Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001736.1 Hibiscus syriacus cultivar Beakdansim tig00003507_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: 1778036
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1290375 original size:19 final size:19
Alignment explanation
Indices: 1290351--1290394 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1290341 AAATTTCATT
*
1290351 ACATAATTCTATCATTACA
1 ACATAATACTATCATTACA
*
1290370 ACATAATACTATCATTATA
1 ACATAATACTATCATTACA
1290389 ACATAA
1 ACATAA
1290395 CACCCACCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (19 bp):
ACATAATACTATCATTACA
Found at i:1297770 original size:2 final size:2
Alignment explanation
Indices: 1297763--1297809 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1297753 ATAATCCATG
1297763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1297805 TA TA T
1 TA TA T
1297810 TTCATTGGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1305339 original size:23 final size:23
Alignment explanation
Indices: 1305312--1305355 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1305302 AGAAAGACCG
1305312 CATAGAAATGCACCGAAGTACCA
1 CATAGAAATGCACCGAAGTACCA
* *
1305335 CATAGAATTGCACCGTAGTAC
1 CATAGAAATGCACCGAAGTAC
1305356 TATATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTACCA
Found at i:1305631 original size:30 final size:30
Alignment explanation
Indices: 1305597--1305659 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
1305587 TTATATCGCG
1305597 TAGACATATTATTTGCATACCTTTATCACA
1 TAGACATATTATTTGCATACCTTTATCACA
*
1305627 TAGACATATTATTTTCATACCTTTATCACA
1 TAGACATATTATTTGCATACCTTTATCACA
1305657 TAG
1 TAG
1305660 CTCATATAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.41
Consensus pattern (30 bp):
TAGACATATTATTTGCATACCTTTATCACA
Found at i:1307491 original size:80 final size:80
Alignment explanation
Indices: 1307390--1307559 Score: 279
Period size: 80 Copynumber: 2.1 Consensus size: 80
1307380 TTCCCTAACT
** *
1307390 TTTTCTTCCACATCTTGAATCAAATCCGGACCAAGAATACTTCGATCTTTGA-GTTCATACCAGT
1 TTTTCTTCCACATCTTGAATCAAATCCAAACCAAGAACACTTCGATCTTT-ATGTTCATACCAGT
*
1307454 TCAATGGCGTACGATA
65 TCAATGGCGTACGACA
*
1307470 TTTTCTTCCACATCTTGAATCAAATCCAAACTAAGAACACTTCGATCTTTATGTTCATACCAGTT
1 TTTTCTTCCACATCTTGAATCAAATCCAAACCAAGAACACTTCGATCTTTATGTTCATACCAGTT
1307535 CAATGGCGTACGACA
66 CAATGGCGTACGACA
1307550 TTTTCTTCCA
1 TTTTCTTCCA
1307560 TATAAATCCT
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
79 1 0.01
80 83 0.99
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (80 bp):
TTTTCTTCCACATCTTGAATCAAATCCAAACCAAGAACACTTCGATCTTTATGTTCATACCAGTT
CAATGGCGTACGACA
Found at i:1311898 original size:21 final size:21
Alignment explanation
Indices: 1311872--1311911 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1311862 TACTACAGTA
*
1311872 CTACAGTGCATCGATGCATTG
1 CTACAGTGCACCGATGCATTG
1311893 CTACAGTGCACCGATGCAT
1 CTACAGTGCACCGATGCAT
1311912 AAAACTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (21 bp):
CTACAGTGCACCGATGCATTG
Found at i:1312806 original size:30 final size:30
Alignment explanation
Indices: 1312770--1312832 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1312760 TCATATAGCG
* *
1312770 TAGACATATTATTTCTATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
1312800 TAGACATATCATTTCCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
1312830 TAG
1 TAG
1312833 CTTATATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (30 bp):
TAGACATATCATTTCCATACCTTTATCACA
Found at i:1317845 original size:24 final size:25
Alignment explanation
Indices: 1317800--1317856 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
1317790 TCAAAACTGT
* *
1317800 CACGTAGAATTTTGCACTGAAGTGC
1 CACGTAGAATTATGCACCGAAGTGC
*
1317825 CACGTAGAA-TATGCACCGAAGTTC
1 CACGTAGAATTATGCACCGAAGTGC
*
1317849 CACATAGA
1 CACGTAGA
1317857 TTTGTCCCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (25 bp):
CACGTAGAATTATGCACCGAAGTGC
Found at i:1321083 original size:2 final size:2
Alignment explanation
Indices: 1321076--1321104 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1321066 ACATTATGCA
1321076 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 A
1321105 AAGATCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1322590 original size:21 final size:21
Alignment explanation
Indices: 1322564--1322606 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1322554 CTGAATTAAT
1322564 TATGAAGCTTTTATCCAAGTA
1 TATGAAGCTTTTATCCAAGTA
*
1322585 TATGAAGCTTTTATCTAAGTA
1 TATGAAGCTTTTATCCAAGTA
1322606 T
1 T
1322607 CTGCACTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (21 bp):
TATGAAGCTTTTATCCAAGTA
Found at i:1322995 original size:25 final size:25
Alignment explanation
Indices: 1322961--1323015 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
1322951 GTATGCATGC
1322961 ATGCATCTTGGGTTGCAGTTCATAT
1 ATGCATCTTGGGTTGCAGTTCATAT
1322986 ATGCATCTTGGGTTGCAGTTCATAT
1 ATGCATCTTGGGTTGCAGTTCATAT
1323011 ATGCA
1 ATGCA
1323016 GTTCTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (25 bp):
ATGCATCTTGGGTTGCAGTTCATAT
Found at i:1324037 original size:2 final size:2
Alignment explanation
Indices: 1324030--1324071 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1324020 TTTCAAAAGT
1324030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1324072 GATGAGTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1324685 original size:9 final size:11
Alignment explanation
Indices: 1324647--1324685 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1324637 AAAAAGTATA
1324647 TTTAT-AATAT
1 TTTATAAATAT
1324657 TTTATAAATAT
1 TTTATAAATAT
1324668 TTTATAAAT-T
1 TTTATAAATAT
1324678 TTTA-AAAT
1 TTTATAAAT
1324686 CAAATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 4 0.14
10 10 0.36
11 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTATAAATAT
Found at i:1324853 original size:26 final size:23
Alignment explanation
Indices: 1324833--1324911 Score: 106
Period size: 23 Copynumber: 3.4 Consensus size: 23
1324823 GATAATTTTA
1324833 AAATAATATTATTTCAAATAATT
1 AAATAATATTATTTCAAATAATT
* *
1324856 AATTAATATTATTTCAAATAAAT
1 AAATAATATTATTTCAAATAATT
* *
1324879 AAATAATATGATTTTAAA-AATT
1 AAATAATATTATTTCAAATAATT
1324901 AAATAAATATT
1 AAAT-AATATT
1324912 TTAAAATAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.15
23 41 0.85
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (23 bp):
AAATAATATTATTTCAAATAATT
Found at i:1324914 original size:20 final size:20
Alignment explanation
Indices: 1324802--1324917 Score: 69
Period size: 23 Copynumber: 5.6 Consensus size: 20
1324792 GGTTCTATAC
*
1324802 AATATTATTTAAAATTAAATA
1 AATATT-TTAAAAATTAAATA
*
1324823 GATAATTTT-AAAA-T-AAT-
1 AAT-ATTTTAAAAATTAAATA
* * *
1324840 ATTATTTCAAATAATTAATTA
1 AATATTTTAAA-AATTAAATA
* *
1324861 ATATTATTTCAAATAAATAAATA
1 A-A-TATTTTAAA-AATTAAATA
1324884 ATATGATTTTAAAAATTAAATA
1 A-AT-ATTTTAAAAATTAAATA
1324906 AATATTTTAAAA
1 AATATTTTAAAA
1324918 TAATTCAGAT
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
16 4 0.05
17 3 0.04
18 5 0.07
19 2 0.03
20 15 0.20
21 7 0.09
22 13 0.17
23 27 0.36
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AATATTTTAAAAATTAAATA
Found at i:1325328 original size:2 final size:2
Alignment explanation
Indices: 1325321--1325376 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1325311 ATCATAGATC
1325321 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1325363 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
1325377 TCCCTTCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1328697 original size:10 final size:11
Alignment explanation
Indices: 1328669--1328695 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1328659 AATGTTAAGG
1328669 AAAAAATTAAA
1 AAAAAATTAAA
1328680 AAAAAATTAAA
1 AAAAAATTAAA
1328691 AAAAA
1 AAAAA
1328696 TTCATACCCA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:1335333 original size:21 final size:20
Alignment explanation
Indices: 1335307--1335356 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1335297 ACTCATAAGG
1335307 GTATCGATACT-TGACCCTAGA
1 GTATCGATACTAT-A-CCTAGA
*
1335328 GTATCGATACTATAGCTAGA
1 GTATCGATACTATACCTAGA
1335348 GTATCGATA
1 GTATCGATA
1335357 TTACCCACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.52
21 12 0.44
22 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (20 bp):
GTATCGATACTATACCTAGA
Found at i:1342816 original size:21 final size:21
Alignment explanation
Indices: 1342790--1342829 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1342780 CCCCCTTTGA
*
1342790 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1342811 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1342830 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1345523 original size:21 final size:21
Alignment explanation
Indices: 1345493--1345532 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1345483 AGAATGCTCG
1345493 GAGGGAACCGATTCCCCCCAA
1 GAGGGAACCGATTCCCCCCAA
*
1345514 GAGGGTACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
1345533 TGTTCAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.40, G:0.25, T:0.12
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAA
Found at i:1346823 original size:14 final size:15
Alignment explanation
Indices: 1346799--1346832 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1346789 TTTATAAAAT
1346799 GAAATATATTTCCTG
1 GAAATATATTTCCTG
*
1346814 GAAA-ATATTTTCTG
1 GAAATATATTTCCTG
1346828 GAAAT
1 GAAAT
1346833 CATTTTACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (15 bp):
GAAATATATTTCCTG
Found at i:1347747 original size:20 final size:20
Alignment explanation
Indices: 1347730--1347787 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1347720 ACATTCTAGG
1347730 ATCTTTCAAAATATTCTAAA
1 ATCTTTCAAAATATTCTAAA
* *
1347750 ATGTTTCAAAGTATTCTAAA
1 ATCTTTCAAAATATTCTAAA
*
1347770 A-CTTTTCATAATATTCTA
1 ATC-TTTCAAAATATTCTA
1347788 TATCCTTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (20 bp):
ATCTTTCAAAATATTCTAAA
Found at i:1349898 original size:24 final size:24
Alignment explanation
Indices: 1349871--1349924 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1349861 CAGTCGAAAC
* *
1349871 TGCCGCGTAGAATTTGCACCAAAG
1 TGCCACGTAGAATATGCACCAAAG
*
1349895 TGCCACGTAGAATATGCACCGAAG
1 TGCCACGTAGAATATGCACCAAAG
1349919 TGCCAC
1 TGCCAC
1349925 ATATATTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.19
Consensus pattern (24 bp):
TGCCACGTAGAATATGCACCAAAG
Found at i:1349973 original size:46 final size:47
Alignment explanation
Indices: 1349900--1349999 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 47
1349890 CAAAGTGCCA
* *
1349900 CGTAGAATATGCACCGAAGTGCCACATATATTTGTCCTGAAGGATCG
1 CGTAGAATATGCACCGAAGTGCCACATAGAATTGTCCTGAAGGATCG
