Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 3 of 135
Found at i:976371 original size:30 final size:29
Alignment explanation
Indices: 976249--976463 Score: 181
Period size: 29 Copynumber: 7.3 Consensus size: 29
976239 TAAAAATCAT
*
976249 ATTTTGACCTCCAAAC-TTTCCAAGATTAC
1 ATTTTGACC-CCAAACTTTTCCAAAATTAC
* ** *
976278 A-TTTAATCCTTAAACTTCTCCAAAATTAC
1 ATTTTGA-CCCCAAACTTTTCCAAAATTAC
* ** *
976307 ACTTT-AGCCTTAAA-TTATTCAAAAATTAC
1 ATTTTGA-CCCCAAACTT-TTCCAAAATTAC
976336 A-TTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCC-AAACTTTTCCAAAATTAC
*
976365 ATTTTGACCCTCAAACTTTTCCAAAATTTC
1 ATTTTGACCC-CAAACTTTTCCAAAATTAC
* * *
976395 ATTTTGCCCCCTAAAC-TTCCCAAAAGTCAC
1 ATTTTGACCCC-AAACTTTTCCAAAA-TTAC
* *
976425 ATTTTGACCCCAAACTCTTCCAAAATTGC
1 ATTTTGACCCCAAACTTTTCCAAAATTAC
976454 ATTTTGACCC
1 ATTTTGACCC
976464 AAAATTCTTT
Statistics
Matches: 153, Mismatches: 21, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
28 15 0.10
29 75 0.49
30 62 0.41
31 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
ATTTTGACCCCAAACTTTTCCAAAATTAC
Found at i:976418 original size:59 final size:59
Alignment explanation
Indices: 976249--976463 Score: 201
Period size: 59 Copynumber: 3.7 Consensus size: 59
976239 TAAAAATCAT
* * * *
976249 ATTTTGA-CCTCCAAAC-TTTCCAAGATTACA-TTTAATCCTTAAACTTCTCCAAAATTAC
1 ATTTTGACCCT-CAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTC-CCAAAATTAC
* * * * * *
976307 ACTTT-AGCCTTAAA-TTATTCAAAAATTACA-TTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCTCAAACTT-TTCCAAAATTACATTTTGACCCCTAAAC-TTCCCAAAATTAC
* * *
976365 ATTTTGACCCTCAAACTTTTCCAAAATTTCATTTTGCCCCCTAAACTTCCCAAAAGTCAC
1 ATTTTGACCCTCAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTCCCAAAA-TTAC
* *
976425 ATTTTGACCC-CAAACTCTTCCAAAATTGCATTTTGACCC
1 ATTTTGACCCTCAAACTTTTCCAAAATTACATTTTGACCC
976464 AAAATTCTTT
Statistics
Matches: 128, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
57 5 0.04
58 42 0.33
59 54 0.42
60 27 0.21
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (59 bp):
ATTTTGACCCTCAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTCCCAAAATTAC
Found at i:976486 original size:28 final size:29
Alignment explanation
Indices: 976328--976472 Score: 123
Period size: 30 Copynumber: 4.9 Consensus size: 29
976318 AAATTATTCA
* *
976328 AAAATTACA-TTTGACCCCAAAACTTTTCC
1 AAAATTGCATTTTGA-CCCAAAACTCTTCC
* * *
976357 AAAATTACATTTTGACCCTCAAACTTTTCC
1 AAAATTGCATTTTGACCC-AAAACTCTTCC
* * * *
976387 AAAATTTCATTTTGCCCCCTAAACT-TCCC
1 AAAATTGCATTTTG-ACCCAAAACTCTTCC
** *
976416 AAAAGTCACATTTTGACCCCAAACTCTTCC
1 AAAA-TTGCATTTTGACCCAAAACTCTTCC
*
976446 AAAATTGCATTTTGACCCAAAATTCTT
1 AAAATTGCATTTTGACCCAAAACTCTT
976473 TGAAACTTCA
Statistics
Matches: 97, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
29 46 0.47
30 48 0.49
31 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAATTGCATTTTGACCCAAAACTCTTCC
Found at i:981705 original size:21 final size:21
Alignment explanation
Indices: 981679--981750 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
981669 TTCACTTACA
981679 TTAATATAAAATTTAAATAAT
1 TTAATATAAAATTTAAATAAT
* *
981700 TTAATAT-TATTTTATAATTTACA-
1 TTAATATAAAATTTA-AA--TA-AT
981723 TTAATATAAAATTTAAATAAT
1 TTAATATAAAATTTAAATAAT
981744 TTAATAT
1 TTAATAT
981751 TATTTTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 6 0.15
21 18 0.44
23 11 0.27
24 6 0.15
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATATAAAATTTAAATAAT
Found at i:981718 original size:18 final size:18
Alignment explanation
Indices: 981695--981763 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 18
981685 TAAAATTTAA
981695 ATAATTTAATATTATTTT
1 ATAATTTAATATTATTTT
*
981713 ATAATTTACATTAATATAAAATTTAA
1 ATAATTTA-A-T-AT-T---ATTT-T
981739 ATAATTTAATATTATTTT
1 ATAATTTAATATTATTTT
981757 ATAATTT
1 ATAATTT
981764 TTTATATGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
18 15 0.37
19 5 0.12
20 1 0.02
21 2 0.05
22 2 0.05
23 2 0.05
24 1 0.02
25 5 0.12
26 8 0.20
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAATTTAATATTATTTT
Found at i:981722 original size:44 final size:44
Alignment explanation
Indices: 981674--981763 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
981664 AAATATTCAC
981674 TTACATTAATATAAAATTTAAATAATTTAATATTATTTTATAAT
1 TTACATTAATATAAAATTTAAATAATTTAATATTATTTTATAAT
981718 TTACATTAATATAAAATTTAAATAATTTAATATTATTTTATAAT
1 TTACATTAATATAAAATTTAAATAATTTAATATTATTTTATAAT
981762 TT
1 TT
981764 TTTATATGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (44 bp):
TTACATTAATATAAAATTTAAATAATTTAATATTATTTTATAAT
Found at i:986811 original size:22 final size:22
Alignment explanation
Indices: 986783--986952 Score: 178
Period size: 22 Copynumber: 7.3 Consensus size: 22
986773 TAGCGCGCTC
* *
986783 TCTGTTTAGCAGTATGTGTGCT
1 TCTGTTTAGCACTGTGTGTGCT
* *
986805 TCTGTTTCCCCAGCACTATGTGTGTT
1 TCTGTTT----AGCACTGTGTGTGCT
*
986831 TCTGTTCAGCACTGTGTGTGCT
1 TCTGTTTAGCACTGTGTGTGCT
*
986853 TCTGTTTAGCACTATGTGTGCT
1 TCTGTTTAGCACTGTGTGTGCT
986875 TCTGTTTCCCCAGCACTGTGTGTGCT
1 TCTGTTT----AGCACTGTGTGTGCT
*
986901 TCTGTTCAGCACTGTGTGTGCT
1 TCTGTTTAGCACTGTGTGTGCT
*
986923 TCTGTTCAGCACTGTGTGTGCCT
1 TCTGTTTAGCACTGTGTGTG-CT
*
986946 ACTGTTT
1 TCTGTTT
986953 CTCAGCATTT
Statistics
Matches: 128, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
22 82 0.64
23 7 0.05
26 39 0.30
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (22 bp):
TCTGTTTAGCACTGTGTGTGCT
Found at i:986959 original size:48 final size:45
Alignment explanation
Indices: 986783--986953 Score: 202
Period size: 48 Copynumber: 3.7 Consensus size: 45
986773 TAGCGCGCTC
* * * *
986783 TCTGTTTAGCAGTATGTGTGCTTCTGTTTCCCCAGCACTATGTGTGTT
1 TCTGTTCAGCACTGTGTGTGCTTCTGTTT---CAGCACTATGTGTGCT
986831 TCTGTTCAGCACTGTGTGTGCTTCTGTTT-AGCACTATGTGTGCT
1 TCTGTTCAGCACTGTGTGTGCTTCTGTTTCAGCACTATGTGTGCT
*
986875 TCTGTTTCCCCAGCACTGTGTGTGCTTCTG-TTCAGCACTGTGTGTGCT
1 TCTG-TT---CAGCACTGTGTGTGCTTCTGTTTCAGCACTATGTGTGCT
*
986923 TCTGTTCAGCACTGTGTGTGCCTACTGTTTC
1 TCTGTTCAGCACTGTGTGTG-CTTCTGTTTC
986954 TCAGCATTTA
Statistics
Matches: 110, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
44 32 0.29
45 7 0.06
46 3 0.03
47 4 0.04
48 64 0.58
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (45 bp):
TCTGTTCAGCACTGTGTGTGCTTCTGTTTCAGCACTATGTGTGCT
Found at i:986959 original size:70 final size:70
Alignment explanation
Indices: 986783--986953 Score: 279
Period size: 70 Copynumber: 2.4 Consensus size: 70
986773 TAGCGCGCTC
* *
986783 TCTGTTTAGCAGTATGTGTGCTTCTGTTTCCCCAGCACTATGTGTGTTTCTGTTCAGCACTGTGT
1 TCTGTTTAGCACTATGTGTGCTTCTGTTTCCCCAGCACTATGTGTGCTTCTGTTCAGCACTGTGT
986848 GTGCT
66 GTGCT
*
986853 TCTGTTTAGCACTATGTGTGCTTCTGTTTCCCCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGT
1 TCTGTTTAGCACTATGTGTGCTTCTGTTTCCCCAGCACTATGTGTGCTTCTGTTCAGCACTGTGT
986918 GTGCT
66 GTGCT
* * *
986923 TCTGTTCAGCACTGTGTGTGCCTACTGTTTC
1 TCTGTTTAGCACTATGTGTG-CTTCTGTTTC
986954 TCAGCATTTA
Statistics
Matches: 94, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 85 0.90
71 9 0.10
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (70 bp):
TCTGTTTAGCACTATGTGTGCTTCTGTTTCCCCAGCACTATGTGTGCTTCTGTTCAGCACTGTGT
GTGCT
Found at i:995565 original size:15 final size:15
Alignment explanation
Indices: 995545--995575 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
995535 TTTTTGTTAT
995545 ATTTAAAAGTTAATA
1 ATTTAAAAGTTAATA
995560 ATTTAAAAGTTAATA
1 ATTTAAAAGTTAATA
995575 A
1 A
995576 AGCCCATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
ATTTAAAAGTTAATA
Found at i:997889 original size:6 final size:6
Alignment explanation
Indices: 997871--997965 Score: 56
Period size: 6 Copynumber: 16.5 Consensus size: 6
997861 TTTAGTTTTA
* * * *
997871 AAATTT ATA-TT AAGTTT AAATTT -ATTTT AAATTT AACTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
** * ** *
997917 ATTTTT AAAATTT AAAATT -GTTTT AAATTT AAA-TT -AGTTT AAATTT
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
997963 AAA
1 AAA
997966 GTGATTTTAA
Statistics
Matches: 63, Mismatches: 20, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
4 1 0.02
5 13 0.21
6 45 0.71
7 4 0.06
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:997893 original size:17 final size:17
Alignment explanation
Indices: 997871--997996 Score: 71
Period size: 17 Copynumber: 7.4 Consensus size: 17
997861 TTTAGTTTTA
*
997871 AAATTTATATTAAGTTT
1 AAATTTAAATTAAGTTT
** *
997888 AAATTTATTTTAAATTT
1 AAATTTAAATTAAGTTT
* **
997905 AACTTTAAATTTATTTTT
