Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021884.1 Corchorus olitorius cultivar O-4 contig21917, 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: 20441
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3429 original size:20 final size:21
Alignment explanation
Indices: 3392--3433 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3382 TTCTATTTCA
3392 GTTTATTTCAGTTTGATCCAG
1 GTTTATTTCAGTTTGATCCAG
3413 GTTTATTTCAG-TTGATCCAG
1 GTTTATTTCAGTTTGATCCAG
3433 G
1 G
3434 GCGATCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.45
Consensus pattern (21 bp):
GTTTATTTCAGTTTGATCCAG
Found at i:3522 original size:36 final size:36
Alignment explanation
Indices: 3413--3773 Score: 335
Period size: 35 Copynumber: 10.4 Consensus size: 36
3403 TTTGATCCAG
* *
3413 GTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCA
1 GTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCA
* * *
3449 GTTTTTTTTCAATTGA-CTTA-GGCGGTC-TTTCTTCA
1 G-TTTATTTCAATTGATC-CAGGGCGATCTTTTCTTCA
* * * * *
3484 GTTTATTTCAGTTGCTCTAGGGCAATATTTTCTTCA
1 GTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCA
* *
3520 GTTTATTTCAATTTATCCAGGGCGGTC-TTTCTTCA
1 GTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCA
*
3555 GTTTATTT-AAGTTGATCCATGGCGATCTTTTCTTCA
1 GTTTATTTCAA-TTGATCCAGGGCGATCTTTTCTTCA
* *
3591 ATTTATTTCAATTGATCCAGGGTGATCTTTTCTTCA
1 GTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCA
*
3627 G----------TTGATCCATGGCGATCTTTTCTTCA
1 GTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCA
*
3653 GTTTATTTCAATTGA-CCTAGGGCGGTC-TTTCTTCA
1 GTTTATTTCAATTGATCC-AGGGCGATCTTTTCTTCA
* *
3688 GTTTATTTGAATTGATCCAGGGCGATC-TTTCCTCA
1 GTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCA
* * * * * *
3723 ATTTACTTCAGTAGATCCAGGGCGATCTTCTCTGCA
1 GTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCA
3759 GTTTATTTCAATTGA
1 GTTTATTTCAATTGA
3774 CTGCAAAATG
Statistics
Matches: 261, Mismatches: 43, Indels: 42
0.75 0.12 0.12
Matches are distributed among these distances:
26 24 0.09
34 15 0.06
35 104 0.40
36 103 0.39
37 15 0.06
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (36 bp):
GTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCA
Found at i:3544 original size:71 final size:71
Alignment explanation
Indices: 3413--3773 Score: 379
Period size: 71 Copynumber: 5.2 Consensus size: 71
3403 TTTGATCCAG
* * *
3413 GTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTTTTTTCAATTGA-CTTA-GGCGGTC
1 GTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAG-TTTATTTCAATTGATC-CAGGGCGGTC
3476 TTTCTTCA
64 TTTCTTCA
* * * * *
3484 GTTTATTTCAGTTGCTCTAGGGCAATATTTTCTTCAGTTTATTTCAATTTATCCAGGGCGGTCTT
1 GTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGGTCTT
3549 TCTTCA
66 TCTTCA
* * * * *
3555 GTTTATTTAAGTTGATCCATGGCGATCTTTTCTTCAATTTATTTCAATTGATCCAGGGTGATC-T
1 GTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGGTCTT
3619 T-TTC-
