Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014318.1 Kokia drynarioides strain JFW-HI SEQ_129355, 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: 92524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 124 characters in sequence are not A, C, G, or T
Found at i:3039 original size:23 final size:22
Alignment explanation
Indices: 3000--3056 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
2990 ACCAGTTATT
3000 ATTATTTTGTAACTCTCCTACC
1 ATTATTTTGTAACTCTCCTACC
* *
3022 ATTATGTTTGTAAGTCTCCTGCC
1 ATTAT-TTTGTAACTCTCCTACC
3045 ATAATATTTTGT
1 AT--TATTTTGT
3057 TTTAAATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.17
23 17 0.57
24 5 0.17
25 3 0.10
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (22 bp):
ATTATTTTGTAACTCTCCTACC
Found at i:4250 original size:19 final size:19
Alignment explanation
Indices: 4226--4266 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
4216 CTAAATAAAC
*
4226 AAACAAAAAAAATTAAATA
1 AAACAAAAAAAACTAAATA
**
4245 AAACAAAACCAACTAAATA
1 AAACAAAAAAAACTAAATA
4264 AAA
1 AAA
4267 AACTAAGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (19 bp):
AAACAAAAAAAACTAAATA
Found at i:5747 original size:2 final size:2
Alignment explanation
Indices: 5742--5766 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5732 CTCTCTTCCT
5742 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
5767 TCACTCACTT
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:9881 original size:19 final size:20
Alignment explanation
Indices: 9858--9917 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 20
9848 ATATTTTTGC
*
9858 ATTTTATAATAATTTTTAAT
1 ATTTTTTAATAATTTTTAAT
*
9878 -TTTTTTTATAA-TTTTAAT
1 ATTTTTTAATAATTTTTAAT
9896 ATTTTTTAATAATTTTTCAAT
1 ATTTTTTAATAATTTTT-AAT
9917 A
1 A
9918 ACTAATGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 7 0.21
19 19 0.56
20 4 0.12
21 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTTTAATAATTTTTAAT
Found at i:9892 original size:10 final size:10
Alignment explanation
Indices: 9858--9918 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
9848 ATATTTTTGC
9858 ATTTTATAATA
1 ATTTT-TAATA
9869 ATTTTTAAT-
1 ATTTTTAATA
* *
9878 TTTTTTTATA
1 ATTTTTAATA
9888 A-TTTTAATA
1 ATTTTTAATA
*
9897 TTTTTTAATA
1 ATTTTTAATA
9907 ATTTTTCAATA
1 ATTTTT-AATA
9918 A
1 A
9919 CTAATGTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
9 14 0.34
10 17 0.41
11 10 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:17765 original size:20 final size:19
Alignment explanation
Indices: 17722--17765 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
17712 ATAAATTATT
*
17722 AAAATTTTAAAAAAATATA
1 AAAATTTTAAAAAAATAAA
* *
17741 CAAATATTTAAAAGAATAAA
1 AAAAT-TTTAAAAAAATAAA
17761 AAAAT
1 AAAAT
17766 CATTCAACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATTTTAAAAAAATAAA
Found at i:26496 original size:10 final size:9
Alignment explanation
Indices: 26479--26503 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
26469 ATCTCTGATG
26479 TATTTTTTT
1 TATTTTTTT
26488 TATTTTTTT
1 TATTTTTTT
26497 TATTTTT
1 TATTTTT
26504 ATATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:26686 original size:24 final size:26
Alignment explanation
Indices: 26640--26687 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
26630 GCATGTCAGA
26640 TAGGCGACACCTATGTGCCTATTTGG
1 TAGGCGACACCTATGTGCCTATTTGG
*
26666 TAGGCGACA-CTA-GTGCTTATTT
1 TAGGCGACACCTATGTGCCTATTT
26688 AAGCACCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 3 0.14
26 9 0.43
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (26 bp):
TAGGCGACACCTATGTGCCTATTTGG
Found at i:27944 original size:22 final size:22
Alignment explanation
Indices: 27919--27966 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
27909 ATTGAGAGGA
* *
27919 TTTT-TTTATTCAGAGGAGGATT
1 TTTTATTTATTCA-AAGAGAATT
*
27941 TTTTATTTGTTCAAAGAGAATT
1 TTTTATTTATTCAAAGAGAATT
27963 TTTT
1 TTTT
27967 GTGGAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (22 bp):
TTTTATTTATTCAAAGAGAATT
Found at i:27995 original size:20 final size:20
Alignment explanation
Indices: 27941--27998 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
27931 GAGGAGGATT
*
27941 TTTTATTTGTTCAAAGAGAA
1 TTTTATTTGTTCAGAGAGAA
27961 -TTT-TTTG-T--G-GAGAA
1 TTTTATTTGTTCAGAGAGAA
27975 TTTTATTTGTTCAGAGAGAA
1 TTTTATTTGTTCAGAGAGAA
27995 TTTT
1 TTTT
27999 TTGTCGAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
14 5 0.16
15 3 0.10
16 4 0.13
17 2 0.06
18 4 0.13
19 4 0.13
20 9 0.29
ACGTcount: A:0.28, C:0.03, G:0.19, T:0.50
Consensus pattern (20 bp):
TTTTATTTGTTCAGAGAGAA
Found at i:28001 original size:18 final size:18
Alignment explanation
Indices: 27946--28002 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
27936 GGATTTTTTA
*
27946 TTTGTTCAAAGAGAATTT
1 TTTGTTCAGAGAGAATTT
27964 TTTG-T--G-GAGAATTTT
1 TTTGTTCAGAGAGAA-TTT
27979 ATTTGTTCAGAGAGAATTT
1 -TTTGTTCAGAGAGAATTT
27998 TTTGT
1 TTTGT
28003 CGAATAAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 5 0.16
15 3 0.09
16 4 0.12
17 2 0.06
18 9 0.28
19 4 0.12
20 5 0.16
ACGTcount: A:0.26, C:0.04, G:0.21, T:0.49
Consensus pattern (18 bp):
TTTGTTCAGAGAGAATTT
Found at i:28034 original size:20 final size:21
Alignment explanation
Indices: 28006--28046 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
27996 TTTTTGTCGA
*
28006 ATAAGATTCAGAG-ATTTTTT
1 ATAACATTCAGAGAATTTTTT
28026 ATAACATTCAGAGAATTTTTT
1 ATAACATTCAGAGAATTTTTT
28047 TTTCCAGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (21 bp):
ATAACATTCAGAGAATTTTTT