1349947 CGTAGAATTAT-C-CCGAAG-GACCACATAGAATTGTCCTGAAGGATCG
1 CGTAGAA-TATGCACCGAAGTG-CCACATAGAATTGTCCTGAAGGATCG
1349993 CGTAGAA
1 CGTAGAA
1350000 CCCTCGACTC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
45 1 0.02
46 37 0.76
47 8 0.16
48 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (47 bp):
CGTAGAATATGCACCGAAGTGCCACATAGAATTGTCCTGAAGGATCG
Found at i:1349998 original size:23 final size:23
Alignment explanation
Indices: 1349931--1349999 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1349921 CCACATATAT
1349931 TTGTCCTGAAGGATCGCGTAGAA
1 TTGTCCTGAAGGATCGCGTAGAA
* * * * *
1349954 TTATCCCGAAGGACCACATAGAA
1 TTGTCCTGAAGGATCGCGTAGAA
1349977 TTGTCCTGAAGGATCGCGTAGAA
1 TTGTCCTGAAGGATCGCGTAGAA
1350000 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.23
Consensus pattern (23 bp):
TTGTCCTGAAGGATCGCGTAGAA
Found at i:1358985 original size:2 final size:2
Alignment explanation
Indices: 1358978--1359036 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1358968 AAATAACGAT
1358978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1359020 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1359037 TAAAGATAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1359055 original size:713 final size:718
Alignment explanation
Indices: 1357623--1360073 Score: 2384
Period size: 713 Copynumber: 3.3 Consensus size: 718
1357613 CATAAAAATT
* * * * * *
1357623 TTATTGGATGGATCAATAAAAATATAAT-AAAAATTGCATAATATCAAAAAATAGGCCATTACGT
1 TTATTGGGTGGACCAATAAAACTATAATAAAAAATTGTATAATATC-AAAAATAGCCCATAACGT
* * *
1357687 TTACTAAAAT-AGTCATTTTGACCCCTATTCA-TTTTTGGAGCATTTTGGCTCCTAATGTTTCAC
65 TTACTAAAATGA-TCATTTTGACCCTTATTCATTTTTTGGAGCATTTTGGCCCCCAATGTTTCAC
*
1357750 TTTAGGGCAAAAAGCTCCCTCTATAAGTGAAAATCATTAGTTAACACATAATTAACA-TTCTAAA
129 TTTAGGGCAAAAAGCTCCCTCTAT-AGTGAAAATCATTAGTTAACACACAATTAACACTT-TAAA
* * * * *
1357814 ATTGAAGCATTTTTAGCCTCAAATTAAACGTTAAGGGCTAAATGCCCAAGAAAAAAGAAAAAAGA
192 ATAGAAGCATTTTTAGCCTTAAATTAAACATTGAGGGCTAAAAGCCC-----------AAAAA-A
* * * * * *
1357879 AAAAATGGACAAAATGATTATTCAGTCAAATGTTATGAGTCTTTTTATCCTAAAA-CAAATTTTG
245 AATAATGGACAAAGTGATTATTCTGTCAAATGTTAAGGGTCTTTTTATCCTAAAATGAAATTTTG
*
1357943 GGGTCAATTTGCTTCAAAAATATAATATGAGACAAAATGACCATTTTAATAAATGTTGAGGGCTA
310 GGGTCAAATTGCTTCAAAAATA-AATATGAGACAAAATGACCATTTTAATAAATGTTGAGGGCTA
* *
1358008 ATTTTGGA-ATTATACATAAAATATTTATCTTAGCATAATTTGTATGCATTTTTAAATTTTTAAA
374 ATTTT-GATATTATACATAAAA-AATTATCTTAGCATAATTTGTATGCATTTTTAAATTTTAAAA
* * **
1358072 TATAA-AAAATAATATATACTTAGACTTAATCTAAAAATATATATATTAGGCCAATATAATTTTT
437 TACAATAAAATAATATATATTTAGACTTAATCTAAAAATATATATACCAGGCCAATATAATTTTT
*
1358136 AATATAATTTATATTTTATTTAAAATATATTTTAACTTTTTAGATTTTTTAAAACATA-GG-GGG
502 AATATAATTTATATTTTATTTAAAATATATTTTAATTTTTTAGATTTTTTAAAACATAGGGTGGG
* * * * ** * *
1358199 ACATAGCCTAGGTAGGCCCATCTCTAAATACGCTACTTTGAATAATGAGTCATGTCCAATAACGA
567 ACATAGCCTAGGTAGGCCCATCCCTAGATAAGCAACTACGAACAATGAGTCATGTCAAATAACGA
* * *
1358264 ATTTATATATACATATATTAAAAATAAGGTAAAAATTCTAACAAGTTTAACGAACAATCAATGGC
632 ATTTATATATACATATATTAAAAATAA-GTAAAAATTATAACAAGTATAACGAACAATCAA--GA
1358329 GAAT---A-AAA-A-AA-A-T-T-A
694 GAATAAGATAAACACAATAGTGTAA
***
1358344 -TATTGGGTGGACCAATAAAACTATAATAAATTTTTTTTGTATAATATCAAAAATAGCCCATAAC
1 TTATTGGGTGGACCAATAAAACTATAATAAA---AAATTGTATAATATCAAAAATAGCCCATAAC
* ** *
1358408 ATTTAGGAAAATGATCATTTTGACCCTTATTCATTTTTTAGAGCATTTTGGCCCCCAATGTTTCA
63 GTTTACTAAAATGATCATTTTGACCCTTATTCATTTTTTGGAGCATTTTGGCCCCCAATGTTTCA
** *
1358473 CTTTAGGATAAAAAACTCCCTCTATAGTTGAAAATCATTAGTTAACACACAATTAACACTTTAAA
128 CTTTAGGGCAAAAAGCTCCCTCTATAG-TGAAAATCATTAGTTAACACACAATTAACACTTTAAA
*
1358538 ATAGAAGCATTTTTAACCTTAAATTAAACATTGAGGGCTAAAAGCCC-AAAAAAATAATGGACAA
192 ATAGAAGCATTTTTAGCCTTAAATTAAACATTGAGGGCTAAAAGCCCAAAAAAAATAATGGACAA
* * *
1358602 AGTGATTATTTTGTCAAATGTTAGGGGTTTTTTTATCCTAAAATGAAATTTTGGGGGTCAAATTG
257 AGTGATTATTCTGTCAAATGTTAAGGGTCTTTTTATCCTAAAATGAAATTTT-GGGGTCAAATTG
* * * *
1358667 CTTCAAAAATAAATTATGAGACAAAATGATCATTTTATTAAATGTTGAGGACTAATTTTGATACT
321 CTTCAAAAATAAA-TATGAGACAAAATGACCATTTTAATAAATGTTGAGGGCTAATTTTGATATT
* *
1358732 ATACATAAACAAATTATCTTAG-ATAATTT-TATGCGTTTTTAAATTTTAAAATACAATGAAATA
385 ATACATAAA-AAATTATCTTAGCATAATTTGTATGCATTTTTAAATTTTAAAATACAATAAAATA
* * * *
1358795 ATATATATTTAGACTTAATCTAAAAATGTATATACCAGGCCAATATAACTTGTAACATAATTTAT
449 ATATATATTTAGACTTAATCTAAAAATATATATACCAGGCCAATATAATTTTTAATATAATTTAT
*
1358860 ATTTTATTTAAAATATATTTTAATTTTTTATA-TTTTTAAAACATAGGGTGGGACATAGCCTAGG
514 ATTTTATTTAAAATATATTTTAATTTTTTAGATTTTTTAAAACATAGGGTGGGACATAGCCTAGG
* * *
1358924 TAGGCCCATCCCTAGATAAACAACTCCGAACAATGAGTCGTGTCAAATAACG-ATTATATATATA
579 TAGGCCCATCCCTAGATAAGCAACTACGAACAATGAGTCATGTCAAATAACGAATT-TATATATA
* * * * *
1358988 TATATATATATATATATATATA-TATATATATATATATATATATATATATTAAAGATA-AGGTAA
643 CATATAT-TA-A-A-A-ATA-AGTA-A-A-A-AT-TATA-ACA-A-GTA-TAACGA-ACA---AT
* * * * * *
1359051 AAATTATAACAAGTTTAACGAGCAATAGTGGTGAA
689 CAA-GAGAATAAGATAAAC-A-CAATAGT-GT-AA
* *
1359086 TTATTGGGTGGACCAATAAAATTATAATAAAAAATTGTATAATATCAAAAATAGCACATAACGTT
1 TTATTGGGTGGACCAATAAAACTATAATAAAAAATTGTATAATATCAAAAATAGCCCATAACGTT
* * * *
1359151 TACTAAAATGGTCATTTTGACCTTTATTCATTTTTTGGGAGCATTTTGGCCCTCAATATTTCACT
66 TACTAAAATGATCATTTTGACCCTTATTCATTTTTT-GGAGCATTTTGGCCCCCAATGTTTCACT
* *
1359216 TTAGGGCAAAAAGCTCCCTCTATAGATGAAAACCATTAGTTAACACACAATTAACACTCTAAAAT
130 TTAGGGCAAAAAGCTCCCTCTATAG-TGAAAATCATTAGTTAACACACAATTAACACTTTAAAAT
* * * *
1359281 AAAAGCCTTTTTAGCCTTAAATTAAACATTGAGGGCTAAAATGCCCAAAAAAAGAATAAGGGGCA
194 AGAAGCATTTTTAGCCTTAAATTAAACATTGAGGGCTAAAA-GCCC-AAAAAA-AATAATGGACA
* * *
1359346 AAGTGGTTATTCTGTCAAATATTAAGGGTCTTTTTATCCTAAAATGAAATTTTAGGGTCAAATTG
256 AAGTGATTATTCTGTCAAATGTTAAGGGTCTTTTTATCCTAAAATGAAATTTTGGGGTCAAATTG
* * *
1359411 CTTCAAAAATGTAATATGAGACAAAATGACCATTTTAATAAACG-TGAAGGGCTAATTTTGGTAT
321 CTTCAAAAAT-AAATATGAGACAAAATGACCATTTTAATAAATGTTG-AGGGCTAATTTTGATAT
*
1359475 TATACATAAAAAAATTATCTTAGCATAATTTGTATGCAATTTTAAATTTTAAAATACAATAAAAT
384 TATACAT-AAAAAATTATCTTAGCATAATTTGTATGCATTTTTAAATTTTAAAATACAATAAAAT
* *
1359540 AATATATATTTAGACCTAATCTAAAAATATATATACC--GCAAATATAATTTTTAATATAATTTA
448 AATATATATTTAGACTTAATCTAAAAATATATATACCAGGCCAATATAATTTTTAATATAATTTA
* * * * * *
1359603 TATTTATAATTATATTATA-TTTAATTTTTTTTAGATTTTTTAAAACGTAGGGTGGGCCATAGTC
513 TATTT-TATTTAAAATATATTTTAA--TTTTTTAGATTTTTTAAAACATAGGGTGGGACATAGCC
* * * * ** *
1359667 TACGAAGACCCACCCCTAGATGTGCCACTACGAACAATGAGTCATGTCGAATAACATATTTTTTG
575 TAGGTAGGCCCATCCCTAGATAAGCAACTACGAACAATGAGTCA--T-G--T--C--A-------
* * * * *
1359732 GATATGAAACTAGATTTTATATATACATATATTAAAAA-AAGGTAAAAACTCTAAAAAGTTTAAC
624 -A-AT--AAC--GAATTTATATATACATATATTAAAAATAA-GTAAAAATTATAACAAGTATAAC
* * * *
1359796 GAACAATTAGTTGTGAAT-ACAT--A-A-AAT--T-T--
682 GAACAATCA--AGAGAATAAGATAAACACAATAGTGTAA
** * * * * *
1359825 TTATT-GGTGGGTCAATTGAAA-TATAATAAAAAATTGCATAATATAAAAAATAACCCATAATGT
1 TTATTGGGTGGACCAA-TAAAACTATAATAAAAAATTGTATAATATCAAAAATAGCCCATAACGT
* * **
1359888 TTAATAAAATGGTCATTTTG-GTCTCTATTCATTTTTTTGGAGCATTTTGGCCCCCAATGTTTCA
65 TTACTAAAATGATCATTTTGACCCT-TATTCA-TTTTTTGGAGCATTTTGGCCCCCAATGTTTCA
** * * * **
1359952 CTTTAGGAAAAAAAG-TCCTTTTATAGATGAAAATCATTAGTTAATACACAATTAACACTCCAAA
128 CTTTAGGGCAAAAAGCTCCCTCTATAG-TGAAAATCATTAGTTAACACACAATTAACACTTTAAA
* * * * * * *
1360016 ATAAAAGCCTTTATAACCTAAAATTAAACTTTGAGAGCTAAAATGCCCCAGAAAAAAA
192 ATAGAAGCATTTTTAGCCTTAAATTAAACATTGAGGGCTAAAA-G-CCCA-AAAAAAA
1360074 GAATAAGAGA
Statistics
Matches: 1448, Mismatches: 184, Indels: 180
0.80 0.10 0.10
Matches are distributed among these distances:
711 86 0.06
712 120 0.08
713 156 0.11
714 3 0.00
715 1 0.00
716 1 0.00
717 3 0.00
718 4 0.00
719 2 0.00
720 25 0.02
721 4 0.00
722 3 0.00
723 45 0.03
724 137 0.09
725 3 0.00
726 6 0.00
727 1 0.00
728 2 0.00
729 3 0.00
732 2 0.00
734 1 0.00
736 2 0.00
737 89 0.06
738 116 0.08
739 15 0.01
740 62 0.04
741 122 0.08
742 6 0.00
743 31 0.02
744 119 0.08
745 79 0.05
746 76 0.05
747 59 0.04
748 1 0.00
749 1 0.00
750 2 0.00
752 5 0.00
753 2 0.00
754 2 0.00
755 6 0.00
756 2 0.00
757 1 0.00
758 2 0.00
759 3 0.00
760 1 0.00
761 1 0.00
762 2 0.00
763 2 0.00
764 4 0.00
765 3 0.00
766 1 0.00
767 4 0.00
768 2 0.00
769 15 0.01
770 2 0.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (718 bp):
TTATTGGGTGGACCAATAAAACTATAATAAAAAATTGTATAATATCAAAAATAGCCCATAACGTT
TACTAAAATGATCATTTTGACCCTTATTCATTTTTTGGAGCATTTTGGCCCCCAATGTTTCACTT
TAGGGCAAAAAGCTCCCTCTATAGTGAAAATCATTAGTTAACACACAATTAACACTTTAAAATAG
AAGCATTTTTAGCCTTAAATTAAACATTGAGGGCTAAAAGCCCAAAAAAAATAATGGACAAAGTG
ATTATTCTGTCAAATGTTAAGGGTCTTTTTATCCTAAAATGAAATTTTGGGGTCAAATTGCTTCA
AAAATAAATATGAGACAAAATGACCATTTTAATAAATGTTGAGGGCTAATTTTGATATTATACAT
AAAAAATTATCTTAGCATAATTTGTATGCATTTTTAAATTTTAAAATACAATAAAATAATATATA
TTTAGACTTAATCTAAAAATATATATACCAGGCCAATATAATTTTTAATATAATTTATATTTTAT
TTAAAATATATTTTAATTTTTTAGATTTTTTAAAACATAGGGTGGGACATAGCCTAGGTAGGCCC
ATCCCTAGATAAGCAACTACGAACAATGAGTCATGTCAAATAACGAATTTATATATACATATATT
AAAAATAAGTAAAAATTATAACAAGTATAACGAACAATCAAGAGAATAAGATAAACACAATAGTG
TAA
Found at i:1359256 original size:741 final size:722
Alignment explanation
Indices: 1358265--1360072 Score: 2065
Period size: 744 Copynumber: 2.4 Consensus size: 722
1358255 CAATAACGAA
* * * * *
1358265 TTTATATATACATATATTAAAAATAAGGTAAAAATTCTAACAAGTTTAACGAACAATCAATGGCG
1 TTTATATATACATATATTAAAAA-AAGGTAAAAACTATAAAAAGTTTAACGAACAATTAGT-G-G
* ***
1358330 AATAAAAAAAATTATATTGGGTGGACCAATAAAACTATAATAAATTTTTTTTGTATAATATCAAA
63 --T-----GAA-TATATTGGGTGGACCAATAAAA-TATAATAAA---AAATTGTATAATATCAAA
* ** * * *
1358395 AATAGCCCATAACATTTAGGAAAATGATCATTTTGACCCTTATTCATTTTTTAGAGCATTTTGGC
116 AATAGCCCATAACGTTTAATAAAATGGTCATTTTGACCTTTATTCATTTTTTGGAGCATTTTGGC
*
1358460 CCCCAATGTTTCACTTTAGGATAAAAAA-CTCCCTCTATAGTTGAAAATCATTAGTTAACACACA
181 CCCCAATGTTTCACTTTAGGA-AAAAAAGCTCCCTCTATAGATGAAAATCATTAGTTAACACACA
* * *
1358524 ATTAACACTTTAAAATAGAAGCATTTTTAACCTTAAATTAAACATTGAGGGCTAAAA-GCCCAAA
245 ATTAACACTCTAAAATAAAAGCCTTTTTAACCTTAAATTAAACATTGAGGGCTAAAATGCCCAAA
* * * * *
1358588 AAAATAATGGACAAAGTGATTATTTTGTCAAATGTTAGGGGTTTTTTTATCCTAAAATGAAATTT
310 AAAATAAGGGACAAAGTGATTATTCTGTCAAATATTAAGGGTCTTTTTATCCTAAAATGAAATTT
* * * *
1358653 TGGGGGTCAAATTGCTTCAAAAAT-AAATTATGAGACAAAATGATCATTTTATTAAATGTTG-AG
375 T-AGGGTCAAATTGCTTCAAAAATGAAA-TATGAGACAAAATGACCATTTTAATAAACG-TGAAG
* **
1358716 GACTAATTTTGATACTATACATAAACAAATTATCTTAG-ATAATTT-TATGCGTTTTTAAATTTT
437 GACTAATTTTGATACTATACATAAAAAAATTATCTTAGCATAATTTGTATGCAATTTTAAATTTT
* * * *
1358779 AAAATACAATGAAATAATATATATTTAGACTTAATCTAAAAATGTATATACCAGGCCAATATAAC
502 AAAATACAATAAAATAATATATATTTAGACCTAATCTAAAAATATATATACC--GCAAATATAAC
* *
1358844 TTGTAACATAATTTATATTT-TATTTAAAATATATTTTAA-TTTTTTATA-TTTTTAAAACATAG
565 TTGTAACATAATTTATATTTATAATTAAAATATA-TTTAATTTTTTTAGATTTTTTAAAACATAG
