Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015083.1 Kokia drynarioides strain JFW-HI SEQ_130127, 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: 241667
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 306 characters in sequence are not A, C, G, or T
Found at i:11341 original size:24 final size:24
Alignment explanation
Indices: 11303--11383 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
11293 CAACTAAGAA
* *
11303 AGAGGAGCAGATTCCAACCGAGGT
1 AGAGGAGCAGCTTCCAACCAAGGT
* * *
11327 AGCA-GAGGAGCTTCCTACCAAAGT
1 AG-AGGAGCAGCTTCCAACCAAGGT
11351 AGAGGAGCAGCTTCCAACCAAGGT
1 AGAGGAGCAGCTTCCAACCAAGGT
*
11375 AGATGAGCA
1 AGAGGAGCA
11384 TTCTCAGCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 1 0.02
24 44 0.96
25 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.30, T:0.14
Consensus pattern (24 bp):
AGAGGAGCAGCTTCCAACCAAGGT
Found at i:12506 original size:63 final size:63
Alignment explanation
Indices: 12411--12530 Score: 240
Period size: 63 Copynumber: 1.9 Consensus size: 63
12401 CAGGCCCTGC
12411 TATATATATATAATGCTTATACAAGGAAGAGTTTCAACATCCATGGCTGAGCCTGTATATATA
1 TATATATATATAATGCTTATACAAGGAAGAGTTTCAACATCCATGGCTGAGCCTGTATATATA
12474 TATATATATATAATGCTTATACAAGGAAGAGTTTCAACATCCATGGCTGAGCCTGTA
1 TATATATATATAATGCTTATACAAGGAAGAGTTTCAACATCCATGGCTGAGCCTGTA
12531 GAAGTATTGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (63 bp):
TATATATATATAATGCTTATACAAGGAAGAGTTTCAACATCCATGGCTGAGCCTGTATATATA
Found at i:16388 original size:31 final size:31
Alignment explanation
Indices: 16353--16411 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
16343 AAAGGGTCTA
*
16353 ATCTTTTCAAAAATGCTCAAATGAGAGCTTC
1 ATCTTTTCAAAAATGCTCAAATAAGAGCTTC
* *
16384 ATCTTTTCGAAAGTGCTCAAATAAGAGC
1 ATCTTTTCAAAAATGCTCAAATAAGAGC
16412 CAAACATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (31 bp):
ATCTTTTCAAAAATGCTCAAATAAGAGCTTC
Found at i:32816 original size:31 final size:30
Alignment explanation
Indices: 32777--32839 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
32767 AAATGTTCAA
* * *
32777 TTTTATTTAGTTTAACTAGTTTATTTTATT
1 TTTTATTTAATATAACAAGTTTATTTTATT
*
32807 TTTTAATTTAATATGACAAGTTTATTTTATT
1 TTTT-ATTTAATATAACAAGTTTATTTTATT
32838 TT
1 TT
32840 GAGCTTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.63
Consensus pattern (30 bp):
TTTTATTTAATATAACAAGTTTATTTTATT
Found at i:33161 original size:32 final size:32
Alignment explanation
Indices: 33098--33161 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
33088 CTAAATTTAG
*
33098 GTATTAAATTGGAAAAGAAAATTATCAATTAA
1 GTATTAAATTGGAAAAGAAAATTAACAATTAA
33130 GTATTAAATTGGATAAA-AAAATTTAAC-ATTAA
1 GTATTAAATTGGA-AAAGAAAA-TTAACAATTAA
33162 ATTAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (32 bp):
GTATTAAATTGGAAAAGAAAATTAACAATTAA
Found at i:39891 original size:29 final size:30
Alignment explanation
Indices: 39854--39911 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
39844 ATTTGTTTGA
39854 TGTGCAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* * *
39883 TGTGTAATTTTATACATGAAATTTTGATT
1 TGTGCAATTGTATACATGAAACTTTGATT
39912 AAATCCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:40123 original size:30 final size:30
Alignment explanation
Indices: 40050--40124 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
40040 TGTATGATTA
* *
40050 AATCAAAATTAAAGTTTTAAGTACATATTTG
1 AATC-AAATTAAAGATTTAAGTACATAATTG
** *
40081 AATCACAATTAAAGATTTCTGTATATAATTG
1 AATCA-AATTAAAGATTTAAGTACATAATTG
*
40112 CATCAAATTAAAG
1 AATCAAATTAAAG
40125 CTCATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 9 0.24
31 28 0.76
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (30 bp):
AATCAAATTAAAGATTTAAGTACATAATTG
Found at i:40554 original size:57 final size:57
Alignment explanation
Indices: 40466--40582 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
40456 AACGCCAGAT
40466 GAAAGTCTTGCCTCCGCTACAAGGAATAACGTACGCATCGATTCCCCTCAAAGCGAC
1 GAAAGTCTTGCCTCCGCTACAAGGAATAACGTACGCATCGATTCCCCTCAAAGCGAC
40523 GAAAGTCTTGCCTCCGCTACAAGGAATAACGTACGCATCGATTCCCCTCAAAGCGAC
1 GAAAGTCTTGCCTCCGCTACAAGGAATAACGTACGCATCGATTCCCCTCAAAGCGAC
40580 GAA
1 GAA
40583 CAGAGCGAGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.19
Consensus pattern (57 bp):
GAAAGTCTTGCCTCCGCTACAAGGAATAACGTACGCATCGATTCCCCTCAAAGCGAC
Found at i:42008 original size:32 final size:32
Alignment explanation
Indices: 41972--42035 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
41962 TCCAAAATAA
* * *
41972 TTATTTTAGATTTTTAAAATTTTCTTTTTTTT
1 TTATTATAGATTTTTAAAATTTTATATTTTTT
** *
42004 TTATTATATTTTTTTAAAGTTTTATATTTTTT
1 TTATTATAGATTTTTAAAATTTTATATTTTTT
42036 AAATATAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (32 bp):
TTATTATAGATTTTTAAAATTTTATATTTTTT
Found at i:43500 original size:15 final size:15
Alignment explanation
Indices: 43450--43500 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
43440 ACAAAATACT
*
43450 AATATAAATAACTAA
1 AATATAAATAATTAA
* *
43465 AACATAACAT-TTTAA
1 AATATAA-ATAATTAA
43480 AA-ATAAATAATTAA
1 AATATAAATAATTAA
43494 AATATAA
1 AATATAA
43501 TTTAAAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 2 0.07
14 10 0.34
15 15 0.52
16 2 0.07
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:51379 original size:23 final size:23
Alignment explanation
Indices: 51336--51380 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
51326 AAAAAAATAC
**
51336 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
51359 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
51381 ATTCGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:54084 original size:6 final size:6
Alignment explanation
Indices: 54073--54097 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54063 AGAATAAAAG
54073 CAATTT CAATTT CAATTT CAATTT C
1 CAATTT CAATTT CAATTT CAATTT C
54098 CATATTCCAA
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:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (6 bp):
CAATTT
