATTTGTTTT
* *
38781068 ATACTTGTTTTTGTTTT
1 A-ACATGTATTTGTTTT
38781085 TTATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.22, C:0.06, G:0.10, T:0.61
Consensus pattern (16 bp):
AACATGTATTTGTTTT
Found at i:38784182 original size:6 final size:6
Alignment explanation
Indices: 38784171--38784204 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
38784161 AGTAGCGATG
38784171 GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAG
1 GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAG
38784205 TAGTAGTCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.50, T:0.00
Consensus pattern (6 bp):
GCAGGA
Found at i:38787339 original size:31 final size:31
Alignment explanation
Indices: 38787304--38787362 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
38787294 ATCCGAATGA
* * *
38787304 TTGGTGATTTAAGTGAAAATTCTTAAATAAT
1 TTGGTGACTTAAATGAAAACTCTTAAATAAT
38787335 TTGGTGACTTAAATGAAAACTCTTAAAT
1 TTGGTGACTTAAATGAAAACTCTTAAAT
38787363 TCGAAATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (31 bp):
TTGGTGACTTAAATGAAAACTCTTAAATAAT
Found at i:38787541 original size:120 final size:120
Alignment explanation
Indices: 38787319--38787595 Score: 430
Period size: 120 Copynumber: 2.3 Consensus size: 120
38787309 GATTTAAGTG
* * * * * * *
38787319 AAAATTCTTAAATAATTTGGTGACTTAAATGAAAACTCTTAAATTCGAAATGATCTCAACTTCAA
1 AAAACTCTCAAATAATTTGATGATTTAAATGAAAACTCTCAAATCCGAAATAATCTCAACTTCAA
* * * *
38787384 AAAGTTACAAAATGATTACTGAATTATTCAAAGTTTTCATTTAGTCAGTTATATA
66 AAAGTTACAAAATGATTACTGAATTATTCAAAGTTTTCATTTAATCACTTAGAAA
*
38787439 AAAACTCTCAAATAATTCGATGATTTAAATGAAAACTCTCAAATCCGAAATAATC-CTAACTTCA
1 AAAACTCTCAAATAATTTGATGATTTAAATGAAAACTCTCAAATCCGAAATAATCTC-AACTTCA
38787503 AAAAGTTACAAAATGATTACTGAATTATTCAAAGTTTTCATTTAATCACTTAGAAA
65 AAAAGTTACAAAATGATTACTGAATTATTCAAAGTTTTCATTTAATCACTTAGAAA
38787559 AAAACTCTCAAATAATTTGATGATTTAAATGAAAACT
1 AAAACTCTCAAATAATTTGATGATTTAAATGAAAACT
38787596 TTCGAATAAT
Statistics
Matches: 143, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
119 1 0.01
120 142 0.99
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (120 bp):
AAAACTCTCAAATAATTTGATGATTTAAATGAAAACTCTCAAATCCGAAATAATCTCAACTTCAA
AAAGTTACAAAATGATTACTGAATTATTCAAAGTTTTCATTTAATCACTTAGAAA
Found at i:38788170 original size:22 final size:22
Alignment explanation
Indices: 38788144--38788194 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
38788134 ATTGAACCAA
38788144 ATTTTATAATTTTATAAT-ATTT
1 ATTTTATAATTTT-TAATAATTT
*
38788166 TTTTTGA-AATTTTTAATAATTT
1 ATTTT-ATAATTTTTAATAATTT
38788188 ATTTTAT
1 ATTTTAT
38788195 TTGAATGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 5 0.21
22 18 0.75
23 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTTATAATTTTTAATAATTT
Found at i:38790258 original size:2 final size:2
Alignment explanation
Indices: 38790251--38790276 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38790241 TTACAAAAGC
38790251 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
38790277 GAATCATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38791674 original size:16 final size:18
Alignment explanation
Indices: 38791638--38791675 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
38791628 GTATTACTTT
*
38791638 TAAAAAGTATTTTTGAGA
1 TAAAAAGTATTTTTGAAA
38791656 TAAAAA-TATTTTT-AAA
1 TAAAAAGTATTTTTGAAA
38791672 TAAA
1 TAAA
38791676 CTGTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 7 0.37
