Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007322.1 Corchorus capsularis cultivar CVL-1 contig07343, 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: 74728
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Found at i:4542 original size:32 final size:33
Alignment explanation
Indices: 4479--4592 Score: 90
Period size: 32 Copynumber: 3.3 Consensus size: 33
4469 CTTTATTGAC
* * * *
4479 TTTACTTAATTACCTTAAATCAAG-TTCTTTAT
1 TTTACTTAATTACCCTGAATTAAGCCTCTTTAT
4511 TTTACTTAATTACCCTGAATTAAGCCT-TTTAT
1 TTTACTTAATTACCCTGAATTAAGCCTCTTTAT
* *
4543 TGATCTCACTTAATTACACTGAAATTAAGCCTGTGTCT-T
1 T--T-T-ACTTAATTACCCTG-AATTAAGCCTCT-T-TAT
4582 TTTACTTAATT
1 TTTACTTAATT
4593 TCCTTGAAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
32 27 0.40
33 1 0.01
34 1 0.01
35 9 0.13
36 14 0.21
37 11 0.16
38 1 0.01
39 3 0.04
40 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (33 bp):
TTTACTTAATTACCCTGAATTAAGCCTCTTTAT
Found at i:4631 original size:36 final size:36
Alignment explanation
Indices: 4582--4794 Score: 259
Period size: 36 Copynumber: 6.0 Consensus size: 36
4572 CCTGTGTCTT
* *
4582 TTTACTTAATTTCCTTGAAACTAAGTCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTC
*
4618 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTC
* * **
4654 TTTACCTAGTTTCCGTGAAACTAAGCCAGTC-CATC
1 TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTC
* * *
4689 TTTACCTAATTTCCTTGAAATTAAGCCAATCTTTCC
1 TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTC
* * * *
4725 TTTACCTAGTTTCCTTGAAACTAATCCAATC-TATC
1 TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTC
* * *
4760 TTTACCTAATTTCTTTGAAATTAAGTCAGTCTTTT
1 TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTT
4795 ATCAGTCTAA
Statistics
Matches: 150, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
35 56 0.37
36 94 0.63
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (36 bp):
TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTC
Found at i:4793 original size:71 final size:71
Alignment explanation
Indices: 4582--4793 Score: 282
Period size: 71 Copynumber: 3.0 Consensus size: 71
4572 CCTGTGTCTT
* * * * *
4582 TTTACTTAATTTCCTTGAAACTAAGT-CAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCA
1 TTTACCTAGTTTCCTTGAAACTAA-TCCAGTC-TATCTTTACCTAATTTCCTTGAAATTAAGCCA
*
4646 GTCTTTTC
64 GTCTTTCC
* * * *
4654 TTTACCTAGTTTCCGTGAAACTAAGCCAGTCCATCTTTACCTAATTTCCTTGAAATTAAGCCAAT
1 TTTACCTAGTTTCCTTGAAACTAATCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGT
4719 CTTTCC
66 CTTTCC
* * *
4725 TTTACCTAGTTTCCTTGAAACTAATCCAATCTATCTTTACCTAATTTCTTTGAAATTAAGTCAGT
1 TTTACCTAGTTTCCTTGAAACTAATCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGT
4790 CTTT
66 CTTT
4794 TATCAGTCTA
Statistics
Matches: 122, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
71 96 0.79
72 26 0.21
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (71 bp):
TTTACCTAGTTTCCTTGAAACTAATCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGT
CTTTCC
Found at i:4808 original size:107 final size:107
Alignment explanation
Indices: 4582--4790 Score: 294
Period size: 107 Copynumber: 2.0 Consensus size: 107
4572 CCTGTGTCTT
* * * * *
4582 TTTACTTAATTTCCTTGAAACTAAGTCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAG
1 TTTACCTAATTTCCTTGAAACTAAGCCAATCTTTCCTTTACCTAGTTTCCTTGAAACTAAGCCAA
* *
4647 TCTTTTCTTTACCTAGTTTCCGTGAAACTAAGCCAGTCCATC
66 TCTTATCTTTACCTAATTTCCGTGAAACTAAGCCAGTCCATC
* *
4689 TTTACCTAATTTCCTTGAAATTAAGCCAATCTTTCCTTTACCTAGTTTCCTTGAAACTAATCCAA
1 TTTACCTAATTTCCTTGAAACTAAGCCAATCTTTCCTTTACCTAGTTTCCTTGAAACTAAGCCAA
** * *
4754 TC-TATCTTTACCTAATTTCTTTGAAATTAAGTCAGTC
66 TCTTATCTTTACCTAATTTCCGTGAAACTAAGCCAGTC
4791 TTTTATCAGT
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
106 29 0.33
107 60 0.67
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.41
Consensus pattern (107 bp):
TTTACCTAATTTCCTTGAAACTAAGCCAATCTTTCCTTTACCTAGTTTCCTTGAAACTAAGCCAA
