Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020302.1 Corchorus olitorius cultivar O-4 contig20335, 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: 29851
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2460 original size:51 final size:51
Alignment explanation
Indices: 2343--2474 Score: 140
Period size: 51 Copynumber: 2.6 Consensus size: 51
2333 CCAAAACTCA
* * *
2343 ACCTAAAGATCCAATTTTTATTGTTAGAATTACCAAGACTAAACATTTGCT
1 ACCTAAAGATCCAATTTTTATTGTTAAAATTACCAAAACTAAACATTTACT
* * ** * *
2394 ACCTAAATATCCAATTTTTGTTGTTAAAATTACCAAAACTCTACCTTTATT
1 ACCTAAAGATCCAATTTTTATTGTTAAAATTACCAAAACTAAACATTTACT
* **
2445 ATCC-AAAGATTCAATTTTTATCATTAAAAT
1 A-CCTAAAGATCCAATTTTTATTGTTAAAAT
2475 CGCGTAGACT
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
51 64 0.97
52 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (51 bp):
ACCTAAAGATCCAATTTTTATTGTTAAAATTACCAAAACTAAACATTTACT
Found at i:3845 original size:15 final size:15
Alignment explanation
Indices: 3825--3853 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3815 GGGAGGTTTT
3825 GGGTTGAGATTTGAA
1 GGGTTGAGATTTGAA
3840 GGGTTGAGATTTGA
1 GGGTTGAGATTTGA
3854 GTCTTGATGT
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:0.24, C:0.00, G:0.41, T:0.34
Consensus pattern (15 bp):
GGGTTGAGATTTGAA
Found at i:8507 original size:112 final size:111
Alignment explanation
Indices: 8378--8591 Score: 295
Period size: 112 Copynumber: 1.9 Consensus size: 111
8368 TCTTCTCGAT
* * ** *
8378 TAACTTAATTGCTCTGAATTAAGCTAATTACT-ATTGATTACTTTTTTTTACTTCTTTTAAACTT
1 TAACTTAATTACTCTGAATTAAGCCAATTACTGATT-ACCACTTTTTTTTACTCCTTTT-AACTT
* * *
8442 AATTATTCTGAATTAAGCCCATTATTGACCACCATTTTTTACTCTTTA
64 AATTACTCTGAATTAAGCACATTACTGACCACCATTTTTTACTCTTTA
*
8490 TAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTTTACTCCTTTTAACTTAA
1 TAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCACTTTTTTTTACTCCTTTTAACTTAA
* **
8555 TTACTCTGAATTGAGCACATTACTGATTACCATTTTT
66 TTACTCTGAATTAAGCACATTACTGACCACCATTTTT
8592 ACTTTTTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
111 38 0.43
112 48 0.54
113 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (111 bp):
TAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCACTTTTTTTTACTCCTTTTAACTTAA
TTACTCTGAATTAAGCACATTACTGACCACCATTTTTTACTCTTTA
Found at i:8577 original size:57 final size:56
Alignment explanation
Indices: 8321--8591 Score: 247
Period size: 57 Copynumber: 4.8 Consensus size: 56
8311 ACTTCTTGAC
* **
8321 TAACTTAATTACTCTGAATTAAGCTA-ATTACTACGGATT-GC-TTTTTTTCTT-CTCGAT
1 TAACTTAATTACTCTGAATTAAGC-ACATTACT---GATTACCATTTTTTT-TTACTCTTT
* ** *
8378 TAACTTAATTGCTCTGAATTAAGCTA-ATTACT-ATTGATTACTTTTTTTTACTTCTTT
1 TAACTTAATTACTCTGAATTAAGC-ACATTACTGATT-ACCATTTTTTTTTAC-TCTTT
* * * **
8435 TAAACTTAATTATTCTGAATTAAGCCCATTATTGACCACCA---TTTTTTACTCTTT
1 T-AACTTAATTACTCTGAATTAAGCACATTACTGATTACCATTTTTTTTTACTCTTT
8489 ATAACTTAATTACTCTGAATTAAGC-CAATTACTGATTACCATTTTTTTTTACTCCTTT
1 -TAACTTAATTACTCTGAATTAAGCAC-ATTACTGATTACCATTTTTTTTTACT-CTTT
*
8547 TAACTTAATTACTCTGAATTGAGCACATTACTGATTACCATTTTT
1 TAACTTAATTACTCTGAATTAAGCACATTACTGATTACCATTTTT
8592 ACTTTTTTTT
Statistics
Matches: 180, Mismatches: 19, Indels: 30
0.79 0.08 0.13
Matches are distributed among these distances:
53 4 0.02
54 38 0.21
55 11 0.06
56 7 0.04
57 86 0.48
58 33 0.18
59 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.46