1 AAATTTAAA-TTAAGTTT
997923 AAAATTTAAAATT--GTTTT
1 -AAATTT-AAATTAAG-TTT
997941 AAATTTAAATT-AGTTT
1 AAATTTAAATTAAGTTT
* * *
997957 AAATTTAAAGTGATTTT
1 AAATTTAAATTAAGTTT
* *
997974 AAACTTAATATTAA-ATT
1 AAATTTAA-ATTAAGTTT
997991 AAATTT
1 AAATTT
997997 GAAAGTCCAA
Statistics
Matches: 86, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
16 18 0.21
17 46 0.53
18 12 0.14
19 7 0.08
20 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
AAATTTAAATTAAGTTT
Found at i:997899 original size:11 final size:11
Alignment explanation
Indices: 997885--997921 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
997875 TTATATTAAG
997885 TTTAAATTTAT
1 TTTAAATTTAT
*
997896 TTTAAATTTAAC
1 TTTAAATTT-AT
997908 TTTAAATTTAT
1 TTTAAATTTAT
997919 TTT
1 TTT
997922 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:997911 original size:23 final size:25
Alignment explanation
Indices: 997880--997931 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 25
997870 AAAATTTATA
*
997880 TTAAGTTTAAATTTA-TTTT-AAAT
1 TTAACTTTAAATTTATTTTTAAAAT
997903 TTAACTTTAAATTTATTTTTAAAAT
1 TTAACTTTAAATTTATTTTTAAAAT
997928 TTAA
1 TTAA
997932 AATTGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 14 0.54
24 4 0.15
25 8 0.31
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAACTTTAAATTTATTTTTAAAAT
Found at i:997923 original size:18 final size:17
Alignment explanation
Indices: 997902--997965 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 17
997892 TTATTTTAAA
* *
997902 TTTAACTTTAAATTTATT
1 TTTAAATTTAAATTT-GT
*
997920 TTTAAAATTTAAAATTGT
1 TTT-AAATTTAAATTTGT
*
997938 TTTAAATTTAAATTAG-
1 TTTAAATTTAAATTTGT
997954 TTTAAATTTAAA
1 TTTAAATTTAAA
997966 GTGATTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 12 0.30
17 11 0.28
18 7 0.17
19 10 0.25
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATTTGT
Found at i:1008209 original size:15 final size:15
Alignment explanation
Indices: 1008189--1008219 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1008179 TTTTTGTTAT
1008189 ATTTAAAAGTTAATA
1 ATTTAAAAGTTAATA
1008204 ATTTAAAAGTTAATA
1 ATTTAAAAGTTAATA
1008219 A
1 A
1008220 AGCCCATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
ATTTAAAAGTTAATA
Found at i:1010553 original size:6 final size:6
Alignment explanation
Indices: 1010535--1010652 Score: 77
Period size: 6 Copynumber: 20.5 Consensus size: 6
1010525 TTTAGTTTTA
* * * *
1010535 AAATTT ATA-TT AAGTTT AAATTT -ATTTT AAATTT AACTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * ** * **
1010581 -ATTTT AAATTT AACTTT AAATTT ATTTTT AAAATTT AAAATT -GTTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT
*
1010628 AAATTT AAA-TT -AGTTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
1010653 GTGGTTTTAA
Statistics
Matches: 81, Mismatches: 24, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
4 1 0.01
5 17 0.21
6 59 0.73
7 4 0.05
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:1010557 original size:17 final size:17
Alignment explanation
Indices: 1010535--1010652 Score: 70
Period size: 17 Copynumber: 7.2 Consensus size: 17
1010525 TTTAGTTTTA
*
1010535 AAATTTATATTAAGTTT
1 AAATTTATATTAAATTT
*
1010552 AAATTTATTTTAAATTT
1 AAATTTATATTAAATTT
* * * *
1010569 AACTTTAAATTTATTTT
1 AAATTTATATTAAATTT
1010586 AAATTTA-ACTTTAAATTT
1 AAATTTATA--TTAAATTT
*
1010604 --ATTT-T-TAAAATTT
1 AAATTTATATTAAATTT
* * *
1010617 AAAATTGTTTTAAATTT
1 AAATTTATATTAAATTT
1010634 AAA-TTAGT-TTAAATTT
1 AAATTTA-TATTAAATTT
1010650 AAA
1 AAA
1010653 GTGGTTTTAA
Statistics
Matches: 79, Mismatches: 14, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
13 7 0.09
15 3 0.04
16 19 0.24
17 44 0.56
18 6 0.08
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
AAATTTATATTAAATTT
Found at i:1010563 original size:11 final size:11
Alignment explanation
Indices: 1010549--1010608 Score: 84
Period size: 11 Copynumber: 5.3 Consensus size: 11
1010539 TTATATTAAG
1010549 TTTAAATTTAT
1 TTTAAATTTAT
*
1010560 TTTAAATTTAAC
1 TTTAAATTT-AT
1010572 TTTAAATTTAT
1 TTTAAATTTAT
*
1010583 TTTAAATTTAAC
1 TTTAAATTT-AT
1010595 TTTAAATTTAT
1 TTTAAATTTAT
1010606 TTT
1 TTT
1010609 TAAAATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
11 23 0.53
12 20 0.47
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:1010575 original size:23 final size:23
Alignment explanation
Indices: 1010544--1010618 Score: 123
Period size: 23 Copynumber: 3.2 Consensus size: 23
1010534 AAAATTTATA
*
1010544 TTAAGTTTAAATTTATTTTAAAT
1 TTAACTTTAAATTTATTTTAAAT
1010567 TTAACTTTAAATTTATTTTAAAT
1 TTAACTTTAAATTTATTTTAAAT
1010590 TTAACTTTAAATTTATTTTTAAAAT
1 TTAACTTTAAATTTA-TTTT-AAAT
1010615 TTAA
1 TTAA
1010619 AATTGTTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
23 37 0.76
24 4 0.08
25 8 0.16
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (23 bp):
TTAACTTTAAATTTATTTTAAAT
Found at i:1010577 original size:12 final size:12
Alignment explanation
Indices: 1010544--1010618 Score: 91
Period size: 12 Copynumber: 6.3 Consensus size: 12
1010534 AAAATTTATA
*
1010544 TTAAGTTTAAAT
1 TTAATTTTAAAT
1010556 TT-ATTTTAAAT
1 TTAATTTTAAAT
*
1010567 TTAACTTTAAAT
1 TTAATTTTAAAT
1010579 TT-ATTTTAAAT
1 TTAATTTTAAAT
*
1010590 TTAACTTTAAAT
1 TTAATTTTAAAT
*
1010602 TTATTTTTAAAAT
1 TTAATTTT-AAAT
1010615 TTAA
1 TTAA
1010619 AATTGTTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
11 20 0.38
12 26 0.49
13 7 0.13
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (12 bp):
TTAATTTTAAAT
Found at i:1010644 original size:16 final size:16
Alignment explanation
Indices: 1010595--1010668 Score: 66
Period size: 16 Copynumber: 4.7 Consensus size: 16
1010585 TAAATTTAAC
1010595 TTTAAATTT--ATT-T
1 TTTAAATTTAAATTGT
*
1010608 TTAAAATTTAAAATTGT
1 TTTAAATTT-AAATTGT
1010625 TTTAAATTTAAATTAG-
1 TTTAAATTTAAATT-GT
*
1010641 TTTAAATTTAAAGTGGT
1 TTTAAATTTAAA-TTGT
*
1010658 TTTAAACTTAA
1 TTTAAATTTAA
1010669 TATTAAATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 8 0.16
16 21 0.42
17 21 0.42
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (16 bp):
TTTAAATTTAAATTGT
Found at i:1010660 original size:33 final size:34
Alignment explanation
Indices: 1010611--1010689 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 34
1010601 TTTATTTTTA
* * * **
1010611 AAATTTAAAATTGTTTTAAATTTAA-ATTAGTTT
1 AAATTTAAAGTGGTTTTAAACTTAATATTAAATT
1010644 AAATTTAAAGTGGTTTTAAACTTAATATTAAATT
1 AAATTTAAAGTGGTTTTAAACTTAATATTAAATT
1010678 AAATTTGAAAGT
1 AAATTT-AAAGT
1010690 CCAAAATACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 22 0.56
34 12 0.31
35 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (34 bp):
AAATTTAAAGTGGTTTTAAACTTAATATTAAATT
Found at i:1010661 original size:17 final size:17
Alignment explanation
Indices: 1010606--1010668 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
1010596 TTAAATTTAT
*
1010606 TTTTAAAATTTAAAATTG
1 TTTT-AAATTTAAAATAG
*
1010624 TTTTAAATTTAAATTAG
1 TTTTAAATTTAAAATAG
* *
1010641 -TTTAAATTTAAAGTGG
1 TTTTAAATTTAAAATAG
*
1010657 TTTTAAACTTAA
1 TTTTAAATTTAA
1010669 TATTAAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 14 0.36
17 21 0.54
18 4 0.10
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (17 bp):
TTTTAAATTTAAAATAG
Found at i:1013969 original size:21 final size:21
Alignment explanation
Indices: 1013932--1013974 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1013922 ATAAATATTG
*
1013932 ATTGTGTGATTAATTGATGAA
1 ATTGTGTGATTAATTGAGGAA
*
1013953 ATTGTG-GATTTATTTGAGGAA
1 ATTGTGTGA-TTAATTGAGGAA
1013974 A
1 A
1013975 CAAATGTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.42
Consensus pattern (21 bp):
ATTGTGTGATTAATTGAGGAA
Found at i:1014049 original size:6 final size:6
Alignment explanation
Indices: 1014038--1014076 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1014028 TGATCAAAAT
* * *
1014038 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
1014077 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:1015300 original size:30 final size:30
Alignment explanation
Indices: 1015261--1015544 Score: 128
Period size: 29 Copynumber: 9.6 Consensus size: 30
1015251 GCCCCCGAAC
1015261 TTCTCAAAAATTCCATTTTTAACCTCGAAA-T
1 TTCT-AAAAATTCCATTTTTAACCTC-AAACT
*
1015292 TTCTAAAAATTCCATTTTTTACCTCAAACT
1 TTCTAAAAATTCCATTTTTAACCTCAAACT
* * *
1015322 TTCCAAAAAATCACCA-TTTTATCC-CAAACT
1 TT-CTAAAAAT-TCCATTTTTAACCTCAAACT
* ** * *
1015352 TCCT-AAAATTGTATTTTTGACCTCGAACT
1 TTCTAAAAATTCCATTTTTAACCTCAAACT
* **
1015381 TT-TAAAAAATCACATTTTTGCCCT-AAAC-
1 TTCTAAAAATTC-CATTTTTAACCTCAAACT