Found at i:57969 original size:23 final size:23
Alignment explanation
Indices: 57935--58037 Score: 93
Period size: 25 Copynumber: 4.3 Consensus size: 23
57925 CTAGCGCACT
* *
57935 CTCTGTTTAGCAC-GTTTCGTGCC
1 CTCTGTTCAGCACTGTGT-GTGCC
57958 CTCTGTTCAGCACTGTGTGTGCC
1 CTCTGTTCAGCACTGTGTGTGCC
* *
57981 CTCTGTTATTAGCACTTTGTGTGCC
1 CTCTG-T-TCAGCACTGTGTGTGCC
*
58006 CTCTGTTACCCAGCACT-TATGTGCC
1 CTCTGTT---CAGCACTGTGTGTGCC
58031 CTCTGTT
1 CTCTGTT
58038 AAGTACTTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
23 23 0.34
24 5 0.07
25 34 0.50
26 6 0.09
ACGTcount: A:0.11, C:0.30, G:0.20, T:0.39
Consensus pattern (23 bp):
CTCTGTTCAGCACTGTGTGTGCC
Found at i:58001 original size:25 final size:25
Alignment explanation
Indices: 57953--58038 Score: 106
Period size: 25 Copynumber: 3.5 Consensus size: 25
57943 AGCACGTTTC
*
57953 GTGCCCTCTG-T-TCAGCACTGTGT
1 GTGCCCTCTGTTATCAGCACTTTGT
*
57976 GTGCCCTCTGTTATTAGCACTTTGT
1 GTGCCCTCTGTTATCAGCACTTTGT
* *
58001 GTGCCCTCTGTTACCCAGCAC-TTAT
1 GTGCCCTCTGTTA-TCAGCACTTTGT
58026 GTGCCCTCTGTTA
1 GTGCCCTCTGTTA
58039 AGTACTTTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 10 0.18
24 1 0.02
25 39 0.71
26 5 0.09
ACGTcount: A:0.12, C:0.30, G:0.21, T:0.37
Consensus pattern (25 bp):
GTGCCCTCTGTTATCAGCACTTTGT
Found at i:58046 original size:48 final size:47
Alignment explanation
Indices: 57935--58047 Score: 126
Period size: 48 Copynumber: 2.4 Consensus size: 47
57925 CTAGCGCACT
* *
57935 CTCTGTT-TAGCACGTTT-CGTGCCCTCTGTTCAGCACTGTGTGTGCC
1 CTCTGTTATAGCAC-TTTGTGTGCCCTCTGTTCAGCACTGTATGTGCC
57981 CTCTGTTATTAGCACTTTGTGTGCCCTCTGTTACCCAGCACT-TATGTGCC
1 CTCTGTTA-TAGCACTTTGTGTGCCCTCTGTT---CAGCACTGTATGTGCC
*
58031 CTCTGTTA-AGTACTTTG
1 CTCTGTTATAGCACTTTG
58048 GTACTTTCTA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
46 7 0.12
47 3 0.05
48 26 0.45
50 15 0.26
51 7 0.12
ACGTcount: A:0.12, C:0.28, G:0.20, T:0.39
Consensus pattern (47 bp):
CTCTGTTATAGCACTTTGTGTGCCCTCTGTTCAGCACTGTATGTGCC
Found at i:60132 original size:5 final size:5
Alignment explanation
Indices: 60122--60149 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
60112 CAGAATTGGT
60122 GTTTG GTTTG GTTTG GTTTG GTTTG GTT
1 GTTTG GTTTG GTTTG GTTTG GTTTG GTT
60150 AGGAGGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.39, T:0.61
Consensus pattern (5 bp):
GTTTG
Found at i:76157 original size:28 final size:28
Alignment explanation
Indices: 76126--76187 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
76116 AAATGAGACT
76126 TTTTGGATACCCGGGGAAAAAATGGTAA
1 TTTTGGATACCCGGGGAAAAAATGGTAA
* * **
76154 TTTTGGATTCTCGGGGGCAAAATGGTAA
1 TTTTGGATACCCGGGGAAAAAATGGTAA
76182 TTTTGG
1 TTTTGG
76188 GAAAATTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.31, T:0.32
Consensus pattern (28 bp):
TTTTGGATACCCGGGGAAAAAATGGTAA
Found at i:76287 original size:29 final size:29
Alignment explanation
Indices: 76255--76587 Score: 199
Period size: 29 Copynumber: 11.5 Consensus size: 29
76245 AAAATCGGGA
*
76255 TAAAAATGGAATTTTTGGACGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTCGGGGG
* **
76284 T-AAAATGGTAGTTTTT-GAGAGTTTTGGGG
1 TAAAAATGG-AATTTTTGGA-AGTTCGGGGG
* *
76313 TCAAAAATGGAGTTTTTGGACA-TTCGAGGG
1 T-AAAAATGGAATTTTTGGA-AGTTCGGGGG
* ** *
76343 T-AAAATGGTAATTTTTAGAAAATC--GGA
1 TAAAAATGG-AATTTTTGGAAGTTCGGGGG
* *
76370 TAAAAATAGAATTTTTGGACA-TTCAGGGG
1 TAAAAATGGAATTTTTGGA-AGTTCGGGGG
*
76399 T-AAAATGGTAATTTTT-GAGAGTTTC-GAGG
1 TAAAAATGG-AATTTTTGGA-AG-TTCGGGGG
* * * *
76428 TCAAAATGGAGTTTTTGGACA-TTTGAGGG
1 TAAAAATGGAATTTTTGGA-AGTTCGGGGG
* * **
76457 T-GAAATGGTAATTTTTGAAAGTTTTGGGG
1 TAAAAATGG-AATTTTTGGAAGTTCGGGGG
* *
76486 TCAAAAATGGAATTTTTGGAGGTTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTCGGGGG
* **
76516 TAAAAATGAAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTCGGGGG
*
76545 T-AAAATAGAATTTTTGGAAGTTC-GGGG
1 TAAAAATGGAATTTTTGGAAGTTCGGGGG
*
76572 TAAAAAATGTAATTTT
1 T-AAAAATGGAATTTT
76588 CAAAAGTTTC
Statistics
Matches: 236, Mismatches: 45, Indels: 46
0.72 0.14 0.14
Matches are distributed among these distances:
27 19 0.08
28 61 0.26
29 98 0.42
30 42 0.18
31 16 0.07
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTCGGGGG
Found at i:76329 original size:59 final size:59
Alignment explanation
Indices: 76193--76576 Score: 361
Period size: 59 Copynumber: 6.7 Consensus size: 59
76183 TTTGGGAAAA
** **
76193 TTTGGGGTTTAAAATGGAA-TTTT--ACATTCGAGGGTAAAAT-GTAATTTTT-AGAAAA
1 TTTGGGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAG-AGT
* * * * * *
76248 ATCGGGAT-AAAAATGGAATTTTTGGACGTTCGGGGGTAAAATGGTAGTTTTTGAGAGT
1 TTTGGGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAGAGT
* *
76306 TTTGGGGTCAAAAATGGAGTTTTTGGACATTCGAGGGTAAAATGGTAATTTTT-AGA-A
1 TTTGGGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAGAGT
** * * *
76363 AATCGGAT-AAAAATAGAATTTTTGGACATTC-AGGGGTAAAATGGTAATTTTTGAGAGT
1 TTTGGGGTCAAAAATGGAATTTTTGGACATTCGA-GGGTAAAATGGTAATTTTTGAGAGT
* * * * * *
76421 TTCGAGGTC-AAAATGGAGTTTTTGGACATTTGAGGGTGAAATGGTAATTTTTGAAAGT
1 TTTGGGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAGAGT
** *
76479 TTTGGGGTCAAAAATGGAATTTTTGGAGGTTCGAGGGTAAAAAT-GAAATTTTTG-GAAGT
1 TTTGGGGTCAAAAATGGAATTTTTGGACATTCGAGGGT-AAAATGGTAATTTTTGAG-AGT
*
76538 TTTGGGGT--AAAATAGAATTTTTGGA-AGTTCG-GGGTAAAA
1 TTTGGGGTCAAAAATGGAATTTTTGGACA-TTCGAGGGTAAAA
76577 AATGTAATTT
Statistics
Matches: 268, Mismatches: 46, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
54 9 0.03
55 14 0.05
56 44 0.16
57 42 0.16
58 68 0.25
59 87 0.32
60 4 0.01
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (59 bp):
TTTGGGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAGAGT
Found at i:76399 original size:115 final size:115
Alignment explanation
Indices: 76216--76476 Score: 411
Period size: 115 Copynumber: 2.3 Consensus size: 115
76206 ATGGAATTTT
* * *
76216 ACATTCGAGGGTAAAAT-GTAATTTTTAGAAAAATCGGGATAAAAATGGAATTTTTGGACGTTCG
1 ACATTCGAGGGTAAAATGGTAATTTTTAG-AAAATCGGGATAAAAATAGAATTTTTGGACATTCA
* * *