Found at i:55685 original size:2 final size:2
Alignment explanation
Indices: 55675--55704 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55665 ATGTGTGAAA
*
55675 AT AT GT 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
55705 TTGTTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58218 original size:21 final size:21
Alignment explanation
Indices: 58180--58221 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58170 AGCTTCCCTT
58180 CAATACTTGTTTTCATCTCCA
1 CAATACTTGTTTTCATCTCCA
*
58201 CAATATTTGCTTTT-ATCTCCA
1 CAATACTTG-TTTTCATCTCCA
58222 ACATTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.24, C:0.26, G:0.05, T:0.45
Consensus pattern (21 bp):
CAATACTTGTTTTCATCTCCA
Found at i:60264 original size:25 final size:26
Alignment explanation
Indices: 60235--60300 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 26
60225 TGGCTCCACC
* *
60235 AAAATA-AAATAATATTTTTAATTTTT
1 AAAATAGAAATAATA-TTTAAAATTTT
*
60261 AAATTAGAAATAA-ATTTAAAATTTT
1 AAAATAGAAATAATATTTAAAATTTT
* *
60286 AAAAAATAAATAATA
1 AAAATAGAAATAATA
60301 AACAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 19 0.59
26 7 0.22
27 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAATAGAAATAATATTTAAAATTTT
Found at i:60383 original size:18 final size:18
Alignment explanation
Indices: 60357--60392 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
60347 CAACCAAAAA
60357 TAAAATATACATTTAAAT
1 TAAAATATACATTTAAAT
* *
60375 TAAACTATATATTTAAAT
1 TAAAATATACATTTAAAT
60393 ATTAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATATACATTTAAAT
Found at i:60476 original size:106 final size:103
Alignment explanation
Indices: 60349--60552 Score: 318
Period size: 106 Copynumber: 2.0 Consensus size: 103
60339 GAGTTGCTCA
*
60349 ACCAAAAATAAAATATACATTTAAATTAAACTATATATTTAAATATTAAATAATAAATAATAATA
1 ACCAAAAATAAAATAAACATTTAAATTAAACTATATATTTAAATATTAAATAATAAAT-A-AA-A
* * * *
60414 AACAAATAAATTAATTGGGTGACACCATTTAAAATGATTCC
63 AACAAAAAAATCAATTGAGTGACACCATATAAAATGATTCC
*
60455 ACCAAAAATAAAATAAACATTTAAATTAAACTATATATTTAAATATTAAATGATAAATAAAAAAC
1 ACCAAAAATAAAATAAACATTTAAATTAAACTATATATTTAAATATTAAATAATAAATAAAAAAC
*
60520 AAAAAAATCAATTGAGTGTCACCATATAAAATG
66 AAAAAAATCAATTGAGTGACACCATATAAAATG
60553 GCTCCATAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
103 32 0.35
104 2 0.02
105 1 0.01
106 56 0.62
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (103 bp):
ACCAAAAATAAAATAAACATTTAAATTAAACTATATATTTAAATATTAAATAATAAATAAAAAAC
AAAAAAATCAATTGAGTGACACCATATAAAATGATTCC
Found at i:62050 original size:30 final size:30
Alignment explanation
Indices: 61982--62059 Score: 142
Period size: 28 Copynumber: 2.7 Consensus size: 30
61972 CTTTTATTAA
61982 TTAAATTGTGTACAAAGTGCAAAGAGGTGC
1 TTAAATTGTGTACAAAGTGCAAAGAGGTGC
62012 TT--ATTGTGTACAAAGTGCAAAGAGGTGC
1 TTAAATTGTGTACAAAGTGCAAAGAGGTGC
62040 TTAAATTGTGTACAAAGTGC
1 TTAAATTGTGTACAAAGTGC
62060 TTATTTAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
28 28 0.61
30 18 0.39
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (30 bp):
TTAAATTGTGTACAAAGTGCAAAGAGGTGC
Found at i:62858 original size:35 final size:35
Alignment explanation
Indices: 62819--62888 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
62809 GTATTACTGA
62819 TGATGTCATTCGTTTAAGATTATTCCCCTTTCACT
1 TGATGTCATTCGTTTAAGATTATTCCCCTTTCACT
62854 TGATGTCATTCGTTTAAGATTATTCCCCTTTCACT
1 TGATGTCATTCGTTTAAGATTATTCCCCTTTCACT
62889 AACCAGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.46
Consensus pattern (35 bp):
TGATGTCATTCGTTTAAGATTATTCCCCTTTCACT
Found at i:67442 original size:21 final size:22
Alignment explanation
Indices: 67416--67457 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
67406 AATCAAAAAG
67416 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
67437 AAAAGAATCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
67458 ACATGTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAC
Found at i:70339 original size:20 final size:21
Alignment explanation
Indices: 70314--70352 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
70304 AACTTCCCTC
70314 CAATACTTG-TTTTATCTCCA
1 CAATACTTGCTTTTATCTCCA
70334 CAATACTTGCTTTTATCTC
1 CAATACTTGCTTTTATCTC
70353 AAGCATTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.23, C:0.26, G:0.05, T:0.46
Consensus pattern (21 bp):
CAATACTTGCTTTTATCTCCA
Found at i:72189 original size:59 final size:59
Alignment explanation
Indices: 71981--72203 Score: 272
Period size: 60 Copynumber: 3.8 Consensus size: 59
71971 GCTTCGAGAA
* * * *
71981 TAAAATGGTAATTTTTCGGAAGGTTTGGGGTTAAAAATGGAATTTATAGACATTCGGGGG
1 TAAAATGGTAATTTTT-GAAAGGTTCGGGGTTAAAAATGGAATTTTTAGACATTTGGGGG
* * *
72041 TAAAATGGTAATTTTTGAAAGGTTCGGGGTTAAAAAATGGAATTTTTAGTCATTCT-AGGA
1 TAAAATGGTAATTTTTGAAAGGTTCGGGGTT-AAAAATGGAATTTTTAGACATT-TGGGGG
* *
72101 TAAAATAGT-ATTTCTTGAAAAGTTCGGGGTTAAAAATGGAATTTTTAGACATTTGGGGG
1 TAAAATGGTAATTT-TTGAAAGGTTCGGGGTTAAAAATGGAATTTTTAGACATTTGGGGG
* * * *
72160 T-AAATGGTAATTTTTGGAAGGTTTGGGGGTAAAAATGTAATTTT
1 TAAAATGGTAATTTTTGAAAGGTTCGGGGTTAAAAATGGAATTTT
72204 CAAAAAATTT
Statistics
Matches: 140, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
58 33 0.24
59 45 0.32
60 62 0.44
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.36
Consensus pattern (59 bp):
TAAAATGGTAATTTTTGAAAGGTTCGGGGTTAAAAATGGAATTTTTAGACATTTGGGGG
Found at i:72227 original size:88 final size:88
Alignment explanation
Indices: 72127--72465 Score: 275
Period size: 88 Copynumber: 3.9 Consensus size: 88
72117 GAAAAGTTCG
* *** *
