Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013282.1 Kokia drynarioides strain JFW-HI SEQ_128303, 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: 308372
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:904 original size:20 final size:20
Alignment explanation
Indices: 879--916 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
869 AATATATATG
879 ATATATGATATATAAATAGT
1 ATATATGATATATAAATAGT
* *
899 ATATATTATGTATAAATA
1 ATATATGATATATAAATA
917 ATTTTAAAAT
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:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (20 bp):
ATATATGATATATAAATAGT
Found at i:7023 original size:22 final size:23
Alignment explanation
Indices: 6998--7044 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
6988 GAATTAGGTA
6998 ATGTCAATATAAT-ATTAAATAT
1 ATGTCAATATAATAATTAAATAT
* *
7020 ATGTCAATGTAATAATTATATAT
1 ATGTCAATATAATAATTAAATAT
7043 AT
1 AT
7045 CAAAGCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (23 bp):
ATGTCAATATAATAATTAAATAT
Found at i:9278 original size:12 final size:12
Alignment explanation
Indices: 9261--9286 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9251 TTTTTTATTC
9261 TTTTTCTTTTTT
1 TTTTTCTTTTTT
9273 TTTTTCTTTTTT
1 TTTTTCTTTTTT
9285 TT
1 TT
9287 ATGTGACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:9889 original size:17 final size:17
Alignment explanation
Indices: 9864--9918 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
9854 TACAATAACA
*
9864 AATGGAAATGCAATGAC
1 AATGAAAATGCAATGAC
* *
9881 AATGCAAATGCAGTGAC
1 AATGAAAATGCAATGAC
* *
9898 AATTAAAATGTAATGAC
1 AATGAAAATGCAATGAC
9915 AATG
1 AATG
9919 GGAATGTGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (17 bp):
AATGAAAATGCAATGAC
Found at i:10072 original size:17 final size:16
Alignment explanation
Indices: 10050--10085 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
10040 CATGGTGCCT
*
10050 TTTCTTCCTTCTCTTCG
1 TTTCTTCCTT-TCTGCG
10067 TTTCTTCCTTTCTGCG
1 TTTCTTCCTTTCTGCG
10083 TTT
1 TTT
10086 TTTGTCCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.31, G:0.08, T:0.61
Consensus pattern (16 bp):
TTTCTTCCTTTCTGCG
Found at i:11330 original size:22 final size:22
Alignment explanation
Indices: 11276--11330 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
11266 CTAACTCACC
*
11276 ATTTTGTAACCTACAAAACATT
1 ATTTTGTAACTTACAAAACATT
11298 ATTTTGTAACTTACAAAACATT
1 ATTTTGTAACTTACAAAACATT
*
11320 ATTTTATAACT
1 ATTTTGTAACT
11331 CTCCTCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (22 bp):
ATTTTGTAACTTACAAAACATT
Found at i:16909 original size:23 final size:22
Alignment explanation
Indices: 16866--16940 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
16856 TGTAACTAAC
* *
16866 TATTTCTGTAAC-CTACACAAAA
1 TATTT-TGTAACTCTCCTCAAAA
* *
16888 TTATTTTGTAATTCTTCTCAAAA
1 -TATTTTGTAACTCTCCTCAAAA
* *
16911 TGTTTTGTAACTCTCCTCATAA
1 TATTTTGTAACTCTCCTCAAAA
*
16933 TGTTTTGT
1 TATTTTGT
16941 TTTAAATTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 31 0.70
23 13 0.30
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (22 bp):
TATTTTGTAACTCTCCTCAAAA
Found at i:16916 original size:22 final size:22
Alignment explanation
Indices: 16891--16940 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
16881 CACAAAATTA
* *
16891 TTTTGTAATTCTTCTCAAAATG
1 TTTTGTAACTCTCCTCAAAATG
*
16913 TTTTGTAACTCTCCTCATAATG
1 TTTTGTAACTCTCCTCAAAATG
16935 TTTTGT
1 TTTTGT
16941 TTTAAATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTTGTAACTCTCCTCAAAATG
Found at i:18768 original size:80 final size:80
Alignment explanation
Indices: 18383--18755 Score: 453
Period size: 80 Copynumber: 4.7 Consensus size: 80
18373 AGTTTAATTG
* * * * * * * *
18383 ACTAGAGCTTGGCTCACTTTCACAGTATATCCGCTAGGCACTGGGTGCC-GAAAATTAACGGATA
1 ACTAGAGCTGGGCTCACTTTCGCAGTTTATCTGCTAGGCATTGGGTGCCAG-GAATTGACAGATA
*
18447 TTTGTTGGCTAATCCA
65 TTTGTTGGTTAATCCA
* * * * *
18463 AATAGAGTTGGGCTCACTTTCGCGGTATATTTGCTAGGCATTGGGTGCCAGGAATTGACAGATAT
1 ACTAGAGCTGGGCTCACTTTCGCAGTTTATCTGCTAGGCATTGGGTGCCAGGAATTGACAGATAT
18528 TTGTTGGTTAATCCA
66 TTGTTGGTTAATCCA
* * * *
18543 ACTAGAGCTGGGCTCACTTTCGCGGTGTATCTGCTAGGCACTGGGTGCCAGGAATTGATAGATAT
1 ACTAGAGCTGGGCTCACTTTCGCAGTTTATCTGCTAGGCATTGGGTGCCAGGAATTGACAGATAT
18608 TTGTTGGTTAATCCA
66 TTGTTGGTTAATCCA
* * * * * * *
18623 ACTAGAGTTGGACTCAATTTTGCAGTTTAT-TCGCTAGGCATTGGGTGCCAGGATTTGACGGTTA
1 ACTAGAGCTGGGCTCACTTTCGCAGTTTATCT-GCTAGGCATTGGGTGCCAGGAATTGACAGATA
18687 TTTGTTGGTTAATCCA
65 TTTGTTGGTTAATCCA
* * * *
18703 ACTAGAGCTGGGTTCACTTTTGCAGTTTATCTGCTAGGCATTAGGTGTCAGGA
1 ACTAGAGCTGGGCTCACTTTCGCAGTTTATCTGCTAGGCATTGGGTGCCAGGA
18756 TCGTCGGTTT
Statistics
Matches: 255, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
79 1 0.00
80 252 0.99
81 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (80 bp):
ACTAGAGCTGGGCTCACTTTCGCAGTTTATCTGCTAGGCATTGGGTGCCAGGAATTGACAGATAT
TTGTTGGTTAATCCA
Found at i:25809 original size:16 final size:17
Alignment explanation
Indices: 25790--25821 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25780 TTTAGGGAAT
25790 ATGT-CAAAATATTCAC
1 ATGTCCAAAATATTCAC
25806 ATGTCCAAAATATTCA
1 ATGTCCAAAATATTCA
25822 TAATTGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (17 bp):
ATGTCCAAAATATTCAC
Found at i:27398 original size:64 final size:64
Alignment explanation
Indices: 27318--27445 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
27308 ACAAAATACC
*
27318 ATACTCATGCTCTATGTATCATTTAAGTTATATTTTGTAAAATGTAAGTGCATTATATATAATT
1 ATACTCATGCTCTATGTATCATTTAAGTTATATTTTGTAAAATGTAAATGCATTATATATAATT
*
27382 ATACTCGTGCTCTATGTATCATTTAAGTTATATTTTGTAAAATGTAAATGCATTATATATAATT
1 ATACTCATGCTCTATGTATCATTTAAGTTATATTTTGTAAAATGTAAATGCATTATATATAATT
27446 TATAATTAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (64 bp):
ATACTCATGCTCTATGTATCATTTAAGTTATATTTTGTAAAATGTAAATGCATTATATATAATT
Found at i:30690 original size:3 final size:3
Alignment explanation
Indices: 30682--30749 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
30672 ATTAAATCAA
30682 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
30730 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
30750 AACAAGATAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:30928 original size:28 final size:30
Alignment explanation
Indices: 30855--30936 Score: 114
Period size: 29 Copynumber: 2.8 Consensus size: 30
30845 GAAAGTTTAA
* *
30855 GGGTTAAATTTGAATTTTTGGAAAGTTTGG
1 GGGTTAAATTTGAATTTTTAGAAAATTTGG
* *
30885 GGGTTAAA-TTCAAATTTTAGAAAATTT-G
1 GGGTTAAATTTGAATTTTTAGAAAATTTGG
30913 GGGTTAAATTTGAATTTTTAGAAA
1 GGGTTAAATTTGAATTTTTAGAAA
30937 GCTCGAGGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 9 0.20
29 28 0.62
30 8 0.18
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.41
Consensus pattern (30 bp):
GGGTTAAATTTGAATTTTTAGAAAATTTGG
Found at i:30947 original size:58 final size:59
Alignment explanation
Indices: 30837--30950 Score: 158
Period size: 58 Copynumber: 1.9 Consensus size: 59
30827 GTCAAATTTA
* * * * * *
30837 AAATTTTGGAAAGTTTAAGGGTTAAATTTGAATTTTTGGAAAGTTTGGGGGTTAAATTC
1 AAATTTTAGAAAATTTAAGGGTTAAATTTGAATTTTTAGAAAGCTCGAGGGTTAAATTC
*
30896 AAATTTTAGAAAATTT-GGGGTTAAATTTGAATTTTTAGAAAGCTCGAGGGTTAAA
1 AAATTTTAGAAAATTTAAGGGTTAAATTTGAATTTTTAGAAAGCTCGAGGGTTAAA
30951 ATATAATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 34 0.71
59 14 0.29
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.39
Consensus pattern (59 bp):
AAATTTTAGAAAATTTAAGGGTTAAATTTGAATTTTTAGAAAGCTCGAGGGTTAAATTC
Found at i:30949 original size:30 final size:30
Alignment explanation
Indices: 30825--30950 Score: 130
Period size: 30 Copynumber: 4.3 Consensus size: 30
30815 CATTAAAATC
* * * * *
30825 GGGTCAAATTTAAAATTTTGGAAAGTTTAA
1 GGGTTAAATTTGAATTTTTAGAAAGTTTGA
* *
30855 GGGTTAAATTTGAATTTTTGGAAAGTTTGG
1 GGGTTAAATTTGAATTTTTAGAAAGTTTGA
* * *
30885 GGGTTAAA-TTCAAATTTTAGAAAATTTG-
1 GGGTTAAATTTGAATTTTTAGAAAGTTTGA
* *
30913 GGGTTAAATTTGAATTTTTAGAAAGCTCGA
1 GGGTTAAATTTGAATTTTTAGAAAGTTTGA
30943 GGGTTAAA
1 GGGTTAAA
30951 ATATAATTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
28 8 0.10
29 31 0.39
30 41 0.51
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGTTAAATTTGAATTTTTAGAAAGTTTGA
Found at i:32804 original size:40 final size:40
Alignment explanation
Indices: 32760--32852 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
32750 TGGTCGAGGC
* * *
32760 AAAAGATTGGATGGTCTTCAATCTACCCTATGATTAGGGT
1 AAAAGATTGGATGGTCCTCAATCTACCCCATGATCAGGGT
* * * *
32800 AAAAGATTGGCTGGTCCTCAATCTGCCCCATGGTCGGGGT
