Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013613.1 Corchorus olitorius cultivar O-4 contig13646, 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: 45631
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:565 original size:64 final size:64
Alignment explanation
Indices: 464--586 Score: 237
Period size: 64 Copynumber: 1.9 Consensus size: 64
454 TTTTTAAATT
*
464 AATTTTGTATTTAATAATAAAAACTATTTCCTTAAAGGACATGTCAATCCTTAACCACCCACAC
1 AATTTTGTATTTAATAATAAAAACTATTTCCCTAAAGGACATGTCAATCCTTAACCACCCACAC
528 AATTTTGTATTTAATAATAAAAACTATTTCCCTAAAGGACATGTCAATCCTTAACCACC
1 AATTTTGTATTTAATAATAAAAACTATTTCCCTAAAGGACATGTCAATCCTTAACCACC
587 GCATGTGTGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (64 bp):
AATTTTGTATTTAATAATAAAAACTATTTCCCTAAAGGACATGTCAATCCTTAACCACCCACAC
Found at i:2944 original size:2 final size:2
Alignment explanation
Indices: 2937--2967 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2927 AAAATTCTAC
2937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2968 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8015 original size:37 final size:38
Alignment explanation
Indices: 7925--8025 Score: 134
Period size: 37 Copynumber: 2.7 Consensus size: 38
7915 CATCAACTTG
**
7925 GTTTTCAAATTGGGAAAGTTCCCA-CCAGTTTTTTTTAA
1 GTTTTCAAATTGGGAAAGTTCCCATCCAG-TTTTTCAAA
* *
7963 GTTTTCAAATCGGGAAAGTTCCCATTCAG-TTTTCAAA
1 GTTTTCAAATTGGGAAAGTTCCCATCCAGTTTTTCAAA
*
8000 GTTTTTAAATTGGGAAAGTTCCCATC
1 GTTTTCAAATTGGGAAAGTTCCCATC
8026 AGGTCCTAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
37 29 0.53
38 23 0.42
39 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (38 bp):
GTTTTCAAATTGGGAAAGTTCCCATCCAGTTTTTCAAA
Found at i:12507 original size:3 final size:3
Alignment explanation
Indices: 12488--12523 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
12478 TGTATCAATG
*
12488 AAT ATAT AAT AAA AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12524 AGTTAGTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12557 original size:3 final size:3
Alignment explanation
Indices: 12549--12588 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12539 ATCAATGGAT
12549 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12589 AATTATTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25859 original size:131 final size:130
Alignment explanation
Indices: 25586--25856 Score: 323
Period size: 131 Copynumber: 2.1 Consensus size: 130
25576 GTAGTTCCTC
* ** * * *
25586 AACCTCAGAATTCGCATTAAATCAAGTCAAAACACAATATCAAATGACTCCATATTGAAAACCAA
1 AACCTCAAAATTTTCATTAAATCAAGTCAAAACAC-ATATAAAAGGACTACATATTGAAAACCAA
* **
25651 GACCTTCAACATAGAAATCTCAAGTTTCCTTCAAGCGTCAGAGCAACCTAAATGACCTGCTCTTC
65 GACCTTCAACATAGAAATCTAAAGTTTCCTTCAAGCGTCAGAGCAACCTAAATGACAAGCTCTTC
25716 A
130 A
* * *
25717 AACCTCAAAATTTTCATTAACTCAAGTCAAAAGAC-TATAAAAGGACTACATACTTGAGAACCTA
1 AACCTCAAAATTTTCATTAAATCAAGTCAAAACACATATAAAAGGACTACATA-TTGAAAACC-A
* * * *
25781 AGACCTTCAACTTAGAAATTTAAAG-TTCCATT-AAGTGTCAGAGCAACCTAAATGATAAGCTCT
64 AGACCTTCAACATAGAAATCTAAAGTTTCC-TTCAAGCGTCAGAGCAACCTAAATGACAAGCTCT
**
25844 TGG
128 TCA
25847 AACCTCAAAA