66 TCTTCA
*
3623 ------TTCAGTTGATCCATGGCGATCTTTTCTTCAGTTTATTTCAATTGA-CCTAGGGCGGTCT
1 GTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCC-AGGGCGGTCT
3681 TTCTTCA
65 TTCTTCA
* * * * * * * *
3688 GTTTATTTGAATTGATCCAGGGCGATC-TTTCCTCAATTTACTTCAGTAGATCCAGGGCGATCTT
1 GTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGGTCTT
*
3752 CTCTGCA
66 -TCTTCA
*
3759 GTTTATTTCAATTGA
1 GTTTATTTCAGTTGA
3774 CTGCAAAATG
Statistics
Matches: 243, Mismatches: 33, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
61 2 0.01
62 50 0.21
63 2 0.01
64 3 0.01
69 3 0.01
70 43 0.18
71 140 0.58
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (71 bp):
GTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGGTCTT
TCTTCA
Found at i:3635 original size:62 final size:61
Alignment explanation
Indices: 3564--3690 Score: 202
Period size: 62 Copynumber: 2.1 Consensus size: 61
3554 AGTTTATTTA
*
3564 AGTTGATCCATGGCGATCTTTTCTTCAATTTATTTCAATTGATCC-AGGGTGATCTTTTCTTC
1 AGTTGATCCATGGCGATCTTTTCTTCAATTTATTTCAATTGA-CCTAGGGCGATC-TTTCTTC
* *
3626 AGTTGATCCATGGCGATCTTTTCTTCAGTTTATTTCAATTGACCTAGGGCGGTCTTTCTTC
1 AGTTGATCCATGGCGATCTTTTCTTCAATTTATTTCAATTGACCTAGGGCGATCTTTCTTC
3687 AGTT
1 AGTT
3691 TATTTGAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
61 13 0.21
62 48 0.79
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (61 bp):
AGTTGATCCATGGCGATCTTTTCTTCAATTTATTTCAATTGACCTAGGGCGATCTTTCTTC
Found at i:3653 original size:26 final size:26
Alignment explanation
Indices: 3597--3655 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
3587 TTCAATTTAT
* *
3597 TTCAATTGATCCAGGGTGATCTTTTC
1 TTCAGTTGATCCAGGGCGATCTTTTC
*
3623 TTCAGTTGATCCATGGCGATCTTTTC
1 TTCAGTTGATCCAGGGCGATCTTTTC
3649 TTCAGTT
1 TTCAGTT
3656 TATTTCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (26 bp):
TTCAGTTGATCCAGGGCGATCTTTTC
Found at i:3654 original size:133 final size:132
Alignment explanation
Indices: 3511--3761 Score: 380
Period size: 133 Copynumber: 1.9 Consensus size: 132
3501 TAGGGCAATA
*
3511 TTTTCTTCAGTTTATTTCAATTTATCC-AGGGCGGTCTTTCTTCAGTTTATTT-AAGTTGATCCA
1 TTTTCTTCAGTTTATTTCAATTGA-CCTAGGGCGGTCTTTCTTCAGTTTATTTGAA-TTGATCCA
* * * * * * *
3574 TGGCGATCTTTTCTTCAATTTATTTCAATTGATCCAGGGTGATCTTTTCTTCAGTTGATCCATGG
64 GGGCGATC-TTTCCTCAATTTACTTCAATAGATCCAGGGCGATCTTCTCTGCAGTTGATCCATGG
3639 CGATC
128 CGATC
3644 TTTTCTTCAGTTTATTTCAATTGACCTAGGGCGGTCTTTCTTCAGTTTATTTGAATTGATCCAGG
1 TTTTCTTCAGTTTATTTCAATTGACCTAGGGCGGTCTTTCTTCAGTTTATTTGAATTGATCCAGG
*
3709 GCGATCTTTCCTCAATTTACTTCAGTAGATCCAGGGCGATCTTCTCTGCAGTT
66 GCGATCTTTCCTCAATTTACTTCAATAGATCCAGGGCGATCTTCTCTGCAGTT
3762 TATTTCAATT
Statistics
Matches: 107, Mismatches: 9, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
132 42 0.39
133 63 0.59
134 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.44
Consensus pattern (132 bp):
TTTTCTTCAGTTTATTTCAATTGACCTAGGGCGGTCTTTCTTCAGTTTATTTGAATTGATCCAGG
