Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019929.1 Corchorus olitorius cultivar O-4 contig19962, 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: 67851
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2823 original size:7 final size:7
Alignment explanation
Indices: 2811--2843 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2801 GCTTTCATAG
2811 AACAAAA
1 AACAAAA
2818 AACAAAA
1 AACAAAA
2825 AAC-AAA
1 AACAAAA
2831 AAC-AAA
1 AACAAAA
2837 AACAAAA
1 AACAAAA
2844 GTACGTACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
AACAAAA
Found at i:3808 original size:44 final size:44
Alignment explanation
Indices: 3740--3864 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 44
3730 TGACAATCAA
** * * * * * *
3740 ACCAAAATCACATAGAAAGATTATCACAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATACAAAGGTTATCAAAATTTCATAGTATAGTT
* *
3784 ACCAAAATTTCATATAAAGGTTATCAAAACTTCATAGTATAGTT
1 ACCAAAATTTCATACAAAGGTTATCAAAATTTCATAGTATAGTT
* * * *
3828 ATCAAAATTTCATACAGAGGTTACCAAAATTTTATAG
1 ACCAAAATTTCATACAAAGGTTATCAAAATTTCATAG
3865 GGAGGGAGGT
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (44 bp):
ACCAAAATTTCATACAAAGGTTATCAAAATTTCATAGTATAGTT
Found at i:4019 original size:22 final size:22
Alignment explanation
Indices: 3760--4214 Score: 134
Period size: 22 Copynumber: 20.6 Consensus size: 22
3750 CATAGAAAGA
* * * *
3760 TTATCACAATTTCGTAGTGTGG
1 TTATCAAAATTTCATAGGGAGG
* ***
3782 TTACCAAAATTTCATATAAAGG
1 TTATCAAAATTTCATAGGGAGG
* * *
3804 TTATCAAAACTTCATA-GTATAG
1 TTATCAAAATTTCATAGGGA-GG
**
3826 TTATCAAAATTTCATACAGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
3848 TTACCAAAATTTTATAGGGAGGGAGG
1 TTATCAAAATTTCAT----AGGGAGG
* *
3874 TTACCAAAATTT-AT-----GC
1 TTATCAAAATTTCATAGGGAGG
*
3890 TTATCAAAATTTCCTAGAGG-GG
1 TTATCAAAATTTCATAG-GGAGG
*
3912 TTAACAAAATTT-ATAGGGAGG
1 TTATCAAAATTTCATAGGGAGG
* * *
3933 TTATGAAAATTTTAT-GGAGAGC
1 TTATCAAAATTTCATAGG-GAGG
* *
3955 TTATCGAAAA-TACATAGAGAGG
1 TTATC-AAAATTTCATAGGGAGG
* *
3977 ATATCACTGTATCATTCTCATAGGGAGG
1 TTATCA----A-AATT-TCATAGGGAGG
* *
4005 TTATCGAAATTTCAT-GGTGTGG
1 TTATCAAAATTTCATAGG-GAGG
* *
4027 TTATCAAAATTTTCATAGTGCGG
1 TTATCAAAA-TTTCATAGGGAGG
* * * * *
4050 TTA-C-CAATTTTATTTAGTGTGA
1 TTATCAAAATTTCA--TAGGGAGG
* * * *
4072 TTATTAAAATTTTATAGGTAGA
1 TTATCAAAATTTCATAGGGAGG
* **
4094 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGGGAGG
* * * * *
4116 TTATCGAAATATCATAGTGTGA
1 TTATCAAAATTTCATAGGGAGG
* * *
4138 TTACCAAAATTTC--AGTGTGG
1 TTATCAAAATTTCATAGGGAGG
* *
4158 TTATCAAATTTTCATATGGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
4180 TTATCGAAATTTCATA-TGAGG
1 TTATCAAAATTTCATAGGGAGG
*
4201 TTATCAAATTTTCA
1 TTATCAAAATTTCA
4215 AAATGTGGTT
Statistics
Matches: 319, Mismatches: 81, Indels: 67
0.68 0.17 0.14
Matches are distributed among these distances:
16 12 0.04
17 1 0.00
20 23 0.07
21 39 0.12
22 179 0.56
23 21 0.07
24 9 0.03
25 3 0.01
26 18 0.06
27 1 0.00
28 13 0.04
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:4156 original size:20 final size:20
Alignment explanation
Indices: 4131--4171 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4121 GAAATATCAT
4131 AGTGTGATTACCAAAATTTC
1 AGTGTGATTACCAAAATTTC
* * *
4151 AGTGTGGTTATCAAATTTTC
1 AGTGTGATTACCAAAATTTC
4171 A
1 A
4172 TATGGAGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (20 bp):
AGTGTGATTACCAAAATTTC
Found at i:4225 original size:43 final size:42
Alignment explanation
Indices: 4094--4235 Score: 126
Period size: 43 Copynumber: 3.3 Consensus size: 42
4084 TATAGGTAGA
* * * *
4094 TTATCAAAATTTCACACTGAGGTTATCGAAA-TATCATAGTGTGA
1 TTATCAAAATTTCA-A-TGAGGTTATC-AAATTTTCAAAATGTGG
* * * * *
4138 TTACCAAAATTTCAGTGTGGTTATCAAATTTTC-ATATGGAGG
1 TTATCAAAATTTCAATGAGGTTATCAAATTTTCAAAAT-GTGG
*
4180 TTATCGAAATTTCATATGAGGTTATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCA-ATGAGGTTATCAAATTTTCAAAATGTGG
*
4223 TTATCAATATTTC
1 TTATCAAAATTTC
4236 TACATTGGAG
Statistics
Matches: 77, Mismatches: 17, Indels: 9
0.75 0.17 0.09
Matches are distributed among these distances:
41 4 0.05
42 26 0.34
43 31 0.40
44 16 0.21
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (42 bp):
TTATCAAAATTTCAATGAGGTTATCAAATTTTCAAAATGTGG
Found at i:4235 original size:22 final size:21
Alignment explanation
Indices: 4094--4234 Score: 99
Period size: 22 Copynumber: 6.5 Consensus size: 21
4084 TATAGGTAGA
* *
4094 TTATCAAAATTTCACACTGAGG
1 TTATCAAATTTTCATA-TGAGG
* * *
4116 TTATCGAAA-TATCATAGTGTGA
1 TTATC-AAATTTTCATA-TGAGG
* * * *
4138 TTACCAAAATTTCA-GTGTGG
1 TTATCAAATTTTCATATGAGG
4158 TTATCAAATTTTCATATGGAGG
