Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012535.1 Corchorus olitorius cultivar O-4 contig12568, 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: 38466
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:401 original size:32 final size:31
Alignment explanation
Indices: 317--407 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 31
307 CTCTATATTT
* * * *
317 TTTCTTTTTCTTATTTTCTCTCTCTCTGACGTG
1 TTTC-TTTTCTTCTTTTCT-TCTTTATGACGCG
*
350 TTTCTTTTCTTCTCCTTCTTCTTTATGACGCG
1 TTTCTTTTCTTCT-TTTCTTCTTTATGACGCG
*
382 TTTCTTTTCTTCTATTTCTTCCTTAT
1 TTTCTTTTCTTCT-TTTCTTCTTTAT
408 TTCTTGGTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
32 41 0.84
33 8 0.16
ACGTcount: A:0.07, C:0.25, G:0.07, T:0.62
Consensus pattern (31 bp):
TTTCTTTTCTTCTTTTCTTCTTTATGACGCG
Found at i:662 original size:2 final size:2
Alignment explanation
Indices: 655--691 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
645 GAGGGATTGA
655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
692 GAAAGCTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7199 original size:2 final size:2
Alignment explanation
Indices: 7194--7219 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7184 ACACACACAC
7194 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
7220 TGATAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10963 original size:50 final size:50
Alignment explanation
Indices: 10888--11030 Score: 259
Period size: 50 Copynumber: 2.9 Consensus size: 50
10878 CACCTCCATA
* *
10888 ACTTTGTTCCTAAGAAATGATGTGATTGGTTATGGGTCGAAATTTCATTC
1 ACTTTGTTCCTAAGAAATGATGTGATTGGATATGGGTGGAAATTTCATTC
*
10938 ACTTTGTTCCTAGGAAATGATGTGATTGGATATGGGTGGAAATTTCATTC
1 ACTTTGTTCCTAAGAAATGATGTGATTGGATATGGGTGGAAATTTCATTC
10988 ACTTTGTTCCTAAGAAATGATGTGATTGGATATGGGTGGAAAT
1 ACTTTGTTCCTAAGAAATGATGTGATTGGATATGGGTGGAAAT
11031 CCTCATACGT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (50 bp):
ACTTTGTTCCTAAGAAATGATGTGATTGGATATGGGTGGAAATTTCATTC
Found at i:11533 original size:50 final size:50
Alignment explanation
Indices: 11458--11552 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
11448 ATCACCTCCA
*
11458 TCACTTTGTTCCTAAGAAATGATGTGATTGGATATATGTGGAAATTTCAT
1 TCACTTTGTTCCTAAGAAATGATGTGATTGGATATAGGTGGAAATTTCAT
* *
11508 TCACTTTGTTCCTAGGAAATGATGTGATTGGATATGGGTGGAAAT
1 TCACTTTGTTCCTAAGAAATGATGTGATTGGATATAGGTGGAAAT
11553 CCTCATACGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.38
Consensus pattern (50 bp):
TCACTTTGTTCCTAAGAAATGATGTGATTGGATATAGGTGGAAATTTCAT
Found at i:12570 original size:11 final size:11
Alignment explanation
Indices: 12554--12578 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12544 TCATCTTTTA
12554 TTTTTCTCTAG
1 TTTTTCTCTAG
12565 TTTTTCTCTAG
1 TTTTTCTCTAG
12576 TTT
1 TTT
12579 AAGAAGAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTCTCTAG
Found at i:14393 original size:50 final size:50
Alignment explanation
Indices: 14314--14408 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
14304 ATCGCCTCCA
* *
14314 TCACTTTGTTCCTAAGAAATGATGTGATTGGATATGGGTGGAAATTTCAT
1 TCACTTTGTTCCTAAGAAATGATGCGATTGGATATGGATGGAAATTTCAT
*
14364 TCACTTTGTTCCTAGGAAATGATGCGATTGGATATGGATGGAAAT
1 TCACTTTGTTCCTAAGAAATGATGCGATTGGATATGGATGGAAAT
14409 CCTCATACGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (50 bp):
TCACTTTGTTCCTAAGAAATGATGCGATTGGATATGGATGGAAATTTCAT
Found at i:15176 original size:42 final size:43
