Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011254.1 Corchorus capsularis cultivar CVL-1 contig11275, 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: 139627
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:716 original size:53 final size:51
Alignment explanation
Indices: 636--776 Score: 187
Period size: 53 Copynumber: 2.7 Consensus size: 51
626 CAACAAATTC
* *
636 ATTTGCACCATTACACCTTTAACTATGTAATAGGAATGCATCATATGACTTCA
1 ATTTGCATCATTACACCTTT-ACTATGTAATAGGAATGCATAATA-GACTTCA
*
689 ATTTGCATCATTACACCTTTCACTATGTAATATGAATGCATAATAGACTTCA
1 ATTTGCATCATTACACCTTT-ACTATGTAATAGGAATGCATAATAGACTTCA
* * *
741 ATTGGCATCATTATACCTTTAGTA--TAATAGGAATGC
1 ATTTGCATCATTACACCTTTACTATGTAATAGGAATGC
777 CAACACTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
49 11 0.14
51 3 0.04
52 25 0.31
53 41 0.51
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (51 bp):
ATTTGCATCATTACACCTTTACTATGTAATAGGAATGCATAATAGACTTCA
Found at i:13716 original size:13 final size:13
Alignment explanation
Indices: 13698--13725 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13688 ACTTTTTCTG
13698 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
13711 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
13724 TT
1 TT
13726 GGTGAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:20927 original size:1 final size:1
Alignment explanation
Indices: 20921--20946 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
20911 AACTTGATTT
20921 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
20947 CCCATGCCCT
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:26328 original size:9 final size:9
Alignment explanation
Indices: 26314--26343 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
26304 ACCTTGATCG
26314 AATCCCTTT
1 AATCCCTTT
26323 AATCCCTTT
1 AATCCCTTT
26332 AAT-CCTTT
1 AATCCCTTT
26340 AATC
1 AATC
26344 AAAGCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (9 bp):
AATCCCTTT
Found at i:29056 original size:35 final size:35
Alignment explanation
Indices: 29010--29081 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
29000 ACATGTTAAC
29010 ATCTTAATCCTTGTCTAGTCTAATAATTACTCAAA
1 ATCTTAATCCTTGTCTAGTCTAATAATTACTCAAA
29045 ATCTTAATCCTTGTCTAGTCTAATAATTACTCAAA
1 ATCTTAATCCTTGTCTAGTCTAATAATTACTCAAA
29080 AT
1 AT
29082 GAAATTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (35 bp):
ATCTTAATCCTTGTCTAGTCTAATAATTACTCAAA
Found at i:33494 original size:15 final size:15
Alignment explanation
Indices: 33474--33502 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33464 ACCAATAACA
33474 ATGGTAATATGATTT
1 ATGGTAATATGATTT
33489 ATGGTAATATGATT
1 ATGGTAATATGATT
33503 CTTGGATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
ATGGTAATATGATTT
Found at i:41981 original size:103 final size:103
Alignment explanation
Indices: 41802--42004 Score: 309
Period size: 103 Copynumber: 2.0 Consensus size: 103
41792 ACTTTTGCGT
* * *
41802 TCAAAATTAGCTTTTGACCCAAACCATGATTTATTTGGTATTGCATTTGGGTTCAAAAGCAGCTT
1 TCAAAATCAGCTTTTGACACAAACCAGGATTTATTTGGTATTGCATTTGGGTTCAAAAGCAGCTT
*
41867 TTTTAATTCCAAACACAATGTCAAACCAGGCCTAAGGA
66 TTTTAATTCCAAACACAATGTCAAACCAAGCCTAAGGA