76280 GGGGTAAAATGGTAGTTTTTGAGAGTTTTGGGGTCAAAAATGGAGTTTTTGG
65 GGGGTAAAATGGTAATTTTTGAGAGTTTCGAGGTC-AAAATGGAGTTTTTGG
76332 ACATTCGAGGGTAAAATGGTAATTTTTAGAAAATC-GGATAAAAATAGAATTTTTGGACATTCAG
1 ACATTCGAGGGTAAAATGGTAATTTTTAGAAAATCGGGATAAAAATAGAATTTTTGGACATTCAG
76396 GGGTAAAATGGTAATTTTTGAGAGTTTCGAGGTCAAAATGGAGTTTTTGG
66 GGGTAAAATGGTAATTTTTGAGAGTTTCGAGGTCAAAATGGAGTTTTTGG
* *
76446 ACATTTGAGGGTGAAATGGTAATTTTT-GAAA
1 ACATTCGAGGGTAAAATGGTAATTTTTAGAAA
76477 GTTTTGGGGT
Statistics
Matches: 136, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
113 4 0.03
114 41 0.30
115 57 0.42
116 23 0.17
117 11 0.08
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (115 bp):
ACATTCGAGGGTAAAATGGTAATTTTTAGAAAATCGGGATAAAAATAGAATTTTTGGACATTCAG
GGGTAAAATGGTAATTTTTGAGAGTTTCGAGGTCAAAATGGAGTTTTTGG
Found at i:76474 original size:173 final size:172
Alignment explanation
Indices: 76257--76630 Score: 452
Period size: 173 Copynumber: 2.2 Consensus size: 172
76247 AATCGGGATA
* * * * *
76257 AAAATGGAATTTTTGGACGTTCGGGGGTAAAATGGTAGTTTTTGAGAGTTTTGGGGTCAAAAATG
1 AAAATGGAATTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATG
* *
76322 GAGTTTTTGGACATTCGAGGGT-AAAATGGTAATTTTTAGAA-AATCGGATAAAAATAGAATTTT
66 GAATTTTTGGACATTCGAGGGTAAAAAT-GAAATTTTTAGAAGAATCGGAT-AAAATAGAATTTT
** * *
76385 TGGACA-TTCAGGGGT-AAAATGGTAATTTTTGAGAGTTTCGAGGTC
129 TGGA-AGTTC-GGGGTAAAAAT-GTAATTTTCAAAAGTTTCGAGATC
* *
76430 AAAATGGAGTTTTTGGACATTTGAGGGTGAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATG
1 AAAATGGAATTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATG
** * ** * *
76495 GAATTTTTGGAGGTTCGAGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGTAAAATAGAATTTTT
66 GAATTTTTGGACATTCGAGGGTAAAAATGAAATTTTTAGAAG-AATCGGATAAAATAGAATTTTT
*
76560 GGAAGTTCGGGGTAAAAAATGTAATTTTCAAAAGTTTCGAGATT
130 GGAAGTTCGGGGT-AAAAATGTAATTTTCAAAAGTTTCGAGATC
76604 AAAATGGAATTTTTGGACAGTTT-AGGG
1 AAAATGGAATTTTTGGACA-TTTGAGGG
76631 ACCTCCAGGG
Statistics
Matches: 172, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
173 94 0.55
174 66 0.38
175 12 0.07
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (172 bp):
AAAATGGAATTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATG
GAATTTTTGGACATTCGAGGGTAAAAATGAAATTTTTAGAAGAATCGGATAAAATAGAATTTTTG
GAAGTTCGGGGTAAAAATGTAATTTTCAAAAGTTTCGAGATC
Found at i:76578 original size:57 final size:58
Alignment explanation
Indices: 76219--76625 Score: 241
Period size: 59 Copynumber: 7.0 Consensus size: 58
76209 GAATTTTACA
* ** * * * *
76219 TTCGAGGGT-AAAATGTAATTTTTAGAAA-AATCGGGATAAAAATGGAATTTTTGGACG
1 TTCGAGGGTAAAAATGAAATTTTT-GAAAGTTTTGGGGTAAAAATAGAATTTTTGGAAG
* * * * * *
76276 TTCGGGGGT-AAAATGGTAGTTTTTGAGAGTTTTGGGGTCAAAAATGGAGTTTTTGGACA-
1 TTCGAGGGTAAAAAT-GAAATTTTTGAAAGTTTTGGGGT-AAAAATAGAATTTTTGGA-AG
* * * *
76335 TTCGAGGGT-AAAATGGTAATTTTTAGAAA---ATCGGATAAAAATAGAATTTTTGGACA-
1 TTCGAGGGTAAAAAT-GAAATTTTT-GAAAGTTTTGGGGTAAAAATAGAATTTTTGGA-AG
* * * * * * *
76391 TTC-AGGGGT-AAAATGGTAATTTTTGAGAGTTTCGAGGTCAAAATGGAGTTTTTGGACA-
1 TTCGA-GGGTAAAAAT-GAAATTTTTGAAAGTTTTGGGGTAAAAATAGAATTTTTGGA-AG
* * * * *
76449 TTTGAGGGT-GAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAGG
1 TTCGAGGGTAAAAAT-GAAATTTTTGAAAGTTTTGGGGT-AAAAATAGAATTTTTGGAAG
*
76508 TTCGAGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGT-AAAATAGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGAAATTTTTGAAAGTTTTGGGGTAAAAATAGAATTTTTGGAAG
* ** * * * * *
76565 TTCG-GGGTAAAAAATGTAATTTTCAAAAGTTTCGAGATTAAAATGGAATTTTTGGACAG
1 TTCGAGGGT-AAAAATGAAATTTTTGAAAGTTTTGGGGTAAAAATAGAATTTTTGGA-AG
76624 TT
1 TT
76626 TAGGGACCTC
Statistics
Matches: 286, Mismatches: 48, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
55 4 0.01
56 44 0.15
57 63 0.22
58 79 0.28
59 89 0.31
60 7 0.02
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (58 bp):
TTCGAGGGTAAAAATGAAATTTTTGAAAGTTTTGGGGTAAAAATAGAATTTTTGGAAG
Found at i:76599 original size:87 final size:86
Alignment explanation
Indices: 76372--76626 Score: 243
Period size: 87 Copynumber: 2.9 Consensus size: 86
76362 AAATCGGATA
* *
76372 AAAATAGAATTTTTGGACA-TTCAGGGGT-AAAATGGTAATTTTTGAGAGTTTCGAGGTCAAAAT
1 AAAATAGAATTTTTGGA-AGTTC-GGGGTAAAAAT-GTAA-TTTTAAGAGTTTCGAGGTAAAAAT
*
76435 GGAGTTTTTGGACA--TTTGAGGGT
62 GGAATTTTTGGACAGTTTTGAGGGT
* * * * * ** *
76458 GAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAGGTTCGAGGGTAAAAAT
1 AAAATAG-AATTTTTGGAAG-TTCGGGGT-AAAAATGTAATTTTAAGAGTTTCGA-GGTAAAAAT
*
76523 GAAATTTTTGGA-AGTTTTG-GGGT
62 GGAATTTTTGGACAGTTTTGAGGGT
* * *
76546 AAAATAGAATTTTTGGAAGTTCGGGGTAAAAAATGTAATTTTCAAAAGTTTCGAGATTAAAATGG
1 AAAATAGAATTTTTGGAAGTTCGGGGT-AAAAATGTAATTTT-AAGAGTTTCGAGGTAAAAATGG
76611 AATTTTTGGACAGTTT
64 AATTTTTGGACAGTTT
76627 AGGGACCTCC
Statistics
Matches: 135, Mismatches: 24, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
86 44 0.33
87 50 0.37
88 32 0.24
89 9 0.07
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (86 bp):
AAAATAGAATTTTTGGAAGTTCGGGGTAAAAATGTAATTTTAAGAGTTTCGAGGTAAAAATGGAA
TTTTTGGACAGTTTTGAGGGT
Found at i:85557 original size:40 final size:39
Alignment explanation
Indices: 85462--85634 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 39
85452 TTCTTGATGT
* * * * * *
85462 TTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATG
1 TTAAAAGGAAGACTTATGACTCGGTA-GAGCATAAGATTG
* *
85502 TGATAAAGGAAGACTTATGACTCGGTAAAGCATAAGATTG
1 TTA-AAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
* *
85542 TTCAAAAGGAAGACTTATAACTCGGTAGAGCATAATATTG
1 TT-AAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
85582 TTAAAAGGAAGACTTATGACTCGGTAGAGCA-AGAGATTG
1 TTAAAAGGAAGACTTATGACTCGGTAGAGCATA-AGATTG
85621 TTAAAAAGGAAGAC
1 TT-AAAAGGAAGAC
85635 ACATAAATCT
Statistics
Matches: 115, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.01
39 35 0.30
40 58 0.50
41 21 0.18
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.24
Consensus pattern (39 bp):
TTAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATTG
Found at i:86352 original size:21 final size:21