Alignment explanation
Indices: 15082--15194 Score: 149
Period size: 42 Copynumber: 2.6 Consensus size: 43
15072 CTGTTATGGA
*
15082 TGTTAT-TCCTTGAATGATGTTAAGTGTTATGATATATACATTAAGT
1 TGTTATGT-CTTGAATGATGTTAAGTGTTATG--A-ATACATTAAGC
*
15128 TGTTATGTCTTGAATGATATTAAGTGTTATG-ATACATTAAGC
1 TGTTATGTCTTGAATGATGTTAAGTGTTATGAATACATTAAGC
*
15170 TGTTATGTCTAGAATGATGTTAAGT
1 TGTTATGTCTTGAATGATGTTAAGT
15195 TTAAGTTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
42 33 0.53
46 28 0.45
47 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.44
Consensus pattern (43 bp):
TGTTATGTCTTGAATGATGTTAAGTGTTATGAATACATTAAGC
Found at i:22330 original size:21 final size:21
Alignment explanation
Indices: 22306--22345 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22296 TCTGTCAAGG
22306 TGGGCTCG-TGAAGAAACCACA
1 TGGGC-CGATGAAGAAACCACA
*
22327 TGGGCGGATGAAGAAACCA
1 TGGGCCGATGAAGAAACCA
22346 ATTGTGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (21 bp):
TGGGCCGATGAAGAAACCACA
Found at i:24332 original size:30 final size:29
Alignment explanation
Indices: 24262--24457 Score: 200
Period size: 29 Copynumber: 6.7 Consensus size: 29
24252 TAGGTCATCT
* * *
24262 AGGGGCATTTTGGTCAATTTTTAAAGAAAATCC
1 AGGGGCATTTTGGTC-ATTTTT---GCATATTC
*
24295 AGGGGCATTTTGGTCATTTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTTGCATATTC
* *
24324 AGGGGGCATTTTGGTCATTTCTGCATATTT
1 A-GGGGCATTTTGGTCATTTTTGCATATTC
24354 AGGGGCATTTTGGTCATTTTTGCATATTC
1 AGGGGCATTTTGGTCATTTTTGCATATTC
* * * *
24383 AAGGGTATTTTGGTCTTTTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCATATTC
* ** *
24412 AGGGGCATTTTAGTCA--TTTGCACGTCC
1 AGGGGCATTTTGGTCATTTTTGCATATTC
24439 A-GGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
24458 AAGTTCACTT
Statistics
Matches: 141, Mismatches: 19, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
26 13 0.09
27 10 0.07
28 2 0.01
29 69 0.49
30 26 0.18
32 6 0.04
33 15 0.11
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCATATTC
Found at i:29848 original size:12 final size:13
Alignment explanation
Indices: 29830--29863 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
29820 TTTTGTTTCT
29830 TCTTTTTGTCTTA
1 TCTTTTTGTCTTA
29843 TCTTTTTGTCTTA
1 TCTTTTTGTCTTA
29856 TCTTTTTG
1 TCTTTTTG
29864 CATATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.15, G:0.09, T:0.71
Consensus pattern (13 bp):
TCTTTTTGTCTTA
Found at i:33378 original size:7 final size:8
Alignment explanation
Indices: 33354--33378 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
33344 ATAATAAATG
33354 AAATGAAA
1 AAATGAAA
33362 AAATGAAA
1 AAATGAAA
33370 AAATGAAA
1 AAATGAAA
33378 A
1 A
33379 TAAAGGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:33790 original size:25 final size:25
Alignment explanation
Indices: 33762--33818 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
33752 AAATTCAAAA
*
33762 AAAAAAAGAAAAAAAACAATCAATC
1 AAAAAAACAAAAAAAACAATCAATC
* *
33787 AAAAAATCAAAAAAATCAATCAATC
1 AAAAAAACAAAAAAAACAATCAATC
33812 AAAAAAA
1 AAAAAAA
33819 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.75, C:0.12, G:0.02, T:0.11
Consensus pattern (25 bp):
AAAAAAACAAAAAAAACAATCAATC
Found at i:33825 original size:25 final size:25
Alignment explanation
Indices: 33770--33848 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
33760 AAAAAAAAAG
33770 AAAAAAAACAATCAATCAAAAAATC
1 AAAAAAAACAATCAATCAAAAAATC
