Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020980.1 Corchorus olitorius cultivar O-4 contig21013, 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: 71083
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6900 original size:115 final size:115
Alignment explanation
Indices: 6771--6989 Score: 384
Period size: 115 Copynumber: 1.9 Consensus size: 115
6761 AAATAAAATA
*
6771 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATTAAATAAAAGTAGAGTTTTTG
1 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATTAAATAAAAGTAGAGTTTTTA
*
6836 ATACAGTAAAACTATAATAGTTTAAACGATAGCACTTAAGAAATATGTTT
66 ATACAGTAAAACTATAATAGTTTAAACAATAGCACTTAAGAAATATGTTT
* * *
6886 GTAAAATGGTAAAAATAGAAACAGTTATAAATATAAGATTTAATTAAATAAAAGTATAGTTTTTA
1 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATTAAATAAAAGTAGAGTTTTTA
*
6951 ATACAGTAAAACTATAATAGTTTAAACAATGGCACTTAA
66 ATACAGTAAAACTATAATAGTTTAAACAATAGCACTTAA
6990 AAAAACAATT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 98 1.00
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (115 bp):
GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATTAAATAAAAGTAGAGTTTTTA
ATACAGTAAAACTATAATAGTTTAAACAATAGCACTTAAGAAATATGTTT
Found at i:7275 original size:104 final size:106
Alignment explanation
Indices: 7107--7397 Score: 464
Period size: 106 Copynumber: 2.8 Consensus size: 106
7097 TAATTATCTA
* ** * * *
7107 ACCCTTAAAATAAAATTTTAATTTTAATTT-GTGCTAAACTTAGTG-AATTAGTTATATGTTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
* *
7170 TTTCTGAAACCCTATAACAAT-ATTATTAATTTTGGAATTT
66 TTTCTAAAACCCTATAACAATAATTATTAATTTTGAAATTT
7210 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA-TTTTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
7274 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTTTGAAATTT
7316 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
*
7381 TTTCTAAAACTCTATAA
66 TTTCTAAAACCCTATAA
7398 TAAAAAACCT
Statistics
Matches: 174, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
103 27 0.16
104 44 0.25
105 5 0.03
106 70 0.40
107 28 0.16
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTTTGAAATTT
Found at i:7447 original size:106 final size:106
Alignment explanation
Indices: 7107--7432 Score: 421
Period size: 106 Copynumber: 3.1 Consensus size: 106
7097 TAATTATCTA
* ** * * *
7107 ACCCTTAAAATAAAATTTTAATTTTAATTT-GTGCTAAACTTAGTG-AATTAGTTATATGTTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA-TTTTATATTTTA
* * * **
7170 TTTCTGAAACCCTATAAC--AATATTATTAATTTTGGAATTT
65 TTTCTAAAACCCTATAACAAAAAACTATTAATTTTCAAATTT
7210 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTATTTTATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTATTTTATATTTTAT
* * *
7275 TTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTCTAAAACCCTATAACAAAAAACTATTAATTTTCAAATTT
7316 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA-TTTTATATTTTA
* *
7381 TTTCTAAAACTCTATAATAAAAAACCT-TTAA-TTTCATAATTT
65 TTTCTAAAACCCTATAACAAAAAA-CTATTAATTTTCA-AATTT
*
7423 ACTCTTAAAA
1 ACCCTTAAAA
7433 ATTAAATTTC
Statistics
Matches: 200, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
103 27 0.14
104 41 0.20
105 5 0.03
106 75 0.38
107 51 0.25
108 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTATTTTATATTTTAT
TTCTAAAACCCTATAACAAAAAACTATTAATTTTCAAATTT
Found at i:7492 original size:15 final size:15
Alignment explanation
Indices: 7472--7501 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7462 AATAAAAACT
*
7472 AAAAAAGAATGAAAA
1 AAAAAAGAAAGAAAA
7487 AAAAAAGAAAGAAAA
1 AAAAAAGAAAGAAAA
7502 GAGAAGACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAGAAAA
Found at i:9178 original size:34 final size:35
Alignment explanation
Indices: 9121--9194 Score: 132
Period size: 34 Copynumber: 2.1 Consensus size: 35
9111 GCCTAACCCT
*
9121 AAATTCAAAAATTTAGGGTATAATAGGCAATTCAA
1 AAATTCAAAAATTAAGGGTATAATAGGCAATTCAA
9156 AAATTCAAAAA-TAAGGGTATAATAGGCAATTCAA
1 AAATTCAAAAATTAAGGGTATAATAGGCAATTCAA
9190 AAATT
1 AAATT
9195 TTAGAAAGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 27 0.71
35 11 0.29
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (35 bp):
AAATTCAAAAATTAAGGGTATAATAGGCAATTCAA
Found at i:9330 original size:21 final size:21
Alignment explanation
Indices: 9280--9383 Score: 82
Period size: 21 Copynumber: 4.9 Consensus size: 21
9270 TGAATATTTT
* *
9280 TATGAAATTTTGATTACTACCC
1 TATGAAATTTTGATAACCA-CC
*
9302 TATTAAATTTTGATAACCACC
1 TATGAAATTTTGATAACCACC
* ** *
9323 TATGAAATTTTCATAATTACT
1 TATGAAATTTTGATAACCACC
* * * *
9344 TATGAAATTGTGATAAACTCGA
1 TATGAAATTTTGATAACCAC-C
*
9366 TATGAAACTTTGATAACC
1 TATGAAATTTTGATAACC
9384 TAATTATAAA
Statistics
Matches: 64, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
21 33 0.52
22 31 0.48
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACCACC
Found at i:11060 original size:20 final size:20
Alignment explanation
Indices: 11033--11080 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
11023 ACCGACCGCC
*
11033 TAATATATA-TAATAT-TTT
1 TAATATATATTAATATGTTA
*
11051 TAATATATATTTATATGTTA
1 TAATATATATTAATATGTTA
11071 TAATATATAT
1 TAATATATAT
11081 CTGATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
19 5 0.19
20 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TAATATATATTAATATGTTA
Found at i:15121 original size:19 final size:19
Alignment explanation
Indices: 15094--15138 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
15084 ATTGCTAATG
15094 GCTGCTGGTATATAATATT
1 GCTGCTGGTATATAATATT
*
15113 GCTGTTGGTATATAATATT
1 GCTGCTGGTATATAATATT
15132 GCTGCTG
1 GCTGCTG
15139 CTTGCTACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.42
Consensus pattern (19 bp):
GCTGCTGGTATATAATATT
Found at i:16183 original size:16 final size:16
Alignment explanation
Indices: 16164--16235 Score: 92
Period size: 16 Copynumber: 4.6 Consensus size: 16
16154 CGGGCTCGGG
*
16164 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTATTTT
16180 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* * *
16196 CGGGCTCGGTTA-TGT
1 CGGGTTCGGGTATTTT
16211 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
16227 CGGATTCGG
1 CGGGTTCGG
16236 TCTCGGGTAG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
15 12 0.26
16 35 0.74
ACGTcount: A:0.06, C:0.15, G:0.39, T:0.40
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:16257 original size:23 final size:23
Alignment explanation
Indices: 16225--16282 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
16215 TTCGGGTATT
* * *
16225 TTCGGATTCGGTCTCGGGTAGGG
1 TTCGGGTTCGGGCTCAGGTAGGG
*
16248 TTCGGGTTCGGGCTCAGGTCGGG
1 TTCGGGTTCGGGCTCAGGTAGGG
*
16271 TTCGGGCTCGGG
1 TTCGGGTTCGGG
16283 TTTGATTTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.05, C:0.21, G:0.47, T:0.28
Consensus pattern (23 bp):
TTCGGGTTCGGGCTCAGGTAGGG
Found at i:16432 original size:13 final size:12
Alignment explanation
Indices: 16409--16455 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
16399 AAGTTTATTG
16409 ATAATATATAAT
1 ATAATATATAAT
16421 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
16434 ATAACAT-TATT
1 ATAATATATAAT
16445 ATCAATATATA
1 AT-AATATATA
16456 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:16744 original size:31 final size:30
Alignment explanation