* * * *
1015409 TTCCAAAAATTACATTTTTACCCCCAAAC-
1 TTCTAAAAATTCCATTTTTAACCTCAAACT
* * * ** *
1015438 TTCCAAAAAATACA-TTTTGCCCCCAAAC-
1 TTCTAAAAATTCCATTTTTAACCTCAAACT
* *
1015466 TTCTAAAAATTACCA-TTTTACCCCCAAAC-
1 TTCTAAAAATT-CCATTTTTAACCTCAAACT
* * *
1015495 TTCGAAAAATAT-CA-TTTTAACCCTTAAAATT
1 TTCTAAAAAT-TCCATTTTTAA-CC-TCAAACT
*
1015526 TTCCAAAAATTGCCATTTT
1 TTCTAAAAATT-CCATTTT
1015545 ACATCGAAAC
Statistics
Matches: 200, Mismatches: 36, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.00
28 53 0.26
29 67 0.34
30 45 0.22
31 26 0.13
32 5 0.03
33 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
TTCTAAAAATTCCATTTTTAACCTCAAACT
Found at i:1015409 original size:29 final size:28
Alignment explanation
Indices: 1015307--1015512 Score: 132
Period size: 29 Copynumber: 7.1 Consensus size: 28
1015297 AAAATTCCAT
* *
1015307 TTTTTACCTCAAACTTTCCAAAAAATCACCA
1 TTTTTGCCCCAAAC-TTCCAAAAAAT-A-CA
* * **
1015338 TTTTAT--CCCAAACTTCCTAAAATTGTA
1 TTTT-TGCCCCAAACTTCCAAAAAATACA
* * **
1015365 TTTTTGACCTCGAACTTTTAAAAAATCACA
1 TTTTTG-CCCCAAACTTCCAAAAAAT-ACA
* *
1015395 TTTTTGCCCTAAACTTCCAAAAATTACA
1 TTTTTGCCCCAAACTTCCAAAAAATACA
*
1015423 TTTTTACCCCCAAACTTCCAAAAAATACA
1 TTTTT-GCCCCAAACTTCCAAAAAATACA
* *
1015452 -TTTTGCCCCCAAACTTCTAAAAATTACCA
1 TTTTTG-CCCCAAACTTCCAAAAAATA-CA
** *
1015481 TTTTACCCCCAAACTT-CGAAAAATATCA
1 TTTTTGCCCCAAACTTCCAAAAAATA-CA
1015509 TTTT
1 TTTT
1015513 AACCCTTAAA
Statistics
Matches: 135, Mismatches: 31, Indels: 21
0.72 0.17 0.11
Matches are distributed among these distances:
26 1 0.01
27 5 0.04
28 42 0.31
29 66 0.49
30 16 0.12
31 4 0.03
32 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (28 bp):
TTTTTGCCCCAAACTTCCAAAAAATACA
Found at i:1015483 original size:58 final size:57
Alignment explanation
Indices: 1015292--1015508 Score: 192
Period size: 58 Copynumber: 3.7 Consensus size: 57
1015282 ACCTCGAAAT
* **
1015292 TTCTAAAAATTCCATTTTTTACCTCAAACTTTCCAAAAAATCACCATTTTATCCCAAAC
1 TTCTAAAAATTCCA-TTTTTACCCCAAAC-TTCCAAAAAATCACCATTTTGCCCCAAAC
** * * ** *
1015351 TTCCT-AAAATTGTATTTTTGACCTCGAACTTTTAAAAAATCA-CATTTTTGCCCTAAAC
1 TT-CTAAAAATTCCATTTTT-ACCCCAAACTTCCAAAAAATCACCA-TTTTGCCCCAAAC
* *
1015409 TTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAAAT-A-CATTTTGCCCCCAAAC
1 TTCTAAAAATTCCATTTTTA-CCCCAAACTTCCAAAAAATCACCATTTTG-CCCCAAAC
*
1015466 TTCTAAAAATTACCA-TTTTACCCCCAAACTTCGAAAAATATCA
1 TTCTAAAAATT-CCATTTTTA-CCCCAAACTTCCAAAAA-ATCA
1015509 TTTTAACCCT
Statistics
Matches: 130, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
56 5 0.04
57 46 0.35
58 59 0.45
59 18 0.14
60 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (57 bp):
TTCTAAAAATTCCATTTTTACCCCAAACTTCCAAAAAATCACCATTTTGCCCCAAAC
Found at i:1015592 original size:29 final size:29
Alignment explanation
Indices: 1015410--1015717 Score: 189
Period size: 29 Copynumber: 10.6 Consensus size: 29
1015400 GCCCTAAACT
* * *
1015410 TCCAAAAATTA-CATTTTTACCCCCAAACT
1 TCCAAAAATTACCA-TTTTACCCTCGAACA
* * * * *
1015439 TCCAAAAAATA-CATTTTGCCCCCAAACT
1 TCCAAAAATTACCATTTTACCCTCGAACA
* * * *
1015467 TCTAAAAATTACCATTTTACCCCCAAACT
1 TCCAAAAATTACCATTTTACCCTCGAACA
* * * *
1015496 TCGAAAAA-TATCATTTTAACCCT-TAAAA
1 TCCAAAAATTACCATTTT-ACCCTCGAACA
* * *
1015524 TTTTCCAAAAATTGCCATTTTA-CATCGAAACT
1 ---TCCAAAAATTACCATTTTACCCTCG-AACA
*
1015556 TCCAAAAATTACCGTTTTACCCTCGAACA
1 TCCAAAAATTACCATTTTACCCTCGAACA
* * * ***
1015585 TCCGAAAATTACAATTTTTCCCTCGAGTG
1 TCCAAAAATTACCATTTTACCCTCGAACA
**
1015614 TCCAAAAATTACCATTTTCACCC-CGATTA
1 TCCAAAAATTACCATTTT-ACCCTCGAACA
* * *
1015643 TCCAAAAATTACCGTTTTATCCTCGAACC
1 TCCAAAAATTACCATTTTACCCTCGAACA
* *
1015672 TCTAAAAATTACCATTTTACCCTCGAGCA
1 TCCAAAAATTACCATTTTACCCTCGAACA
* *
1015701 TCCGAAAATCA-CATTTT
1 TCCAAAAATTACCATTTT
1015718 TTGACTCTGT
Statistics
Matches: 221, Mismatches: 47, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
28 42 0.19
29 153 0.69
30 9 0.04
31 8 0.04
32 9 0.04
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTCGAACA
Found at i:1015709 original size:87 final size:86
Alignment explanation
Indices: 1015556--1015717 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 86
1015546 CATCGAAACT
* * **
1015556 TCCAAAAATTACCGTTTTACCCTCGAACATCCGAAAATTACAATTTTTCCCTCGAGTGTCCAAAA
1 TCCAAAAATTACCGTTTTACCCTCGAACATCCAAAAATTACAATTTTACCCTCGAGCATCCAAAA
*
1015621 ATTACCATTTTCACCCCGATTA
66 ATCA-CATTTTCACCCCGATTA
* * * * *
1015643 TCCAAAAATTACCGTTTTATCCTCGAACCTCTAAAAATTACCATTTTACCCTCGAGCATCCGAAA
1 TCCAAAAATTACCGTTTTACCCTCGAACATCCAAAAATTACAATTTTACCCTCGAGCATCCAAAA
1015708 ATCACATTTT
66 ATCACATTTT
1015718 TTGACTCTGT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
86 6 0.09
87 59 0.91
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.31
Consensus pattern (86 bp):
TCCAAAAATTACCGTTTTACCCTCGAACATCCAAAAATTACAATTTTACCCTCGAGCATCCAAAA
ATCACATTTTCACCCCGATTA
Found at i:1020779 original size:19 final size:19
Alignment explanation
Indices: 1020757--1020801 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1020747 TTATATTAGG
1020757 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
1020776 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
1020795 ATTTAAT
1 ATTTAAT
1020802 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:1028045 original size:2 final size:2
Alignment explanation
Indices: 1028040--1028072 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1028030 GTATATATAT
*
1028040 AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1028073 CCCGCGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1028109 original size:9 final size:9
Alignment explanation
Indices: 1028097--1028133 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1028087 TGCGACCCAT
1028097 GGTGGCGGC
1 GGTGGCGGC
1028106 GGTGGCGGC
1 GGTGGCGGC
1028115 GGTGGCGGC
1 GGTGGCGGC
*
1028124 GGTGGTGGC
1 GGTGGCGGC
1028133 G
1 G
1028134 AGATTTCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.68, T:0.14
Consensus pattern (9 bp):
GGTGGCGGC
Found at i:1034038 original size:142 final size:142
Alignment explanation
Indices: 1033815--1034094 Score: 542
Period size: 142 Copynumber: 2.0 Consensus size: 142
1033805 AATAAAAAAC
1033815 TAATTTCCTCTTTAACCTAATATACCATGATAAACTTTTTTATTTTTTAATAAAAACGATAAAAT
1 TAATTTCCTCTTTAACCTAATATACCATGATAAACTTTTTTATTTTTTAATAAAAACGATAAAAT
*
1033880 ACAATATTACTTTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGTTGAAGGATTTAAAT
66 ACAATATTACTCTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGTTGAAGGATTTAAAT
1033945 GTAATCTTATAA
131 GTAATCTTATAA
*
1033957 TAATTTCCTCTTTAACCTAATATACCATGATAAACTTTTTTATTTTTTAATAAAAATGATAAAAT
1 TAATTTCCTCTTTAACCTAATATACCATGATAAACTTTTTTATTTTTTAATAAAAACGATAAAAT
1034022 ACAATATTACTCTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGTTGAAGGATTTAAAT
66 ACAATATTACTCTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGTTGAAGGATTTAAAT
1034087 GTAATCTT
131 GTAATCTT
1034095 GTAAAATATA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 136 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (142 bp):
TAATTTCCTCTTTAACCTAATATACCATGATAAACTTTTTTATTTTTTAATAAAAACGATAAAAT
ACAATATTACTCTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGTTGAAGGATTTAAAT
GTAATCTTATAA
Found at i:1034154 original size:142 final size:141
Alignment explanation
Indices: 1033866--1034154 Score: 325
Period size: 142 Copynumber: 2.0 Consensus size: 141
1033856 ATTTTTTAAT
*
1033866 AAAAACGATAAAATACAATATTACTTTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGT
1 AAAAACGATAAAATACAATATTACTCTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGT
* * ** ** * **
1033931 TGAAGGATTTAAATGTAATCTTATAATAATTTCCTCTTTAACCTAATATACCATGATAAACTTTT
66 TGAAGGATTTAAATGTAATCTTAAAATAATGTCCTCTTTAA-CTAATATAAAAAAAAAAACTAAT
* ***** *
1033996 TTATTTTTTAAT
130 CTAAGGGGTAAG
*
1034008 AAAAATGATAAAATACAATATTACTCTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGT
1 AAAAACGATAAAATACAATATTACTCTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGT
*
1034073 TGAAGGATTTAAATGTAATCTTGTAAAATATATGTCATTTCTTT-A-T-ATATAAAAAAAAAAAC
66 TGAAGGATTTAAATGTAATC-T-TAAAATA-ATGTC--CTCTTTAACTAATATAAAAAAAAAAAC
1034135 TAATCTAAGGGGT-AG
126 TAATCTAAGGGGTAAG
1034150 AAAAA
1 AAAAA
1034155 GGTAGAAGCA
Statistics
Matches: 123, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
142 89 0.72
143 17 0.14
144 7 0.06
145 4 0.03
146 1 0.01
147 5 0.04
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (141 bp):
AAAAACGATAAAATACAATATTACTCTTAATACGAGAGTACTTTTAGAGGTCAATTTATTAGAGT
