Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010611.1 Kokia drynarioides strain JFW-HI SEQ_125544, 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: 95356
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1736 original size:205 final size:200
Alignment explanation
Indices: 1271--1800 Score: 700
Period size: 205 Copynumber: 2.6 Consensus size: 200
1261 CCTCGAACTC
*
1271 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCTTGATGAGATACAGAGAAGCG
1 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCG
* * **
1336 AATTGAAACAAATGACGCGGTCTTCTTCCTGACAAGATATTGAGAAGAAGGCCAAATCAAACCCA
66 AATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGGCCAAATCAAACCCA
* *
1401 CACTCGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAA
131 CACTCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGGCGAAGCAATAA
*
1466 AAGGT
196 AAAGT
1471 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCG
1 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCG
* * * * *
1536 AATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCA
66 AATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGGCCAAATCAAACCCA
* * * *
1601 TGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGC
131 --CAC--T-CGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGGCGAAGC
1666 AATAAAAAGT
191 AATAAAAAGT
* * * * ** * * * *
1676 TAGCTTCCTGATGAAATACGGGGAAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGAAGCG
1 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCG
* ** * ** * *
1741 GATCAAAACAAGTGATATGGTCGTCTTCTTGATGAGATATTGAGAAGAAGGCCAAATCAA
66 AATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGGCCAAATCAA
1801 TGAAACCAGA
Statistics
Matches: 286, Mismatches: 39, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
200 120 0.42
202 2 0.01
204 1 0.00
205 163 0.57
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (200 bp):
TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCG
AATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGGCCAAATCAAACCCA
CACTCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGGCGAAGCAATAA
AAAGT
Found at i:1748 original size:37 final size:37
Alignment explanation
Indices: 1679--1749 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
1669 AAAAAGTTAG
* * * *
1679 CTTCCTGATGAAATACGGGGAAGTGAACCAAAACCAT
1 CTTCCTGATGAAACACAGAGAAGCGAACCAAAACCAT
* *
1716 CTTCCTGATGAAACACAGAGAAGCGGATCAAAAC
1 CTTCCTGATGAAACACAGAGAAGCGAACCAAAAC
1750 AAGTGATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (37 bp):
CTTCCTGATGAAACACAGAGAAGCGAACCAAAACCAT
Found at i:2163 original size:34 final size:34
Alignment explanation
Indices: 2125--2244 Score: 101
Period size: 34 Copynumber: 3.7 Consensus size: 34
2115 TAAAATCATT
*
2125 TTTAAATTTATTATAAGATTT-AATTTATTTTAAA
1 TTTAAATTTATTATAA-ATTTAAATTTACTTTAAA
* * *
2159 TTTAAACTTATTTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTATTATAAATTTAAATTTACTTTAAA
*
2193 TTT-AA---A-T-TAAGTTTAAATTTACTTTTAAA
1 TTTAAATTTATTATAAATTTAAATTTAC-TTTAAA
* * *
2222 ATTAAAATTATTTTAAATTTAAA
1 TTTAAATTTATTATAAATTTAAA
2245 AAGTCTCATT
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
28 13 0.19
29 9 0.13
30 3 0.04
33 7 0.10
34 29 0.41
35 9 0.13
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTATAAATTTAAATTTACTTTAAA
Found at i:2164 original size:6 final size:6
Alignment explanation
Indices: 2125--2244 Score: 67
Period size: 6 Copynumber: 21.0 Consensus size: 6
2115 TAAAATCATT
* * *
2125 TTTAAA TTT--A TTATAAGA TTT-AA TTT-AT TTTAAA TTTAAA CTT-AT
1 TTTAAA TTTAAA TT-TAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * **
2170 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA -TTAAG TTTAAA TTTACT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
2216 TTTAAA ATTAAA ATT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2245 AAGTCTCATT
Statistics
Matches: 85, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
4 3 0.04
5 22 0.26
6 56 0.66
7 1 0.01
8 3 0.04
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:2244 original size:17 final size:17
Alignment explanation
Indices: 2125--2245 Score: 85
Period size: 17 Copynumber: 7.4 Consensus size: 17
2115 TAAAATCATT
* *
2125 TTTAAATTTATTATAAGA
1 TTTAAAATTATTTTAA-A
*
2143 TTT-AATTTATTTTAAA
1 TTTAAAATTATTTTAAA
*
2159 TTTAAACTTATTTTAAA
1 TTTAAAATTATTTTAAA
* **
2176 TTTAAATTTGCTTTAAA
1 TTTAAAATTATTTTAAA
*
2193 TTT-AAATTAAGTTTAAA
1 TTTAAAATT-ATTTTAAA
*
2210 TTT---A--CTTTTAAA
1 TTTAAAATTATTTTAAA
*
2222 ATTAAAATTATTTTAAA
1 TTTAAAATTATTTTAAA
2239 TTTAAAA
1 TTTAAAA
2246 AGTCTCATTA
Statistics
Matches: 83, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
12 8 0.10
15 2 0.02
16 8 0.10
17 62 0.75
18 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:2971 original size:3 final size:3
Alignment explanation
Indices: 2951--3012 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
2941 AATGGCAACT
* *
2951 ATA ATTA ATA TTA TTA ATA AT- ATA ATA ATA ATA ATA ATA ATA GATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* *
2997 TTA TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
3013 ACCGAAAGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:4059 original size:30 final size:31
Alignment explanation
Indices: 4018--4198 Score: 218
Period size: 30 Copynumber: 6.1 Consensus size: 31
4008 GGACTGTCCG
* *
4018 AAAATTTCATTTTTGA-CCTGGAAACTTCCA
1 AAAATTCCATTTTTGACCCTCGAAACTTCCA
4048 AAAATTCCATTTTT-A-CCTCCG-AACTTCCA
1 AAAATTCCATTTTTGACCCT-CGAAACTTCCA
*
4077 AAAATTCCATTTTTAACCCT-GAAACTTCCA
1 AAAATTCCATTTTTGACCCTCGAAACTTCCA
*
4107 AAAATTCCATTTTTGACCCTC-AAACTTCTA
1 AAAATTCCATTTTTGACCCTCGAAACTTCCA
* *
4137 AAAATTGCATTTTT-ACCCTCG-AATTTCCA
1 AAAATTCCATTTTTGACCCTCGAAACTTCCA