1 TTATCAAATTTTCATAT-GAGG
4180 TTATCGAAA-TTTCATATGAGG
1 TTATC-AAATTTTCATATGAGG
* *
4201 TTATCAAATTTTCAAAATGTGG
1 TTATCAAATTTTC-ATATGAGG
4223 TTATCAATATTT
1 TTATCAA-ATTT
4235 CTACATTGGA
Statistics
Matches: 96, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
20 19 0.20
21 17 0.18
22 50 0.52
23 10 0.10
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (21 bp):
TTATCAAATTTTCATATGAGG
Found at i:5287 original size:23 final size:24
Alignment explanation
Indices: 5255--5317 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 24
5245 CACAATTGCT
5255 TGGCGCCCGACCACTTCCA-AAC-C
1 TGGCG-CCGACCACTTCCATAACGC
5278 TGGCGACCGACCACTTCCATAACGC
1 TGGCG-CCGACCACTTCCATAACGC
5303 -GGCGCTCGACCACTT
1 TGGCGC-CGACCACTT
5318 GTGACCACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 19 0.53
24 16 0.44
25 1 0.03
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.16
Consensus pattern (24 bp):
TGGCGCCGACCACTTCCATAACGC
Found at i:6533 original size:22 final size:22
Alignment explanation
Indices: 6508--7036 Score: 126
Period size: 22 Copynumber: 23.6 Consensus size: 22
6498 ACATAGGAAT
*
6508 GTTATTAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
6530 GTTACCAAAATTTCATA-TGGAG
1 GTTATCAAAATTTCATAGT-GTG
* * *
6552 GTTATCAAAACTTCGTAGTGTA
1 GTTATCAAAATTTCATAGTGTG
** *
6574 GTTATCAAAATTTCATACAGAG
1 GTTATCAAAATTTCATAGTGTG
* ****
6596 GTTACCAAAATTTCATAAAAAAG
1 GTTATCAAAATTTCAT-AGTGTG
*
6619 GTTATCAAAATTTCTTA-TG-G
1 GTTATCAAAATTTCATAGTGTG
**
6639 AGATTATCAAAATTTCATACG-AAG
1 -G-TTATCAAAATTTCATA-GTGTG
** * * *
6663 GTTATTGAACTTTTATAGTTTG
1 GTTATCAAAATTTCATAGTGTG
* * ***
6685 ATTATCAAAA-TTAATTAG-AAC
1 GTTATCAAAATTTCA-TAGTGTG
* *
6706 GTTGA-CAAAATTTCATAGGGAG
1 GTT-ATCAAAATTTCATAGTGTG
* * * *
6728 GTTATGAAAATATT-ATGGAGAG
1 GTTATCAAAAT-TTCATAGTGTG
* **
6750 GTTATCAAAATTACATA-TAAAG
1 GTTATCAAAATTTCATAGT-GTG
** * * **
6772 AATATCACAGTTTCATTCTCATAGGGAA
1 GTTATCA-A----AATT-TCATAGTGTG
* *
6800 GTTATCGAAATTTCATGGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
6822 CTTATCAAAATTTTCATAGTGCG
1 GTTATCAAAA-TTTCATAGTGTG
* * * *
6845 ATTA-C-CAATTTTATAATGTG
1 GTTATCAAAATTTCATAGTGTG
* *
6865 ATTATCAAAATTTCATAGACACTGAG
1 GTTATCAAAATTTCATAG----TGTG
* * *
6891 CTTATCAAAACTTCATTGTGTG
1 GTTATCAAAATTTCATAGTGTG
* * *
6913 GTTAGCAGAATTTCACAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* * *
6935 GTTATCAAAATTTTACATTGTG
1 GTTATCAAAATTTCATAGTGTG
* * *
6957 GTTATCAAATTTTCATAGGGAG
1 GTTATCAAAATTTCATAGTGTG
* * * * **
6979 GTTATCAAGATTCCACAATAAG
1 GTTATCAAAATTTCATAGTGTG
* **
7001 GTTATCAAATTTTCGCAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
7023 GCTATCAATATTTC
1 GTTATCAAAATTTC
7037 TACGTTGGAG
Statistics
Matches: 362, Mismatches: 114, Indels: 62
0.67 0.21 0.12
Matches are distributed among these distances:
20 14 0.04
21 21 0.06
22 256 0.71
23 39 0.11
24 1 0.00
26 18 0.05
27 4 0.01
28 9 0.02
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTG
Found at i:6556 original size:44 final size:44
Alignment explanation
Indices: 6489--6657 Score: 160
Period size: 44 Copynumber: 3.8 Consensus size: 44
6479 TGACATTCAA
* * *
6489 ACCAAAATTACATA-GGAATGTTATTAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATATGG-AGGTTATCAAAATTTCATAGTGTGGTT
* * *
6533 ACCAAAATTTCATATGGAGGTTATCAAAACTTCGTAGTGTAGTT
1 ACCAAAATTTCATATGGAGGTTATCAAAATTTCATAGTGTGGTT
* ** * ****
6577 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAAAAAGGTT
1 ACCAAAATTTCATATGGAGGTTATCAAAATTTCAT-AGTGTGGTT
* * *
6622 ATCAAAATTTCTTATGGAGATTATCAAAATTTCATA
1 ACCAAAATTTCATATGGAGGTTATCAAAATTTCATA
6658 CGAAGGTTAT
Statistics
Matches: 101, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
44 65 0.64
45 36 0.36
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (44 bp):
ACCAAAATTTCATATGGAGGTTATCAAAATTTCATAGTGTGGTT
Found at i:6656 original size:67 final size:65
Alignment explanation
Indices: 6508--6666 Score: 185
Period size: 67 Copynumber: 2.4 Consensus size: 65
6498 ACATAGGAAT
* * * *** *
6508 GTTATTAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGAGGTTATCAAAACTTCGTAGTGT
1 GTTATCAAAATTTCATA-CGAGGTTACCAAAATTTCATAAAAAGGTTATCAAAACTTCGTAGTGG
6573 A
65 A
* *
6574 GTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAAAAAGGTTATCAAAATTTCTTA-TG
1 GTTATCAAAATTTCATAC-GAGGTTACCAAAATTTCAT-AAAAAGGTTATCAAAACTTCGTAGTG
6638 GA
64 GA
6640 GATTATCAAAATTTCATACGAAGGTTA
1 G-TTATCAAAATTTCATACG-AGGTTA
6667 TTGAACTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
66 39 0.49
67 41 0.51
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (65 bp):
GTTATCAAAATTTCATACGAGGTTACCAAAATTTCATAAAAAGGTTATCAAAACTTCGTAGTGGA