72127 GGGTTAAAAATGGAATTTTTAGACA-TTT-GGGGGTAAATGGTAATTTTTGGAAGGTTTGGGGGT
1 GGGTTAAAAATGGAATTTTTAGAAAGTTTAGGGAAAAAATGG-AA-TTTTGGAAGGTTTAGGGGT
72190 AAAAATGTAATTT-TCAAAAAATTTA
64 AAAAATGTAATTTCT-AAAAAATTTA
* *
72215 GGGTAAAAAATGGAA-TTTTAGAAAGTTTTAGGGAAAAAATGGAATTTTGGAATGTTTAGGGGTA
1 GGGTTAAAAATGGAATTTTTAGAAAG-TTTAGGGAAAAAATGGAATTTTGGAAGGTTTAGGGGTA
*
72279 AAAATGTAATTTCTAAAAAGTTTA
65 AAAATGTAATTTCTAAAAAATTTA
* * * * ** * * *
72303 GGGTTAAAAA--GAAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTCTAAAAAGTTTAAGGTT
1 GGGTTAAAAATGGAATTTTTAGAAAGTTT-AGGGAAAAAATGGAATTT-TGGAAGGTTTAGGGGT
* ** *
72366 AAAAATGGAATTT-TGGAAAGTTTA
64 AAAAATGTAATTTCTAAAAAATTTA
* * * * * *
72390 GGGGT-AAAATGTAATTTTT-GAAAAGTTTAGGGTTATAAATAGAATTTTGGAAAGTTT-GGTGG
1 GGGTTAAAAATGGAATTTTTAG-AAAGTTTAGGG-AAAAAATGGAATTTTGGAAGGTTTAGG-GG
*
72452 TAAAAATGGAATTT
63 TAAAAATGTAATTT
72466 TGGAAAAGTT
Statistics
Matches: 209, Mismatches: 30, Indels: 25
0.79 0.11 0.09
Matches are distributed among these distances:
86 11 0.05
87 74 0.35
88 109 0.52
89 6 0.03
90 9 0.04
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (88 bp):
GGGTTAAAAATGGAATTTTTAGAAAGTTTAGGGAAAAAATGGAATTTTGGAAGGTTTAGGGGTAA
AAATGTAATTTCTAAAAAATTTA
Found at i:72436 original size:117 final size:115
Alignment explanation
Indices: 72128--72476 Score: 375
Period size: 117 Copynumber: 3.0 Consensus size: 115
72118 AAAAGTTCGG
* * * * * * *
72128 GGTTAAAAATGGAATTTTTAGACA-TTTGGGGGT-AAATGGTAATTTTTGGAAGGTTTGGGGGTA
1 GGTTAAAAATGGAA-TTTTGGAAAGTTTAGGGGTAAAAT-GTAATTTTTGAAAAGTTTAGGGTTA
* ** * * *
72191 AAA-ATGTAATTTTCAAAAAATTTAGGGTAAAAAATGGAATTTTAGAAAGTTTTA
64 AAATA-GAAATTTT-GGAAAGTTTAGGGT-AAAAATGGAATTTTAAAAAGTTTAA
** * * *
72245 GGGAAAAAATGGAATTTTGGAATGTTTAGGGGTAAAAATGTAATTTCTAAAAAGTTTAGGGTTAA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT-AAAATGTAATTTTTGAAAAGTTTAGGGTTAA
*
72310 AA-AGAAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTCTAAAAAGTTTAA
65 AATAGAAATTTTGGAAAGTTT-AGGGTAAAAATGGAATTT-TAAAAAGTTTAA
72362 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGAAAAGTTTAGGGTTATA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGAAAAGTTTAGGGTTA-A
* *
72427 AATAG-AATTTTGGAAAGTTTGGTGGTAAAAATGGAATTTTGGAAAAGTTT
65 AATAGAAATTTTGGAAAGTTTAG-GGTAAAAATGGAATTTT-AAAAAGTTT
72477 GGTGGTCAAA
Statistics
Matches: 196, Mismatches: 27, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
116 54 0.28
117 113 0.58
118 25 0.13
119 4 0.02
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (115 bp):
GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGAAAAGTTTAGGGTTAAA
ATAGAAATTTTGGAAAGTTTAGGGTAAAAATGGAATTTTAAAAAGTTTAA
Found at i:72476 original size:30 final size:29
Alignment explanation
Indices: 72126--72506 Score: 294
Period size: 29 Copynumber: 13.0 Consensus size: 29
72116 TGAAAAGTTC
* * *
72126 GGGGTTAAAAATGGAATTTTTAGACA-TTTG
1 GGGG-TAAAAATGGAA-TTTTGGAAAGTTTA
* *
72156 GGGGT--AAATGGTAATTTTTGGAAGGTTTG
1 GGGGTAAAAATGG-AA-TTTTGGAAAGTTTA
* ** *
72185 GGGGTAAAAATGTAATTTTCAAAAAATTTA
1 GGGGTAAAAATGGAATTTT-GGAAAGTTTA
*
72215 -GGGTAAAAAATGGAATTTTAGAAAGTTTTA
1 GGGGT-AAAAATGGAATTTTGGAAAG-TTTA
* *
72245 -GGGAAAAAATGGAATTTTGGAATGTTTA
1 GGGGTAAAAATGGAATTTTGGAAAGTTTA
* **
72273 GGGGTAAAAATGTAATTTCTAAAAAGTTTA
1 GGGGTAAAAATGGAATTT-TGGAAAGTTTA
* *
72303 GGGTTAAAAA-GAAATTTTGGAAAGTTTA
1 GGGGTAAAAATGGAATTTTGGAAAGTTTA
* * **
72331 AGGGTAAAAATGTAATTTCTAAAAAGTTTA
1 GGGGTAAAAATGGAATTT-TGGAAAGTTTA
* *
72361 AGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAAATGGAATTTTGGAAAGTTTA
* *
72390 GGGGT-AAAATGTAATTTTTGAAAAGTTTA
1 GGGGTAAAAATGGAA-TTTTGGAAAGTTTA
* * *
72419 GGGTTATAAATAGAATTTTGGAAAGTTT-
1 GGGGTAAAAATGGAATTTTGGAAAGTTTA
72447 GGTGGTAAAAATGGAATTTTGGAAAAGTTT-
1 GG-GGTAAAAATGGAATTTTGG-AAAGTTTA
* * *
72477 GGTGGTCAAAATGTAATTTTTGAAAAGTTT
1 GG-GGTAAAAATGGAA-TTTTGGAAAGTTT
72507 GAGTGTTAAA
Statistics
Matches: 287, Mismatches: 48, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
27 6 0.02
28 40 0.14
29 124 0.43
30 107 0.37
31 10 0.03
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTGGAAAGTTTA
Found at i:72507 original size:30 final size:29
Alignment explanation
Indices: 72102--72507 Score: 253
Period size: 30 Copynumber: 13.8 Consensus size: 29
72092 ATTCTAGGAT
*
72102 AAAATAGT-ATTTCTTGAAAAGTTCGGGGTTA
1 AAAAT-GTAATTT-TTGAAAAGTTTGGGG-TA
* *
72133 AAAATGGAATTTTT-AGACA-TTTGGGGGT-
1 AAAATGTAATTTTTGA-AAAGTTT-GGGGTA
* *
72161 -AAATGGTAATTTTTGGAAGGTTTGGGGGTA
1 AAAAT-GTAATTTTTGAAAAGTTT-GGGGTA
** * *
72191 AAAATGTAATTTTCAAAAAATTTAGGGTAA
1 AAAATGTAATTTTTGAAAAGTTTGGGGT-A
* * * *
72221 AAAATGGAATTTTAG-AAAGTTTTAGGGAA
1 AAAATGTAATTTTTGAAAAG-TTTGGGGTA
* * *
72250 AAAATGGAA-TTTTGGAATGTTTAGGGGTA
1 AAAATGTAATTTTTGAAAAGTTT-GGGGTA
* * *
72279 AAAATGTAATTTCTAAAAAGTTTAGGGTTA
1 AAAATGTAATTTTTGAAAAGTTT-GGGGTA
* * *
72309 AAAA-G-AAATTTTGGAAAGTTTAAGGGTA
1 AAAATGTAATTTTTGAAAAGTTT-GGGGTA
* * * *
72337 AAAATGTAATTTCTAAAAAGTTTAAGGTTA
1 AAAATGTAATTTTTGAAAAGTTT-GGGGTA
* *
72367 AAAATGGAA-TTTTGGAAAGTTTAGGGGT-
1 AAAATGTAATTTTTGAAAAGTTT-GGGGTA
*
72395 AAAATGTAATTTTTGAAAAGTTTAGGGTTA
1 AAAATGTAATTTTTGAAAAGTTT-GGGGTA
* *
72425 TAAATAG-AA-TTTTGGAAAGTTTGGTGGTA
1 AAAAT-GTAATTTTTGAAAAGTTTGG-GGTA
* * *
72454 AAAATGGAATTTTGGAAAAGTTTGGTGGTC
1 AAAATGTAATTTTTGAAAAGTTTGG-GGTA
72484 AAAATGTAATTTTTGAAAAGTTTG
1 AAAATGTAATTTTTGAAAAGTTTG
72508 AGTGTTAAAA
Statistics
Matches: 297, Mismatches: 57, Indels: 43
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.01
28 48 0.16
29 99 0.33
30 132 0.44
31 14 0.05
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAAGTTTGGGGTA
Found at i:72526 original size:30 final size:29
Alignment explanation
Indices: 72403--72535 Score: 96
Period size: 30 Copynumber: 4.5 Consensus size: 29
72393 GTAAAATGTA
72403 ATTTTTGAAAAGTTTAGG-GTTATAAAT-AG
1 ATTTTTGAAAAGTTT-GGTGTTA-AAATAAG
* * * *
72432 AATTTTGGAAAGTTTGGTGGTAAAA-ATGG
1 ATTTTTGAAAAGTTTGGTGTTAAAATA-AG
* * *
72461 AATTTTGGAAAAGTTTGGTGGTCAAAATGTA-
1 -ATTTTTGAAAAGTTTGGT-GTTAAAAT-AAG
72492 ATTTTTGAAAAGTTTGAGTGTTAAAATAAG
1 ATTTTTGAAAAGTTTG-GTGTTAAAATAAG
72522 ATTTTT-AAACAGTT
1 ATTTTTGAAA-AGTT
72536 CAAGGACTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
28 5 0.06
29 21 0.26
30 47 0.59
31 7 0.09
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (29 bp):
ATTTTTGAAAAGTTTGGTGTTAAAATAAG
Found at i:74144 original size:11 final size:11
Alignment explanation
Indices: 74128--74170 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
74118 AAACCATTTC
*
74128 AAATTTAAACT
1 AAATTTAAAAT
*
74139 AAATTTAAATTT
1 AAATTTAAA-AT
74151 AAATTTAAAAT
1 AAATTTAAAAT
74162 AAATTTAAA
1 AAATTTAAA
74171 TTCAAGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:74148 original size:17 final size:18
Alignment explanation
Indices: 74144--74188 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
74134 AAACTAAATT
*
74144 TAAATTTAAATTTAA-AA
1 TAAATTTAAATTCAAGAA
74161 TAAATTTAAATTCAAGAA
1 TAAATTTAAATTCAAGAA
74179 TAAATTTAAA
1 TAAATTTAAA
74189 ACCAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAATTTAAATTCAAGAA
Found at i:74182 original size:23 final size:23
Alignment explanation
Indices: 74125--74175 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
74115 TTAAAACCAT
* *
74125 TTCAAATTTAAACTAAATTTAAA
1 TTCAAATATAAAATAAATTTAAA
* *
74148 TTTAAATTTAAAATAAATTTAAA
1 TTCAAATATAAAATAAATTTAAA
74171 TTCAA
1 TTCAA
74176 GAATAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (23 bp):
TTCAAATATAAAATAAATTTAAA
Found at i:74188 original size:6 final size:6
Alignment explanation
Indices: 74123--74172 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
74113 GTTTAAAACC
* *
74123 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
74170 ATT
1 ATT
74173 CAAGAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 8 0.22
6 25 0.68
7 4 0.11
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:74198 original size:29 final size:28
Alignment explanation
Indices: 74150--74217 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
74140 AATTTAAATT
*
74150 TAAATTTAAAATAAATTTAAA-TTCAAGAA
1 TAAATTTAAAACAAATTTAAACTT-AA-AA
*
74179 TAAATTTAAAACCAAA-TTAAACTTAATA
1 TAAATTTAAAA-CAAATTTAAACTTAAAA
74207 TAAATTTAAAA
1 TAAATTTAAAA
74218 ATCGAAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 12 0.34
29 18 0.51
30 5 0.14
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (28 bp):
TAAATTTAAAACAAATTTAAACTTAAAA
Found at i:74872 original size:26 final size:26
Alignment explanation
Indices: 74834--74887 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
74824 AAAAAAAATA
*
74834 GGATGGCTACAATCTGCCCCAGGCTC
1 GGATGGCTACAATCTGCCCCAAGCTC
* *
74860 GGATGGTTGCAATCTGCCCCAAGCTC
1 GGATGGCTACAATCTGCCCCAAGCTC
74886 GG
1 GG
74888 GGTAAGAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (26 bp):
GGATGGCTACAATCTGCCCCAAGCTC
Found at i:74918 original size:39 final size:39
Alignment explanation
Indices: 74871--75098 Score: 163
Period size: 39 Copynumber: 5.8 Consensus size: 39
74861 GATGGTTGCA
*
74871 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGACT-GTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGA-TAGTG
* * * * * **
74910 ATATGCCCCATGCTCGGGGTAAGAGATCGAATGGTAGCA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATAGTG
* * * *
74949 ATCTTCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATAGTG
* * * * * * * **
74988 ATTTGCCCCAAACTCTGAGTAAAAGATTGAATGGCT-GCA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGAT-GATAGTG
* * * *
75027 ATCTGCCGCAGGTTCGGGGTAAGAGATTGGCTGATAGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATAGTG
* * * *
75066 ATCTGCCCTAAACTCGGGGTAAAAGATCGGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATG
75099 GTTTTCAATC
Statistics
Matches: 135, Mismatches: 51, Indels: 6
0.70 0.27 0.03
Matches are distributed among these distances:
38 3 0.02
39 130 0.96
40 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATAGTG
Found at i:74995 original size:78 final size:76
Alignment explanation
Indices: 74862--75100 Score: 289
Period size: 78 Copynumber: 3.1 Consensus size: 76
74852 CCAGGCTCGG
* **
74862 ATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGACTGTGATATGCCCCATGCTCGG
1 ATGG-TGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGA-TGTGATATGCCCCAAACTCGG
*
74927 GGTAAGAGATCGA
64 GGTAAAAGATCGA
* * *
74940 ATGGTAGCAATCTTCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATTTGCCCCAAACTCTG
1 ATGGT-GCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGAT-GTGATATGCCCCAAACTCGG
* *
75005 AGTAAAAGATTGA
64 GGTAAAAGATCGA
* * * * *
75018 ATGGCTGCAATCTGCCGCAGGTTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCTAAACTCGG
1 ATGG-TGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGAT-GTGATATGCCCCAAACTCGG
*
75083 GGTAAAAGATCGG
64 GGTAAAAGATCGA
75096 ATGGT
1 ATGGT
75101 TTTCAATCTG
Statistics
Matches: 138, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
77 3 0.02
78 134 0.97
79 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (76 bp):
ATGGTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGTGATATGCCCCAAACTCGGGG
TAAAAGATCGA
Found at i:75436 original size:49 final size:49
Alignment explanation