* *
4166 AAAATTCCATTTTTGA-CCTCAAAACTTACA
1 AAAATTCCATTTTTGACCCTCGAAACTTCCA
4196 AAA
1 AAA
4199 TTTTTATTTT
Statistics
Matches: 132, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
29 56 0.42
30 73 0.55
31 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (31 bp):
AAAATTCCATTTTTGACCCTCGAAACTTCCA
Found at i:4110 original size:59 final size:61
Alignment explanation
Indices: 4018--4236 Score: 247
Period size: 59 Copynumber: 3.7 Consensus size: 61
4008 GGACTGTCCG
* * *
4018 AAAATTTCATTTTTGA-CCTGGAAACTTCCAAAAATTCCATTTTT-ACCTCCGAACTTCCA
1 AAAATTTCATTTTTAACCCTCGAAACTTCCAAAAATTCCATTTTTGACCTCCAAACTTCCA
* *
4077 AAAATTCCATTTTTAACCCT-GAAACTTCCAAAAATTCCATTTTTGACC-CTCAAACTTCTA
1 AAAATTTCATTTTTAACCCTCGAAACTTCCAAAAATTCCATTTTTGACCTC-CAAACTTCCA
* * * *
4137 AAAATTGCATTTTT-ACCCTCG-AATTTCCAAAAATTCCATTTTTGACCTCAAAACTTACA
1 AAAATTTCATTTTTAACCCTCGAAACTTCCAAAAATTCCATTTTTGACCTCCAAACTTCCA
* * *
4196 AAATTTTTATTTTTAA-CCTCG-AACTTTCCCAAAATTACCAT
1 AAAATTTCATTTTTAACCCTCGAAAC-TTCCAAAAATT-CCAT
4237 ATTGCCCCTA
Statistics
Matches: 138, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
59 94 0.68
60 40 0.29
61 4 0.03
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (61 bp):
AAAATTTCATTTTTAACCCTCGAAACTTCCAAAAATTCCATTTTTGACCTCCAAACTTCCA
Found at i:4199 original size:29 final size:29
Alignment explanation
Indices: 4018--4236 Score: 208
Period size: 30 Copynumber: 7.3 Consensus size: 29
4008 GGACTGTCCG
* *
4018 AAAATTTCATTTTTGACCTGGAAACTTCCA
1 AAAATTCCATTTTTGACCT-CAAACTTCCA
*
4048 AAAATTCCATTTTT-ACCTCCGAACTTCCA
1 AAAATTCCATTTTTGACCT-CAAACTTCCA
* *
4077 AAAATTCCATTTTTAACCCTGAAACTTCCA
1 AAAATTCCATTTTTGA-CCTCAAACTTCCA
*
4107 AAAATTCCATTTTTGACCCTCAAACTTCTA
1 AAAATTCCATTTTTGA-CCTCAAACTTCCA
* * *
4137 AAAATTGCATTTTT-ACCCTCGAATTTCCA
1 AAAATTCCATTTTTGA-CCTCAAACTTCCA
*
4166 AAAATTCCATTTTTGACCTCAAAACTTACA
1 AAAATTCCATTTTTGACCTC-AAACTTCCA
* ** * * *
4196 AAATTTTTATTTTTAACCTCGAACTTTCCC
1 AAAATTCCATTTTTGACCTCAAAC-TTCCA
4226 AAAATTACCAT
1 AAAATT-CCAT
4237 ATTGCCCCTA
Statistics
Matches: 156, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
29 58 0.37
30 93 0.60
31 5 0.03
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAATTCCATTTTTGACCTCAAACTTCCA
Found at i:4230 original size:89 final size:87
Alignment explanation
Indices: 4018--4236 Score: 235
Period size: 89 Copynumber: 2.4 Consensus size: 87
4008 GGACTGTCCG
* *
4018 AAAATTTCATTTTTGACCTGGAAACTTCCAAAAATTCCATTTTTACCTCCGAACTTCCAAAAATT
1 AAAATTTCATTTTTAACCTCG-AACTTCCAAAAATTCCATTTTTACCTCCGAACTTCCAAAAATT
* *
4083 CCATTTTTAACCCTGAAACTTCC
65 CCATTTTTAACCCTAAAACTTAC
* * * * * *
4106 AAAAATTCCATTTTTGACCCTCAAACTTCTAAAAATTGCATTTTTACC-CTCGAATTTCCAAAAA
1 -AAAATTTCATTTTT-AACCTCGAACTTCCAAAAATTCCATTTTTACCTC-CGAACTTCCAAAAA
*
4170 TTCCATTTTTGA-CCTCAAAACTTAC
63 TTCCATTTTTAACCCT-AAAACTTAC
* *
4195 AAAATTTTTATTTTTAACCTCGAACTTTCCCAAAATTACCAT
1 AAAA-TTTCATTTTTAACCTCGAAC-TTCCAAAAATT-CCAT
4237 ATTGCCCCTA
Statistics
Matches: 106, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
88 16 0.15
89 84 0.79
90 6 0.06
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (87 bp):
AAAATTTCATTTTTAACCTCGAACTTCCAAAAATTCCATTTTTACCTCCGAACTTCCAAAAATTC
CATTTTTAACCCTAAAACTTAC
Found at i:6731 original size:117 final size:116
Alignment explanation
Indices: 6568--7031 Score: 359
Period size: 117 Copynumber: 4.0 Consensus size: 116
6558 TAGCTGATGG
* * * * * *
6568 TGATCTACCCCAAGCTCGAGGTAAAAGATC-GAATGGTTGCAATCTGCCCTAGGCTTGGGGTAAG
1 TGATCTGCCCCATGATCGGGGTAAGAGATCAG-ATGGTTG-AATCTGCCCTAGGCTCGGGGTAAG
* * *
6632 AGATTGGCTGATGGTGACCTGCCTCAAGCTTGGGGTAAAAGATCGAATGACTA
64 AGATTGGCTGATGGTGACTTGCCTCAAGCTCGGGGTAAAAGATCGGATGACTA
* * * *
6685 TGATCTACCCCATGATCGGGGTAAGAGATTGGCTA-ATGG-TG-ATCTGCCCCAAGCTCGGAGTA
1 TGATCTGCCCCATGATCGGGGTAAGAGA-T--C-AGATGGTTGAATCTGCCCTAGGCTCGGGGTA
** * * * * * * * *
6747 AGAGA-T--CAAATGGTTACAATTTGTCTCAGGCTCGAGGTAAGAGATTGGCT-AATA
62 AGAGATTGGCTGATGGTGAC---TTGCCTCAAGCTCGGGGTAAAAGATCGGATGACTA
* * * *
6801 GTGATATGCCCCAAGCTCGGAGTAAGAGATCAGATGGTTGCAATCTGCCCTAGGCTCGGGGTAAG
1 -TGATCTGCCCCATGATCGGGGTAAGAGATCAGATGGTTG-AATCTGCCCTAGGCTCGGGGTAAG
* * * * *
6866 AGATTGGATGATGGTGATTTGCCCCAAGCTCGGGGTGAAAGATCGGATGACTG
64 AGATTGGCTGATGGTGACTTGCCTCAAGCTCGGGGTAAAAGATCGGATGACTA
* * * * * * ** *
6919 TGATCTGCCCCATGATCGGGGTAAGAAATCGGATGGTTGTAATTTGTCTTAAGCTCATGGTAAAA
1 TGATCTGCCCCATGATCGGGGTAAGAGATCAGATGGTTG-AATCTGCCCTAGGCTCGGGGTAAGA
* * * *
6984 GATTGGTTGATGGTGATTTGCCCCAAGCTCAGGGTAAAAGATCGGATG
65 GATTGGCTGATGGTGACTTGCCTCAAGCTCGGGGTAAAAGATCGGATG
7032 GCTGCAATCT
Statistics
Matches: 269, Mismatches: 61, Indels: 34
0.74 0.17 0.09
Matches are distributed among these distances:
113 1 0.00
114 13 0.05
115 2 0.01
116 5 0.02
117 231 0.86
118 4 0.01
119 2 0.01
120 11 0.04
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (116 bp):
TGATCTGCCCCATGATCGGGGTAAGAGATCAGATGGTTGAATCTGCCCTAGGCTCGGGGTAAGAG
ATTGGCTGATGGTGACTTGCCTCAAGCTCGGGGTAAAAGATCGGATGACTA
Found at i:6850 original size:39 final size:39
Alignment explanation
Indices: 6726--6869 Score: 110
Period size: 39 Copynumber: 3.7 Consensus size: 39
6716 GCTAATGGTG
* *
6726 ATCTGCCCCAAGCTCGGAGTAAGAGATCAAATGGTTACA
1 ATCTGCCCCAAGCTCGGAGTAAGAGATCAGATGGTTGCA
* * * * ** * ** * **
6765 ATTTGTCTCAGGCTC-GAGGTAAGAGATTGGCTAATAGTG
1 ATCTGCCCCAAGCTCGGA-GTAAGAGATCAGATGGTTGCA
*
6804 ATATGCCCCAAGCTCGGAGTAAGAGATCAGATGGTTGCA
1 ATCTGCCCCAAGCTCGGAGTAAGAGATCAGATGGTTGCA
* * *
6843 ATCTGCCCTAGGCTCGGGGTAAGAGAT
1 ATCTGCCCCAAGCTCGGAGTAAGAGAT
6870 TGGATGATGG
Statistics
Matches: 73, Mismatches: 30, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
38 2 0.03
39 69 0.95
40 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGAGTAAGAGATCAGATGGTTGCA