Indices: 16709--16780 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
16699 TAAATTATTG
*
16709 CAAATTAAAACAATCTAAG-CATTAAATTAAA
1 CAAATTAAAA-AATCAAAGTC-TTAAATTAAA
*
16740 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA--AAAATCAAAGTCTTAAATTAAA
16771 CAAATTAAAA
1 CAAATTAAAA
16781 GCTGATAGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
30 5 0.14
31 24 0.69
32 6 0.17
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.26
Consensus pattern (30 bp):
CAAATTAAAAAATCAAAGTCTTAAATTAAA
Found at i:17101 original size:21 final size:22
Alignment explanation
Indices: 17060--17101 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
17050 CTTTTTATAT
*
17060 TGATCAATTAATTAATTAATTG
1 TGATCAATTAATTAATAAATTG
17082 TGATC-ATT-ATTATATAAATT
1 TGATCAATTAATTA-ATAAATT
17102 TTATATATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (22 bp):
TGATCAATTAATTAATAAATTG
Found at i:17251 original size:17 final size:17
Alignment explanation
Indices: 17229--17268 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17219 CAGGTTTGGA
17229 CTCGGG-TCGGGATCGGG
1 CTCGGGATCGGG-TCGGG
17246 CTCGGGATCGGGTCGGG
1 CTCGGGATCGGGTCGGG
*
17263 TTCGGG
1 CTCGGG
17269 CTGCCTCGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.05, C:0.23, G:0.53, T:0.20
Consensus pattern (17 bp):
CTCGGGATCGGGTCGGG
Found at i:17261 original size:11 final size:11
Alignment explanation
Indices: 17230--17268 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
17220 AGGTTTGGAC
17230 TCGGGTCGGGA
1 TCGGGTCGGGA
17241 TCGGGCTCGGGA
1 TCGGG-TCGGGA
*
17253 TCGGGTCGGGT
1 TCGGGTCGGGA
17264 TCGGG
1 TCGGG
17269 CTGCCTCGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.05, C:0.21, G:0.54, T:0.21
Consensus pattern (11 bp):
TCGGGTCGGGA
Found at i:18054 original size:9 final size:9
Alignment explanation
Indices: 18040--18064 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18030 TTTCGCAGTC
18040 AAAAATATA
1 AAAAATATA
18049 AAAAATATA
1 AAAAATATA
18058 AAAAATA
1 AAAAATA
18065 ATGACTTCAT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATATA
Found at i:26517 original size:41 final size:41
Alignment explanation
Indices: 26465--26542 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
26455 ACCTTACCTT
* *
26465 TTTTTTTTCTTTCTTAAATGAAATTTTAACTTATTGATACC
1 TTTTTCTTCTTTCTTAAATAAAATTTTAACTTATTGATACC
26506 TTTTTCTTCTTTCTTAAATAAAATTTTAACTTATTGA
1 TTTTTCTTCTTTCTTAAATAAAATTTTAACTTATTGA
26543 AATTTTTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (41 bp):
TTTTTCTTCTTTCTTAAATAAAATTTTAACTTATTGATACC
Found at i:29598 original size:53 final size:54
Alignment explanation
Indices: 29453--30281 Score: 1063
Period size: 54 Copynumber: 15.6 Consensus size: 54
29443 TTACTACTAA
* * * *
29453 TTACTGCTTACTTTTACTCTTTAGTTTAATTAGCCAGAATTAAACTAGTTACTGT
1 TTACTCCTT-CTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
**
29508 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAAAAACTGT
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
29562 TTACTCCTT-TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
*
29615 TTACTCCTT-TTTTACTATTTAGTTTAATTACTCAGAATTAAACTAATTACTGT
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
* *
29668 TTACTCCTT-TTTTACTCTTTAGTTTAATTATCCAGAATTAAAC----TACTGT
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
* * * * *
29717 TTACT-CTTTTTTTACTATTTAGTTTAATTACCCGGAATTAAACTATTTTCTGC
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
* * * * * *
29770 TTACTTCTTCTCTTACTCTTTAGTTTAATTACCCAAAATTAAACTAGTTATTGT
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
29824 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