* * *
41905 TCAAAATCAGCTTTTGACACGAATCAGGATTTATTTGGTATTGCGTTTGGGTTCAAAAGCAGCTT
1 TCAAAATCAGCTTTTGACACAAACCAGGATTTATTTGGTATTGCATTTGGGTTCAAAAGCAGCTT
* *
41970 TTTT-ATCTCCAAACGCAATGTCAAACTAAGCCTAA
66 TTTTAAT-TCCAAACACAATGTCAAACCAAGCCTAA
42005 ATCACCCATA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 2 0.02
103 88 0.98
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (103 bp):
TCAAAATCAGCTTTTGACACAAACCAGGATTTATTTGGTATTGCATTTGGGTTCAAAAGCAGCTT
TTTTAATTCCAAACACAATGTCAAACCAAGCCTAAGGA
Found at i:51168 original size:20 final size:21
Alignment explanation
Indices: 51133--51172 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
51123 AAGGTTTTTC
51133 TTTTTTTTTGCCATAAATATT
1 TTTTTTTTTGCCATAAATATT
*
51154 TTTTTTTTTG-GATAAATAT
1 TTTTTTTTTGCCATAAATAT
51173 ATATTATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTTTTTTTGCCATAAATATT
Found at i:54523 original size:2 final size:2
Alignment explanation
Indices: 54516--54545 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54506 ACAATTTCAC
54516 AT AT 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 AT AT
54546 CCAAACATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62608 original size:109 final size:111
Alignment explanation
Indices: 62455--62752 Score: 449
Period size: 109 Copynumber: 2.6 Consensus size: 111
62445 TAAATTAAAA
** *
62455 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
62519 AGAATAAAATTGTATATTAGAAAAAA-TTTTAATATATCCAAA-TTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTTAATATATCCAAATTTTTT
62566 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
62631 ATAAAATTGTATATTAGAAAAAATTTTTAGTATATCCAAATTTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTTAATATATCCAAATTTTTT
* *
62677 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
62742 GTAGAATAAAA
61 GTAGAATAAAA
62753 CTATAATAGT
Statistics
Matches: 173, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
109 63 0.36
110 26 0.15
111 53 0.31
112 2 0.01
113 1 0.01
116 28 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (111 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTTAATATATCCAAATTTTTT
Found at i:64361 original size:6 final size:6
Alignment explanation
Indices: 64341--64375 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
64331 CATGTTGTTC
*
64341 TTTAAG TTTAA- TTTAAT TTTAAT TTTAAT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
64376 GGCATACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (6 bp):
TTTAAT
Found at i:64361 original size:11 final size:11
Alignment explanation
Indices: 64341--64375 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
64331 CATGTTGTTC
*
64341 TTTAAGTTTAA
1 TTTAATTTTAA
64352 TTTAATTTTAA
1 TTTAATTTTAA
64363 TTTTAATTTTAA
1 -TTTAATTTTAA
64375 T
1 T
64376 GGCATACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
TTTAATTTTAA
Found at i:72846 original size:32 final size:34
Alignment explanation
Indices: 72810--72874 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
72800 TATGTTACTC
*
72810 AGATATAATCAGATATC-TT-TTTTTTTTTGGCA
1 AGATATAATCAGATATCGTTCATTTTTTTTGGCA
72842 AGATATAATCAGATATCGTTCATTTTTTTTGGC
1 AGATATAATCAGATATCGTTCATTTTTTTTGGC