Found at i:6925 original size:78 final size:78
Alignment explanation
Indices: 6532--7455 Score: 521
Period size: 78 Copynumber: 11.9 Consensus size: 78
6522 GGTGGTTGCA
* * * * * *
6532 ATCTGCCTCAAGCTC-GAGTAAGAGATTAGCTGATGGTGATCTACCCCAAGCTCGAGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
* * **
6596 TCGAATGGTTGCA
66 TCGGATGATTGTG
* * * * * * *
6609 ATCTGCCCTAGGCTTGGGGTAAGAGATTGGCTGATGGTGACCTGCCTCAAGCTTGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
* * *
6674 TCGAATGACTATG
66 TCGGATGATTGTG
* * * * * * *
6687 ATCTACCCCATGATCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAAGCTCGGAGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
** * ***
6752 TCAAATGGTTACA
66 TCGGATGATTGTG
* * * * * * * * * * *
6765 ATTTGTCTCAGGCTCGAGGTAAGAGATTGGCTAATAGTGATATGCCCCAAGCTCGGAGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
* * **
6830 TCAGATGGTTGCA
66 TCGGATGATTGTG
* * * *
6843 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGATGATGGTGATTTGCCCCAAGCTCGGGGTGAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
*
6908 TCGGATGACTGTG
66 TCGGATGATTGTG
* * * * * * * * * ** **
6921 ATCTGCCCCATGATCGGGGTAAGAAATCGGATGGTTGTAATTTGTCTTAAGCTCATGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
* * *
6986 TTGGTTGATGGTG
66 TCGGATGATTGTG
* * * * * ** * * *
6999 ATTTGCCCCAAGCTCAGGGTAAAAGATCGGATG--GCTGCAATCTGCCTTAGGCTTGGGGTAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTG--ATCTGCCCCAAGCTCGGGGTAAAA
* **
7062 GAT-TGACTGATAATG
64 GATCGGA-TGATTGTG
* * * * * * * * * *
7077 ATCTGCCTCAAGCTCGAGGTAAAAGATCGAATGGCT-GTAATCTGCCCCAGGTTTGGGGTAAAAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGAT-GATGGTGATCTGCCCCAAGCTCGGGGTAAAAG
* * *
7141 ATTGGATGGTTGTA
65 ATCGGATGATTGTG
* * * *
7155 ATTTACCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
*
7220 TCGGATGACTGTG
66 TCGGATGATTGTG
* * * * * ** * * * *
7233 ATCTACCCCATGATCGGAGTAAGAGATTAGATGACT-GCAATCTGTCCTAGGCTCGGGGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGA-TGGTGATCTGCCCCAAGCTCGGGGTAAAAG
* * *
7297 ATTGGTTGATGGTG
65 ATCGGATGATTGTG
* * * * * * * * * *
7311 ATCTGCCCTAAGCTCGCGGTAAAAGATCGAATGGAT-GTAATCTGCGCTAAGCTTGGGGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGAT-GATGGTGATCTGCCCCAAGCTCGGGGTAAAAG
* * *
7375 ATTGGTTGATGGTG
65 ATCGGATGATTGTG
* * * * * * * * *
7389 ATCTGCCTCAAGCTCGAGGTAAAAGATCGGATGATTGTGATCTACCCCATGATCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
7454 TC
66 TC
7456 AAAATCTTCA
Statistics
Matches: 659, Mismatches: 176, Indels: 23
0.77 0.21 0.03
Matches are distributed among these distances:
76 1 0.00
77 17 0.03
78 634 0.96
79 6 0.01
80 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (78 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
TCGGATGATTGTG
Found at i:7090 original size:117 final size:115
Alignment explanation
Indices: 6860--7376 Score: 372
Period size: 117 Copynumber: 4.4 Consensus size: 115
6850 CTAGGCTCGG
* * * * **
6860 GGTAAGAGATTGGATGATGGTGATTTGCCCCAAGCTCGGGGTGAAAGATCGGATGACTGTGATCT
1 GGTAAAAGATCGGATGAT-GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGACTGCAATCT
* * * * * * * * * *
6925 GCCCCATGATCGGGGTAAGAAATCGGA-TGGTTGTAATTTGTCTTAAGCTCA
65 GCCCCAGGCTCGGGGTAAGAGAT-TGACTGATGGTGATCTGCCTCAAGCTCA
* * * * *
6976 TGGTAAAAGATTGGTTGATGGTGATTTGCCCCAAGCTCAGGGTAAAAGATCGGATGGCTGCAATC
1 -GGTAAAAGATCGGATGAT-GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGACTGCAATC
** * **
7041 TGCCTTAGGCTTGGGGTAAGAGATTGACTGATAATGATCTGCCTCAAGCTCGA
64 TGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCAAGCTC-A
* * * * * * * ** * *
7094 GGTAAAAGATCGAATGGCTGTAATCTGCCCCAGGTTTGGGGTAAAAGATTGGATGGTTGTAATTT
1 GGTAAAAGATCGGAT-GATGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGACTGCAATCT
* * * * * *
7159 ACCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGG
65 GCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCAAGCTC-A
* * * * * **
7211 GGTAAAAGATCGGATGACTGTGATCTACCCCATGATCGGAGTAAGAGATTAGATGACTGCAATCT
1 GGTAAAAGATCGGATGA-TGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGACTGCAATCT
* * ** *
7276 GTCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCC-CTAAGCTCGC
65 GCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTC-AAGCTC-A
* * * * * *
7328 GGTAAAAGATCGAATGGATGTAATCTGCGCTAAGCTTGGGGTAAGAGAT
1 GGTAAAAGATCGGAT-GATGTGATCTGCCCCAAGCTCGGGGTAAAAGAT
7377 TGGTTGATGG
Statistics
Matches: 318, Mismatches: 76, Indels: 12
0.78 0.19 0.03
Matches are distributed among these distances:
116 4 0.01
117 309 0.97
118 5 0.02
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (115 bp):
GGTAAAAGATCGGATGATGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGACTGCAATCTG
CCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCAAGCTCA
Found at i:7449 original size:117 final size:116
Alignment explanation
Indices: 7037--7455 Score: 385
Period size: 117 Copynumber: 3.6 Consensus size: 116
7027 GGATGGCTGC
* * * ** * * *
7037 AATCTGCCTTAGGCTTGGGGTAAGAGATT-GACTGATAATGATCTGCCTCAAGCTCGAGGTAAAA
1 AATCTGCCTCAAGCTCGGGGTAAGAGATTGGA-TGATGGTGATCTACCCCAAGCTCGGGGTAAAA
* * * * *
7101 GATCGAATGGCTGTAATCTGCCCCAGGTTTGGGGTAAAAGATTGGATGGTTGT
65 GATCGAATGGATGTAATCTGCCCCAAGATTGGGGTAAGAGATTGGAT-GATGT
* * * *
7154 AATTTACCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAG
1 AATCTGCCTCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAAGCTCGGGGTAAAAG
* * * * * * * *
7219 ATCGGAT-GACTGTGATCTACCCCATGATCGGAGTAAGAGATTAGATGACTGC
66 ATCGAATGGA-TGTAATCTGCCCCAAGATTGGGGTAAGAGATTGGATGA-TGT
* * * * *
7271 AATCTGTCCT-AGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCGCGGTAAAA
1 AATCTG-CCTCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAAGCTCGGGGTAAAA
* * * *
7335 GATCGAATGGATGTAATCTGCGCTAAGCTTGGGGTAAGAGATTGGTTGATGGT
65 GATCGAATGGATGTAATCTGCCCCAAGATTGGGGTAAGAGATTGGATGAT-GT
* * * * * * * *
7388 GATCTGCCTCAAGCTCGAGGTAAAAGATCGGATGATTGTGATCTACCCCATGATCGGGGTAAGAG
1 AATCTGCCTCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAAGCTCGGGGTAAAAG
7453 ATC
66 ATC
7456 AAAATCTTCA
Statistics
Matches: 238, Mismatches: 57, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
116 6 0.03
117 227 0.95
118 5 0.02
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (116 bp):
AATCTGCCTCAAGCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAAGCTCGGGGTAAAAG
ATCGAATGGATGTAATCTGCCCCAAGATTGGGGTAAGAGATTGGATGATGT
Found at i:16356 original size:30 final size:30
Alignment explanation
Indices: 16321--16604 Score: 212
Period size: 30 Copynumber: 9.5 Consensus size: 30
16311 ATTTTTCGAT
16321 ATTTTTGAGAAGTTTAGGGGTTAAAATGTA
1 ATTTTTGAGAAGTTTAGGGGTTAAAATGTA
* **
16351 ATTTTTGAGAAATTTAAAGGTTAAAATGTA
1 ATTTTTGAGAAGTTTAGGGGTTAAAATGTA
* * *
16381 ATTTTT-ATGAAGTTTAGGGGTCAAAATATG
1 ATTTTTGA-GAAGTTTAGGGGTTAAAATGTA
* * * *
16411 ATTTTTGATAAG-TTCGAGGGTTAAAATATG
1 ATTTTTGAGAAGTTTAG-GGGTTAAAATGTA
16441 ATTTTTGAGAAGTTT-GGGAGTTAAAATGTA
1 ATTTTTGAGAAGTTTAGGG-GTTAAAATGTA
* * *
16471 ATTTTT-ACGATGTTTAGTGGTCAAAATGTA
1 ATTTTTGA-GAAGTTTAGGGGTTAAAATGTA
* * *
16501 ATTTTT-ACGAAG-TTCGAGTGTCAAAATGTA
1 ATTTTTGA-GAAGTTTAG-GGGTTAAAATGTA
* * *
16531 ATTTATCA-AA-TTTTGGGGTTTAAAATGTA
1 ATTTTTGAGAAGTTTAGGGG-TTAAAATGTA
* * *
16560 A-TTTTGCA-AAGTTT-GAGGGTCAAAATATG
1 ATTTTTG-AGAAGTTTAG-GGGTTAAAATGTA
16589 ATTTTTGAGAAGTTTA
1 ATTTTTGAGAAGTTTA
16605 AGGACCTTCT
Statistics
Matches: 206, Mismatches: 31, Indels: 33
0.76 0.11 0.12
Matches are distributed among these distances:
28 5 0.02
29 38 0.18
30 157 0.76
31 6 0.03
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (30 bp):
ATTTTTGAGAAGTTTAGGGGTTAAAATGTA
Found at i:16437 original size:90 final size:88
Alignment explanation
Indices: 16321--16602 Score: 295
Period size: 90 Copynumber: 3.2 Consensus size: 88
16311 ATTTTTCGAT
* **
16321 ATTTTTGAGAAGTT-TAGGGGTTAAAATGTAATTTTTGAGAAATTTAAAGGTTAAAATGTAATTT
1 ATTTTTGAGAAGTTCGA-GGGTTAAAATGTAATTTTTGAGAAATTT-GGGGTTAAAATGTAATTT
16385 TTATGAAGTTTAGGGGTCAAAATATG
64 TTA-GAAGTTTAGGGGTCAAAATATG
* * * *
16411 ATTTTTGATAAGTTCGAGGGTTAAAATATGATTTTTGAGAAGTTTGGGAGTTAAAATGTAATTTT
1 ATTTTTGAGAAGTTCGAGGGTTAAAATGTAATTTTTGAGAAATTTGGG-GTTAAAATGTAATTTT
* * * *
16476 TACGATGTTTAGTGGTCAAAATGTA
65 TA-GAAGTTTAGGGGTCAAAATATG
* * * * *
16501 ATTTTT-ACGAAGTTCGAGTGTCAAAATGTAATTTATCA-AATTTTGGGGTTTAAAATGTAATTT
1 ATTTTTGA-GAAGTTCGAGGGTTAAAATGTAATTTTTGAGAAATTTGGGG-TTAAAATGTAATTT
*
16564 TGCA-AAGTTT-GAGGGTCAAAATATG
64 T-TAGAAGTTTAG-GGGTCAAAATATG
16589 ATTTTTGAGAAGTT
1 ATTTTTGAGAAGTT
16603 TAAGGACCTT
Statistics
Matches: 160, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
87 1 0.01
88 28 0.17
89 26 0.16
90 104 0.65
91 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (88 bp):
ATTTTTGAGAAGTTCGAGGGTTAAAATGTAATTTTTGAGAAATTTGGGGTTAAAATGTAATTTTT
AGAAGTTTAGGGGTCAAAATATG
Found at i:16569 original size:29 final size:30
Alignment explanation
Indices: 16523--16579 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
16513 TTCGAGTGTC
*
16523 AAAATGTAATTTATCAAATTTTG-GGGTTT
1 AAAATGTAATTTATCAAAGTTTGAGGGTTT
16552 AAAATGTAATTT-TGCAAAGTTTGAGGGT
1 AAAATGTAATTTAT-CAAAGTTTGAGGGT
16580 CAAAATATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 20 0.80
30 4 0.16
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (30 bp):
AAAATGTAATTTATCAAAGTTTGAGGGTTT
Found at i:17433 original size:3 final size:3
Alignment explanation
Indices: 17425--17455 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
17415 ATATGTGTAA
17425 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17456 TGTATTATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17601 original size:11 final size:11
Alignment explanation
Indices: 17578--17616 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
17568 TTCAAATCTG
*
17578 TTTTTTGTT-A
1 TTTTTTATTGA
17588 TTTTTTATTGA
1 TTTTTTATTGA
17599 TTTTTTATTGTA
1 TTTTTTATTG-A
17611 TTTTTT
1 TTTTTT
17617 TTTTAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 8 0.31
11 11 0.42
12 7 0.27
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (11 bp):
TTTTTTATTGA
Found at i:17603 original size:12 final size:12
Alignment explanation
Indices: 17586--17616 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
17576 TGTTTTTTGT
17586 TATTTTTTATTG
1 TATTTTTTATTG
17598 -ATTTTTTATTG
1 TATTTTTTATTG
17609 TATTTTTT
1 TATTTTTT
17617 TTTTAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (12 bp):
TATTTTTTATTG
Found at i:22347 original size:59 final size:59
Alignment explanation
Indices: 22223--22680 Score: 552
Period size: 59 Copynumber: 7.8 Consensus size: 59
22213 TTGTTTAAGC
* * * * * *
22223 AAATGATAAAATATATAAATAATGTGTAAAAAAAAATTC-AAAGTAAACTTCTCTTTTATT
1 AAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAG--AACTTTTATTTTATT
* *
22283 TAATGATAGAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTTTATTTTATT
1 AAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTTTATTTTATT
* * *
22342 AAATGATACAATAGAAAAATAATGTGTACAAAAA-ATTCAAAACAAACTTCTATTTTATT
1 AAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAA-GAACTTTTATTTTATT
* * * * *
22401 AAATGATAGAATATAAAAATAATCTGTACAAAAATATTCAATAGAATTTTTATTTTGTT
1 AAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTTTATTTTATT
* * *
22460 AAATGATACAATATAAAAATAATGTGGACAAAAA-ATTTC--AA-AACTTCTATTTTGTT
1 AAATGATACAATATAAAAATAATGTGTACAAAAATA-TTCAAAAGAACTTTTATTTTATT
* * * *