Alignment explanation
Indices: 86325--86373 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
86315 AAGACTTGTT
*
86325 TCAGTAGAAGAGTCACTTGCA
1 TCAGTAGAACAGTCACTTGCA
* *
86346 TCGGTAGAACTGTCACTTGCA
1 TCAGTAGAACAGTCACTTGCA
86367 TCAGTAG
1 TCAGTAG
86374 TGGTCTGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (21 bp):
TCAGTAGAACAGTCACTTGCA
Found at i:91736 original size:22 final size:22
Alignment explanation
Indices: 91694--91744 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
91684 TTAAATATTT
*
91694 TTTAAACAATTAATATTAAATA
1 TTTAAACAATTAATATCAAATA
*
91716 TTTATACAATTTAAT-TCAAATA
1 TTTAAACAA-TTAATATCAAATA
*
91738 TATAAAC
1 TTTAAAC
91745 TACATCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAACAATTAATATCAAATA
Found at i:92362 original size:2 final size:2
Alignment explanation
Indices: 92355--92390 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
92345 TCAATAACAT
92355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92391 AATTGATGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:99691 original size:57 final size:58
Alignment explanation
Indices: 99581--99691 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 58
99571 CACTTCAACA
* **
99581 TTAACAGTTTCACCTCCATTTATTTGAACAGAAGCGGAGCTTTTATTGTGCTGCACAT
1 TTAACAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTTTTATTCAGCTGCACAT
*
99639 TTAA-AGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 TTAACAGTTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTTTTATTCAGCTGC
99692 TCTTCAACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
57 42 0.88
58 6 0.12
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (58 bp):
TTAACAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTTTTATTCAGCTGCACAT
Found at i:99706 original size:57 final size:58
Alignment explanation
Indices: 99578--99706 Score: 158
Period size: 57 Copynumber: 2.3 Consensus size: 58
99568 CTCCACTTCA
* **
99578 ACATT-AACAGTTTCACCTCCATTTATTTGAACAGAAGCGGAGCTTTTATTGTGCTGC
1 ACATTCAACAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTTTTATTCAGCTGC
* *
99635 ACATTTAA-AGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 ACATTCAACAGTTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTTTTATTCAGCTGC
* *
99692 TC-TTCAACATTTTCA
1 ACATTCAACAGTTTCA
99707 ATTGTCTTCC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
56 4 0.06
57 54 0.87
58 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.36
Consensus pattern (58 bp):
ACATTCAACAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTTTTATTCAGCTGC
Found at i:104528 original size:35 final size:35
Alignment explanation
Indices: 104459--104528 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
104449 CAAAAGAGGC
* *
104459 TGAGAGTCGGAGCAGGGACAAGAAAATAAACAAAT
1 TGAGAGTCGAAGCAGGGACAAGAAAACAAACAAAT
* * *
104494 TGAGAGTCGAAGCAGTGACAAGAGAACAAGCAAAT
1 TGAGAGTCGAAGCAGGGACAAGAAAACAAACAAAT
104529 GGTCAACAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.47, C:0.13, G:0.29, T:0.11
Consensus pattern (35 bp):
TGAGAGTCGAAGCAGGGACAAGAAAACAAACAAAT
Found at i:105546 original size:15 final size:15
Alignment explanation
Indices: 105528--105563 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
105518 AAAATTAAAG
105528 AAAAATGAATATGGT
1 AAAAATGAATATGGT
*
105543 AAAAATGAATGTGGT
1 AAAAATGAATATGGT
105558 AAAAAT
1 AAAAAT
105564 TTTGGTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (15 bp):
AAAAATGAATATGGT
Found at i:108387 original size:62 final size:56
Alignment explanation
Indices: 108275--108446 Score: 247
Period size: 62 Copynumber: 3.0 Consensus size: 56
108265 ATTTCTTGAA
*
108275 CCATAATAATATCCTATAATATCCCATTAGGAATTAAATTGTTAAGAGATAATATT
1 CCATAATAATATCCTATAATATCCCATTAGGAATTAAATTGCTAAGAGATAATATT
*
108331 CCATAATAATATCCTATAATATCCCATTAGGAATAGGAATCAAATTGCTAATAGATAATATT
1 CCATAATAATATCCTATAATATCCCATTAGGAAT-----T-AAATTGCTAAGAGATAATATT
* *
108393 CCATAATAATATCCTATAATATCTCATTAGGAATTAAATTGCTAA-AAATAATAT
1 CCATAATAATATCCTATAATATCCCATTAGGAATTAAATTGCTAAGAGATAATAT
108447 CTAACAACCT
Statistics
Matches: 106, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
55 8 0.08
56 44 0.42
57 1 0.01
61 1 0.01
62 52 0.49
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (56 bp):
CCATAATAATATCCTATAATATCCCATTAGGAATTAAATTGCTAAGAGATAATATT
Found at i:113390 original size:56 final size:56
Alignment explanation
Indices: 113255--113407 Score: 155
Period size: 56 Copynumber: 2.7 Consensus size: 56
113245 AGTTACATAG
* * * * * *
113255 AAATCAAAATTGCTGAAAGATAATATCCCATAA-AAGTATCCTATAATATCTCATTAA
1 AAATC-AAATTACTAAAAAATAATATCACATAATAA-TATTCTATAATATCCCATTAA
** ***
113312 AAATCAAATTGTTAAGGGATAATATCACATAATAATATTCTATAATATCCCATTAA
1 AAATCAAATTACTAAAAAATAATATCACATAATAATATTCTATAATATCCCATTAA
* * *
113368 GAATTAAATTACTAAAAAATAATATCGCATAATAATATTC
1 AAATCAAATTACTAAAAAATAATATCACATAATAATATTC
113408 CAAATAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
56 73 0.91
57 7 0.09
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (56 bp):
AAATCAAATTACTAAAAAATAATATCACATAATAATATTCTATAATATCCCATTAA
Found at i:125645 original size:8 final size:7
Alignment explanation
Indices: 125624--125653 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
125614 TCTTTTTTTT
125624 AAAGAAA
1 AAAGAAA
125631 AAAGAAA
1 AAAGAAA
*
125638 AAAGGAA
1 AAAGAAA
125645 AAAGAAA
1 AAAGAAA
125652 AA
1 AA
125654 GGAATGGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:125646 original size:14 final size:13
Alignment explanation
Indices: 125624--125657 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
125614 TCTTTTTTTT
*
125624 AAAGAAAAAAGAAA
1 AAAGGAAAAAG-AA
125638 AAAGGAAAAAGAA
1 AAAGGAAAAAGAA
125651 AAAGGAA
1 AAAGGAA
125658 TGGGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGGAAAAAGAA
Found at i:127645 original size:98 final size:97
Alignment explanation
Indices: 127471--127665 Score: 295
Period size: 98 Copynumber: 2.0 Consensus size: 97
127461 AACTTTGGAA