Found at i:17128 original size:22 final size:22
Alignment explanation
Indices: 17102--17147 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
17092 TTCACCAACA
17102 TCTCCTTTCCTTCATGCTAAAC
1 TCTCCTTTCCTTCATGCTAAAC
17124 TCTCCTTTCCTTCATGCTAAAC
1 TCTCCTTTCCTTCATGCTAAAC
17146 TC
1 TC
17148 AAAAGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.37, G:0.04, T:0.41
Consensus pattern (22 bp):
TCTCCTTTCCTTCATGCTAAAC
Found at i:29116 original size:31 final size:31
Alignment explanation
Indices: 29081--29176 Score: 156
Period size: 31 Copynumber: 3.1 Consensus size: 31
29071 AAGGGACTGA
*
29081 TTTGTCCCAAAAGATAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
29112 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
* * *
29143 TTTGTCTCAAAAGAAAAATATAAGAGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
29174 TTT
1 TTT
29177 TAGTATTTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:30274 original size:33 final size:32
Alignment explanation
Indices: 30226--30323 Score: 128
Period size: 30 Copynumber: 3.1 Consensus size: 32
30216 ACTAAATACT
* * **
30226 AAAAAAATTCTCTTATACTTTTCTTTTGGGGAC
1 AAAAAAAATCCCTTATGTTTTTCTTTT-GGGAC
*
30259 AAAAAAAATCCCTTATGTTTTTCTTTTGCGAC
1 AAAAAAAATCCCTTATGTTTTTCTTTTGGGAC
30291 --AAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAAATCCCTTATGTTTTTCTTTTGGGAC
30321 AAA
1 AAA
30324 TCAATCCCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
30 29 0.51
32 5 0.09
33 23 0.40
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (32 bp):
AAAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:30333 original size:31 final size:30
Alignment explanation
Indices: 30244--30333 Score: 126
Period size: 30 Copynumber: 2.9 Consensus size: 30
30234 TCTCTTATAC
30244 TTTTCTTTTGGGGACAAAAAAAATCCCTTATGT
1 TTTTCTTTT-GGGAC--AAAAAATCCCTTATGT
*
30277 TTTTCTTTTGCGACAAAAAATCCCTTATGT
1 TTTTCTTTTGGGACAAAAAATCCCTTATGT
*
30307 TTTTCTTTTGGGACAAATCAATCCCTT
1 TTTTCTTTTGGGACAAA-AAATCCCTT
30334 GCTGACGTGG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 32 0.60
31 8 0.15
32 4 0.08
33 9 0.17
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (30 bp):
TTTTCTTTTGGGACAAAAAATCCCTTATGT
Found at i:30489 original size:29 final size:30
Alignment explanation
Indices: 30447--30520 Score: 123
Period size: 29 Copynumber: 2.5 Consensus size: 30
30437 CTCATTTTTG
30447 AAACATAAGGGATTAATTTGTCCCAAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
*
30476 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
30507 AAACATAAGGGATT
1 AAACATAAGGGATT
30521 TTTTTGGGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 27 0.64
31 15 0.36
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:44404 original size:1 final size:1
Alignment explanation
Indices: 44398--44423 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
44388 GCTGAAATTT
44398 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
44424 CGGAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:45110 original size:15 final size:15
Alignment explanation
Indices: 45090--45120 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45080 TACTGATTCT
45090 TGGAAGATATTCAAA
1 TGGAAGATATTCAAA
*
45105 TGGAAGGTATTCAAA
1 TGGAAGATATTCAAA
45120 T
1 T
45121 ATGTTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (15 bp):
TGGAAGATATTCAAA
Found at i:46113 original size:16 final size:16
Alignment explanation
Indices: 46094--46124 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46084 ATTAACATGC
46094 AAAGTCTAAAACAAAG
1 AAAGTCTAAAACAAAG
*
46110 AAAGTCTAAAGCAAA
1 AAAGTCTAAAACAAA
46125 CACATCTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAGTCTAAAACAAAG
Found at i:50404 original size:16 final size:16
Alignment explanation
Indices: 50385--50415 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50375 ATTAACATGC
50385 AAAGTCTAAAACAAAG
1 AAAGTCTAAAACAAAG
*
50401 AAAGTCTAAAGCAAA
1 AAAGTCTAAAACAAA
50416 CACATCTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAGTCTAAAACAAAG
Found at i:51648 original size:29 final size:31
Alignment explanation
Indices: 51616--51682 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
51606 ACGCAATTTG
51616 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
51645 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
51676 GGATATA
1 GGATATA
51683 GTCAGTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:51840 original size:31 final size:30
Alignment explanation
Indices: 51802--51879 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
51792 CTAACTGATT
51802 ATATCCTTAATTGCTTGAAATCGAAAACATC