TCTTATCTTTACCTAATTTCCGTGAAACTAAGCCAGTCCATC
Found at i:4864 original size:11 final size:11
Alignment explanation
Indices: 4796--5045 Score: 111
Period size: 11 Copynumber: 23.0 Consensus size: 11
4786 CAGTCTTTTA
4796 TCAGTCTAATT
1 TCAGTCTAATT
* **
4807 TCAATCTTCTT
1 TCAGTCTAATT
* *
4818 TCAGCCTGATT
1 TCAGTCTAATT
*
4829 TCAGTTTAATAT
1 TCAGTCTAAT-T
4841 TC-GTCCT--TT
1 TCAGT-CTAATT
4850 TCAGTCTAATT
1 TCAGTCTAATT
** *
4861 TCAGTCTTCTA
1 TCAGTCTAATT
* **
4872 TCAGTTTTCTT
1 TCAGTCTAATT
*
4883 TCAGTCTGATT
1 TCAGTCTAATT
*
4894 TCAGTTTAATAT
1 TCAGTCTAAT-T
4906 TCA-TCCT--TT
1 TCAGT-CTAATT
4915 TCAGTCTAATT
1 TCAGTCTAATT
** *
4926 TCAGTCTTCTA
1 TCAGTCTAATT
* **
4937 TCAGTTTTCTT
1 TCAGTCTAATT
*
4948 TCAGTCTGATT
1 TCAGTCTAATT
* *
4959 TCAGTTTAATA
1 TCAGTCTAATT
*
4970 TCCGTCCT--TT
1 TCAGT-CTAATT
4980 TCAGTCTAATT
1 TCAGTCTAATT
** *
4991 TCAGTCTTCTA
1 TCAGTCTAATT
* **
5002 TCAGTTTTCTT
1 TCAGTCTAATT
*
5013 TTAGTCTAATT
1 TCAGTCTAATT
*
5024 TCAGTCTTATT
1 TCAGTCTAATT
5035 TCAGTCTAATT
1 TCAGTCTAATT
5046 GTCAATCCTC
Statistics
Matches: 177, Mismatches: 49, Indels: 26
0.70 0.19 0.10
Matches are distributed among these distances:
9 13 0.07
10 10 0.06
11 144 0.81
12 10 0.06
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (11 bp):
TCAGTCTAATT
Found at i:4888 original size:33 final size:33
Alignment explanation
Indices: 4848--5031 Score: 216
Period size: 33 Copynumber: 5.6 Consensus size: 33
4838 TATTCGTCCT
4848 TTTCAGTCTAATTTCAGTCTTCTATCAGTTTTC
1 TTTCAGTCTAATTTCAGTCTTCTATCAGTTTTC
* * **
4881 TTTCAGTCTGATTTCAGT-TTAATATTCA-TCCT-
1 TTTCAGTCTAATTTCAGTCTT-CTA-TCAGTTTTC
4913 TTTCAGTCTAATTTCAGTCTTCTATCAGTTTTC
1 TTTCAGTCTAATTTCAGTCTTCTATCAGTTTTC
* * * **
4946 TTTCAGTCTGATTTCAGT-TTAATATCCGTCCT-
1 TTTCAGTCTAATTTCAGTCTT-CTATCAGTTTTC
4978 TTTCAGTCTAATTTCAGTCTTCTATCAGTTTTC
1 TTTCAGTCTAATTTCAGTCTTCTATCAGTTTTC
*
5011 TTTTAGTCTAATTTCAGTCTT
1 TTTCAGTCTAATTTCAGTCTT
5032 ATTTCAGTCT
Statistics
Matches: 124, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
31 3 0.02
32 49 0.40
33 69 0.56
34 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.10, T:0.51
Consensus pattern (33 bp):
TTTCAGTCTAATTTCAGTCTTCTATCAGTTTTC
Found at i:4892 original size:65 final size:65
Alignment explanation
Indices: 4813--5028 Score: 387
Period size: 65 Copynumber: 3.3 Consensus size: 65
4803 AATTTCAATC
*
4813 TTCTTTCAGCCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTATCAGTT
1 TTCTTTCAGTCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTATCAGTT
*
4878 TTCTTTCAGTCTGATTTCAGTTTAATATTCATCCTTTTCAGTCTAATTTCAGTCTTCTATCAGTT
1 TTCTTTCAGTCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTATCAGTT
*
4943 TTCTTTCAGTCTGATTTCAGTTTAATATCCGTCCTTTTCAGTCTAATTTCAGTCTTCTATCAGTT
1 TTCTTTCAGTCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTATCAGTT
* *
5008 TTCTTTTAGTCTAATTTCAGT
1 TTCTTTCAGTCTGATTTCAGT
5029 CTTATTTCAG
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 145 1.00
ACGTcount: A:0.19, C:0.20, G:0.10, T:0.50
Consensus pattern (65 bp):
TTCTTTCAGTCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTATCAGTT
Found at i:5239 original size:49 final size:49
Alignment explanation
Indices: 5176--5298 Score: 124
Period size: 49 Copynumber: 2.5 Consensus size: 49
5166 CCTTAATTTC
** *
5176 ATTAAGATCCACTTCTCTTAATTTCCTTTA-TGTCCCTTTA-TTTCACTGA
1 ATTAAGATTTACTTCTCTTAATTTCCTTTATTGTCCC-TAACTTT-ACTGA
* * * *
5225 ATTAAGATTTACTTCTCTCAATTTCTTTTATTTTCCCTAACTTTGCTGA
1 ATTAAGATTTACTTCTCTTAATTTCCTTTATTGTCCCTAACTTTACTGA
* *
5274 ATTAAGAATTACTTTTTCTTAATTT
1 ATTAAGATTTAC-TTCTCTTAATTT
5299 TCTTCAATCA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
49 43 0.70
50 18 0.30
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (49 bp):
ATTAAGATTTACTTCTCTTAATTTCCTTTATTGTCCCTAACTTTACTGA
Found at i:9667 original size:13 final size:13
Alignment explanation
Indices: 9649--9683 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