Consensus pattern (56 bp):
TAACTTAATTACTCTGAATTAAGCACATTACTGATTACCATTTTTTTTTACTCTTT
Found at i:8642 original size:34 final size:35
Alignment explanation
Indices: 8575--8662 Score: 115
Period size: 34 Copynumber: 2.5 Consensus size: 35
8565 TTGAGCACAT
*
8575 TACTGATTACCATTTTTACTTTTTTTTTTAACTTAAC
1 TACTGATTACCATTTTTAC--TTCTTTTTAACTTAAC
* **
8612 TACTGATTACGATTTTTAC-TCTTTTTAACTTAGT
1 TACTGATTACCATTTTTACTTCTTTTTAACTTAAC
8646 TACTGATTACCATTTTT
1 TACTGATTACCATTTTT
8663 TTGAATTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 28 0.61
37 18 0.39
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.55
Consensus pattern (35 bp):
TACTGATTACCATTTTTACTTCTTTTTAACTTAAC
Found at i:8707 original size:32 final size:31
Alignment explanation
Indices: 8607--9227 Score: 560
Period size: 32 Copynumber: 19.6 Consensus size: 31
8597 TTTTTTTAAC
* * * *
8607 TTAACTACTGATTACGATTTTTACTCTTTTTAAC
1 TTAATTACTGATTACCA-TTTTA--CTTTTGAAT
*
8641 TTAGTTACTGATTACCA-TTT--TTTTGAAT
1 TTAATTACTGATTACCATTTTACTTTTGAAT
* * * * *
8669 TGAATTACTAATTTCCATTTTCCTTATTGAAC
1 TTAATTACTGATTACCATTTTACTT-TTGAAT
8701 TTAATTACTGATTACCA--TTACTTTTTGAAT
1 TTAATTACTGATTACCATTTTAC-TTTTGAAT
* * *
8731 TTACTTATTGATTTCCATTTTACTCTTTGAAT
1 TTAATTACTGATTACCATTTTACT-TTTGAAT
* * *
8763 TTAATTACTGATTACTATTTTACTCTTCGATT
1 TTAATTACTGATTACCATTTTACT-TTTGAAT
*
8795 TTAATTACTGATTCCCA--TTACCTTTTGAAT
1 TTAATTACTGATTACCATTTTA-CTTTTGAAT
* * *
8825 TGAATTATTGATTGCCA--TTACTTTTTGAAT
1 TTAATTACTGATTACCATTTTAC-TTTTGAAT
* * * *
8855 TGATTTACTGATTTCCATTTTCCTTATTGAAT
1 TTAATTACTGATTACCATTTTACTT-TTGAAT
* *
8887 TTAGTTACTGATTACCATTTTACTCTTTAAAT
1 TTAATTACTGATTACCATTTTACT-TTTGAAT
* *
8919 TTAATTACTGATTACTATTTTACTTTTTAAACT
1 TTAATTACTGATTACCATTTTAC-TTTTGAA-T
*
8952 TGAATTACTGATTACCATTTTACTTTTTGAAT
1 TTAATTACTGATTACCATTTTAC-TTTTGAAT
* * *
8984 TGAATTACTGATTTCCATTTTCCTTATTGAAT
1 TTAATTACTGATTACCATTTTACTT-TTGAAT
*
9016 TTAATTACTGATTACCATTTGACTCTTTGAAT
1 TTAATTACTGATTACCATTTTACT-TTTGAAT
* * * *
9048 TTGATTATTGATCACCAGTTTACTTTTTGAACT
1 TTAATTACTGATTACCATTTTAC-TTTTGAA-T
* * *
9081 TGAATTATTGATTACCATTTTACTCTCTGAAT
1 TTAATTACTGATTACCATTTTACT-TTTGAAT
*
9113 TTAATTACTGATTACCTTTTTACTCTTTGAAT
1 TTAATTACTGATTACCATTTTACT-TTTGAAT
* *
9145 TGAATTACTGATTTCCATTTTACTCTTATG-AT
1 TTAATTACTGATTACCATTTTACT-TT-TGAAT
*
9177 TTAATTACTGATTATCATTTTACTCTTTGAAT
1 TTAATTACTGATTACCATTTTACT-TTTGAAT
*
9209 TTGATTACTGATTACCATT
1 TTAATTACTGATTACCATT
9228 ACTTTTTACA
Statistics
Matches: 491, Mismatches: 73, Indels: 48
0.80 0.12 0.08
Matches are distributed among these distances:
28 19 0.04
29 4 0.01
30 69 0.14
31 13 0.03
32 312 0.64
33 60 0.12
34 14 0.03
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (31 bp):
TTAATTACTGATTACCATTTTACTTTTGAAT
Found at i:9013 original size:129 final size:127
Alignment explanation
Indices: 8625--9234 Score: 695
Period size: 129 Copynumber: 4.8 Consensus size: 127
8615 TGATTACGAT
* * * * * *
8625 TTTTACTCTTTTTAACTTAGTTACTGATTACCA-TTT--T-TTTGAATTGAATTACTAATTTCCA
1 TTTTACTC-TTTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACTGATTACCA
* * * * *
8686 TTTTCCTTATTGAACTT-AATTACTGATTACCATTACTTTTTGAATTTACTTATTGATTTCCA
65 TTTTACTTTTTGAACTTGAATTACTGATTACCATTACTTTTTGAATTGAATTACTGATTTCCA
* * * *
8748 TTTTACTCTTTGAATTTAATTACTGATTACTATTTTACTCTTCGATTTTAATTACTGATTCCCA-
1 TTTTACTCTTTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACTGATTACCAT
* * * *