72875 TGAATCAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 17 0.57
33 2 0.07
34 11 0.37
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.48
Consensus pattern (34 bp):
AGATATAATCAGATATCGTTCATTTTTTTTGGCA
Found at i:78184 original size:3 final size:3
Alignment explanation
Indices: 78176--78208 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
78166 AACCCACCTT
78176 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
78209 GTTTGATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:78318 original size:104 final size:99
Alignment explanation
Indices: 78210--78407 Score: 301
Period size: 104 Copynumber: 1.9 Consensus size: 99
78200 TTCTTCTTCG
*
78210 TTTGATCTTTTATGCCCTAAATTTCGTCTTGTTTCTCCTCTGCAACTGCAACCCACCCTATTACC
1 TTTGATCTTTTATGCCCTAAATTTCGTCTTGTTTCTCCTCTACAA---C--CCCACCCTATTACC
*
78275 AGATCTTCGATCAAATCT-TCGTCTTCGA-CCAAAACGCGA
61 AGATCTT-GATCAAATCTCT-GGCTTCGACCCAAAACGCGA
78314 TTTGATCTTTTATGCCCTAAATTTCGTCTTGTTTCTCCTCTACAACCCCACCCTATTACCAGATC
1 TTTGATCTTTTATGCCCTAAATTTCGTCTTGTTTCTCCTCTACAACCCCACCCTATTACCAGATC
78379 TTGATCAAATCTCTGGCTTCGACCCAAAA
66 TTGATCAAATCTCTGGCTTCGACCCAAAA
78408 AAAAAAGGGA
Statistics
Matches: 90, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
98 17 0.19
99 28 0.31
101 1 0.01
104 44 0.49
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.35
Consensus pattern (99 bp):
TTTGATCTTTTATGCCCTAAATTTCGTCTTGTTTCTCCTCTACAACCCCACCCTATTACCAGATC
TTGATCAAATCTCTGGCTTCGACCCAAAACGCGA
Found at i:79747 original size:72 final size:72
Alignment explanation
Indices: 79630--79774 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
79620 AAATTCAATA
79630 CCGGATTGTTGTCCCCAAGGGGACACTAAGAGCTTGGGATTTCCTCCGTCCGGGTTTGAATCCTG
1 CCGGATTGTTGTCCCCAAGGGGACACTAAGAGCTTGGGATTTCCTCCGTCCGGGTTTGAATCCTG
79695 GGAGGGG
66 GGAGGGG
79702 CCGGATTGTTGTCCCCAAGGGGACACTAAGAGCTTGGGATTTCCTCCGTCCGGGTTTGAATCCTG
1 CCGGATTGTTGTCCCCAAGGGGACACTAAGAGCTTGGGATTTCCTCCGTCCGGGTTTGAATCCTG
79767 GGAGGGG
66 GGAGGGG
79774 C
1 C
79775 GTGGTGGGAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.17, C:0.24, G:0.34, T:0.25
Consensus pattern (72 bp):
CCGGATTGTTGTCCCCAAGGGGACACTAAGAGCTTGGGATTTCCTCCGTCCGGGTTTGAATCCTG
GGAGGGG
Found at i:104157 original size:5 final size:5
Alignment explanation
Indices: 104147--104177 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
104137 ATTGGCCTTG
104147 TCTTT TCTTT TCTTT TCTTT TCTTT T-TTT TC
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TC
104178 AAAAGCTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:116802 original size:15 final size:16
Alignment explanation
Indices: 116753--116807 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
116743 TTGGAACCAT
116753 ATGACCCAAAACCGAAAA
1 ATGACCC-AAACC-AAAA
*
116771 A-CACCCAAACCAAAA
1 ATGACCCAAACCAAAA
*
116786 ATGACCCAAACC-CAA
1 ATGACCCAAACCAAAA
116801 ATGACCC
1 ATGACCC
116808 GACATTTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 14 0.42
16 14 0.42
17 4 0.12
18 1 0.03
ACGTcount: A:0.51, C:0.36, G:0.07, T:0.05
Consensus pattern (16 bp):
ATGACCCAAACCAAAA
Found at i:133379 original size:5 final size:5
Alignment explanation