TGAAGGATTTAAATGTAATCTTAAAATAATGTCCTCTTTAACTAATATAAAAAAAAAAACTAATC
TAAGGGGTAAG
Found at i:1035015 original size:28 final size:25
Alignment explanation
Indices: 1034977--1035042 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 25
1034967 CGGTAGTTGA
*
1034977 TTTTTTTTAATTAATAC-TTGAATTT
1 TTTTTTTTAATTAA-ACATTGAAGTT
1035002 TATTTTGTCTTAATTAAACATTGAAGTT
1 T-TTTT-T-TTAATTAAACATTGAAGTT
1035030 TTTTTTTTAATTA
1 TTTTTTTTAATTA
1035043 TGCATTCATG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 8 0.22
26 5 0.14
27 7 0.19
28 16 0.44
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.61
Consensus pattern (25 bp):
TTTTTTTTAATTAAACATTGAAGTT
Found at i:1035835 original size:29 final size:28
Alignment explanation
Indices: 1035782--1035836 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
1035772 TGTATTTTTA
* *
1035782 TTATATTTAGAATTTAGTTTTTTTATAC
1 TTATATTTAGAATTTAATTTCTTTATAC
*
1035810 TTATTTTTAAGAATTTAATTTCTTTAT
1 TTATATTT-AGAATTTAATTTCTTTAT
1035837 CTTTCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (28 bp):
TTATATTTAGAATTTAATTTCTTTATAC
Found at i:1039870 original size:28 final size:29
Alignment explanation
Indices: 1039826--1039880 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
1039816 TGAGTATTCG
*
1039826 AAAGTTTAGGATGTAA-TTAGAATAATTT
1 AAAGTTTAGGATGTAATTTAAAATAATTT
1039854 AAAGTTTAGGTAT-TAATTTAAAATAAT
1 AAAGTTTAGG-ATGTAATTTAAAATAAT
1039881 GGGTATAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (29 bp):
AAAGTTTAGGATGTAATTTAAAATAATTT
Found at i:1043667 original size:17 final size:17
Alignment explanation
Indices: 1043622--1043670 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1043612 ATTTCTTATA
1043622 ATATTTATATATTT-AAT
1 ATATTTAT-TATTTAAAT
*
1043639 -TA--TATTAATTAAAT
1 ATATTTATTATTTAAAT
1043653 ATATTTATTATTTAAAT
1 ATATTTATTATTTAAAT
1043670 A
1 A
1043671 ATAATTCAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 4 0.15
14 6 0.23
15 2 0.08
16 2 0.08
17 12 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTATTATTTAAAT
Found at i:1044204 original size:3 final size:3
Alignment explanation
Indices: 1044196--1044222 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1044186 CCCTAAAATA
1044196 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1044223 CCATTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1047208 original size:16 final size:16
Alignment explanation
Indices: 1047187--1047220 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1047177 TATATAAGGA
*
1047187 TTAATTTGTCTATTTT
1 TTAATTTGTCCATTTT
1047203 TTAATTTGTCCATTTT
1 TTAATTTGTCCATTTT
1047219 TT
1 TT
1047221 GAATAGGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.68
Consensus pattern (16 bp):
TTAATTTGTCCATTTT
Found at i:1056311 original size:21 final size:23
Alignment explanation
Indices: 1056271--1056313 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1056261 AATTGAGTGA
*
1056271 TTTTAATATAATTTATCTTTTAT
1 TTTTAATATAATTTACCTTTTAT
1056294 TTTTAATA-AATTT-CCTTTTA
1 TTTTAATATAATTTACCTTTTA
1056314 ATATTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTAATATAATTTACCTTTTAT
Found at i:1071188 original size:15 final size:16
Alignment explanation
Indices: 1071168--1071197 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1071158 CTCAATGCAT
1071168 AATTTT-TTTAATATG
1 AATTTTCTTTAATATG
1071183 AATTTTCTTTAATAT
1 AATTTTCTTTAATAT
1071198 TGATGATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
AATTTTCTTTAATATG
Found at i:1072331 original size:2 final size:2
Alignment explanation
Indices: 1072324--1072359 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1072314 ATTTCACCAT
1072324 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
1072360 GTTTTTAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1092425 original size:19 final size:21
Alignment explanation
Indices: 1092386--1092425 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1092376 TTATTATATG
*
1092386 ATTTTATTATGTGTGAGTTTA
1 ATTTAATTATGTGTGAGTTTA
1092407 ATTTAATTATGT-T-AGTTTA
1 ATTTAATTATGTGTGAGTTTA
1092426 TCAATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
ATTTAATTATGTGTGAGTTTA
Found at i:1092453 original size:21 final size:21
Alignment explanation
Indices: 1092420--1092460 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1092410 TAATTATGTT
1092420 AGTTTATCAA-TTTTAGTTTG
1 AGTTTATCAATTTTTAGTTTG
*
1092440 AGTTGTATCTATTTTTAGTTT
1 AGTT-TATCAATTTTTAGTTT
1092461 TATTATGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 9 0.50
ACGTcount: A:0.22, C:0.05, G:0.15, T:0.59
Consensus pattern (21 bp):
AGTTTATCAATTTTTAGTTTG
Found at i:1092587 original size:2 final size:2
Alignment explanation
Indices: 1092580--1092646 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1092570 AATTAAAATT
1092580 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
1092622 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1092647 GTGTGTTTAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1108271 original size:3 final size:3
Alignment explanation
Indices: 1108263--1108288 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1108253 AGGGAGATTC
1108263 GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GG
1108289 AAGAGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:1115026 original size:15 final size:16
Alignment explanation
Indices: 1115006--1115035 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1114996 TTTAGTGCAT
1115006 AAAAAATAA-ATAAAC
1 AAAAAATAATATAAAC
1115021 AAAAAATAATATAAA
1 AAAAAATAATATAAA
1115036 ACATAAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAAATAATATAAAC
Found at i:1115781 original size:17 final size:18
Alignment explanation
Indices: 1115759--1115797 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1115749 TTAACATTAT
*
1115759 TTTTTAT-TCAAAAGTGC
1 TTTTTATATCAAAAGTAC
1115776 TTTTTATATCAAAAGTAC
1 TTTTTATATCAAAAGTAC
1115794 TTTT
1 TTTT
1115798 AAAAAGCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (18 bp):
TTTTTATATCAAAAGTAC
Found at i:1117419 original size:13 final size:13
Alignment explanation
Indices: 1117401--1117428 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1117391 TAACCTTAAA
1117401 CCTACCTTGTAAG
1 CCTACCTTGTAAG
1117414 CCTACCTTGTAAG
1 CCTACCTTGTAAG
1117427 CC
1 CC
1117429 GTTTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (13 bp):
CCTACCTTGTAAG
Found at i:1117708 original size:24 final size:23
Alignment explanation
Indices: 1117664--1117708 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1117654 TTTATTTGAA
*
1117664 CAAAAAAATTATTTTTTGAAAAG
1 CAAAAAAATTATTTTTCGAAAAG
1117687 CAAATAAAATT-TATTTTCGAAA
1 CAAA-AAAATTAT-TTTTCGAAA
1117709 TTAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (23 bp):
CAAAAAAATTATTTTTCGAAAAG
Found at i:1124840 original size:2 final size:2
Alignment explanation
Indices: 1124833--1124857 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1124823 TGGGCTTTAC
1124833 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1124858 TCCTGCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1133645 original size:20 final size:20
Alignment explanation
Indices: 1133608--1133645 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1133598 TTATGTTCAA
*
1133608 ATGTTACGTTTTATTTACTT
1 ATGTTACGTTTTAGTTACTT
1133628 ATGTTATCGTTTT-GTTAC
1 ATGTTA-CGTTTTAGTTAC
1133646 GAAGTGGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.18, C:0.11, G:0.13, T:0.58
Consensus pattern (20 bp):
ATGTTACGTTTTAGTTACTT
Found at i:1133786 original size:18 final size:18
Alignment explanation
Indices: 1133763--1133802 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1133753 TAGATTTTTC
1133763 ATTAAATAAATTT-AATTA
1 ATTAAA-AAATTTAAATTA
1133781 ATTAAAAAATTTAAATTA
1 ATTAAAAAATTTAAATTA
1133799 ATTA
1 ATTA
1133803 CACATTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTAAAAAATTTAAATTA
Found at i:1137098 original size:17 final size:18
Alignment explanation
Indices: 1137076--1137118 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1137066 AATTTACTTC
*
1137076 AAAATTTTTTTAACGA-T
1 AAAATTTTTTGAACGAGT
* *
1137093 AAAATTGTTTGAACTAGT
1 AAAATTTTTTGAACGAGT
1137111 AAAATTTT
1 AAAATTTT
1137119 AATGACATCG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (18 bp):
AAAATTTTTTGAACGAGT
Found at i:1145065 original size:20 final size:22
Alignment explanation
Indices: 1145040--1145084 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1145030 TATTTGGGTC
1145040 AAAACTAAAA-T-ATCGAAATA