8812 -TTACCTTTTGAA-TTGAATTATTGATTGCCATTACTTTTTGAATTGATTTACTGATTTCCA
66 TTTACTTTTTGAACTTGAATTACTGATTACCATTACTTTTTGAATTGAATTACTGATTTCCA
* * * *
8872 TTTTCCT-TATTGAATTTAGTTACTGATTACCATTTTACTCTTTAAATTTAATTACTGATTACTA
1 TTTTACTCT-TTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACTGATTACCA
*
8936 TTTTACTTTTTAAACTTGAATTACTGATTACCATTTTACTTTTTGAATTGAATTACTGATTTCCA
65 TTTTACTTTTTGAACTTGAATTACTGATTACCA--TTACTTTTTGAATTGAATTACTGATTTCCA
* * * * *
9001 TTTTCCT-TATTGAATTTAATTACTGATTACCATTTGACTCTTTGAATTTGATTATTGATCACCA
1 TTTTACTCT-TTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACTGATTACCA
* * * * * * *
9065 GTTTACTTTTTGAACTTGAATTATTGATTACCATTTTACTCTCTGAATTTAATTACTGATTACCT
65 TTTTACTTTTTGAACTTGAATTACTGATTACCA--TTACTTTTTGAATTGAATTACTGATTTCCA
* * *
9130 TTTTACTCTTTGAATTGAATTACTGATTTCCATTTTACTCTTATG-ATTTAATTACTGATTATCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCATTTTACTCTT-TGAATTTAATTACTGATTACCA
* *
9194 TTTTACTCTTTGAATTTG-ATTACTGATTACCATTACTTTTT
65 TTTTACTTTTTGAACTTGAATTACTGATTACCATTACTTTTT
9235 ACAGATTACC
Statistics
Matches: 415, Mismatches: 59, Indels: 23
0.84 0.12 0.05
Matches are distributed among these distances:
122 20 0.05
123 14 0.03
124 103 0.25
125 1 0.00
126 36 0.09
127 16 0.04
128 13 0.03
129 209 0.50
130 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (127 bp):
TTTTACTCTTTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACTGATTACCAT
TTTACTTTTTGAACTTGAATTACTGATTACCATTACTTTTTGAATTGAATTACTGATTTCCA
Found at i:9121 original size:161 final size:157
Alignment explanation
Indices: 8607--9227 Score: 679
Period size: 161 Copynumber: 3.9 Consensus size: 157
8597 TTTTTTTAAC
* * * * *
8607 TTAACTACTGATTACGATTTTTACTCTTTTTAACTTAGTTACTGATTACCATT--TTTTTGAATT
1 TTAATTACTGATTACTA-TTTTACTC--TTGAATTTAATTACTGATTACCATTACTTTTTGAATT
* * *
8670 GAATTACTAATTTCCATTTTCCTTATTGAACTTAATTACTGATTACCA--TTACTTTTTGAATTT
63 GAATTACTGATTTCCATTTTCCTTATTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTT
* *
8733 ACTTATTGATTTCCATTTTACTCTTTGAAT
128 ACTTACTGATTACCATTTTACTCTTTGAAT
* * *
8763 TTAATTACTGATTACTATTTTACTCTTCGATTTTAATTACTGATTCCCATTACCTTTTGAATTGA
1 TTAATTACTGATTACTATTTTACTCTT-GAATTTAATTACTGATTACCATTACTTTTTGAATTGA
* * * * * * * *
8828 ATTATTGATTGCCA--TTACTTTTTGAATTGATTTACTGATTTCCATTTTCCT-TATTGAATTTA
65 ATTACTGATTTCCATTTTCCTTATTGAATTTAATTACTGATTACCATTTTACTCT-TTGAATTTA
* *
8890 GTTACTGATTACCATTTTACTCTTTAAAT
129 CTTACTGATTACCATTTTACTCTTTGAAT
* * *
8919 TTAATTACTGATTACTATTTTACTTTTTAAACTTGAATTACTGATTACCATTTTACTTTTTGAAT
1 TTAATTACTGATTACTATTTTAC-TCTTGAA-TTTAATTACTGATTACCA--TTACTTTTTGAAT
*
8984 TGAATTACTGATTTCCATTTTCCTTATTGAATTTAATTACTGATTACCATTTGACTCTTTGAATT
62 TGAATTACTGATTTCCATTTTCCTTATTGAATTTAATTACTGATTACCATTTTACTCTTTGAATT
* * * *
9049 TGA-TTATTGATCACCAGTTTACTTTTTGAACT
127 T-ACTTACTGATTACCATTTTACTCTTTGAA-T
* * * * *
9081 TGAATTATTGATTACCATTTTACTCTCTGAATTTAATTACTGATTACCTTTTTACTCTTTGAATT
1 TTAATTACTGATTACTATTTTACTCT-TGAATTTAATTACTGATTACC--ATTACTTTTTGAATT
*
9146 GAATTACTGATTTCCATTTTACTCTTA-TG-ATTTAATTACTGATTATCATTTTACTCTTTGAAT
63 GAATTACTGATTTCCATTTT-C-CTTATTGAATTTAATTACTGATTACCATTTTACTCTTTGAAT
9209 TTGA-TTACTGATTACCATT
126 TT-ACTTACTGATTACCATT
9228 ACTTTTTACA
Statistics
Matches: 390, Mismatches: 55, Indels: 35
0.81 0.11 0.07
Matches are distributed among these distances:
153 2 0.01
154 42 0.11
155 9 0.02
156 99 0.25
157 19 0.05
159 27 0.07
161 159 0.41