Indices: 133369--133413 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
133359 TTAAAGCTCA
*
133369 TTTCT TTTCT TTTCT TTTCT TTTCT TTT-T TTT-T TTT-T TGTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
133414 GGGAGAACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 11 0.30
5 26 0.70
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (5 bp):
TTTCT
Found at i:136820 original size:389 final size:389
Alignment explanation
Indices: 136092--136867 Score: 1444
Period size: 389 Copynumber: 2.0 Consensus size: 389
136082 AACAAAACAC
*
136092 AAGTATATATAACAAACAATAATAATTGAAGTGTGGATTACCAAAAAACCAATAAGGATTCTCAC
1 AAGTATATATAACAAACAATAATAATTGAAGTGTGGATTACCAAAAAACCAATAAGGACTCTCAC
* * *
136157 CACATTCAATTGGGGTATCATTTATTTGGTTTTTTTGGTCTTTTTACCCTTGGCTTTTTTGTTAT
66 CACATTCAATTGGGGTACCATTTATATGGTTTTTTTGGTCTTTTTACCCTTGACTTTTTTGTTAT
136222 TTCGTTGAACTCTCAAGGGTGATATGGGGAAAAAAGTCAAAAGTTAAAAATTAAAAATACAAAGC
131 TTCGTTGAACTCTCAAGGGTGATATGGGGAAAAAAGTCAAAAGTTAAAAATTAAAAATACAAAGC
**
136287 CAATCATGCGGGTTATAATCATTGTGTTGTACTTGTACATGAAAGCCTTGGTCTGTTTACTCTGT
196 CAATCATGCGGGTTATAATCATTGTGTTGTACTTGTACATGAAAGCAATGGTCTGTTTACTCTGT
136352 CAAAAACAAGGCGTATCCTAAAACCTAAATTACTAATTATTATTATTACTTGAAAAGCCAAAGCC
261 CAAAAACAAGGCGTATCCTAAAACCTAAATTACTAATTATTATTATTACTTGAAAAGCCAAAGCC
* *
136417 AATTGTGCGGGTTATAATCATTGTGTTGTAATTGTACATGAAAGCATTGGGTATTCTACTCACT
326 AATCGTGCGGGTTATAATCATTATGTTGTAATTGTACATGAAAGCATTGGGTATTCTACTCACT
136481 AAGTATATATAACAAACAATAATAATTGAAGTGTGGATTACCAAAAAACCAATAAGGACTCTCAC
1 AAGTATATATAACAAACAATAATAATTGAAGTGTGGATTACCAAAAAACCAATAAGGACTCTCAC
136546 CACATTCAATTGGGGTACCATTTATATGGTTTTTTTGGTCTTTTTACCCTTGACTTTTTTGTTAT
66 CACATTCAATTGGGGTACCATTTATATGGTTTTTTTGGTCTTTTTACCCTTGACTTTTTTGTTAT
*
136611 TTCGTTGAACTCTCAAGGGTGATATGGGGAAAAGAGTCAAAAGTTAAAAATTAAAAATACAAAGC
131 TTCGTTGAACTCTCAAGGGTGATATGGGGAAAAAAGTCAAAAGTTAAAAATTAAAAATACAAAGC
*
136676 CAATCATGCGGGTTATAATCATTGTGTTGTACTTGTACATGAAAGCAATGGTTTGTTTACTCTGT
196 CAATCATGCGGGTTATAATCATTGTGTTGTACTTGTACATGAAAGCAATGGTCTGTTTACTCTGT
*
136741 CAAAAACAAGGCGTATCCTAAAATCTAAATTACTAATTATTATTATTACTTGAAAAGCCAAAGCC
261 CAAAAACAAGGCGTATCCTAAAACCTAAATTACTAATTATTATTATTACTTGAAAAGCCAAAGCC
*
136806 AATCGTGTGGGTTATAATCATTATGTTGTAATTGTACATGAAAGCATTGGGTATTCTACTCA
326 AATCGTGCGGGTTATAATCATTATGTTGTAATTGTACATGAAAGCATTGGGTATTCTACTCA
136868 ACAAGATTGT
Statistics
Matches: 375, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
389 375 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (389 bp):
AAGTATATATAACAAACAATAATAATTGAAGTGTGGATTACCAAAAAACCAATAAGGACTCTCAC
CACATTCAATTGGGGTACCATTTATATGGTTTTTTTGGTCTTTTTACCCTTGACTTTTTTGTTAT
TTCGTTGAACTCTCAAGGGTGATATGGGGAAAAAAGTCAAAAGTTAAAAATTAAAAATACAAAGC
CAATCATGCGGGTTATAATCATTGTGTTGTACTTGTACATGAAAGCAATGGTCTGTTTACTCTGT
CAAAAACAAGGCGTATCCTAAAACCTAAATTACTAATTATTATTATTACTTGAAAAGCCAAAGCC
AATCGTGCGGGTTATAATCATTATGTTGTAATTGTACATGAAAGCATTGGGTATTCTACTCACT
Found at i:137205 original size:32 final size:32
Alignment explanation
Indices: 137168--137229 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
137158 GGGGTATTTC
* *
137168 TTTATCTCACTTAGGGTTTATATATCATGTAT
1 TTTATCTCACTTAGGGATTAAATATCATGTAT