* * * * * *
1358906 GGTGGGACATAGCCTAGGTAGGCCCATCCCTAGATAAACAACTCCGAACAATGAGTCGTGTCAAA
629 GGTGGGACATAGCCTACGAAGACCCACCCCTAGATAAACAACTACGAACAATGAGTCATGTCAAA
* * *
1358971 TAACGATTATATATATATATATATATATATATATATATATAT
694 TAAC----ATAT-T-T-T-T-TAGATAT-GA-A-A-ATAGAT
* * * *
1359013 ATATATATATATATATATATATATTAAAGATAAGGTAAAAATTATAACAAGTTTAACGAGCAA-T
1 -T-T-TATATATACATATAT-TA--AAA-A-AAGGTAAAAACTATAAAAAGTTTAACGAACAATT
1359077 AGTGGTGAAT-TATTGGGTGGACCAATAAAATTATAATAAAAAATTGTATAATATCAAAAATAGC
58 AGTGGTGAATATATTGGGTGGACCAATAAAA-TATAATAAAAAATTGTATAATATCAAAAATAGC
* * *
1359141 ACATAACGTTTACTAAAATGGTCATTTTGACCTTTATTCATTTTTTGGGAGCATTTTGGCCCTCA
122 CCATAACGTTTAATAAAATGGTCATTTTGACCTTTATTCATTTTTT-GGAGCATTTTGGCCCCCA
* ** *
1359206 ATATTTCACTTTAGGGCAAAAAGCTCCCTCTATAGATGAAAACCATTAGTTAACACACAATTAAC
186 ATGTTTCACTTTAGGAAAAAAAGCTCCCTCTATAGATGAAAATCATTAGTTAACACACAATTAAC
*
1359271 ACTCTAAAATAAAAGCCTTTTTAGCCTTAAATTAAACATTGAGGGCTAAAATGCCCAAAAAAAGA
251 ACTCTAAAATAAAAGCCTTTTTAACCTTAAATTAAACATTGAGGGCTAAAATGCCC--AAAAA-A
* *
1359336 ATAAGGGGCAAAGTGGTTATTCTGTCAAATATTAAGGGTCTTTTTATCCTAAAATGAAATTTTAG
313 ATAAGGGACAAAGTGATTATTCTGTCAAATATTAAGGGTCTTTTTATCCTAAAATGAAATTTTAG
* *
1359401 GGTCAAATTGCTTCAAAAATGTAATATGAGACAAAATGACCATTTTAATAAACGTGAAGGGCTAA
378 GGTCAAATTGCTTCAAAAATGAAATATGAGACAAAATGACCATTTTAATAAACGTGAAGGACTAA
* *
1359466 TTTTGGTATTATACATAAAAAAATTATCTTAGCATAATTTGTATGCAATTTTAAATTTTAAAATA
443 TTTTGATACTATACATAAAAAAATTATCTTAGCATAATTTGTATGCAATTTTAAATTTTAAAATA
* * *
1359531 CAATAAAATAATATATATTTAGACCTAATCTAAAAATATATATACCGCAAATATAATTTTTAATA
508 CAATAAAATAATATATATTTAGACCTAATCTAAAAATATATATACCGCAAATATAACTTGTAACA
* * * *
1359596 TAATTTATATTTATAATTATATTATATTTAATTTTTTTTAGATTTTTTAAAACGTAGGGTGGGCC
573 TAATTTATATTTATAATTAAAATATATTTAA-TTTTTTTAGATTTTTTAAAACATAGGGTGGGAC
* *** * *
1359661 ATAGTCTACGAAGACCCACCCCTAGATGTGCCACTACGAACAATGAGTCATGTCGAATAACATAT
637 ATAGCCTACGAAGACCCACCCCTAGATAAACAACTACGAACAATGAGTCATGTCAAATAACATAT
* *
1359726 TTTTTGGATATGAAACTAGAT
702 TTTTTAGATATGAAAATAGAT
* *
1359747 TTTATATATACATATATTAAAAAAAGGTAAAAACTCTAAAAAGTTTAACGAACAATTAGTTGTGA
1 TTTATATATACATATATTAAAAAAAGGTAAAAACTATAAAAAGTTTAACGAACAATTAGTGGTGA
* ** * * *
1359812 ATACATAAAATTTTTATTGGTGGGTCAATTGAAATATAATAAAAAATTGCATAATATAAAAAATA
66 AT--AT---A----T-TGGGTGGACCAA-TAAAATATAATAAAAAATTGTATAATATCAAAAATA
* * ** *
1359877 ACCCATAATGTTTAATAAAATGGTCATTTTGGTCTCTATTCATTTTTTTGGAGCATTTTGGCCCC
120 GCCCATAACGTTTAATAAAATGGTCATTTTGACCTTTATTCA-TTTTTTGGAGCATTTTGGCCCC
* * *
1359942 CAATGTTTCACTTTAGGAAAAAAAG-TCCTTTTATAGATGAAAATCATTAGTTAATACACAATTA
184 CAATGTTTCACTTTAGGAAAAAAAGCTCCCTCTATAGATGAAAATCATTAGTTAACACACAATTA
* * * * *
1360006 ACACTCCAAAATAAAAGCCTTTATAACCTAAAATTAAACTTTGAGAGCTAAAATGCCCCAGAAAA
249 ACACTCTAAAATAAAAGCCTTTTTAACCTTAAATTAAACATTGAGGGCTAAAATG-CCCA-AAAA
1360071 AA
312 AA
1360073 AGAATAAGAG
Statistics
Matches: 915, Mismatches: 108, Indels: 85
0.83 0.10 0.08
Matches are distributed among these distances:
726 28 0.03
727 11 0.01
728 3 0.00
730 3 0.00
731 14 0.02
732 1 0.00
733 2 0.00
734 4 0.00
735 1 0.00
736 4 0.00
737 90 0.10
738 118 0.13
739 11 0.01
740 67 0.07
741 118 0.13
742 5 0.01
743 35 0.04
744 122 0.13
745 78 0.09
746 73 0.08
747 69 0.08
749 1 0.00
750 2 0.00
751 14 0.02
752 3 0.00
753 1 0.00
754 5 0.01
755 32 0.03
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (722 bp):
TTTATATATACATATATTAAAAAAAGGTAAAAACTATAAAAAGTTTAACGAACAATTAGTGGTGA
ATATATTGGGTGGACCAATAAAATATAATAAAAAATTGTATAATATCAAAAATAGCCCATAACGT
TTAATAAAATGGTCATTTTGACCTTTATTCATTTTTTGGAGCATTTTGGCCCCCAATGTTTCACT
TTAGGAAAAAAAGCTCCCTCTATAGATGAAAATCATTAGTTAACACACAATTAACACTCTAAAAT
AAAAGCCTTTTTAACCTTAAATTAAACATTGAGGGCTAAAATGCCCAAAAAAATAAGGGACAAAG
TGATTATTCTGTCAAATATTAAGGGTCTTTTTATCCTAAAATGAAATTTTAGGGTCAAATTGCTT
CAAAAATGAAATATGAGACAAAATGACCATTTTAATAAACGTGAAGGACTAATTTTGATACTATA
CATAAAAAAATTATCTTAGCATAATTTGTATGCAATTTTAAATTTTAAAATACAATAAAATAATA
TATATTTAGACCTAATCTAAAAATATATATACCGCAAATATAACTTGTAACATAATTTATATTTA
TAATTAAAATATATTTAATTTTTTTAGATTTTTTAAAACATAGGGTGGGACATAGCCTACGAAGA
CCCACCCCTAGATAAACAACTACGAACAATGAGTCATGTCAAATAACATATTTTTTAGATATGAA
AATAGAT
Found at i:1360242 original size:155 final size:155
Alignment explanation
Indices: 1359973--1360264 Score: 503
Period size: 155 Copynumber: 1.9 Consensus size: 155
1359963 AAAGTCCTTT
* *
1359973 TATAGATGAAAATCATTAGTTAATACACAATTAACACTCCAAAATAAAAGCCTTTATAACCTAAA
1 TATAGATGAAAATCAATAGTTAATACACAATTAACACTCCAAAATAAAAGACTTTATAACCTAAA
* * * *
1360038 ATTAAACTTTGAGAGCTAAAATGCCCCAGAAAAAAAGAATAAGAGATAAAATGATTATTCTTTTT
66 ATTAAACGTTAAGAGCTAAAATGCCCCAGAAAAAAAGAATAAGAGATAAAATGATTATTATGTTT
1360103 AATGTTATGGGCAAAAAGCTCCCTC
131 AATGTTATGGGCAAAAAGCTCCCTC
* * *
1360128 TATAGATGAAAATCAATAGTTAATACACAATTAACACTCCAAAATAGAAGATTTTTTAACCTAAA
1 TATAGATGAAAATCAATAGTTAATACACAATTAACACTCCAAAATAAAAGACTTTATAACCTAAA
1360193 ATTAAACGTTAAGAGCTAAAATGCCCCAGAAAAAAAGAATAAGAGATAAAATGATTATTATGTTT
66 ATTAAACGTTAAGAGCTAAAATGCCCCAGAAAAAAAGAATAAGAGATAAAATGATTATTATGTTT
1360258 AATGTTA
131 AATGTTA
1360265 GGGGTCTTTT
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
155 128 1.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (155 bp):
TATAGATGAAAATCAATAGTTAATACACAATTAACACTCCAAAATAAAAGACTTTATAACCTAAA
ATTAAACGTTAAGAGCTAAAATGCCCCAGAAAAAAAGAATAAGAGATAAAATGATTATTATGTTT
AATGTTATGGGCAAAAAGCTCCCTC
Found at i:1360810 original size:20 final size:20
Alignment explanation
Indices: 1360750--1360813 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1360740 AGAGATAACG
*
1360750 AATTGGACAAAATC-GATTGA
1 AATTTGACAAAATCGGA-TGA
* * *
1360770 AAATTGACAAAATTGGTTGA
1 AATTTGACAAAATCGGATGA
*
1360790 AATTTGAGAAAATCGGATGA
1 AATTTGACAAAATCGGATGA
1360810 AATT
1 AATT
1360814 CGATAAAACT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 34 0.97
21 1 0.03
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.28
Consensus pattern (20 bp):
AATTTGACAAAATCGGATGA
Found at i:1360890 original size:11 final size:11
Alignment explanation
Indices: 1360874--1360898 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1360864 ATATTCTAGG
1360874 AATTTAAAAGA
1 AATTTAAAAGA
1360885 AATTTAAAAGA
1 AATTTAAAAGA
1360896 AAT
1 AAT
1360899 GAAAAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (11 bp):
AATTTAAAAGA
Found at i:1361948 original size:229 final size:230
Alignment explanation
Indices: 1361569--1361999 Score: 677
Period size: 229 Copynumber: 1.9 Consensus size: 230
1361559 ATAATAATAC
* * ** *
1361569 AAAATAGGGGTTAGGTTTATGGGGTTTGGGTTTTTTTAAGTAAAGAAGCATTTGGGACTGATTGC
1 AAAATAGGGATTAGGTTTATGGGGTTTGGGGTTTTCGAAGTAAAGAAGCATTTGGGACTGATTAC
* * ** *
1361634 AATTAGAAAGTGATATTCTAGGTAGAATTTAAATATCGATACTTTTATATAATATTATAGGTAGA
66 AATTAGAAAGTAACATTCTAGGTAGAAAATAAATATCGATACTTTTATATAATATTATAGGTAAA
* * *
1361699 AAATGTTATTGTAGGTTGTATAAAGGTACTGGTACTTGTAGTAGAGAATATTCTCATTCCTTTGA
131 AAATGATATTGTAGGTTGTATAAAGGTACTGATACTTGTAGTAGAGAATATTCCCATTCCTTTGA
1361764 AGAAAACCCTAGTTTTTTTAGCATTGTAGTATTCA
196 AGAAAACCCTAGTTTTTTTAGCATTGTAGTATTCA
*
1361799 AAAATAGGGATTAGGTTTAT-GGGTTTGGGGTTTTCGAAGTAAAGAAGGATTTGGGA-TCGATTA
1 AAAATAGGGATTAGGTTTATGGGGTTTGGGGTTTTCGAAGTAAAGAAGCATTTGGGACT-GATTA
*
1361862 CAGTTAGAAAGTAACATTCTAGGTAGAAAATAAATATCGATACTTTTATATAATATTATAGGTAA
65 CAATTAGAAAGTAACATTCTAGGTAGAAAATAAATATCGATACTTTTATATAATATTATAGGTAA
* *
1361927 AAAATGATATTGTAGGTTGTATAAAGGTATTGATACTTGTAGTAGAGAGTATTCCCATTCCTTTG
130 AAAATGATATTGTAGGTTGTATAAAGGTACTGATACTTGTAGTAGAGAATATTCCCATTCCTTTG
*
1361992 AAGGAAAC
195 AAGAAAAC
1362000 TGTTTTACTA
Statistics
Matches: 182, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
228 1 0.01
229 162 0.89
230 19 0.10
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.36
Consensus pattern (230 bp):
AAAATAGGGATTAGGTTTATGGGGTTTGGGGTTTTCGAAGTAAAGAAGCATTTGGGACTGATTAC
AATTAGAAAGTAACATTCTAGGTAGAAAATAAATATCGATACTTTTATATAATATTATAGGTAAA
AAATGATATTGTAGGTTGTATAAAGGTACTGATACTTGTAGTAGAGAATATTCCCATTCCTTTGA
AGAAAACCCTAGTTTTTTTAGCATTGTAGTATTCA
Found at i:1363481 original size:18 final size:18
Alignment explanation
Indices: 1363454--1363493 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1363444 GGTAAAATTG
*
1363454 AAGCTTGAAAGACCGAGT
1 AAGCTGGAAAGACCGAGT
1363472 AAGCTGGAAAGACCGAGT
1 AAGCTGGAAAGACCGAGT
1363490 AAGC
1 AAGC
1363494 AAGAAAGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.30, T:0.12
Consensus pattern (18 bp):
AAGCTGGAAAGACCGAGT
Found at i:1363499 original size:18 final size:18
Alignment explanation
Indices: 1363460--1363500 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1363450 ATTGAAGCTT
**
1363460 GAAAGACCGAGTAAGCTG
1 GAAAGACCGAGTAAGCAA
1363478 GAAAGACCGAGTAAGCAA
1 GAAAGACCGAGTAAGCAA
1363496 GAAAG
1 GAAAG
1363501 TGTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.32, T:0.07
Consensus pattern (18 bp):
GAAAGACCGAGTAAGCAA
Found at i:1368665 original size:200 final size:199
Alignment explanation
Indices: 1368243--1368673 Score: 535
Period size: 200 Copynumber: 2.2 Consensus size: 199
1368233 ATTTCGATAT
1368243 TTTTTTATATGTATCGATACTTTTGGTAC-AATATGATACCCAAACGACATGCACGCAGAAAGTA
1 TTTTTTATATGTATCGATACTTTTGGT-CTAATATGATACCCAAACGACATGCACGCAGAAAGTA
*
1368307 TCGATACACATATCACAAGTATCGATACTCATAACTTCGAAACCGATTATTTTAAAGTAATAGGT
65 TCGATACACATATCACAAGTATCGATACTCATAACTTCGAAACCGATTACTTTAAAGTAATAGGT
* * * *
1368372 AAATTTACAATATAACCCGTAAAAATATATCGATTTAATGACAAAATGCGTAAACATAAAGTTAC
130 AAATTTACAATATAACCCGTAAAAATATACCGATTTAATGACAAAAGGCATAAACAAAAAGTTAC
1368437 AATAC
195 AATAC
* * * * *
1368442 TTTTTATATATGTATCAATACTTTTGGTCTAGTATGCTTCCCAAACGAGATGCACGCAGAAAGTA
1 TTTTT-TATATGTATCGATACTTTTGGTCTAATATGATACCCAAACGACATGCACGCAGAAAGTA
** * * *
1368507 TCGATACATGTATCACAAGT-TTGATTCTTATAACTTCGAAACCGATTACTTTAAAGTAATAGGT
65 TCGATACACATATCACAAGTATCGATACTCATAACTTCGAAACCGATTACTTTAAAGTAATAGGT
* * * * * * ** * *
1368571 AAATTTACAATGTAAGCGGTAAAAATCTACCGGTTTAATGATAGTAGGCATTAGCAAAAAAG-TA
130 AAATTTACAATATAACCCGTAAAAATATACCGATTTAATGACAAAAGGCATAAAC-AAAAAGTTA
**
1368635 TTGATAC
194 -CAATAC
* *
1368642 TTCTTTTATAGGTATCGATACTTTTGATCTAA
1 TT-TTTTATATGTATCGATACTTTTGGTCTAA
1368674 ACATCACTGA
Statistics
Matches: 196, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
199 90 0.46
200 103 0.53
201 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (199 bp):
TTTTTTATATGTATCGATACTTTTGGTCTAATATGATACCCAAACGACATGCACGCAGAAAGTAT
CGATACACATATCACAAGTATCGATACTCATAACTTCGAAACCGATTACTTTAAAGTAATAGGTA
AATTTACAATATAACCCGTAAAAATATACCGATTTAATGACAAAAGGCATAAACAAAAAGTTACA
ATAC
Found at i:1368917 original size:280 final size:280
Alignment explanation
Indices: 1368416--1368978 Score: 1108
Period size: 280 Copynumber: 2.0 Consensus size: 280
1368406 TTAATGACAA
1368416 AATGCGTAAACATAAAGTTACAATACTTTTTATATATGTATCAATACTTTTGGTCTAGTATGCTT
1 AATGCGTAAACATAAAGTTACAATACTTTTTATATATGTATCAATACTTTTGGTCTAGTATGCTT
