Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020344.1 Corchorus olitorius cultivar O-4 contig20377, 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: 66812
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1802 original size:11 final size:11
Alignment explanation
Indices: 1759--1796 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1749 TTCCTATATA
*
1759 AAATAAATTAT
1 AAATTAATTAT
1770 CAAA-TAATTAT
1 -AAATTAATTAT
1781 AAATTAATTAT
1 AAATTAATTAT
1792 AAATT
1 AAATT
1797 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:3170 original size:42 final size:42
Alignment explanation
Indices: 3111--3193 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
3101 ATTATACTTT
*
3111 CCTTTCACATAAATGTTACTATAATAAATCCTATCCACCTTC
1 CCTTTCACATAAATGTTACTATAATAAATCATATCCACCTTC
*
3153 CCTTTCACATAAATGTTACTATAATAAATCATATCCCCCTT
1 CCTTTCACATAAATGTTACTATAATAAATCATATCCACCTT
3194 ATCTCTACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (42 bp):
CCTTTCACATAAATGTTACTATAATAAATCATATCCACCTTC
Found at i:7131 original size:49 final size:48
Alignment explanation
Indices: 7059--7187 Score: 172
Period size: 49 Copynumber: 2.7 Consensus size: 48
7049 CAAGCAATCC
7059 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTACAACAAAATTGAACT
1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTACAACAAAATTGAACT
** *
7107 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAGGACAAAATTGATCT
1 TTTATTTTTACTTGCA-CTTTTTCTCAATTTTTACAACAAAATTGAACT
* *
7156 TTTAATTTT-CATTGCACTTTTTATCAATTTTT
1 TTTATTTTTAC-TTGCACTTTTTCTCAATTTTT
7188 GGACAAAATT
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
47 7 0.10
48 24 0.33
49 42 0.58
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (48 bp):
TTTATTTTTACTTGCACTTTTTCTCAATTTTTACAACAAAATTGAACT
Found at i:9163 original size:15 final size:15
Alignment explanation
Indices: 9143--9184 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
9133 CGCTCAAATA
9143 TCGGGTCATTTGGGT
1 TCGGGTCATTTGGGT
9158 TCGGGTCAATTCTGGGT
1 TCGGGTC-ATT-TGGGT
9175 T-GGGTCATTT
1 TCGGGTCATTT
9185 TCGGTTTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 10 0.40
16 8 0.32
17 6 0.24
ACGTcount: A:0.10, C:0.14, G:0.36, T:0.40
Consensus pattern (15 bp):
TCGGGTCATTTGGGT
Found at i:9181 original size:16 final size:16
Alignment explanation
Indices: 9143--9197 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
9133 CGCTCAAATA
9143 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
9158 TCGGGTCAATTCTGGGT
1 TCGGGTCAATT-TGGGT
* *
9175 T-GGGTCATTTTCGGTT
1 TCGGGTCAATTT-GGGT
9191 TCGGGTC
1 TCGGGTC
9198 GTACGGTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 8 0.24
16 15 0.44
17 11 0.32
ACGTcount: A:0.07, C:0.16, G:0.36, T:0.40
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:10824 original size:17 final size:16
Alignment explanation
Indices: 10788--10857 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
10778 GTCGGGTTGA
10788 TCGGGTTCGGGTCATT
1 TCGGGTTCGGGTCATT
*
10804 TCGGGTTTGGGTCATTT
1 TCGGGTTCGGGTCA-TT
*
10821 TCGGGTTCGGGTCGTT
1 TCGGGTTCGGGTCATT
* *
10837 T-GGATTCGGGTAATT
1 TCGGGTTCGGGTCATT
10852 TCGGGT