Indices: 75383--76094 Score: 552
Period size: 49 Copynumber: 14.7 Consensus size: 49
75373 AGGTTAGTCA
*
75383 TTGCGACTTAAA-CATTTCCCTTCAAATCTTCATGGTACTAGATTCGTCG
1 TTGCGACTTAAATC-TTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
* * * * *
75432 TTGCGACTTAAATCTTTCCCATCATAT-TCTCGTGGTACTGGATTCACCG
1 TTGCGACTTAAATCTTTCCCTTCAAATCT-TCATGGTACTAGATTCGCCG
* * *
75481 TTGCTG-CTTAAATCTTTCCCTTCATATCTTCGTGGTACTAGATTCGCCA
1 TTGC-GACTTAAATCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
* * *
75530 TTGC-AGCTTAAATCTTTCTCTTCAAATCTTCGTGGTTCTAG----GCCG
1 TTGCGA-CTTAAATCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
* * * * * * *
75575 TTACGGCTTAAATCTCTCCTTTC--ATGCTTC-TGAGGTACAAGGTTCACCG
1 TTGCGACTTAAATCTTTCCCTTCAAAT-CTTCAT--GGTACTAGATTCGCCG
* * * * *
75624 TTGCGACTTAAACCTTTCCTTTCAAATTTTCATGGTACAAGATTCACCG
1 TTGCGACTTAAATCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
* * * * *
75673 TTGCGGCTTAAATCTTTCCCTTCATATCCTT-GTGGTACTGGATTCACCG
1 TTGCGACTTAAATCTTTCCCTTCAAAT-CTTCATGGTACTAGATTCGCCG
* * * * *
75722 TTGTGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCG
1 TTGCGACTTAAATCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
** * * * * *
75771 TTATGGCTTAAATCTTTCCCTTC--ATGCTTCTAAGGTACAAGGTTCGTCG
1 TTGCGACTTAAATCTTTCCCTTCAAAT-CTTC-ATGGTACTAGATTCGCCG
* * * *
75820 TTGCAACTTAAACCTTTCCCTTCAAATTTTCATGGTACTAGATTCACCG
1 TTGCGACTTAAATCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
* * * * *
75869 TTGCCG-CTTAAATCTTTTCCTTCATATCCTCGTGGTACTGGATTCGCCG
1 TTG-CGACTTAAATCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
* * * **
75918 TTGCGGCTTAAATCTTTCCCTTC--AT-ATCATGGTATTAGATTCATCG
1 TTGCGACTTAAATCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
* * * * *
75964 ATGCGGCTTAAATCTTTCCCTTC--ATGCTTCTAAGGTACAAG-TACGCCG
1 TTGCGACTTAAATCTTTCCCTTCAAAT-CTTC-ATGGTACTAGATTCGCCG
**
76012 TTGCGACTTAAA-CTTTTCCCTTCAAATCTTTGTGGTACTAGATTCGCCG
1 TTGCGACTTAAATC-TTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
* *
76061 TT-CCAGCTTAAATCTTTCCCTTCAAATCATCATG
1 TTGCGA-CTTAAATCTTTCCCTTCAAATCTTCATG
76095 TTTTTCTCAG
Statistics
Matches: 538, Mismatches: 91, Indels: 68
0.77 0.13 0.10
Matches are distributed among these distances:
43 3 0.01
44 4 0.01
45 26 0.05
46 39 0.07
47 5 0.01
48 44 0.08
49 397 0.74
50 15 0.03
51 5 0.01
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.38
Consensus pattern (49 bp):
TTGCGACTTAAATCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCG
Found at i:75518 original size:98 final size:98
Alignment explanation
Indices: 75383--76084 Score: 616
Period size: 98 Copynumber: 7.2 Consensus size: 98
75373 AGGTTAGTCA
* * * *
75383 TTGCGACTTAAA-CATTTCCCTTCAAATCTTCATGGTACTAGATTCGTCGTTGCGACTTAAATCT
1 TTGCGGCTTAAATC-TTTCCCTTCATATCTTCGTGGTACTAGATTCGCCGTTGCGACTTAAATCT
* *
75447 TTCCCATCATATTCTCGTGGTACTGGATTCACCG
65 TTCCCTTCATATTCTCGTGGTACTAGATTCACCG
* *
75481 TTGCTGCTTAAATCTTTCCCTTCATATCTTCGTGGTACTAGATTCGCCATTGC-AGCTTAAATCT
1 TTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACTAGATTCGCCGTTGCGA-CTTAAATCT
* * * *
75545 TTCTCTTCA-AATCTTCGTGGTTCTAG----GCCG
65 TTCCCTTCATATTC-TCGTGGTACTAGATTCACCG
* * * * * * * * *
75575 TTACGGCTTAAATCTCTCCTTTCAT-GCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCT
1 TTGCGGCTTAAATCTTTCCCTTCATATCTTC-GTGGTACTAGATTCGCCGTTGCGACTTAAATCT
* * * * *
75639 TTCCTTTCAAATTTTCATGGTACAAGATTCACCG
65 TTCCCTTCATATTCTCGTGGTACTAGATTCACCG
* * * *
75673 TTGCGGCTTAAATCTTTCCCTTCATATCCTT-GTGGTACTGGATTCACCGTTGTGGCTTAAATCT
1 TTGCGGCTTAAATCTTTCCCTTCATAT-CTTCGTGGTACTAGATTCGCCGTTGCGACTTAAATCT
* *
75737 TTCCCTTCATA-TCTTCGTGGTACTGGATTCGCCG
65 TTCCCTTCATATTC-TCGTGGTACTAGATTCACCG
** * * * * * *
75771 TTATGGCTTAAATCTTTCCCTTCAT-GCTTC-TAAGGTACAAGGTTCGTCGTTGCAACTTAAACC
1 TTGCGGCTTAAATCTTTCCCTTCATATCTTCGT--GGTACTAGATTCGCCGTTGCGACTTAAATC
* * *
75834 TTTCCCTTCAAATTTTCATGGTACTAGATTCACCG
64 TTTCCCTTCATATTCTCGTGGTACTAGATTCACCG
* * * * *
75869 TTGCCGCTTAAATCTTTTCCTTCATATCCTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTT
1 TTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACTAGATTCGCCGTTGCGACTTAAATCTT
* * *
75934 TCCCTTCATA---TCATGGTATTAGATTCATCG
66 TCCCTTCATATTCTCGTGGTACTAGATTCACCG
* * * *
75964 ATGCGGCTTAAATCTTTCCCTTCAT-GCTTC-TAAGGTACAAG-TACGCCGTTGCGACTTAAA-C
1 TTGCGGCTTAAATCTTTCCCTTCATATCTTCGT--GGTACTAGATTCGCCGTTGCGACTTAAATC
* * *
76025 TTTTCCCTTCA-AATCTTTGTGGTACTAGATTCGCCG
64 -TTTCCCTTCATATTC-TCGTGGTACTAGATTCACCG
* *
76061 TTCCAGCTTAAATCTTTCCCTTCA
1 TTGCGGCTTAAATCTTTCCCTTCA
76085 AATCATCATG
Statistics
Matches: 479, Mismatches: 99, Indels: 53
0.76 0.16 0.08
Matches are distributed among these distances:
93 7 0.01
94 95 0.20
95 49 0.10
96 4 0.01
97 41 0.09
98 274 0.57
99 5 0.01
100 4 0.01
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (98 bp):
TTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACTAGATTCGCCGTTGCGACTTAAATCTT
TCCCTTCATATTCTCGTGGTACTAGATTCACCG
Found at i:77046 original size:6 final size:6
Alignment explanation
Indices: 77037--77130 Score: 71
Period size: 6 Copynumber: 14.3 Consensus size: 6
77027 CAACCTCTCC
* *
77037 TTTTCT TTTTCCATT TTTTCT TTTTGT TTTTCCT CTTTCTT TTTTCT TTTTCTT
1 TTTTCT TTTT-C--T TTTTCT TTTTCT TTTT-CT TTTTC-T TTTTCT TTTTC-T
* * *
77091 TTCTTCT TCTTCT TCTTCT TCTTCT TTTTCTT TTTTCT TT
1 TT-TTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TT
77131 ATTCATTGAA
Statistics
Matches: 74, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
6 44 0.59
7 21 0.28
8 4 0.05
9 5 0.07
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:77068 original size:12 final size:12