9639 TTAATTATTG
9649 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
9662 TTTGCTTAATTAA
1 TTTGCTTTATTAA
*
9675 TCTGCTTTA
1 TTTGCTTTA
9684 GATTTAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:13718 original size:27 final size:26
Alignment explanation
Indices: 13661--13736 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 26
13651 AAATGAACTT
* *
13661 AAAATGACCAAAATACCTCCTAAATGC
1 AAAATGACCAAAATGCC-CCTGAATGC
*
13688 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATG-C
*
13715 AAAATAACCAACAATGCCCCTG
1 AAAATGACCAA-AATGCCCCTG
13737 GATGACCCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 7 0.16
27 26 0.60
28 10 0.23
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.17
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTGAATGC
Found at i:14628 original size:59 final size:59
Alignment explanation
Indices: 14008--14611 Score: 788
Period size: 59 Copynumber: 10.2 Consensus size: 59
13998 TCAGTCTAAA
* * * **
14008 TCTTAA-ACGCTTTCAGGAACTGTCTTCAGATCCC-TCTACGAGCAGTCTTCACACTCAT
1 TCTTAATAC-CTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
* * *** * *
14066 ACTTCATTTGTTTTAGGAACTGTCTTCAGAACCCATCTACGAGCAGTCTTCATACTCAT
1 TCTTAATACCTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
* * * * *
14125 ACTTAATATCTTTTAGGAACTGTCTTCAGAACCCATCCACGAGCAGTCTTCATACTCAT
1 TCTTAATACCTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
* * * *
14184 ACTTAATATCTTTTAGGAACTGTCTTCAGAACCCATCTACGAGCAGTCTTCATACTCAT
1 TCTTAATACCTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
* * * *
14243 ACTTAATACCTTTTAGGAACTGTCCTCAGAACCCGTCTATGAGCAGTCTTCGTAATCAT
1 TCTTAATACCTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
* * * *
14302 TCTTAATACCTTTTAGGAACTGTCTTCAGAATCCATCCACGAGCAGTCTTCATACTCAT
1 TCTTAATACCTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
* * * *
14361 ACTTAATATCTTTTAGGAACTGTCTTCATGAACTCGTCTATGAGCAGTCTTCGTACTCAT
1 TCTTAATACCTTTTAGGAACTGTCTTCA-GAACCCATCTATGAGCAGTCTTCGTACTCAT
*
14421 TCTTAATACCTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAATCTTCGTACTCAT
1 TCTTAATACCTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
*
14480 TCTTAAATA-CTTTTCAGGAACTGTCTCCAGAA-CCATCTATGAGCAGTCTTCGTACTCAT
1 TCTT-AATACCTTTT-AGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
*
14539 TCTTAAATACCTTTCAGGAACTGTCTTCAGAA-CCATCTATGAGCAGTCTTCGTACTCAT
1 TCTT-AATACCTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
14598 TCTTAAATA-CTTTT
1 TCTT-AATACCTTTT
14612 CAGGTTCCGT
Statistics
Matches: 495, Mismatches: 45, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
58 30 0.06
59 390 0.79
60 75 0.15
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.35
Consensus pattern (59 bp):
TCTTAATACCTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCAGTCTTCGTACTCAT
Found at i:19401 original size:27 final size:27
Alignment explanation
Indices: 19371--19425 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
19361 GGATAGGAAT
*
19371 AAAGAATCAATAGAATATGAGACAAGA
1 AAAGAATCAAAAGAATATGAGACAAGA
*
19398 AAAGAATCAAAAGGATATGAGACAAGA
1 AAAGAATCAAAAGAATATGAGACAAGA
19425 A
1 A
19426 CGTGGGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.13
Consensus pattern (27 bp):
AAAGAATCAAAAGAATATGAGACAAGA
Found at i:24666 original size:9 final size:9
Alignment explanation
Indices: 24652--24690 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
24642 TTAATTTCTT
*
24652 TTAATTTAA
1 TTAATTAAA
24661 TTAATTAAA
1 TTAATTAAA
*
24670 TTAAATAAA
1 TTAATTAAA
*
24679 TTAAGTAAA
1 TTAATTAAA
24688 TTA
1 TTA
24691 TGTTGAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:26134 original size:6 final size:6
Alignment explanation
Indices: 26125--26160 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
26115 CTTTTATTAT
26125 TATAAA TATAAATA TATAAA TATAAA TATAAA TATA
1 TATAAA TAT-AA-A TATAAA TATAAA TATAAA TATA
26161 TAAATGTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 20 0.71