22516 AAATGATAGAATATAAAAATAATGCGTACAAAAATATTTAAAAG-ATTTTCTATTTTATT
1 AAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTT-TATTTTATT
* * * * *
22575 TAATGATACAATGTAAAAATGATGTGTACAAGAACATTCAAAAGAACTTTTATTTTATT
1 AAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTTTATTTTATT
* *
22634 AAATGATATAATATAAAAATAATGTGTACAAAAAAATTCAAAAGAAC
1 AAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAAC
22681 ATCAATGCAT
Statistics
Matches: 340, Mismatches: 48, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
56 46 0.14
57 2 0.01
58 14 0.04
59 229 0.67
60 45 0.13
61 4 0.01
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (59 bp):
AAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAAGAACTTTTATTTTATT
Found at i:22812 original size:33 final size:33
Alignment explanation
Indices: 22752--22814 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
22742 ATTCCTTCTT
* * *
22752 GGTTCAACTTTTGGTCGGGGTTATGGTTGTCGG
1 GGTTCAACTTTCGGGCGAGGTTATGGTTGTCGG
* *
22785 GGTTCAGCTTTCGGGCGAGGTTGTGGTTGT
1 GGTTCAACTTTCGGGCGAGGTTATGGTTGT
22815 GGTTGTTGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.08, C:0.13, G:0.41, T:0.38
Consensus pattern (33 bp):
GGTTCAACTTTCGGGCGAGGTTATGGTTGTCGG
Found at i:23698 original size:24 final size:25
Alignment explanation
Indices: 23666--23716 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
23656 ATTCAAACTA
*
23666 TATAAACATGATA-AAAACATTAGT
1 TATAAACATAATACAAAACATTAGT
* * *
23690 TATATACATAATACTAAATATTAGT
1 TATAAACATAATACAAAACATTAGT
23715 TA
1 TA
23717 CAAAATCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (25 bp):
TATAAACATAATACAAAACATTAGT
Found at i:24678 original size:21 final size:22
Alignment explanation
Indices: 24652--24693 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
24642 CTGTTCACAT
*
24652 AAAAATTATAAAAA-TGAAATA
1 AAAAATTAAAAAAATTGAAATA
24673 AAAAATTAAAAAAATTGAAAT
1 AAAAATTAAAAAAATTGAAAT
24694 TAATTCTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAAATTAAAAAAATTGAAATA
Found at i:25429 original size:18 final size:17
Alignment explanation
Indices: 25390--25433 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
25380 AAAATTGTAA
*
25390 AAAAAATAATAAATTTT
1 AAAAAATAATAAATTAT
25407 AAAAAATATATAAATTAT
1 AAAAAATA-ATAAATTAT
*
25425 GAAAAATAA
1 AAAAAATAA
25434 AAAAAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAAAATAATAAATTAT
Found at i:25447 original size:18 final size:18
Alignment explanation
Indices: 25356--25517 Score: 76
Period size: 19 Copynumber: 8.5 Consensus size: 18
25346 AAAATTTATA
*
25356 AAAAAAAATTAGAGAAAAAT
1 AAAAAAAATT-G-TAAAAAT
**
25376 ATTAAAAATTGTAAAAA-
1 AAAAAAAATTGTAAAAAT
*
25393 AAATAATAAATTTTAAAAA-
1 AAA-AA-AAATTGTAAAAAT
* * *
25412 ATATATAAATTATGAAAAAT
1 A-AAAAAAATTGT-AAAAAT
25432 AAAAAAAATTGTAAAAAT
1 AAAAAAAATTGTAAAAAT
* *
25450 AATGAAAAAAATGTTTAAAAT
1 AA--AAAAAATTG-TAAAAAT
* * *
25471 ATAGAAAATTATTAAAAAT
1 AAAAAAAATT-GTAAAAAT
* *
25490 AGAAAAAATTATAGAAAAT
1 AAAAAAAATTGTA-AAAAT
*
25509 AGAAAAAAT
1 AAAAAAAAT
25518 ATAGAAAATT
Statistics
Matches: 110, Mismatches: 22, Indels: 21
0.72 0.14 0.14
Matches are distributed among these distances:
17 1 0.01
18 23 0.21
19 61 0.55
20 18 0.16
21 7 0.06
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (18 bp):
AAAAAAAATTGTAAAAAT
Found at i:25488 original size:19 final size:18
Alignment explanation
Indices: 25370--25585 Score: 74
Period size: 19 Copynumber: 11.7 Consensus size: 18
25360 AAAATTAGAG
* *
25370 AAAAATATTAAAAATTGTA
1 AAAAATA-TAAAAATTATT
*
25389 AAAAAAATAATAAATT-TT
1 AAAAATATAA-AAATTATT
* *
25407 AAAAAATATATAAATTATG
1 -AAAAATATAAAAATTATT
* *
25426 AAAAATAAAAAAAATT-GT
1 AAAAAT-ATAAAAATTATT
* *
25444 AAAAATAATGAAAAAAATGTT
1 AAAAAT-AT--AAAAATTATT
*
25465 TAAAATATAGAAAATTATT
1 AAAAATATA-AAAATTATT
*
25484 AAAAATAGAAAAAATTA-T
1 AAAAATA-TAAAAATTATT
* *
25502 AGAAAATAGAAAAAATA-T
1 A-AAAATATAAAAATTATT
* *
25520 AGAAAATTACAAAAAATATT
1 A-AAAA-TATAAAAATTATT
*
25540 ----AT-TAAAAGTTATT
1 AAAAATATAAAAATTATT
*
25553 GAAAAATAATATAAAATTA-C
1 -AAAAAT-ATA-AAAATTATT
25573 AAAAATATAAAAA
1 AAAAATATAAAAA
25586 AAAAAATGTT
Statistics
Matches: 152, Mismatches: 25, Indels: 42
0.69 0.11 0.19
Matches are distributed among these distances:
13 8 0.05
14 1 0.01
15 1 0.01
17 4 0.03
18 45 0.30
19 69 0.45
20 12 0.08
21 12 0.08
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAAATATAAAAATTATT
Found at i:25520 original size:18 final size:18
Alignment explanation
Indices: 25485--25538 Score: 81
Period size: 19 Copynumber: 2.9 Consensus size: 18
25475 AAAATTATTA
25485 AAAATAGAAAAAATTATAG
1 AAAATAGAAAAAA-TATAG
25504 AAAATAGAAAAAATATAG
1 AAAATAGAAAAAATATAG
*
25522 AAAATTACAAAAAATAT
1 AAAA-TAGAAAAAATAT
25539 TATTAAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 9 0.27
19 24 0.73
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (18 bp):
AAAATAGAAAAAATATAG
Found at i:25905 original size:19 final size:19
Alignment explanation
Indices: 25883--25929 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
25873 ATGCTTCTTA
25883 TAATATTTT-ATAAATTTAT
1 TAATATTTTAATAAATTT-T
25902 TAATATTTCTAATAAATTTT
1 TAATATTT-TAATAAATTTT
25922 T-ATATTTT
1 TAATATTTT
25930 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 3 0.12
21 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATATTTTAATAAATTTT
Found at i:26038 original size:20 final size:19
Alignment explanation
Indices: 25983--26041 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
25973 ACATTTCTTA
* * *
25983 TAATTTATATATATATTTTT
1 TAATTTATTTA-AAATTTAT
26003 TAATTTATTTAAAATTTAT
1 TAATTTATTTAAAATTTAT
* *
26022 TAATTATTTTTAGAATTTAT
1 TAATT-TATTTAAAATTTAT