127471 AAGGATATTCGATTATCTCGATTTGAAGAAAATTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAATTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* *
127536 GAATCAGAAATAAAGGAATATTGCCTCGATTT
66 AAATCAGAAATAAAAGAATATTGCCTCGATTT
* *
127568 AAGGGTATTCGATTATTTCGATTTGAAGAAAAAATT-GCACCTAGTAAGTTAAGGCACAAATTTT
1 AAGGATATTCGATTATCTCGATTTGAAG--AAAATTCGCACCTAGTAAGTTAAGGCACAAATTTT
* *
127632 CAAAACTCA-AAATAAAATAATATTGTCTCGATTT
64 CAAAA-TCAGAAATAAAAGAATATTGCCTCGATTT
127666 TAAAGTTTTC
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
97 26 0.29
98 54 0.61
99 9 0.10
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAATTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAATCAGAAATAAAAGAATATTGCCTCGATTT
Found at i:127964 original size:30 final size:31
Alignment explanation
Indices: 127922--128262 Score: 131
Period size: 28 Copynumber: 11.6 Consensus size: 31
127912 CTCGGGGGGC
*
127922 AAAATGGTAATTTTGGGAAAATTAGGGGTCA
1 AAAATGGTAATTTTTGGAAAATTAGGGGTCA
* * * *
127953 AAAATGG-AATTTTTAGACATTTGGGGGT--
1 AAAATGGTAATTTTTGGAAAATTAGGGGTCA
* * * *
127981 AAGATGGTACTTTTTGGAAGAATCA-AGGTCA
1 AAAATGGTAATTTTTGGAA-AATTAGGGGTCA
**
128012 AAAATGG-AATTTTTGGAAGTTTAGGGGT--
1 AAAATGGTAATTTTTGGAAAATTAGGGGTCA
* **
128040 AAAATGGTAATTTTTGGAAAA-AAGTAGTCA
1 AAAATGGTAATTTTTGGAAAATTAGGGGTCA
* * * *
128070 AAAATGG-AATTTTTAG-AATTTCA-AGGT-T
1 AAAATGGTAATTTTTGGAAAATT-AGGGGTCA
** * * *
128098 AAAATGGTTTTTTTTTTGGAAAAATCGAGGTCA
1 AAAATGG--TAATTTTTGGAAAATTAGGGGTCA
* *
128131 AAAATGG-AA-TTTTGG-AAGTTCGGGAGT--
1 AAAATGGTAATTTTTGGAAAATTAGGG-GTCA
* *
128158 AAAATGGTAATTTTTTGAAAAATTA-GGGTTA
1 AAAATGGTAA-TTTTTGGAAAATTAGGGGTCA
* * * *
128189 AAAATAG-AA-TTTTGGAAAGTTCGAGG--A
1 AAAATGGTAATTTTTGGAAAATTAGGGGTCA
* * *
128216 TAAAATGGTAATTTTTAG-AAATCA-GAGTC-
1 -AAAATGGTAATTTTTGGAAAATTAGGGGTCA
128245 AAAATGG-AATTTTTGGAA
1 AAAATGGTAATTTTTGGAA
128263 TTTCAAGGGT
Statistics
Matches: 222, Mismatches: 58, Indels: 63
0.65 0.17 0.18
Matches are distributed among these distances:
27 16 0.07
28 59 0.27
29 51 0.23
30 53 0.24
31 29 0.13
32 7 0.03
33 7 0.03
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.33
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGAAAATTAGGGGTCA
Found at i:128101 original size:58 final size:57
Alignment explanation
Indices: 127922--128276 Score: 283
Period size: 59 Copynumber: 6.1 Consensus size: 57
127912 CTCGGGGGGC
* * * * **
127922 AAAATGGTAATTTTGGGAAAATTAGGGGTCAAAAATGGAATTTTTAGACATTT-GGGGGT
1 AAAATGGTAATTTTTGGAAAA--AAGAGTCAAAAATGGAATTTTTGGA-ATTTCAAGGGT
* * *
127981 AAGATGGTACTTTTTGGAAGAATCAAG-GTCAAAAATGGAATTTTTGGAAGTTT-AGGGGT
1 AAAATGGTAATTTTTGGAA-AA--AAGAGTCAAAAATGGAATTTTTGGAA-TTTCAAGGGT
* *
128040 AAAATGGTAATTTTTGGAAAAAAGTAGTCAAAAATGGAATTTTTAGAATTTCAAGGTT
1 AAAATGGTAATTTTTGGAAAAAAG-AGTCAAAAATGGAATTTTTGGAATTTCAAGGGT
** * * *
128098 AAAATGGTTTTTTTTTTGGAAAAATCGAGGTCAAAAATGGAA-TTTTGGAAGTTC-GGGAGT
1 AAAATGG--TAATTTTTGGAAAAA-AGA-GTCAAAAATGGAATTTTTGGAATTTCAAGG-GT
* * * * * * *
128158 AAAATGGTAATTTTTTGAAAAATTAGGGTTAAAAATAGAA-TTTTGGAAAGTTCGAGGAT
1 AAAATGGTAATTTTTGGAAAAA--AGAGTCAAAAATGGAATTTTTGG-AATTTCAAGGGT
* **
128217 AAAATGGTAATTTTTAGAAATCAGAGTC-AAAATGGAATTTTTGGAATTTCAAGGGT
1 AAAATGGTAATTTTTGGAAAAAAGAGTCAAAAATGGAATTTTTGGAATTTCAAGGGT
128273 AAAA
1 AAAA
128277 ATATGATTTC
Statistics
Matches: 245, Mismatches: 37, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
56 24 0.10
57 13 0.05
58 64 0.26
59 91 0.37
60 39 0.16
61 14 0.06
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTTGGAAAAAAGAGTCAAAAATGGAATTTTTGGAATTTCAAGGGT
Found at i:128148 original size:118 final size:116
Alignment explanation
Indices: 127917--128276 Score: 331
Period size: 118 Copynumber: 3.1 Consensus size: 116
127907 GGTCACTCGG
* * * * **
127917 GGGGCAAAATGGTAATTTTGGGAAAATTAGGGGTCAAAAATGGAATTTTTAGACATTTGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGAAAA-AAGGAGTCAAAAATGGAATTTTTAGACATTTAAGGGTA
* *
127982 AGATGGTACTTTTTGGAAGAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTA
65 AAATGGTACTTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAG-TTA
* *
128035 GGGGTAAAATGGTAATTTTTGGAAAAAAGTAGTCAAAAATGGAATTTTTAGA-ATTTCAAGGTTA
1 GGGGTAAAATGGTAATTTTTGGAAAAAAGGAGTCAAAAATGGAATTTTTAGACATTT-AAGGGTA
** * *
128099 AAATGGTTTTTTTTTTGGAAAAATCGAGGTCAAAAATGGAA-TTTTGGAAGTTC
65 AAATGG--TACTTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTA
* * * * * **
128152 GGGAGTAAAATGGTAATTTTTTGAAAAATTAGG-GTTAAAAATAGAA-TTTTGGAAAGTTCGAGG
1 GGG-GTAAAATGGTAATTTTTGGAAAAA--AGGAGTCAAAAATGGAATTTTTAGACA-TTTAAGG
* * * *
128215 ATAAAATGGTAATTTTT--AGAAATC-AGAGTC-AAAATGGAATTTTTGGAATTTCA
62 GTAAAATGGTACTTTTTGGAAAAATCAAG-GTCAAAAATGGAATTTTTGGAAGTT-A
*
128268 AGGGTAAAA
1 GGGGTAAAA
128277 ATATGATTTC
Statistics
Matches: 203, Mismatches: 28, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
114 11 0.05
115 25 0.12
116 6 0.03
117 43 0.21
118 62 0.31
119 52 0.26
120 4 0.02
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (116 bp):
GGGGTAAAATGGTAATTTTTGGAAAAAAGGAGTCAAAAATGGAATTTTTAGACATTTAAGGGTAA
AATGGTACTTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTA
Found at i:128220 original size:119 final size:119
Alignment explanation
Indices: 127991--128276 Score: 306
Period size: 119 Copynumber: 2.4 Consensus size: 119
127981 AAGATGGTAC
*
127991 TTTTTGGAAGAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTG
1 TTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTG
* * * *
128056 GAAAAAAGTAGTCAAAAATGGAATTTTTAGAATTTCAAGGTTAAAATGGTTTTT
66 GAAAAAAGTAGTCAAAAATAGAATTTTGAGAAGTTCAAGGATAAAATGGTTTTT
* *
128110 TTTTTGGAAAAATCGAGGTCAAAAATGGAA-TTTTGGAAG-TTCGGGAGTAAAATGGTAATTTTT
1 TTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTAGGG-GTAAAATGGTAATTTTT
* * * * **
128173 TGAAAAATTAG-GGTTAAAAATAGAATTTTG-GAAAGTTCGAGGATAAAATGG--TAA
65 GGAAAAA--AGTAGTCAAAAATAGAATTTTGAG-AAGTTCAAGGATAAAATGGTTTTT
* *
128227 TTTTT--AGAAATC-AGAGTC-AAAATGGAATTTTTGGAA-TTTCAAGGGTAAAA
1 TTTTTGGAAAAATCAAG-GTCAAAAATGGAATTTTTGGAAGTTT-AGGGGTAAAA
128277 ATATGATTTC
Statistics