1 ATATCCTTAATTGCTTGAAATC-AAAACATC
* *
51833 ATATCCTTAATTGCTTGAAATCAAAACGTT
1 ATATCCTTAATTGCTTGAAATCAAAACATC
51863 ATATCCTTAATTGCTTG
1 ATATCCTTAATTGCTTG
51880 TTTTGTAACA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 23 0.51
31 22 0.49
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (30 bp):
ATATCCTTAATTGCTTGAAATCAAAACATC
Found at i:51867 original size:30 final size:31
Alignment explanation
Indices: 51799--51935 Score: 145
Period size: 31 Copynumber: 4.5 Consensus size: 31
51789 AGTCTAACTG
51799 ATTATATCCTTAATTGCTTGAAATCGAAAAC
1 ATTATATCCTTAATTGCTTGAAATCGAAAAC
*
51830 ATCATATCCTTAATTGCTTGAAATC-AAAAC
1 ATTATATCCTTAATTGCTTGAAATCGAAAAC
* ** * *
51860 GTTATATCCTTAATTGCTTG-TTTTG-TAAC
1 ATTATATCCTTAATTGCTTGAAATCGAAAAC
** * *
51889 ATTATATCCTTAATTGCTTGTGATAGCAAAC
1 ATTATATCCTTAATTGCTTGAAATCGAAAAC
* *
51920 GTTATATCCTAAATTG
1 ATTATATCCTTAATTG
51936 ATTATTCAAC
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
29 23 0.26
30 25 0.28
31 41 0.46
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (31 bp):
ATTATATCCTTAATTGCTTGAAATCGAAAAC
Found at i:51905 original size:59 final size:61
Alignment explanation
Indices: 51800--51935 Score: 161
Period size: 59 Copynumber: 2.2 Consensus size: 61
51790 GTCTAACTGA
51800 TTATATCCTTAATTGCTTGAAATCGAAAACATCATATCCTTAATTGCTTGAAAT-CAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACATCATATCCTTAATTGCTTGAAATAC-AAACG
** * * * **
51861 TTATATCCTTAATTGCTTG-TTTTG-TAACATTATATCCTTAATTGCTTGTGATAGCAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACATCATATCCTTAATTGCTTGAAATA-CAAACG
*
51921 TTATATCCTAAATTG
1 TTATATCCTTAATTG
51936 ATTATTCAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
59 24 0.37
60 21 0.32
61 20 0.31
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.40
Consensus pattern (61 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACATCATATCCTTAATTGCTTGAAATACAAACG
Found at i:52704 original size:11 final size:11
Alignment explanation
Indices: 52661--52698 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
52651 TTCCTATATA
*
52661 AAATAAATTAT
1 AAATTAATTAT
52672 CAAA-TAATTAT
1 -AAATTAATTAT
52683 AAATTAATTAT
1 AAATTAATTAT
52694 AAATT
1 AAATT
52699 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:53717 original size:15 final size:17
Alignment explanation
Indices: 53692--53724 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53682 TAAAAAGTGA
53692 TTTAAATAAAA-TATTT
1 TTTAAATAAAATTATTT
53708 TTTAAA-AAAATTATTT
1 TTTAAATAAAATTATTT
53724 T
1 T
53725 CTTCTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAATAAAATTATTT
Found at i:53852 original size:31 final size:31
Alignment explanation
Indices: 53814--53894 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
53804 CGTTACAAAA
**
53814 CAAGCAATTAAGGATATAACATTTTTTATTT
1 CAAGCAATTAAGGATATAACATTTTCGATTT
* *
53845 CAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACATTTTCGATTT
53876 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
53895 TAAGTTAGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACATTTTCGATTT
Found at i:53853 original size:60 final size:62
Alignment explanation
Indices: 53754--53894 Score: 160
Period size: 60 Copynumber: 2.3 Consensus size: 62
53744 AGATGATAAG
* * *
53754 CAAGCAATTTAGGATATAACGTTTTATGCTGCAAACAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACATTTTATACTGCAAACAATTAAGGATATAACGTTTACGAAAA
* * * * * * ***
53814 CAAGCAATTAAGGATATAACATTTTTTATTTCAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACATTTTATACTGCAAACAATTAAGGATATAACGTTTACGAAAA
53876 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
53895 TAAGTTAGGG
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 44 0.66
61 3 0.04
62 20 0.30
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (62 bp):
CAAGCAATTAAGGATATAACATTTTATACTGCAAACAATTAAGGATATAACGTTTACGAAAA
Found at i:54087 original size:29 final size:31
Alignment explanation
Indices: 54024--54090 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
54014 TCTTACGGAC
*
54024 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAACTGCTCGCTTTTCGTAACGT
*
54055 TATATCCTTAACTGCTTG-TTTT-GTAACGT
1 TATATCCTTAACTGCTCGCTTTTCGTAACGT
54084 TATATCC
1 TATATCC
54091 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (31 bp):
TATATCCTTAACTGCTCGCTTTTCGTAACGT
Found at i:54490 original size:5 final size:5
Alignment explanation
Indices: 54480--54525 Score: 78
Period size: 5 Copynumber: 9.6 Consensus size: 5
54470 TGAGATCTCG
54480 TTATC TTATC TTA-C -TATC TTATC TTATC TTATC TTATC TTATC TTA
1 TTATC TTATC TTATC TTATC TTATC TTATC TTATC TTATC TTATC TTA