Alignment explanation
Indices: 77037--77130 Score: 71
Period size: 13 Copynumber: 7.2 Consensus size: 12
77027 CAACCTCTCC
77037 TTTTCTTTTTCCATT
1 TTTTCTTTTT-C--T
*
77052 TTTTCTTTTTGT
1 TTTTCTTTTTCT
*
77064 TTTTCCTCTTTCTT
1 TTTT-CTTTTTC-T
77078 TTTTCTTTTTCTT
1 TTTTCTTTTTC-T
*
77091 TTCTTCTTCTTCT
1 TT-TTCTTTTTCT
* *
77104 TCTTCTTCTTCT
1 TTTTCTTTTTCT
77116 TTTTCTTTTTTCT
1 TTTTC-TTTTTCT
77129 TT
1 TT
77131 ATTCATTGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
12 19 0.28
13 25 0.37
14 13 0.19
15 10 0.15
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:77099 original size:3 final size:3
Alignment explanation
Indices: 77080--77122 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
77070 TCTTTCTTTT
* *
77080 TTC TTT TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
77123 TTTTCTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:77928 original size:244 final size:244
Alignment explanation
Indices: 77499--77986 Score: 949
Period size: 244 Copynumber: 2.0 Consensus size: 244
77489 GGCTGTTCTA
*
77499 ATAGAAAACTCGATAAACCTCGAAGGCAAATGGTGATTTCTCATGCCGAGCTTTTGTAGGTCTTT
1 ATAGAAAACTCGATAAACCTCGAAGGCAAATGGTGATTTCTCATGCCGAGCTTTTGTAAGTCTTT
77564 GCTATTTTCCAATCAATCCTTTGTTGTCTTTATTGGTCCCCACCAATGCCCCATTTTTTGGCGAT
66 GCTATTTTCCAATCAATCCTTTGTTGTCTTTATTGGTCCCCACCAATGCCCCATTTTTTGGCGAT
*
77629 GTGGTAATGAGTTGTGATATTTGCTCTTGAATTGATTGTAGATTTTGCTCTCGTGCTGTTGTTCA
131 GTGGTAATGAGTTGTGATATTTGCTCTTGAATTGACTGTAGATTTTGCTCTCGTGCTGTTGTTCA
77694 GATTCAAGTTATCGTTGGATATGATCCTTTCTTGGCATTCCATATCGGC
196 GATTCAAGTTATCGTTGGATATGATCCTTTCTTGGCATTCCATATCGGC
*
77743 ATAGAAAACTCGATAAATCTCGAAGGCAAATGGTGATTTCTCATGCCGAGCTTTTGTAAGTCTTT
1 ATAGAAAACTCGATAAACCTCGAAGGCAAATGGTGATTTCTCATGCCGAGCTTTTGTAAGTCTTT
77808 GCTATTTTCCAATCAATCCTTTGTTGTCTTTATTGGTCCCCACCAATGCCCCATTTTTTGGCGAT
66 GCTATTTTCCAATCAATCCTTTGTTGTCTTTATTGGTCCCCACCAATGCCCCATTTTTTGGCGAT
77873 GTGGTAATGAGTTGTGATATTTGCTCTTGAATTGACTGTAGATTTTGCTCTCGTGCTGTTGTTCA
131 GTGGTAATGAGTTGTGATATTTGCTCTTGAATTGACTGTAGATTTTGCTCTCGTGCTGTTGTTCA
77938 GATTCAAGTTATCGTTGGATATGATCCTTTCTTGGCATTCCATATCGGC
196 GATTCAAGTTATCGTTGGATATGATCCTTTCTTGGCATTCCATATCGGC
77987 CTATAATCTC
Statistics
Matches: 241, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
244 241 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (244 bp):
ATAGAAAACTCGATAAACCTCGAAGGCAAATGGTGATTTCTCATGCCGAGCTTTTGTAAGTCTTT
GCTATTTTCCAATCAATCCTTTGTTGTCTTTATTGGTCCCCACCAATGCCCCATTTTTTGGCGAT
GTGGTAATGAGTTGTGATATTTGCTCTTGAATTGACTGTAGATTTTGCTCTCGTGCTGTTGTTCA
GATTCAAGTTATCGTTGGATATGATCCTTTCTTGGCATTCCATATCGGC
Found at i:81913 original size:59 final size:60
Alignment explanation
Indices: 81805--82085 Score: 290
Period size: 59 Copynumber: 4.8 Consensus size: 60
81795 CTTCGGGAAC
* * *
81805 AAAATGGTAATTTTTCGAAAGG-TTCGAGGTTAAAAATGAAATTTTTAGACATTCTG-GGGT
1 AAAATGGTAATTTTT-GGAAGGTTTAG-GGTTAAAAATGGAATTTTTAGACATTCTGAGGGT
*
81865 AAAATGGTAA-TTTTGGAAGGTTTAGGGTCTAAAAATGGAATTCTTAGACATT-TGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTTAGGGT-TAAAAATGGAATTTTTAGACATTCTGAGGGT
* * *
81924 AAAATGGTAATTTCTAGAAAGTTTAGGGTTAAAAATGGAATTTTTAGACA-TCTGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTTAGGGTTAAAAATGGAATTTTTAGACATTCTGAGGGT
** * * * * * * *
81983 AAAATGGTAATTTTTGGAATATTTGGGGGTAAAAATGTAATTTTCA-AAATTTTGAGGTT
1 AAAATGGTAATTTTTGGAAGGTTTAGGGTTAAAAATGGAATTTTTAGACATTCTGAGGGT
* * **
82042 AAAAATGG-AA-TTTTGGAAAGTTTAGGGGTAAAAATATAATTTTT
1 -AAAATGGTAATTTTTGGAAGGTTTAGGGTTAAAAATGGAATTTTT
82086 GAAAAGTTTA
Statistics
Matches: 190, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
58 42 0.22
59 116 0.61
60 32 0.17
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (60 bp):
AAAATGGTAATTTTTGGAAGGTTTAGGGTTAAAAATGGAATTTTTAGACATTCTGAGGGT
Found at i:81966 original size:30 final size:29
Alignment explanation
Indices: 81805--82400 Score: 348
Period size: 29 Copynumber: 20.1 Consensus size: 29
81795 CTTCGGGAAC
* * *
81805 AAAATGGTAATTTTTCGAAAGGTTCGAGGTTA
1 AAAATGG-AA-TTTTAGAAAGTTTAG-GGTTA
* * *
81837 AAAATGAAATTTTTAGACA-TTCT-GGGGT-
1 AAAATGGAA-TTTTAGAAAGTT-TAGGGTTA
* *
81865 AAAATGGTAATTTTGGAAGGTTTAGGGTCTA
1 AAAATGG-AATTTTAGAAAGTTTAGGGT-TA
*
81896 AAAATGGAATTCTTAGACA-TTTGAGGG-T-
1 AAAATGGAATT-TTAGAAAGTTT-AGGGTTA
81924 AAAATGGTAATTTCTAGAAAGTTTAGGGTTA
1 AAAATGG-AATTT-TAGAAAGTTTAGGGTTA
* *
81955 AAAATGGAATTTTTAGACA-TCTGAGGG-T-
1 AAAATGGAA-TTTTAGAAAGT-TTAGGGTTA
* * *
81983 AAAATGGTAATTTTTGGAATA-TTTGGGGGTA
1 AAAATGG-AA-TTTTAGAA-AGTTTAGGGTTA
* *
82014 AAAATGTAATTTTCA-AAA-TTTTGAGGTTA
1 AAAATGGAATTTT-AGAAAGTTTAG-GGTTA
* *
82043 AAAATGGAATTTTGGAAAGTTTAGGGGTA
1 AAAATGGAATTTTAGAAAGTTTAGGGTTA
** * **
82072 AAAATATAATTTTTGAAAAGTTTAATGTTA
1 AAAATGGAATTTTAG-AAAGTTTAGGGTTA
* *
82102 AAAATGGAATTTTGGAAAGTTTAGGGGTA
1 AAAATGGAATTTTAGAAAGTTTAGGGTTA
*
82131 AAAATGTAAGTTTT-GAAAAGTTTAGGGTTA
1 AAAATGGAA-TTTTAG-AAAGTTTAGGGTTA
* *
82161 AAAATGGAAATTTGGAAAGTTTAAGGG-TA
1 AAAATGGAATTTTAGAAAGTTT-AGGGTTA
* *
82190 AAAATGTAATTTTTGAAAAGTTTAGGGTTA
1 AAAATGGAATTTTAG-AAAGTTTAGGGTTA
* *
82220 AAAATGGAAATTTGGAAAGTTTAAGGGTT-
1 AAAATGGAATTTTAGAAAGTTT-AGGGTTA
* * *
82249 AAAATGTAATTTTTGAAAATTTTAGGGTT-
1 AAAATGGAATTTTAG-AAAGTTTAGGGTTA
* * * *
82278 AAAATGGAATTTTGGAATGTTTGGGGGTA
1 AAAATGGAATTTTAGAAAGTTTAGGGTTA
* * *
82307 AAAATGTAATTTCCAAAAAGTTTAAGGGTT-
1 AAAATGGAATTT-TAGAAAGTTT-AGGGTTA
* * * *
82337 AAAATGTAATTTCCAAAAAGTTTAAGGGTCA
1 AAAATGGAATTT-TAGAAAGTTT-AGGGTTA
*
82368 AAATAT--AATTTTTAGAAAGTTTGAGGGTCA
1 AAA-ATGGAA-TTTTAGAAAGTTT-AGGGTTA
82398 AAA
1 AAA