26042 ATATTTTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 11 0.33
20 22 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TAATTTATTTAAAATTTAT
Found at i:26055 original size:35 final size:35
Alignment explanation
Indices: 26016--26083 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
26006 TTTATTTAAA
*
26016 ATTTATTAATTATTTTTAGAA-TTTATATATTTTTC
1 ATTTA-TAATAATTTTTAGAACTTTATATATTTTTC
* *
26051 ATTTATAATAATTTTTATAACTTTCTATATTTT
1 ATTTATAATAATTTTTAGAACTTTATATATTTT
26084 ATAATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (35 bp):
ATTTATAATAATTTTTAGAACTTTATATATTTTTC
Found at i:26099 original size:26 final size:27
Alignment explanation
Indices: 26070--26120 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
26060 AATTTTTATA
*
26070 ACTTTCTATAT-TTTATAAT-TTTTTGC
1 ACTTT-TATATCTGTATAATATTTTTGC
26096 ACTTTTATATCTGTATAATATTTTT
1 ACTTTTATATCTGTATAATATTTTT
26121 ATGATATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 12 0.55
27 5 0.23
ACGTcount: A:0.25, C:0.10, G:0.04, T:0.61
Consensus pattern (27 bp):
ACTTTTATATCTGTATAATATTTTTGC
Found at i:36869 original size:17 final size:17
Alignment explanation
Indices: 36849--36885 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
36839 ACGCCAAAAG
36849 AAAGAATCAA-AGAAGAC
1 AAAGAATCAAGA-AAGAC
36866 AAAGAATCAAGAAAGAC
1 AAAGAATCAAGAAAGAC
36883 AAA
1 AAA
36886 AACCACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.68, C:0.11, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAGAATCAAGAAAGAC
Found at i:37243 original size:18 final size:18
Alignment explanation
Indices: 37209--37244 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
37199 ATGACACCAA
37209 TATATTAAAAAATAATAT
1 TATATTAAAAAATAATAT
37227 TATA-TAAAAAATGAATAT
1 TATATTAAAAAAT-AATAT
37245 ATAATTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TATATTAAAAAATAATAT
Found at i:42512 original size:24 final size:24
Alignment explanation
Indices: 42480--42543 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
42470 CACATTTCCA
* * *
42480 CTCGTCAGCTAATGTATGTTTATG
1 CTCGTCAGCCAATATACGTTTATG
*
42504 CTCGTCAGCCACTATACGTTTATG
1 CTCGTCAGCCAATATACGTTTATG
* *
42528 CTCGCCAGCCACTATA
1 CTCGTCAGCCAATATA
42544 AGATACACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (24 bp):
CTCGTCAGCCAATATACGTTTATG
Found at i:47858 original size:21 final size:21
Alignment explanation
Indices: 47832--47878 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
47822 TTTTTAGTAC
* *
47832 CGGTAGAAGCATGATTTGTTT
1 CGGTAGAAGCATGACTTGTAT
*
47853 CGGTAGAAGCTTGACTTGTAT
1 CGGTAGAAGCATGACTTGTAT
47874 CGGTA
1 CGGTA
47879 AAACTATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (21 bp):
CGGTAGAAGCATGACTTGTAT
Found at i:49047 original size:21 final size:19
Alignment explanation
Indices: 49023--49081 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
49013 AATCAAAATT
49023 TTATAAGAATTTCATAAAAAC
1 TTATAA-AATTT-ATAAAAAC
*
49044 TTAT-AAATATTGTAAAAAC
1 TTATAAAAT-TTATAAAAAC
*
49063 TTATAAAAAATTATAAAAA
1 TTAT-AAAATTTATAAAAA
49082 AAATTATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 14 0.44
20 11 0.34
21 7 0.22
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (19 bp):
TTATAAAATTTATAAAAAC
Found at i:49082 original size:10 final size:10
Alignment explanation
Indices: 49036--49114 Score: 61
Period size: 10 Copynumber: 7.8 Consensus size: 10
49026 TAAGAATTTC
*
49036 ATAAAAACTT
1 ATAAAAAATT
*
49046 AT-AAATATT
1 ATAAAAAATT
* *
49055 GTAAAAACTT
1 ATAAAAAATT
49065 ATAAAAAATT
1 ATAAAAAATT
49075 ATAAAAAAAATT
1 AT--AAAAAATT
* *
49087 ATAATAAGTT
1 ATAAAAAATT
* *
49097 CTAATAAATT
1 ATAAAAAATT
49107 ATAAAAAA
1 ATAAAAAA
49115 AACTATGATT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
9 6 0.11
10 37 0.70
12 10 0.19
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:49135 original size:30 final size:30
Alignment explanation
Indices: 49070--49143 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 30
49060 AACTTATAAA
*
49070 AAATTATAAAAAAAATTATAATAAGTTCTAAT
1 AAATTATAAAAAAAACTATAAT-A-TTCTAAT
* *
49102 AAATTATAAAAAAAACTATGAT-TTTTAATT
1 AAATTATAAAAAAAACTATAATATTCTAA-T
49132 AAATTATAAAAA
1 AAATTATAAAAA
49144 TTCATTCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 5 0.13
30 13 0.34
32 20 0.53
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (30 bp):
AAATTATAAAAAAAACTATAATATTCTAAT
Found at i:49723 original size:48 final size:47
Alignment explanation
Indices: 49664--49810 Score: 133
Period size: 48 Copynumber: 3.3 Consensus size: 47
49654 ATTAGAATTT
49664 TTTATT-A-TTTATAAGTTTTTATAGTATTTAAATATTTTAAATATGC
1 TTTATTAATTTTATAAGTTTTTATA-TATTTAAATATTTTAAATATGC
*
49710 TTTATTAATTTTATAAATTTTTATA-A-TT---TA--TTAGAAT-T--
1 TTTATTAATTTTATAAGTTTTTATATATTTAAATATTTTA-AATATGC
*
49748 TTT-TT-ATCATTATAAGTTTTTATAATATTTAAATATTTTAAATATGC
1 TTTATTAAT-TTTATAAGTTTTTAT-ATATTTAAATATTTTAAATATGC
*
49795 TTTATTATTTTTATAA
1 TTTATTAATTTTATAA
49811 ATTTATTTAT
Statistics
Matches: 79, Mismatches: 5, Indels: 32
0.68 0.04 0.28
Matches are distributed among these distances:
36 2 0.03
37 15 0.19
38 4 0.05
39 1 0.01
40 6 0.08
41 3 0.04
42 2 0.03
43 2 0.03
44 3 0.04
45 6 0.08
46 7 0.09
47 4 0.05
48 23 0.29
49 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (47 bp):
TTTATTAATTTTATAAGTTTTTATATATTTAAATATTTTAAATATGC
Found at i:49740 original size:85 final size:85
Alignment explanation
Indices: 49651--49814 Score: 285
Period size: 85 Copynumber: 1.9 Consensus size: 85
49641 ATAACATTAT
* *
49651 TTTATTAGAA-TTTTTTATTATTTATAAGTTTTTATAGTATTTAAATATTTTAAATATGCTTTAT
1 TTTATTAGAATTTTTTTATCA-TTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTAT
49715 TAATTTTATAAATTTTTATAA
65 TAATTTTATAAATTTTTATAA