54526 CTACTATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 35 0.90
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATC
Found at i:55676 original size:22 final size:22
Alignment explanation
Indices: 55651--55990 Score: 71
Period size: 22 Copynumber: 15.3 Consensus size: 22
55641 AATTTCCGTA
55651 TGATAAC-CTCCTTAT-AAACTTT
1 TGATAACACTCC-TATGAAA-TTT
*
55673 TGATAACATTCCTATGAAATTT
1 TGATAACACTCCTATGAAATTT
** * **
55695 TGATAA-TGTACTATGTTATTT
1 TGATAACACTCCTATGAAATTT
* * * * *
55716 TGAAAACATTCCTATCAAAATA
1 TGATAACACTCCTATGAAATTT
* *
55738 TAAGAACA-TCCCTATGAAATTT
1 TGATAACACT-CCTATGAAATTT
*
55760 TGTTAAC-CTCCCTAT-ACAATTT
1 TGATAACACT-CCTATGA-AATTT
* * * *
55782 TGAAAACATTACTATAAAATTT
1 TGATAACACTCCTATGAAATTT
* * *
55804 TGATAA-TCTCCATGTGAAATGT
1 TGATAACACTCC-TATGAAATTT
* * *
55826 TGGTAAGCAC-ACTATGAACTTTT
1 TGATAA-CACTCCTATGAA-ATTT
*
55849 TTATAAC-CTCCCTATGAAATCTT
1 TGATAACACT-CCTATGAAAT-TT
* *
55872 AGTGAT--CAC-ACTGTGAAATTT
1 --TGATAACACTCCTATGAAATTT
* *
55893 TGATAATCACACACTATGAAATTG
1 TGATAA-CACTC-CTATGAAATTT
* * *
55917 T-A-AAGACCTCGGTATAAAATTT
1 TGATAACA-CTC-CTATGAAATTT
* * *
55939 TGATAAACATTCATATAAAATTT
1 TGAT-AACACTCCTATGAAATTT
* *
55962 TTATAA-ACCTCCCTATAAAATTT
1 TGATAACA-CT-CCTATGAAATTT
55985 TGATAA
1 TGATAA
55991 TCACAAATTT
Statistics
Matches: 226, Mismatches: 63, Indels: 57
0.65 0.18 0.16
Matches are distributed among these distances:
19 4 0.02
21 24 0.11
22 122 0.54
23 56 0.25
24 14 0.06
25 6 0.03
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (22 bp):
TGATAACACTCCTATGAAATTT
Found at i:55937 original size:46 final size:46
Alignment explanation
Indices: 55887--55995 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 46
55877 TCACACTGTG
* **
55887 AAATTTTGATAATCACACACTATGAAA-TTGTA-AAGACCTCGGTATA
1 AAATTTTGATAATCACACA-TATAAAATTTGTATAA-ACCTCCCTATA
* ** *
55933 AAATTTTGATAAACATTCATATAAAATTTTTATAAACCTCCCTATA
1 AAATTTTGATAATCACACATATAAAATTTGTATAAACCTCCCTATA
55979 AAATTTTGATAATCACA
1 AAATTTTGATAATCACA
55996 AATTTCGATA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
45 6 0.12
46 43 0.84
47 2 0.04
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (46 bp):
AAATTTTGATAATCACACATATAAAATTTGTATAAACCTCCCTATA
Found at i:55956 original size:23 final size:23
Alignment explanation
Indices: 55929--55990 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
55919 AAGACCTCGG
*
55929 TATAAAATTTTGATAAACATTCA
1 TATAAAATTTTGATAAACATCCA
* * *
55952 TATAAAATTTTTATAAACCTCCC
1 TATAAAATTTTGATAAACATCCA
55975 TATAAAATTTTGATAA
1 TATAAAATTTTGATAA
55991 TCACAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.40
Consensus pattern (23 bp):
TATAAAATTTTGATAAACATCCA
Found at i:59924 original size:5 final size:5
Alignment explanation
Indices: 59914--59974 Score: 108
Period size: 5 Copynumber: 12.6 Consensus size: 5
59904 TGAGAACTCG
59914 TTATC TTATC TTA-C -TATC TTATC TTATC TTATC TTATC TTATC TTATC
1 TTATC TTATC TTATC TTATC TTATC TTATC TTATC TTATC TTATC TTATC
59962 TTATC TTATC TTA
1 TTATC TTATC TTA
59975 CTACTATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 50 0.93
ACGTcount: A:0.21, C:0.20, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATC
Found at i:61110 original size:22 final size:22
Alignment explanation
Indices: 61085--61570 Score: 73
Period size: 22 Copynumber: 22.3 Consensus size: 22
61075 AATCTCCGTA
61085 TGATAAC-CTCCTTAT-AAACTTT
1 TGATAACACTCC-TATGAAA-TTT
*
61107 TGATAACATTCCTATGAAATTT
1 TGATAACACTCCTATGAAATTT
** * **
61129 TGATAA-TGTACTATGTTATTT
1 TGATAACACTCCTATGAAATTT
* * * * *
61150 TGAAAACATTCCTATCAAAATA
1 TGATAACACTCCTATGAAATTT
* *
61172 TAAGAACA-TCCCTATGAAATTT
1 TGATAACACT-CCTATGAAATTT
*
61194 TGTTAAC-CTCCCTAT-ACAATTT
1 TGATAACACT-CCTATGA-AATTT
* * * *
61216 TGAAAACATTACTATAAAATTT
1 TGATAACACTCCTATGAAATTT
* * *
61238 TGATAA-TCTCCATGTGAAATGT
1 TGATAACACTCC-TATGAAATTT
* * *
61260 TGGTAAGCAC-ACTATGAACTTTT
1 TGATAA-CACTCCTATGAA-ATTT
*
61283 TTATAAC-CTCCCTATGAAATCTT
1 TGATAACACT-CCTATGAAAT-TT
* *
61306 AGTGAT--CAC-ACTGTGAAATTT
1 --TGATAACACTCCTATGAAATTT
* *
61327 TGATAATCACACACTATGAAATTG
1 TGATAA-CACTC-CTATGAAATTT
* * *
61351 T-A-AAGACCTCGGTATAAAATTT
1 TGATAACA-CTC-CTATGAAATTT
* * *
61373 TGATAAACATTCATATAAAATTT
1 TGAT-AACACTCCTATGAAATTT
* *
61396 TTATAA-ACCTCCCTATAAAATTT
1 TGATAACA-CT-CCTATGAAATTT
*
61419 TGAT-A-A-T-C-A-CAAATTT
1 TGATAACACTCCTATGAAATTT
* *
61435 CGATAAC-CTTCCTATG-ATTTT
1 TGATAACAC-TCCTATGAAATTT
* *
61456 TCGATAAC-TTCATTATGAAA-TT
1 T-GATAACACTC-CTATGAAATTT
*
61478 TCATTAAC-CTCCGTATGAAATTT
1 TGA-TAACACTCC-TATGAAATTT
*