162 29 0.07
163 4 0.01
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (157 bp):
TTAATTACTGATTACTATTTTACTCTTGAATTTAATTACTGATTACCATTACTTTTTGAATTGAA
TTACTGATTTCCATTTTCCTTATTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTACT
TACTGATTACCATTTTACTCTTTGAAT
Found at i:10454 original size:51 final size:51
Alignment explanation
Indices: 10209--10459 Score: 306
Period size: 51 Copynumber: 4.9 Consensus size: 51
10199 TAATCTCCCC
* * * *
10209 AAGATCCAATTGTTATTGTTAAAATTACCAAAACCCAACACTTACTATCTA
1 AAGATCCAATTTTTATTGTTAAAATTACCAAAACTCAACATTTACTACCTA
* *
10260 GAGATCCAATTTTTATTGTTAAAATTACCAAAACTCAACATTTGCTACCTA
1 AAGATCCAATTTTTATTGTTAAAATTACCAAAACTCAACATTTACTACCTA
* * *
10311 AAGATCCAATTTTTATTGTTATAATTACCAAGACTCAACATTTGCTACCTA
1 AAGATCCAATTTTTATTGTTAAAATTACCAAAACTCAACATTTACTACCTA
* * * *
10362 AAGCTCCAATTTTTATTGTTAAAATTACCAAAACTCTACCTTTATTATCC-A
1 AAGATCCAATTTTTATTGTTAAAATTACCAAAACTCAACATTTACTA-CCTA
* * ** * * *
10413 AAGATTCAATTTTCATCATTAAAATCACCAAGACTCAACCTTTACTA
1 AAGATCCAATTTTTATTGTTAAAATTACCAAAACTCAACATTTACTA
10460 TTTAGAGATC
Statistics
Matches: 174, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
51 172 0.99
52 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (51 bp):
AAGATCCAATTTTTATTGTTAAAATTACCAAAACTCAACATTTACTACCTA
Found at i:12628 original size:37 final size:37
Alignment explanation
Indices: 12586--12660 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
12576 TACATATCAA
12586 TTGCATAAATCTAAAACAAAACAAAATCTTTTTCTTT
1 TTGCATAAATCTAAAACAAAACAAAATCTTTTTCTTT
12623 TTGCATAAATCTAAAACAAAACAAAATCTTTTTCTTT
1 TTGCATAAATCTAAAACAAAACAAAATCTTTTTCTTT
12660 T
1 T
12661 GGCACGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.39
Consensus pattern (37 bp):
TTGCATAAATCTAAAACAAAACAAAATCTTTTTCTTT
Found at i:12675 original size:37 final size:37
Alignment explanation
Indices: 12592--12683 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
12582 TCAATTGCAT
* * *
12592 AAATCTAAAACAAAACAAAATCTTTTTCTTTTTGCAT
1 AAATATAAAACAAAACAAAATCTTTTTCTTTTGGCAG
*
12629 AAATCTAAAACAAAACAAAATCTTTTTCTTTTGGCACG
1 AAATATAAAACAAAACAAAATCTTTTTCTTTTGGCA-G
12667 AAA-ATAAAAC-AAACAAA
1 AAATATAAAACAAAACAAA
12684 CAAAAAACTT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 7 0.14
37 41 0.80
38 3 0.06
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.29
Consensus pattern (37 bp):
AAATATAAAACAAAACAAAATCTTTTTCTTTTGGCAG
Found at i:13577 original size:54 final size:54
Alignment explanation
Indices: 13510--14328 Score: 847
Period size: 54 Copynumber: 15.4 Consensus size: 54
13500 TGGATCAAAT
* *
13510 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACCGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
13564 TAGAGATCAACTCTGATCTTTGAAAACTTCTTGAAATGACCGCACTGTATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
13618 TGGAGATCAACTTTGATCTTCGAAAACTTCTTGAAATGACTGCACCGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
*
13672 TGGAGATCAACTCTGATCTTCGAAAACTTCTT-AGATGGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAAT-GACCGCACTGGATCATC
*
13726 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACTGCA-TCGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACT-GGATCATC
* * * *
13780 TGAAGATCAACTCTGATCTTTGAAAACTTCTTG-GATGGACCGTACTGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAAT-GACCGCACTGGATCATC
* * * **
13834 TGGAGATCAATTCTGATCATT-GAAAACTTTTTGGAATGA-C-CACCAGATCATC