82401 TATTTTTTTT
Statistics
Matches: 455, Mismatches: 71, Indels: 78
0.75 0.12 0.13
Matches are distributed among these distances:
28 42 0.09
29 177 0.39
30 176 0.39
31 52 0.11
32 8 0.02
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTAGAAAGTTTAGGGTTA
Found at i:81984 original size:118 final size:118
Alignment explanation
Indices: 81805--82203 Score: 326
Period size: 118 Copynumber: 3.4 Consensus size: 118
81795 CTTCGGGAAC
* * *
81805 AAAATGGTAATTTTTCGAAAGGTTCGAGGTTAAAAATGAAATTTTTAGACATTCTGGGGTAAAAT
1 AAAATGGTAA-TTTTAGAAAGTTTAG-GGTTAAAAATGAAATTTTTAGACATTCTGGGGTAAAAT
* * *
81870 GGTAA-TTTTGGAAGGTTTAGGGTCTAAAAATGGAATTCTT-AGACA-TTTGAGGGT-
64 GGTAATTTTTGGAAGATTT-GGGGCTAAAAATGGAATT-TTCA-AAATTTTGAGGGTA
*
81924 AAAATGGTAATTTCTAGAAAGTTTAGGGTTAAAAATGGAATTTTTAGACA-TCTGAGGGTAAAAT
1 AAAATGGTAATTT-TAGAAAGTTTAGGGTTAAAAATGAAATTTTTAGACATTCTG-GGGTAAAAT
* * * *
81988 GGTAATTTTTGGAATATTTGGGGGTAAAAATGTAATTTTCAAAATTTTGAGGTTA
64 GGTAATTTTTGGAAGATTTGGGGCTAAAAATGGAATTTTCAAAATTTTGAGGGTA
* * * ** *
82043 AAAATGG-AATTTTGGAAAGTTTAGGGGTAAAAAT-ATAATTTTT-GAAAAGTT-TAATGTTAAA
1 AAAATGGTAATTTTAGAAAGTTTAGGGTTAAAAATGA-AATTTTTAG-ACA-TTCT-GGGGT-AA
* * *
82104 AATGG-AA-TTTTGGAA-AGTTTAGGGG-TAAAAATGTAAGTTTTGAAAAGTTT-AGGGTTA
61 AATGGTAATTTTTGGAAGA-TTT-GGGGCTAAAAATGGAA-TTTTCAAAATTTTGAGGG-TA
* * *
82161 AAAATGG-AAATTTGGAAAGTTTAAGGG-TAAAAATGTAATTTTT
1 AAAATGGTAATTTTAGAAAGTTT-AGGGTTAAAAATGAAATTTTT
82204 GAAAAGTTTA
Statistics
Matches: 239, Mismatches: 23, Indels: 37
0.80 0.08 0.12
Matches are distributed among these distances:
116 2 0.01
117 62 0.26
118 126 0.53
119 49 0.21
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (118 bp):
AAAATGGTAATTTTAGAAAGTTTAGGGTTAAAAATGAAATTTTTAGACATTCTGGGGTAAAATGG
TAATTTTTGGAAGATTTGGGGCTAAAAATGGAATTTTCAAAATTTTGAGGGTA
Found at i:82110 original size:59 final size:59
Alignment explanation
Indices: 81865--82389 Score: 487
Period size: 59 Copynumber: 8.9 Consensus size: 59
81855 ATTCTGGGGT
* * * * * * *
81865 AAAATGGTAATTTTGGAAGGTTTAGGGTCTAAAAATGGAATTCTT-AGACA-TTTGAGGGT-
1 AAAATGG-AATTTTGGAAAGTTTAGGG-GTAAAAATGTAATTTTTGA-AAAGTTTAAGGTTA
* * * * * * *
81924 AAAATGGTAATTTCTAGAAAGTTTAGGGTTAAAAATGGAATTTTT-AGACA-TCTGAGGGT-
1 AAAATGG-AATTT-TGGAAAGTTTAGGGGTAAAAATGTAATTTTTGA-AAAGTTTAAGGTTA
* * * *
81983 AAAATGGTAATTTTTGGAATA-TTTGGGGGTAAAAATGTAA-TTTTCAAAATTTTGAGGTTA
1 AAAATGG-AA-TTTTGGAA-AGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGTTA
* *
82043 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATATAATTTTTGAAAAGTTTAATGTTA
1 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGTTA
* *
82102 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAAGTTTTGAAAAGTTTAGGGTTA
1 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGTTA
* * *
82161 AAAATGGAAATTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGTTTAGGGTTA
1 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGTTA
* * * * *
82220 AAAATGGAAATTTGGAAAGTTTAAGGGTTAAAATGTAATTTTTGAAAATTTTAGGGTT-
1 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGTTA
* * ***
82278 AAAATGGAATTTTGGAATGTTTGGGGGTAAAAATGTAATTTCCAAAAAGTTTAAGGGTT-
1 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAA-GGTTA
* *** * * *
82337 AAAATGTAATTTCCAAAAAGTTTAAGGGTCAAAATATAATTTTT-AGAAAGTTT
1 AAAATGGAATTT-TGGAAAGTTTAGGGGTAAAAATGTAATTTTTGA-AAAGTTT
82390 GAGGGTCAAA
Statistics
Matches: 407, Mismatches: 48, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
57 1 0.00
58 75 0.18
59 280 0.69
60 51 0.13
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGTTA
Found at i:82403 original size:30 final size:30
Alignment explanation
Indices: 81805--82401 Score: 362
Period size: 30 Copynumber: 20.2 Consensus size: 30
81795 CTTCGGGAAC
* * *
81805 AAAATGGTAATTTTTCGAAAGGTTCGAGGTTA
1 AAAAT-GTAATTTTTAGAAA-GTTTGAGGGTA
* *
81837 AAAATGAAATTTTTAGACA-TTCTG-GGGT-
1 AAAATGTAATTTTTAGAAAGTT-TGAGGGTA
* *
81865 AAAATGGTAA-TTTTGGAAGGTTT-AGGGTCTA
1 AAAAT-GTAATTTTTAGAAAGTTTGAGGG--TA
* * *
81896 AAAATGGAATTCTTAGACA-TTTGAGGGT-
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
*
81924 AAAATGGTAATTTCTAGAAAGTTT-AGGGTTA
1 AAAAT-GTAATTTTTAGAAAGTTTGAGGG-TA
* * *
81955 AAAATGGAATTTTTAGACA-TCTGAGGGT-
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
* *
81983 AAAATGGTAATTTTTGGAATA-TTTGGGGGTA
1 AAAAT-GTAATTTTTAGAA-AGTTTGAGGGTA
* * *
82014 AAAATGTAATTTTCA-AAATTTTGAGGTTA
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
* *
82043 AAAATGGAA-TTTTGGAAAGTTT-AGGGGTA
1 AAAATGTAATTTTTAGAAAGTTTGA-GGGTA
* * * *
82072 AAAATATAATTTTT-GAAAAGTTTAATGTTA
1 AAAATGTAATTTTTAG-AAAGTTTGAGGGTA
* *
82102 AAAATGGAA-TTTTGGAAAGTTT-AGGGGTA
1 AAAATGTAATTTTTAGAAAGTTTGA-GGGTA
*
82131 AAAATGTAAGTTTT-GAAAAGTTT-AGGGTTA
1 AAAATGTAATTTTTAG-AAAGTTTGAGGG-TA
* * * *
82161 AAAATGGAA-ATTTGGAAAGTTTAAGGGTA
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
82190 AAAATGTAATTTTT-GAAAAGTTT-AGGGTTA
1 AAAATGTAATTTTTAG-AAAGTTTGAGGG-TA
* * * * *
82220 AAAATGGAA-ATTTGGAAAGTTTAAGGGTT
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
* * *
82249 AAAATGTAATTTTT-GAAAATTTTAGGGTT
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
* * * *
82278 AAAATGGAA-TTTTGGAATGTTTGGGGGTA
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
** * * *
82307 AAAATGTAATTTCCAAAAAGTTTAAGGGTT
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
** * * *
82337 AAAATGTAATTTCCAAAAAGTTTAAGGGTC
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
* *
82367 AAAATATAATTTTTAGAAAGTTTGAGGGTC
1 AAAATGTAATTTTTAGAAAGTTTGAGGGTA
82397 AAAAT
1 AAAAT
82402 ATTTTTTTTA
Statistics