* *
33795 AAAAAAATCAATCAATCAAAAAAATT
1 AAAAAAAACAATCAATC-AAAAAATC
*
33821 TAAAAAAA-AA-C-A--AAAAAATC
1 AAAAAAAACAATCAATCAAAAAATC
33841 AAAAAAAA
1 AAAAAAAA
33849 ATCAAAATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 14 0.30
23 1 0.02
24 1 0.02
25 18 0.38
26 13 0.28
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (25 bp):
AAAAAAAACAATCAATCAAAAAATC
Found at i:33834 original size:20 final size:20
Alignment explanation
Indices: 33788--33855 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
33778 CAATCAATCA
33788 AAAAATCAAAAAAATC---A
1 AAAAATCAAAAAAATCAAAA
** *
33805 ATCAATCAAAAAAATTTAAAA
1 AAAAATCAAAAAAA-TCAAAA
33826 AAAAA-CAAAAAAATCAAAA
1 AAAAATCAAAAAAATCAAAA
33845 AAAAATCAAAA
1 AAAAATCAAAA
33856 TCAAAATCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
17 12 0.30
18 1 0.03
19 10 0.25
20 13 0.32
21 4 0.10
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAATCAAAAAAATCAAAA
Found at i:33836 original size:11 final size:11
Alignment explanation
Indices: 33760--33867 Score: 78
Period size: 12 Copynumber: 9.4 Consensus size: 11
33750 AGAAATTCAA
**
33760 AAAAAAAAAGA
1 AAAAAAAAATC
33771 AAAAAAACAATC
1 AAAAAAA-AATC
*
33783 AATCAAAAAATC
1 AA-AAAAAAATC
33795 AAAAAAATCAATC
1 AAAAAAA--AATC
*
33808 AATCAAAAAAATTT
1 AA--AAAAAAA-TC
33822 AAAAAAAAA-C
1 AAAAAAAAATC
33832 --AAAAAAATC
1 AAAAAAAAATC
33841 AAAAAAAAATC
1 AAAAAAAAATC
*
33852 AAAATCAAAATC
1 AAAA-AAAAATC
33864 AAAA
1 AAAA
33868 GAGAATTGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 21
0.74 0.07 0.20
Matches are distributed among these distances:
8 7 0.09
9 1 0.01
11 24 0.30
12 27 0.34
13 12 0.15
14 3 0.04
15 5 0.06
ACGTcount: A:0.76, C:0.11, G:0.01, T:0.12
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:33844 original size:6 final size:6
Alignment explanation
Indices: 33835--33867 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
33825 AAAAAACAAA
*
33835 AAAATC AAAA-A AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
33868 GAGAATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:33844 original size:17 final size:17
Alignment explanation
Indices: 33783--33861 Score: 61
Period size: 17 Copynumber: 4.5 Consensus size: 17
33773 AAAAACAATC
*
33783 AATCAAAAAATCAAAAA
1 AATCAAAAAAACAAAAA
** *
33800 AATCAATCAATCAAAAA
1 AATCAAAAAAACAAAAA
*
33817 AATTTAAAAAAAAACAAAAA
1 AA--T-CAAAAAAACAAAAA
*
33837 AATCAAAAAAA-AATCAA
1 AATCAAAAAAACAA-AAA
33854 AATCAAAA
1 AATCAAAA
33862 TCAAAAGAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.04
17 34 0.68
18 1 0.02
19 1 0.02
20 12 0.24
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (17 bp):
AATCAAAAAAACAAAAA
Found at i:33855 original size:9 final size:9
Alignment explanation
Indices: 33783--33847 Score: 62
Period size: 9 Copynumber: 7.2 Consensus size: 9
33773 AAAAACAATC
33783 AATC-AAAA
1 AATCAAAAA
33791 AATCAAAAA
1 AATCAAAAA
**
33800 AATC-AATC
1 AATCAAAAA
33808 AATCAAAAA
1 AATCAAAAA
*
33817 AATTTAAAAAA
1 AA--TCAAAAA
*
33828 AAACAAAAA
1 AATCAAAAA
33837 AATCAAAAA
1 AATCAAAAA
33846 AA
1 AA
33848 AATCAAAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
8 10 0.22
9 27 0.60
11 8 0.18
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (9 bp):
AATCAAAAA
Found at i:34526 original size:50 final size:50
Alignment explanation
Indices: 34451--34596 Score: 222
Period size: 50 Copynumber: 2.9 Consensus size: 50
34441 TTACAATAAG
*