1 AAAAGATTGGATGGTCCTCAATCTACCCCATGATCAGGGT
*
32840 AAAAGATTTGATG
1 AAAAGATTGGATG
32853 TAGTGACTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (40 bp):
AAAAGATTGGATGGTCCTCAATCTACCCCATGATCAGGGT
Found at i:32804 original size:79 final size:78
Alignment explanation
Indices: 32638--32852 Score: 234
Period size: 79 Copynumber: 2.7 Consensus size: 78
32628 ATAGCTTTAG
* * * *
32638 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCGAATGGTTTTCAAT
1 GGGTAAAAGATTGGATT-CTTCAATCTGCCCCATGGTCGAGGTAAAAGATTGGATGGTCTTCAAT
* *
32703 CTGCCCTCTAGTTA
65 CTACCCTATAGTTA
*** * * *
32717 GTAAAAAAGATTGAATTACTTCAATTTGCCCCATGGTCGAGGCAAAAGATTGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATT-CTTCAATCTGCCCCATGGTCGAGGTAAAAGATTGGATGGTCTTCAAT
32782 CTACCCTAT-GATTA
65 CTACCCTATAG-TTA
* * * *
32796 GGGTAAAAGATTGGCTGGTCCTCAATCTGCCCCATGGTCGGGGTAAAAGATTTGATG
1 GGGTAAAAGATTGGAT--TCTTCAATCTGCCCCATGGTCGAGGTAAAAGATTGGATG
32853 TAGTGACTTC
Statistics
Matches: 110, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
78 1 0.01
79 75 0.68
80 33 0.30
81 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (78 bp):
GGGTAAAAGATTGGATTCTTCAATCTGCCCCATGGTCGAGGTAAAAGATTGGATGGTCTTCAATC
TACCCTATAGTTA
Found at i:44721 original size:18 final size:17
Alignment explanation
Indices: 44674--44722 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
44664 ATTTACAAGT
44674 ATAAATAATAAGAAAACA
1 ATAAATAATAA-AAAACA
* *
44692 ATATATACATAAAATACA
1 ATAAATA-ATAAAAAACA
44710 ATAAAATAATAAA
1 AT-AAATAATAAA
44723 TTGAGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (17 bp):
ATAAATAATAAAAAACA
Found at i:44753 original size:20 final size:21
Alignment explanation
Indices: 44730--44781 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
44720 AAATTGAGTA
* *
44730 AATAAATAATCG-AATAAATG
1 AATAAATAATAGAAACAAATG
44750 AATAAATAA-AGAAACAAATG
1 AATAAATAATAGAAACAAATG
44770 AATAAAATAATA
1 AAT-AAATAATA
44782 TACATATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 19 0.70
21 6 0.22
22 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (21 bp):
AATAAATAATAGAAACAAATG
Found at i:44914 original size:30 final size:30
Alignment explanation
Indices: 44843--44999 Score: 194
Period size: 30 Copynumber: 5.3 Consensus size: 30
44833 AAAATAAAAT
* *
44843 AGGGTCAAATTTGAATTTTTGGAAAATTTG
1 AGGGTTAAATTTGAATTTTTGGAAAGTTTG
* *
44873 -GGG-TCAATTGGAATTTTTGGAAAGTTTG
1 AGGGTTAAATTTGAATTTTTGGAAAGTTTG
*
44901 AGGGTTAAATTGGAATTTTTGGAAAGTTT-
1 AGGGTTAAATTTGAATTTTTGGAAAGTTTG
*
44930 AGGGGTTAAATTTGAATTTTTAGAAAGTTTG
1 A-GGGTTAAATTTGAATTTTTGGAAAGTTTG
* * *
44961 AGAGTTAAATTTAAATTTTTAGAAAGTTTG
1 AGGGTTAAATTTGAATTTTTGGAAAGTTTG
*
44991 GGGGTTAAA
1 AGGGTTAAA
45000 GCATAATTTC
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
28 21 0.19
29 7 0.06
30 83 0.74
31 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.26, T:0.40
Consensus pattern (30 bp):
AGGGTTAAATTTGAATTTTTGGAAAGTTTG
Found at i:46580 original size:715 final size:714
Alignment explanation
Indices: 45210--46641 Score: 2334
Period size: 715 Copynumber: 2.0 Consensus size: 714
45200 TTACCCAATT
* * *
45210 TTAGAAAAAAACAAATATCTTCTCCTTTAAACAATGTTGTTTCAATGGTATTATATAACCTATAT
1 TTAGAAAAAAACAAATATCCTCTCCTTTAAACAATGTCGTTTCAATGGTATTATATAACCCATAT
* *
45275 TTTTTTTATGTTTTTCATTTTCCTTTCTTTCTCAAAAACAAACCCAAATCCCATTTCTTTTTTTC
66 TTTTTTTATGTTATTCATTTTCCTTTCTTTCTCAAAAACAAACACAAATCCCATTTCTTTTTTTC
*
45340 TCTCAAAATCAAAGTTTTTTCCTTTCTTTTTTTTTTCTCTCCACAAAATAAAAAACACAACCTTC
131 TCTCAAAATCAAAGTTTTTTCCTTTC-TTTTTTTTTCTCTCCACAAAATAAAAAACAAAACCTTC
45405 CCTTCTTTTTCAATGGTCAACCATGGGTTTCAAACCCGTACCCCCGACGACTCCTCCAACGGACG
195 CCTTCTTTTTCAATGGTCAACCATGGGTTTCAAACCCGTACCCCCGACGACTCCTCCAACGGACG
*
45470 ACCAAGGCGGCAGGGCAAGGAGATTAGCGTGAAAAGGTAAAGAAATCAACCCCAAAATCTTCTTT
260 ACCAAGGCGGCAGGGCAAGGAGATTAGCGCGAAAAGGTAAAGAAATCAACCCCAAAATCTTCTTT
* *
45535 TATTTATACTTTTGAAAATGACAAAAAAAGAAAAAAAATTATTAGTATCGAAATATAAAAAAAAA
325 CATTTATACTTTTGAAAATGACAAAAAAAGAAAAAAAATTATTAGTACCGAAATATAAAAAAAAA
*
45600 CCCAAGAAAATACCTTGCTTGGTTGCTAAAGAACTTTTGCTGCTGATTTTTCTATTAATTTCGTG
390 CCCAAGAAAATACCTTGCTTGGTTGCTAAAGAACTTTTGCTGCTGATTTTTCTATTAATTTCCTG
45665 TATATTCGTATCAAGTTCGTGTGTGTTTACATCTAATCTTTTTTTGTTTTCATAACACATTTGTA
455 TATATTCGTATCAAGTTCGTGTGTGTTTACATCTAATCTTTTTTTGTTTTCATAACACATTTGTA
* * * * *
45730 CAATGAATTTTTGGATTTTTCGGAGTGAAATCAAATAATGTGCGCATGGTGGATTTCGAATGCGA
520 CAATGAATTTTTAGATATTTCGGAGTGAAATCAAATAACGTGCGCATGGTGGATTTCAAATCCGA
**
45795 AGGCCATGGCGACAACAGCGACAGTGCAAGCATGGTGTGGTTGCTGACAGCGGCGGCAGCTGGAG
585 AGGCCATGGCGACAACAGCGACAGCACAAGCATGGTGTGGTTGCTGACAGCGGCGGCAGCTGGAG
*
45860 ACCAAAAGGGTGCTACGGCTTGTGTTTAGTCTTTAGGGTTTGTAAGACTGGGCTAGTATTTGGGC
650 ACCAAAACGGTGCTACGGCTTGTGTTTAGTCTTTAGGGTTTGTAAGACTGGGCTAGTATTTGGGC
** * * *
45925 TTAGAAAAAAGTAAATATCCTCTCCTTTAAACAATGTCGTTTTAGTGGTATTGTATAACCCATAT
1 TTAGAAAAAAACAAATATCCTCTCCTTTAAACAATGTCGTTTCAATGGTATTATATAACCCATA-
*
45990 TTTTTTTTATGTTATTCATTTTCCTTTCTTTCTCAAAAACAAACACAAATCTCATTTCTTTTTTT
65 TTTTTTTTATGTTATTCATTTTCCTTTCTTTCTCAAAAACAAACACAAATCCCATTTCTTTTTTT
46055 CTCTCAAAATCAAAGTTTTTTCCTTTC-TTTTTTTTCTCTCCACAAAATAAAAAA-AAAACCTTC
130 CTCTCAAAATCAAAGTTTTTTCCTTTCTTTTTTTTTCTCTCCACAAAATAAAAAACAAAACCTTC
* * *
46118 CCTTCTTTTTTAATGGTCAACCATGGGTTTCAAACCTGTACCCCTGACGACTCCTCCAACGGACG
195 CCTTCTTTTTCAATGGTCAACCATGGGTTTCAAACCCGTACCCCCGACGACTCCTCCAACGGACG
* * * *
46183 ACCAAGGTGGCGGGGCAAGGAGATTGGTGCGAAAAGGTAAAGAAATCAA-CCCAAAATCTTCTTT
260 ACCAAGGCGGCAGGGCAAGGAGATTAGCGCGAAAAGGTAAAGAAATCAACCCCAAAATCTTCTTT
* * *
46247 CATTTATATTTTTGAAAAT-ACCAAAAAAGAAAAATAATTATTAGTACCGAAATATAAAAAAAAA
325 CATTTATACTTTTGAAAATGACAAAAAAAGAAAAAAAATTATTAGTACCGAAATAT--AAAAAAA
* * * * *
46311 AACCCACGAAAATACCTTGCTTTGTTGTTAATGAACTTTTGTTGCTGATTTTTCTATTAATTTCC
388 AACCCAAGAAAATACCTTGCTTGGTTGCTAAAGAACTTTTGCTGCTGATTTTTCTATTAATTTCC
* *
46376 TGTGTATTCGTATCAAGTTCATGTGTGTGTTTACATCTAATCTTTTTTTGTTTTTATAACACATT
453 TGTATATTCGTATCAAGTTC--GTGTGTGTTTACATCTAATCTTTTTTTGTTTTCATAACACATT
46441 TGTACAATGAATTTTTAGATATTTCGGAGTGAAATCAAATAACGTGCGCATGGTGGATTTCAAAT
516 TGTACAATGAATTTTTAGATATTTCGGAGTGAAATCAAATAACGTGCGCATGGTGGATTTCAAAT
* * * * ** *
46506 CCGAAGGCCATGGTGACGACGGCGGCAGCACAAGTGTGGTGTGGTTGCTGAC-GACGGCGGCGGC
581 CCGAAGGCCATGGCGACAACAGCGACAGCACAAGCATGGTGTGGTTGCTGACAG-CGGCGGCAGC
46570 TGGAGACCAAAACGGTGCTACGGCTTGTGTTTAGTCTTTAGGGTTTGTAAGACTGGGCTAGTATT
645 TGGAGACCAAAACGGTGCTACGGCTTGTGTTTAGTCTTTAGGGTTTGTAAGACTGGGCTAGTATT
46635 TGGGC
710 TGGGC
46640 TT
1 TT
46642 GTTTGCGTAT
Statistics
Matches: 663, Mismatches: 48, Indels: 12
0.92 0.07 0.02
Matches are distributed among these distances:
711 33 0.05
712 32 0.05
713 199 0.30
714 28 0.04
715 282 0.43
716 89 0.13
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (714 bp):
TTAGAAAAAAACAAATATCCTCTCCTTTAAACAATGTCGTTTCAATGGTATTATATAACCCATAT
TTTTTTTATGTTATTCATTTTCCTTTCTTTCTCAAAAACAAACACAAATCCCATTTCTTTTTTTC
TCTCAAAATCAAAGTTTTTTCCTTTCTTTTTTTTTCTCTCCACAAAATAAAAAACAAAACCTTCC
CTTCTTTTTCAATGGTCAACCATGGGTTTCAAACCCGTACCCCCGACGACTCCTCCAACGGACGA
CCAAGGCGGCAGGGCAAGGAGATTAGCGCGAAAAGGTAAAGAAATCAACCCCAAAATCTTCTTTC
ATTTATACTTTTGAAAATGACAAAAAAAGAAAAAAAATTATTAGTACCGAAATATAAAAAAAAAC
CCAAGAAAATACCTTGCTTGGTTGCTAAAGAACTTTTGCTGCTGATTTTTCTATTAATTTCCTGT
ATATTCGTATCAAGTTCGTGTGTGTTTACATCTAATCTTTTTTTGTTTTCATAACACATTTGTAC
AATGAATTTTTAGATATTTCGGAGTGAAATCAAATAACGTGCGCATGGTGGATTTCAAATCCGAA
GGCCATGGCGACAACAGCGACAGCACAAGCATGGTGTGGTTGCTGACAGCGGCGGCAGCTGGAGA
CCAAAACGGTGCTACGGCTTGTGTTTAGTCTTTAGGGTTTGTAAGACTGGGCTAGTATTTGGGC
Found at i:49591 original size:94 final size:95
Alignment explanation
Indices: 49369--49584 Score: 292
Period size: 94 Copynumber: 2.3 Consensus size: 95
49359 TTTTGAAGAC
* * *
49369 TCACTCCATTCCACTATAACCTTAGGGACATTGA-TTTCTACTTCATTATTTTCATCCTACCCAC
1 TCACTCCATTCCACTGTAACCTTAGGGACATTGAGCTTCTACTTCATTATTTTCATCCAACCCAC
* *
49433 TGCAACTCAGGGGTATAGGATCTTGGTGCT
66 TACAAATCAGGGGTATAGGATCTTGGTGCT
* * * * *
49463 TCACTCCACTCCACTGTAACCTTATGGACATTGAGCTT-TGCTTCATTATTTTTATCCAACCTAC
1 TCACTCCATTCCACTGTAACCTTAGGGACATTGAGCTTCTACTTCATTATTTTCATCCAACCCAC
* * *
49527 TACAAATTAGGGGTATAGGATTTTGGTTCT
66 TACAAATCAGGGGTATAGGATCTTGGTGCT
*
49557 TCACTCCATTCCACTGTAACCTCAGGGA
1 TCACTCCATTCCACTGTAACCTTAGGGA
49585 TGTTGAGATC
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 103 0.98
95 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (95 bp):
TCACTCCATTCCACTGTAACCTTAGGGACATTGAGCTTCTACTTCATTATTTTCATCCAACCCAC
TACAAATCAGGGGTATAGGATCTTGGTGCT
Found at i:49968 original size:19 final size:19
Alignment explanation
Indices: 49931--49969 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