Matches: 450, Mismatches: 77, Indels: 78
0.74 0.13 0.13
Matches are distributed among these distances:
28 35 0.08
29 183 0.41
30 191 0.42
31 36 0.08
32 5 0.01
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTAGAAAGTTTGAGGGTA
Found at i:83768 original size:20 final size:20
Alignment explanation
Indices: 83745--83792 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
83735 GCAATGGCAA
*
83745 GTTGCTGGTGGTGCAACTTG
1 GTTGCTGATGGTGCAACTTG
83765 GTTGCTGATGGTGCAACTTG
1 GTTGCTGATGGTGCAACTTG
83785 GTTGCTGA
1 GTTGCTGA
83793 CGTGGCGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.15, G:0.38, T:0.35
Consensus pattern (20 bp):
GTTGCTGATGGTGCAACTTG
Found at i:84000 original size:17 final size:17
Alignment explanation
Indices: 83980--84065 Score: 95
Period size: 17 Copynumber: 5.0 Consensus size: 17
83970 CAATATTGAG
*
83980 TTTAAAAC-CATTTCAAA
1 TTTAAAACAAATTT-AAA
83997 TTT-AAACTAAATTTAAA
1 TTTAAAAC-AAATTTAAA
84014 TTTAAAACAAATTTAAA
1 TTTAAAACAAATTTAAA
*
84031 TTTAAAATAAATTTAAA
1 TTTAAAACAAATTTAAA
* *
84048 TTCAAGAATAAATTTAAA
1 TTTAA-AACAAATTTAAA
84066 ATGAATTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
16 4 0.06
17 38 0.61
18 20 0.32
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (17 bp):
TTTAAAACAAATTTAAA
Found at i:84015 original size:6 final size:6
Alignment explanation
Indices: 83989--84093 Score: 60
Period size: 6 Copynumber: 18.2 Consensus size: 6
83979 GTTTAAAACC
* **
83989 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * * * *
84036 A-ATAA ATTTAA ATTCAA GA-ATAA ATTTAA A-ATGA ATTTAA ACTT-A
1 ATTTAA ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
84081 ATATAA ATTTAA A
1 ATTTAA ATTTAA A
84094 AATCGAAAGT
Statistics
Matches: 71, Mismatches: 20, Indels: 15
0.67 0.19 0.14
Matches are distributed among these distances:
5 18 0.25
6 48 0.68
7 5 0.07
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (6 bp):
ATTTAA
Found at i:84018 original size:34 final size:34
Alignment explanation
Indices: 83980--84065 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
83970 CAATATTGAG
* *
83980 TTTAAAAC-CATTTCAAATTTAAACTAAATTTAAA
1 TTTAAAACAAATTT-AAATTTAAAATAAATTTAAA
84014 TTTAAAACAAATTTAAATTTAAAATAAATTTAAA
1 TTTAAAACAAATTTAAATTTAAAATAAATTTAAA
* *
84048 TTCAAGAATAAATTTAAA
1 TTTAA-AACAAATTTAAA
84066 ATGAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
34 31 0.67
35 15 0.33
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (34 bp):
TTTAAAACAAATTTAAATTTAAAATAAATTTAAA
Found at i:84093 original size:17 final size:17
Alignment explanation
Indices: 83989--84065 Score: 109
Period size: 17 Copynumber: 4.4 Consensus size: 17
83979 GTTTAAAACC
*
83989 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAAATAA
*
84007 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAATAA
84024 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
84041 ATTTAAATTCAAGAATAA
1 ATTTAAATTTAA-AATAA
84059 ATTTAAA
1 ATTTAAA
84066 ATGAATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
17 38 0.70
18 16 0.30
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:84096 original size:29 final size:29
Alignment explanation
Indices: 84027--84094 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
84017 AAAACAAATT
84027 TAAATTTAAAATAAATTTAAATTCAAGAA
1 TAAATTTAAAATAAATTTAAATTCAAGAA
* *
84056 TAAATTTAAAATGAATTTAAACTT-AA-TA
1 TAAATTTAAAATAAATTTAAA-TTCAAGAA
84084 TAAATTTAAAA
1 TAAATTTAAAA
84095 ATCGAAAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 12 0.33
29 22 0.61
30 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
TAAATTTAAAATAAATTTAAATTCAAGAA
Found at i:84576 original size:24 final size:23
Alignment explanation
Indices: 84541--84591 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
84531 TAAGAGTGTT
*
84541 AAATTAAAAAATAAAACAAAATA
1 AAATGAAAAAATAAAACAAAATA
**
84564 AAATGAAACAAATAAAGTAAAATA
1 AAATGAAA-AAATAAAACAAAATA
84588 AAAT
1 AAAT
84592 ATTGTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (23 bp):
AAATGAAAAAATAAAACAAAATA
Found at i:88185 original size:24 final size:24
Alignment explanation
Indices: 88152--88199 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
88142 ATGTGACTCG
*
88152 ATTGTACAATGATAGTAGCAGCCA
1 ATTGTACAATGACAGTAGCAGCCA
* **
88176 ATTGTGCAATTCCAGTAGCAGCCA
1 ATTGTACAATGACAGTAGCAGCCA
88200 CTAAAGGGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
ATTGTACAATGACAGTAGCAGCCA
Found at i:90703 original size:21 final size:22
Alignment explanation
Indices: 90677--90719 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
90667 ATCTTCCTTT
*
90677 TAATACTTG-TTTTTATGTTCA
1 TAATACTTGCTTTTTATCTTCA
90698 TAATACTTGCTTTTTATCTTCA
1 TAATACTTGCTTTTTATCTTCA
90720 ACATTTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (22 bp):
TAATACTTGCTTTTTATCTTCA
Found at i:91295 original size:18 final size:17
Alignment explanation
Indices: 91257--91295 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
91247 GCTATCTTAG
**
91257 TTTTCCCTTTTTTTGGT
1 TTTTCCCTTTTTTTGCA
91274 TTTTCCCTTTTTCTTGCA
1 TTTTCCCTTTTT-TTGCA
91292 TTTT
1 TTTT
91296 GAGCTTCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.69
Consensus pattern (17 bp):
TTTTCCCTTTTTTTGCA
Found at i:91957 original size:20 final size:21
Alignment explanation
Indices: 91932--91971 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
91922 TTCATTTTTA
*
91932 GCATTTT-TAACTTAGTGATT
1 GCATTTTCTAACTCAGTGATT
91952 GCATTTTCTAACTCAGTGAT
1 GCATTTTCTAACTCAGTGAT
91972 GCTCGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGATT
Done.