1 AACCTCAAAA
25857 ATTGCACTAA
Statistics
Matches: 119, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
129 14 0.12
130 50 0.42
131 55 0.46
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (130 bp):
AACCTCAAAATTTTCATTAAATCAAGTCAAAACACATATAAAAGGACTACATATTGAAAACCAAG
ACCTTCAACATAGAAATCTAAAGTTTCCTTCAAGCGTCAGAGCAACCTAAATGACAAGCTCTTCA
Found at i:30301 original size:40 final size:40
Alignment explanation
Indices: 30155--30578 Score: 636
Period size: 40 Copynumber: 10.7 Consensus size: 40
30145 TCCCGATGAA
** * * *
30155 GAAGGGCAAACTAAGAATTTAGACAACACTTTCCGGTAGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
* * * *
30195 GAAAGACAAACT-GGTATTTAAACAACACCTTCAGGTGGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
* *
30234 GAAGGGCAAACT-GGTATTTAAACAACACCTTCCAGTGGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
30273 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
*
30313 GAAGGGCAAATTGGGTATTTAGACAACACCTTCCGGTGGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
* *
30353 GAAGGGTAAACTGGGTATTTAAACAACACCTTCCGGTGGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
*
30393 GAAGGGCAAATTGGGTATTTAGACAACACCTTCCGGTGGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
* * * *
30433 GAAAGGCAAACTGGTTATTTAAACAACACCTTCCAGTGGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
* *
30473 GAAGGGCAAATTGGGTATTTAGACAACACCTTCCGATGGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
30513 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
1 GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
*
30553 GAAGGGCAAACTGGGTATTTAAACAA
1 GAAGGGCAAACTGGGTATTTAGACAA
30579 GACAAGACTG
Statistics
Matches: 348, Mismatches: 35, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 68 0.20
40 280 0.80
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (40 bp):
GAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGGG
Found at i:34424 original size:25 final size:25
Alignment explanation
Indices: 34388--34437 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
34378 TTAGTCGATT
34388 AAATCAGATTTGAGCTACATGAATG
1 AAATCAGATTTGAGCTACATGAATG
*
34413 AAATCAGCTTTGAGCTACATGAATG
1 AAATCAGATTTGAGCTACATGAATG
34438 CAAAATACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (25 bp):
AAATCAGATTTGAGCTACATGAATG
Found at i:34632 original size:26 final size:26
Alignment explanation
Indices: 34575--34673 Score: 76
Period size: 26 Copynumber: 3.7 Consensus size: 26
34565 AAGTGGACTC
* *
34575 AAAATGACCAACATGCCCCTAAATATG-
1 AAAATGACCAA-ATG-CCCTGAATGTGA
* * *
34602 CAAATGACCGAAATGCCCTTAGTGT-A
1 AAAATGACC-AAATGCCCTGAATGTGA
34628 AAAATGACCATAATGCCACTGAATGTGA
1 AAAATGACCA-AATGCC-CTGAATGTGA
*
34656 AAAATGATCAAAATGCCC
1 AAAATGA-CCAAATGCCC
34674 CTGGATTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
25 1 0.02
26 21 0.36
27 18 0.31
28 16 0.28
29 2 0.03
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.20
Consensus pattern (26 bp):
AAAATGACCAAATGCCCTGAATGTGA
Found at i:35144 original size:31 final size:31
Alignment explanation
Indices: 35100--35170 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