49736 TTTATTAGAATTTTTTTATCATTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
1 TTTATTAGAATTTTTTTATCATTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
*
49801 ATTTTTATAAATTT
66 AATTTTATAAATTT
49815 ATTTATTATA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
85 66 0.88
86 9 0.12
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (85 bp):
TTTATTAGAATTTTTTTATCATTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
AATTTTATAAATTTTTATAA
Found at i:49834 original size:8 final size:9
Alignment explanation
Indices: 49659--49850 Score: 75
Period size: 9 Copynumber: 21.0 Consensus size: 9
49649 ATTTTATTAG
49659 AATTTTT-T
1 AATTTTTAT
49667 -ATTATTTAT
1 AATT-TTTAT
49676 AAGTTTTTAT
1 AA-TTTTTAT
* *
49686 AGTATTTA-
1 AATTTTTAT
49694 AATATTTTA-
1 AAT-TTTTAT
49703 AATATGCTTTATT
1 AAT-T--TTTA-T
49716 AA-TTTTAT
1 AATTTTTAT
49724 AAATTTTTAT
1 -AATTTTTAT
*
49734 AATTTATTAG
1 AATTT-TTAT
49744 AATTTTT-T
1 AATTTTTAT
* **
49752 TATCATTAT
1 AATTTTTAT
49761 AAGTTTTTAT
1 AA-TTTTTAT
*
49771 AATATTTA-
1 AATTTTTAT
49779 AATATTTTA-
1 AAT-TTTTAT
49788 AATATGCTTTAT
1 AAT-T--TTTAT
*
49800 TATTTTTAT
1 AATTTTTAT
*
49809 AA-ATTTAT
1 AATTTTTAT
*
49817 --TTATTAT
1 AATTTTTAT
49824 AATTTTT-T
1 AATTTTTAT
49832 AATTTTTAT
1 AATTTTTAT
49841 ATATTTTTAT
1 A-ATTTTTAT
49851 GAGAAAATAT
Statistics
Matches: 141, Mismatches: 20, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
7 7 0.05
8 26 0.18
9 56 0.40
10 36 0.26
11 12 0.09
12 2 0.01
13 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
AATTTTTAT
Found at i:49860 original size:85 final size:83
Alignment explanation
Indices: 49651--49834 Score: 268
Period size: 85 Copynumber: 2.2 Consensus size: 83
49641 ATAACATTAT
* *
49651 TTTATTAGAATTTTTT-ATTATTTATAAGTTTTTATAGTATTTAAATATTTTAAATATGCTTTAT
1 TTTATTAGAATTTTTTAATCA-TTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTAT
49715 TAATTTTATAAATTTTTATAA
65 TAATTTTATAAA--TTTATAA
*
49736 TTTATTAGAATTTTTTTATCATTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
1 TTTATTAGAATTTTTTAATCATTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
*
49801 ATTTTTATAAA-TT-T-A
66 AATTTTATAAATTTATAA
*
49816 TTTATTATAATTTTTTAAT
1 TTTATTAGAATTTTTTAAT
49835 TTTTATATAT
Statistics
Matches: 93, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
80 18 0.19
81 1 0.01
82 2 0.02
85 69 0.74
86 3 0.03
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (83 bp):
TTTATTAGAATTTTTTAATCATTATAAGTTTTTATAATATTTAAATATTTTAAATATGCTTTATT
AATTTTATAAATTTATAA
Found at i:52040 original size:21 final size:21
Alignment explanation
Indices: 52006--52055 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
51996 ATAATAGCAT
* * *
52006 AATCAAAATATAAAGTTTAGA
1 AATCCAAACATAAAATTTAGA
* *
52027 AATTCAAACATAAAATTTATA
1 AATCCAAACATAAAATTTAGA
52048 AATCCAAA
1 AATCCAAA
52056 TTACATAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.28
Consensus pattern (21 bp):
AATCCAAACATAAAATTTAGA
Found at i:53474 original size:25 final size:25
Alignment explanation
Indices: 53441--53490 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
53431 TTGTAAATCA
53441 GAAAAATATC-TCTAGAG-ATTTTCT
1 GAAAAATATCTTC-AGAGAATTTTCT
53465 GAAATAATATCTTCAGAGAATTTTCT
1 GAAA-AATATCTTCAGAGAATTTTCT
53491 CTCTGTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 10 0.43
26 9 0.39
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (25 bp):
GAAAAATATCTTCAGAGAATTTTCT
Found at i:58956 original size:21 final size:21
Alignment explanation
Indices: 58930--59004 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
58920 GGATGCAGAT
58930 TTCTACCGATACAAGTGATAG
1 TTCTACCGATACAAGTGATAG
* *
58951 TTCTACCGATTCAAGTG-TCAC
1 TTCTACCGATACAAGTGAT-AG
* * *
58972 TTTTACCGACACAAGTCAT-G
1 TTCTACCGATACAAGTGATAG
58992 CTTCTACCGATAC
1 -TTCTACCGATAC
59005 TAAAAACTCT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (21 bp):
TTCTACCGATACAAGTGATAG
Found at i:61749 original size:16 final size:16
Alignment explanation
Indices: 61728--61761 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61718 TTCGTAGCTA
*
61728 TTGTTGGAATAAACTC
1 TTGTTGAAATAAACTC
*
61744 TTGTTGAAATCAACTC
1 TTGTTGAAATAAACTC
61760 TT
1 TT
61762 TACTCTTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (16 bp):
TTGTTGAAATAAACTC
Found at i:66669 original size:28 final size:28
Alignment explanation
Indices: 66635--66706 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 28
66625 ATACTCGAGA
*
66635 TATTTTTCAGAACTC-ATATTGTCAAAAT
1 TATTTTTCAGAAC-CAATATCGTCAAAAT
*
66663 TATTTTTTTCAAAACCAATATCGTCAAAAT
1 TA--TTTTTCAGAACCAATATCGTCAAAAT
* *
66693 TATTGTTAAGAACC
1 TATTTTTCAGAACC
66707 CCTAAACCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
28 11 0.31
29 1 0.03
30 24 0.67
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (28 bp):
TATTTTTCAGAACCAATATCGTCAAAAT
Found at i:66671 original size:30 final size:30
Alignment explanation
Indices: 66637--66696 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
66627 ACTCGAGATA
* *
66637 TTTTTCAGAACTC-ATATTGTCAAAATTATT
1 TTTTTCAAAAC-CAATATCGTCAAAATTATT
66667 TTTTTCAAAACCAATATCGTCAAAATTATT
1 TTTTTCAAAACCAATATCGTCAAAATTATT
66697 GTTAAGAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (30 bp):
TTTTTCAAAACCAATATCGTCAAAATTATT
Found at i:66812 original size:23 final size:22
Alignment explanation
Indices: 66786--66857 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 22
66776 CCTTAAAACT
66786 TTAAAACCTTAATTAATAAACAC
1 TTAAAA-CTTAATTAATAAACAC
* *
66809 TTAAAAATTAAAT-A-AAACAC
1 TTAAAACTTAATTAATAAACAC
* *
66829 TAAAAATCATAATTAATAAACAC
1 TTAAAA-CTTAATTAATAAACAC
66852 TTAAAA
1 TTAAAA
66858 AATAAATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