1 TGGAGATCAACTCTGATC-TTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
*
13886 TGGAGATCAACTCTGGTCTTCGAAAACTTCTTTGAAA-GACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTC-TTGAAATGACCGCACTGGATCATC
* * * *
13940 TGGAGATCAATTCTGATCTTCAAAAACTTCTTGGAAGGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * * *
13994 TAGG-GATCAACTGTGATC-TCTAAACACTTCTTGGAATGACCGCACTAGTTTATC
1 T-GGAGATCAACTCTGATCTTCGAAA-ACTTCTTGAAATGACCGCACTGGATCATC
*** ** *
14048 TGG-GATCAACTCTGATCAAAGAAAACTAATTGGAATGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* *
14101 TGG-GATCAACTCTGATC-TCTAAAAACTTCTT-AGAATGACTGCACTAGG-TCATC
1 TGGAGATCAACTCTGATCTTC-GAAAACTTCTTGA-AATGACCGCACT-GGATCATC
**** * * *
14154 TGG-GATCAACTCTGAT-AAAAAAAACTACTTGGAATGACCGCACTGAATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
14206 TGTG-GATCAACTCTGATC-ACTGAAAACTTATTGAAAT-ATCGCACTAGAT--T-
1 TG-GAGATCAACTCTGATCTTC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * * *
14256 TGGGGATAAACTCTGATCATTC-AAAACTTCTTGGAATGATCACACTAGATCATC
1 TGGAGATCAACTCTGATC-TTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* *
14310 TGGGGATCAACTCTAATCT
1 TGGAGATCAACTCTGATCT
14329 CTAAGAACTT
Statistics
Matches: 651, Mismatches: 83, Indels: 63
0.82 0.10 0.08
Matches are distributed among these distances:
49 1 0.00
50 28 0.04
51 15 0.02
52 64 0.10
53 145 0.22
54 388 0.60
55 10 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (54 bp):
TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
Found at i:13971 original size:214 final size:216
Alignment explanation
Indices: 13510--14328 Score: 929
Period size: 214 Copynumber: 3.8 Consensus size: 216
13500 TGGATCAAAT
* *
13510 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACCGGATCATCTAGAGATCAAC
1 TGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGACCGCACTGGATCATCTAGAGATCAAC
* *
13575 TCTGATCTTTGAAAACTTCTTGAAATGACCGCACT-GTATCATCTGGAGATCAACTTTGATC-TT
66 TCTGATCTCTGAAAACTTCTTGAAATGACCGCACTAG-ATCATCTGGAGATCAACTCTGATCATT
* * *
13638 CGAAAACTTCTTGAAATGACTGCACCGGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCT
130 -GAAAACTTCTTGGAATGACCGCACCAGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCT
**
13703 TAGATGGACCGCACTGGATCATC
194 TAGAAAGACCGCACTGGATCATC
* * *
13726 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACTGCA-TCGGATCATCT-GAAGATCA
1 TGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGACCGCACT-GGATCATCTAG-AGATCA
* * * * *
13789 ACTCTGATCTTTGAAAACTTCTTG-GATGGACCGTACTGGATCATCTGGAGATCAATTCTGATCA
64 ACTCTGATCTCTGAAAACTTCTTGAAAT-GACCGCACTAGATCATCTGGAGATCAACTCTGATCA
* *
13853 TTGAAAACTTTTTGGAATGA-C-CACCAGATCATCTGGAGATCAACTCTGGTCTTCGAAAACTTC
128 TTGAAAACTTCTTGGAATGACCGCACCAGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTC
*
13916 TTTGAAAGACCGCACTGGATCATC
193 TTAGAAAGACCGCACTGGATCATC
* * * * *
13940 TGGAGATCAATTCTGATCTTCAAAAACTTCTTGGAAGGACCGCACTGGATCATCTAGGGATCAAC
1 TGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGACCGCACTGGATCATCTAGAGATCAAC
* * * * **
14005 TGTGATCTCT-AAACACTTCTTGGAATGACCGCACTAGTTTATCTGG-GATCAACTCTGATCAAA
66 TCTGATCTCTGAAA-ACTTCTTGAAATGACCGCACTAGATCATCTGGAGATCAACTCTGATCATT
** ** *
14068 GAAAACTAATTGGAATGACCGCACTGGATCATCTGG-GATCAACTCTGATC-TCTAAAAACTTCT
130 GAAAACTTCTTGGAATGACCGCACCAGATCATCTGGAGATCAACTCTGATCTTC-GAAAACTTCT
* *
14131 TAGAATGACTGCACTAGG-TCATC
194 TAGAAAGACCGCACT-GGATCATC