1 AAAACTAAAATTAATCGAAATA
*
1145060 AAAACTAAAATTAATCGAATTA
1 AAAACTAAAATTAATCGAAATA
1145082 AAA
1 AAA
1145085 TACAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 1 0.05
22 11 0.50
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAACTAAAATTAATCGAAATA
Found at i:1145371 original size:3 final size:3
Alignment explanation
Indices: 1145363--1145395 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1145353 CCATAAAGTA
1145363 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1145396 ATGTGAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1160088 original size:29 final size:30
Alignment explanation
Indices: 1160037--1160102 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
1160027 TAGGGACTGG
* * * *
1160037 ATCAAATTAGTCCCTCTATTATT-AAATGA
1 ATCAAATTAGTACCTATAGTATTAAAAAGA
*
1160066 ATCAATTTAGTACCTATAGTATTAAAAAGA
1 ATCAAATTAGTACCTATAGTATTAAAAAGA
1160096 ATCAAAT
1 ATCAAAT
1160103 ATGTCCAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.35
Consensus pattern (30 bp):
ATCAAATTAGTACCTATAGTATTAAAAAGA
Found at i:1173877 original size:13 final size:13
Alignment explanation
Indices: 1173861--1173885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1173851 TATGAAAAAA
1173861 ATATTAAAAATAT
1 ATATTAAAAATAT
1173874 ATATTAAAAATA
1 ATATTAAAAATA
1173886 AAGATACATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATTAAAAATAT
Found at i:1180340 original size:151 final size:151
Alignment explanation
Indices: 1180062--1180347 Score: 434
Period size: 151 Copynumber: 1.9 Consensus size: 151
1180052 TTTTAGCCGT
* *
1180062 CTTTAGACAACACAATTCAAGTGAGCATTACATATGAATGTGTTAACAACTTAGTATTACGAAAC
1 CTTTAGACAACACAATTCAAGTGAGCATTACATATGAATCTGTTAACAACTTAGTATTACAAAAC
* *
1180127 TGACATGGTTGCTTTCTTTTAATAATGATGTTTATTTTAGGTGGTATACATATTATACCTTGTTT
66 AGACATGGTTGCTTTCTTTTAATAATGATGTTTATTTTAGGTGGTATACATATTATAACTTGTTT
1180192 AAAGGGGAATTTGATGTTCAC
131 AAAGGGGAATTTGATGTTCAC
* * *
1180213 CTTTAGACAACACAATTCAAGTGATCATTACATATGAATCTGTTCACAACTTTGTATTACAAAAC
1 CTTTAGACAACACAATTCAAGTGAGCATTACATATGAATCTGTTAACAACTTAGTATTACAAAAC
* * *
1180278 AGACATTGTTGCTTT-TTCTTAGTAATGATGATGTTATTTTAGGT-GT-TATATATTATAACTTG
66 AGACATGGTTGCTTTCTT-TTAATAATGATG-T-TTATTTTAGGTGGTATACATATTATAACTTG
1180340 TTTAAAGG
128 TTTAAAGG
1180348 AAGGTAAATA
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
150 2 0.02
151 106 0.87
152 3 0.02
153 11 0.09
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (151 bp):
CTTTAGACAACACAATTCAAGTGAGCATTACATATGAATCTGTTAACAACTTAGTATTACAAAAC
AGACATGGTTGCTTTCTTTTAATAATGATGTTTATTTTAGGTGGTATACATATTATAACTTGTTT
AAAGGGGAATTTGATGTTCAC
Found at i:1180414 original size:15 final size:15
Alignment explanation
Indices: 1180390--1180419 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1180380 GTTTCGAAAG
*
1180390 TAATGCTTTGTGTGA
1 TAATGATTTGTGTGA
1180405 TAATGATTTGTGTGA
1 TAATGATTTGTGTGA
1180420 ATTTCAAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (15 bp):
TAATGATTTGTGTGA
Found at i:1181855 original size:26 final size:27
Alignment explanation
Indices: 1181819--1181869 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1181809 TAGAAAAAAT
*
1181819 TAAAAATAACTTTTAATTATGTTATTC
1 TAAAAATAACTTGTAATTATGTTATTC
1181846 TAAAAA-AACTTGTAATTATGTTAT
1 TAAAAATAACTTGTAATTATGTTAT
1181870 ATGATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (27 bp):
TAAAAATAACTTGTAATTATGTTATTC
Found at i:1182479 original size:15 final size:15
Alignment explanation
Indices: 1182458--1182501 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1182448 TCATAAAATT
1182458 AAATTTTAATTTTTA
1 AAATTTTAATTTTTA
*
1182473 TAATTTTAATTTTTA
1 AAATTTTAATTTTTA
*
1182488 AAATTTTAGTTTTT
1 AAATTTTAATTTTT
1182502 TATTTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
AAATTTTAATTTTTA
Found at i:1183436 original size:12 final size:12
Alignment explanation
Indices: 1183419--1183446 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1183409 GAAAGTTCTA
1183419 CTTCAGTTTCAG
1 CTTCAGTTTCAG
1183431 CTTCAGTTTCAG
1 CTTCAGTTTCAG
1183443 CTTC
1 CTTC
1183447 TTTAACAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (12 bp):
CTTCAGTTTCAG
Found at i:1186667 original size:3 final size:3
Alignment explanation
Indices: 1186661--1186705 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1186651 TTTATAATGT
* *
1186661 TTA TTA TTA TTA TTG TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1186706 AATTTGGCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1186780 original size:5 final size:6
Alignment explanation
Indices: 1186765--1186794 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1186755 AAACAAACAA
*
1186765 AAAAAG AAAAAG AAAAAG AAAAAG GAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1186795 CGAGGTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1187815 original size:12 final size:12
Alignment explanation
Indices: 1187784--1187826 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1187774 ATAATATTAT
*
1187784 TATAAAGAATCA
1 TATAAAAAATCA
* *
1187796 AATTAAAAATCA
1 TATAAAAAATCA
*
1187808 TGTAAAAAATCA
1 TATAAAAAATCA
1187820 TATAAAA
1 TATAAAA
1187827 TCAAAGTTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.26
Consensus pattern (12 bp):
TATAAAAAATCA
Found at i:1188107 original size:18 final size:19
Alignment explanation
Indices: 1188059--1188107 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1188049 AAAATAATTT
*
1188059 AATAAATACAATAAATATG
1 AATAAATACAATAAAGATG
1188078 AA-AAATACAATACAAGA-G
1 AATAAATACAATA-AAGATG
1188096 AATAAATA-AATA
1 AATAAATACAATA
1188108 TGCCAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.20
Consensus pattern (19 bp):
AATAAATACAATAAAGATG
Found at i:1199788 original size:4 final size:5
Alignment explanation
Indices: 1199760--1199789 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1199750 TTGGATTGGT
1199760 GGTGG GGTGG GGTGG GGTGG GGT-G GGTGG G
1 GGTGG GGTGG GGTGG GGTGG GGTGG GGTGG G
1199790 ATGCGATGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (5 bp):
GGTGG
Found at i:1202113 original size:16 final size:16
Alignment explanation
Indices: 1202090--1202129 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1202080 CGTTTGGTTC
*
1202090 GCTGTAATGAAATAGA
1 GCTGTAATAAAATAGA
*
1202106 GGTGTAATAAAATAGA
1 GCTGTAATAAAATAGA
1202122 GCTGTAAT
1 GCTGTAAT
1202130 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (16 bp):
GCTGTAATAAAATAGA
Found at i:1202202 original size:44 final size:46
Alignment explanation
Indices: 1202116--1202204 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 46
1202106 GGTGTAATAA
* *
1202116 AATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGATTGGAATGG
1 AATAGAGCTGTAATCAATAATTCAATTGTTTGGTTGAATGGAATGG
*
1202162 AATAGAGCTGTAAT-AAT-ATTC-TTGTGTTTGGTTGAATGGAATG
1 AATAGAGCTGTAATCAATAATTCAAT-TGTTTGGTTGAATGGAATG
1202205 ATGCTGTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 22 0.56
45 2 0.05
46 14 0.36
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (46 bp):
AATAGAGCTGTAATCAATAATTCAATTGTTTGGTTGAATGGAATGG
Found at i:1202324 original size:26 final size:26
Alignment explanation
Indices: 1202292--1202431 Score: 86
Period size: 26 Copynumber: 5.1 Consensus size: 26
1202282 CTTATTAAAT
*
1202292 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAAATTATTATTAAATATAA
* *
1202318 TTTAATAAAAATATTAATT-AATTTAA
1 TTTAATAAAATTATT-ATTAAATATAA
*** *
1202344 -TTATATTTTATTATTATTAAATAAAA
1 TTTA-ATAAAATTATTATTAAATATAA
* *
1202370 TTTAATAAAATAATATATAATTTAATAATATT
1 TTTAATAAAAT--TAT-T-ATTAAAT-ATA-A
*
1202402 TTTAATATAATTATTATTAAAATATGAA
1 TTTAATAAAATTATTATT-AAATAT-AA
1202430 TT
1 TT
1202432 AGTAAAAATT
Statistics
Matches: 84, Mismatches: 18, Indels: 22
0.68 0.15 0.18
Matches are distributed among these distances:
25 6 0.07
26 35 0.42
27 6 0.07
28 10 0.12
29 6 0.07
30 9 0.11
31 2 0.02
32 10 0.12
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TTTAATAAAATTATTATTAAATATAA
Found at i:1202405 original size:52 final size:52
Alignment explanation
Indices: 1202301--1202403 Score: 156
Period size: 51 Copynumber: 2.0 Consensus size: 52
1202291 TTTTAATAAG
* * *
1202301 ATTATTATTAAATATAATTTAATAAAAATATTAATTAATTTAATTATATTTT
1 ATTATTATTAAATAAAATTTAATAAAAATAATAATTAATTTAATAATATTTT
1202353 ATTATTATTAAATAAAATTTAAT-AAAATAAT-ATATAATTTAATAATATTTT
1 ATTATTATTAAATAAAATTTAATAAAAATAATAAT-TAATTTAATAATATTTT
1202404 TAATATAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
50 2 0.04
51 23 0.49