Matches: 143, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
114 11 0.08
115 25 0.17
116 2 0.01
117 11 0.08
118 33 0.23
119 59 0.41
120 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (119 bp):
TTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTG
GAAAAAAGTAGTCAAAAATAGAATTTTGAGAAGTTCAAGGATAAAATGGTTTTT
Found at i:129403 original size:3 final size:3
Alignment explanation
Indices: 129397--129432 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
129387 TTTTTGATAC
* *
129397 TTA TTA TTA ATA TTA TTA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
129433 ATGCCGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:129410 original size:9 final size:9
Alignment explanation
Indices: 129398--129434 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
129388 TTTTGATACT
129398 TATTATTAA
1 TATTATTAA
129407 TATTATTAA
1 TATTATTAA
*
129416 TATTATTAT
1 TATTATTAA
129425 TATTATTAA
1 TATTATTAA
129434 T
1 T
129435 GCCGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:129996 original size:17 final size:17
Alignment explanation
Indices: 129974--130016 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
129964 GACTCTCTTT
129974 TTATTGGGCCAAACATG
1 TTATTGGGCCAAACATG
129991 TTATTGGGCCAAACATG
1 TTATTGGGCCAAACATG
130008 TTATTGGGC
1 TTATTGGGC
130017 TTGCTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (17 bp):
TTATTGGGCCAAACATG
Found at i:130157 original size:17 final size:17
Alignment explanation
Indices: 130114--130164 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
130104 ATTATTTATG
**
130114 ATAAATTTAAATTTCTA
1 ATAAATTTAAATTTAAA
*
130131 ATTAATTTAAATTTAAA
1 ATAAATTTAAATTTAAA
*
130148 ATAAACTTAAATTTAAA
1 ATAAATTTAAATTTAAA
130165 TTTTATTGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAAATTTAAATTTAAA
Found at i:136204 original size:173 final size:176
Alignment explanation
Indices: 135870--136222 Score: 613
Period size: 175 Copynumber: 2.0 Consensus size: 176
135860 AATCATAATG
*
135870 TAATACCTAGAGATAATGTTTTTTTTTTTTCTATTACTGCTCAAGAATATAGTTCATGCCCTCTC
1 TAATACCTAGAGATAATG-TTTTTTTTTTTCTATTACTGCTCAAGAATATAGTTCATGCCCTATC
* *
135935 AAAAGTAAAATTCTAACTTTTTTTTTTATAATTTCAAAATTATATATATTTTCACGTGTTATTAT
65 AAAAGTAAAATTCTAACTCTTTTTTTTATAATTTCAAAATTATACATATTTTCACGTGTTATTAT
*
136000 TAATTAGTTTCAAACCATATGTTTGATTATTTATTATATATTATTTT
130 TAATTAGTTTCAAACCATATGTTTCATTATTTATTATATATTATTTT
*
136047 TAATACCTAGAGATAATG-TTTTTTTTTTCTATTACTGCTCAAGAATATAGTTCATGCCTTATCA
1 TAATACCTAGAGATAATGTTTTTTTTTTTCTATTACTGCTCAAGAATATAGTTCATGCCCTATCA
*
136111 AAAGTAAAATTCTAACTCTTTTTTTT-TAATTTCAAAATTATACATA-TTTCACGTGTTATTGTT
66 AAAGTAAAATTCTAACTCTTTTTTTTATAATTTCAAAATTATACATATTTTCACGTGTTATTATT
*
136174 AATTAGTTTCAAATCATATGTTTCATTATTTATTATATATTATTTT
131 AATTAGTTTCAAACCATATGTTTCATTATTTATTATATATTATTTT
136220 TAA
1 TAA
136223 ACACGTATTT
Statistics
Matches: 169, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
173 63 0.37
174 19 0.11
175 69 0.41
177 18 0.11
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.49
Consensus pattern (176 bp):
TAATACCTAGAGATAATGTTTTTTTTTTTCTATTACTGCTCAAGAATATAGTTCATGCCCTATCA
AAAGTAAAATTCTAACTCTTTTTTTTATAATTTCAAAATTATACATATTTTCACGTGTTATTATT
AATTAGTTTCAAACCATATGTTTCATTATTTATTATATATTATTTT
Found at i:137970 original size:15 final size:15
Alignment explanation
Indices: 137950--138016 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
137940 AAATAAAACT
137950 TTATTTTGAATATAA
1 TTATTTTGAATATAA
* * *
137965 TTATTTCGGATGTAA
1 TTATTTTGAATATAA
*
137980 TTATTTCT-AA-ACAA
1 TTATTT-TGAATATAA
*
137994 TTATTTTGAATAATTA
1 TTATTTTGAAT-ATAA
138010 TTATTTT
1 TTATTTT
138017 TCTAAAAGAT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 19 0.49
16 9 0.23
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.54
Consensus pattern (15 bp):
TTATTTTGAATATAA
Found at i:161392 original size:11 final size:11
Alignment explanation
Indices: 161376--161400 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
161366 CAAGGAGAAG
161376 CAATTAAGGAA
1 CAATTAAGGAA
161387 CAATTAAGGAA
1 CAATTAAGGAA
161398 CAA
1 CAA
161401 AGATGGTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (11 bp):
CAATTAAGGAA
Found at i:164518 original size:19 final size:17
Alignment explanation
Indices: 164491--164536 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
164481 CTTCAAAATC
* *
164491 AATACAATTAAATTTATTT
1 AATATAATTAAA--TATTA
164510 AATATAATTAAATATTA
1 AATATAATTAAATATTA
164527 AATATAATTA
1 AATATAATTA
164537 TTTATTTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.56
19 11 0.44
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATAATTAAATATTA
Found at i:164542 original size:17 final size:17
Alignment explanation
Indices: 164502--164542 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
164492 ATACAATTAA
*
164502 ATTTATTTAATATAATT
1 ATTTATTAAATATAATT
**
164519 AAATATTAAATATAATT
1 ATTTATTAAATATAATT
164536 ATTTATT
1 ATTTATT
164543 TCTCTTTCAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATTAAATATAATT
Found at i:164584 original size:14 final size:14
Alignment explanation
Indices: 164561--164599 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
164551 AAGTGTTGGG
*
164561 TTTTAGATTTTGAA
1 TTTTAAATTTTGAA
* *
164575 TTTTGAATTTTGGA
1 TTTTAAATTTTGAA
164589 TTTTAAATTTT
1 TTTTAAATTTT
164600 AACTTTCAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (14 bp):
TTTTAAATTTTGAA
Found at i:178273 original size:14 final size:15
Alignment explanation
Indices: 178242--178281 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
178232 TGTATAAATT
*
178242 TATTAAATATTAAAA
1 TATTTAATATTAAAA
*
178257 TATTTATTATT-AAA
1 TATTTAATATTAAAA
178271 TATTTAATATT
1 TATTTAATATT
178282 TTATAATACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATATTAAAA
Found at i:178285 original size:22 final size:22
Alignment explanation
Indices: 178241--178282 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
178231 ATGTATAAAT
178241 TTATTAAATATTAAAATATTTA
1 TTATTAAATATTAAAATATTTA