** * * * *
14154 TGG-GATCAACTCTGAT-AAAAAAAACTACTTGGAATGACCGCACTGAATCATCT-GTGGATCAA
1 TGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGACCGCACTGGATCATCTAG-AGATCAA
* * * * *
14216 CTCTGATCACTGAAAACTTATTGAAAT-ATCGCACTAGAT--T-TGGGGATAAACTCTGATCATT
65 CTCTGATCTCTGAAAACTTCTTGAAATGACCGCACTAGATCATCTGGAGATCAACTCTGATCATT
* * * * * *
14277 CAAAACTTCTTGGAATGATCACACTAGATCATCTGGGGATCAACTCTAATCT
130 GAAAACTTCTTGGAATGACCGCACCAGATCATCTGGAGATCAACTCTGATCT
14329 CTAAGAACTT
Statistics
Matches: 522, Mismatches: 63, Indels: 41
0.83 0.10 0.07
Matches are distributed among these distances:
208 3 0.01
209 45 0.09
210 13 0.02
211 11 0.02
212 57 0.11
213 50 0.10
214 191 0.37
215 22 0.04
216 127 0.24
217 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (216 bp):
TGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGACCGCACTGGATCATCTAGAGATCAAC
TCTGATCTCTGAAAACTTCTTGAAATGACCGCACTAGATCATCTGGAGATCAACTCTGATCATTG
AAAACTTCTTGGAATGACCGCACCAGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCTTA
GAAAGACCGCACTGGATCATC
Found at i:14508 original size:50 final size:53
Alignment explanation
Indices: 14439--14559 Score: 149
Period size: 50 Copynumber: 2.3 Consensus size: 53
14429 GCACTGAATC
* * *
14439 ATCTGTGGATCAACTCTGATCACTGAAAACTTATTGAAAT-ATCGCACTAGAT
1 ATCTGGGGATCAACTCTGATCACTCAAAACTTATTGAAATGATCACACTAGAT
* * * *
14491 -T-TGGGGATAAACTCTGATCATTCAAAACTTCTTGGAATGATCACACTAGAT
1 ATCTGGGGATCAACTCTGATCACTCAAAACTTATTGAAATGATCACACTAGAT
14542 CATCTGGGGATCAACTCT
1 -ATCTGGGGATCAACTCT
14560 AATCTCTAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
50 31 0.54
51 12 0.21
53 1 0.02
54 13 0.23
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (53 bp):
ATCTGGGGATCAACTCTGATCACTCAAAACTTATTGAAATGATCACACTAGAT
Found at i:14574 original size:54 final size:53
Alignment explanation
Indices: 14436--14574 Score: 144
Period size: 50 Copynumber: 2.7 Consensus size: 53
14426 ACCGCACTGA
* * * *
14436 ATCATCTGTGGATCAACTCTGATCACTGAAAACTTATTGAAATATCGCACTAG
1 ATCATCTGGGGATCAACTCTGATCTCTCAAAACTTATTGAAATATCACACTAG
* * *
14489 AT--T-TGGGGATAAACTCTGATCAT-TCAAAACTTCTTGGAATGATCACACTAG
1 ATCATCTGGGGATCAACTCTGATC-TCTCAAAACTTATTGAAAT-ATCACACTAG
*
14540 ATCATCTGGGGATCAACTCTAATCTCT-AAGAACTT
1 ATCATCTGGGGATCAACTCTGATCTCTCAA-AACTT
14575 TTATGAAAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
50 30 0.43
51 12 0.17
53 6 0.09
54 22 0.31
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (53 bp):
ATCATCTGGGGATCAACTCTGATCTCTCAAAACTTATTGAAATATCACACTAG
Found at i:14599 original size:236 final size:236
Alignment explanation
Indices: 14186--14660 Score: 932
Period size: 236 Copynumber: 2.0 Consensus size: 236
14176 AACTACTTGG
14186 AATGACCGCACTGAATCATCTGTGGATCAACTCTGATCACTGAAAACTTATTGAAATATCGCACT
1 AATGACCGCACTGAATCATCTGTGGATCAACTCTGATCACTGAAAACTTATTGAAATATCGCACT
14251 AGATTTGGGGATAAACTCTGATCATTCAAAACTTCTTGGAATGATCACACTAGATCATCTGGGGA
66 AGATTTGGGGATAAACTCTGATCATTCAAAACTTCTTGGAATGATCACACTAGATCATCTGGGGA
14316 TCAACTCTAATCTCTAAGAACTTTTATGAAAGAAAACACCGAGTCATCTGAAGATCAACTTAGAT
131 TCAACTCTAATCTCTAAGAACTTTTATGAAAGAAAACACCGAGTCATCTGAAGATCAACTTAGAT
*
14381 CTCTGAAAGTTTTTATGAAAGTTCGAACAGGATCATCATAA
196 CTCTGAAAGCTTTTATGAAAGTTCGAACAGGATCATCATAA
14422 AATGACCGCACTGAATCATCTGTGGATCAACTCTGATCACTGAAAACTTATTGAAATATCGCACT
1 AATGACCGCACTGAATCATCTGTGGATCAACTCTGATCACTGAAAACTTATTGAAATATCGCACT
14487 AGATTTGGGGATAAACTCTGATCATTCAAAACTTCTTGGAATGATCACACTAGATCATCTGGGGA