52 22 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (52 bp):
ATTATTATTAAATAAAATTTAATAAAAATAATAATTAATTTAATAATATTTT
Found at i:1202442 original size:25 final size:24
Alignment explanation
Indices: 1202414--1202464 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1202404 TAATATAATT
*
1202414 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
1202439 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
1202463 AT
1 AT
1202465 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:1208540 original size:16 final size:16
Alignment explanation
Indices: 1208516--1208546 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1208506 ATTAATTCTA
1208516 AAATGGAAAATAAAAT
1 AAATGGAAAATAAAAT
*
1208532 AAATTGAAAATAAAA
1 AAATGGAAAATAAAA
1208547 ATGATTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
AAATGGAAAATAAAAT
Found at i:1209405 original size:19 final size:19
Alignment explanation
Indices: 1209347--1209406 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
1209337 CAACAGCTAA
1209347 AAGTTACATATTAAGTTGT
1 AAGTTACATATTAAGTTGT
* * **
1209366 AAGAT-CAT-TAACAGCAAGT
1 AAGTTACATATTA-AG-TTGT
1209385 AAGTTACATATTAAGTTGT
1 AAGTTACATATTAAGTTGT
1209404 AAG
1 AAG
1209407 ATATTGCAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
19 15 0.52
20 5 0.17
21 2 0.07
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (19 bp):
AAGTTACATATTAAGTTGT
Found at i:1220614 original size:22 final size:22
Alignment explanation
Indices: 1220589--1220631 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1220579 TATTCAAATA
1220589 ATAAT-AACAAATTAGTAGCAAT
1 ATAATGAACAAA-TAGTAGCAAT
*
1220611 ATAATGACCAAATAGTAGCAA
1 ATAATGAACAAATAGTAGCAA
1220632 AATAGTAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAATGAACAAATAGTAGCAAT
Found at i:1222609 original size:17 final size:17
Alignment explanation
Indices: 1222573--1222622 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1222563 GATGAAAATT
* **
1222573 AAAATTTAAAAATTTTA
1 AAAATATAAAAATTAAA
1222590 AAAATATAAAAATTAAA
1 AAAATATAAAAATTAAA
*
1222607 AAAATAT-CAAATTAAA
1 AAAATATAAAAATTAAA
1222623 TTTACAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATATAAAAATTAAA
Found at i:1223324 original size:20 final size:20
Alignment explanation
Indices: 1223295--1223341 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1223285 TGTTTAAAAT
*
1223295 AAAAAT-AAAATATTACTTA
1 AAAAATAAAAATATAACTTA
*
1223314 AAAAATAAAAATATAATTTA
1 AAAAATAAAAATATAACTTA
*
1223334 AAACATAA
1 AAAAATAA
1223342 TATTCGACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATAAAAATATAACTTA
Found at i:1223336 original size:19 final size:20
Alignment explanation
Indices: 1223294--1223341 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1223284 ATGTTTAAAA
*
1223294 TAAAAAT-AAAATATTACTT
1 TAAAAATAAAAATATTAATT
*
1223313 AAAAAATAAAAATA-TAATT
1 TAAAAATAAAAATATTAATT
1223332 TAAAACATAA
1 TAAAA-ATAA
1223342 TATTCGACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAATAAAAATATTAATT
Found at i:1226584 original size:22 final size:22
Alignment explanation
Indices: 1226541--1226585 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1226531 AAATGAATTG
*
1226541 TTTTATTTCAATTTTTTCTCTT
1 TTTTATTTCAATTTATTCTCTT
*
1226563 TTTTTTTTCATATTTATT-TCTT
1 TTTTATTTCA-ATTTATTCTCTT
1226585 T
1 T
1226586 ACTATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTATTTCAATTTATTCTCTT
Found at i:1233765 original size:33 final size:34
Alignment explanation
Indices: 1233686--1233770 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 34
1233676 TTTCGATCAA
1233686 GAGATTAAATTT-TTATTTTTAAAGAGATAAAATAT
1 GAGATT-AATTTATTATTTTTAAAGAGA-AAAATAT
*
1233721 GAGA--AAATTATTATTTTTAAAGAG-AAAATAT
1 GAGATTAATTTATTATTTTTAAAGAGAAAAATAT
*
1233752 GAGATTAATTTATTGTTTT
1 GAGATTAATTTATTATTTT
1233771 AAAAAAACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
31 11 0.25
32 4 0.09
33 25 0.57
35 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (34 bp):
GAGATTAATTTATTATTTTTAAAGAGAAAAATAT
Found at i:1242603 original size:37 final size:38
Alignment explanation
Indices: 1242546--1242622 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 38
1242536 TAATTTTGAA
* *
1242546 TTTAAAATTTTTTGGATTTTTTTTAAAT-ATAAAA-AT
1 TTTAAAAGTTTTTGGATTTTTTTGAAATAATAAAATAT
1242582 TTTAAAAGTTTTTGGATTTTTTTGAAATAATAAAATAT
1 TTTAAAAGTTTTTGGATTTTTTTGAAATAATAAAATAT
1242620 TTT
1 TTT
1242623 GGGATTTGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 26 0.70
37 6 0.16
38 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (38 bp):
TTTAAAAGTTTTTGGATTTTTTTGAAATAATAAAATAT
Found at i:1253022 original size:2 final size:2
Alignment explanation
Indices: 1253015--1253039 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1253005 GTCAAAACGA
1253015 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1253040 TTCTATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1258464 original size:6 final size:6
Alignment explanation
Indices: 1258453--1258478 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1258443 TCAATTATAA
1258453 AAATAT AAATAT AAATAT AAATAT AA
1 AAATAT AAATAT AAATAT AAATAT AA
1258479 TATTTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:1258607 original size:28 final size:27
Alignment explanation
Indices: 1258554--1258608 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1258544 ATATTAAGTT
** *
1258554 AATTTTATTTTATTAAAATTTGAAATA
1 AATTTTATTTTATTAAAAAATAAAATA
*
1258581 AATTTTATATTTTTTAAAAAATAAAATA
1 AATTTTAT-TTTATTAAAAAATAAAATA
1258609 TTTAAATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
AATTTTATTTTATTAAAAAATAAAATA
Found at i:1259955 original size:20 final size:19
Alignment explanation
Indices: 1259919--1259957 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1259909 CCATAGCAAT
*
1259919 AAAATGTTTATATTAAATG
1 AAAATGTTTATAATAAATG
*
1259938 AAAATAGTTTTTAATAAATG
1 AAAAT-GTTTATAATAAATG
1259958 GTATTGTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (19 bp):
AAAATGTTTATAATAAATG
Found at i:1264472 original size:2 final size:2
Alignment explanation
Indices: 1264460--1264493 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1264450 TCCATACATA
*
1264460 TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1264494 ATTTTGAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:1267073 original size:72 final size:72
Alignment explanation
Indices: 1266956--1267103 Score: 242
Period size: 72 Copynumber: 2.1 Consensus size: 72
1266946 TGCCTTTCAG
* *
1266956 TCTTCGGGTTCTACATTGGGTAATGCGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTCAA
1 TCTTCGGGTTCTACACTGGGTAACGCGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTCAA
*
1267021 TAGCAGC
66 TAACAGC
* *
1267028 TCTTCGGGTTCTACACTGGGTAACGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
1 TCTTCGGGTTCTACACTGGGTAACGCGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTCAA
*
1267093 TAACAGT
66 TAACAGC
1267100 TCTT
1 TCTT
1267104 ACCCTAGTCT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.30
Consensus pattern (72 bp):
TCTTCGGGTTCTACACTGGGTAACGCGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTCAA
TAACAGC
Found at i:1268112 original size:24 final size:24
Alignment explanation
Indices: 1268085--1268171 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 24
1268075 GTTTACTACC
*
1268085 CCAGCTGCCTCTCCTGTTCCAGTT
1 CCAGCTCCCTCTCCTGTTCCAGTT
1268109 CCAGCTCCCGCTGCCGTTCCTGTTCCAGTT
1 CCAGCT-CC-CT--C--TCCTGTTCCAGTT
* *
1268139 CCAGCTCCCGCTGCC-GTTCCCGTT
1 CCAGCTCCCTCT-CCTGTTCCAGTT
1268163 CCAGCTCCC
1 CCAGCTCCC
1268172 GCTGTCACTG
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
24 24 0.45
25 3 0.06
26 3 0.06
28 2 0.04
29 2 0.04
30 19 0.36
ACGTcount: A:0.07, C:0.47, G:0.18, T:0.28
Consensus pattern (24 bp):
CCAGCTCCCTCTCCTGTTCCAGTT
Found at i:1268130 original size:30 final size:30
Alignment explanation
Indices: 1268088--1268166 Score: 133
Period size: 30 Copynumber: 2.6 Consensus size: 30
1268078 TACTACCCCA
1268088 GCTGCC-TCTCCTGTTCCAGTTCCAGCTCCC
1 GCTGCCGT-TCCTGTTCCAGTTCCAGCTCCC
1268118 GCTGCCGTTCCTGTTCCAGTTCCAGCTCCC
1 GCTGCCGTTCCTGTTCCAGTTCCAGCTCCC
*
1268148 GCTGCCGTTCCCGTTCCAG
1 GCTGCCGTTCCTGTTCCAG
1268167 CTCCCGCTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 46 0.98
31 1 0.02
ACGTcount: A:0.06, C:0.44, G:0.20, T:0.29
Consensus pattern (30 bp):
GCTGCCGTTCCTGTTCCAGTTCCAGCTCCC
Found at i:1268172 original size:24 final size:24
Alignment explanation
Indices: 1268100--1268175 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 24