34451 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
1 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAAGTAAA
* * * **
34501 ATTGCTTTCCATTTGTAAGTTCAAGATCAAAATTC-ATTTTTCAAAGTAGG
1 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGA-TTTTCAAAGTAAA
34551 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAAG
1 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAAG
34597 GGCATTTAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
50 84 0.99
51 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (50 bp):
ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAAGTAAA
Found at i:35142 original size:80 final size:80
Alignment explanation
Indices: 34994--35360 Score: 546
Period size: 80 Copynumber: 4.6 Consensus size: 80
34984 AAAGCAACAG
* * * *
34994 TCAAAAAG-TTTCAATCCCAACAACATACCAGAGTTATTTTTTT-AAGTTGACCACACATTGGTC
1 TCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACACATTGGTC
35057 CTTTTTCATCATCAA
66 CTTTTTCATCATCAA
**
35072 TCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACGTATTGGTC
1 TCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACACATTGGTC
35137 CTTTTTCATCATCAA
66 CTTTTTCATCATCAA
* *
35152 TCAAGAAGTTTTTAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACGCATTGGTC
1 TCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACACATTGGTC
35217 CTTTTTCATCATCAA
66 CTTTTTCATCATCAA
* * * *
35232 CCAAGAGGTTTTCAGTTACAACATCAGACCAGAGTTA-TTTTTTCAAGTTGACCACACATTGGTC
1 TCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACACATTGGTC
35296 CTTTTTCATCATCAA
66 CTTTTTCATCATCAA
* * * *
35311 TCAAGAGGTTTTCAGTTACAACATTAGACTCAGAGTTA--TTTTTCAAGTTG
1 TCAAGAAGTTTTCAATCACAACATCAGAC-CAGAGTTATTTTTTTCAAGTTG
35361 TTTTTCAAAG
Statistics
Matches: 270, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
78 7 0.03
79 112 0.41
80 151 0.56
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (80 bp):
TCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACACATTGGTC
CTTTTTCATCATCAA
Found at i:35219 original size:160 final size:160
Alignment explanation
Indices: 34994--35444 Score: 561
Period size: 159 Copynumber: 2.8 Consensus size: 160
34984 AAAGCAACAG
* * * * *
34994 TCAAAAAG-TTTCAATCCCAACAACATACCAGAGTTATTTTTTT-AAGTTGACCACACATTGGTC
1 TCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACGCATTGGTC
35057 CTTTTTCATCATCAATCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTT
66 CTTTTTCATCATCAATCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTT
**
35122 GACCACGTATTGGTCCTTTTTCATCATCAA
131 GACCACACATTGGTCCTTTTTCATCATCAA
*
35152 TCAAGAAGTTTTTAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACGCATTGGTC
1 TCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACGCATTGGTC
* * * *
35217 CTTTTTCATCATCAACCAAGAGGTTTTCAGTTACAACATCAGACCAGAGTTA-TTTTTTCAAGTT
66 CTTTTTCATCATCAATCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTT
35281 GACCACACATTGGTCCTTTTTCATCATCAA
131 GACCACACATTGGTCCTTTTTCATCATCAA
* * * *
35311 TCAAGAGGTTTTCAGTTACAACATTAGACTCAGAGTTATTTTTCAAGTTGTTTTTCAAAGTTGAC
1 TCAAGAAGTTTTCAATCACAACATCAGAC-CAGAG------TT--A-TT-TTTTTC-AAGTTGAC
* * * *
35376 CA-GACATTGGTCCTTTTCCATCATCAATCAAGAA-ATTTCAAACACAACATCAGATTCAGAGTT
54 CACG-CATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAATCACAACATCAGA-CCAGAGTT
35439 ATTTTT
117 ATTTTT
35445 CAAAGGTATT
Statistics
Matches: 251, Mismatches: 25, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