7 4 0.14
8 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:26144 original size:14 final size:14
Alignment explanation
Indices: 26125--26199 Score: 70
Period size: 14 Copynumber: 5.5 Consensus size: 14
26115 CTTTTATTAT
26125 TATAAATATAAATA
1 TATAAATATAAATA
26139 TATAAATAT-AA-A
1 TATAAATATAAATA
26151 TATAAATATATAA-A
1 TATAAATATA-AATA
* *
26165 TGTAAGTA-AAGCAT-
1 TATAAATATAA--ATA
26179 TATAAATATAAATA
1 TATAAATATAAATA
26193 TATAAAT
1 TATAAAT
26200 GTAAGTAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
12 11 0.22
13 5 0.10
14 32 0.64
15 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (14 bp):
TATAAATATAAATA
Found at i:26150 original size:20 final size:20
Alignment explanation
Indices: 26125--26194 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
26115 CTTTTATTAT
26125 TATAAATATAAATATATAAA
1 TATAAATATAAATATATAAA
26145 TATAAATATAAATATATAAA
1 TATAAATATAAATATATAAA
* *
26165 TGTAAGTA-AAGCAT-TATAAA
1 TATAAATATAA--ATATATAAA
26185 TATAAATATA
1 TATAAATATA
26195 TAAATGTAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
19 2 0.05
20 38 0.88
21 3 0.07
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (20 bp):
TATAAATATAAATATATAAA
Found at i:26183 original size:34 final size:34
Alignment explanation
Indices: 26145--26213 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
26135 AATATATAAA
26145 TATAAATATAAATATATAAATGTAAGTAAAGCAT
1 TATAAATATAAATATATAAATGTAAGTAAAGCAT
26179 TATAAATATAAATATATAAATGTAAGTAAAGCAT
1 TATAAATATAAATATATAAATGTAAGTAAAGCAT
26213 T
1 T
26214 TTGGTTACCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (34 bp):
TATAAATATAAATATATAAATGTAAGTAAAGCAT
Found at i:27164 original size:14 final size:15
Alignment explanation
Indices: 27145--27173 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27135 ATTTTTATAA
27145 CTATTTTATT-TTTT
1 CTATTTTATTGTTTT
27159 CTATTTTATTGTTTT
1 CTATTTTATTGTTTT
27174 AGAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (15 bp):
CTATTTTATTGTTTT
Found at i:30759 original size:4 final size:4
Alignment explanation
Indices: 30750--30774 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
30740 AATGCAAGAT
30750 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
30775 GACTCAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:31445 original size:7 final size:7
Alignment explanation
Indices: 31435--31459 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31425 TTTTCTTTTC
31435 TTTTCCT
1 TTTTCCT
31442 TTTTCCT
1 TTTTCCT
31449 TTTTCCT
1 TTTTCCT
31456 TTTT
1 TTTT
31460 GGTGATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCCT
Found at i:32937 original size:21 final size:21
Alignment explanation
Indices: 32913--32967 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
32903 TTTCTTTACT
*
32913 TTTTTCTTAGATTTTCTTGCA
1 TTTTTCTTAGATTTTCTTCCA
*
32934 -TTTTCTATCGATTTTCTTCCA
1 TTTTTCT-TAGATTTTCTTCCA
*
32955 TTTTCTCGTAGAT
1 TTTT-TCTTAGAT
32968 CTGTTTGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 6 0.22
21 12 0.44
22 7 0.26
23 2 0.07
ACGTcount: A:0.15, C:0.18, G:0.09, T:0.58
Consensus pattern (21 bp):
TTTTTCTTAGATTTTCTTCCA
Found at i:40529 original size:19 final size:18
Alignment explanation
Indices: 40496--40532 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
40486 TTGAAATAAT
40496 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
40514 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
40533 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:43992 original size:26 final size:26
Alignment explanation
Indices: 43957--44007 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
43947 AATGTTACAT
43957 CATACGTGAAACCTTATTATTATTAA
1 CATACGTGAAACCTTATTATTATTAA
43983 CATACGTGAAACCTTATTATTATTA
1 CATACGTGAAACCTTATTATTATTA
44008 TTTTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (26 bp):
CATACGTGAAACCTTATTATTATTAA
Found at i:51561 original size:19 final size:18