66 AGATTTGGGGATAAACTCTGATCATTCAAAACTTCTTGGAATGATCACACTAGATCATCTGGGGA
14552 TCAACTCTAATCTCTAAGAACTTTTATGAAAGAAAACACCGAGTCATCTGAAGATCAACTTAGAT
131 TCAACTCTAATCTCTAAGAACTTTTATGAAAGAAAACACCGAGTCATCTGAAGATCAACTTAGAT
*
14617 CTTTGAAAGCTTTTATGAAAGTTCGAACAGGATCATCATAA
196 CTCTGAAAGCTTTTATGAAAGTTCGAACAGGATCATCATAA
14658 AAT
1 AAT
14661 CAACTTAGAT
Statistics
Matches: 237, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
236 237 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (236 bp):
AATGACCGCACTGAATCATCTGTGGATCAACTCTGATCACTGAAAACTTATTGAAATATCGCACT
AGATTTGGGGATAAACTCTGATCATTCAAAACTTCTTGGAATGATCACACTAGATCATCTGGGGA
TCAACTCTAATCTCTAAGAACTTTTATGAAAGAAAACACCGAGTCATCTGAAGATCAACTTAGAT
CTCTGAAAGCTTTTATGAAAGTTCGAACAGGATCATCATAA
Found at i:14653 original size:54 final size:54
Alignment explanation
Indices: 14541--15108 Score: 680
Period size: 54 Copynumber: 10.6 Consensus size: 54
14531 TCACACTAGA
** * *** * *
14541 TCATCTGGGGATCAACTCT-AATCTCT-AAGAACTTTTATGAAAGAAAACACCGAG
1 TCATCTGAAGATCAACT-TAAATCTCTGAA-AACTTCTATGAAAGACCGCACAGGG
* * * * ** * *
14595 TCATCTGAAGATCAACTTAGATCTTTGAAAGCTTTTATGAAAGTTCGAACAGGA
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * *
14649 TCATCAT-AAAATCAACTTAGATCTCAGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATC-TGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* *
14703 TCATCTGAAGATCAACTTAAATCTTTGAAAACTTTTATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
*
14757 TCATCTGAAGATCAACTTAAATCTTTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* *
14811 TCATCTGAAGATCAACTTAAATATCTGAAAACTTCTATGAAAGACCGCACAGGA
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * * *
14865 TTATGTGAAGATCAACTTATACCTCTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * * *
14919 TCATGTGAAGATCAACTTAAACCTCTGAAAACTTCTATGAAAGACTGCACAGGT
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * *
14973 TCATTTGAAGATCAACTTAAATCTCTGAAAACATGTATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * * * *
15027 TTATTTGAAGATCAACTTATACCTCTGAAAACTTCTATGAAAGACCGCACCGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* *
15081 CCA--TGAACG-TCAACTTAGATCTCTGAAA
1 TCATCTGAA-GATCAACTTAAATCTCTGAAA
15109 GTTTCTAAAA
Statistics
Matches: 452, Mismatches: 57, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
52 21 0.05
53 3 0.01
54 425 0.94
55 3 0.01
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (54 bp):
TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
Found at i:16197 original size:37 final size:39
Alignment explanation
Indices: 16121--16199 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 39
16111 ATCTTTTTGA
** * *
16121 AAAACATTTTTTCTCTTTTGAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
16160 AAAACA-TTTTTC-CTTTTGAAAAGATCACACCTAGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
16197 AAA
1 AAA
16200 GTTTCATTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 24 0.67
38 6 0.17
39 6 0.17
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
Found at i:16402 original size:21 final size:21
Alignment explanation
Indices: 16378--16423 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
16368 CTTTCCTCCG
16378 TCTTTTGCTTTTTCAACT-TTT
1 TCTTTT-CTTTTTCAACTCTTT
*
16399 TCTTTTCTTTTTCAATTCTTT
1 TCTTTTCTTTTTCAACTCTTT
16420 TCTT
1 TCTT
16424 CTTTGTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (21 bp):