49921 GATTAAGGGT
* *
49931 AAAAGACTGGATGGCTTCA
1 AAAAGACTGGATAGATTCA
49950 AAAAGACTGGATAGATTCA
1 AAAAGACTGGATAGATTCA
49969 A
1 A
49970 TCTGCCCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAGACTGGATAGATTCA
Found at i:49997 original size:43 final size:43
Alignment explanation
Indices: 49950--50181 Score: 240
Period size: 43 Copynumber: 5.5 Consensus size: 43
49940 GATGGCTTCA
* *
49950 AAAAGACTGGATAGA-TTCAATCTGCCCCTACTGGATTAAGGGT
1 AAAAGACTGGAT-GACTTCAATCTACCCCTACTAGATTAAGGGT
* * * *
49993 AAAAGACTGAATGACTTCAATTTATCCCTACT-G--TAGGGGT
1 AAAAGACTGGATGACTTCAATCTACCCCTACTAGATTAAGGGT
* * *
50033 AAAAGATTGGATGACTTCAATCTACCCCTACTGGATTATGGGT
1 AAAAGACTGGATGACTTCAATCTACCCCTACTAGATTAAGGGT
* * * * * *
50076 AAAAGA-TCAGATGATTTCAATCTGCCTCTACTAAATTAGGGGT
1 AAAAGACT-GGATGACTTCAATCTACCCCTACTAGATTAAGGGT
* ** *
50119 AAAAGAATGGATGGTTTCAATCTACCCCTATTAGATTAAGGGT
1 AAAAGACTGGATGACTTCAATCTACCCCTACTAGATTAAGGGT
50162 AAAAGACTGGATGACTTCAA
1 AAAAGACTGGATGACTTCAA
50182 AAAAACTGGA
Statistics
Matches: 156, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
40 34 0.22
41 1 0.01
42 4 0.03
43 116 0.74
44 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (43 bp):
AAAAGACTGGATGACTTCAATCTACCCCTACTAGATTAAGGGT
Found at i:50175 original size:86 final size:83
Alignment explanation
Indices: 49950--50181 Score: 263
Period size: 83 Copynumber: 2.8 Consensus size: 83
49940 GATGGCTTCA
* * * * *
49950 AAAAGACTGGATAGATTCAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGAATGACTTCAATT
1 AAAAGAATGGATGGATTCAATCTACCCCTACTGGATTAAGGGTAAAAGACTGGATGACTTCAATC
*
50015 TATCCCTACTGTAGGGGT
66 TAGCCCTACTGTAGGGGT
* * * *
50033 AAAAGATTGGAT-GACTTCAATCTACCCCTACTGGATTATGGGTAAAAGA-TCAGATGATTTCAA
1 AAAAGAATGGATGGA-TTCAATCTACCCCTACTGGATTAAGGGTAAAAGACT-GGATGACTTCAA
*
50096 TCT-GCCTCTACTAAATTAGGGGT
64 TCTAGCC-CTACT---GTAGGGGT
* * *
50119 AAAAGAATGGATGGTTTCAATCTACCCCTATTAGATTAAGGGTAAAAGACTGGATGACTTCAA
1 AAAAGAATGGATGGATTCAATCTACCCCTACTGGATTAAGGGTAAAAGACTGGATGACTTCAA
50182 AAAAACTGGA
Statistics
Matches: 125, Mismatches: 16, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
82 5 0.04
83 59 0.47
86 59 0.47
87 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (83 bp):
AAAAGAATGGATGGATTCAATCTACCCCTACTGGATTAAGGGTAAAAGACTGGATGACTTCAATC
TAGCCCTACTGTAGGGGT
Found at i:50234 original size:43 final size:43
Alignment explanation
Indices: 50181--50321 Score: 185
Period size: 43 Copynumber: 3.3 Consensus size: 43
50171 GATGACTTCA
* * *
50181 AAAAAACTGGATAGCTTCAATTTGCTCTTATTGGATTAGGGGT
1 AAAAGACTGGATAGCTTCAATTTGCTCCTACTGGATTAGGGGT
*
50224 AAAAGACTGGAT-GACTTCAATTTGCCCCTACTGGATTAGGGGT
1 AAAAGACTGGATAG-CTTCAATTTGCTCCTACTGGATTAGGGGT
* * *
50267 AAAAGACTAGATAGCTTCAATCTGCTCCTACTGGATTAAGGGT
1 AAAAGACTGGATAGCTTCAATTTGCTCCTACTGGATTAGGGGT
* *
50310 AAATGATTGGAT
1 AAAAGACTGGAT
50322 GAGGTGACGT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.01
43 83 0.98
44 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.30
Consensus pattern (43 bp):
AAAAGACTGGATAGCTTCAATTTGCTCCTACTGGATTAGGGGT
Found at i:56425 original size:14 final size:15
Alignment explanation
Indices: 56399--56432 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
56389 AAGAAAATTG
56399 GAAAACAATTTTAAT
1 GAAAACAATTTTAAT
*
56414 TAAAAC-ATTTTAAT
1 GAAAACAATTTTAAT
56428 GAAAA
1 GAAAA
56433 ATGAATGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (15 bp):
GAAAACAATTTTAAT
Found at i:56690 original size:20 final size:20
Alignment explanation
Indices: 56667--56706 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56657 TAGGGGCAAA
56667 AATTAAATTTTTGAAGAGTT
1 AATTAAATTTTTGAAGAGTT
56687 AATTAAATTTTTGAAGAGTT
1 AATTAAATTTTTGAAGAGTT
56707 TAGGGGCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
AATTAAATTTTTGAAGAGTT
Found at i:61688 original size:23 final size:23
Alignment explanation
Indices: 61646--61689 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
61636 TAACAATATA
*
61646 ATAAAATTTTCATTTCTATTTTT
1 ATAAAATTTTAATTTCTATTTTT
61669 ATAACAATTTTAATTT-TATTT
1 ATAA-AATTTTAATTTCTATTT
61690 AACGGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (23 bp):
ATAAAATTTTAATTTCTATTTTT
Found at i:73885 original size:23 final size:23
Alignment explanation
Indices: 73855--73902 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
73845 GTATAGGGTT
*
73855 CTTTCCACCGAGATTTGAGCTTC
1 CTTTCCACCGAGATGTGAGCTTC
*
73878 CTTTCCACCGGGATGTGAGCTTC
1 CTTTCCACCGAGATGTGAGCTTC
73901 CT
1 CT
73903 AGGAAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.15, C:0.31, G:0.21, T:0.33
Consensus pattern (23 bp):
CTTTCCACCGAGATGTGAGCTTC
Found at i:82067 original size:25 final size:25
Alignment explanation
Indices: 82039--82087 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
82029 GGGTCAAAGT
*
82039 AATTAAATTAACCCAATTAATTAAC
1 AATTAAATAAACCCAATTAATTAAC
* *
82064 AATTTAATAAACCCAATTTATTAA
1 AATTAAATAAACCCAATTAATTAA
82088 TGAAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTAAATAAACCCAATTAATTAAC
Found at i:84391 original size:16 final size:16
Alignment explanation
Indices: 84370--84403 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
84360 ATCATTCTAA
84370 CTTAAATAAAATTAAG
1 CTTAAATAAAATTAAG
84386 CTTAAATAAAATTAAG
1 CTTAAATAAAATTAAG
84402 CT
1 CT
84404 ACCATTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (16 bp):
CTTAAATAAAATTAAG
Found at i:85101 original size:19 final size:19
Alignment explanation
Indices: 85079--85123 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
85069 TTATATTAGG
85079 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
85098 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
85117 ATTTAAT
1 ATTTAAT
85124 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:85939 original size:15 final size:16
Alignment explanation
Indices: 85921--85950 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
85911 CTTCCCTATT
85921 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
85936 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
85951 TTTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:85943 original size:22 final size:22
Alignment explanation
Indices: 85916--85976 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
85906 TTCGACTTCC
85916 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
85938 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
*
85960 -T-TGTTTCTTTTATTTTT
1 CTAT-TTTCTTTTACTTTT
85977 CCTTAGATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 1 0.03
21 18 0.50
22 17 0.47
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.74
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:86609 original size:21 final size:21
Alignment explanation
Indices: 86585--86650 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
86575 TATGTCCAAA
86585 ATTAACATTTAAGAAAAATTC
1 ATTAACATTTAAGAAAAATTC
**
86606 ATT-A-ATTTATTAAACAATT-
1 ATTAACATTTAAGAAA-AATTC
*
86625 ACTAACATTTAAGAAAAATTC
1 ATTAACATTTAAGAAAAATTC
86646 ATTAA
1 ATTAA
86651 TTTATTGAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 10 0.29
20 10 0.29
21 15 0.43
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (21 bp):
ATTAACATTTAAGAAAAATTC
Found at i:86613 original size:19 final size:19
Alignment explanation
Indices: 86591--86654 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
86581 CAAAATTAAC
86591 ATTTAAGAAAAATTCATTA
1 ATTTAAGAAAAATTCATTA
** *
86610 ATTTATTAAACAATT-ACTAA
1 ATTTAAGAAA-AATTCA-TTA
86630 CATTTAAGAAAAATTCATTA
1 -ATTTAAGAAAAATTCATTA
86650 ATTTA
1 ATTTA
86655 TTGAAGAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 14 0.40
20 12 0.34
21 9 0.26
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (19 bp):
ATTTAAGAAAAATTCATTA
Found at i:86676 original size:40 final size:40
Alignment explanation
Indices: 86587--86667 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
86577 TGTCCAAAAT
86587 TAACATTTAAGAAAAATTCATTAATTTATTAAACAATTAC
1 TAACATTTAAGAAAAATTCATTAATTTATTAAACAATTAC
* *
86627 TAACATTTAAGAAAAATTCATTAATTTATTGAAGAATTAC
1 TAACATTTAAGAAAAATTCATTAATTTATTAAACAATTAC
86667 T
1 T
86668 CGGTTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (40 bp):
TAACATTTAAGAAAAATTCATTAATTTATTAAACAATTAC
Found at i:93304 original size:16 final size:16
Alignment explanation
Indices: 93283--93315 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
93273 TTTGAAACCC
93283 TAAATAT-TAACCATTA
1 TAAATATCTAA-CATTA
93299 TAAATATCTAACATTA
1 TAAATATCTAACATTA
93315 T
1 T
93316 CCTAACTCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATATCTAACATTA
Found at i:100239 original size:35 final size:35
Alignment explanation
Indices: 100196--100264 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
100186 CTTGTTTGAA
*
100196 AAACATTTTGA-A-GTATTAAAATAATTTTGACTTC
1 AAACATTTTGACATGT-TTAAAATAATTTTAACTTC
*
100230 AAACTATTTTGACATGTTTAAAATCATTTTAACTT
1 AAAC-ATTTTGACATGTTTAAAATAATTTTAACTT
100265 GATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 4 0.13
35 7 0.23
36 17 0.57
37 2 0.07
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (35 bp):
AAACATTTTGACATGTTTAAAATAATTTTAACTTC
Found at i:102470 original size:20 final size:20
Alignment explanation
Indices: 102442--102495 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
102432 AAAGCCAATG
* *
102442 GTATCGATATTTTTTTACAA
1 GTATCGATATTTTTATAAAA
*
102462 GTATTGATATTTTTATAAAA
1 GTATCGATATTTTTATAAAA
102482 GTATCGATAATTTT
1 GTATCGAT-ATTTT
102496 CAATCGGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (20 bp):
GTATCGATATTTTTATAAAA
Found at i:102873 original size:37 final size:37
Alignment explanation
Indices: 102823--102897 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
102813 CAAGGTAAGG
102823 TGGTCAAACCTAGTTCTCTACTAAGTGTCCAAAATCT
1 TGGTCAAACCTAGTTCTCTACTAAGTGTCCAAAATCT
102860 TGGTCAAACCTAGTTCTCTACTAAGTGTCCAAAATCT
1 TGGTCAAACCTAGTTCTCTACTAAGTGTCCAAAATCT
102897 T
1 T
102898 TCTTTGTCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (37 bp):
TGGTCAAACCTAGTTCTCTACTAAGTGTCCAAAATCT
Found at i:114863 original size:3 final size:3
Alignment explanation
Indices: 114855--114881 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
114845 TTTCCCTCTA
114855 TGC TGC TGC TGC TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC
114882 AAATTGAGGT
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:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
TGC
Found at i:115337 original size:29 final size:30
Alignment explanation
Indices: 115286--115357 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
115276 AATAAATTAT
* *
115286 TTTTATAATTTTTAAAAAATTAAATTAAAA
1 TTTTATTATTTTTAAAAAATTAAAATAAAA
* * ** *
115316 TTTTATTATTTTT-GAAGATTAAAATGTAG
1 TTTTATTATTTTTAAAAAATTAAAATAAAA
115345 TTTTATTATTTTT
1 TTTTATTATTTTT
115358 TTAAAAGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (30 bp):
TTTTATTATTTTTAAAAAATTAAAATAAAA
Found at i:115625 original size:30 final size:29
Alignment explanation
Indices: 115587--115653 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
115577 TTTAATATTT
*
115587 ATTG-ATTTTT-ATTTATAAAATATTTTTTA
1 ATTGAATTTTTAATTT-T-AAATATTTTTAA
*
115616 ATTTAATTTTTTAATTTTAAATATTTTTAA
1 ATTGAA-TTTTTAATTTTAAATATTTTTAA
115646 ATTGAATT
1 ATTGAATT
115654 ATGATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 5 0.16
30 17 0.53
31 6 0.19
32 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (29 bp):
ATTGAATTTTTAATTTTAAATATTTTTAA
Found at i:115626 original size:13 final size:13
Alignment explanation
Indices: 115608--115632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
115598 TTTATAAAAT
115608 ATTTTTTAATTTA
1 ATTTTTTAATTTA
115621 ATTTTTTAATTT
1 ATTTTTTAATTT
115633 TAAATATTTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTAATTTA
Found at i:117953 original size:26 final size:28
Alignment explanation
Indices: 117898--117962 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
117888 TTAAAAATAA
117898 TATATATTTTATTATAAAAAATAAACTTT
1 TATAT-TTTTATTATAAAAAATAAACTTT
* *
117927 TATATTTTTA-TAT-AAAAATTAATTTT
1 TATATTTTTATTATAAAAAATAAACTTT
*
117953 TTTATTTTTA
1 TATATTTTTA
117963 GAATTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.61
27 3 0.09
28 5 0.15
29 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TATATTTTTATTATAAAAAATAAACTTT
Found at i:118510 original size:20 final size:20
Alignment explanation
Indices: 118471--118508 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
118461 TAAAATTCAA
*
118471 AAAAATCTAAAAATATAAAT
1 AAAAATATAAAAATATAAAT
118491 AAAAATAT-AAAATATAAA
1 AAAAATATAAAAATATAAA
118509 ATGCATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATATAAAAATATAAAT
Found at i:126320 original size:22 final size:23
Alignment explanation
Indices: 126288--126331 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
126278 ATTATTATAA
126288 AACAAAGAG-A-AATATAAAATG
1 AACAAAGAGAAGAATATAAAATG
126309 AACAAGAGAGAAGAATATAAAAT
1 AACAA-AGAGAAGAATATAAAAT
126332 AAAAAAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 1 0.05
24 10 0.50
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.14
Consensus pattern (23 bp):
AACAAAGAGAAGAATATAAAATG
Found at i:129633 original size:18 final size:18
Alignment explanation
Indices: 129610--129656 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
129600 CGAAAGGAAT
*
129610 AGCATACTAGCTCGTTAG
1 AGCATACTAGCTCGTAAG
* *
129628 AGCATATTGGCTCGTAAG
1 AGCATACTAGCTCGTAAG
129646 AGCAATACTAG
1 AGC-ATACTAG
129657 ATCACAAGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (18 bp):
AGCATACTAGCTCGTAAG
Found at i:133725 original size:15 final size:15
Alignment explanation
Indices: 133705--133752 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
133695 TTTCACACAA
133705 ATCATATAT-TATCAT
1 ATCATA-ATGTATCAT
133720 ATCATAATGTATCAT
1 ATCATAATGTATCAT
*
133735 AACATAA-GATATCAT
1 ATCATAATG-TATCAT
133750 ATC
1 ATC
133753 GAATCACAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 3 0.10
15 26 0.90
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (15 bp):
ATCATAATGTATCAT
Found at i:133776 original size:25 final size:25
Alignment explanation
Indices: 133717--133777 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
133707 CATATATTAT
* *
133717 CATATCATAAT-GTATCATAACATAA
1 CATATCAT-ATCGAATCACAACATAA
*
133742 GATATCATATCGAATCACAACATAA
1 CATATCATATCGAATCACAACATAA
133767 CATATCATATC
1 CATATCATATC
133778 ATACCATGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 2 0.06
25 29 0.94
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.30
Consensus pattern (25 bp):
CATATCATATCGAATCACAACATAA
Found at i:135106 original size:34 final size:34
Alignment explanation
Indices: 135068--135135 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
135058 AAATAAATGG
135068 CAAAATCACAATGAGAGAAAAAAGAAAGAAAAAT
1 CAAAATCACAATGAGAGAAAAAAGAAAGAAAAAT
135102 CAAAATCACAATGAGAGAAAAAAGAAAGAAAAAT
1 CAAAATCACAATGAGAGAAAAAAGAAAGAAAAAT
135136 AGAGTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.68, C:0.09, G:0.15, T:0.09
Consensus pattern (34 bp):
CAAAATCACAATGAGAGAAAAAAGAAAGAAAAAT
Found at i:148426 original size:15 final size:15
Alignment explanation
Indices: 148408--148448 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
148398 GAACATATCT
148408 TATCATATCATAACA
1 TATCATATCATAACA
*
148423 TATCATAAT-ATAAGA
1 TATCAT-ATCATAACA
148438 TATCATATCAT
1 TATCATATCAT
148449 GTCCTATCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 19 0.83
16 2 0.09
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (15 bp):
TATCATATCATAACA
Found at i:152826 original size:49 final size:49
Alignment explanation
Indices: 152754--152852 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
152744 TTTTTAAGAT
152754 TGATTATGTAAAGTTACATTCACTTTAGGGAATGAAGCATATCTAATGA
1 TGATTATGTAAAGTTACATTCACTTTAGGGAATGAAGCATATCTAATGA
*
152803 TGATTATGTAATGTTACATTCACTTTAGGGAATGAAGCATATCTAATGA
1 TGATTATGTAAAGTTACATTCACTTTAGGGAATGAAGCATATCTAATGA
152852 T
1 T
152853 AATTTTTTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (49 bp):
TGATTATGTAAAGTTACATTCACTTTAGGGAATGAAGCATATCTAATGA
Found at i:159529 original size:48 final size:48
Alignment explanation
Indices: 159468--159581 Score: 178
Period size: 46 Copynumber: 2.4 Consensus size: 48
159458 ATTAAATATT
* * *
159468 TTTATGGTAAATATTTTTTTTTATTTATGATTGATTGGATTTAGTGTG
1 TTTATGATAAATATTTTTTTTCATTTATGAATGATTGGATTTAGTGTG
159516 TTTATGATAAATA--TTTTTTCATTTATGAATGATTGGATTTAGTGTG
1 TTTATGATAAATATTTTTTTTCATTTATGAATGATTGGATTTAGTGTG
*
159562 TTTATAATAAATATTTTTTT
1 TTTATGATAAATATTTTTTT
159582 CTTAAATAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
46 43 0.72
48 17 0.28
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.57
Consensus pattern (48 bp):
TTTATGATAAATATTTTTTTTCATTTATGAATGATTGGATTTAGTGTG
Found at i:159565 original size:25 final size:25
Alignment explanation
Indices: 159491--159566 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
159481 TTTTTTTTTA
*
159491 TTTATGATTGATTGGATTTAGTGTG
1 TTTATGAATGATTGGATTTAGTGTG
* * * *
159516 TTTATG-ATAAAT--ATTT--TTTCA
1 TTTATGAATGATTGGATTTAGTGT-G