Alignment explanation
Indices: 51537--51573 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
51527 TTGAAGATTT
51537 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
51556 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
51574 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:57206 original size:17 final size:17
Alignment explanation
Indices: 57177--57222 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
57167 GAAAAGTTTG
*
57177 TAAT-TTATATTATTTT
1 TAATATTATTTTATTTT
57193 TAATATTATTTTA-TTT
1 TAATATTATTTTATTTT
57209 TATATATT-TTTTAT
1 TA-ATATTATTTTAT
57223 AAACAATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TAATATTATTTTATTTT
Found at i:66992 original size:31 final size:31
Alignment explanation
Indices: 66957--67022 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
66947 AACTTTATGT
* *
66957 TTTCCGATTTTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
*
66988 TTTCCAATTGTACCCTTTTTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
67019 TTTC
1 TTTC
67023 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:67188 original size:24 final size:22
Alignment explanation
Indices: 67110--67219 Score: 80
Period size: 22 Copynumber: 4.9 Consensus size: 22
67100 ATTTTACTTT
* *
67110 GGTTATTATAATTCCATGAGG-A
1 GGTTATTAAAATTTCAT-AGGTA
* *
67132 GGTTATCAAAATTCCATAGTGT-
1 GGTTATTAAAATTTCATAG-GTA
**
67154 GGTTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGG-T-A
* *
67178 GGTTATTAAAATTTCTTAGGTT
1 GGTTATTAAAATTTCATAGGTA
* *
67200 GGTTATTGAAATTTTATAGG
1 GGTTATTAAAATTTCATAGG
67220 GTGCGTGGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 3 0.04
22 51 0.71
23 1 0.01
24 17 0.24
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGTA
Found at i:67319 original size:22 final size:22
Alignment explanation
Indices: 67269--67399 Score: 90
Period size: 22 Copynumber: 6.0 Consensus size: 22
67259 AAAAAGATTT
* *
67269 CAAAATCTCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
67292 C-GAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
*
67313 CAAAATTTCATTAG-AAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * *
67334 CTAATATTTCATCGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * *
67357 CAAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
67379 CAAAATTTCATA-TGAAGGTTA
1 CAAAATTTCATAGTG-AGGTTA
67400 TAAAAGTCTC
Statistics
Matches: 84, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
21 8 0.10
22 71 0.85
23 5 0.06
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:67400 original size:22 final size:22
Alignment explanation
Indices: 67294--67650 Score: 122
Period size: 22 Copynumber: 16.0 Consensus size: 22
67284 AGGTTATACG
* *
67294 AATTTCATAGTG-TGGTTAACAA
1 AATTTCATA-TGAAGGTTATCAA
67316 AATTTCAT-TAGAAGGTTA-CTAA
1 AATTTCATAT-GAAGGTTATC-AA
* ** *
67338 TATTTCATCGGGAGGTTATCAA
1 AATTTCATATGAAGGTTATCAA
* *
67360 AATTTTATAGTG-TGGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
67382 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
* * *
67403 AAGTCTCAATTTCAT-AAGGAGTACCAA
1 AA-TTTC-A--T-ATGAAGG-TTATCAA
* *
67430 AATCTGATA-GAAGGTTATC-A
1 AATTTCATATGAAGGTTATCAA
67450 AATCTT-ATA-G-AGTGATTATCAA
1 AAT-TTCATATGAAG-G-TTATCAA
* *
67472 AATTTCATAAAGATATGATTATCAA
1 AATTTCAT-ATGA-A-GGTTATCAA
*
67497 AATTT-ATATGAAGATTATCAA
1 AATTTCATATGAAGGTTATCAA
**
67518 AATTTCATAGTG-TTGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
* *
67540 AATTTCAAACCG-AGGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
* * *
67562 AATTACATAATG-TGATTATCAA
1 AATTTCAT-ATGAAGGTTATCAA
* * *
67584 AATTTCATA-GAGGGGTCAACAA
1 AATTTCATATGA-AGGTTATCAA
*
67606 AATTT--TATAAAGATGTTATCAA
1 AATTTCATATGAAG--GTTATCAA
*
67628 AATTTCATA-AAGAGGTTATCAA
1 AATTTCATATGA-AGGTTATCAA
67650 A
1 A
67651 TTTTTAAAAT
Statistics
Matches: 257, Mismatches: 42, Indels: 72
0.69 0.11 0.19
Matches are distributed among these distances:
19 2 0.01