18 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAAAAAGTATTTTTGAAA
Found at i:38795052 original size:23 final size:22
Alignment explanation
Indices: 38795025--38795077 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 22
38795015 GATATTTTTA
38795025 AATTAAATAATAAAATCAAATTT
1 AATTAAAT-ATAAAATCAAATTT
38795048 AA-T---TATAAAATCAAATTT
1 AATTAAATATAAAATCAAATTT
38795066 AATTAAAT-TAAA
1 AATTAAATATAAA
38795078 CCATTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 16 0.62
19 2 0.08
21 4 0.15
22 2 0.08
23 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTAAATATAAAATCAAATTT
Found at i:38795055 original size:18 final size:18
Alignment explanation
Indices: 38795024--38795070 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
38795014 CGATATTTTT
* *
38795024 AAATTAAATAATAAAATC
1 AAATTTAATTATAAAATC
38795042 AAATTTAATTATAAAATC
1 AAATTTAATTATAAAATC
38795060 AAATTTAATTA
1 AAATTTAATTA
38795071 AATTAAACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTTAATTATAAAATC
Found at i:38799560 original size:23 final size:22
Alignment explanation
Indices: 38799508--38799561 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
38799498 TGACACTTTT
38799508 ATATTA-AAATTAAATTAAAAA
1 ATATTATAAATTAAATTAAAAA
**
38799529 ATAGAATAAATTACAATTAAAATA
1 ATATTATAAATTA-AATTAAAA-A
38799553 A-ATTATAAA
1 ATATTATAAA
38799562 AAGTAAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.15
22 6 0.23
23 14 0.54
24 2 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
ATATTATAAATTAAATTAAAAA
Found at i:38800083 original size:13 final size:12
Alignment explanation
Indices: 38800074--38800104 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
38800064 TTCTATTATT
38800074 ATTTTATATTTA
1 ATTTTATATTTA
38800086 ATTATTATATTTA
1 ATT-TTATATTTA
38800099 ATTTTA
1 ATTTTA
38800105 AAGATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTATATTTA
Found at i:38800091 original size:18 final size:18
Alignment explanation
Indices: 38800068--38800102 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38800058 ACTTTTTTCT
38800068 ATTATTAT-TTTATATTTA
1 ATTATTATATTTA-ATTTA
38800086 ATTATTATATTTAATTT
1 ATTATTATATTTAATTT
38800103 TAAAGATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTATTATATTTAATTTA
Found at i:38802940 original size:30 final size:31
Alignment explanation
Indices: 38802898--38802993 Score: 103
Period size: 30 Copynumber: 3.2 Consensus size: 31
38802888 TCACGAGGGC
38802898 AAAATGGTAATTTTCGGTGAAATCGAGGTCG
1 AAAATGGTAATTTTCGGTGAAATCGAGGTCG
** *
38802929 AAAATGG-AATTTT-GG-GAAATTTAGG-GG
1 AAAATGGTAATTTTCGGTGAAATCGAGGTCG
* *
38802956 TAAAATGGTAATTTTC-GTGAAATCGAAGTCA
1 -AAAATGGTAATTTTCGGTGAAATCGAGGTCG
38802987 AAAATGG
1 AAAATGG
38802994 AATCTTGGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
27 1 0.02
28 15 0.29
29 9 0.17
30 20 0.38
31 7 0.13
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.29
Consensus pattern (31 bp):
AAAATGGTAATTTTCGGTGAAATCGAGGTCG
Found at i:38803014 original size:58 final size:58
Alignment explanation
Indices: 38802898--38803347 Score: 557
Period size: 58 Copynumber: 7.7 Consensus size: 58
38802888 TCACGAGGGC
* ** * * *
38802898 AAAATGGTAATTTTCGGTGAAATCGAGGTCGAAAATGGAATTTTGGGAAA-TTTAGGGGT
1 AAAATGGTAATTTT-GATGAAATCGAGGTTAAAAATGGAATCTT-AGAAAGTTTGGGGGT
* * * *
38802957 AAAATGGTAATTTTCG-TGAAATCGAAGTCAAAAATGGAATCTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTT-GATGAAATCGAGGTTAAAAATGGAATCTTAGAAAGTTTGGGGGT