1 TCGGGT
10858 CATTTATGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
15 12 0.27
16 19 0.42
17 14 0.31
ACGTcount: A:0.07, C:0.14, G:0.39, T:0.40
Consensus pattern (16 bp):
TCGGGTTCGGGTCATT
Found at i:10900 original size:58 final size:57
Alignment explanation
Indices: 10793--10904 Score: 127
Period size: 58 Copynumber: 1.9 Consensus size: 57
10783 GTTGATCGGG
* ***
10793 TTCGGGTCATTTCGGGTTTGGGTCATTTTCGGGTTCGGGTCGTTTGGATTCGGGTAAT
1 TTCGGGTCATTTCGGGTTTGGGTCAGTTTCGGGTTCGGGTCGGGCGGATT-GGGTAAT
* * * *
10851 TTCGGGTCATTTATGGG-TTGGGTGAGTTTCGGTTTCGGGTTGGGCGGATTGGGT
1 TTCGGGTCATTT-CGGGTTTGGGTCAGTTTCGGGTTCGGGTCGGGCGGATTGGGT
10905 TTGTTGACTT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
57 4 0.09
58 38 0.84
59 3 0.07
ACGTcount: A:0.08, C:0.12, G:0.40, T:0.40
Consensus pattern (57 bp):
TTCGGGTCATTTCGGGTTTGGGTCAGTTTCGGGTTCGGGTCGGGCGGATTGGGTAAT
Found at i:11126 original size:13 final size:12
Alignment explanation
Indices: 11099--11151 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
11089 GAGGAATTGT
*
11099 TTTTATT-ATTG
1 TTTTATTAAATG
11110 TTTTATTAACATG
1 TTTTATTAA-ATG
11123 TTTTA-TAAATG
1 TTTTATTAAATG
11134 ATTTTATTAAATG
1 -TTTTATTAAATG
11147 ATTTT
1 -TTTT
11152 GGCTGCATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
11 10 0.27
12 9 0.24
13 18 0.49
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTTATTAAATG
Found at i:11140 original size:12 final size:13
Alignment explanation
Indices: 11110--11151 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
11100 TTTATTATTG
11110 TTTTATTAACATG-
1 TTTTATTAA-ATGA
11123 TTTTA-TAAATGA
1 TTTTATTAAATGA
11135 TTTTATTAAATGA
1 TTTTATTAAATGA
11148 TTTT
1 TTTT
11152 GGCTGCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.11
12 8 0.30
13 16 0.59
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (13 bp):
TTTTATTAAATGA
Found at i:16003 original size:2 final size:2
Alignment explanation
Indices: 15996--16024 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15986 AATTCAGATC
15996 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 A
16025 GGATCCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17028 original size:129 final size:129
Alignment explanation
Indices: 16798--17053 Score: 503
Period size: 129 Copynumber: 2.0 Consensus size: 129
16788 CAAGTCTTCC
16798 AATTTGTCAATTTGGTCAATTGAACCCTTTAAGAAATTAATTAATGGTAAACTAATAAAACCATT
1 AATTTGTCAATTTGGTCAATTGAACCCTTTAAGAAATTAATTAATGGTAAACTAATAAAACCATT
16863 TGTTCCCCCACGTGGTGGTTTACCTGGAATTTCCATGTGGTGCAAGGGCCACTCACATGAACCA
66 TGTTCCCCCACGTGGTGGTTTACCTGGAATTTCCATGTGGTGCAAGGGCCACTCACATGAACCA
16927 AATTTGTCAATTTGGTCAATTGAACCCTTTAAGAAATTAATTAATGGTAAACTAATAAAACCATT
1 AATTTGTCAATTTGGTCAATTGAACCCTTTAAGAAATTAATTAATGGTAAACTAATAAAACCATT
*
16992 TGTTCCCCCACGTGGTGGTTTACCTGGAATTTCCATGTGGTGCAAGGGCTACTCACATGAAC
66 TGTTCCCCCACGTGGTGGTTTACCTGGAATTTCCATGTGGTGCAAGGGCCACTCACATGAAC
17054 TAAAACCTCA
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 126 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (129 bp):
AATTTGTCAATTTGGTCAATTGAACCCTTTAAGAAATTAATTAATGGTAAACTAATAAAACCATT
TGTTCCCCCACGTGGTGGTTTACCTGGAATTTCCATGTGGTGCAAGGGCCACTCACATGAACCA