20 14 0.05
21 35 0.14
22 155 0.60
23 13 0.05
24 7 0.03
25 18 0.07
26 8 0.03
27 5 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:67451 original size:21 final size:22
Alignment explanation
Indices: 67427--67474 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
67417 TAAGGAGTAC
67427 CAAAATCTGATAGAAG-G-TTAT
1 CAAAATCTGATAG-AGTGATTAT
*
67448 C-AAATCTTATAGAGTGATTAT
1 CAAAATCTGATAGAGTGATTAT
67469 CAAAAT
1 CAAAAT
67475 TTCATAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 11 0.48
21 6 0.26
22 4 0.17
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (22 bp):
CAAAATCTGATAGAGTGATTAT
Found at i:67507 original size:18 final size:19
Alignment explanation
Indices: 67484--67522 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
67474 TTTCATAAAG
67484 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
67502 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
67523 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:67647 original size:66 final size:65
Alignment explanation
Indices: 67469--67650 Score: 172
Period size: 66 Copynumber: 2.7 Consensus size: 65
67459 GAGTGATTAT
* **
67469 CAAAATTTCATAAAGATATGATTATCAAAATTT-ATATGAAGA-TTATCAAAATTTCATAGTGTT
1 CAAAATTTCATAAAG--ATG-TTATCAAAATTTCATA--AAGAGTTATCAAAATTTCATAGAGGG
* *
67532 GTTAT
61 GTCAA
* * * * *
67537 CAAAATTTCA-AACCGAGGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGAGGGGTC
1 CAAAATTTCATAA-AGATGTTATCAAAATTTCATAAAGAG-TTATCAAAATTTCATAGAGGGGTC
67601 AA
64 AA
*
67603 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAA
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGA-GTTATCAAA
67651 TTTTTAAAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
64 2 0.02
65 11 0.12
66 63 0.68
67 5 0.05
68 11 0.12
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (65 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGTTATCAAAATTTCATAGAGGGGTCAA
Found at i:67656 original size:44 final size:45
Alignment explanation
Indices: 67465--67650 Score: 179
Period size: 44 Copynumber: 4.2 Consensus size: 45
67455 TATAGAGTGA
67465 TTATCAAAATTTCATAAAGATATGATTATCAAAATTT-ATATGAAGA--
1 TTATCAAAATTTCATAAAG--ATGATTATCAAAATTTCATA--AAGAGG
** * *
67511 TTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCA-AACCGAGG
1 TTATCAAAATTTCATAAAGATGATTATCAAAATTTCATAA-AGAGG
* * * *
67555 TTATCAAAATTACATAATG-TGATTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGATGATTATCAAAATTTCATAAAGAGG
* * *
67599 TCAACAAAATTTTATAAAGATG-TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGATGATTATCAAAATTTCATAAAGAGG
67643 TTATCAAA
1 TTATCAAA
67651 TTTTTAAAAT
Statistics
Matches: 115, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 15 0.13
44 77 0.67
45 3 0.03
46 17 0.15
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (45 bp):
TTATCAAAATTTCATAAAGATGATTATCAAAATTTCATAAAGAGG
Found at i:67792 original size:19 final size:19
Alignment explanation
Indices: 67762--67828 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
67752 TGATGGAGTA
67762 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
* *
67782 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
67801 ATCAAAATTC-AGTGAGGAT
1 ATCAAAATTCAAG-GAGGAT
67820 ATCAAAATT
1 ATCAAAATT
67829 TCATACGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 1 0.02
19 35 0.83
20 6 0.14
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:67847 original size:22 final size:20
Alignment explanation
Indices: 67762--68110 Score: 160
Period size: 22 Copynumber: 16.5 Consensus size: 20
67752 TGATGGAGTA
*
67762 ATCAAAATTTCA-AGGAGGAT
1 ATCAAAATTTCATA-GAGGTT
* ** *
67782 ACCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCATAGAGGTT
*
67801 ATCAAAA-TTCAGT-GAGGAT
1 ATCAAAATTTCA-TAGAGGTT
67820 ATCAAAATTTCATACGAAGGTT
1 ATCAAAATTTCATA-G-AGGTT
*
67842 ATCAAATTTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG---AGGTT
*
67864 TTCAAAATTTCATAAGAGAGTT
1 ATCAAAATTTCAT-AGAG-GTT