* * * *
38803015 AAAATGTTAATTTTTATGAAATTGGGGTTAAAAATGGAATCTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATCTTAGAAAGTTTGGGGGT
*
38803073 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATCTTAGAAAGTTTGGGGGT
* * * *
38803131 AAAATGGTAATTTTGATAAAATTGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATCTTAGAAAGTTTGGGGGT
* * * * *
38803189 AAAATGGTAATTTTTGGTGAAACCAAGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGT
1 AAAATGGTAA-TTTTGATGAAATCGAGGTTAAAAATGGAATCTTAGAAAGTTTGGGGGT
* * * *
38803248 AAAATGGTAATTTTGATAAAATCGGGGTT-AAAATGGAATTTTAGAAAGTTTAGGGGT
1 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATCTTAGAAAGTTTGGGGGT
* *
38803305 AAAATGGTAGTTTTGATGAAATTTG-GGTTAAAAATGGAATCTT
1 AAAATGGTAATTTTGATGAAA-TCGAGGTTAAAAATGGAATCTT
38803348 GGAATAATTC
Statistics
Matches: 345, Mismatches: 41, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
57 54 0.16
58 226 0.66
59 65 0.19
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATCTTAGAAAGTTTGGGGGT
Found at i:38803046 original size:29 final size:28
Alignment explanation
Indices: 38803001--38803203 Score: 137
Period size: 29 Copynumber: 7.0 Consensus size: 28
38802991 TGGAATCTTG
38803001 GAAAGTTCGGGGGTAAAATGTTAATTTTTA
1 GAAAGTT-GGGGGTAAAATG-TAATTTTTA
* * *
38803031 TGAAA-TTGGGGTTAAAAATGGAA-TCTTA
1 -GAAAGTTGGGGGT-AAAATGTAATTTTTA
*
38803059 GAAAGTTTGGGGGTAAAATGGTAATTTTGA
1 GAAAG-TTGGGGGTAAAAT-GTAATTTTTA
* * * *
38803089 TGAAA-TCGAGGTTAAAAATGGAA-TTTTA
1 -GAAAGTTGGGGGT-AAAATGTAATTTTTA
*
38803117 GAAAGTTTGGGGGTAAAATGGTAATTTTGA
1 GAAAG-TTGGGGGTAAAAT-GTAATTTTTA
* * * *
38803147 TAAAATTGGGGTTAAAAATGGAA-TTTTA
1 GAAAGTTGGGGGT-AAAATGTAATTTTTA
38803175 GAAAGTTTGGGGGTAAAATGGTAATTTTT
1 GAAAG-TTGGGGGTAAAAT-GTAATTTTT
38803204 GGTGAAACCA
Statistics
Matches: 131, Mismatches: 26, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
27 8 0.06
28 30 0.23
29 53 0.40
30 32 0.24
31 8 0.06
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.34
Consensus pattern (28 bp):
GAAAGTTGGGGGTAAAATGTAATTTTTA
Found at i:38803110 original size:174 final size:173
Alignment explanation
Indices: 38802898--38803351 Score: 617
Period size: 174 Copynumber: 2.6 Consensus size: 173
38802888 TCACGAGGGC
* * *
38802898 AAAATGGTAATTTTCGGTGAAATCGAGGTCGAAAATGGAATTTTGGGAAA-TTTAGGGGTAAAAT
1 AAAATGGTAATTTT-GATGAAATCGAGGT-TAAAATGGAATTTT-AGAAAGTTTAGGGGTAAAAT
* * * *
38802962 GGTAATTTTCG-TGAAATCGAAGTCAAAAATGGAATCTTGGAAAGTTCGGGGGTAAAATGTTAAT
63 GGTAATTTT-GATGAAATTG-GGTTAAAAATGGAATCTTGGAAAGTTCGGGGGTAAAATGGTAAT
**** *
38803026 TTTT-ATGAAATTGGGGTTAAAAATGGAATCTTAGAAAGTTTGGGGGT
126 TTTTGATGAAACCAAGGTTAAAAATGGAATCTTAGAAAGTTTAGGGGT
*
38803073 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGG
1 AAAATGGTAATTTTGATGAAATCGAGGTT-AAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGG
* * * *
38803138 TAATTTTGATAAAATTGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTT
65 TAATTTTGATGAAATT-GGGTTAAAAATGGAATCTTGGAAAGTTCGGGGGTAAAATGGTAATTTT
* *
38803203 TGGTGAAACCAAGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGT
129 TGATGAAACCAAGGTTAAAAATGGAATCTTAGAAAGTTTAGGGGT
* *
38803248 AAAATGGTAATTTTGATAAAATCGGGGTTAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGT
1 AAAATGGTAATTTTGATGAAATCGAGGTTAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGT
*
38803313 AGTTTTGATGAAATTTGGGTTAAAAATGGAATCTTGGAA
66 AATTTTGATGAAA-TTGGGTTAAAAATGGAATCTTGGAA
38803352 TAATTCAGGG
Statistics