159537 TTTATGAATGATTGGATTTAGTGTG
1 TTTATGAATGATTGGATTTAGTGTG
159562 TTTAT
1 TTTAT
159567 AATAAATATT
Statistics
Matches: 36, Mismatches: 9, Indels: 12
0.63 0.16 0.21
Matches are distributed among these distances:
20 2 0.06
21 6 0.17
22 8 0.22
24 7 0.19
25 11 0.31
26 2 0.06
ACGTcount: A:0.25, C:0.01, G:0.20, T:0.54
Consensus pattern (25 bp):
TTTATGAATGATTGGATTTAGTGTG
Found at i:160947 original size:5 final size:5
Alignment explanation
Indices: 160939--160963 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
160929 CAATTCAACG
160939 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
160964 CAATTGGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:162758 original size:19 final size:20
Alignment explanation
Indices: 162727--162765 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
162717 TTTTTATACA
162727 ATAATAATATTTT-AATTTT
1 ATAATAATATTTTAAATTTT
162746 ATAAT-ATATTTTTAAATTTT
1 ATAATAATA-TTTTAAATTTT
162766 TAAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 9 0.50
20 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATAATAATATTTTAAATTTT
Found at i:162772 original size:18 final size:18
Alignment explanation
Indices: 162732--162772 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
162722 ATACAATAAT
162732 AATA-TTTTAATTTTATA
1 AATATTTTTAATTTTATA
162749 ATATATTTTTAAATTTT-TA
1 A-ATATTTTT-AATTTTATA
162768 AATAT
1 AATAT
162773 AATTATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 7 0.33
19 7 0.33
20 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATATTTTTAATTTTATA
Found at i:163103 original size:2 final size:2
Alignment explanation
Indices: 163098--163126 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
163088 TGGATTAACA
163098 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
163127 CACGATGGTT
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:164448 original size:22 final size:22
Alignment explanation
Indices: 164403--164449 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
164393 AATACTACTC
* *
164403 TAATGTAAACATTAAATTATGT
1 TAATGTAAACATTAAATAACGT
164425 TAATGTAAACATTAAATAACGT
1 TAATGTAAACATTAAATAACGT
164447 TAA
1 TAA
164450 GATGAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (22 bp):
TAATGTAAACATTAAATAACGT
Found at i:165848 original size:28 final size:28
Alignment explanation
Indices: 165802--165864 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 28
165792 AAAAAAAATA
165802 TTTATATTATATTATTTTAATTTAATAA-TT
1 TTTATATTATATTATTTT-A-TTAA-AATTT
*
165832 TTTATATT-TTTTA-TTTATTAAAATTT
1 TTTATATTATATTATTTTATTAAAATTT
165858 TTTATAT
1 TTTATAT
165865 AATCATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 2 0.06
26 13 0.42
27 1 0.03
28 3 0.10
29 4 0.13
30 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTATATTATATTATTTTATTAAAATTT
Found at i:173101 original size:21 final size:21
Alignment explanation
Indices: 173064--173113 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
173054 ATCATATGTT
* *
173064 ACATAACA-TTATCATAGATT
1 ACATAACACTTATAATAGATC
*
173084 GCATAACACTTATAATAGATC
1 ACATAACACTTATAATAGATC
173105 ACATAACAC
1 ACATAACAC
173114 ATATCACGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (21 bp):
ACATAACACTTATAATAGATC
Found at i:174265 original size:12 final size:12
Alignment explanation
Indices: 174240--174272 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
174230 GTAAGGTGAG
174240 AAAACAATGGAGT
1 AAAACAA-GGAGT
174253 AAAACAAGGAGT
1 AAAACAAGGAGT
174265 AAAA-AAGG
1 AAAACAAGG
174273 GGATTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.61, C:0.06, G:0.24, T:0.09
Consensus pattern (12 bp):
AAAACAAGGAGT
Found at i:174573 original size:19 final size:19
Alignment explanation
Indices: 174549--174586 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
174539 TTTAACTAAC
*
174549 TTAATTAATTAATTAAAAA
1 TTAATTAACTAATTAAAAA
*
174568 TTAATTAACTACTTAAAAA
1 TTAATTAACTAATTAAAAA
174587 AATTGAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAATTAACTAATTAAAAA
Found at i:179971 original size:28 final size:28
Alignment explanation
Indices: 179940--179997 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
179930 ACCATAATCC
* *
179940 AAAACATCCCAA-AATTAA-AATTTAGAT
1 AAAAAATCCCAATAA-TAATAATCTAGAT
*
179967 AAAAAATCTCAATAATAATAATCTAGAT
1 AAAAAATCCCAATAATAATAATCTAGAT
179995 AAA
1 AAA
179998 TCACACTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (28 bp):
AAAAAATCCCAATAATAATAATCTAGAT
Found at i:180543 original size:21 final size:21
Alignment explanation
Indices: 180519--180594 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
180509 GGACAAGCCA
180519 CCACATATTTTCCAATAATGG
1 CCACATATTTTCCAATAATGG
* *
180540 CCACATAGTTTATACAATAAAATTG
1 CCACATA-TTT-TCCAAT--AATGG
* * * *
180565 CCAAATATTTGCTAATGATGG
1 CCACATATTTTCCAATAATGG
180586 CCACATATT
1 CCACATATT
180595 CCTCCTTTCA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
21 18 0.43
22 3 0.07
23 8 0.19
24 3 0.07
25 10 0.24
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (21 bp):
CCACATATTTTCCAATAATGG
Found at i:180739 original size:46 final size:46
Alignment explanation
Indices: 180677--180792 Score: 135
Period size: 46 Copynumber: 2.5 Consensus size: 46
180667 TTAGCCTTTT
* * * * *
180677 TCATACTCAGATATCACTTGTCACGATTTTCACATTTTAGTC-TGTA
1 TCATACTCACATATCACATATCACGATTTCCACATGTTAG-CATGTA
* *
180723 TCATGCTCACATATCACATATCATGATTTCCACATGTTAGCATGTA
1 TCATACTCACATATCACATATCACGATTTCCACATGTTAGCATGTA
* *
180769 TTATACTCATATATCACATATCAC
1 TCATACTCACATATCACATATCAC
180793 ATAATCTCAC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 1 0.02
46 57 0.98
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (46 bp):
TCATACTCACATATCACATATCACGATTTCCACATGTTAGCATGTA
Found at i:180963 original size:20 final size:20
Alignment explanation
Indices: 180931--180996 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
180921 GAAATCACAC
*
180931 ATCATACATCATATAACATT
1 ATCATAGATCATATAACATT
*
180951 ATCGTAGATCATATAACACTT
1 ATCATAGATCATATAACA-TT
* *
180972 ATAATAGATCACATAACAATT
1 ATCATAGATCATATAAC-ATT
180993 ATCA
1 ATCA
180997 CGATTTTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.42
21 21 0.55
22 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (20 bp):
ATCATAGATCATATAACATT
Found at i:184840 original size:21 final size:21
Alignment explanation
Indices: 184815--184870 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
184805 TTGAAGTTTG
184815 TTGTATCGGTAGAAGTAATAA
1 TTGTATCGGTAGAAGTAATAA
* ** *
184836 TTGTATCGGTAGTAGTTTTAC
1 TTGTATCGGTAGAAGTAATAA
184857 TTGTATCGGTAGAA
1 TTGTATCGGTAGAA
184871 CCTTCCCAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.39
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTAATAA
Found at i:189389 original size:101 final size:101
Alignment explanation
Indices: 189214--189417 Score: 390
Period size: 101 Copynumber: 2.0 Consensus size: 101
189204 TCAATGCAAT
189214 TTGCCCATTCTCTTTAACATTGTACGCCAGTAGCCTTTCTGCCATATTCATTTTATTTTTCTTTC
1 TTGCCCATTCTCTTTAACATTGTACGCCAGTAGCCTTTCTGCCATATTCATTTTATTTTTCTTTC
*
189279 CTTTTCATCAATTAGTTTTATTGCTTTCTAAAGCCC
66 CATTTCATCAATTAGTTTTATTGCTTTCTAAAGCCC
*
189315 TTGCCCATTCTCTTTAATATTGTACGCCAGTAGCCTTTCTGCCATATTCATTTTATTTTTCTTTC
1 TTGCCCATTCTCTTTAACATTGTACGCCAGTAGCCTTTCTGCCATATTCATTTTATTTTTCTTTC
189380 CATTTCATCAATTAGTTTTATTGCTTTCTAAAGCCC
66 CATTTCATCAATTAGTTTTATTGCTTTCTAAAGCCC
189416 TT
1 TT
189418 CTCCTTTCCA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.19, C:0.24, G:0.09, T:0.48
Consensus pattern (101 bp):
TTGCCCATTCTCTTTAACATTGTACGCCAGTAGCCTTTCTGCCATATTCATTTTATTTTTCTTTC
CATTTCATCAATTAGTTTTATTGCTTTCTAAAGCCC
Found at i:190104 original size:14 final size:14
Alignment explanation
Indices: 190077--190119 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
190067 ATATATTTTC
* *
190077 TCTCATTTATTTTA
1 TCTCAATTAATTTA
*
190091 TCTTAATTAATTTA
1 TCTCAATTAATTTA
190105 TCTCAATTAATTTA
1 TCTCAATTAATTTA
190119 T
1 T
190120 TTTGCAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (14 bp):
TCTCAATTAATTTA
Found at i:191070 original size:21 final size:20
Alignment explanation
Indices: 191028--191070 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
191018 GATTTTCCTT
*
191028 AACCAAAAATATTTTGCAAC
1 AACCAAAAATATTTTACAAC
191048 AACC-AAAATACTTTCTACAAC
1 AACCAAAAATA-TTT-TACAAC
191069 AA
1 AA
191071 AAACAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 7 0.35
21 7 0.35
ACGTcount: A:0.51, C:0.23, G:0.02, T:0.23
Consensus pattern (20 bp):
AACCAAAAATATTTTACAAC
Found at i:191073 original size:18 final size:19