35090 ATTTTTAACC
*
35100 ACCAACTTGAGTCTAAACCTTTCAAAAGTTG
1 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
35131 -CTCAATTTGAGTCTAAACCTTTCAAAAGTTG
1 AC-CAATTTGAGTCTAAACCTTTCAAAAGTTG
35162 ACCAATTTG
1 ACCAATTTG
35171 CGGCTAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
30 1 0.03
31 35 0.95
32 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (31 bp):
ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
Found at i:35178 original size:31 final size:31
Alignment explanation
Indices: 35106--35178 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
35096 AACCACCAAC
*
35106 TTGAGTCTAAACCTTTCAAAAGTTGCTCAAT
1 TTGAGGCTAAACCTTTCAAAAGTTGCTCAAT
*
35137 TTGAGTCTAAACCTTTCAAAAGTTGAC-CAAT
1 TTGAGGCTAAACCTTTCAAAAGTTG-CTCAAT
*
35168 TTGCGGCTAAA
1 TTGAGGCTAAA
35179 ATAGAAACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (31 bp):
TTGAGGCTAAACCTTTCAAAAGTTGCTCAAT
Found at i:37194 original size:52 final size:52
Alignment explanation
Indices: 37113--37215 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
37103 ATAGAGAAAA
37113 CAAAAATTGACAAGATTATAATAGAAAAAATATATTATTTCATTTGCTATAG
1 CAAAAATTGACAAGATTATAATAGAAAAAATATATTATTTCATTTGCTATAG
* * *
37165 CAAAAATTGGCAAGATTATAATAGGAAAAATATATTATTTCATTTGTTATA
1 CAAAAATTGACAAGATTATAATAGAAAAAATATATTATTTCATTTGCTATA
37216 TCCATGCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.36
Consensus pattern (52 bp):
CAAAAATTGACAAGATTATAATAGAAAAAATATATTATTTCATTTGCTATAG
Found at i:39159 original size:21 final size:21
Alignment explanation
Indices: 39135--39177 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
39125 TTGGGAGATC
39135 AAAGCCCAGATT-CAATTGCAA
1 AAAGCCCA-ATTCCAATTGCAA
39156 AAAGCCCAATTCCAATTGCAA
1 AAAGCCCAATTCCAATTGCAA
39177 A
1 A
39178 GTAACCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.19
Consensus pattern (21 bp):
AAAGCCCAATTCCAATTGCAA
Found at i:39216 original size:16 final size:17
Alignment explanation
Indices: 39190--39227 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
39180 AACCCATTTG
*
39190 ATTTGATTTTTTTTATT
1 ATTTTATTTTTTTTATT
39207 -TTTTATTTTTTTTATT
1 ATTTTATTTTTTTTATT
39223 ATTTT
1 ATTTT
39228 TATGGAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
ATTTTATTTTTTTTATT
Found at i:42466 original size:36 final size:36
Alignment explanation
Indices: 42390--42469 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
42380 TTTAACTCTT
* * * *
42390 TTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAGTT
1 TTCAATTTGGGAAAGTTCCCATCAAGTTTTAAAATA
*
42426 TTCAATTTGGGAAAGTTCCCA-CCAGTTTTCAAAATA
1 TTCAATTTGGGAAAGTTCCCATCAAGTTTT-AAAATA
42462 TTCAATTT
1 TTCAATTT
42470 AGCTCCTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 7 0.18
36 31 0.82
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (36 bp):
TTCAATTTGGGAAAGTTCCCATCAAGTTTTAAAATA
Found at i:42529 original size:87 final size:87
Alignment explanation
Indices: 42362--42542 Score: 260
Period size: 87 Copynumber: 2.1 Consensus size: 87
42352 TTTCCTTCAA
* ** *
42362 AGTTTTCAAAGTATTCAATTTAACTCTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAGTTT
1 AGTTTTCAAAATATTCAATTTAACTCTTTTCAAATTAAGAAAGTTCCCATCAAGGTTTTAAGTTT
42427 TCAATTTGGGAAAGTTCCCACC
66 TCAATTTGGGAAAGTTCCCACC
* *
42449 AGTTTTCAAAATATTCAATTTAGCTCCTTTTCAAATTAAGAAAGTTCCCATC-AGGTTTT-GGTT
1 AGTTTTCAAAATATTCAATTTAACT-CTTTTCAAATTAAGAAAGTTCCCATCAAGGTTTTAAGTT
*
42512 TTCAATTTAGGGAAAGTTCCCATC
65 TTCAATTT-GGGAAAGTTCCCACC
42536 A-TTTTCA
1 AGTTTTCA
42543 GTTTTAGTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
86 17 0.20
87 44 0.52
88 24 0.28
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (87 bp):
AGTTTTCAAAATATTCAATTTAACTCTTTTCAAATTAAGAAAGTTCCCATCAAGGTTTTAAGTTT
TCAATTTGGGAAAGTTCCCACC
Found at i:43130 original size:40 final size:39
Alignment explanation
Indices: 43069--43599 Score: 589
Period size: 40 Copynumber: 13.3 Consensus size: 39
43059 CGTTACGATG
* * * *
43069 ATTAAGTTGATAAAGCAATGATCCTGAG-TGTGATTTTGAA
1 ATTAATTTGATAAA-AAATGATCCTGAGCAG-GGTTTTGAA
* *
43109 ATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAA
1 ATTAATTTGATAAAAA-ATGATCCTGAGCAGGGTTTTGAA
* *
43149 ATTAATTTGATAAAAAGATGGTCCTGAGCAGGGTTCTGAA
1 ATTAATTTGATAAAAA-ATGATCCTGAGCAGGGTTTTGAA
* *
43189 ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAA
1 ATTAATTTGATAAA-AAATGATCCTGAGCAGGGTTTTGAA
** * * *
43229 ATCGA-CTGATAAAGAAATGATCTTGAACAGGGTTTTGAA
1 ATTAATTTGATAAA-AAATGATCCTGAGCAGGGTTTTGAA
* *
43268 ATTAATTTGATAAAGCAATGATCCTGAACAGGGTTTTGAA
1 ATTAATTTGATAAA-AAATGATCCTGAGCAGGGTTTTGAA
* * *
43308 ATTAATTTGATAAAAAGATGATCCTGAGAAGGGTCTCGAA
1 ATTAATTTGATAAAAA-ATGATCCTGAGCAGGGTTTTGAA
* *
43348 ATTGATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAG
1 ATTAATTTGATAAAA-AATGATCCTGAGCAGGGTTTTGAA
* * * *
43388 ATTAATTTGATAAAGCAATGATCCTGAACAGGATTCTGAA
1 ATTAATTTGATAAA-AAATGATCCTGAGCAGGGTTTTGAA
* * *
43428 ATTGATTTGATAAAACAATGATCCGGAGCAAGGTTTTGAA
1 ATTAATTTGATAAAA-AATGATCCTGAGCAGGGTTTTGAA
* **
43468 ATTAATTTGATAAAGCAATGATCCTGAGCAGAATTTTTTGAA
1 ATTAATTTGATAAA-AAATGATCCTGAGCAG--GGTTTTGAA
* *
43510 ATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAA
1 ATTAATTTGATAAAAA-ATGATCCTGAGCAGGGTTTTGAA
*
43550 ATTAATTTGATAAAAAGATGGTCCTGAGCAGGGTTTTGAA
1 ATTAATTTGATAAAAA-ATGATCCTGAGCAGGGTTTTGAA
43590 ATTAATTTGA
1 ATTAATTTGA
43600 GCAGGATTCT
Statistics
Matches: 421, Mismatches: 58, Indels: 24
0.84 0.12 0.05
Matches are distributed among these distances:
39 34 0.08
40 348 0.83
41 4 0.01
42 35 0.08
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (39 bp):
ATTAATTTGATAAAAAATGATCCTGAGCAGGGTTTTGAA
Found at i:43409 original size:120 final size:119
Alignment explanation
Indices: 43069--44134 Score: 1083
Period size: 120 Copynumber: 9.0 Consensus size: 119
43059 CGTTACGATG
* * *
43069 ATTAAGTTGATAAAGCAATGATCCTGAG-TGTGATTTTGAAATTAATTTGATAAAA-AGATGATC
1 ATTAATTTGATAAAGCAATGATCCTGAGCAG-GGTTTTGAAATTAATTTGATAAAACA-ATGATC
* * * * *
43132 CTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGGTCCTGAGCAGGGTTCTGAA
64 CTGAGCAGGGTTTTGAAATTAATTTGATAAAAA-ATGATCCTGAACAGGATTCTGAA
* ** * *
43189 ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATCGA-CTGATAAAGA-AATGATCT
1 ATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAA-ACAATGATCC