Matches: 247, Mismatches: 26, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
173 5 0.02
174 162 0.66
175 80 0.32
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.32
Consensus pattern (173 bp):
AAAATGGTAATTTTGATGAAATCGAGGTTAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGT
AATTTTGATGAAATTGGGTTAAAAATGGAATCTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTG
ATGAAACCAAGGTTAAAAATGGAATCTTAGAAAGTTTAGGGGT
Found at i:38803714 original size:98 final size:98
Alignment explanation
Indices: 38803493--38803702 Score: 260
Period size: 98 Copynumber: 2.1 Consensus size: 98
38803483 GTTGAATTAG
* * * * *
38803493 GGATTAGATTAAAACAAATTAAAAATAAAAGGTACTAATTGCACAAATAAGCCAAAATAGTGCTA
1 GGATTAAATTAAAATAAATTAAAAATAAAAGGGACTAATTGCACAAATAAGCCAAAACAATGCTA
* *
38803558 CGTGGCAACCTCTGATGCATTCAAAAAGTTAAA
66 CGTGGCAACCTCTGATGCAGTCAAAAAGTCAAA
* * * *
38803591 GGATTAAATTAAAATAAATTAAAAATAAAAGGGACTAATTTCATAGATATGCCAAAACAATGAC-
1 GGATTAAATTAAAATAAATTAAAAATAAAAGGGACTAATTGCACAAATAAGCCAAAACAATG-CT
** * *
38803655 ACGTGGCGGCCTCTGGTGCAGTCAAACAGTCAAA
65 ACGTGGCAACCTCTGATGCAGTCAAAAAGTCAAA
*
38803689 GGATTAATTTAAAA
1 GGATTAAATTAAAA
38803703 ACCAATCAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
98 94 0.99
99 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.24
Consensus pattern (98 bp):
GGATTAAATTAAAATAAATTAAAAATAAAAGGGACTAATTGCACAAATAAGCCAAAACAATGCTA
CGTGGCAACCTCTGATGCAGTCAAAAAGTCAAA
Found at i:38805257 original size:6 final size:6
Alignment explanation
Indices: 38805210--38805314 Score: 67
Period size: 6 Copynumber: 18.0 Consensus size: 6
38805200 TTTTGGGCTT
* * * *
38805210 TTTAAT TTTAAT TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
** * * *
38805256 TTTAAA AATGAA TTTAAA TTTAAA TTTAAA -GTAAA TTTAAT TTTAGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA
*
38805304 -ATAAA TTTAAA
1 TTTAAA TTTAAA
38805315 AATCATTTTA
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
4 3 0.04
5 10 0.13
6 57 0.76
7 5 0.07
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:38805258 original size:35 final size:35
Alignment explanation
Indices: 38805213--38805279 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
38805203 TGGGCTTTTT
* * *
38805213 AATTTTAATTTTAAAAT-TATTTCAAATTTAAACTA
1 AATTTAAATTTAAAAATGAATTT-AAATTTAAACTA
38805248 AATTTAAATTTAAAAATGAATTTAAATTTAAA
1 AATTTAAATTTAAAAATGAATTTAAATTTAAA
38805280 TTTAAAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (35 bp):
AATTTAAATTTAAAAATGAATTTAAATTTAAACTA
Found at i:38805281 original size:41 final size:42
Alignment explanation
Indices: 38805231--38805340 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 42
38805221 TTTTAAAATT
*
38805231 ATTTCAAATTTAAACTAAATTTAAATTTAAAAATGAATTTAA
1 ATTTCAAATTTAAACTAAATTTAAATTTAAAAATAAATTTAA
* * *
38805273 ATTT-AAATTTAAAGTAAATTTAATTTTAGAAATAAATTTAA
1 ATTTCAAATTTAAACTAAATTTAAATTTAAAAATAAATTTAA
** * *
38805314 AAATC-ATTTTAAACTTAAATTAAAATT
1 ATTTCAAATTTAAAC-TAAATTTAAATT
38805341 GACCCAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
41 42 0.75
42 14 0.25
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.42
Consensus pattern (42 bp):
ATTTCAAATTTAAACTAAATTTAAATTTAAAAATAAATTTAA
Found at i:38805292 original size:17 final size:18
Alignment explanation
Indices: 38805270--38805314 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
38805260 AAAATGAATT
*
38805270 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