Alignment explanation
Indices: 191031--191073 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
191021 TTTCCTTAAC
*
191031 CAAAAATATTTTGCAACAA
1 CAAAAATACTTTGCAACAA
* *
191050 CCAAAATACTTT-CTACAA
1 CAAAAATACTTTGCAACAA
191068 CAAAAA
1 CAAAAA
191074 CAATATTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.53, C:0.21, G:0.02, T:0.23
Consensus pattern (19 bp):
CAAAAATACTTTGCAACAA
Found at i:191448 original size:32 final size:31
Alignment explanation
Indices: 191411--191471 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
191401 TTTTTGGTCC
191411 AATTTGGTACCCAAACTTGACACTTTTTTCCT
1 AATTTGGTACCCAAACTTGACA-TTTTTTCCT
* *
191443 AATTTGGTACCTAAACTTGATATTTTTTC
1 AATTTGGTACCCAAACTTGACATTTTTTC
191472 TTAAGTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (31 bp):
AATTTGGTACCCAAACTTGACATTTTTTCCT
Found at i:191489 original size:31 final size:32
Alignment explanation
Indices: 191418--191491 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
191408 TCCAATTTGG
* * *
191418 TACCCAAACTTGACACTTTTTTCCTAATTTGG
1 TACCTAAACTTGACACTTTTTTCCTAAGTTGA
* *
191450 TACCTAAACTTGATA-TTTTTTCTTAAGTTGA
1 TACCTAAACTTGACACTTTTTTCCTAAGTTGA
*
191481 TACTTAAACTT
1 TACCTAAACTT
191492 TTTGGGGATC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (32 bp):
TACCTAAACTTGACACTTTTTTCCTAAGTTGA
Found at i:192064 original size:58 final size:58
Alignment explanation
Indices: 191934--192085 Score: 166
Period size: 58 Copynumber: 2.6 Consensus size: 58
191924 AACATTTAAT
* * *
191934 AAATTTAGGTACCAAATTAGGAAAAA-TGACAAGTTCAGGTATCAAATTGGGCCCCAAAA
1 AAATTTAGGTACCAAATTAGAAAAAAGTGTCAAG-TCAGGTATCAAATTAGG-CCCAAAA
* * **
191993 AAGTTTAGGTACCAAATTAGAAAAAAGTGTCAAGTCCGGTTATCAAATTAGG-TGAAAA
1 AAATTTAGGTACCAAATTAGAAAAAAGTGTCAAGTCAGG-TATCAAATTAGGCCCAAAA
* *
192051 AAATTTAAGTACCAAATTA-AGAAAATGTGTCAAGT
1 AAATTTAGGTACCAAATTAGA-AAAAAGTGTCAAGT
192086 TCAAATACCA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 34 0.43
59 28 0.35
60 17 0.21
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (58 bp):
AAATTTAGGTACCAAATTAGAAAAAAGTGTCAAGTCAGGTATCAAATTAGGCCCAAAA
Found at i:192098 original size:58 final size:58
Alignment explanation
Indices: 191989--192099 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 58
191979 ATTGGGCCCC
* * *** *
191989 AAAAAAGTTTAGGTACCAAATTAGAAAAAAGTGTCAAGTCCGGTTATCAAATTAGGTG
1 AAAAAAATTTAAGTACCAAATTAGAAAAAAGTGTCAAGTCCAAATACCAAATTAGGTG
* *
192047 AAAAAAATTTAAGTACCAAATTA-AGAAAATGTGTCAAGTTCAAATACCAAATT
1 AAAAAAATTTAAGTACCAAATTAGA-AAAAAGTGTCAAGTCCAAATACCAAATT
192100 TTATATTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
57 1 0.02
58 43 0.98
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (58 bp):
AAAAAAATTTAAGTACCAAATTAGAAAAAAGTGTCAAGTCCAAATACCAAATTAGGTG
Found at i:192879 original size:22 final size:22
Alignment explanation
Indices: 192854--192896 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
192844 TAGAATACTA
* * *
192854 CGAATTGTATTGTAGTATACCG
1 CGAACTGTACTGTAGGATACCG
192876 CGAACTGTACTGTAGGATACC
1 CGAACTGTACTGTAGGATACC
192897 ACTATCATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (22 bp):
CGAACTGTACTGTAGGATACCG
Found at i:193412 original size:75 final size:74
Alignment explanation
Indices: 193237--193424 Score: 223
Period size: 74 Copynumber: 2.5 Consensus size: 74
193227 TCAGCGAGCT
* * * *
193237 TTAAAAATGACAGTCGCAATCGTAAATCAGTGACCTGTTAGAAAATCGAAGGTTGTGTCGTAAAT
1 TTAAAAATGACAGTCGCGATCGTAAATCAATGAACTGTTAGAAAATCGAAGGCTGTGTCGTAAAT
193302 CAACAAACC
66 CAACAAACC
* * * * * *
193311 GTAAAAATGAGAGTCGTGATCATAAATCAATGAATTGTTTGAAAATCGAAGGCTGTGATCGTAAA
1 TTAAAAATGACAGTCGCGATCGTAAATCAATGAACTGTTAGAAAATCGAAGGCTGTG-TCGTAAA
***
193376 TCAATGGACC
65 TCAACAAACC
* * *
193386 TTAAAAATGACAGTTGCGATCGTAAATCGACGAACTGTT
1 TTAAAAATGACAGTCGCGATCGTAAATCAATGAACTGTT
193425 TAAGTGGAGA
Statistics
Matches: 92, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
74 47 0.51
75 45 0.49
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (74 bp):
TTAAAAATGACAGTCGCGATCGTAAATCAATGAACTGTTAGAAAATCGAAGGCTGTGTCGTAAAT
CAACAAACC
Found at i:193425 original size:75 final size:73
Alignment explanation
Indices: 193237--193425 Score: 216
Period size: 75 Copynumber: 2.5 Consensus size: 73
193227 TCAGCGAGCT
* * * *
193237 TTAAAAATGACAGTCGCAATCGTAAATCAGTGACCTGTTAGAAAATCGAAGGTTGTGTCGTAAAT
1 TTAAAAATGACAGTCGCGATCGTAAATCA-TGAACTGTTTGAAAATCGAAGGCTGTGTCGTAAAT
193302 CAACAAACC
65 CAACAAACC
* * * * *
193311 GTAAAAATGAGAGTCGTGATCATAAATCAATGAATTGTTTGAAAATCGAAGGCTGTGATCGTAAA
1 TTAAAAATGACAGTCGCGATCGTAAATC-ATGAACTGTTTGAAAATCGAAGGCTGTG-TCGTAAA
***
193376 TCAATGGACC
64 TCAACAAACC
* *
193386 TTAAAAATGACAGTTGCGATCGTAAATCGACGAACTGTTT
1 TTAAAAATGACAGTCGCGATCGTAAATC-ATGAACTGTTT
193426 AAGTGGAGAC
Statistics
Matches: 93, Mismatches: 20, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
74 46 0.49
75 47 0.51
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (73 bp):
TTAAAAATGACAGTCGCGATCGTAAATCATGAACTGTTTGAAAATCGAAGGCTGTGTCGTAAATC
AACAAACC
Found at i:193586 original size:139 final size:139
Alignment explanation
Indices: 193323--193619 Score: 343
Period size: 139 Copynumber: 2.1 Consensus size: 139
193313 AAAAATGAGA
* * * * *
193323 GTCGTGATCATAAATCAATGAATTGTTTGAAAATCGAAGGCTGTGATCGTAAATCAATGGACCTT
1 GTCGTGATCATAAATCAATGAAATG-TTGAAAACCGAAGGCTGTGATCGTAAATCAACGAACCAT
* * * *
193388 AAAAATGACAGTTGCGATCGTAAATCGACGAACTGTTTAAGTGGAGACATAGTCATAAATCT-AT
65 AAAAATGACAGTTGCGATCGTAAATAGACGAACTGTTCAAGTGGAGACACAATCATAAAT-TGAT
*
193452 GAAGTT-TTTAT
129 GAA-TTCTTTAC
* * *
193463 GTCTTGATCATAAATCAATGGACAATG-TG-AAACCGAAGG-TCGTGATCTTAAATCAGCGAACC
1 GTCGTGATCATAAATCAAT-GA-AATGTTGAAAACCGAAGGCT-GTGATCGTAAATCAACGAACC
* * * *
193525 ATAAAAATGACAGTTGCGATCGTAAATAGATGAATTGTTCAAGTGGAGTCACAATCGTAAATTGA
63 ATAAAAATGACAGTTGCGATCGTAAATAGACGAACTGTTCAAGTGGAGACACAATCATAAATTGA
193590 TGAATTCTTTAC
128 TGAATTCTTTAC
*
193602 GTCGTGATCGTAAATCAA
1 GTCGTGATCATAAATCAA
193620 CGAACAATTA
Statistics
Matches: 133, Mismatches: 19, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
138 4 0.03
139 104 0.78
140 20 0.15
141 2 0.02
142 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (139 bp):
GTCGTGATCATAAATCAATGAAATGTTGAAAACCGAAGGCTGTGATCGTAAATCAACGAACCATA
AAAATGACAGTTGCGATCGTAAATAGACGAACTGTTCAAGTGGAGACACAATCATAAATTGATGA
ATTCTTTAC
Found at i:193659 original size:39 final size:39
Alignment explanation
Indices: 193605--193698 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
193595 TCTTTACGTC
* *
193605 GTGATCGTAAATCAACGAACAATTAGAAAAT-TAATGGTT
1 GTGATAGTAAATCAACGAACAATTAGAAAATCGAA-GGTT
*
193644 GTGATAGTAAATCAACGAACTATTAGAAAATCGAAGGTT
1 GTGATAGTAAATCAACGAACAATTAGAAAATCGAAGGTT
* *
193683 ATGATTGTAAATCAAC
1 GTGATAGTAAATCAAC
193699 AAACCGTAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 47 0.96
40 2 0.04
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.28
Consensus pattern (39 bp):
GTGATAGTAAATCAACGAACAATTAGAAAATCGAAGGTT
Found at i:193711 original size:39 final size:39
Alignment explanation
Indices: 193606--193725 Score: 98
Period size: 39 Copynumber: 3.1 Consensus size: 39
193596 CTTTACGTCG
* * * * * *
193606 TGATCGTAAATCAACGAACAATTAGAAAAT-TAATGGTTG
1 TGATAGTAAATCAACAAACCATAAGAAAATCGAA-GGTTA
* * *
193645 TGATAGTAAATCAACGAACTATTAGAAAATCGAAGGTTA
1 TGATAGTAAATCAACAAACCATAAGAAAATCGAAGGTTA
* * * * *
193684 TGATTGTAAATCAACAAACCGTAAGAAAGTCGATGGTCA
1 TGATAGTAAATCAACAAACCATAAGAAAATCGAAGGTTA
193723 TGA
1 TGA
193726 CAAGACCATA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 66 0.97
40 2 0.03
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (39 bp):
TGATAGTAAATCAACAAACCATAAGAAAATCGAAGGTTA
Found at i:193787 original size:39 final size:38
Alignment explanation
Indices: 193744--193843 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 38
193734 TAAAAAAGTT
*
193744 AAAGGTCGTGGTCATAAATCAACA-AATCATAAGAAAACC
1 AAAGGTCGTGATCATAAATCAA-AGAA-CATAAGAAAACC
*
193783 AAAGGTCGTGATCATAAATCAAAGGAACATAAGAAAATC
1 AAAGGTCGTGATCATAAATCAAA-GAACATAAGAAAACC
* *
193822 GAAGGTTGTGATCATAAATCAA
1 AAAGGTCGTGATCATAAATCAA
193844 TAGACTACAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
38 1 0.02
39 52 0.95
40 2 0.04
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (38 bp):
AAAGGTCGTGATCATAAATCAAAGAACATAAGAAAACC
Found at i:194013 original size:87 final size:87
Alignment explanation
Indices: 193853--194021 Score: 239
Period size: 87 Copynumber: 1.9 Consensus size: 87
193843 ATAGACTACA
* * **
193853 AGATTCGTAAAATCTCATAAATAAAAGATTGTGATCGTAAATCAGTAAACCATAAGAGAGCTGAA