* * * *
43252 TGAACAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAACAGGGTTTTGAA
65 TGAGCAGGGTTTTGAAATTAATTTGATAAA-AAATGATCCTGAACAGGATTCTGAA
* * * * *
43308 ATTAATTTGATAAA-AAGATGATCCTGAGAAGGGTCTCGAAATTGATTTGATAAAACAATGATCC
1 ATTAATTTGATAAAGCA-ATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCC
* *
43372 TGAGCAGGGTTTTGAGATTAATTTGATAAAGCAATGATCCTGAACAGGATTCTGAA
65 TGAGCAGGGTTTTGAAATTAATTTGATAAA-AAATGATCCTGAACAGGATTCTGAA
* * * * *
43428 ATTGATTTGATAAAACAATGATCCGGAGCAAGGTTTTGAAATTAATTTGATAAAGCAATGATCCT
1 ATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCCT
** *
43493 GAGCAGAATTTTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAA
66 GAGCAG--GGTTTTGAAATTAATTTGATAAAAA-ATGATCCTGAACAGGATTCTGAA
* * * * *
43550 ATTAATTTGATAAA-AAGATGGTCCTGAGCAGGGTTTTGAAATTAATTTG----AGC-AGGATTC
1 ATTAATTTGATAAAGCA-ATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCC
* **** * ** * ** ** * * *
43609 TGA-AATTAATTTGATAA-AAAGATGGTCCTGAGCAGGGTTCTG---A--A-----A-
65 TGAGCAGGGTTTTGA-AATTAATTTGAT--AAAAAATGATCCTGAACAGGATTCTGAA
* * * *
43654 -TTAATTTGATAGAGCAATGATCCTGAGCAGGATTTTGAAATCAATTTGATAAAGCAATGATCCT
1 ATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCCT
** * * *
43718 -AGCAGGGTTTTGAAATCGA-CTGATAAAGAAATGATCCTGAACAGGGTTTTGAA
66 GAGCAGGGTTTTGAAATTAATTTGATAAA-AAATGATCCTGAACAGGATTCTGAA
* *
43771 ATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTTTGAAATTAATTTGATAAAA-AGATGAT
1 ATTAATTTGATAAAGCAATGATCCTGAGCAGG--GTTTTGAAATTAATTTGATAAAACA-ATGAT
* *
43835 CCTGAGCA-GGATTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAA
63 CCTGAGCAGGGTTTTGAAATTAATTTGATAAAAA-ATGATCCTGAACAGGATTCTGAA
* *
43892 ATTGATTTGACAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCCT
1 ATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCCT
*
43957 GAGCAGGGTTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAA
66 GAGCAGGGTTTTGAAATTAATTTGATAAAAA-ATGATCCTGAACAGGATTCTGAA
* *
44012 ATTGATTTGACAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCCT
1 ATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCCT
* *
44077 GAGCAGGGTTTTGAAATTAATTTGATAAAAAAATGATCCTGAGCAAGATTCTGAA
66 GAGCAGGGTTTTGAAATTAATTTGAT-AAAAAATGATCCTGAACAGGATTCTGAA
44132 ATT
1 ATT
44135 GATCTGACAA
Statistics
Matches: 799, Mismatches: 103, Indels: 88
0.81 0.10 0.09
Matches are distributed among these distances:
103 41 0.05
104 1 0.00
105 2 0.00
106 6 0.01
107 9 0.01
108 13 0.02
109 1 0.00
110 1 0.00
112 1 0.00
114 11 0.01
115 8 0.01
116 3 0.00
117 8 0.01
118 33 0.04
119 134 0.17
120 374 0.47
121 69 0.09
122 84 0.11
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (119 bp):
ATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCCT
GAGCAGGGTTTTGAAATTAATTTGATAAAAAATGATCCTGAACAGGATTCTGAA
Found at i:43604 original size:23 final size:23
Alignment explanation
Indices: 43574--43622 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
43564 AAGATGGTCC
* *
43574 TGAGCAGGGTTTTGAAATTAATT
1 TGAGCAGGATTCTGAAATTAATT
43597 TGAGCAGGATTCTGAAATTAATT
1 TGAGCAGGATTCTGAAATTAATT
43620 TGA
1 TGA
43623 TAAAAAGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (23 bp):