*
29878 TTACTCCTT-TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTATTGT
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
* * * * * *
29931 TTACTGCTT-TTTTACTATTTAGTTTAATTACCCGGAATT-AACTATTTTCGGC
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
* *
29983 TTACTCCTT-TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAGTTACCGT
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
* ** * * *
30036 GTACTCCTTCTTTTACTATTTAGTTTAATTACCTGGAATTAAACTATTTTCTGC
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
* * * * * *
30090 TTACTTCTTCTCTTACTCTTTAGTTTAATTACCCAAAATTAAACTAGTTACTGC
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
* * * * *
30144 TTACTCCTTCTTTTACTATTTAGTTTAATTATCCGGAATTAAACTATTTTCTGC
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
* * * * *
30198 TTAATTCTTCTCTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTT-CTAT
1 TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-TTACTGT
* * *
30252 TTATTTCTTCTTTTACTCTTTAGTTTAATT
1 TTACTCCTTCTTTTACTATTTAGTTTAATT
30282 GTTCTGATTT
Statistics
Matches: 684, Mismatches: 81, Indels: 19
0.87 0.10 0.02
Matches are distributed among these distances:
48 3 0.00
49 42 0.06
52 45 0.07
53 240 0.35
54 344 0.50
55 10 0.01
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (54 bp):
TTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACTGT
Found at i:30532 original size:29 final size:29
Alignment explanation
Indices: 30500--30577 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
30490 AGGATCACCT
*
30500 AGGGCCATTTTGGTCATTTTTAAAAACCC
1 AGGGGCATTTTGGTCATTTTTAAAAACCC
* ** * **
30529 AGGGGTATTTTGGTCATTTTTGCATATTC
1 AGGGGCATTTTGGTCATTTTTAAAAACCC
30558 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
30578 AAGTTCACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTAAAAACCC
Found at i:36123 original size:41 final size:41
Alignment explanation
Indices: 36036--36215 Score: 222
Period size: 41 Copynumber: 4.4 Consensus size: 41
36026 ACAATTTATG
* * * *
36036 GTGTCAATA-GTAATTATAATTTACTAGAGTAAC-ACTTCTA
1 GTGTCAA-AGGTAATTTTAATTTACCAAAGTGACAACTTCTA
36076 GTGTCAAAGGTAATTTTAATTTACCAAAGTGACAACTTCTA
1 GTGTCAAAGGTAATTTTAATTTACCAAAGTGACAACTTCTA
*
36117 GTGTCAAAGGTAATTTTAATTTACCAAGGTGACAACTTCTA
1 GTGTCAAAGGTAATTTTAATTTACCAAAGTGACAACTTCTA
* * * *
36158 GTGTCAGCA-GTAATTTTAATTTACCGAAGTGATAACTTCTG
1 GTGTCA-AAGGTAATTTTAATTTACCAAAGTGACAACTTCTA
* *
36199 GTATCAAAGATAATTTT
1 GTGTCAAAGGTAATTTT
36216 CAATATTATT
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 28 0.23
41 93 0.76
42 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (41 bp):
GTGTCAAAGGTAATTTTAATTTACCAAAGTGACAACTTCTA
Found at i:40279 original size:21 final size:21
Alignment explanation
Indices: 40228--40271 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
40218 ATGCTTTAGA
* *
40228 TTTAATTTAATTTGTTTTATT
1 TTTAGTTTAAATTGTTTTATT
40249 TTTAGTTTAAATTGTTTTATT
1 TTTAGTTTAAATTGTTTTATT
40270 TT
1 TT
40272 CTTTTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTAGTTTAAATTGTTTTATT
Found at i:40281 original size:20 final size:20
Alignment explanation
Indices: 40228--40284 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
40218 ATGCTTTAGA
*
40228 TTTAATTTAATTTGTTTTATT
1 TTTATTTTAA-TTGTTTTATT
*
40249 TTTAGTTTAAATTGTTTTATT
1 TTTA-TTTTAATTGTTTTATT
40270 TTCT-TTTTAATTGTT
1 TT-TATTTTAATTGTT
40285 CTGTTTAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 10 0.32
21 16 0.52
22 5 0.16
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (20 bp):
TTTATTTTAATTGTTTTATT
Found at i:43608 original size:26 final size:26
Alignment explanation