1368481 CCCAAACGAGATGCACGCAGAAAGTATCGATACATGTATCACAAGTTTGATTCTTATAACTTCGA
66 CCCAAACGAGATGCACGCAGAAAGTATCGATACATGTATCACAAGTTTGATTCTTATAACTTCGA
1368546 AACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATCTACCGGTTTAATG
131 AACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATCTACCGGTTTAATG
1368611 ATAGTAGGCATTAGCAAAAAAGTATTGATACTTCTTTTATAGGTATCGATACTTTTGATCTAAAC
196 ATAGTAGGCATTAGCAAAAAAGTATTGATACTTCTTTTATAGGTATCGATACTTTTGATCTAAAC
1368676 ATCACTGATACTTTTAACAC
261 ATCACTGATACTTTTAACAC
*
1368696 AATGCGTAAACATAAAGTTACAATACTTTTTATATATGTATCGATACTTTTGGTCTAGTATGCTT
1 AATGCGTAAACATAAAGTTACAATACTTTTTATATATGTATCAATACTTTTGGTCTAGTATGCTT
1368761 CCCAAACGAGATGCACGCAGAAAGTATCGATACATGTATCACAAGTTTGATTCTTATAACTTCGA
66 CCCAAACGAGATGCACGCAGAAAGTATCGATACATGTATCACAAGTTTGATTCTTATAACTTCGA
1368826 AACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATCTACCGGTTTAATG
131 AACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATCTACCGGTTTAATG
*
1368891 ATAGTAGGCATTAGCAAAAAAGTATTGATACTTCTTTTATAGGTATCGATGCTTTTGATCTAAAC
196 ATAGTAGGCATTAGCAAAAAAGTATTGATACTTCTTTTATAGGTATCGATACTTTTGATCTAAAC
1368956 ATCACTGATACTTTTAACAC
261 ATCACTGATACTTTTAACAC
1368976 AAT
1 AAT
1368979 TACCGATATT
Statistics
Matches: 281, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
280 281 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (280 bp):
AATGCGTAAACATAAAGTTACAATACTTTTTATATATGTATCAATACTTTTGGTCTAGTATGCTT
CCCAAACGAGATGCACGCAGAAAGTATCGATACATGTATCACAAGTTTGATTCTTATAACTTCGA
AACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATCTACCGGTTTAATG
ATAGTAGGCATTAGCAAAAAAGTATTGATACTTCTTTTATAGGTATCGATACTTTTGATCTAAAC
ATCACTGATACTTTTAACAC
Found at i:1370423 original size:108 final size:108
Alignment explanation
Indices: 1370253--1370755 Score: 458
Period size: 108 Copynumber: 4.6 Consensus size: 108
1370243 ATTATGGTTG
* * * *
1370253 ATAACAAATCAAGTAATTAATCGGTTATGTTATCATCGGATTTCTAAGG-CTCCATCAACTTAAA
1 ATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCCT-CATCAGCTTAAA
* *
1370317 CTTTGGTAACATTTTAGGTGTTATCTAATATGTTGATAATACTA
65 CTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTA
* * *
1370361 ATAACAAATTAAGTAATTAACCGGTTATATTATCGTCAGATTTCTAAGGCCTTATCAGCTTAAAC
1 ATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCCTCATCAGCTTAAAC
* *
1370426 TTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATAATG
66 TTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTA
** * * *
1370469 ATAACAAATTAAGTAATTAACCTATTTTGTTATCATCGGATTTCTAAGGCCCCATCAGCTTTAAA
1 ATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCCTCATCAGC-TT---
* * * * * ** * ** *
1370534 AAGGCACTCCTT-ATTACGTTACATAAGCACTACCTAATATGTT-ATTATGGTTT
62 AA---ACT--TTGGTAACATT--TTAGGCGTTACCTAATATGTTGATAAT-ACTA
* ** * * *
1370587 ATAACAAATCAAACAATTAATCGGCTATGTTATCGTCGGATTTCTAAGG-CTCCATTAGCTTAAA
1 ATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCCT-CATCAGCTTAAA
* * *
1370651 CTTTGGTAACATTTTAGGTGTTAGCTCATATGTTGATAATAC-A
65 CTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTA
** * * * *
1370694 GATAACAAATTAAGTAATTAACCTATTTTGTTATTGTCAGATTTCTAAGGCCCCATCAGCTT
1 -ATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCCTCATCAGCTT
1370756 TAAAAAAAGC
Statistics
Matches: 310, Mismatches: 67, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
108 206 0.66
109 11 0.04
110 5 0.02
111 3 0.01
112 2 0.01
114 2 0.01
115 3 0.01
116 5 0.02
117 9 0.03
118 64 0.21
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (108 bp):
ATAACAAATTAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCCTCATCAGCTTAAAC
TTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTA
Found at i:1370656 original size:226 final size:224
Alignment explanation
Indices: 1370341--1370856 Score: 716
Period size: 226 Copynumber: 2.3 Consensus size: 224
1370331 TAGGTGTTAT
* * * * * *
1370341 CTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCGGTTATATTATCGTCAGATTTCT
1 CTAATATGTT-ATTATAGTTATAACAAATCAAGTAATTAATCGGTTATGTTATCGTCAGATTTCT
*
1370406 AAGGCCTTATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATA-ATGA
65 AAGGCCTCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACA-GA
*
1370470 TAACAAATTAAGTAATTAACCTATTTTGTTATCATCGGATTTCTAAGGCCCCATCAGCTTT-AAA
129 TAACAAATTAAGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGCCCCATCAGCTTTAAAA
* * *
1370534 AAGGCACTCCTTATTACGTTACATAAGCA-CTAC
194 AAAG--CTACATATTACGTTACATAAG-AGCTAC
* ** * *
1370567 CTAATATGTTATTATGGTTTATAACAAATCAAACAATTAATCGGCTATGTTATCGTCGGATTTCT
1 CTAATATGTTATTATAG-TTATAACAAATCAAGTAATTAATCGGTTATGTTATCGTCAGATTTCT
* * * *
1370632 AAGG-CTCCATTAGCTTAAACTTTGGTAACATTTTAGGTGTTAGCTCATATGTTGATAATACAGA
65 AAGGCCT-CATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACAGA
**
1370696 TAACAAATTAAGTAATTAACCTATTTTGTTATTGTCAGATTTCTAAGGCCCCATCAGCTTTAAAA
129 TAACAAATTAAGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGCCCCATCAGCTTTAAAA
*
1370761 AAAGCTACATATTATGTTACATAAGAGCTAC
194 AAAGCTACATATTACGTTACATAAGAGCTAC
*
1370792 CTAATATGTTATTATAGTTATTAACAAATCAAGTAATTAATTGGTTATGTTATCGTCAGATTTCT
1 CTAATATGTTATTATAGTTA-TAACAAATCAAGTAATTAATCGGTTATGTTATCGTCAGATTTCT
1370857 CAAGATCGGA
Statistics
Matches: 255, Mismatches: 29, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
224 4 0.02
225 83 0.33
226 161 0.63
227 7 0.03
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (224 bp):
CTAATATGTTATTATAGTTATAACAAATCAAGTAATTAATCGGTTATGTTATCGTCAGATTTCTA
AGGCCTCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACAGATA
ACAAATTAAGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGCCCCATCAGCTTTAAAAAA
AGCTACATATTACGTTACATAAGAGCTAC
Found at i:1370745 original size:334 final size:334
Alignment explanation
Indices: 1370136--1370755 Score: 929
Period size: 334 Copynumber: 1.9 Consensus size: 334
1370126 TATACACGAT
* ** ** *
1370136 TAACAAATTAAATAATTAACTTATTTTGTTATTGTAGGATTTCTAAGGCCCTGTCAACTTTTAAA
1 TAACAAATTAAATAATTAACCTATTTTGTTATCATAGGATTTCTAAGGCCCCATCAACTTTAAAA
* ** * *
1370201 ATGTGCTACCTATTACGTTACATAAACGCTACCTAATAGGTTATTATGGTTGATAACAAATCAAG
66 AGGCACTACCTATTACGTTACATAAACACTACCTAATAGGTTATTATGGTTGATAACAAATCAAA
* *
1370266 TAATTAATCGGTTATGTTATCATCGGATTTCTAAGGCTCCATCAACTTAAACTTTGGTAACATTT
131 CAATTAATCGGCTATGTTATCATCGGATTTCTAAGGCTCCATCAACTTAAACTTTGGTAACATTT
* *
1370331 TAGGTGTTATCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCGGTTATATTATCG
196 TAGGTGTTAGCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCGATTATATTATCG
**
1370396 TCAGATTTCTAAGGCCTTATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGA
261 TCAGATTTCTAAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGA
1370461 TAATAATGA
326 TAATAATGA
* * *
1370470 TAACAAATTAAGTAATTAACCTATTTTGTTATCATCGGATTTCTAAGGCCCCATCAGCTTTAAAA
1 TAACAAATTAAATAATTAACCTATTTTGTTATCATAGGATTTCTAAGGCCCCATCAACTTTAAAA
* * *
1370535 AGGCACT-CCTTATTACGTTACATAAGCACTACCTAATATGTTATTATGGTTTATAACAAATCAA
66 AGGCACTACC-TATTACGTTACATAAACACTACCTAATAGGTTATTATGGTTGATAACAAATCAA
* * *
1370599 ACAATTAATCGGCTATGTTATCGTCGGATTTCTAAGGCTCCATTAGCTTAAACTTTGGTAACATT
130 ACAATTAATCGGCTATGTTATCATCGGATTTCTAAGGCTCCATCAACTTAAACTTTGGTAACATT
* * * *
1370664 TTAGGTGTTAGCTCATATGTTGATAATAC-AGATAACAAATTAAGTAATTAACCTATTTTGTTAT
195 TTAGGTGTTAGCTAATATGTTGATAATACTA-ATAACAAATTAAGTAATTAACCGATTATATTAT
*
1370728 TGTCAGATTTCTAAGGCCCCATCAGCTT
259 CGTCAGATTTCTAAGGCCCCATCAGCTT
1370756 TAAAAAAAGC
Statistics
Matches: 253, Mismatches: 31, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
333 3 0.01
334 250 0.99
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (334 bp):
TAACAAATTAAATAATTAACCTATTTTGTTATCATAGGATTTCTAAGGCCCCATCAACTTTAAAA
AGGCACTACCTATTACGTTACATAAACACTACCTAATAGGTTATTATGGTTGATAACAAATCAAA
CAATTAATCGGCTATGTTATCATCGGATTTCTAAGGCTCCATCAACTTAAACTTTGGTAACATTT
TAGGTGTTAGCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCGATTATATTATCG
TCAGATTTCTAAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGA
TAATAATGA
Found at i:1371352 original size:23 final size:21
Alignment explanation
Indices: 1371303--1371378 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 21
1371293 AATATTTTAA
*
1371303 AATATTATTTAAG-TTTTAAAAT
1 AATATTATTT--GTTTTTTAAAT
*
1371325 CATATTATTTGTTTATTTTAAAT
1 AATATTATTTG-TT-TTTTAAAT
1371348 AATATTATTTGTTTTTTAAAT
1 AATATTATTTGTTTTTTAAAT
1371369 AATATTATTT
1 AATATTATTT
1371379 TTAAATTATC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.02
21 18 0.38
22 12 0.25
23 17 0.35
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (21 bp):
AATATTATTTGTTTTTTAAAT
Found at i:1371367 original size:45 final size:42
Alignment explanation
Indices: 1371295--1371378 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 42
1371285 ATTATAAAAA
*
1371295 TATTTTAAAATATTATTTAAGTTTTAAAATCATATTATTTGTT
1 TATTTTAAAATATTATTTAAGTTTT-AAATAATATTATTTGTT
***
1371338 TATTTTAAATAATATTATTTGTTTTTTAAATAATATTATTT
1 TATTTT-AA-AATATTATTTAAGTTTTAAATAATATTATTT
1371379 TTAAATTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 6 0.17
44 15 0.43
45 14 0.40
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (42 bp):
TATTTTAAAATATTATTTAAGTTTTAAATAATATTATTTGTT
Found at i:1371381 original size:16 final size:16
Alignment explanation
Indices: 1371360--1371411 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1371350 TATTATTTGT
1371360 TTTTTAAATAATATTA
1 TTTTTAAATAATATTA
*
1371376 TTTTTAAATTATCTATTTA
1 TTTTTAAA-TA-ATA-TTA
*
1371395 ATTTTAAATAATATTA
1 TTTTTAAATAATATTA
1371411 T
1 T
1371412 GTGGAACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 11 0.38
17 4 0.14
18 4 0.14
19 10 0.34
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTAAATAATATTA
Found at i:1371508 original size:16 final size:15
Alignment explanation
Indices: 1371487--1371539 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
1371477 TAAATAGATA
1371487 ATTTCAAAATAATATT
1 ATTTC-AAATAATATT
1371503 ATTTC-AATAAT-TT
1 ATTTCAAATAATATT
*
1371516 A---AAAATAATATT
1 ATTTCAAATAATATT
1371528 ATTTCAAATAAT
1 ATTTCAAATAAT
1371540 TAATTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
11 6 0.20
12 3 0.10
13 3 0.10
14 6 0.20
15 7 0.23
16 5 0.17
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTTCAAATAATATT
Found at i:1371512 original size:25 final size:26
Alignment explanation
Indices: 1371484--1371561 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 26
1371474 AATTAAATAG
*
1371484 ATAATTTCAAAATAATATTATTTC-A
1 ATAATTTAAAAATAATATTATTTCAA
1371509 ATAATTTAAAAATAATATTATTTCAA
1 ATAATTTAAAAATAATATTATTTCAA
* *
1371535 ATAA-TT--AATTAATATTATTTAAA
1 ATAATTTAAAAATAATATTATTTCAA
1371558 ATAA
1 ATAA
1371562 ATAAACATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
23 19 0.39
25 25 0.51
26 5 0.10
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATTTAAAAATAATATTATTTCAA
Found at i:1374495 original size:20 final size:20
Alignment explanation
Indices: 1374470--1374528 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
1374460 ATTTTTAAAG
1374470 CAAAATTAGATTTTGAAAAA
1 CAAAATTAGATTTTGAAAAA
*
1374490 CAAAATGAGATTTTGAAAAA
1 CAAAATTAGATTTTGAAAAA
*
1374510 CAAAA-TGGAATTTTGAAAA
1 CAAAATTAG-ATTTTGAAAA
1374529 GTGATTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (20 bp):
CAAAATTAGATTTTGAAAAA
Found at i:1380858 original size:74 final size:74
Alignment explanation
Indices: 1380741--1380883 Score: 205
Period size: 74 Copynumber: 1.9 Consensus size: 74
1380731 AGCAAAGGCA
* * * ** *
1380741 TTATTTGACTAATATTTAAATTAAAAATTACCTAAAATACTATTATATCAAAAAGTTTGGGAGGG
1 TTATTTAACTAACATTTAAACTAAAAAGAACCTAAAATACTATTATAACAAAAAGTTTGGGAGGG
1380806 GCAAAAACC
66 GCAAAAACC
* * *
1380815 TTATTTAACTAACATTTAAACTAAAAAGAACCTAAAATGCTATTATAACAAAAATTTTGGGTGGG
1 TTATTTAACTAACATTTAAACTAAAAAGAACCTAAAATACTATTATAACAAAAAGTTTGGGAGGG
1380880 GCAA
66 GCAA
1380884 CAGCCCCTCC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (74 bp):
TTATTTAACTAACATTTAAACTAAAAAGAACCTAAAATACTATTATAACAAAAAGTTTGGGAGGG
GCAAAAACC
Found at i:1382155 original size:18 final size:19
Alignment explanation
Indices: 1382132--1382175 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1382122 AATAAATTCT
*
1382132 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATATTAC
*
1382150 ATTCCCACTGGTAATATTAT
1 ATT-CCACTGGTAATATTAC
1382170 ATTCCA
1 ATTCCA
1382176 TGAACCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 3 0.14
19 5 0.23
20 14 0.64
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (19 bp):
ATTCCACTGGTAATATTAC
Found at i:1382162 original size:20 final size:20
Alignment explanation
Indices: 1382137--1382174 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1382127 ATTCTATTCC
*
1382137 CTGGTAATCTTACATTCCCA
1 CTGGTAATATTACATTCCCA
*
1382157 CTGGTAATATTATATTCC
1 CTGGTAATATTACATTCC
1382175 ATGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATATTACATTCCCA
Found at i:1382416 original size:83 final size:83
Alignment explanation
Indices: 1382277--1382440 Score: 328
Period size: 83 Copynumber: 2.0 Consensus size: 83
1382267 AGCATAGAGT
1382277 ACCAATATGTATCTTAAGTTATCAATACTCTTGGGTGGAGTTCAAATTGACATTTTAGAATCTAA
1 ACCAATATGTATCTTAAGTTATCAATACTCTTGGGTGGAGTTCAAATTGACATTTTAGAATCTAA
1382342 CATTTTACCTAGGTATAA
66 CATTTTACCTAGGTATAA
1382360 ACCAATATGTATCTTAAGTTATCAATACTCTTGGGTGGAGTTCAAATTGACATTTTAGAATCTAA
1 ACCAATATGTATCTTAAGTTATCAATACTCTTGGGTGGAGTTCAAATTGACATTTTAGAATCTAA
1382425 CATTTTACCTAGGTAT
66 CATTTTACCTAGGTAT
1382441 CGATATAGGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (83 bp):
ACCAATATGTATCTTAAGTTATCAATACTCTTGGGTGGAGTTCAAATTGACATTTTAGAATCTAA
CATTTTACCTAGGTATAA
Found at i:1385417 original size:27 final size:28
Alignment explanation
Indices: 1385385--1385437 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1385375 TCTTGAAGAA
1385385 GAAGAG-AAAAAGA-GAAATGAAGATATT
1 GAAGAGAAAAAAGATGAAAT-AAGATATT
1385412 GAAGAGAAAAAAGATGAAATAAGATA
1 GAAGAGAAAAAAGATGAAATAAGATA
1385438 CAACTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 6 0.25
28 13 0.54
29 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.13
Consensus pattern (28 bp):
GAAGAGAAAAAAGATGAAATAAGATATT
Found at i:1387029 original size:21 final size:22
Alignment explanation
Indices: 1386984--1387033 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1386974 TTAACTTCAG
1386984 TTCAAGC-TTCTAATAACATAA
1 TTCAAGCATTCTAATAACATAA
* *
1387005 -TCAAGCATTCTAA-CATATAA
1 TTCAAGCATTCTAATAACATAA
1387025 TTCAAGCAT
1 TTCAAGCAT
1387034 AACATATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (22 bp):
TTCAAGCATTCTAATAACATAA
Found at i:1394773 original size:21 final size:22
Alignment explanation
Indices: 1394726--1394777 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1394716 ATTTAACTTC
*
1394726 AATTCAAGC-TTCTAATAACAT
1 AATTCAAGCATTCTAACAACAT
*
1394747 AA-TCAAGCATTCTAACATC-T
1 AATTCAAGCATTCTAACAACAT
1394767 AATTCAAGCAT
1 AATTCAAGCAT
1394778 AACACATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (22 bp):
AATTCAAGCATTCTAACAACAT
Found at i:1395993 original size:28 final size:29
Alignment explanation
Indices: 1395921--1396008 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 29
1395911 CTAAAATACA
* * * *
1395921 TAACTTTTTAAA-ATTAGATTTTGGTCCC
1 TAACTTTTCAAATTTTATATTTTGGTCAC
**
1395949 TAAACTTTTCCCATTTTATATTTTGGTCAC
1 T-AACTTTTCAAATTTTATATTTTGGTCAC
*
1395979 TAAC-TTTCAAATTTTATATTTTGTTCAC
1 TAACTTTTCAAATTTTATATTTTGGTCAC
1396007 TA
1 TA
1396009 GCAAAAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 24 0.49
29 11 0.22
30 14 0.29
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (29 bp):
TAACTTTTCAAATTTTATATTTTGGTCAC
Found at i:1400599 original size:13 final size:13
Alignment explanation
Indices: 1400581--1400607 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1400571 TTGTATTAGG
1400581 TTATTGGAAATCA
1 TTATTGGAAATCA
1400594 TTATTGGAAATCA
1 TTATTGGAAATCA
1400607 T
1 T
1400608 CTCCAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TTATTGGAAATCA
Found at i:1404658 original size:12 final size:12
Alignment explanation
Indices: 1404641--1404676 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1404631 GCAACAGTCA
* *
1404641 TAGGAGCTGAGC
1 TAGGAGCAGACC
1404653 TAGGAGCAGACC
1 TAGGAGCAGACC
1404665 TAGGAGCAGACC
1 TAGGAGCAGACC
1404677 GTTCCATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.22, G:0.36, T:0.11
Consensus pattern (12 bp):
TAGGAGCAGACC
Found at i:1405921 original size:19 final size:19
Alignment explanation
Indices: 1405897--1405934 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1405887 ATAACTCTAG
1405897 GACAGATTGTCTTGAACCA
1 GACAGATTGTCTTGAACCA
1405916 GACAGATTGTCTTGAACCA
1 GACAGATTGTCTTGAACCA
1405935 CTGTGTAAAG
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:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (19 bp):
GACAGATTGTCTTGAACCA
Found at i:1408088 original size:27 final size:27
Alignment explanation
Indices: 1408058--1408127 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 27
1408048 TTGCATTTTC
1408058 TATTTCAATGAATGT-ATTTGTTTATAA
1 TATTTCAATGAATGTAATTT-TTTATAA
*
1408085 TATTTAAATGTAAT-TACATTTTTTATAA
1 TATTTCAATG-AATGTA-ATTTTTTATAA
*
1408113 T-TTCTCAATGTATGT
1 TATT-TCAATGAATGT
1408128 GTATTTTCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 14 0.40
28 17 0.49
29 4 0.11
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.53
Consensus pattern (27 bp):
TATTTCAATGAATGTAATTTTTTATAA
Found at i:1414198 original size:31 final size:31
Alignment explanation
Indices: 1414163--1414263 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
1414153 GATCCGATCT
1414163 GAAAATTGATAGATTGAATTTGACTTGACTC
1 GAAAATTGATAGATTGAATTTGACTTGACTC
* * * *
1414194 GAAAAGTAATCGTTATG-ATATTGA-TCTGA-TC
1 GAAAATTGATAGAT-TGAAT-TTGACT-TGACTC
* * *
1414225 TGAAAATTGATTGACTCAATTTGACTTGACTC
1 -GAAAATTGATAGATTGAATTTGACTTGACTC
1414257 GAAAATT
1 GAAAATT
1414264 AATTGTTCCA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
31 30 0.57
32 23 0.43
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (31 bp):
GAAAATTGATAGATTGAATTTGACTTGACTC
Found at i:1414278 original size:63 final size:63
Alignment explanation
Indices: 1414149--1414278 Score: 179
Period size: 63 Copynumber: 2.1 Consensus size: 63
1414139 ACTAACTTGG
* * **
1414149 TATTGATCCGATCTGAAAATTGATAGATTGAATTTGACTTGACTCGAAAAGTAATCGTTATGA
1 TATTGATCCGATCTGAAAATTGATAGACTCAATTTGACTTGACTCGAAAAGTAATCGTTACAA
* * * * *
1414212 TATTGATCTGATCTGAAAATTGATTGACTCAATTTGACTTGACTCGAAAATTAATTGTTCCAA
1 TATTGATCCGATCTGAAAATTGATAGACTCAATTTGACTTGACTCGAAAAGTAATCGTTACAA
1414275 TATT
1 TATT
1414279 AACCCAATGA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (63 bp):
TATTGATCCGATCTGAAAATTGATAGACTCAATTTGACTTGACTCGAAAAGTAATCGTTACAA
Found at i:1417339 original size:15 final size:15
Alignment explanation
Indices: 1417279--1417358 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
1417269 ATTTTATATA
1417279 TATATATATATAATAT
1 TATATATATATAAT-T
* *
1417295 TA-ATAAATTTAATT
1 TATATATATATAATT
* *
1417309 TA-A-AT-TAAAATA
1 TATATATATATAATT
1417321 TATATATA-AT-ATT
1 TATATATATATAATT
1417334 TATATAT-T-TAATT
1 TATATATATATAATT
*
1417347 TAAATATATATA
1 TATATATATATA
1417359 TCCGACCCGA
Statistics
Matches: 48, Mismatches: 9, Indels: 15
0.67 0.12 0.21
Matches are distributed among these distances:
12 7 0.15
13 20 0.42
14 8 0.17
15 11 0.23
16 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:1418531 original size:18 final size:19
Alignment explanation
Indices: 1418508--1418550 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1418498 CCAGTAATCC
*
1418508 TATTCT-CTGGTAATCTTT
1 TATTCTACTGGTAATCTTA
1418526 TATTCTCACTGGTAATCTTA
1 TATTCT-ACTGGTAATCTTA
1418546 TATTC
1 TATTC
1418551 CGTGAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (19 bp):
TATTCTACTGGTAATCTTA
Found at i:1424436 original size:30 final size:30
Alignment explanation
Indices: 1424367--1424472 Score: 108
Period size: 30 Copynumber: 3.6 Consensus size: 30
1424357 CAGAAAATAT
* * *
1424367 AATTTATTTTACATAAAATAGTTTT-AGGC
1 AATTCATTTTACATAAAAAAGTTTTCAGGA
*
1424396 AATTCATTTTACATAAAAAAGTTTTCATGA
1 AATTCATTTTACATAAAAAAGTTTTCAGGA
* * *
1424426 AATTCGTTTTACGTAAAACAA-TTTTCAGGT
1 AATTCATTTTACATAAAA-AAGTTTTCAGGA
* *
1424456 AATCCATTTTACGTAAA
1 AATTCATTTTACATAAA
1424473 TTATTTTTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 23 0.35
30 40 0.62
31 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (30 bp):
AATTCATTTTACATAAAAAAGTTTTCAGGA
Found at i:1425765 original size:21 final size:22
Alignment explanation
Indices: 1425741--1425783 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1425731 TCAGTTTGGT
*
1425741 AATA-ATTTAAAAAAATAAAAA
1 AATATATTCAAAAAAATAAAAA
1425762 AATATATTCAAAAAAATAAAAA
1 AATATATTCAAAAAAATAAAAA
1425784 TATTAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
AATATATTCAAAAAAATAAAAA
Found at i:1427103 original size:106 final size:105
Alignment explanation
Indices: 1426911--1427101 Score: 275
Period size: 106 Copynumber: 1.8 Consensus size: 105
1426901 ACTTATATAT
1426911 ATATAATAAATTATAATTTAATAGAATAAAAAAATCCTCAATATATAAATATTAATATAATTCAT
1 ATATAATAAATTATAATTTAATAGAATAAAAAAATCCTCAATATATAAATATTAATATAATT-AT
1426976 TAGAAAAAAATAATTCTTAATAAATATTAAAAGTTATAAAG
65 TAGAAAAAAATAATTCTTAATAAATATTAAAAGTTATAAAG
* * * *
1427017 ATATAATAAATTATAATTT-ATAAGAA-GAAATAATTCTTAATATATAAACTATTAATATAA-T-
1 ATATAATAAATTATAATTTAAT-AGAATAAAAAAATCCTCAATATATAAA-TATTAATATAATTA
1427078 TTA-ATAAAAAATAATTCTTAATAA
64 TTAGA-AAAAAATAATTCTTAATAA
1427102 TATGAAATTA
Statistics
Matches: 78, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