*
137200 TTTATCTCACTTAGGGATTAAATTTCATGT
1 TTTATCTCACTTAGGGATTAAATATCATGT
137230 CATGTCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (32 bp):
TTTATCTCACTTAGGGATTAAATATCATGTAT
Found at i:137402 original size:32 final size:32
Alignment explanation
Indices: 137361--137421 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
137351 GGAAATTTCT
*
137361 TTATCTCACTTAGGGTTTATATATCATGTATC
1 TTATCTCACTTAGGGTTTAGATATCATGTATC
*
137393 TTATCTCACTTAGGGTTTAGATTTCATGT
1 TTATCTCACTTAGGGTTTAGATATCATGT
137422 CATGTCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.48
Consensus pattern (32 bp):
TTATCTCACTTAGGGTTTAGATATCATGTATC
Found at i:137419 original size:192 final size:193
Alignment explanation
Indices: 137078--137458 Score: 604
Period size: 192 Copynumber: 2.0 Consensus size: 193
137068 ACAATTTTTA
*
137078 AAATTATGACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAGACTATCTCACTTAGG
1 AAATTATGACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAAACTATCTCACTTAGG
** *
137143 ATTTAATATAGTTTTGGGGTATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTTTATCTC
66 ATTTAATATAGTTTTGGGAAATTTCTTTATCTCACTTAGGGTTTATATATCATGTATCTTATCTC
137208 ACTTAGGGATTAAATTTCATGTCATGTC-A-TTTTTTGTCTCTCATAGCCATTTTTTTATTTG
131 ACTTAGGGATTAAATTTCATGTCATGTCAATTTTTTTGTCTCTCATAGCCATTTTTTTATTTG
* * * * *
137269 AAATTTTGACTCTTCCACCACTTTTTATGATATAGAATGTTGAAATTTAAAGTATCTCACTTAGG
1 AAATTATGACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAAACTATCTCACTTA-G
*
137334 GTTTTAATATAGTTTTGGGAAATTTCTTTATCTCACTTAGGGTTTATATATCATGTATCTTATCT
65 GATTTAATATAGTTTTGGGAAATTTCTTTATCTCACTTAGGGTTTATATATCATGTATCTTATCT
* * **
137399 CACTTAGGGTTTAGATTTCATGTCATGTCAATTTTTTTTGTCTCTCATAGCTTTTTTTTT
130 CACTTAGGGATTAAATTTCATGTCATGTCAA-TTTTTTTGTCTCTCATAGCCATTTTTTT
137459 TTTAAAAATT
Statistics
Matches: 172, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
191 57 0.33
192 89 0.52
193 1 0.01
195 25 0.15
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.48
Consensus pattern (193 bp):
AAATTATGACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAAACTATCTCACTTAGG
ATTTAATATAGTTTTGGGAAATTTCTTTATCTCACTTAGGGTTTATATATCATGTATCTTATCTC
ACTTAGGGATTAAATTTCATGTCATGTCAATTTTTTTGTCTCTCATAGCCATTTTTTTATTTG
Found at i:138459 original size:25 final size:26
Alignment explanation
Indices: 138411--138461 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
138401 AACCTAAAAC
**
138411 CGAAAATTAACCAAACCCTTATAACT
1 CGAAAATTAACCAAACCCAGATAACT
*
138437 CGAAAA-TAACCTAACCCAGATAACT
1 CGAAAATTAACCAAACCCAGATAACT
138462 GGATCCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.47, C:0.27, G:0.06, T:0.20
Consensus pattern (26 bp):
CGAAAATTAACCAAACCCAGATAACT
Found at i:139076 original size:21 final size:22
Alignment explanation
Indices: 139050--139094 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
139040 ACTTAGGGTG
139050 TTGCTAAACACCGCCACA-TTT
1 TTGCTAAACACCGCCACACTTT
** *
139071 TTGCTATTCACCGCCTCACTTT
1 TTGCTAAACACCGCCACACTTT
139093 TT
1 TT
139095 ACACTTTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.20, C:0.33, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAAACACCGCCACACTTT
Done.