1268090 TGCCTCTCCT
*
1268100 GTTCCAGTTCCAGCTCCCGCTGCC
1 GTTCCCGTTCCAGCTCCCGCTGCC
1268124 GTTCCTGTTCCAGTTCCAGCTCCCGCTGCC
1 GTT-C----CC-GTTCCAGCTCCCGCTGCC
1268154 GTTCCCGTTCCAGCTCCCGCTG
1 GTTCCCGTTCCAGCTCCCGCTG
1268176 TCACTGACCC
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
24 19 0.42
25 3 0.07
29 2 0.04
30 21 0.47
ACGTcount: A:0.07, C:0.45, G:0.21, T:0.28
Consensus pattern (24 bp):
GTTCCCGTTCCAGCTCCCGCTGCC
Found at i:1268229 original size:6 final size:6
Alignment explanation
Indices: 1268214--1268274 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
1268204 AATGTTTACT
* * * * *
1268214 GCTCCA GCTCCC GCTCCC GCTCCC GCTCCC GCTCCA GTTCCA GCTCCA
1 GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC
1268262 GCTCCC GCTCCC G
1 GCTCCC GCTCCC G
1268275 TTGTCACTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.07, C:0.57, G:0.18, T:0.18
Consensus pattern (6 bp):
GCTCCC
Found at i:1268326 original size:96 final size:96
Alignment explanation
Indices: 1268166--1268566 Score: 478
Period size: 96 Copynumber: 4.0 Consensus size: 96
1268156 TCCCGTTCCA
**
1268166 GCTCCCGCTGTCACTGACCCACTCAAAGATGTACTCCGAATGTTTACTGCTCCAGCTCCCGCTCC
1 GCTCCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCA------GCTCC
* *
1268231 CGCTCCCGCTCCCGCTCCAGTTCCAGCTCCAGCTCCC
60 CGCTCCAGCTCCAGCTCCAGTTCCAGCTCCAGCTCCC
*
1268268 GCTCCCGTTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCAGCTCCCGCTCC
1 GCTCCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCAGCTCCCGCTCC
* * *
1268333 AGTTCCAGTTCCAGTTCCAGCTCCCGCTCTCGTTCC
66 AGCTCCAGCTCCAGTTCCAGCTCCAG--CTC---CC
*
1268369 AGCTCCAGCTCCAACTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCAGCTC
1 -GCT----C-CC-GCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCAGCTC
* * *
1268434 CCGCTCCCGCTCCCGCTCCAGTTCCAGCTCCAGCTCCA
59 CCGCTCCAGCTCCAGCTCCAGTTCCAGCTCCAGCTCCC
* * * *
1268472 ACTCCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCCGCTCCAGTTCC
1 GCTCCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCAGCTCCCGCTCC
* *
1268537 AGTTCCAGCTCCCGTTCCAGCTCCAGCTCC
66 AGCTCCAGCTCCAGTTCCAGCTCCAGCTCC
1268567 AGCTGTATAT
Statistics
Matches: 262, Mismatches: 25, Indels: 30
0.83 0.08 0.09
Matches are distributed among these distances:
96 113 0.43
97 2 0.01
98 4 0.02
101 2 0.01
102 56 0.21
103 1 0.00
106 4 0.02
107 2 0.01
108 78 0.30
ACGTcount: A:0.15, C:0.43, G:0.17, T:0.24
Consensus pattern (96 bp):
GCTCCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCAGCTCCCGCTCC
AGCTCCAGCTCCAGTTCCAGCTCCAGCTCCC
Found at i:1268331 original size:6 final size:6
Alignment explanation
Indices: 1268316--1268381 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
1268306 AATGTTTACT
* * * * *
1268316 GCTCCA GCTCCC GCTCCA GTTCCA GTTCCA GTTCCA GCTCCC GCTCTC-
1 GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTC-CA
*
1268364 GTTCCA GCTCCA GCTCCA
1 GCTCCA GCTCCA GCTCCA
1268382 ACTGTCACTG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
5 1 0.02
6 49 0.96
7 1 0.02
ACGTcount: A:0.12, C:0.47, G:0.17, T:0.24
Consensus pattern (6 bp):
GCTCCA
Found at i:1268352 original size:30 final size:30
Alignment explanation
Indices: 1268316--1268381 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1268306 AATGTTTACT
*
1268316 GCTCCAGCTCCCGCTC-CAGTTCCAGTTCCA
1 GCTCCAGCTCCCGCTCTC-GTTCCAGCTCCA
*
1268346 GTTCCAGCTCCCGCTCTCGTTCCAGCTCCA
1 GCTCCAGCTCCCGCTCTCGTTCCAGCTCCA
1268376 GCTCCA
1 GCTCCA
1268382 ACTGTCACTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.12, C:0.47, G:0.17, T:0.24
Consensus pattern (30 bp):
GCTCCAGCTCCCGCTCTCGTTCCAGCTCCA
Found at i:1268402 original size:108 final size:104
Alignment explanation
Indices: 1268108--1268566 Score: 510
Period size: 108 Copynumber: 4.4 Consensus size: 104
1268098 CTGTTCCAGT
* * * *
1268108 TCCAGCTCCCGCTGCC-GTTCCTGTTCCAGTTCCAGCTCCCGCTGCCGTTCCCGTTCCAGCTCCC
1 TCCAGCTCCCGCT-CCAGTTCCAGCTCCAGTTCCAGCT-CCGCT-CC--TCCAGCTCCAGCTCCC
**
1268172 GCTGTCACTGACCCACTCAAAGATGTACTCCGAATGTTTACTGC
61 GCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGC
* * * * * * * *
1268216 TCCAGCTCCCGCTCCCGCTCCCGCTCCCGCTCCAGTTCCAG---CTCCAGCTCCCGCTCCCGTTG
1 TCCAGCTCCCGCTCCAGTTCCAGCTCCAGTTCCAGCTCC-GCTCCTCCAGCTCCAGCTCCCGCTG
1268278 TCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGC
65 TCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGC
* **
1268318 TCCAGCTCCCGCTCCAGTTCCAGTTCCAGTTCCAGCTCCCGCTCTCGTTCCAGCTCCAGCTCCAA
1 TCCAGCTCCCGCTCCAGTTCCAGCTCCAGTTCCAGCT-CCGCTC-C--TCCAGCTCCAGCTCCCG
1268383 CTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGC
62 CTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGC
* * * *
1268426 TCCAGCTCCCGCTCCCGCTCCCGCTCCAGTTCCA-----G---CTCCAGCTCCAACTCCCGCTGT
1 TCCAGCTCCCGCTCCAGTTCCAGCTCCAGTTCCAGCTCCGCTCCTCCAGCTCCAGCTCCCGCTGT
1268483 CACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGC
66 CACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGC
* * * *
1268522 TCCCGCTCCAGTTCCAGTTCCAGCTCCCGTTCCAGCTCCAGCTCC
1 TCCAGCTCCCGCTCCAGTTCCAGCTCCAGTTCCAGCTCC-GCTCC
1268567 AGCTGTATAT
Statistics
Matches: 296, Mismatches: 37, Indels: 39
0.80 0.10 0.10
Matches are distributed among these distances:
96 84 0.28
98 1 0.00
102 87 0.29
103 2 0.01
104 1 0.00
105 1 0.00
106 1 0.00
107 4 0.01
108 115 0.39
ACGTcount: A:0.14, C:0.44, G:0.17, T:0.25
Consensus pattern (104 bp):
TCCAGCTCCCGCTCCAGTTCCAGCTCCAGTTCCAGCTCCGCTCCTCCAGCTCCAGCTCCCGCTGT
CACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGC
Found at i:1268439 original size:6 final size:6
Alignment explanation
Indices: 1268424--1268476 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
1268414 AATGTTTACT
* * * *
1268424 GCTCCA GCTCCC GCTCCC GCTCCC GCTCCA GTTCCA GCTCCA GCTCCA
1 GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA
*
1268472 ACTCC
1 GCTCC
1268477 CGCTGTCACT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.11, C:0.55, G:0.15, T:0.19
Consensus pattern (6 bp):
GCTCCA
Found at i:1268451 original size:18 final size:18
Alignment explanation
Indices: 1268424--1268480 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
1268414 AATGTTTACT
*
1268424 GCTCCAGCTCCCGCTCCC
1 GCTCCAGCTCCAGCTCCC
* * *
1268442 GCTCCCGCTCCAGTTCCA
1 GCTCCAGCTCCAGCTCCC
*
1268460 GCTCCAGCTCCAACTCCC
1 GCTCCAGCTCCAGCTCCC
1268478 GCT
1 GCT
1268481 GTCACTGACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.11, C:0.54, G:0.16, T:0.19
Consensus pattern (18 bp):
GCTCCAGCTCCAGCTCCC
Found at i:1268486 original size:204 final size:204
Alignment explanation
Indices: 1268108--1268566 Score: 688
Period size: 204 Copynumber: 2.2 Consensus size: 204
1268098 CTGTTCCAGT
* * * *
1268108 TCCAGCTCCCGCTGCC-GTTCCTGTTCCAGTTCCAGCTCCCGCTGCCGTTCCCGTTCCAGCTCCC
1 TCCAGCTCCCGCT-CCAGTTCCAGTTCCAGTTCCAGCTCCCGCT-CCGTTCCAGCTCCAGCTCCA
*
1268172 GCTGTCACTGACCCACTCAAAGATGTACTCCGAATGTTTACTGCTCCAGCTCCCGCTCCCGCTCC
64 ACTGTCACTGACCCACTCAAAGATGTACTCCGAATGTTTACTGCTCCA-----CGCTCCCGCTCC
** *
1268237 CGCTCCCGCTCCAGTTCCAGCTCCAGCTCCCGCTCCCGTTGTCACTGACCCACTCAGCGATGTAC
124 CGCTCCCGCTCCAGTTCCAGCTCCAGCTCCAACTCCCGCTGTCACTGACCCACTCAGCGATGTAC
1268302 TCCGAATGTTTACTGC
189 TCCGAATGTTTACTGC
1268318 TCCAGCTCCCGCTCCAGTTCCAGTTCCAGTTCCAGCTCCCGCTCTCGTTCCAGCTCCAGCTCCAA
1 TCCAGCTCCCGCTCCAGTTCCAGTTCCAGTTCCAGCTCCCGCTC-CGTTCCAGCTCCAGCTCCAA
**
1268383 CTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCA-GCTCCCGCTCCCGCTCC
65 CTGTCACTGACCCACTCAAAGATGTACTCCGAATGTTTACTGCTCCACGCTCCCGCTCCCGCTCC
1268447 CGCTCCAGTTCCAGCTCCAGCTCCAACTCCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAA
130 CGCTCCAGTTCCAGCTCCAGCTCCAACTCCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAA
1268512 TGTTTACTGC
195 TGTTTACTGC
* * * * * *
1268522 TCCCGCTCCAGTTCCAGTTCCAGCTCCCGTTCCAGCTCCAGCTCC
1 TCCAGCTCCCGCTCCAGTTCCAGTTCCAGTTCCAGCTCCCGCTCC
1268567 AGCTGTATAT
Statistics
Matches: 231, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
203 1 0.00
204 127 0.55
209 3 0.01
210 100 0.43
ACGTcount: A:0.14, C:0.44, G:0.17, T:0.25
Consensus pattern (204 bp):
TCCAGCTCCCGCTCCAGTTCCAGTTCCAGTTCCAGCTCCCGCTCCGTTCCAGCTCCAGCTCCAAC
TGTCACTGACCCACTCAAAGATGTACTCCGAATGTTTACTGCTCCACGCTCCCGCTCCCGCTCCC
GCTCCAGTTCCAGCTCCAGCTCCAACTCCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAAT
GTTTACTGC
Found at i:1268537 original size:6 final size:6
Alignment explanation
Indices: 1268520--1268570 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
1268510 AATGTTTACT
* * * * *
1268520 GCTCCC GCTCCA GTTCCA GTTCCA GCTCCC GTTCCA GCTCCA GCTCCA