*
178263 TTATTAAATATT-TAATATTT
1 TTATTAAATATTAAAATATTT
178283 TATAATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTAAATATTAAAATATTTA
Found at i:183341 original size:14 final size:14
Alignment explanation
Indices: 183318--183352 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
183308 ATATATTAGT
183318 TAATAATAATAAAA
1 TAATAATAATAAAA
* *
183332 TAATACTAATTAAA
1 TAATAATAATAAAA
183346 TAATAAT
1 TAATAAT
183353 TTATATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:186338 original size:24 final size:24
Alignment explanation
Indices: 186310--186356 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
186300 AGAATTTGAC
186310 TAAAACAAATAAACAGAGTTTAAT
1 TAAAACAAATAAACAGAGTTTAAT
186334 TAAAACAAATAAACAGAGTTTAA
1 TAAAACAAATAAACAGAGTTTAA
186357 CTGAAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (24 bp):
TAAAACAAATAAACAGAGTTTAAT
Found at i:191569 original size:15 final size:16
Alignment explanation
Indices: 191548--191587 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
191538 TAATTAAATT
191548 TAATATTAAATTAAGA
1 TAATATTAAATTAAGA
191564 -AATATT--ATTAAGA
1 TAATATTAAATTAAGA
191577 TAATTATTAAA
1 TAA-TATTAAA
191588 ATAAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 7
0.74 0.00 0.26
Matches are distributed among these distances:
13 7 0.35
14 2 0.10
15 10 0.50
17 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
TAATATTAAATTAAGA
Found at i:192637 original size:60 final size:58
Alignment explanation
Indices: 192493--192684 Score: 215
Period size: 60 Copynumber: 3.2 Consensus size: 58
192483 TTAATATAAT
* * * * *
192493 ATTTGATACCTGAATTTGACATTTTTTCTTAATTTAATACTTAAATTTTTTTTACCCA
1 ATTTGATACCTAAACTTGACATTTTTTCCTAATTTGATACTTAAATTTTTTTGACCCA
* * *
192551 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACTTAAATATTTTTTGGACCCA
1 ATTTGATACCTAAACTTGACATTTTTTCCTAATTTGATACTTAAAT-TTTTTT-GACCCA
* * **
192611 ATTTGATACCTAAACTT-AGCATTTTTTCCTAATTTGATACCTAATCTTTTTTTAGATTCA
1 ATTTGATACCTAAACTTGA-CATTTTTTCCTAATTTGATACTTAA-ATTTTTTT-GACCCA
*
192671 ATTTGGTACCTAAA
1 ATTTGATACCTAAA
192685 TTTATTAAAT
Statistics
Matches: 113, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
58 39 0.35
59 7 0.06
60 66 0.58
61 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (58 bp):
ATTTGATACCTAAACTTGACATTTTTTCCTAATTTGATACTTAAATTTTTTTGACCCA
Found at i:194254 original size:18 final size:18
Alignment explanation
Indices: 194231--194267 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
194221 TTTGTGATCA
194231 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
194249 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
194267 A
1 A
194268 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:195329 original size:22 final size:22
Alignment explanation
Indices: 195279--195358 Score: 124
Period size: 23 Copynumber: 3.5 Consensus size: 22
195269 CTGGGGAAAT
*
195279 AGTAAGCACACACAGTGCAATCC
1 AGTAGGCACACACAGTGCAAT-C
195302 AGTAGGCACACACAGTGCAATC
1 AGTAGGCACACACAGTGCAATC
*
195324 AGTAGGCACACATAGTGCAAATC
1 AGTAGGCACACACAGTGC-AATC
195347 AGTAGGCACACA
1 AGTAGGCACACA
195359 AGGTGCGGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
22 18 0.33
23 36 0.67
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (22 bp):
AGTAGGCACACACAGTGCAATC
Found at i:195364 original size:23 final size:23
Alignment explanation
Indices: 195275--195396 Score: 121
Period size: 23 Copynumber: 5.4 Consensus size: 23
195265 AGTGCTGGGG
*
195275 AAAT-AGTAAGCACACACAGTGC
1 AAATCAGTAGGCACACACAGTGC
195297 -AATCCAGTAGGCACACACAGTGC
1 AAAT-CAGTAGGCACACACAGTGC
*
195320 -AATCAGTAGGCACACATAGTGC
1 AAATCAGTAGGCACACACAGTGC
195342 AAATCAGTAGGCACACA-AGGTGC
1 AAATCAGTAGGCACACACA-GTGC
* * *
195365 GGAA-CAGTAAGCACACAAAGTGC
1 -AAATCAGTAGGCACACACAGTGC
195388 GAAA-CAGTA
1 -AAATCAGTA
195397 AGCGTGCTAG
Statistics
Matches: 89, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
21 3 0.03
22 19 0.21
23 64 0.72
24 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.13
Consensus pattern (23 bp):
AAATCAGTAGGCACACACAGTGC
Found at i:202026 original size:17 final size:18
Alignment explanation
Indices: 202004--202039 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
201994 TAAATGAGTT
202004 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
202021 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
202039 A
1 A
202040 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:202363 original size:18 final size:18
Alignment explanation
Indices: 202340--202376 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
202330 TTTGTGATCA
202340 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
202358 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
202376 A
1 A
202377 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:205956 original size:46 final size:45
Alignment explanation
Indices: 205906--206011 Score: 112
Period size: 46 Copynumber: 2.3 Consensus size: 45
205896 TTAAATAAAT
*
205906 TTTATTAATTTTAT-AGTTTTTAT-AATTTATTAGA-AATTTTATAATA
1 TTTATTAATTTTATAAGTTTATATCAA-TT-TTA-ATAATTTT-TAATA
205952 TTTA-TAAGTTTTAATAAGTTTATATCAATTTTAATAATTTTTAATA
1 TTTATTAA-TTTT-ATAAGTTTATATCAATTTTAATAATTTTTAATA
*
205998 TTTATAAATTTTAT
1 TTTATTAATTTTAT
206012 GAAAAAATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
45 5 0.10
46 22 0.42
47 13 0.25
48 10 0.19
49 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.58
Consensus pattern (45 bp):
TTTATTAATTTTATAAGTTTATATCAATTTTAATAATTTTTAATA
Found at i:205982 original size:38 final size:36
Alignment explanation
Indices: 205902--205992 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 36
205892 ACTTTTAAAT
*
205902 AAATTTTATTAATTTTATAGTTTTTATAATTTATTAG
1 AAATTTTA-TAATTTTATAGTTTTAATAATTTATTAG
*
205939 AAATTTTATAATATTTATAAGTTTTAATAAGTTTA-TAT
1 AAATTTTATAAT-TTTAT-AGTTTTAATAA-TTTATTAG
*
205977 CAATTTTAATAATTTT
1 AAATTTT-ATAATTTT
205993 TAATATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
36 4 0.09
37 13 0.28
38 21 0.45
39 9 0.19