Indices: 43578--43634 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
43568 AAAATTGGAT
43578 AGTTCCGGTTCTACATGGACGGATTC
1 AGTTCCGGTTCTACATGGACGGATTC
*
43604 AGTTCCGGTTCTACATGGACGGTTTC
1 AGTTCCGGTTCTACATGGACGGATTC
43630 AGTTC
1 AGTTC
43635 GATTCTTCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (26 bp):
AGTTCCGGTTCTACATGGACGGATTC
Found at i:51256 original size:2 final size:2
Alignment explanation
Indices: 51249--51277 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51239 TTGTGATAAT
51249 CA CA 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 CA CA C
51278 TATTTGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:57895 original size:22 final size:22
Alignment explanation
Indices: 57844--58048 Score: 90
Period size: 22 Copynumber: 9.2 Consensus size: 22
57834 GTGATTTTTT
57844 TTATCAAAATTTCATA-ACG-TGG
1 TTATCAAAATTTCATAGA-GAT-G
*
57866 TTACCAAAATTTCATAGAGATG
1 TTATCAAAATTTCATAGAGATG
* * *
57888 TTATCAAAATTTTAAAGCA-AGG
1 TTATCAAAATTTCATAG-AGATG
57910 TTATCAAAAATTTCCA-ATGAGA--
1 TTATC-AAAATTT-CATA-GAGATG
* *
57932 TTATCAAAATTTTTCACA-AAATGTGG
1 TTATCAAAA--TTTCATAGAGA--T-G
* *
57958 TTATCAAAATTTTATATG-GAGG
1 TTATCAAAATTTCATA-GAGATG
*
57980 TTA-C-AAATTTCATAG-TATG
1 TTATCAAAATTTCATAGAGATG
*
57999 ATTATCAAAATTTCATAGAGAGG
1 -TTATCAAAATTTCATAGAGATG
* * * *
58022 TTAACAAAATTTTATAGGGAAG
1 TTATCAAAATTTCATAGAGATG
58044 TTATC
1 TTATC
58049 GTAGTTTTTA
Statistics
Matches: 141, Mismatches: 21, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
19 3 0.02
20 12 0.09
21 8 0.06
22 82 0.58
23 18 0.13
24 8 0.06
25 1 0.01
26 9 0.06
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGATG
Found at i:58211 original size:22 final size:22
Alignment explanation
Indices: 58129--58696 Score: 275
Period size: 22 Copynumber: 25.7 Consensus size: 22
58119 AGAGAGAGAC
*
58129 TATCAAAATTTCATAGTG-TGTT
1 TATCAAAATTTCATAGGGATG-T
* * * *
58151 TACCAAAATTTCATATGAATAT
1 TATCAAAATTTCATAGGGATGT
* * *
58173 TATTTAAGATCTCATAGGGATGT
1 TA-TCAAAATTTCATAGGGATGT
**
58196 TATCAAAATTTCATA-GTTTAGT
1 TATCAAAATTTCATAGGGAT-GT
*
58218 TTTCAAAATTTCATAGGG--GT
1 TATCAAAATTTCATAGGGATGT
* *
58238 CATCAAAATTTCATA-GTATGGT
1 TATCAAAATTTCATAGGGAT-GT
**
58260 TATC--AATCACATAGGGA-G-
1 TATCAAAATTTCATAGGGATGT
* ** **
58278 -ATTAAAATTTCAT-GATTAACT
1 TATCAAAATTTCATAG-GGATGT
** *
58299 TAT-AAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGGGATGT
* ** * *
58320 TATCAAAAATTTTATTTGAAGGT
1 TATC-AAAATTTCATAGGGATGT
* *
58343 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGGATG-T
* *
58366 TATCAAAATTTTATAGGAATGTT
1 TATCAAAATTTCATAGGGATG-T
* *
58389 TATCAAAATTTCATAGTGAGGT
1 TATCAAAATTTCATAGGGATGT
* *
58411 TATCAAAATTTTATA-GGATCCTT
1 TATCAAAATTTCATAGGGAT--GT
*
58434 TATCAAAATTTCATAGGGAGGT
1 TATCAAAATTTCATAGGGATGT
* *** *
58456 TAACAAAATTTCATAATTAGGT
1 TATCAAAATTTCATAGGGATGT
* ** * *
58478 TATAAAAAAATCATAGGTAGGT
1 TATCAAAATTTCATAGGGATGT
* *
58500 TATCAAAATTTCATATGGAGGTT
1 TATCAAAATTTCATAGGGATG-T
* * *
58523 TATCAAAATTTTATATGAATGTT
1 TATCAAAATTTCATAGGGATG-T
* *
58546 TATCAAGATTTCATAGTGA-GAT
1 TATCAAAATTTCATAGGGATG-T
* * *
58568 TATTAAAATTTCATAAGAATGTT
1 TATCAAAATTTCATAGGGATG-T
* *
58591 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGGATG-T
* **
58614 TATCAAAATTTTATAGAAATGTT
1 TATCAAAATTTCATAGGGATG-T
*
58637 TATCAAAATTTCAT-GGTGAGGT
1 TATCAAAATTTCATAGG-GATGT
* *
58659 TATCACAATTTCATAGTGATGT
1 TATCAAAATTTCATAGGGATGT
* *
58681 TTTCACAATTTCATAG
1 TATCAAAATTTCATAG
58697 TGTGATTATT
Statistics
Matches: 415, Mismatches: 106, Indels: 50
0.73 0.19 0.09
Matches are distributed among these distances:
17 2 0.00
18 1 0.00