102 1 0.01
103 22 0.28
105 21 0.27
106 34 0.44
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (105 bp):
ATATAATAAATTATAATTTAATAGAATAAAAAAATCCTCAATATATAAATATTAATATAATTATT
AGAAAAAAATAATTCTTAATAAATATTAAAAGTTATAAAG
Found at i:1427121 original size:30 final size:30
Alignment explanation
Indices: 1427098--1427154 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1427088 ATAATTCTTA
1427098 ATAATATGAAATTATAATTAATAAATATAT
1 ATAATATGAAATTATAATTAATAAATATAT
* *
1427128 ATAATATTACATTATAATTAATAAATA
1 ATAATATGAAATTATAATTAATAAATA
1427155 AAAATTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
ATAATATGAAATTATAATTAATAAATATAT
Found at i:1428213 original size:67 final size:65
Alignment explanation
Indices: 1428141--1428315 Score: 174
Period size: 65 Copynumber: 2.7 Consensus size: 65
1428131 TGGGAGCGTG
* * * * *
1428141 GTGCATCGATGCATAGTCAAG-GTATATATGTACACTAATTACATTTGATGTTTCAAAAGAGCCA
1 GTGCATCGATGCATAGTC-AGTGCAT-T-GGTACACAAAATACATTCGATGTTTCAAAAGAGCCA
1428205 AGA
63 AGA
* * * * **
1428208 GTGCATCGATGCATGGTCTGTGCATTGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGA
1 GTGCATCGATGCATAGTCAGTGCATTGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGA
* * *
1428273 GTGCATCGATGCATAG-CTTGTGCATCGGTACACAAAATGCATT
1 GTGCATCGATGCATAGTC-AGTGCATTGGTACACAAAATACATT
1428316 TGAAATGGGT
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
64 1 0.01
65 70 0.75
66 2 0.02
67 20 0.22
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAGTCAGTGCATTGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGA
Found at i:1428259 original size:65 final size:65
Alignment explanation
Indices: 1428182--1428315 Score: 198
Period size: 65 Copynumber: 2.1 Consensus size: 65
1428172 ACACTAATTA
* * *
1428182 CATTTGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCAT-GGTCTGTGCATTGGTACACAAAAT
1 CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCT-TGTGCATCGGTACACAAAAT
1428246 G
65 G
* **
1428247 CATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATAGCTTGTGCATCGGTACACAAAATG
1 CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCTTGTGCATCGGTACACAAAATG
1428312 CATT
1 CATT
1428316 TGAAATGGGT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
65 60 0.97
66 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (65 bp):
CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCTTGTGCATCGGTACACAAAATG
Found at i:1429895 original size:13 final size:13
Alignment explanation
Indices: 1429877--1429902 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1429867 TAATATAAAT
1429877 ATTAAATTCATCA
1 ATTAAATTCATCA
1429890 ATTAAATTCATCA
1 ATTAAATTCATCA
1429903 TTTTTCTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAAATTCATCA
Found at i:1435643 original size:43 final size:43
Alignment explanation
Indices: 1435582--1435676 Score: 181
Period size: 43 Copynumber: 2.2 Consensus size: 43
1435572 ACTTCATTGG
1435582 AAAAGTGTTTATTTTTTACTATACAACTTATGTACGAGATTTT
1 AAAAGTGTTTATTTTTTACTATACAACTTATGTACGAGATTTT
1435625 AAAAGTGTTTATTTTTTACTATACAACTTATGTACGAGATTTT
1 AAAAGTGTTTATTTTTTACTATACAACTTATGTACGAGATTTT
1435668 AAGAAGTGT
1 AA-AAGTGT
1435677 ATTTATAATC
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 45 0.88
44 6 0.12
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (43 bp):
AAAAGTGTTTATTTTTTACTATACAACTTATGTACGAGATTTT
Found at i:1444806 original size:21 final size:21
Alignment explanation
Indices: 1444780--1444921 Score: 173
Period size: 21 Copynumber: 6.7 Consensus size: 21
1444770 AGAGTGACAA
* *
1444780 AGTGCATCCATGTACCCTTGC
1 AGTGCATCCATGCACCCCTGC
1444801 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
1444822 AGTGCATCAATACACCCCTGC
1 AGTGCATCCATGCACCCCTGC
1444843 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
1444864 AGTGCATCCATGCACTTTCCACT--
1 AGTGCATCCATGCAC---CC-CTGC
* *
1444887 AGTGCATCGATGCA-CCATGC
1 AGTGCATCCATGCACCCCTGC
1444907 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1444922 TCAAACACCG
Statistics
Matches: 105, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 13 0.12
21 72 0.69
23 13 0.12
24 2 0.02
25 2 0.02
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1445054 original size:21 final size:21
Alignment explanation
Indices: 1445030--1445083 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1445020 GAAGGGGTAT
1445030 CGATGCACCATGATAGTGCAC
1 CGATGCACCATGATAGTGCAC
1445051 CGATGCACCATGATAGTGCAC
1 CGATGCACCATGATAGTGCAC
1445072 CGATGCACCATG
1 CGATGCACCATG
1445084 TTATGGGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.19
Consensus pattern (21 bp):
CGATGCACCATGATAGTGCAC
Found at i:1448082 original size:19 final size:20
Alignment explanation
Indices: 1448038--1448085 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1448028 AAGTTTGGTT
1448038 TGAAAAAGTCAATTTCTTAA
1 TGAAAAAGTCAATTTCTTAA
*
1448058 TGAAAAATTCAATTTCTTAA
1 TGAAAAAGTCAATTTCTTAA
*
1448078 TAAAAAAG
1 TGAAAAAG
1448086 GGGGAGCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (20 bp):
TGAAAAAGTCAATTTCTTAA
Found at i:1448150 original size:21 final size:21
Alignment explanation
Indices: 1448124--1448163 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1448114 CAACAATTGG
1448124 TAACAATTGATATCATTTTGC
1 TAACAATTGATATCATTTTGC
*
1448145 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
1448164 CATTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGC
Found at i:1448412 original size:21 final size:21
Alignment explanation
Indices: 1448386--1448485 Score: 132
Period size: 21 Copynumber: 4.7 Consensus size: 21
1448376 AGAGTGTCAA
1448386 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
1448407 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1448428 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTGC
* *
1448450 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
1448471 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1448486 TCAAGCACCG
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
20 14 0.20
21 38 0.55
22 2 0.03
23 15 0.22
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1454746 original size:25 final size:25
Alignment explanation
Indices: 1454712--1454763 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1454702 ATTATCTGAG
1454712 GTGGAAATAGCTGGCATCCATGTCA
1 GTGGAAATAGCTGGCATCCATGTCA
1454737 GTGGAAATAGCTGGCATCCATGTCA
1 GTGGAAATAGCTGGCATCCATGTCA
1454762 GT
1 GT
1454764 AAAAACTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (25 bp):
GTGGAAATAGCTGGCATCCATGTCA
Found at i:1464296 original size:20 final size:20
Alignment explanation
Indices: 1464267--1464305 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1464257 AGAGCTCATA
*
1464267 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1464287 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1464306 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1470190 original size:7 final size:7
Alignment explanation
Indices: 1470171--1470204 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1470161 AGAAAAGTAA
1470171 ATTTTAT
1 ATTTTAT
1470178 ATTTTTAT
1 A-TTTTAT
1470186 ATTTTAT
1 ATTTTAT
*
1470193 ATTATAT
1 ATTTTAT
1470200 ATTTT
1 ATTTT
1470205 TTATATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTAT
Found at i:1470213 original size:15 final size:15
Alignment explanation
Indices: 1470171--1470213 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1470161 AGAAAAGTAA
* *
1470171 ATTTTATATTTTTAT
1 ATTTTATATATATAT
1470186 ATTTTATAT-TATAT
1 ATTTTATATATATAT
*
1470200 ATTTTTTATATATA
1 ATTTTATATATATA
1470214 ATCATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTATATATATAT
Found at i:1470378 original size:21 final size:21
Alignment explanation
Indices: 1470354--1470396 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1470344 ATAAAAATAA
1470354 TTTTAAAAATATTAAATTTAT
1 TTTTAAAAATATTAAATTTAT
* *
1470375 TTTTATACATATTAAATTTAT
1 TTTTAAAAATATTAAATTTAT
1470396 T
1 T
1470397 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAAAAATATTAAATTTAT
Found at i:1470401 original size:21 final size:21
Alignment explanation
Indices: 1470362--1470401 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1470352 AATTTTAAAA
*
1470362 ATATTAAATTTATTTTTATAC
1 ATATTAAATTTATTATTATAC
1470383 ATATTAAATTTATTATTAT
1 ATATTAAATTTATTATTAT
1470402 TTTAAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTAAATTTATTATTATAC
Found at i:1472525 original size:16 final size:17
Alignment explanation
Indices: 1472504--1472539 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1472494 TTAATGTTAT
1472504 TTTAAAATTAAATT-AA
1 TTTAAAATTAAATTGAA
*
1472520 TTTAAATTTAAATTGAA
1 TTTAAAATTAAATTGAA
1472537 TTT
1 TTT
1472540 TTCTCATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAATTAAATTGAA
Found at i:1473018 original size:15 final size:15
Alignment explanation
Indices: 1473000--1473048 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1472990 TGATGATGAT
* *
1473000 GATGACGACGATAAC
1 GATGATGACGACAAC
1473015 GATGATGACGACAAC
1 GATGATGACGACAAC
*
1473030 GATGATGACGACGAC
1 GATGATGACGACAAC
1473045 GATG
1 GATG
1473049 CCGATGATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.31, T:0.14
Consensus pattern (15 bp):
GATGATGACGACAAC
Found at i:1473053 original size:21 final size:19
Alignment explanation
Indices: 1472994--1473057 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 19
1472984 TGATGATGAT
*
1472994 GATGATGATGACGACGATAAC
1 GATGATGACGACGACGAT--C
1473015 GATGATGACGAC-A--A-C
1 GATGATGACGACGACGATC
1473030 GATGATGACGACGACGATGCC
1 GATGATGACGACGACGAT--C
1473051 GATGATG
1 GATGATG
1473058 GTGGTGGTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
15 13 0.36
16 1 0.03
18 2 0.06
20 1 0.03
21 19 0.53
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (19 bp):
GATGATGACGACGACGATC
Found at i:1473605 original size:23 final size:23
Alignment explanation
Indices: 1473578--1473624 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1473568 TAAGATGTAA
1473578 ATTTTTTATATTTAT-AGTTATGT
1 ATTTTTT-TATTTATAAGTTATGT
* *
1473601 ATTTTTTTCTTTCTAAGTTATGT
1 ATTTTTTTATTTATAAGTTATGT
1473624 A
1 A
1473625 AAATGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (23 bp):
ATTTTTTTATTTATAAGTTATGT
Found at i:1473606 original size:22 final size:23
Alignment explanation
Indices: 1473580--1473624 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1473570 AGATGTAAAT
1473580 TTTTTATATTTAT-AGTTATGTA
1 TTTTTATATTTATAAGTTATGTA
* * *
1473602 TTTTTTTCTTTCTAAGTTATGTA
1 TTTTTATATTTATAAGTTATGTA
1473625 AAATGATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.22, C:0.04, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTTTATATTTATAAGTTATGTA
Found at i:1476587 original size:2 final size:2
Alignment explanation