TCTTTTCTTTTTCAACTCTTT
Found at i:16410 original size:20 final size:19
Alignment explanation
Indices: 16378--16443 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
16368 CTTTCCTCCG
16378 TCTTTTGCTTTTTCAACTTTT
1 TCTTTT-CTTTTTCAA-TTTT
16399 TCTTTTCTTTTTCAATTCTT
1 TCTTTTCTTTTTCAATT-TT
*
16419 T-TCTTCTTTGTTC-ATTTT
1 TCTTTTCTTT-TTCAATTTT
16437 TCTTTTC
1 TCTTTTC
16444 CTCTCCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 3 0.08
19 16 0.40
20 15 0.38
21 6 0.15
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTTTTCAATTTT
Found at i:16615 original size:27 final size:27
Alignment explanation
Indices: 16577--16646 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
16567 TTTGTTTCTT
16577 ATTTTGGTCATTTGCATGT-CCGAGGGC
1 ATTTTGGTCATTTGCATGTCCCG-GGGC
16604 ATTTTGGTCATTTGCATGTCCCGGGGC
1 ATTTTGGTCATTTGCATGTCCCGGGGC
*
16631 GTTTTGGTCATTTGCA
1 ATTTTGGTCATTTGCA
16647 CATCCACGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 38 0.93
28 3 0.07
ACGTcount: A:0.13, C:0.19, G:0.29, T:0.40
Consensus pattern (27 bp):
ATTTTGGTCATTTGCATGTCCCGGGGC
Found at i:16662 original size:27 final size:27
Alignment explanation
Indices: 16577--16667 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
16567 TTTGTTTCTT
16577 ATTTTGGTCATTTGCATGTCCGA-GGGC
1 ATTTTGGTCATTTGCATGTCC-ACGGGC
16604 ATTTTGGTCATTTGCATGTCC-CGGGGC
1 ATTTTGGTCATTTGCATGTCCAC-GGGC
* ** *
16631 GTTTTGGTCATTTGCACATCCACGTGC
1 ATTTTGGTCATTTGCATGTCCACGGGC
16658 ATTTTGGTCA
1 ATTTTGGTCA
16668 CTTCAAATAC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
27 55 0.98
28 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.38
Consensus pattern (27 bp):
ATTTTGGTCATTTGCATGTCCACGGGC
Found at i:17986 original size:18 final size:17
Alignment explanation
Indices: 17956--17989 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17946 AGAGCACAAG
17956 CAAGAAAACAGAGTTGT
1 CAAGAAAACAGAGTTGT
*
17973 CAAGCAAAATAGAGTTG
1 CAAG-AAAACAGAGTTG
17990 GTACCAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
CAAGAAAACAGAGTTGT
Found at i:27833 original size:50 final size:50
Alignment explanation
Indices: 27772--27998 Score: 366
Period size: 50 Copynumber: 4.5 Consensus size: 50
27762 AGATATCCAG
* *
27772 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
*
27822 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
*
27872 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAAACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
*
27922 AAGATTAAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* * *
27972 TATATTTAATTGGAAGAC-GATTCAAAG
1 AAGATTGAATTGGAAGACAG-TTCAAAG
27999 AAGTAGAGTC
Statistics
Matches: 166, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
49 1 0.01
50 165 0.99
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (50 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:28311 original size:27 final size:27
Alignment explanation
Indices: 28273--28363 Score: 110
Period size: 27 Copynumber: 3.4 Consensus size: 27
28263 TTTGCTTCTT
**
28273 ATTTTGGTCATTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTGCACATCCAGGGGC
** *
28300 ATTTTGGTCATTTGCACATCTTGGGAC
1 ATTTTGGTCATTTGCACATCCAGGGGC
* * *
28327 GTTTTGGTCATTTACACATCCAAGGGC
1 ATTTTGGTCATTTGCACATCCAGGGGC
28354 ATTTTGGTCA
1 ATTTTGGTCA
28364 CTTCAGGTAC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (27 bp):
ATTTTGGTCATTTGCACATCCAGGGGC
Done.