20 11 0.28
21 5 0.13
22 6 0.15
23 17 0.44
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (22 bp):
TTAAAACTTAATTAATAAACAC
Found at i:66819 original size:18 final size:19
Alignment explanation
Indices: 66803--66869 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 19
66793 CTTAATTAAT
66803 AAACACTTAAAAATTAAATA
1 AAACAC-TAAAAATTAAATA
*
66823 AAACACTAAAAATCATAATTAA
1 AAACACTAAAAAT--TAAAT-A
*
66845 TAAACACTTAAAAAATAAATA
1 -AAACAC-TAAAAATTAAATA
66866 AAAC
1 AAAC
66870 CTTAATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 7 0.18
20 10 0.26
21 5 0.13
22 5 0.13
23 6 0.15
24 6 0.15
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (19 bp):
AAACACTAAAAATTAAATA
Found at i:66873 original size:19 final size:20
Alignment explanation
Indices: 66803--66874 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 20
66793 CTTAATTAAT
*
66803 AAACACTTAAAAATTAAATA
1 AAACACTTAAAAAATAAATA
*
66823 AAACAC-TAAAAATCATAATTAA
1 AAACACTTAAAAA--ATAAAT-A
66845 TAAACACTTAAAAAATAAATA
1 -AAACACTTAAAAAATAAATA
66866 AAAC-CTTAA
1 AAACACTTAA
66875 TTTAAATTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
19 11 0.25
20 10 0.23
21 5 0.11
22 6 0.14
23 6 0.14
24 6 0.14
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (20 bp):
AAACACTTAAAAAATAAATA
Found at i:74830 original size:12 final size:12
Alignment explanation
Indices: 74791--74821 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
74781 AGGTTTGCTT
*
74791 GCAGGGGCAGTA
1 GCAGGAGCAGTA
74803 GCAGGAGCAGTA
1 GCAGGAGCAGTA
74815 GCAGGAG
1 GCAGGAG
74822 TAGTCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.48, T:0.06
Consensus pattern (12 bp):
GCAGGAGCAGTA
Found at i:75682 original size:31 final size:31
Alignment explanation
Indices: 75644--75709 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
75634 AACAACTCAA
* *
75644 TGACTTAAATAAAAACTTTCGAATAGTTCAG
1 TGACTTAAATAAAAACTTTCGAAAAATTCAG
* * *
75675 TGACTTAAATGAAAAGTTTTGAAAAATTCAG
1 TGACTTAAATAAAAACTTTCGAAAAATTCAG
75706 TGAC
1 TGAC
75710 CATGTTGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCGAAAAATTCAG
Found at i:78653 original size:20 final size:20
Alignment explanation
Indices: 78628--78665 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
78618 GTCAAAATTT
*
78628 AATAGAAAGTATATGTAATC
1 AATAGAAAATATATGTAATC
78648 AATAGAAAATATATGTAA
1 AATAGAAAATATATGTAA
78666 GTGTGGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (20 bp):
AATAGAAAATATATGTAATC
Found at i:79057 original size:58 final size:58
Alignment explanation
Indices: 78988--79120 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 58
78978 GAAAACCCAT
* * * **
78988 CATAAACTAAACCCAAATATGTATAAACTCAAATATAATTTCATTTTTAAAAAACATT
1 CATAAATTAAACCCAAATATGTATAAACCCAAATATAATTTCATTCTTAAAAAACACG
* * * * *
79046 CATAGATTAAACCCAATTATTTTTAAACCCAAATATAATTTTATTCTTAAAAAACACG
1 CATAAATTAAACCCAAATATGTATAAACCCAAATATAATTTCATTCTTAAAAAACACG
*
79104 CATAAATTAAACTCAAA
1 CATAAATTAAACCCAAA
79121 ATCAATTTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (58 bp):
CATAAATTAAACCCAAATATGTATAAACCCAAATATAATTTCATTCTTAAAAAACACG
Found at i:79954 original size:19 final size:19
Alignment explanation
Indices: 79926--79987 Score: 81
Period size: 20 Copynumber: 3.3 Consensus size: 19
79916 TGTTGTGTTA
*
79926 TTGTTG-TTACTTGGACTT
1 TTGTTGTTTACTTGAACTT
* *
79944 ATGTTGTTTACTAGAACTT
1 TTGTTGTTTACTTGAACTT
79963 TTGTTTGTTTACTTGAACTT
1 TTG-TTGTTTACTTGAACTT
79983 TTGTT
1 TTGTT
79988 TATTTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 5 0.14
19 14 0.38
20 18 0.49
ACGTcount: A:0.16, C:0.10, G:0.18, T:0.56
Consensus pattern (19 bp):
TTGTTGTTTACTTGAACTT
Found at i:83247 original size:30 final size:32
Alignment explanation
Indices: 83196--83261 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
83186 TCATTAAATG
*
83196 TATACAATTGAATTAAAAATAAAATT-TTATA
1 TATACAATTGAATTAAAAATAAAATTGTAATA
* *
83227 TATACATTTGAA-TCAAAATAAAATTGTAATA
1 TATACAATTGAATTAAAAATAAAATTGTAATA
83258 TATA
1 TATA
83262 TGTATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (32 bp):
TATACAATTGAATTAAAAATAAAATTGTAATA
Found at i:85971 original size:13 final size:13
Alignment explanation
Indices: 85953--85988 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
85943 TATTCAATTG
* *
85953 AAATTAAACTTGA
1 AAATTAAAATTAA
85966 AAATTAAAATTAA
1 AAATTAAAATTAA
85979 AAATTAAAAT
1 AAATTAAAAT
85989 GAATTTGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (13 bp):
AAATTAAAATTAA
Found at i:93818 original size:32 final size:33
Alignment explanation
Indices: 93754--93819 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
93744 TCCATCACAG
93754 CATTCCCGGTTTGGATGTGCAATGAAATGAGCA
1 CATTCCCGGTTTGGATGTGCAATGAAATGAGCA
*
93787 CATTCCCGGTTTGGATGTGCGA-GAAATGAGCA
1 CATTCCCGGTTTGGATGTGCAATGAAATGAGCA
93819 C
1 C
93820 CTCGAGATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 11 0.34
33 21 0.66
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (33 bp):
CATTCCCGGTTTGGATGTGCAATGAAATGAGCA
Found at i:94286 original size:46 final size:47
Alignment explanation
Indices: 94234--94332 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 47
94224 CTTATTTTTT
* *
94234 GTGCAAGTCA-TTTCTTTTGCACACGTA-TTCTTTACCTATATTATTG
1 GTGCAAGTCATTTTCTTTTGCACACGTACGT-TTTACCTACATTATTG
* * **
94280 GTGCAAGTTATTTTTTTTTGCACGTGTACGTTTTACCTACATTATTG
1 GTGCAAGTCATTTTCTTTTGCACACGTACGTTTTACCTACATTATTG
94327 GTGCAA
1 GTGCAA
94333 ATAATGTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 9 0.20
47 35 0.78
48 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.45
Consensus pattern (47 bp):
GTGCAAGTCATTTTCTTTTGCACACGTACGTTTTACCTACATTATTG
Done.