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (36 bp):
AAATTTTATAATTTTATAGTTTTAATAATTTATTAG
Found at i:208945 original size:21 final size:22
Alignment explanation
Indices: 208921--208984 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 22
208911 AAAACGCATA
*
208921 AAAAAATAACATTC-AAATAAC
1 AAAAAATAACAATCAAAATAAC
208942 -AAAAATAACAATCAAAATAAC
1 AAAAAATAACAATCAAAATAAC
*
208963 AGCAAAAACAACAA-CAAAATAA
1 A--AAAAATAACAATCAAAATAA
208985 TAGAAAAAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 12 0.32
21 7 0.19
23 8 0.22
24 10 0.27
ACGTcount: A:0.70, C:0.16, G:0.02, T:0.12
Consensus pattern (22 bp):
AAAAAATAACAATCAAAATAAC
Found at i:208960 original size:12 final size:11
Alignment explanation
Indices: 208935--208984 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
208925 AATAACATTC
208935 AAATAAC-A-A
1 AAATAACAACA
208944 AAATAACAATCA
1 AAATAACAA-CA
*
208956 AAATAACAGCAA
1 AAATAACAAC-A
*
208968 AAACAACAACA
1 AAATAACAACA
208979 AAATAA
1 AAATAA
208985 TAGAAAAAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 7 0.21
10 1 0.03
11 7 0.21
12 18 0.55
ACGTcount: A:0.72, C:0.16, G:0.02, T:0.10
Consensus pattern (11 bp):
AAATAACAACA
Found at i:208980 original size:23 final size:22
Alignment explanation
Indices: 208942--209038 Score: 97
Period size: 23 Copynumber: 4.3 Consensus size: 22
208932 TTCAAATAAC
* *
208942 AAAAATAACAATCAAAATAACAG
1 AAAAACAACAA-CAAAATAATAG
208965 CAAAAACAACAACAAAATAATAG
1 -AAAAACAACAACAAAATAATAG
* * *
208988 AAAAAGCAGCACCAAAATAGTA-
1 AAAAA-CAACAACAAAATAATAG
* *
209010 AAAAACAACACCAAAATAATAA
1 AAAAACAACAACAAAATAATAG
209032 AAAAACA
1 AAAAACA
209039 GAACCAAAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
21 14 0.22
22 17 0.27
23 23 0.36
24 10 0.16
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAAACAACAACAAAATAATAG
Found at i:209012 original size:20 final size:20
Alignment explanation
Indices: 208966--209038 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
208956 AAATAACAGC
* *
208966 AAAAACAACAACAAAATAAT
1 AAAAACAACACCAAAATAGT
*
208986 AGAAAAAGCAGCACCAAAATAGT
1 --AAAAA-CAACACCAAAATAGT
*
209009 AAAAAACAACACCAAAATAAT
1 -AAAAACAACACCAAAATAGT
209030 AAAAA-AACA
1 AAAAACAACA
209039 GAACCAAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.09
20 5 0.11
21 13 0.30
22 10 0.23
23 12 0.27
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.08
Consensus pattern (20 bp):
AAAAACAACACCAAAATAGT
Found at i:209013 original size:22 final size:22
Alignment explanation
Indices: 208935--209099 Score: 122
Period size: 22 Copynumber: 7.5 Consensus size: 22
208925 AATAACATTC
*
208935 AAATAACAAAAATAACA--ATCA
1 AAATAACAAAAA-AACAGCACCA
* * *
208956 AAATAACAGCAAAAACAACAACA
1 AAATAACA-AAAAAACAGCACCA
* *
208979 AAATAATAGAAAAAGCAGCACCA
1 AAATAACA-AAAAAACAGCACCA
** *
209002 AAAT-AGTAAAAAACAACACCA
1 AAATAACAAAAAAACAGCACCA
* *
209023 AAATAATAAAAAAACAGAACCA
1 AAATAACAAAAAAACAGCACCA
* *
209045 AAACAACAAAAAAATAGCACCA
1 AAATAACAAAAAAACAGCACCA
* *
209067 AAACAGCAAAAAAACA-CACCAA
1 AAATAACAAAAAAACAGCACC-A
*
209089 AAATAGCAAAA
1 AAATAACAAAA
209100 GACAGCAATA
Statistics
Matches: 117, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
21 32 0.27
22 60 0.51
23 25 0.21
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.07
Consensus pattern (22 bp):
AAATAACAAAAAAACAGCACCA
Found at i:209837 original size:11 final size:11
Alignment explanation
Indices: 209811--209843 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
209801 AGTTACACAA
*
209811 AATTTTAAAA-
1 AATTATAAAAT
209821 AATTATAAAAT
1 AATTATAAAAT
209832 AATTATAAAAT
1 AATTATAAAAT
209843 A
1 A
209844 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTATAAAAT
Found at i:213536 original size:19 final size:19
Alignment explanation
Indices: 213512--213554 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
213502 AAACATAAAT
213512 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
213531 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
213550 TAAAT
1 TAAAT
213555 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:216000 original size:20 final size:18
Alignment explanation
Indices: 215953--216001 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
215943 CAATATAAAC
215953 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
215970 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
215990 ATTAAATTAATA
1 ATTAAATTAATA
216002 AAATACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:218616 original size:19 final size:19
Alignment explanation
Indices: 218594--218630 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
218584 CAATGATCAA
218594 ATTTAAAAAAAATTAAAAG
1 ATTTAAAAAAAATTAAAAG
*
218613 ATTTAAAAAAATTTAAAA
1 ATTTAAAAAAAATTAAAA
218631 ACATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
ATTTAAAAAAAATTAAAAG
Found at i:218656 original size:10 final size:10
Alignment explanation
Indices: 218592--218641 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
218582 AACAATGATC
218592 AAATTTAAAA
1 AAATTTAAAA
*
218602 AAAATT-AAA
1 AAATTTAAAA
*
218611 AGATTTAAAA
1 AAATTTAAAA
218621 AAATTTAAAA
1 AAATTTAAAA
*
218631 ACATATTAAAA
1 AAAT-TTAAAA
218642 CAAAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
9 7 0.21
10 20 0.61
11 6 0.18
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAATTTAAAA
Found at i:237045 original size:3 final size:3
Alignment explanation
Indices: 237037--237063 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
237027 AAGTAACAAA
237037 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
237064 TTTTGATATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:241218 original size:3 final size:3
Alignment explanation
Indices: 241210--241275 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
241200 TGCTAGCTAC
*
241210 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
241258 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
241276 TTACACTATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.