1 AGATTCGTAAAATCTCATAAATAAAAGATTGTGATCGTAAATCAGGAAACCATAAGAAAGCCAAA
193918 GATCGTGATCGCAAATACCTCG
66 GATCGTGATCGCAAATACCTCG
* * * *
193940 AGATTCGTAAAATCTCGTATATAAAAGGTTGTGATTGTAAATCAGGAAACCATAAGAAAGCCAAA
1 AGATTCGTAAAATCTCATAAATAAAAGATTGTGATCGTAAATCAGGAAACCATAAGAAAGCCAAA
* * *
194005 GGTTGTGATCGTAAATA
66 GATCGTGATCGCAAATA
194022 ACGGACTGTA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (87 bp):
AGATTCGTAAAATCTCATAAATAAAAGATTGTGATCGTAAATCAGGAAACCATAAGAAAGCCAAA
GATCGTGATCGCAAATACCTCG
Found at i:200186 original size:40 final size:40
Alignment explanation
Indices: 200142--200237 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
200132 AAATTGGCAG
* * *
200142 TGACACTATAAACACTACGACATTACAACTGAACTGGTAA
1 TGACACTGTAAACACTACGACAATACAACTAAACTGGTAA
* * *
200182 TGACACTGTAAACACTTCGATAATACAACTAAACTGGTAG
1 TGACACTGTAAACACTACGACAATACAACTAAACTGGTAA
*
200222 TGACATTGTAAACACT
1 TGACACTGTAAACACT
200238 GCAATGCTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (40 bp):
TGACACTGTAAACACTACGACAATACAACTAAACTGGTAA
Found at i:200249 original size:40 final size:40
Alignment explanation
Indices: 200165--200279 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 40
200155 ACTACGACAT
* * * *
200165 TACAACTGAACTGGTAATGACACTGTAAACACTTCGATAA
1 TACAACTGAACTGGTAGTGACATTGTAAACACTGCAATAA
* **
200205 TACAACTAAACTGGTAGTGACATTGTAAACACTGCAATGC
1 TACAACTGAACTGGTAGTGACATTGTAAACACTGCAATAA
* *
200245 TACAACTGAACTAGCAGTGACATTGTAAACACTGC
1 TACAACTGAACTGGTAGTGACATTGTAAACACTGC
200280 TAGATTACCA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (40 bp):
TACAACTGAACTGGTAGTGACATTGTAAACACTGCAATAA
Found at i:202661 original size:25 final size:23
Alignment explanation
Indices: 202632--202677 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
202622 GTTGGATCCA
202632 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
202657 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
202678 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:208157 original size:43 final size:43
Alignment explanation
Indices: 208078--208164 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
208068 CACATAGGTT
* * ** ***
208078 GGACACACGGGCGTGTGTCTGGTCGTGTGTGTATATTGTCTTG
1 GGACACACGGGCGTGTGCCAGACCGTGTGAAAATATTGTCTTG
*
208121 GGACACACGGGCGTGTGCCAGACCGTGTGAAAATATTGTTTTG
1 GGACACACGGGCGTGTGCCAGACCGTGTGAAAATATTGTCTTG
208164 G
1 G
208165 CATTTTAGGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (43 bp):
GGACACACGGGCGTGTGCCAGACCGTGTGAAAATATTGTCTTG
Found at i:208653 original size:40 final size:40
Alignment explanation
Indices: 208516--208656 Score: 151
Period size: 40 Copynumber: 3.5 Consensus size: 40
208506 AGTTAAATTG
* * * *
208516 GCAATGACACTGTAAACA-TGCGACATTACAATTGAACTA
1 GCAATGACACTATAAACACTGCGATACTACAACTGAACTA
* * * * *
208555 GCAGTGATACTGTAAACATTGCGATAAC-ACAACTGAACTG
1 GCAATGACACTATAAACACTGCGAT-ACTACAACTGAACTA
* **
208595 GCAGTGACACTATAAACACTGTAATACTACAACTGAACTA
1 GCAATGACACTATAAACACTGCGATACTACAACTGAACTA
208635 GCAATGACACTATAAACACTGC
1 GCAATGACACTATAAACACTGC
208657 TAGATTACCA
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 18 0.21
40 66 0.78
41 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (40 bp):
GCAATGACACTATAAACACTGCGATACTACAACTGAACTA
Found at i:212182 original size:23 final size:24
Alignment explanation
Indices: 212129--212182 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
212119 GTTAGGGGTT
*
212129 AAAATT-AAATTATAATTTTTAAG
1 AAAATTAAAAATATAATTTTTAAG
**
212152 ATGA-TAAAAATATAATTTTTAA-
1 AAAATTAAAAATATAATTTTTAAG
212174 AAAATTAAA
1 AAAATTAAA
212183 TAAAAATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
AAAATTAAAAATATAATTTTTAAG
Found at i:212282 original size:21 final size:21
Alignment explanation
Indices: 212258--212305 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
212248 TTTTTAATTT
*
212258 TTTTTTAAATTTAAATGAAAA
1 TTTTTTAAACTTAAATGAAAA
* *
212279 TTTTTCAGACTTAAATGAAAA
1 TTTTTTAAACTTAAATGAAAA
*
212300 ATTTTT
1 TTTTTT
212306 CATTTTAAGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (21 bp):
TTTTTTAAACTTAAATGAAAA
Found at i:212313 original size:21 final size:21
Alignment explanation
Indices: 212266--212307 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
212256 TTTTTTTTAA
212266 ATTTAAATGAAAATTTTTCAG
1 ATTTAAATGAAAATTTTTCAG
*
212287 ACTTAAATGAAAAATTTTTCA
1 ATTTAAATG-AAAATTTTTCA
212308 TTTTAAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
ATTTAAATGAAAATTTTTCAG
Found at i:212642 original size:19 final size:18
Alignment explanation
Indices: 212612--212658 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
212602 TTAGTAACCG
212612 TAAAATAAATATGAAAAGTA
1 TAAAA-AAATATGAAAA-TA
* *
212632 TAAAAAAATATTATAATA
1 TAAAAAAATATGAAAATA
212650 TAAAAAAAT
1 TAAAAAAAT
212659 TACTTTGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.44
19 9 0.36
20 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
TAAAAAAATATGAAAATA
Found at i:213300 original size:39 final size:43
Alignment explanation
Indices: 213209--213304 Score: 110
Period size: 45 Copynumber: 2.3 Consensus size: 43
213199 TTTGTATGTG
* * *
213209 TATTTGAAAAAAATTATTTGAAATATTTCACATATAAACATAATGA
1 TATTTG-AAATAATTAATTGAAATATTTCACACAT-AACATAA-GA
213255 TATTTGAAATAATTAATTGAAATATTTCACACAT-A-A-AA-A
1 TATTTGAAATAATTAATTGAAATATTTCACACATAACATAAGA
213294 TATTTGAAATA
1 TATTTGAAATA
213305 TCATACCCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
39 12 0.26
41 2 0.04
42 1 0.02
43 1 0.02
45 25 0.53
46 6 0.13
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (43 bp):
TATTTGAAATAATTAATTGAAATATTTCACACATAACATAAGA
Found at i:221267 original size:26 final size:26
Alignment explanation
Indices: 221231--221283 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
221221 GATTAGAAGG
221231 TTACTAAAGTTACTTTGACGTTTCCT
1 TTACTAAAGTTACTTTGACGTTTCCT
221257 TTACTAAAGTTACTTTGACGTTTCCT
1 TTACTAAAGTTACTTTGACGTTTCCT
221283 T
1 T
221284 AAGAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (26 bp):
TTACTAAAGTTACTTTGACGTTTCCT
Found at i:223347 original size:82 final size:81
Alignment explanation
Indices: 223204--223445 Score: 283
Period size: 82 Copynumber: 3.0 Consensus size: 81
223194 CATTAACTAA
* *
223204 TTTCGTCAATTCGTGGCACCCAA-TGCCTAGC-GAATAAATCATAATAAGTGAG-TCCAACTCTA
1 TTTCGTCAATTCCTGGCA-CCAAGTGCCTAGCAG-ATAAATCATAATAAGTGAGCT-CAGCTCTA
223266 GTTGGATTAACCAACGATAG
63 GTTGGATTAACCAACG-TAG
* * * * *
223286 TTTTGTCAATTCCTGGCATCAAGTGCTTAGCAGATAAACCACAATAAGTGAGCTCAGCTCTAGTT
1 TTTCGTCAATTCCTGGCACCAAGTGCCTAGCAGATAAATCATAATAAGTGAGCTCAGCTCTAGTT
* *
223351 TGATTAACCAATTGTAG
66 GGATTAACCAA-CGTAG
* * ** *
223368 TTTCGTCAATTCCTGGCACCTAGTGCCTAGCGGATAAATTGTAATAAGTGAGCCCAGCTCTAGTT
1 TTTCGTCAATTCCTGGCACCAAGTGCCTAGCAGATAAATCATAATAAGTGAGCTCAGCTCTAGTT
*
223433 GGATTAGCCAACG
66 GGATTAACCAACG
223446 GTTTTGCGCC
Statistics
Matches: 134, Mismatches: 22, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
81 4 0.03
82 127 0.95
83 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (81 bp):
TTTCGTCAATTCCTGGCACCAAGTGCCTAGCAGATAAATCATAATAAGTGAGCTCAGCTCTAGTT
GGATTAACCAACGTAG
Found at i:225087 original size:15 final size:15
Alignment explanation
Indices: 225067--225097 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
225057 TCTAATTTGC
225067 ATTTTAATCACCTAA
1 ATTTTAATCACCTAA
225082 ATTTTAATCACCTAA
1 ATTTTAATCACCTAA
225097 A
1 A
225098 AACGTAATTA
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:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTTTAATCACCTAA
Found at i:227471 original size:17 final size:17
Alignment explanation
Indices: 227417--227471 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
227407 TATATATGGA
*
227417 AATGCAATGACAAT-GT
1 AATGCAATGACAATAAT
* *
227433 AGATGCAACGACAATAAA
1 A-ATGCAATGACAATAAT
*
227451 AATGCAATGACATTAAT
1 AATGCAATGACAATAAT
227468 AATG
1 AATG
227472 TAGGAATGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 1 0.03
17 29 0.94
18 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (17 bp):
AATGCAATGACAATAAT
Found at i:227941 original size:92 final size:92
Alignment explanation
Indices: 227784--227968 Score: 361
Period size: 92 Copynumber: 2.0 Consensus size: 92
227774 ATTCCTTAGC
227784 CGAATTTGTCACGACATCAGGTCCTTCTCTTCTTTCTTCTTTTACTTTTGTTTGAGCTTCGCATG
1 CGAATTTGTCACGACATCAGGTCCTTCTCTTCTTTCTTCTTTTACTTTTGTTTGAGCTTCGCATG
227849 AACTGTAGACTACTCCTCAATTTCTAT
66 AACTGTAGACTACTCCTCAATTTCTAT
227876 CGAATTTGTCACGACATCAGGTCCTTCTCTTCTTTCTTCTTTTACTTTTGTTTGAGCTTCGCATG