TGAGCAGGATTCTGAAATTAATT
Found at i:43633 original size:63 final size:63
Alignment explanation
Indices: 43534--43662 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 63
43524 AAGATGATCC
*
43534 TGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGGTCCTGAGCAGGGTTTTGAAATTAATT
1 TGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGGTCCTGAGCAGGGTTCTGAAATTAATT
43597 TGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGGTCCTGAGCAGGGTTCTGAAATTAATT
1 TGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGGTCCTGAGCAGGGTTCTGAAATTAATT
43660 TGA
1 TGA
43663 TAGAGCAATG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.33
Consensus pattern (63 bp):
TGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGGTCCTGAGCAGGGTTCTGAAATTAATT
Found at i:43690 original size:103 final size:103
Alignment explanation
Indices: 43506--43702 Score: 315
Period size: 103 Copynumber: 1.9 Consensus size: 103
43496 CAGAATTTTT
*
43506 TGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGG
1 TGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGA
* *
43571 TCCTGAGCAGGGTTTTGAAATTAATTTGAGCAGGATTC
66 TCCTGAGCAGGATTTTGAAATCAATTTGAGCAGGATTC
* * **
43609 TGAAATTAATTTGATAAAAAGATGGTCCTGAGCAGGGTTCTGAAATTAATTTGATAGAGCA-ATG
1 TGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTGATA-AAAAGATG
43673 ATCCTGAGCAGGATTTTGAAATCAATTTGA
65 ATCCTGAGCAGGATTTTGAAATCAATTTGA
43703 TAAAGCAATG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 84 0.98
104 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (103 bp):
TGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGA
TCCTGAGCAGGATTTTGAAATCAATTTGAGCAGGATTC
Found at i:44132 original size:40 final size:40
Alignment explanation
Indices: 43597--44134 Score: 678
Period size: 40 Copynumber: 13.5 Consensus size: 40
43587 GAAATTAATT
* *
43597 TGAGCAGGATTCTGAAATTAATTTGATAAAA-AGATGGTCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACA-ATGATCC
* * * *
43637 TGAGCAGGGTTCTGAAATTAATTTGATAGAGCAATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCC
* *
43677 TGAGCAGGATTTTGAAATCAATTTGATAAAGCAATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCC
* ** *
43717 T-AGCAGGGTTTTGAAATCGA-CTGATAAAGA-AATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAA-ACAATGATCC
* * *
43755 TGAACAGGGTTTTGAAATTAATTTGATAAAGCAATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCC
*
43795 TGAGTAGGATTTTTTGAAATTAATTTGATAAAA-AGATGATCC
1 TGAGCAGGA--TTTTGAAATTAATTTGATAAAACA-ATGATCC
43837 TGAGCAGGA-TTTGAAATTAATTTGATAAAA-AGATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACA-ATGATCC
* * * *
43876 TGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCC
*
43916 TGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCC
*
43956 TGAGCAGGGTTTTGAAATTAATTTGATAAAA-AGATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACA-ATGATCC
* * * *
43996 TGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCC
*
44036 TGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCC
* *
44076 TGAGCAGGGTTTTGAAATTAATTTGATAAAAAAATGATCC
1 TGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCC
* *
44116 TGAGCAAGATTCTGAAATT
1 TGAGCAGGATTTTGAAATT
44135 GATCTGACAA
Statistics
Matches: 441, Mismatches: 45, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
38 16 0.04
39 73 0.17
40 312 0.71
41 4 0.01
42 36 0.08
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (40 bp):
TGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCC
Found at i:44141 original size:23 final size:24
Alignment explanation
Indices: 44110--44157 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
44100 GATAAAAAAA
44110 TGATCCTGAGCAA-GATTCTGAAAT
1 TGATCCTGA-CAAGGATTCTGAAAT
*
44134 TGAT-CTGACAAGGATTTTGAAAT
1 TGATCCTGACAAGGATTCTGAAAT
44157 T
1 T
44158 AATTTGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 15 0.68
24 4 0.18
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (24 bp):
TGATCCTGACAAGGATTCTGAAAT
Found at i:44208 original size:39 final size:39
Alignment explanation
Indices: 44144--44306 Score: 236
Period size: 39 Copynumber: 4.2 Consensus size: 39
44134 TGATCTGACA
* * *
44144 AGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGC
1 AGGATTTTGAAATTAA-CTGGTAAAGAAATGATCCTGAGC
* *
44184 AGGGTTTTGAAATTAATTGGTAAAGAAATGATCCTGAGC
1 AGGATTTTGAAATTAACTGGTAAAGAAATGATCCTGAGC
*
44223 AGGATTTTGAAATTAACTGGTAAAGAAAAGATCCTGAGC
1 AGGATTTTGAAATTAACTGGTAAAGAAATGATCCTGAGC
**
44262 AGGATTTTGAAATCGACTGGTAAAGAAATGATCCTGAGC
1 AGGATTTTGAAATTAACTGGTAAAGAAATGATCCTGAGC
*
44301 GGGATT
1 AGGATT
44307 CTGGAATCGA
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 98 0.87
40 15 0.13
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (39 bp):
AGGATTTTGAAATTAACTGGTAAAGAAATGATCCTGAGC
Found at i:44315 original size:39 final size:39
Alignment explanation
Indices: 44144--44333 Score: 218
Period size: 39 Copynumber: 4.8 Consensus size: 39
44134 TGATCTGACA
* * * *
44144 AGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGC
1 AGGATTTTGAAATCAA-CTGGTAAAGAAATGATCCTGAGC
* * *
44184 AGGGTTTTGAAATTAATTGGTAAAGAAATGATCCTGAGC
1 AGGATTTTGAAATCAACTGGTAAAGAAATGATCCTGAGC
* *
44223 AGGATTTTGAAATTAACTGGTAAAGAAAAGATCCTGAGC
1 AGGATTTTGAAATCAACTGGTAAAGAAATGATCCTGAGC
*
44262 AGGATTTTGAAATCGACTGGTAAAGAAATGATCCTGAGC
1 AGGATTTTGAAATCAACTGGTAAAGAAATGATCCTGAGC
* * * * ** *
44301 GGGATTCTGGAATCGACTAATAAAGCAATGATC
1 AGGATTTTGAAATCAACTGGTAAAGAAATGATC
44334 ATGAATAGAA
Statistics
Matches: 135, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 120 0.89
40 15 0.11
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (39 bp):
AGGATTTTGAAATCAACTGGTAAAGAAATGATCCTGAGC
Found at i:44857 original size:141 final size:140
Alignment explanation
Indices: 44408--44950 Score: 858
Period size: 141 Copynumber: 3.9 Consensus size: 140
44398 GGAGGACAAG
* * * *
44408 TCAGAATTGATACCCGGAGGTTTCTGAAATTGTGCCCGGTGGTCTCACAAATGCAAACTCGACCT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
* * * *
44473 TGAGCAAGGTTTATTTGAAATTTAAACGCAAATTTGATTAACAACATGATGAAATGAGATGATAC
66 TGAGCAAGG-TT-TTTGAAATTTAAACGCAACTTTGATTAAAAACTTGATGAAATGAAATGATAC
44538 CCGGAGGATTTA
129 CCGGAGGATTTA
44550 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
* *