158 7 0.03
159 95 0.38
160 72 0.29
166 2 0.01
168 1 0.00
169 2 0.01
170 23 0.09
171 45 0.18
172 4 0.02
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (160 bp):
TCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTTGACCACGCATTGGTC
CTTTTTCATCATCAATCAAGAAGTTTTCAATCACAACATCAGACCAGAGTTATTTTTTTCAAGTT
GACCACACATTGGTCCTTTTTCATCATCAA
Found at i:35457 original size:91 final size:90
Alignment explanation
Indices: 35270--35447 Score: 250
Period size: 92 Copynumber: 2.0 Consensus size: 90
35260 CCAGAGTTAT
* ** ***
35270 TTTTTCAAGTTGACCACACATTGGTCCTTTTTCATCATCAATCAAGAGGTTTTCAGTTACAACAT
1 TTTTTCAAGTTGACCACACATTGGTCCTTTTCCATCATCAATCAAGAGAATTTCAAACACAACAT
*
35335 TAGACTCAGAGTTATTTTTCAAGTTG
66 CAGACTCAGAGTTATTTTTCAAG-TG
*
35361 TTTTTCAAAGTTGACCAGACATTGGTCCTTTTCCATCATCAATCAAGA-AATTTCAAACACAACA
1 TTTTTC-AAGTTGACCACACATTGGTCCTTTTCCATCATCAATCAAGAGAATTTCAAACACAACA
*
35425 TCAGATTCAGAGTTATTTTTCAA
65 TCAGACTCAGAGTTATTTTTCAA
35448 AGGTATTTTC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 38 0.49
92 39 0.51
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (90 bp):
TTTTTCAAGTTGACCACACATTGGTCCTTTTCCATCATCAATCAAGAGAATTTCAAACACAACAT
CAGACTCAGAGTTATTTTTCAAGTG
Found at i:36074 original size:69 final size:69
Alignment explanation
Indices: 35569--36051 Score: 750
Period size: 69 Copynumber: 7.0 Consensus size: 69
35559 CAAGTCAATT
* * *
35569 AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCATTGGTCCCA
1 AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
35634 TCCA
66 TCCA
* * * *
35638 AGCCATATAGGCTTTTCCACAAGCCAATCTCGTTTCCACACGAGGCAGTTCAAGCATTGGTTCCA
1 AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
35703 TCCA
66 TCCA
* * * *
35707 AGCCACATAGGCTTTTCCATAAGCCAGACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCA
1 AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
35772 TCCA
66 TCCA
* *
35776 AGCCATATAGGTTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
1 AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
35841 TCCA
66 TCCA
* **
35845 AGCCACATAGGCTTTTCCACAAGCCAAACTCGTTTCTGTACGAGTCAGTTCAAGCCTTGGTTCCA
1 AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
35910 TCCA
66 TCCA
*
35914 AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTCA
1 AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
35979 TCCA
66 TCCA
* * * * * * *
35983 AGCCATATAGACTTTTCCATAAGTCAAACTCGTTTCCATGCGAGTCAGTTTAAACATTGGTTCCA
1 AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
36048 TCCA
66 TCCA
36052 TACAGCAGTG
Statistics
Matches: 378, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 378 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (69 bp):
AGCCATATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
TCCA
Found at i:37414 original size:69 final size:69
Alignment explanation
Indices: 37303--37442 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
37293 AAGTATATTG
37303 AATCTTTTTTGGGTAAATATAGAATACTTTTGTTAAATAAGGTATACAAAACAAAAATAATATAA
1 AATCTTTTTTGGGTAAATATAGAATACTTTTGTTAAATAAGGTATACAAAACAAAAATAATATAA
37368 ATAA
66 ATAA
*
37372 AATCTTTTTTGGGTAAATATAGAATACTTTTGTTAAATAAGGTATACAAAACAAAAATAGTATAA
1 AATCTTTTTTGGGTAAATATAGAATACTTTTGTTAAATAAGGTATACAAAACAAAAATAATATAA
37437 ATAA
66 ATAA
37441 AA
1 AA
37443 CACCAAGATG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (69 bp):
AATCTTTTTTGGGTAAATATAGAATACTTTTGTTAAATAAGGTATACAAAACAAAAATAATATAA
ATAA
Done.