1 CGAATTTGTCACGACATCAGGTCCTTCTCTTCTTTCTTCTTTTACTTTTGTTTGAGCTTCGCATG
*
227941 AACTGTAGACTACTCCTCAGTTTCTAT
66 AACTGTAGACTACTCCTCAATTTCTAT
227968 C
1 C
227969 TCTGCTCTGG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.43
Consensus pattern (92 bp):
CGAATTTGTCACGACATCAGGTCCTTCTCTTCTTTCTTCTTTTACTTTTGTTTGAGCTTCGCATG
AACTGTAGACTACTCCTCAATTTCTAT
Found at i:229479 original size:14 final size:15
Alignment explanation
Indices: 229442--229481 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
229432 CATATTTCAC
229442 TAAAA-GAAA-AATG
1 TAAAAGGAAACAATG
*
229455 TAAAAGTAAACAATG
1 TAAAAGGAAACAATG
229470 -AAAAGGAAACAA
1 TAAAAGGAAACAA
229482 GTTAGTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 5 0.22
14 14 0.61
15 4 0.17
ACGTcount: A:0.68, C:0.05, G:0.15, T:0.12
Consensus pattern (15 bp):
TAAAAGGAAACAATG
Found at i:233697 original size:37 final size:37
Alignment explanation
Indices: 233644--233714 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
233634 GTTGCTGCAT
*
233644 GAGCACTTCTAGATTGCACCCAAAAC-TATCACCGTAA
1 GAGCACTTCTAAATTGCACCCAAAACAT-TCACCGTAA
*
233681 GAGCACTTCTAAATTGCACCTAAAACATTCACCG
1 GAGCACTTCTAAATTGCACCCAAAACATTCACCG
233715 CAGGAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.23
Consensus pattern (37 bp):
GAGCACTTCTAAATTGCACCCAAAACATTCACCGTAA
Found at i:237146 original size:17 final size:17
Alignment explanation
Indices: 237124--237189 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
237114 TTGTAGTATA
*
237124 ATTGTCCTTGCTTTTTT
1 ATTGTCCTTGCATTTTT
237141 ATTGTCAC-TGCATTTTT
1 ATTGTC-CTTGCATTTTT
* * *
237158 ATTGTCGTTGCATCTAT
1 ATTGTCCTTGCATTTTT
**
237175 ATTGTGATTGCATTT
1 ATTGTCCTTGCATTT
237190 CCATATATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 39 0.98
18 1 0.03
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (17 bp):
ATTGTCCTTGCATTTTT
Found at i:238347 original size:37 final size:37
Alignment explanation
Indices: 238306--238416 Score: 116
Period size: 37 Copynumber: 3.0 Consensus size: 37
238296 TCACCAGAGG
* *
238306 AATATTTTTGAAATGCACCCAAGACTGTCGCTGCATA
1 AATATTATTCAAATGCACCCAAGACTGTCGCTGCATA
* * *
238343 AATATTCTTCAAATTGCATCC-AGAACTATCGCTGCATA
1 AATATTATTCAAA-TGCACCCAAG-ACTGTCGCTGCATA
* * * *
238381 AGTATTATTCAATTGCACCCAGGAATGTCGCTGCAT
1 AATATTATTCAAATGCACCCAAGACTGTCGCTGCAT
238417 GAACATGTAC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
37 30 0.50
38 30 0.50
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (37 bp):
AATATTATTCAAATGCACCCAAGACTGTCGCTGCATA
Found at i:238376 original size:38 final size:37
Alignment explanation
Indices: 238319--238416 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 37
238309 ATTTTTGAAA
* * * *
238319 TGCACCCAAGACTGTCGCTGCATAAATATTCTTCAAAT
1 TGCACCCAGGAATATCGCTGCATAAATATTATTC-AAT
* *
238357 TGCATCCA-GAACTATCGCTGCATAAGTATTATTCAAT
1 TGCACCCAGGAA-TATCGCTGCATAAATATTATTCAAT
*
238394 TGCACCCAGGAATGTCGCTGCAT
1 TGCACCCAGGAATATCGCTGCAT
238417 GAACATGTAC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 22 0.43
38 29 0.57
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (37 bp):
TGCACCCAGGAATATCGCTGCATAAATATTATTCAAT
Found at i:244069 original size:17 final size:17
Alignment explanation
Indices: 244045--244080 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
244035 AACTCTAGAC
244045 TAAAACCTT-TTTATTT
1 TAAAACCTTATTTATTT
244061 TAAATACCTTATTTATTT
1 TAAA-ACCTTATTTATTT
244079 TA
1 TA
244081 TTTAGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 5 0.28
18 9 0.50
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAAACCTTATTTATTT
Found at i:245104 original size:15 final size:12
Alignment explanation
Indices: 245070--245101 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
245060 AGAAGAAGAA
245070 GAAGAAGATCTT
1 GAAGAAGATCTT
245082 GAAGAAGATCTT
1 GAAGAAGATCTT
*
245094 GAGGAAGA
1 GAAGAAGA
245102 AGAAGATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (12 bp):
GAAGAAGATCTT
Found at i:247694 original size:12 final size:12
Alignment explanation
Indices: 247679--247703 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
247669 GCTCTCTAGC
247679 TTTCCCTTCCAT
1 TTTCCCTTCCAT
247691 TTTCCCTTCCAT
1 TTTCCCTTCCAT
247703 T
1 T
247704 CCTTTTCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTCCCTTCCAT
Found at i:248625 original size:5 final size:6
Alignment explanation
Indices: 248609--248633 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
248599 ATTGAAATAA
248609 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
248634 ACTTAGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:258362 original size:15 final size:15
Alignment explanation
Indices: 258337--258387 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
258327 GGTTCGAGAT
*
258337 GGTAAATTGCATCCA
1 GGTAAACTGCATCCA
*
258352 GGTAAGCTGCATCCA
1 GGTAAACTGCATCCA
258367 GGTAAACTGCATCCA
1 GGTAAACTGCATCCA
258382 GGTAAA
1 GGTAAA
258388 TTATGGCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (15 bp):
GGTAAACTGCATCCA
Found at i:260292 original size:17 final size:18
Alignment explanation
Indices: 260270--260309 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
260260 GTTTGCATGT
260270 ATTTTTA-ATGTCATTGC
1 ATTTTTATATGTCATTGC
*
260287 ATTTTTATTTTGTCATTGC
1 ATTTTTA-TATGTCATTGC
260306 ATTT
1 ATTT
260310 CTTTTGTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
19 13 0.65
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (18 bp):
ATTTTTATATGTCATTGC
Found at i:260919 original size:18 final size:18
Alignment explanation
Indices: 260895--260939 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
260885 GTCACTTGAA
260895 AAAAGAAAATGAGAAAA-AG
1 AAAAGAAAA--AGAAAAGAG
260914 -AAAGAAAAAGAAAAGAG
1 AAAAGAAAAAGAAAAGAG
260931 AAAAGAAAA
1 AAAAGAAAA
260940 GAAGGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.25
17 2 0.08
18 16 0.67
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGAG
Found at i:260942 original size:23 final size:24
Alignment explanation
Indices: 260894--260938 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
260884 AGTCACTTGA
260894 AAAAAGAAAATGAGAAAAAGAAAG
1 AAAAAGAAAATGAGAAAAAGAAAG
260918 AAAAAGAAAA-GAG-AAAAGAAA
1 AAAAAGAAAATGAGAAAAAGAAA
260939 AGAAGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (24 bp):
AAAAAGAAAATGAGAAAAAGAAAG
Found at i:263774 original size:14 final size:15
Alignment explanation
Indices: 263757--263789 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
263747 TAGTTGGTTT
263757 TAAA-GATCATAAAA
1 TAAACGATCATAAAA
263771 TAAACGATCATAAAA
1 TAAACGATCATAAAA
263786 TAAA
1 TAAA
263790 AGAGTTGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.21
Consensus pattern (15 bp):
TAAACGATCATAAAA
Found at i:263798 original size:44 final size:44
Alignment explanation
Indices: 263739--263822 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
263729 GCTAAAGTAG
* *
263739 AAATTAAATAGTTGGTTTTAAAGATCATAAAATAAACGATCATA
1 AAATAAAAGAGTTGGTTTTAAAGATCATAAAATAAACGATCATA
263783 AAATAAAAGAGTTGGTTTTAAAGATCATAAAATAAACGAT
1 AAATAAAAGAGTTGGTTTTAAAGATCATAAAATAAACGAT
263823 AAGCTAAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (44 bp):
AAATAAAAGAGTTGGTTTTAAAGATCATAAAATAAACGATCATA
Found at i:264413 original size:12 final size:13
Alignment explanation
Indices: 264385--264416 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
264375 ATCTCGTTTC
264385 AAAACTGAAAATA
1 AAAACTGAAAATA
*
264398 AAAACTGAAACTA
1 AAAACTGAAAATA
264411 AAAACT
1 AAAACT
264417 AAAGTCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.12, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAACTGAAAATA
Found at i:269531 original size:15 final size:16
Alignment explanation
Indices: 269511--269540 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
269501 GCATCTCACA
269511 ATCTTCATA-ATATCC
1 ATCTTCATAGATATCC
269526 ATCTTCATAGATATC
1 ATCTTCATAGATATC
269541 GGCATCATAA
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:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (16 bp):
ATCTTCATAGATATCC
Found at i:277628 original size:24 final size:21
Alignment explanation
Indices: 277567--277624 Score: 53
Period size: 24 Copynumber: 2.6 Consensus size: 21
277557 CGACAAAAAT
* *
277567 TTCTTCATGCTCTCCTTTTCC
1 TTCTTCTTGCTCTCCTTGTCC
**
277588 TTCTTCTTTTTCCTCCTTCGTCTC
1 TTCTTCTTGCT-CTCCTT-GTC-C
277612 TTCTTCTTGCTCT
1 TTCTTCTTGCTCT
277625 TCCTCAATAC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
21 8 0.29
22 6 0.21
23 4 0.14
24 10 0.36
ACGTcount: A:0.02, C:0.36, G:0.05, T:0.57
Consensus pattern (21 bp):
TTCTTCTTGCTCTCCTTGTCC
Done.