* *
67886 ATCAAAATTTCATAGTATGTAG
1 ATCAAAATTTCATAG-AGGT-T
*
67908 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATA--GAGGTT
*
67930 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCAT-A-GAGGTT
** *
67952 ATCAAAAAATCATAGGGAGCTT
1 ATCAAAATTTCATA--GAGGTT
*
67974 ATCAAAATTT-GT--A-GTT
1 ATCAAAATTTCATAGAGGTT
* *
67990 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCAT-AG-AGGTT
*
68012 ATCAAAATTTTATAGGAGGTTT
1 ATCAAAATTTCATA-GAGG-TT
* *
68034 ATTAAAATATT-ATAGAAAGATTT
1 ATCAAAAT-TTCATAG--AG-GTT
68057 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATA--GAGGTT
* *
68079 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGAG-G-TT
68101 ATCAAAATTT
1 ATCAAAATTT
68111 TAAAGTGTGA
Statistics
Matches: 256, Mismatches: 39, Indels: 66
0.71 0.11 0.18
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
19 34 0.13
20 13 0.05
21 14 0.05
22 156 0.61
23 24 0.09
24 1 0.00
25 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (20 bp):
ATCAAAATTTCATAGAGGTT
Found at i:67913 original size:44 final size:43
Alignment explanation
Indices: 67819--68372 Score: 204
Period size: 44 Copynumber: 12.8 Consensus size: 43
67809 TCAGTGAGGA
* *
67819 TATCAAAATTTCATACGA-AGGTTATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATAAGAGA-GTTATCAAAATTTCATAG--TAGGT
* *
67863 TTTCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGTATGT
1 TATCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGTAGGT
* * * *
67906 AGATCAAAATTTCAT-AGGGAGATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATAAGAGAG-TTATCAAAATTTCATAGT-AGGT
** *
67951 TATCAAAAAATCAT-AGGGAGCTTATCAAAA-TT--T-GTA-GT
1 TATCAAAATTTCATAAGAGAG-TTATCAAAATTTCATAGTAGGT
* * * *
67989 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGAGGTT
1 TATCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGTAGG-T
* * * *
68033 TATTAAAATATT-ATAGAAAGATTTATCAAAATTTCATAGCGAGGT
1 TATCAAAAT-TTCATA-AGAGAGTTATCAAAATTTCATAG-TAGGT
* * * * *
68078 TATCACAATTTCAT-AGTGTGATTATCAAAATTTTAAAGT-GTGAT
1 TATCAAAATTTCATAAGAGAG-TTATCAAAATTTCATAGTAG-G-T
* * * *
68122 TA-CTAACAA-TTCATATG-GAGGTT-TTAAATTTTTATAAAGT-GGT
1 TATC-AA-AATTTCATAAGAGA-GTTATCAAAATTTCAT--AGTAGGT
* * * * * *
68165 TATCAATATATCATATG-GAGGTTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAAGAGA-GTTATCAAAATTTCATA--GTAGGT
** * *
68210 TATCAAAATTTCATTGGAAAGTTATCAAAATTTCATATTGAGGT
1 TATCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGT-AGGT
* * * * * * *
68254 CT-TCGAAA-TTCCTTAGGGAG--AACAAAATTTCATAAGAAAGT
1 -TATCAAAATTTCATAAGAGAGTTATCAAAATTTCAT-AGTAGGT
* * * * ** * *
68295 TTTAAAAATTT-ATAAAAG-GATTCTTGAAATTCCATAGTACCGT
1 TATCAAAATTTCATAAGAGAG-TTATCAAAATTTCATAGTA-GGT
*
68338 TATCAAAATTTCATAGGAG-GTTATCAAAATTTCAT
1 TATCAAAATTTCATAAGAGAGTTATCAAAATTTCAT
68373 GATGGGATCA
Statistics
Matches: 380, Mismatches: 88, Indels: 85
0.69 0.16 0.15
Matches are distributed among these distances:
38 22 0.06
39 7 0.02
40 3 0.01
41 24 0.06
42 13 0.03
43 80 0.21
44 151 0.40
45 75 0.20
46 5 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGTAGGT
Found at i:68041 original size:126 final size:127
Alignment explanation
Indices: 67859--68110 Score: 301
Period size: 126 Copynumber: 2.0 Consensus size: 127
67849 TTTCATAGTT
* * * *
67859 TAGTTTTCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGTATGTAGATCAAAAT-TTCATAG
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATATT-ATAG
** * *
67923 GGAGA-TTAACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGCTTATCAAAATTTG
65 AAAGATTTAACAAAATTTCATAACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTG
* * ** *
67985 TAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGAGGTTTATTAAAATATTATAGA
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATATTATAGA
* * * ** * *
68050 AAGATTTATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTGTGATTATCAAAATTT
66 AAGATTTAACAAAATTTCATAACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTT
68111 TAAAGTGTGA
Statistics
Matches: 104, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
126 55 0.53
127 49 0.47
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (127 bp):
TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATATTATAGA
AAGATTTAACAAAATTTCATAACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTG
Found at i:68117 original size:22 final size:22
Alignment explanation
Indices: 68055--68123 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
68045 ATAGAAAGAT
* * * *
68055 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCAAAGTGTGA
* *
68077 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
*
68099 TTATCAAAATTTTAAAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
68121 TTA
1 TTA
68124 CTAACAATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAAAGTGTGA
Found at i:68190 original size:22 final size:22
Alignment explanation
Indices: 68131--68253 Score: 88
Period size: 22 Copynumber: 5.6 Consensus size: 22
68121 TTACTAACAA
* *
68131 TTCATATGGAGGTT-TTAAATT
1 TTCATATGGAGGTTATCAAAAT
* ** * *
68152 TTTATAAAGTGGTTATCAATAT
1 TTCATATGGAGGTTATCAAAAT
* *
68174 ATCATATGGAGGTTATCAACAT
1 TTCATATGGAGGTTATCAAAAT
* **
68196 CTCATAGTGTTGGTTATCAAAAT
1 TTCATA-TGGAGGTTATCAAAAT
*
68219 TTCAT-TGGAAAGTTATCAAAAT
1 TTCATATGG-AGGTTATCAAAAT
*
68241 TTCATATTGAGGT
1 TTCATATGGAGGT
68254 CTTCGAAATT
Statistics
Matches: 75, Mismatches: 23, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
21 12 0.16
22 44 0.59
23 19 0.25
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (22 bp):
TTCATATGGAGGTTATCAAAAT
Found at i:68234 original size:45 final size:45
Alignment explanation
Indices: 68161--68246 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
68151 TTTTATAAAG
* * *
68161 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
68206 TGGTTATCAAAATTTCAT-TGGAAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATATGG-AAGTTATCAAAATCTCATA
68247 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:68352 original size:22 final size:21
Alignment explanation
Indices: 68321--68372 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
68311 AGGATTCTTG
* *
68321 AAATTCCATAGTACCGTTATCA
1 AAATTTCATAGGA-CGTTATCA
*
68343 AAATTTCATAGGAGGTTATCA
1 AAATTTCATAGGACGTTATCA
68364 AAATTTCAT
1 AAATTTCAT
68373 GATGGGATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
AAATTTCATAGGACGTTATCA
Found at i:68955 original size:18 final size:19
Alignment explanation
Indices: 68932--68967 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
68922 ATATAATAAT
*
68932 TATTAGTGTTA-TTATTAA
1 TATTAGTATTATTTATTAA
68950 TATTAGTATTATTTATTA
1 TATTAGTATTATTTATTA
68968 TTACTAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TATTAGTATTATTTATTAA
Found at i:72780 original size:26 final size:26
Alignment explanation
Indices: 72743--72796 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
72733 GATGATATTG
*
72743 TAAAAATTGAATTTTTCTAAATAAAA
1 TAAAAATAGAATTTTTCTAAATAAAA
*
72769 TAAAAATAGAATTTTTCTGAATAAAA
1 TAAAAATAGAATTTTTCTAAATAAAA
72795 TA
1 TA
72797 TTTTAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (26 bp):
TAAAAATAGAATTTTTCTAAATAAAA
Found at i:73955 original size:18 final size:18
Alignment explanation
Indices: 73934--73968 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
73924 TTATATATGT
73934 TTTATAAAAAGAATATTA
1 TTTATAAAAAGAATATTA
*
73952 TTTATAACAAGAATATT
1 TTTATAAAAAGAATATT
73969 TAAATGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (18 bp):
TTTATAAAAAGAATATTA
Found at i:74534 original size:24 final size:24
Alignment explanation
Indices: 74500--74546 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
74490 CAAAATTCTA
74500 TCAAATAATTTCTAACTTTCTAAC
1 TCAAATAATTTCTAACTTTCTAAC
*
74524 TCAAATCATTTCTAACTTTCTAA
1 TCAAATAATTTCTAACTTTCTAA
74547 ATTTTTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (24 bp):
TCAAATAATTTCTAACTTTCTAAC
Done.