61501 TGAT-A-AC-CCTATAAAATTT
1 TGATAACACTCCTATGAAATTT
*
61520 TGA-AA-ACTAAACTATGAAATTT
1 TGATAACACT--CCTATGAAATTT
* *
61542 TGATAATC-CCCCTTTGAAATTT
1 TGATAA-CACTCCTATGAAATTT
*
61564 TAATAAC
1 TGATAAC
61571 CTTCATACAA
Statistics
Matches: 332, Mismatches: 82, Indels: 101
0.64 0.16 0.20
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 1 0.00
19 20 0.06
20 4 0.01
21 35 0.11
22 179 0.54
23 61 0.18
24 15 0.05
25 6 0.02
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TGATAACACTCCTATGAAATTT
Found at i:61371 original size:46 final size:46
Alignment explanation
Indices: 61321--61429 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 46
61311 TCACACTGTG
* **
61321 AAATTTTGATAATCACACACTATGAAA-TTGTA-AAGACCTCGGTATA
1 AAATTTTGATAATCACACA-TATAAAATTTGTATAA-ACCTCCCTATA
* ** *
61367 AAATTTTGATAAACATTCATATAAAATTTTTATAAACCTCCCTATA
1 AAATTTTGATAATCACACATATAAAATTTGTATAAACCTCCCTATA
61413 AAATTTTGATAATCACA
1 AAATTTTGATAATCACA
61430 AATTTCGATA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
45 6 0.12
46 43 0.84
47 2 0.04
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (46 bp):
AAATTTTGATAATCACACATATAAAATTTGTATAAACCTCCCTATA
Found at i:61390 original size:23 final size:23
Alignment explanation
Indices: 61363--61424 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
61353 AAGACCTCGG
*
61363 TATAAAATTTTGATAAACATTCA
1 TATAAAATTTTGATAAACATCCA
* * *
61386 TATAAAATTTTTATAAACCTCCC
1 TATAAAATTTTGATAAACATCCA
61409 TATAAAATTTTGATAA
1 TATAAAATTTTGATAA
61425 TCACAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.40
Consensus pattern (23 bp):
TATAAAATTTTGATAAACATCCA
Found at i:61733 original size:44 final size:42
Alignment explanation
Indices: 61659--61754 Score: 97
Period size: 44 Copynumber: 2.2 Consensus size: 42
61649 ATAATAACAT
* * * * *
61659 TATGAAATTTCGATAACCTTCTTATGAAATTTTGCTAACCTCTC-
1 TATGAAATTTAGATAACATACTTAT-AAAATTTG-AAACCTC-CA
61703 TATGAAATTTAGATAATCATAC-TATAAAATTTGAAACCTCCA
1 TATGAAATTTAGATAA-CATACTTATAAAATTTGAAACCTCCA
61745 TATGAAATTT
1 TATGAAATTT
61755 TAATGACCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.02
42 16 0.36
43 7 0.16
44 18 0.40
45 3 0.07
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (42 bp):
TATGAAATTTAGATAACATACTTATAAAATTTGAAACCTCCA
Found at i:61843 original size:22 final size:22
Alignment explanation
Indices: 61663--61852 Score: 77
Period size: 22 Copynumber: 8.6 Consensus size: 22
61653 TAACATTATG
* * *
61663 AAATTTCGATAACCTTC-TTATG
1 AAATTTTGATAACC-TCGCTATA
* * *
61685 AAATTTTGCTAACCTCTCTATG
1 AAATTTTGATAACCTCGCTATA
* * *
61707 AAATTTAGATAATCAT-ACTATA
1 AAATTTTGATAA-CCTCGCTATA
*
61729 AAA-TTTGA-AACCTC-CATATG
1 AAATTTTGATAACCTCGC-TATA
* * * **
61749 AAATTTTAATGACCACAATATGA
1 AAATTTTGATAACCTCGCTAT-A
* * * **
61772 AAATTTTTCAGAACCTCACTGGA
1 AAA-TTTTGATAACCTCGCTATA
*
61795 AAATTTTGATAACCTCGCTTTA
1 AAATTTTGATAACCTCGCTATA
*
61817 AAATTTTGATAACCTTC-CTATG
1 AAATTTTGATAACC-TCGCTATA
*
61839 TAATTTTGATAACC
1 AAATTTTGATAACC
61853 ACATTATGGA
Statistics
Matches: 127, Mismatches: 31, Indels: 20
0.71 0.17 0.11
Matches are distributed among these distances:
19 3 0.02
20 8 0.06
21 10 0.08
22 84 0.66
23 11 0.09
24 11 0.09
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCTCGCTATA
Found at i:61860 original size:22 final size:22
Alignment explanation
Indices: 61796--61937 Score: 64
Period size: 22 Copynumber: 6.4 Consensus size: 22
61786 CTCACTGGAA
* **
61796 AATTTTGATAACCT-CGCTTTAA
1 AATTTTGATAACCTAC-CTATGT
*
61818 AATTTTGATAACCTTCCTATGT
1 AATTTTGATAACCTACCTATGT
*
61840 AATTTTGATAACC-ACATTATG-
1 AATTTTGATAACCTAC-CTATGT
* * * *
61861 GA-TTTGATAACTTTCCTATGC
1 AATTTTGATAACCTACCTATGT
* *
61882 AATTTTGGTAATCTGATCTCTATG-
1 AATTTTGATAACCT-A-C-CTATGT
61906 AATTTTTGATAA-CTACTCTATG-
1 AA-TTTTGATAACCTAC-CTATGT
61928 AGATTTTGAT
1 A-ATTTTGAT
61938 TGCTTCCTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
20 13 0.14
21 4 0.04
22 57 0.60
23 3 0.03
24 5 0.05
25 13 0.14
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.44
Consensus pattern (22 bp):
AATTTTGATAACCTACCTATGT
Found at i:61910 original size:24 final size:21
Alignment explanation
Indices: 61818--61937 Score: 77
Period size: 22 Copynumber: 5.4 Consensus size: 21
61808 CTCGCTTTAA
*
61818 AATTTTGATAACCTTC-CTATG
1 AATTTTGATAA-CTACTCTATG
*
61839 TAATTTTGATAACCACAT-TATG
1 -AATTTTGATAACTAC-TCTATG
* *
61861 GA-TTTGATAACT-TTCCTATG
1 AATTTTGATAACTACT-CTATG
*
61881 CAATTTTGGTAATCTGATCTCTATG
1 -AATTTTGATAA-CT-A-CTCTATG
61906 AATTTTTGATAACTACTCTATG
1 AA-TTTTGATAACTACTCTATG
61928 AGATTTTGAT
1 A-ATTTTGAT
61938 TGCTTCCTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