19 9 0.02
20 22 0.05
21 19 0.05
22 181 0.44
23 178 0.43
24 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
TATCAAAATTTCATAGGGATGT
Found at i:58342 original size:23 final size:22
Alignment explanation
Indices: 58310--58674 Score: 243
Period size: 23 Copynumber: 16.2 Consensus size: 22
58300 ATAAAAAATC
*
58310 ATAGGGAGGTTATCAAAAATTTT
1 ATAGGAAGGTTATC-AAAATTTT
**
58333 ATTTGAAGGTTATCAAAATTTT
1 ATAGGAAGGTTATCAAAATTTT
*
58355 ATAGGGAGGTTTATCAAAATTTT
1 ATAGGAAGG-TTATCAAAATTTT
* *
58378 ATAGGAATGTTTATCAAAATTTC
1 ATAGGAA-GGTTATCAAAATTTT
58401 ATAGTG-AGGTTATCAAAATTTT
1 ATAG-GAAGGTTATCAAAATTTT
*** *
58423 ATAGGATCCTTTATCAAAATTTC
1 ATAGGA-AGGTTATCAAAATTTT
* * *
58446 ATAGGGAGGTTAACAAAATTTC
1 ATAGGAAGGTTATCAAAATTTT
*** * ** *
58468 ATAATTAGGTTATAAAAAAATC
1 ATAGGAAGGTTATCAAAATTTT
* *
58490 ATAGGTAGGTTATCAAAATTTC
1 ATAGGAAGGTTATCAAAATTTT
58512 ATATGG-AGGTTTATCAAAATTTT
1 ATA-GGAAGG-TTATCAAAATTTT
* * * *
58535 ATATGAATGTTTATCAAGATTTC
1 ATAGGAA-GGTTATCAAAATTTT
* * *
58558 ATAGTG-AGATTATTAAAATTTC
1 ATAG-GAAGGTTATCAAAATTTT
* *
58580 ATAAGAATGTTTATCAAAATTTT
1 ATAGGAA-GGTTATCAAAATTTT
*
58603 ATAGGGAGGTTTATCAAAATTTT
1 ATAGGAAGG-TTATCAAAATTTT
* * *
58626 ATAGAAATGTTTATCAAAATTTC
1 ATAGGAA-GGTTATCAAAATTTT
* * *
58649 AT-GGTGAGGTTATCACAATTTC
1 ATAGG-AAGGTTATCAAAATTTT
58671 ATAG
1 ATAG
58675 TGATGTTTTC
Statistics
Matches: 270, Mismatches: 56, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
21 2 0.01
22 115 0.43
23 148 0.55
24 5 0.02
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
ATAGGAAGGTTATCAAAATTTT
Found at i:58361 original size:45 final size:44
Alignment explanation
Indices: 58129--58674 Score: 274
Period size: 45 Copynumber: 12.4 Consensus size: 44
58119 AGAGAGAGAC
* * * * * **
58129 TATCAAAATTTCATAGTGTGTTTACCAAAATTTCATATGAATAT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTTATATGAAGGT
* * * * * **
58173 TATTTAAGATCTCATAGGGATGTTATCAAAATTTCATAGTTTA-GT
1 TA-TCAAAATTTCATAGGGAGGTTATCAAAATTTTATA-TGAAGGT
* * * *
58218 TTTCAAAATTTCATA-GG-GGTCATCAAAATTTCATA-GTATGGT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTTATATG-AAGGT
** * * * *
58260 TATC--AATCACATAGGGA-G--ATTAAAATTTCATGATTAA-CT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTTAT-ATGAAGGT
** *
58299 TAT-AAAAAATCATAGGGAGGTTATCAAAAATTTTATTTGAAGGT
1 TATCAAAATTTCATAGGGAGGTTATC-AAAATTTTATATGAAGGT
* * *
58343 TATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAATGTT
1 TATCAAAATTTCATAGGGAGG-TTATCAAAATTTTATATGAA-GGT
* * ***
58389 TATCAAAATTTCATAGTGAGGTTATCAAAATTTTATAGGATCCTT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTTATATGA-AGGT
* * *
58434 TATCAAAATTTCATAGGGAGGTTAACAAAATTTCATAAT-TAGGT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTTAT-ATGAAGGT
* ** * * *
58478 TATAAAAAAATCATAGGTAGGTTATCAAAATTTCATATGGAGGTT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTTATATGAAGG-T
* * * * * * *
58523 TATCAAAATTTTATATGAATGTTTATCAAGATTTCATAGTG-AGAT
1 TATCAAAATTTCATAGGGA-GGTTATCAAAATTTTATA-TGAAGGT
* * * * * *
58568 TATTAAAATTTCATAAGAATGTTTATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGGA-GGTTATCAAAATTTTATATGAAGG-T
* ** * * *
58614 TATCAAAATTTTATAGAAATGTTTATCAAAATTTCATGGTG-AGGT
1 TATCAAAATTTCATAGGGA-GGTTATCAAAATTTTAT-ATGAAGGT
*
58659 TATCACAATTTCATAG
1 TATCAAAATTTCATAG
58675 TGATGTTTTC
Statistics
Matches: 391, Mismatches: 84, Indels: 53
0.74 0.16 0.10
Matches are distributed among these distances:
39 16 0.04
40 19 0.05
41 4 0.01
42 21 0.05
43 9 0.02
44 61 0.16
45 175 0.45
46 83 0.21
47 3 0.01
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (44 bp):
TATCAAAATTTCATAGGGAGGTTATCAAAATTTTATATGAAGGT