Indices: 1476580--1476613 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1476570 CTAACATGCC
1476580 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1476614 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1476618 original size:2 final size:2
Alignment explanation
Indices: 1476613--1476647 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1476603 TCTCTCTCTC
1476613 TA TA 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 TA TA T
1476648 TCAAACTACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1478964 original size:10 final size:10
Alignment explanation
Indices: 1478951--1478995 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
1478941 GGTCATCCGA
*
1478951 CCGAGACCAT
1 CCGAGAACAT
*
1478961 CCGAGAGCAT
1 CCGAGAACAT
**
1478971 CCGAGGTCAT
1 CCGAGAACAT
1478981 CCGAGAACAT
1 CCGAGAACAT
1478991 CCGAG
1 CCGAG
1478996 GTCATCCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (10 bp):
CCGAGAACAT
Found at i:1478981 original size:20 final size:20
Alignment explanation
Indices: 1478958--1479004 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1478948 CGACCGAGAC
*
1478958 CATCCGAGAGCATCCGAGGT
1 CATCCGAGAACATCCGAGGT
1478978 CATCCGAGAACATCCGAGGT
1 CATCCGAGAACATCCGAGGT
1478998 CATCCGA
1 CATCCGA
1479005 ACGAGCTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.15
Consensus pattern (20 bp):
CATCCGAGAACATCCGAGGT
Found at i:1478992 original size:30 final size:33
Alignment explanation
Indices: 1478936--1479004 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 33
1478926 AGATTGTATG
1478936 TCCGAGGTCATCCGACCGAGACCATCCGAGAG-CA
1 TCCGAGGTCATCCGA-CGAGACCATCCGAG-GTCA
1478970 TCCGAGGTCATCCGA-GA-A-CATCCGAGGTCA
1 TCCGAGGTCATCCGACGAGACCATCCGAGGTCA
1479000 TCCGA
1 TCCGA
1479005 ACGAGCTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 1 0.03
30 15 0.44
31 1 0.03
32 2 0.06
34 15 0.44
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.14
Consensus pattern (33 bp):
TCCGAGGTCATCCGACGAGACCATCCGAGGTCA
Found at i:1479001 original size:10 final size:10
Alignment explanation
Indices: 1478958--1479004 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
1478948 CGACCGAGAC
1478958 CATCCGAGAG-
1 CATCCGAG-GT
1478968 CATCCGAGGT
1 CATCCGAGGT
**
1478978 CATCCGAGAA
1 CATCCGAGGT
1478988 CATCCGAGGT
1 CATCCGAGGT
1478998 CATCCGA
1 CATCCGA
1479005 ACGAGCTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 1 0.03
10 31 0.97
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.15
Consensus pattern (10 bp):
CATCCGAGGT
Found at i:1479153 original size:29 final size:29
Alignment explanation
Indices: 1479069--1479145 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
1479059 GAGCGAGGGT
* *
1479069 AGGTCGTCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
1479098 AGGTCACCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
1479127 AGGTCGCCCGGAGGGCATG
1 AGGTCGCCCGGAGGGCATG
1479146 ACGGCCTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.21, C:0.29, G:0.38, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:1479255 original size:29 final size:29
Alignment explanation
Indices: 1479212--1479268 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1479202 GAGCAAGGGT
*
1479212 AGGTCGTCCGAAGTGCATGGCGACTTACA
1 AGGTCGCCCGAAGTGCATGGCGACTTACA
*
1479241 AGGTCGCCCGGAGTGCATGGCGACTTAC
1 AGGTCGCCCGAAGTGCATGGCGACTTAC
1479269 GGCCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.19
Consensus pattern (29 bp):
AGGTCGCCCGAAGTGCATGGCGACTTACA
Found at i:1480291 original size:18 final size:18
Alignment explanation
Indices: 1480262--1480301 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
1480252 AATATTAAGA
1480262 AAAACAAAAAAAATAAACG
1 AAAACAAAAAAAATAAA-G
1480281 AAAACAAAAAAAATAAAG
1 AAAACAAAAAAAATAAAG
1480299 AAA
1 AAA
1480302 CGTATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.82, C:0.07, G:0.05, T:0.05
Consensus pattern (18 bp):
AAAACAAAAAAAATAAAG
Found at i:1480405 original size:16 final size:16
Alignment explanation
Indices: 1480367--1480407 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1480357 TAGTAATAGT
*
1480367 TATATTAATATATATA
1 TATAATAATATATATA
* *
1480383 AAAAATAATATATATA
1 TATAATAATATATATA
1480399 TATAATAAT
1 TATAATAAT
1480408 TTGTAAACAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAATAATATATATA
Found at i:1482376 original size:105 final size:105
Alignment explanation
Indices: 1482138--1483017 Score: 1571
Period size: 105 Copynumber: 8.4 Consensus size: 105
1482128 TGTTTTGAGG
* * * * *
1482138 CCAATATCTTTCGTTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAA-TGTTTGTTGACAACCAG
*
1482203 CGGTCCCTTCGTTGTGAAGTTGAACTTTGCGTTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAAC-TTGCGTTGTCTGGAGT
*
1482245 CCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
*
1482310 GGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
1482350 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTGTTTGTTGACAACCAAC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1482415 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1482455 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG-TTTGTTGACAACCAG
*
1482520 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCGGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
1482561 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1482626 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
1482666 CCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGAAAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
*
1482731 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1482771 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
*
1482836 GGTCCCTTCGTCGCGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
1482876 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1482941 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1482981 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1483018 GTAAAACCTG
Statistics
Matches: 743, Mismatches: 29, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
105 560 0.75
106 142 0.19
107 41 0.06
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:1482736 original size:316 final size:316
Alignment explanation
Indices: 1482138--1483017 Score: 1566
Period size: 316 Copynumber: 2.8 Consensus size: 316
1482128 TGTTTTGAGG
* * * * *
1482138 CCAATATCTTTCGTTATGAAGTTGAAATTGGCTCCGAAATTGGGAAAT-TGTTTGTTGACAACCA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGT-TTTGTTGACAACCA
* *
1482202 GCGGTCCCTTCGTTGTGAAGTTGAACTTTGCGTTGTCTGGAGTCCAATATCCTTTGTTGTGAAGT
65 GCGGTCCCTTCGTCGTGAAGTTGAAC-TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
1482267 TGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAA
129 TGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
*
1482332 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAG
194 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAA
* *
1482397 TGTTTGTTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
259 TGTTCGTTGAAAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1482455 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTTGTTGACAACCAG
*
1482520 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCGGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
*
1482585 AAATTGGCTCTGAATTTGAGAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
1482650 TTGCGTTGTCTGGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
* *
1482715 TTCGTTGAAAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
261 TTCGTTGAAAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1482771 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG-TTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTTGTTGACAACCAG
*
1482835 CGGTCCCTTCGTCGCGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
*
1482900 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
1482965 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1483018 GTAAAACCTG
Statistics
Matches: 541, Mismatches: 21, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
315 193 0.36
316 265 0.49
317 82 0.15
318 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (316 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
TTCGTTGAAAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:1496817 original size:3 final size:3
Alignment explanation
Indices: 1496804--1496850 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
1496794 GTAGTGTAAT
*
1496804 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1496850 T
1 T
1496851 TCGGACAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1498980 original size:19 final size:19
Alignment explanation
Indices: 1498956--1498992 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1498946 ATGACCAACA
1498956 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
1498975 AAATCGCAATGCGATCTC
1 AAATCGCAATGCGATCTC
1498993 CAGTATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:1499162 original size:20 final size:20
Alignment explanation
Indices: 1499110--1499154 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1499100 GAATATGTAA
*
1499110 ATCGCAACACGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1499130 ATCGCAACGCGATTCTTACT
1 ATCGCAACGCGATTCTGACT
1499150 ATCGC
1 ATCGC
1499155 GTTGCGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1499358 original size:22 final size:22
Alignment explanation
Indices: 1499333--1499379 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1499323 GGCGACATCT
*
1499333 GTCCCCATCTCCGACGAAATTC
1 GTCCCCATCTCCGACGAAATCC
1499355 GTCCCCATCTCCGACGAAATCC
1 GTCCCCATCTCCGACGAAATCC
1499377 GTC
1 GTC
1499380 TATCTCCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.43, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCC
Found at i:1499805 original size:20 final size:19
Alignment explanation
Indices: 1499780--1499831 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
1499770 CGATTTTAGT
1499780 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTC-AA
*
1499800 TTCGCGTTGCGATAGTCAT
1 TTCGCGTTGCGATAGTCAA
*
1499819 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
1499832 TTTCATTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTCAA
Found at i:1499843 original size:20 final size:19
Alignment explanation
Indices: 1499769--1499854 Score: 75
Period size: 20 Copynumber: 4.4 Consensus size: 19
1499759 AAATCGCAAA
1499769 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
** *
1499788 GCGATAGTCAAATTCGCGTT
1 GCGATTTTC-ATTTCGCGTT
** *
1499808 GCGATAGTCATTTCGTGTT
1 GCGATTTTCATTTCGCGTT
*
1499827 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCA-TTTCGCGTT
1499847 GCGATTTT
1 GCGATTTT
1499855 AAGTTTCAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.39
20 34 0.60
21 1 0.02