Found at i:20327 original size:17 final size:18
Alignment explanation
Indices: 20307--20344 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
20297 ATCTCACTAG
*
20307 TATTTTATTTTGTT-ATT
1 TATTTTATTTAGTTAATT
*
20324 TATTTTGTTTAGTTAATT
1 TATTTTATTTAGTTAATT
20342 TAT
1 TAT
20345 CCATAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (18 bp):
TATTTTATTTAGTTAATT
Found at i:20560 original size:20 final size:18
Alignment explanation
Indices: 20535--20595 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 18
20525 TTTCCTTTAG
20535 TTTTGTTTTTATTTTTCGT
1 TTTTGTTTTTATTTTT-GT
*
20554 ATTTTGTTTTTGTTTTTGT
1 -TTTTGTTTTTATTTTTGT
* *
20573 TTTTG-TGTT-TTTGTGT
1 TTTTGTTTTTATTTTTGT
20589 TTTTGTT
1 TTTTGTT
20596 AATTTTGCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 11 0.30
17 4 0.11
18 5 0.14
19 2 0.05
20 15 0.41
ACGTcount: A:0.03, C:0.02, G:0.16, T:0.79
Consensus pattern (18 bp):
TTTTGTTTTTATTTTTGT
Found at i:20564 original size:6 final size:6
Alignment explanation
Indices: 20535--20595 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
20525 TTTCCTTTAG
* *
20535 TTTTGT TTTTAT TTTTCGT ATTTTGT TTTTGT TTTTGT TTTTG- TGTT-T
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
*
20583 TTGTGT TTTTGT T
1 TTTTGT TTTTGT T
20596 AATTTTGCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 5 0.11
6 33 0.73
7 3 0.07
8 4 0.09
ACGTcount: A:0.03, C:0.02, G:0.16, T:0.79
Consensus pattern (6 bp):
TTTTGT
Found at i:20569 original size:26 final size:28
Alignment explanation
Indices: 20535--20595 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
20525 TTTCCTTTAG
20535 TTTTGTTTTTATTTTT-CGTATTT-TGT
1 TTTTGTTTTTATTTTTGCGTATTTGTGT
* * *
20561 TTTTGTTTTTGTTTTTGTGTTTTTGTGT
1 TTTTGTTTTTATTTTTGCGTATTTGTGT
20589 TTTTGTT
1 TTTTGTT
20596 AATTTTGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 15 0.50
27 5 0.17
28 10 0.33
ACGTcount: A:0.03, C:0.02, G:0.16, T:0.79
Consensus pattern (28 bp):
TTTTGTTTTTATTTTTGCGTATTTGTGT
Found at i:20583 original size:8 final size:8
Alignment explanation
Indices: 20566--20594 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
20556 TTTGTTTTTG
20566 TTTT-TGT
1 TTTTGTGT
20573 TTTTGTGT
1 TTTTGTGT
20581 TTTTGTGT
1 TTTTGTGT
20589 TTTTGT
1 TTTTGT
20595 TAATTTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (8 bp):
TTTTGTGT
Found at i:24338 original size:14 final size:14
Alignment explanation
Indices: 24319--24347 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
24309 CAACTTTGGG
24319 AGGAGGAGAAAAAA
1 AGGAGGAGAAAAAA
24333 AGGAGGAGAAAAAA
1 AGGAGGAGAAAAAA
24347 A
1 A
24348 AGTGAGAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AGGAGGAGAAAAAA
Found at i:25768 original size:25 final size:21
Alignment explanation
Indices: 25742--25783 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
25732 AGGCTTGGTC
25742 AATCAATTACTTTGATTGCTT
1 AATCAATTACTTTGATTGCTT
25763 AATCAATTACTTTGATTGCTT
1 AATCAATTACTTTGATTGCTT
25784 TGATTGCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (21 bp):
AATCAATTACTTTGATTGCTT
Found at i:30393 original size:2 final size:2
Alignment explanation