38805287 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
38805305 TAAATTTAAA
1 TAAATTTAAA
38805315 AATCATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:38805332 original size:24 final size:24
Alignment explanation
Indices: 38805246--38805338 Score: 75
Period size: 24 Copynumber: 3.7 Consensus size: 24
38805236 AAATTTAAAC
38805246 TAAATTTAAATTTAAAAATGAA-TT
1 TAAATTTAAATTTAAAAAT-AATTT
38805270 TAAATTTAAATTTAAAGTAAATTTAATTT
1 TAAATTTAAATTT-AA--AAA--TAATTT
* *
38805299 TAGAA-ATAAATTTAAAAATCATTT
1 TA-AATTTAAATTTAAAAATAATTT
*
38805323 TAAACTTAAA-TTAAAA
1 TAAATTTAAATTTAAAA
38805339 TTGACCCAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
23 8 0.14
24 24 0.41
25 2 0.03
26 3 0.05
27 3 0.05
28 4 0.07
29 12 0.21
30 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (24 bp):
TAAATTTAAATTTAAAAATAATTT
Found at i:38807711 original size:13 final size:13
Alignment explanation
Indices: 38807693--38807742 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
38807683 TTAAACCAAG
38807693 CTTTTCAAAAGTA
1 CTTTTCAAAAGTA
38807706 CTTTTCAAAA-TCA
1 CTTTTCAAAAGT-A
*
38807719 CTTTTTAAAAGTA
1 CTTTTCAAAAGTA
*
38807732 CTTCTCAAAAG
1 CTTTTCAAAAG
38807743 CAATACTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 1 0.03
13 30 0.94
14 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (13 bp):
CTTTTCAAAAGTA
Found at i:38812531 original size:29 final size:30
Alignment explanation
Indices: 38812499--38812557 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
38812489 TTCATTCAGA
* *
38812499 AAATTATACA-AAATTAAAATTCATATATG
1 AAATTAGACATAAACTAAAATTCATATATG
*
38812528 AAATTAGACATTAAACTAAAATTTATATAT
1 AAATTAGACA-TAAACTAAAATTCATATAT
38812558 AATTTTAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
31 16 0.64
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (30 bp):
AAATTAGACATAAACTAAAATTCATATATG
Found at i:38818823 original size:30 final size:30
Alignment explanation
Indices: 38818789--38818850 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
38818779 CAACTTAACA
*
38818789 AACAAATACCTCTAAAATAGTAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
* *
38818819 AACAAATGCCTCTAAAATAATAACAAATTT
1 AACAAATACCTCTAAAATAATAACAAAATT
38818849 AA
1 AA
38818851 TAGTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
AACAAATACCTCTAAAATAATAACAAAATT
Found at i:38823088 original size:26 final size:26
Alignment explanation
Indices: 38823059--38823133 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 26
38823049 TGTCTTCTTC
38823059 TTTTTTCTTTTTCTTTTTTTTTCCAA
1 TTTTTTCTTTTTCTTTTTTTTTCCAA
** *
38823085 TTTTTT-TCAATTC-TTTTTTTT-CAT
1 TTTTTTCT-TTTTCTTTTTTTTTCCAA
*
38823109 TTTTTTCTTTTCGACTTTTTTTTTC
1 TTTTTTCTTTT--TCTTTTTTTTTC
38823134 TAAATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
24 9 0.24
25 10 0.27
26 10 0.27
27 8 0.22
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (26 bp):
TTTTTTCTTTTTCTTTTTTTTTCCAA
Found at i:38823114 original size:13 final size:14
Alignment explanation
Indices: 38823085--38823132 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
38823075 TTTTTTCCAA
*
38823085 TTTTTTTCAATTCT
1 TTTTTTTCAATTTT
38823099 TTTTTTTC-ATTTT
1 TTTTTTTCAATTTT
*
38823112 TTTCTTTTCGACTTTT
1 TTT-TTTTC-AATTTT
38823128 TTTTT
1 TTTTT
38823133 CTAAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 7 0.24
14 13 0.45
15 2 0.07
16 7 0.24
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTTTCAATTTT
Done.