ACGTcount: A:0.15, C:0.16, G:0.24, T:0.44
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:1499861 original size:20 final size:20
Alignment explanation
Indices: 1499818--1499861 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1499808 GCGATAGTCA
* *
1499818 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1499838 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1499858 TTTC
1 TTTC
1499862 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1501773 original size:20 final size:20
Alignment explanation
Indices: 1501750--1501788 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1501740 AAACTTAAAA
1501750 TCGCAACGCGAAAATGACTT
1 TCGCAACGCGAAAATGACTT
* *
1501770 TCGCAATGCGGAAATGACT
1 TCGCAACGCGAAAATGACT
1501789 ATCGTAACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTT
Found at i:1501897 original size:19 final size:20
Alignment explanation
Indices: 1501868--1501906 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1501858 GTAACACGAA
*
1501868 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
1501888 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
1501907 ATCTTGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:1501918 original size:14 final size:14
Alignment explanation
Indices: 1501899--1501933 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1501889 TTATTTCGCA
1501899 TTGCGATTATCTTG
1 TTGCGATTATCTTG
1501913 TTGCGATTATCTTG
1 TTGCGATTATCTTG
1501927 TTGCGAT
1 TTGCGAT
1501934 AGTCATTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (14 bp):
TTGCGATTATCTTG
Found at i:1501951 original size:20 final size:20
Alignment explanation
Indices: 1501926--1501973 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1501916 CGATTATCTT
1501926 GTTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTCCGC
*
1501946 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTCCGC
1501966 GTTGCGAT
1 GTTGCGAT
1501974 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGC
Found at i:1501983 original size:20 final size:20
Alignment explanation
Indices: 1501960--1502003 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1501950 CGATAGTCAT
1501960 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
1501980 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
1502000 TTTC
1 TTTC
1502004 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:1502556 original size:21 final size:21
Alignment explanation
Indices: 1502532--1502601 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
1502522 CTATAATCCC
1502532 TCAAGAGTCCCCTCCCATCGT
1 TCAAGAGTCCCCTCCCATCGT
* **
1502553 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGTCCCCTCCCATCGT
* * *
1502574 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCATCGT
1502595 TCAAGAG
1 TCAAGAG
1502602 CCCGATTCAC
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCATCGT
Found at i:1502580 original size:42 final size:42
Alignment explanation
Indices: 1502479--1502601 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1502469 GCCCGACTCA
* ** *
1502479 CCTGTCATCGTTCAAGAGGCCTATCCTAACGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCAACGTTCAAGAGGCC
* * ** *
1502521 CCTATAATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCAACGTTCAAGAGGCC
* * *
1502563 CCTGTCATCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGA-GTCCCCTCCCAACGTTCAAGAG
1502602 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 62 0.97
43 2 0.03
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.23
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCCAACGTTCAAGAGGCC
Found at i:1504018 original size:13 final size:13
Alignment explanation
Indices: 1503980--1504019 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1503970 CATTTTTTGC
1503980 TTGTTTAATTGAT
1 TTGTTTAATTGAT
**
1503993 TTGTAAAAATTGAT
1 TTGT-TTAATTGAT
1504007 TTGTTTAATTGAT
1 TTGTTTAATTGAT
1504020 GTGTAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (13 bp):
TTGTTTAATTGAT
Found at i:1504167 original size:20 final size:20
Alignment explanation
Indices: 1504130--1504227 Score: 133
Period size: 20 Copynumber: 4.9 Consensus size: 20
1504120 AGGTACACTT
* * *
1504130 TCGCAACGCTAAACTCAAAA
1 TCGCAATGCGAAAGTCAAAA
* *
1504150 TTGCAATGCGAAATTCAAAA
1 TCGCAATGCGAAAGTCAAAA
*
1504170 TCGCAATGCGAAAGCCAAAA
1 TCGCAATGCGAAAGTCAAAA
*
1504190 TCGCAATGCGAAAGCCAAAA
1 TCGCAATGCGAAAGTCAAAA
1504210 TCGCAATGCGAAAGTCAA
1 TCGCAATGCGAAAGTCAA
1504228 TTCGCGTTGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAATGCGAAAGTCAAAA
Found at i:1504259 original size:20 final size:19
Alignment explanation
Indices: 1504216--1504408 Score: 82
Period size: 20 Copynumber: 10.3 Consensus size: 19
1504206 AAAATCGCAA
* *
1504216 TGCGAAAGTCAATTCGCGT
1 TGCGATAGTCAATACGCGT
*
1504235 TGCGATAGTCTAATACGCTT
1 TGCGATAGTC-AATACGCGT
* *
1504255 TGCGAT--T---TTCTCGT
1 TGCGATAGTCAATACGCGT
* *
1504269 TGCGATAGTCAAATTCCCGT
1 TGCGATAGTC-AATACGCGT
* * **
1504289 TGCGATAATCAAATTCATGT
1 TGCGATAGTC-AATACGCGT
*
1504309 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTC-AATACGCGT
* * *
1504329 TGTGATAGTTAAATTCGCGT
1 TGCGATAG-TCAATACGCGT
**
1504349 TGCGAT--T-TTTA--CGT
1 TGCGATAGTCAATACGCGT
*
1504363 TGCGATAGTCATATTCGCGT
1 TGCGATAGTCA-ATACGCGT
*
1504383 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTC-AATACGCGT
1504403 TGCGAT
1 TGCGAT
1504409 TTTTGAGTTA
Statistics
Matches: 137, Mismatches: 22, Indels: 29
0.73 0.12 0.15
Matches are distributed among these distances:
14 19 0.14
16 3 0.02
17 1 0.01
18 2 0.01
19 9 0.07
20 101 0.74
21 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (19 bp):
TGCGATAGTCAATACGCGT
Found at i:1504322 original size:40 final size:40
Alignment explanation
Indices: 1504216--1504408 Score: 169
Period size: 34 Copynumber: 5.2 Consensus size: 40
1504206 AAAATCGCAA
* * * *
1504216 TGCGAAAGTC-AATTCGCGTTGCGATAGTCTAATACGCTT
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGT
* *
1504255 TGCGAT--T----TTCTCGTTGCGATAGTCAAATTCCCGT
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGT
* **
1504289 TGCGATAATCAAATTCATGTTGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGT
* * **
1504329 TGTGATAGTTAAATTCGCGTTGCGAT--T----TTTACGT
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGT
*
1504363 TGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGT
1504403 TGCGAT
1 TGCGAT
1504409 TTTTGAGTTA
Statistics
Matches: 121, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
34 56 0.46
36 2 0.02
37 1 0.01
38 1 0.01
39 5 0.04
40 56 0.46
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (40 bp):
TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGT
Found at i:1504352 original size:94 final size:93
Alignment explanation
Indices: 1504216--1504408 Score: 264
Period size: 94 Copynumber: 2.1 Consensus size: 93
1504206 AAAATCGCAA
* *
1504216 TGCGAAAGTCAATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCT-CGTTGCGATAGTCA
1 TGCGATAGTCAATTCGCGTTGCGATAGTCTAATACGCGTTGCGATTTT-TACGTTGCGATAGTCA
*
1504280 AATTCCCGTTGCGATAATCAAATTCATGT
65 AATTCCCGTTGCGATAATCAAATTCACGT
* *
1504309 TGCGATAGTCAAATTCGCGTTGTGATAGT-TAAATTCGCGTTGCGATTTTTACGTTGCGATAGTC
1 TGCGATAGTC-AATTCGCGTTGCGATAGTCT-AATACGCGTTGCGATTTTTACGTTGCGATAGTC
* * * *
1504373 ATATTCGCGTTGCGATAGTCAAATTCGCGT
64 AAATTCCCGTTGCGATAATCAAATTCACGT
1504403 TGCGAT
1 TGCGAT
1504409 TTTTGAGTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
93 11 0.12
94 77 0.88
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (93 bp):
TGCGATAGTCAATTCGCGTTGCGATAGTCTAATACGCGTTGCGATTTTTACGTTGCGATAGTCAA
ATTCCCGTTGCGATAATCAAATTCACGT
Found at i:1504390 original size:54 final size:54
Alignment explanation
Indices: 1504266--1504450 Score: 210
Period size: 54 Copynumber: 3.3 Consensus size: 54
1504256 GCGATTTTCT
* * *
1504266 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCATGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T---TTTGA-GTTGCGATAGTCAAATTCG
* * *
1504326 CGTTGTGATAGTTAAATTCGCGTTGCGATTTTT-ACGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA-GTTGCGATAGTCAAATTCG
**
1504380 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTATGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTGCGATAGTCAAATTCG
* *
1504434 CATTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1504451 GAATGTGTAA
Statistics
Matches: 111, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
54 81 0.73
55 3 0.03
58 1 0.01
60 26 0.23
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTGCGATAGTCAAATTCG
Found at i:1504440 original size:74 final size:71
Alignment explanation
Indices: 1504205--1504448 Score: 175
Period size: 74 Copynumber: 3.3 Consensus size: 71
1504195 ATGCGAAAGC
* * * * * * *
1504205 CAAAATCGCAATGCGAAAGTCAATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTT
1 CAAATTCGCATTGCGATAGTCAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TAGTT
1504270 GCGATAGT
65 -CGATAGT
* * * ** * * * *
1504278 CAAATTCCCGTTGCGATAATCAAATTCATGTTGCGATAGTCAAATTCGCGTTGTGATAGTTAAAT
1 CAAATTCGCATTGCGATAGTC-AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT-TTTTAGT
* *
1504343 TCGCGTTG-
64 TCG-ATAGT
** ** *
1504351 CGATTTTTACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAG
1 C-AAATTCGCATTGCGATAGTCA-ATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT-AG
*
1504416 TTATGATAGT
63 TT-CGATAGT
*
1504426 CAAATTCGCATTGCGATATTCAA
1 CAAATTCGCATTGCGATAGTCAA
1504449 ATGAATGTGT
Statistics
Matches: 125, Mismatches: 38, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
73 22 0.18
74 99 0.79
75 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (71 bp):
CAAATTCGCATTGCGATAGTCAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTAGTTC
GATAGT
Found at i:1504673 original size:140 final size:140
Alignment explanation
Indices: 1504421--1504703 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
1504411 TTGAGTTATG
*
1504421 ATAGTCAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1504486 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
1504551 AATACACATA
131 AATACACATA
* *
1504561 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAATAACTGAACAGATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
* *
1504626 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
1504691 AATACACATA
131 AATACACATA
1504701 ATA
1 ATA
1504704 CAACGTTTGC
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCACATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1504784 original size:18 final size:18
Alignment explanation
Indices: 1504761--1504795 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1504751 AAGCCGGTTG
*
1504761 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1504779 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1504796 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Done.