Indices: 30388--30413 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30378 GTGTGTGTGT
30388 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
30414 AGGGAAAGCA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:32177 original size:28 final size:30
Alignment explanation
Indices: 32133--32207 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 30
32123 AAAGTTGTTG
*
32133 GTTTGAGGTGTTATTCACAGAAG-A-ATAA
1 GTTTGAGGTGTTGTTCACAGAAGTATATAA
* *
32161 GTTTGAGGTGTTGTTCATAGCAGTTAATATAA
1 GTTTGAGGTGTTGTTCACAGAAG-T-ATATAA
32193 GTTTGAGGTGTTGTT
1 GTTTGAGGTGTTGTT
32208 TTTCTGCTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 20 0.50
31 1 0.03
32 19 0.47
ACGTcount: A:0.27, C:0.05, G:0.28, T:0.40
Consensus pattern (30 bp):
GTTTGAGGTGTTGTTCACAGAAGTATATAA
Found at i:35614 original size:30 final size:30
Alignment explanation
Indices: 35571--35678 Score: 119
Period size: 30 Copynumber: 3.6 Consensus size: 30
35561 ACGTTCATTG
* *
35571 TTCCTTTAG-CAAGGTCCTGGACATTCATCA
1 TTCCTTT-GCCAAGGTCCTGGACGTTCGTCA
* *
35601 TTCCATTGCCAAGGTCCTGGACGTTCGTCC
1 TTCCTTTGCCAAGGTCCTGGACGTTCGTCA
* * * * *
35631 TTTCTTTGTCAAAGTCCTAGACGTTCGTCG
1 TTCCTTTGCCAAGGTCCTGGACGTTCGTCA
35661 TTCCTTTGCCAAGGTCCT
1 TTCCTTTGCCAAGGTCCT
35679 CAAAATTGGA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 1 0.02
30 63 0.98
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (30 bp):
TTCCTTTGCCAAGGTCCTGGACGTTCGTCA
Found at i:37824 original size:46 final size:46
Alignment explanation
Indices: 37736--37824 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
37726 AACAAAAGTC
* *
37736 TAATTTTCTTTAACCTATTAAATATTGAATTTCGGCCTTAAAAGGT
1 TAATTTTCTTTAACCTATTAAATATTGAAATTCGGCCCTAAAAGGT
* * * *
37782 TAATTTTGTTTTACCTATTAAA-ATTTAAGATTGGGCCCTAAAA
1 TAATTTTCTTTAACCTATTAAATATTGAA-ATTCGGCCCTAAAA
37825 AGTTGTTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
45 5 0.14
46 31 0.86
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (46 bp):
TAATTTTCTTTAACCTATTAAATATTGAAATTCGGCCCTAAAAGGT
Found at i:38280 original size:17 final size:17
Alignment explanation
Indices: 38258--38303 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
38248 CACCCCCCAA
**
38258 ATCACCAGTGATTTAAG
1 ATCACCAGTGATGCAAG
38275 ATCACCAGTGATGCAAG
1 ATCACCAGTGATGCAAG
*
38292 ATCACCGGTGAT
1 ATCACCAGTGAT
38304 CAAAGATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (17 bp):
ATCACCAGTGATGCAAG
Found at i:38429 original size:17 final size:16
Alignment explanation
Indices: 38375--38425 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
38365 ATCACCCCCC
38375 AGATCACTAGTGATCTA
1 AGATCACTAGTGATC-A
* *
38392 GGATCACCAGTGATGCA
1 AGATCACTAGTGAT-CA
*
38409 AGATCACTGGTGATCA
1 AGATCACTAGTGATCA
38425 A
1 A
38426 AGATTACATG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 3 0.11
17 24 0.86
18 1 0.04
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (16 bp):
AGATCACTAGTGATCA
Found at i:38439 original size:119 final size:120
Alignment explanation
Indices: 38228--38471 Score: 391
Period size: 119 Copynumber: 2.0 Consensus size: 120
38218 ATACACTGTT
*
38228 AGGGGGCGTTTGGTTAGAATCACCCCCCAAATCACCAGTGATTTAAGATCACCAGTGATGCAAGA