44615 TGAGCAAGG-TTTTGAAATTTAAACGCAGCTTTGATT-AAAACTTGAAGAAATGAAATGATACCC
66 TGAGCAAGGTTTTTGAAATTTAAACGCAACTTTGATTAAAAACTTGATGAAATGAAATGATACCC
44678 GGAGGATTTA
131 GGAGGATTTA
* * * * *
44688 TCAGAACTAATACCCGAAGATTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACACAAACT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
44753 TGAGCAAGGTTTTTGAAATTTTAAACGCAACTTTGATTAAAAACTTGATGAAATGAAATGATACC
66 TGAGCAAGGTTTTTGAAA-TTTAAACGCAACTTTGATTAAAAACTTGATGAAATGAAATGATACC
*
44818 TGGAGGATTTA
130 CGGAGGATTTA
* * *
44829 TCAGAATTAATACCTGGAGGTTTTTGAAATTGTGCCCGGAGGTCCTACAAATGCAAACTCAACCT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
*
44894 TGAGCAAGGTTTTTGAAATTTAAACGCAGCTTTGATTAAAAACTTGATGAAAT-AAAT
66 TGAGCAAGGTTTTTGAAATTTAAACGCAACTTTGATTAAAAACTTGATGAAATGAAAT
44951 TTTGTCTTCG
Statistics
Matches: 371, Mismatches: 27, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
138 102 0.27
139 36 0.10
140 53 0.14
141 110 0.30
142 70 0.19
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (140 bp):
TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
TGAGCAAGGTTTTTGAAATTTAAACGCAACTTTGATTAAAAACTTGATGAAATGAAATGATACCC
GGAGGATTTA
Found at i:44880 original size:279 final size:281
Alignment explanation
Indices: 44408--44950 Score: 878
Period size: 279 Copynumber: 1.9 Consensus size: 281
44398 GGAGGACAAG
* * * * * * * *
44408 TCAGAATTGATACCCGGAGGTTTCTGAAATTGTGCCCGGTGGTCTCACAAATGCAAACTCGACCT
1 TCAGAACTAATACCCGAAGATTTCTGAAATTGTGCCCGGAGGTCTCACAAATGCAAACACAAACT
* *
44473 TGAGCAAGGTTTATTTGAAATTTAAACGCAAATTTGATTAACAACATGATGAAATGAGATGATAC
66 TGAGCAAGGTTTATTTGAAATTTAAACGCAAATTTGATTAAAAACATGATGAAATGAAATGATAC
*
44538 CCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATG
131 CCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCCTACAAATG
44603 CAAACTCAACCTTGAGCAAGG-TTTTGAAATTTAAACGCAGCTTTGATT-AAAACTTGAAGAAAT
196 CAAACTCAACCTTGAGCAAGGTTTTTGAAATTTAAACGCAGCTTTGATTAAAAACTTGAAGAAAT
44666 GAAATGATACCCGGAGGATTTA
261 -AAATGATACCCGGAGGATTTA
*
44688 TCAGAACTAATACCCGAAGATTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACACAAACT
1 TCAGAACTAATACCCGAAGATTTCTGAAATTGTGCCCGGAGGTCTCACAAATGCAAACACAAACT
* *
44753 TGAGCAAGG-TT-TTTGAAATTTTAAACGCAACTTTGATTAAAAACTTGATGAAATGAAATGATA
66 TGAGCAAGGTTTATTTGAAA-TTTAAACGCAAATTTGATTAAAAACATGATGAAATGAAATGATA
* * *
44816 CCTGGAGGATTTATCAGAATTAATACCTGGAGGTTTTTGAAATTGTGCCCGGAGGTCCTACAAAT
130 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCCTACAAAT
*
44881 GCAAACTCAACCTTGAGCAAGGTTTTTGAAATTTAAACGCAGCTTTGATTAAAAACTTGATGAAA
195 GCAAACTCAACCTTGAGCAAGGTTTTTGAAATTTAAACGCAGCTTTGATTAAAAACTTGAAGAAA
44946 TAAAT
260 TAAAT
44951 TTTGTCTTCG
Statistics
Matches: 242, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
278 7 0.03
279 125 0.52
280 96 0.40
281 14 0.06
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (281 bp):
TCAGAACTAATACCCGAAGATTTCTGAAATTGTGCCCGGAGGTCTCACAAATGCAAACACAAACT
TGAGCAAGGTTTATTTGAAATTTAAACGCAAATTTGATTAAAAACATGATGAAATGAAATGATAC
CCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCCTACAAATG
CAAACTCAACCTTGAGCAAGGTTTTTGAAATTTAAACGCAGCTTTGATTAAAAACTTGAAGAAAT
AAATGATACCCGGAGGATTTA
Done.