1 GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA
1268568 GCT
1 GCT
1268571 GTATATAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.12, C:0.47, G:0.18, T:0.24
Consensus pattern (6 bp):
GCTCCA
Found at i:1268547 original size:24 final size:24
Alignment explanation
Indices: 1268520--1268570 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1268510 AATGTTTACT
* *
1268520 GCTCCCGCTCCAGTTCCAGTTCCA
1 GCTCCCGCTCCAGCTCCAGCTCCA
*
1268544 GCTCCCGTTCCAGCTCCAGCTCCA
1 GCTCCCGCTCCAGCTCCAGCTCCA
1268568 GCT
1 GCT
1268571 GTATATAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.47, G:0.18, T:0.24
Consensus pattern (24 bp):
GCTCCCGCTCCAGCTCCAGCTCCA
Found at i:1268553 original size:18 final size:18
Alignment explanation
Indices: 1268520--1268568 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1268510 AATGTTTACT
*
1268520 GCTCCCGCTCCAGTTCCA
1 GCTCCAGCTCCAGTTCCA
* *
1268538 GTTCCAGCTCCCGTTCCA
1 GCTCCAGCTCCAGTTCCA
1268556 GCTCCAGCTCCAG
1 GCTCCAGCTCCAG
1268569 CTGTATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.12, C:0.47, G:0.18, T:0.22
Consensus pattern (18 bp):
GCTCCAGCTCCAGTTCCA
Found at i:1277962 original size:3 final size:3
Alignment explanation
Indices: 1277954--1278007 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1277944 CCTAATGGTA
1277954 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1278002 AAT AAT
1 AAT AAT
1278008 TAACAAAGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1278872 original size:24 final size:24
Alignment explanation
Indices: 1278837--1278883 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1278827 AATAATTAGC
* *
1278837 TTTTTAACTTATTTA-TTATATAT
1 TTTTTAAATTATATATTTATATAT
1278860 TTTTTGAAATTATATATTTATATA
1 TTTTT-AAATTATATATTTATATA
1278884 ATTTCAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 8 0.40
25 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTTAAATTATATATTTATATAT
Found at i:1279034 original size:24 final size:25
Alignment explanation
Indices: 1278988--1279042 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1278978 TGAACCGGGT
* * *
1278988 AATAAAATAATAATTTAAGTATCAA
1 AATAAAATAAAAAATTAAATATCAA
1279013 AATAAAA-AAAAAATTAAATATCAA
1 AATAAAATAAAAAATTAAATATCAA
*
1279037 AGTAAA
1 AATAAA
1279043 TTCAAGTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (25 bp):
AATAAAATAAAAAATTAAATATCAA
Found at i:1280707 original size:16 final size:16
Alignment explanation
Indices: 1280686--1280730 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
1280676 TGATGTTTAA
1280686 TTTATATATTTTATTT
1 TTTATATATTTTATTT
* *
1280702 TTTATATAATTTAATT
1 TTTATATATTTTATTT
1280718 TTTATAT-TTTTAT
1 TTTATATATTTTAT
1280731 AATGTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATATATTTTATTT
Found at i:1290099 original size:2 final size:2
Alignment explanation
Indices: 1290092--1290125 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1290082 CTTTGCTACC
1290092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1290126 TAATACAATC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1296120 original size:2 final size:2
Alignment explanation
Indices: 1296115--1296139 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1296105 ACACACACAC
1296115 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1296140 CACGTACGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1302260 original size:31 final size:31
Alignment explanation
Indices: 1302192--1302258 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1302182 CTACTCAAAA
* * *
1302192 ATTTATATTTAAGCTATTGAATTATTTAAAT
1 ATTTTTATTTAAACTATTAAATTATTTAAAT
*
1302223 ATTTTTATTTAAATTATTAAATTA-TTAAAT
1 ATTTTTATTTAAACTATTAAATTATTTAAAT
*
1302253 TTTTTT
1 ATTTTT
1302259 TAAAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (31 bp):
ATTTTTATTTAAACTATTAAATTATTTAAAT
Found at i:1308650 original size:24 final size:26
Alignment explanation
Indices: 1308614--1308661 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
1308604 GAAAAATTGT
1308614 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
1308638 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
1308662 TCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:1308807 original size:24 final size:25
Alignment explanation
Indices: 1308778--1308831 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1308768 TGTGTGCCTA
* *
1308778 CTGTTT-CCCAGCAGTTACGTGCTT
1 CTGTTTCCCCAGCACTTACGCGCTT
*
1308802 CTGTTTCCCCAGCACTTATGCGCTT
1 CTGTTTCCCCAGCACTTACGCGCTT
1308827 CTGTT
1 CTGTT
1308832 AAGTATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.11, C:0.31, G:0.19, T:0.39
Consensus pattern (25 bp):
CTGTTTCCCCAGCACTTACGCGCTT
Found at i:1314923 original size:45 final size:45
Alignment explanation
Indices: 1314872--1315017 Score: 138
Period size: 45 Copynumber: 3.2 Consensus size: 45
1314862 ATTTTAGTTT
1314872 ATTTTCATTTGTATCTCATTCACATTTCTGTGATTATAGAAGATC
1 ATTTTCATTTGTATCTCATTCACATTTCTGTGATTATAGAAGATC
* * * *** * *
1314917 ATTTTCATTTGTATCTGCAGT-AAATTTAT-T-ACTTTATTTTCA-TTG
1 ATTTTCATTTGTATCT-CATTCACATTTCTGTGA--TTA-TAGAAGATC
*
1314962 ATTTTCATGTGTATCTCATTCACATTTCTGTGATTATAGAAGATC
1 ATTTTCATTTGTATCTCATTCACATTTCTGTGATTATAGAAGATC
1315007 ATTTTCTATTT
1 ATTTTC-ATTT
1315018 CTCTATGTAT
Statistics
Matches: 74, Mismatches: 18, Indels: 17
0.68 0.17 0.16
Matches are distributed among these distances:
43 1 0.01
44 6 0.08
45 57 0.77
46 9 0.12
47 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (45 bp):
ATTTTCATTTGTATCTCATTCACATTTCTGTGATTATAGAAGATC
Found at i:1314991 original size:90 final size:91
Alignment explanation
Indices: 1314838--1315017 Score: 310
Period size: 90 Copynumber: 2.0 Consensus size: 91
1314828 TATATAATGT
* *
1314838 TATCTGCAGTAAATTCATTACTTTATTTTAGTTTATTTTCATTTGTATCTCATTCACATTTCTGT
1 TATCTGCAGTAAATTCATTACTTTATTTTAGTTGATTTTCATGTGTATCTCATTCACATTTCTGT
1314903 GATTATAGAAGATCATTTTC-ATTTG
66 GATTATAGAAGATCATTTTCTATTTG
*
1314928 TATCTGCAGTAAATTTATTACTTTATTTTCA-TTGATTTTCATGTGTATCTCATTCACATTTCTG
1 TATCTGCAGTAAATTCATTACTTTATTTT-AGTTGATTTTCATGTGTATCTCATTCACATTTCTG
1314992 TGATTATAGAAGATCATTTTCTATTT
65 TGATTATAGAAGATCATTTTCTATTT
1315018 CTCTATGTAT
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
90 80 0.94
91 5 0.06
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (91 bp):
TATCTGCAGTAAATTCATTACTTTATTTTAGTTGATTTTCATGTGTATCTCATTCACATTTCTGT
GATTATAGAAGATCATTTTCTATTTG
Found at i:1344404 original size:2 final size:2
Alignment explanation
Indices: 1344397--1344430 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1344387 AAAGGAATGC
1344397 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1344431 TTTGATATTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1345447 original size:76 final size:76
Alignment explanation
Indices: 1345356--1345513 Score: 237
Period size: 76 Copynumber: 2.1 Consensus size: 76
1345346 TAAAAAGCTG
* *
1345356 AAAATCAGGAGGAAAAATCTGATTTGTCATTCTCCTATTGAAAAGGGATAGGGATGAA-ATGAAA
1 AAAATCAGGAAGAAAAATCTGATTTGTCATTCTCCTATTGAAAAGAGATAGGGAT-AACATGAAA
* *
1345420 TCACGATTTCAT
65 TCACAATATCAT
* *
1345432 AAAATCAGGAAGAAAAATCTGATTTGTCATTCTCTTATTGGAAAGAGATAGGGATAACATGAAAT
1 AAAATCAGGAAGAAAAATCTGATTTGTCATTCTCCTATTGAAAAGAGATAGGGATAACATGAAAT
1345497 CACAATATCAT
66 CACAATATCAT
*
1345508 ACAATC
1 AAAATC
1345514 CCTTCTCATT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
75 2 0.03
76 72 0.97
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (76 bp):
AAAATCAGGAAGAAAAATCTGATTTGTCATTCTCCTATTGAAAAGAGATAGGGATAACATGAAAT
CACAATATCAT
Found at i:1347116 original size:3 final size:3
Alignment explanation
Indices: 1347108--1347137 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1347098 TCCCCATACT
1347108 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1347138 AGAACACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1356198 original size:29 final size:30
Alignment explanation
Indices: 1356152--1356246 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
1356142 GTTAATAATT
* *
1356152 TATAAGAATTGCATC-AAATCAAAATTTCATA
1 TATAA-AATTACATCAAAATC-AAAGTTCATA
1356183 TATAAAATTACA-CAAAATCAAAGTTCATA
1 TATAAAATTACATCAAAATCAAAGTTCATA
* * * *
1356212 TATACAATTGCAT-ATTAAATCAAAGTCCATC
1 TATAAAATTACATCA--AAATCAAAGTTCATA
1356243 TATA
1 TATA
1356247 GTTTTGAGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 21 0.39
30 11 0.20
31 22 0.41
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (30 bp):
TATAAAATTACATCAAAATCAAAGTTCATA
Done.