18 1 0.01
20 13 0.17
21 4 0.05
22 37 0.48
23 4 0.05
24 4 0.05
25 13 0.17
26 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.44
Consensus pattern (21 bp):
AATTTTGATAACTACTCTATG
Found at i:62013 original size:28 final size:29
Alignment explanation
Indices: 61972--62026 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
61962 CCAACTATAA
*
61972 AATTTTGATAACATTCGTATGAAATTTAG
1 AATTTTGATAACATTAGTATGAAATTTAG
*
62001 AATTTT-ATAACATTATTATGAAATTT
1 AATTTTGATAACATTAGTATGAAATTT
62027 TGGTTACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.45
Consensus pattern (29 bp):
AATTTTGATAACATTAGTATGAAATTTAG
Found at i:62072 original size:45 final size:44
Alignment explanation
Indices: 62021--62123 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 44
62011 CATTATTATG
* * *
62021 AAATTTTGGTTACCACACTATGAAATCTTTAATAACCTC-CTGATA
1 AAATTTTGATAACCACACTATGAAAT-TCTAATAACCTCGCT-ATA
** * *
62066 AAATTTTGATAACGGCACTATGAAATTCTGATAACCTCGCTATG
1 AAATTTTGATAACCACACTATGAAATTCTAATAACCTCGCTATA
*
62110 AAATTTTAATAACC
1 AAATTTTGATAACC
62124 TCTTTGATAG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
44 24 0.50
45 24 0.50
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (44 bp):
AAATTTTGATAACCACACTATGAAATTCTAATAACCTCGCTATA
Found at i:62077 original size:22 final size:22
Alignment explanation
Indices: 62017--62125 Score: 94
Period size: 22 Copynumber: 4.9 Consensus size: 22
62007 ATAACATTAT
** * *
62017 TATGAAATTTTGGTTACCACAC
1 TATGAAATTTTAATAACCTCAC
62039 TATGAAATCTTTAATAACCTC-C
1 TATGAAAT-TTTAATAACCTCAC
* * **
62061 TGATAAAATTTTGATAACGGCAC
1 T-ATGAAATTTTAATAACCTCAC
* * *
62084 TATGAAATTCTGATAACCTCGC
1 TATGAAATTTTAATAACCTCAC
62106 TATGAAATTTTAATAACCTC
1 TATGAAATTTTAATAACCTC
62126 TTTGATAGCC
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
22 53 0.77
23 16 0.23
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTAATAACCTCAC
Found at i:62115 original size:44 final size:44
Alignment explanation
Indices: 62017--62123 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 44
62007 ATAACATTAT
* * *
62017 TATGAAATTTTGGTTACCACACTATGAAATCTTTAATAACCTCC
1 TATGAAATTTTGATAACCACACTATGAAATCTCTAATAACCTCC
* ** *
62061 TGATAAAATTTTGATAACGGCACTATGAAAT-TCTGATAACCTCGC
1 T-ATGAAATTTTGATAACCACACTATGAAATCTCTAATAACCTC-C
*
62106 TATGAAATTTTAATAACC
1 TATGAAATTTTGATAACC
62124 TCTTTGATAG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
44 25 0.49
45 26 0.51
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACACTATGAAATCTCTAATAACCTCC
Found at i:62248 original size:22 final size:23
Alignment explanation
Indices: 62140--62246 Score: 112
Period size: 22 Copynumber: 4.7 Consensus size: 23
62130 ATAGCCTCTT
*
62140 TATGAAATTTTGATAACCAC-AC
1 TATGAAATTTTGATAACCACTCC
**
62162 TATGAAATTTTGATAA-CTTTCC
1 TATGAAATTTTGATAACCACTCC
* *
62184 TATGAAATTTTAATAACCTAATCC
1 TATGAAATTTTGATAACC-ACTCC
*
62208 ATATGAAATTTTGATAATCACT-C
1 -TATGAAATTTTGATAACCACTCC
*
62231 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
62247 TCTTTTGATG
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.01
22 47 0.66
23 2 0.03
24 5 0.07
25 16 0.23
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.39
Consensus pattern (23 bp):
TATGAAATTTTGATAACCACTCC
Found at i:62375 original size:44 final size:43
Alignment explanation
Indices: 62304--62492 Score: 150
Period size: 44 Copynumber: 4.3 Consensus size: 43
62294 AACCTAATCC
* * *
62304 CTAT-AAATTTTGATAACCACTCAATGAAAATTTGATAACCTTT
1 CTATGAAATTTTGATAACCTC-CTATGAAAATTTGATAACCTTA
* * * ** **
62347 CTATGAAATTTTGGTAACCGCACTATGAAATTTTGGCAACCACA
1 CTATGAAATTTTGATAACCTC-CTATGAAAATTTGATAACCTTA
* * * *
62391 ATATGAATTTTTGATAACCTCCCTAT-AAAATTTGGTAA-CTGGA
1 CTATGAAATTTTGATAACCT-CCTATGAAAATTTGATAACCT-TA
* **
62434 CTATGAAATTTTGATAACCTCCTTATGAAATTTTGATAATGTTA
1 CTATGAAATTTTGATAACCTCC-TATGAAAATTTGATAACCTTA
*
62478 TTATGAAATTTTGAT
1 CTATGAAATTTTGAT
62493 TACCACCCAA
Statistics
Matches: 115, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
42 3 0.03
43 36 0.31
44 74 0.64
45 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTCCTATGAAAATTTGATAACCTTA
Found at i:62425 original size:43 final size:43
Alignment explanation
Indices: 62348--62466 Score: 121
Period size: 43 Copynumber: 2.7 Consensus size: 43
62338 ATAACCTTTC
* * * *
62348 TATGAAATTTTGGTAACCGCACTATGAAATTTTGGCAACCACAA
1 TATGAAATTTTGATAACCTCCCTAT-AAAATTTGGCAACCACAA
* * *** *
62392 TATGAATTTTTGATAACCTCCCTATAAAATTTGGTAACTGGAC
1 TATGAAATTTTGATAACCTCCCTATAAAATTTGGCAACCACAA
* *
62435 TATGAAATTTTGATAACCTCCTTATGAAATTT
1 TATGAAATTTTGATAACCTCCCTATAAAATTT