1 AGGGGGCGTTTGGTTAGAATCACCCCCCAAATCACCAGTGATCTAAGATCACCAGTGATGCAAGA
* *
38293 TCACCGGTGATCAAAGATTTCATGGGTTAATGGTGGTAATCCAGATTACCATTA-
66 TCACCGGTGATCAAAGATTACATGGGTTAATGGTGGTAATCCAGATCACCATTAG
* * * *
38347 AGGGGGCGTTTGGTTAGGATCACCCCCCAGATCACTAGTGATCTAGGATCACCAGTGATGCAAGA
1 AGGGGGCGTTTGGTTAGAATCACCCCCCAAATCACCAGTGATCTAAGATCACCAGTGATGCAAGA
* * *
38412 TCACTGGTGATCAAAGATTACATGGGTTTATGGTGGTAATCCAGATCACCCTTAG
66 TCACCGGTGATCAAAGATTACATGGGTTAATGGTGGTAATCCAGATCACCATTAG
38467 AGGGG
1 AGGGG
38472 TGATCAGGGG
Statistics
Matches: 114, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
119 109 0.96
120 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (120 bp):
AGGGGGCGTTTGGTTAGAATCACCCCCCAAATCACCAGTGATCTAAGATCACCAGTGATGCAAGA
TCACCGGTGATCAAAGATTACATGGGTTAATGGTGGTAATCCAGATCACCATTAG
Found at i:38653 original size:110 final size:110
Alignment explanation
Indices: 38460--38665 Score: 340
Period size: 110 Copynumber: 1.9 Consensus size: 110
38450 ATCCAGATCA
* * *
38460 CCCTTAGAGGGGTGATCAGGGGGTAATCCGGATTACCATACTAAACCAAAAAGTGTAACCAAACA
1 CCCTTAGAGGGGTGATCAGGGGGTAATCCGGATTACCACACCAAACCAAAAAGTGTAACAAAACA
*
38525 GGGTGATCTGAGATCACCTGCCAAGATCACCCCCAACCAAACACC
66 GGGTGATCTGAGATCACCTGCCAAAATCACCCCCAACCAAACACC
* * **
38570 CCCTTAGATGGGTGATCAGGGGGTAATCCGGATTACCACACCAAACCACAAAGTGTAACAAAATG
1 CCCTTAGAGGGGTGATCAGGGGGTAATCCGGATTACCACACCAAACCAAAAAGTGTAACAAAACA
38635 GGGTGATCTGAGATCACCTGCCAAAATCACC
66 GGGTGATCTGAGATCACCTGCCAAAATCACC
38666 ACAAGTGATC
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 88 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (110 bp):
CCCTTAGAGGGGTGATCAGGGGGTAATCCGGATTACCACACCAAACCAAAAAGTGTAACAAAACA
GGGTGATCTGAGATCACCTGCCAAAATCACCCCCAACCAAACACC
Found at i:39430 original size:19 final size:20
Alignment explanation
Indices: 39408--39449 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
39398 ATAATTATTC
39408 TTAAATG-GTAGTTTTCTTT
1 TTAAATGAGTAGTTTTCTTT
*
39427 TTAAATGAGTAGTTTTTTTT
1 TTAAATGAGTAGTTTTCTTT
39447 TTA
1 TTA
39450 GAGTAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (20 bp):
TTAAATGAGTAGTTTTCTTT
Found at i:44698 original size:29 final size:29
Alignment explanation
Indices: 44656--44714 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
44646 TAAATGACTT
*
44656 AGAATTTTTACTAAGTAAGCATTTTTTGG
1 AGAATTTTTACTAAGCAAGCATTTTTTGG
44685 AGAATTTTTACTAAGCAAGCATTTTTTGG
1 AGAATTTTTACTAAGCAAGCATTTTTTGG
44714 A
1 A
44715 TAAAGACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.42
Consensus pattern (29 bp):
AGAATTTTTACTAAGCAAGCATTTTTTGG
Found at i:66073 original size:26 final size:28
Alignment explanation
Indices: 66016--66079 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
66006 AGCTGACACC
*
66016 CCACACGTGACCTCCAAACGTACGACCT
1 CCACACGTGACCTCCAAACGGACGACCT
* *
66044 -CACACGTGACCTCC-AACGGA-TATCT
1 CCACACGTGACCTCCAAACGGACGACCT
66069 CCACACGTGAC
1 CCACACGTGAC
66080 ATCGCGCGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 3 0.09
26 15 0.47
27 14 0.44
ACGTcount: A:0.28, C:0.41, G:0.16, T:0.16
Consensus pattern (28 bp):
CCACACGTGACCTCCAAACGGACGACCT
Done.