Found at i:58505 original size:157 final size:158
Alignment explanation
Indices: 58339--58624 Score: 450
Period size: 157 Copynumber: 1.8 Consensus size: 158
58329 TTTTATTTGA
*
58339 AGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAATGTTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATAGGGAGGTTTATCAAAATTTTATAGGAATGTTTATCAAAATTTCATA
* * *
58404 GTGAGGTTATCAAAATTTTAT-AGGATCCTTTATCAAAATTTCATAGGGAGG-TTAACAAAATTT
66 GTGAGATTATCAAAATTTCATAAGAAT-CTTTATCAAAATTTCATAGGGAGGTTTAACAAAATTT
58467 CATAATTAGGTTATAAAAAAATCATAGGT
130 CATAATTAGGTTATAAAAAAATCATAGGT
* * *
58496 AGGTTATCAAAATTTCATATGGAGGTTTATCAAAATTTTATATGAATGTTTATCAAGATTTCATA
1 AGGTTATCAAAATTTCATAGGGAGGTTTATCAAAATTTTATAGGAATGTTTATCAAAATTTCATA
* * * *
58561 GTGAGATTATTAAAATTTCATAAGAATGTTTATCAAAATTTTATAGGGAGGTTTATCAAAATTT
66 GTGAGATTATCAAAATTTCATAAGAATCTTTATCAAAATTTCATAGGGAGGTTTAACAAAATTT
58625 TATAGAAATG
Statistics
Matches: 116, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
157 101 0.87
158 15 0.13
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (158 bp):
AGGTTATCAAAATTTCATAGGGAGGTTTATCAAAATTTTATAGGAATGTTTATCAAAATTTCATA
GTGAGATTATCAAAATTTCATAAGAATCTTTATCAAAATTTCATAGGGAGGTTTAACAAAATTTC
ATAATTAGGTTATAAAAAAATCATAGGT
Found at i:58681 original size:45 final size:45
Alignment explanation
Indices: 58339--58856 Score: 237
Period size: 45 Copynumber: 11.4 Consensus size: 45
58329 TTTTATTTGA
* * * * *
58339 AGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGG-A
1 AGGTTATCAAAATTTCATAGTGATGTTTATCAAAATTTCAT-GGTG
* * *
58384 ATGTTTATCAAAATTTCATAGTGA-GGTTATCAAAATTTTATAGGAT-
1 A-GGTTATCAAAATTTCATAGTGATGTTTATCAAAATTTCAT-GG-TG
*** * * * ** *
58430 CCTTTATCAAAATTTCATAGGGA-GGTTAACAAAATTTCATAATT
1 AGGTTATCAAAATTTCATAGTGATGTTTATCAAAATTTCATGGTG
* ** * *
58474 AGGTTATAAAAAAATCATAG-G-TAGGTTATCAAAATTTCAT-ATGG
1 AGGTTATCAAAATTTCATAGTGAT-GTTTATCAAAATTTCATGGT-G
* * *
58518 AGGTTTATCAAAATTTTATA-TGAATGTTTATCAAGATTTCATAGTG
1 AGG-TTATCAAAATTTCATAGTG-ATGTTTATCAAAATTTCATGGTG
* * * *
58564 AGATTATTAAAATTTCATAAG-AATGTTTATCAAAATTTTATAGG-G
1 AGGTTATCAAAATTTCAT-AGTGATGTTTATCAAAATTTCAT-GGTG
* **
58609 AGGTTTATCAAAATTTTATAGAAATGTTTATCAAAATTTCATGGTG
1 AGG-TTATCAAAATTTCATAGTGATGTTTATCAAAATTTCATGGTG
* * *
58655 AGGTTATCACAATTTCATAGTGATGTTT-TCACAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTGATGTTTATCAAAATTTCATGGTG
* * * * * *
58699 TGATTATTAACATTTTACA-ATGTGATTACGAGGTTATCAAAATTTCATGGTC
1 AGGTTATCAA-AATTT-CATA-GTGA-T----GTTTATCAAAATTTCATGGTG
* * * * * *
58751 TGCTTATCAACATTTCACAAG-GA-GGTTATCAAAATTTCAT--AG
1 AGGTTATCAAAATTTCA-TAGTGATGTTTATCAAAATTTCATGGTG
* *
58793 ATGGTTATCAAAA-TTCATTAG-GA-GGTTATCAAAATTTCATAGTG
1 A-GGTTATCAAAATTTCA-TAGTGATGTTTATCAAAATTTCATGGTG
* * *
58837 AGGTAATTAAAATTCCATAG
1 AGGTTATCAAAATTTCATAG
58857 GAAGGTTCTT
Statistics
Matches: 373, Mismatches: 67, Indels: 68
0.73 0.13 0.13
Matches are distributed among these distances:
42 25 0.07
43 25 0.07
44 75 0.20
45 131 0.35
46 81 0.22
47 3 0.01
50 4 0.01
51 7 0.02
52 22 0.06
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (45 bp):
AGGTTATCAAAATTTCATAGTGATGTTTATCAAAATTTCATGGTG
Found at i:58779 original size:22 final size:21
Alignment explanation
Indices: 58754--58863 Score: 116
Period size: 22 Copynumber: 5.1 Consensus size: 21
58744 CATGGTCTGC
* *
58754 TTATCAACATTTCACAAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
58776 TTATCAAAATTTCATA-GATGG
1 TTATCAAAATTTCATAGGA-GG
58797 TTATCAAAA-TTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
58818 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAG-GAGG
* * *
58840 TAATTAAAATTCCATAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
58862 TT
1 TT
58864 CTTGAAATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.08
21 29 0.38
22 41 0.54
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:58800 original size:21 final size:20
Alignment explanation
Indices: 58728--58834 Score: 99
Period size: 22 Copynumber: 5.0 Consensus size: 20
58718 ATGTGATTAC
*
58728 GAGGTTATCAAAATTTCATG
1 GAGGTTATCAAAATTTCATA
* * * *
58748 GTCTGCTTATCAACATTTCACAA
1 G--AGGTTATCAAAATTTCA-TA
58771 GGAGGTTATCAAAATTTCATA
1 -GAGGTTATCAAAATTTCATA
58792 GATGGTTATCAAAA-TTCATTA
1 GA-GGTTATCAAAATTTCA-TA
58813 GGAGGTTATCAAAATTTCATA
1 -GAGGTTATCAAAATTTCATA
58834 G
1 G
58835 TGAGGTAATT
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
20 8 0.11
21 27 0.39
22 34 0.49
24 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (20 bp):
GAGGTTATCAAAATTTCATA
Found at i:58829 original size:42 final size:44
Alignment explanation
Indices: 58723--58835 Score: 149
Period size: 42 Copynumber: 2.6 Consensus size: 44
58713 TTACAATGTG
* * * *
58723 ATTACGAGGTTATCAAAATTTCATGGTCTGCTTATCAACATTTC
1 ATTAGGAGGTTATCAAAATTTCATAGTATGCTTATCAACAATTC
** *
58767 ACAAGGAGGTTATCAAAATTTCATAG-ATGGTTATCAA-AATTC
1 ATTAGGAGGTTATCAAAATTTCATAGTATGCTTATCAACAATTC
58809 ATTAGGAGGTTATCAAAATTTCATAGT
1 ATTAGGAGGTTATCAAAATTTCATAGT
58836 GAGGTAATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 28 0.47
43 9 0.15
44 22 0.37
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (44 bp):
ATTAGGAGGTTATCAAAATTTCATAGTATGCTTATCAACAATTC
Found at i:58925 original size:22 final size:21
Alignment explanation
Indices: 58900--58961 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
58890 TGCATAATAT
58900 TGTTATCAAAATTTTATGGAAA-
1 TGTTATCAAAATTTTAT--AAAG
*
58922 TGTTATCAAAATTTCATAAAG
1 TGTTATCAAAATTTTATAAAG
*
58943 AGTTTATCAAAATTTTATA
1 TG-TTATCAAAATTTTATA
58962 GGGAGATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.09
21 1 0.03
22 31 0.89
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (21 bp):
TGTTATCAAAATTTTATAAAG
Found at i:58973 original size:22 final size:21
Alignment explanation
Indices: 58904--58979 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 21
58894 TAATATTGTT
*
58904 ATCAAAATTTTAT-GGAAATG
1 ATCAAAATTTTATAGGAGATG
* * * *
58924 TTATCAAAATTTCATAAAGAGTTT
1 --ATCAAAATTTTAT-AGGAGATG
58948 ATCAAAATTTTATAGGGAGATG
1 ATCAAAATTTTATA-GGAGATG
*
58970 ATCACAATTT
1 ATCAAAATTT
58980 CATAATAATA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
21 1 0.02
22 37 0.90
24 3 0.07
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (21 bp):
ATCAAAATTTTATAGGAGATG
Found at i:60587 original size:40 final size:41
Alignment explanation
Indices: 60497--60588 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 41
60487 TTCTCCATTG
*
60497 TTGAAGGATATTTAAGAATATATTGTTTAAAGAATTTATTT
1 TTGAAGGATATTTAACAATATATTGTTTAAAGAATTTATTT
* *
60538 TTGAAGGATATTTAACAATGTATT-TCTTAAAGGA-TTATTT
1 TTGAAGGATATTTAACAATATATTGT-TTAAAGAATTTATTT
60578 TTGAAGGATAT
1 TTGAAGGATAT
60589 ATTATGATGA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
40 18 0.38
41 29 0.62
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (41 bp):
TTGAAGGATATTTAACAATATATTGTTTAAAGAATTTATTT
Found at i:67005 original size:29 final size:30
Alignment explanation
Indices: 66941--66997 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
66931 AGTTCGTGAT
66941 TGAAGATTAATTGAAGATAATTTCAAGTCA
1 TGAAGATTAATTGAAGATAATTTCAAGTCA
*
66971 TGAAGATT-ATTGAAGAATTATTTCAAG
1 TGAAGATTAATTGAAG-ATAATTTCAAG
66998 GAGAAAGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAAGATTAATTGAAGATAATTTCAAGTCA
Done.