62467 TGATAATGTT
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
43 41 0.66
44 21 0.34
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTCCCTATAAAATTTGGCAACCACAA
Found at i:62461 original size:65 final size:65
Alignment explanation
Indices: 62304--62472 Score: 180
Period size: 65 Copynumber: 2.6 Consensus size: 65
62294 AACCTAATCC
* * * ** *
62304 CTAT-AAATTTTGATAACCACTCAATGAAAATTTGATAACCTTTCTATGAAATTTTGGTAACCGC
1 CTATGAAATTTTGATAACCCCT-TATGAAATTTTGATAACCTCCCTATGAAAATTTGGTAACCGC
62368 A
65 A
** ** * * *
62369 CTATGAAATTTTGGCAACCACAATATGAATTTTTGATAACCTCCCTAT-AAAATTTGGTAACTGG
1 CTATGAAATTTTGATAACC-CCTTATGAAATTTTGATAACCTCCCTATGAAAATTTGGTAACCGC
62433 A
65 A
62434 CTATGAAATTTTGATAACCTCCTTATGAAATTTTGATAA
1 CTATGAAATTTTGATAACC-CCTTATGAAATTTTGATAA
62473 TGTTATTATG
Statistics
Matches: 83, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
65 51 0.61
66 32 0.39
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (65 bp):
CTATGAAATTTTGATAACCCCTTATGAAATTTTGATAACCTCCCTATGAAAATTTGGTAACCGCA
Found at i:62481 original size:22 final size:22
Alignment explanation
Indices: 62308--62492 Score: 119
Period size: 22 Copynumber: 8.5 Consensus size: 22
62298 TAATCCCTAT
62308 AAATTTTGATAACCACTCA--ATG
1 AAATTTTGATAA-C-CTCATTATG
* *
62330 AAAATTTGATAACCT-TTCTATG
1 AAATTTTGATAACCTCAT-TATG
* * *
62352 AAATTTTGGTAACCGCACTATG
1 AAATTTTGATAACCTCATTATG
** * *
62374 AAATTTTGGCAACCACAATATG
1 AAATTTTGATAACCTCATTATG
* **
62396 AATTTTTGATAACCTCCCTAT-
1 AAATTTTGATAACCTCATTATG
* * * *
62417 AAAATTTGGTAA-CTGGACTATG
1 AAATTTTGATAACCT-CATTATG
*
62439 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCATTATG
** *
62461 AAATTTTGATAATGTTATTATG
1 AAATTTTGATAACCTCATTATG
62483 AAATTTTGAT
1 AAATTTTGAT
62493 TACCACCCAA
Statistics
Matches: 126, Mismatches: 30, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
20 4 0.03
21 14 0.11
22 106 0.84
23 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCATTATG
Found at i:62594 original size:22 final size:22
Alignment explanation
Indices: 62568--62618 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
62558 TAAATTTTCC
*
62568 TCATGAAAACTTGATAATCTCA
1 TCATGAAAACTTGAAAATCTCA
**
62590 TCATG-AAGTTTGAAAATCTCA
1 TCATGAAAACTTGAAAATCTCA
*
62611 TTATGAAA
1 TCATGAAA
62619 TTTTTTGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
TCATGAAAACTTGAAAATCTCA
Found at i:62607 original size:21 final size:21
Alignment explanation
Indices: 62578--62617 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
62568 TCATGAAAAC
*
62578 TTGATAATCTCATCATGAAGT
1 TTGAAAATCTCATCATGAAGT
*
62599 TTGAAAATCTCATTATGAA
1 TTGAAAATCTCATCATGAA
62618 ATTTTTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (21 bp):
TTGAAAATCTCATCATGAAGT
Found at i:63237 original size:20 final size:19
Alignment explanation
Indices: 63192--63228 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
63182 CTATATAAAA
*
63192 ATAGTGTGATTATCAATTG
1 ATAGTGTGATTACCAATTG
*
63211 ATAGTGTGGTTACCAATT
1 ATAGTGTGATTACCAATT
63229 TTATAGTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (19 bp):
ATAGTGTGATTACCAATTG
Found at i:63298 original size:21 final size:22
Alignment explanation
Indices: 63249--63387 Score: 118
Period size: 22 Copynumber: 6.4 Consensus size: 22
63239 TGAGATTTTT
63249 AAAATTTCACAGTGTGGTTATC
1 AAAATTTCACAGTGTGGTTATC
* *
63271 AAAATTTCGCTGTGTGGTTATC
1 AAAATTTCACAGTGTGGTTATC
* * * * *
63293 AAATTTTCATAGGGAGATTATC
1 AAAATTTCACAGTGTGGTTATC
* * * *
63315 AAATTTTCATAGGGAGGTTATC
1 AAAATTTCACAGTGTGGTTATC
* * * *
63337 AAAATTTCATAATGAGATTATC
1 AAAATTTCACAGTGTGGTTATC
*
63359 -AATTTTCACAGTGTGGTTATC
1 AAAATTTCACAGTGTGGTTATC
*
63380 AATATTTC
1 AAAATTTC
63388 TACATTAGAG
Statistics
Matches: 95, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
21 16 0.17
22 79 0.83
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (22 bp):
AAAATTTCACAGTGTGGTTATC
Found at i:63387 original size:43 final size:43
Alignment explanation
Indices: 63266--63387 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 43
63256 CACAGTGTGG
* * * *
63266 TTATCAAAATTTCGCTGTGTGGTTATCAAATTTTCATAGGGAGA
1 TTATCAAATTTTCACAGTGTGGTTATCAAA-TTTCATAAGGAGA
* * * *
63310 TTATCAAATTTTCATAGGGAGGTTATCAAAATTTCATAATGAGA
1 TTATCAAATTTTCACAGTGTGGTTATC-AAATTTCATAAGGAGA
63354 TTATC-AATTTTCACAGTGTGGTTATCAATATTTC
1 TTATCAAATTTTCACAGTGTGGTTATCAA-ATTTC
63388 TACATTAGAG
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 2 0.03
43 23 0.35
44 37 0.57
45 3 0.05
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (43 bp):
TTATCAAATTTTCACAGTGTGGTTATCAAATTTCATAAGGAGA
Done.