GCGATCTTTCCTCAATTTACTTCAATAGATCCAGGGCGATCTTCTCTGCAGTTGATCCATGGCGA
TC
Found at i:4073 original size:30 final size:29
Alignment explanation
Indices: 4037--4748 Score: 662
Period size: 30 Copynumber: 23.6 Consensus size: 29
4027 GCTTTATCAG
4037 CTTCATTTTAATCCTGTTCGAGGATCATTA
1 CTTCATTTTAATCCTGTT-GAGGATCATTA
*
4067 CTTCATTTTTAATCTTGTTTGAGGATCATTA
1 CTTCA-TTTTAATCCTG-TTGAGGATCATTA
* * * *
4098 CTTCGTTTTAATCCTGTTTGAGGAGCACTG
1 CTTCATTTTAATCCTG-TTGAGGATCATTA
* *
4128 C-TAATTTTAATCTTGTTTGAGGATCATTA
1 CTTCATTTTAATCCTG-TTGAGGATCATTA
4157 CTTCATTTTAATCCTGTTTGAGGATCATTA
1 CTTCATTTTAATCCTG-TTGAGGATCATTA
*
4187 CTTCATTTTTAATCCTGTTTAAGGATCATTA
1 CTTCA-TTTTAATCCTG-TTGAGGATCATTA
4218 CTTCATTTTAATCCTGTTTGAGGATCATTA
1 CTTCATTTTAATCCTG-TTGAGGATCATTA
4248 CTTCATTTTAATCCTGTTTGAGGATCATTA
1 CTTCATTTTAATCCTG-TTGAGGATCATTA
4278 CTTCATTTTAATCCTGTTTGAGGATCATTA
1 CTTCATTTTAATCCTG-TTGAGGATCATTA
* *
4308 CTTTATTTTAAATCCTGTTCGAGGATCATTG
1 CTTCATTTT-AATCCTGTT-GAGGATCATTA
* * * *
4339 CTTTATTTTAAATCCTATTTAGGATCATTG
1 CTTCATTTT-AATCCTGTTGAGGATCATTA
* *
4369 CTTTATTTTAAATCCTGTTTGAGGATCATTG
1 CTTCATTTT-AATCCTG-TTGAGGATCATTA
* * *
4400 CTTTATGTTAATCCTGGTTGAGGATCATTG
1 CTTCATTTTAATCCT-GTTGAGGATCATTA
* * * *
4430 CTTTATGTTAGTCCTGGTCGAGGATCATTA
1 CTTCATTTTAATCCT-GTTGAGGATCATTA
* * * * * *
4460 TTTTATTTCAATCCTGGTTTAAGATCATTG
1 CTTCATTTTAATCCT-GTTGAGGATCATTA
* **
4490 CTTTATTTTAACTCCTGTTTGAGGATCATGG
1 CTTCATTTTAA-TCCTG-TTGAGGATCATTA
**
4521 CTTCATTTTAATCCTGGTTGAGGATCATGG
1 CTTCATTTTAATCCT-GTTGAGGATCATTA
*
4551 CTTCATTTTAATCCTGGTTGAGGATCATTG
1 CTTCATTTTAATCCT-GTTGAGGATCATTA
* *
4581 CTTCATTTTAATCCTGGTTAAGGA-CATTG
1 CTTCATTTTAATCCT-GTTGAGGATCATTA
**
4610 CGTTTTTTTTTTTAATCCTGGTTGAGGATCATTGA
1 C----TTCATTTTAATCCT-GTTGAGGATCATT-A
* *
4645 -TTTATTTTAATCTTGGTTGAGGATCATTA
1 CTTCATTTTAATCCT-GTTGAGGATCATTA
4674 C-TCTATTTTAATCCTGGTTGAGGATCATTGA
1 CTTC-ATTTTAATCCT-GTTGAGGATCATT-A
* *
4705 -TTTATTTTAATCCTGGTTTAGGATCATT-
1 CTTCATTTTAATCCT-GTTGAGGATCATTA
* *
4733 GTTTATTTTAATCCTG
1 CTTCATTTTAATCCTG
4749 GTTAATTGCT
Statistics
Matches: 608, Mismatches: 52, Indels: 46
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.00
29 45 0.07
30 399 0.66
31 137 0.23
32 2 0.00
33 20 0.03
34 4 0.01
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.46
Consensus pattern (29 bp):
CTTCATTTTAATCCTGTTGAGGATCATTA
Found at i:4255 original size:91 final size:90
Alignment explanation
Indices: 4036--4832 Score: 769
Period size: 91 Copynumber: 8.9 Consensus size: 90
4026 TGCTTTATCA
* *
4036 GCTTCATTTTAATCCTGTTCGAGGATCATTACTTCATTTTTAATCTTGTTTGAGGATCATTACTT
1 GCTTCATTTTAATCCTGTTTGAGGATCATTACTTCA-TTTTAATCCTGTTTGAGGATCATTACTT
* * *
4101 CGTTTTAATCCTGTTTGAGGAGCACT
65 CATTTTAATCCTGTTTGAGGATCATT
* *
4127 GC-TAATTTTAATCTTGTTTGAGGATCATTACTTCATTTTAATCCTGTTTGAGGATCATTACTTC
1 GCTTCATTTTAATCCTGTTTGAGGATCATTACTTCATTTTAATCCTGTTTGAGGATCATTACTTC
*
4191 ATTTTTAATCCTGTTTAAGGATCATT
66 A-TTTTAATCCTGTTTGAGGATCATT
*
4217 ACTTCATTTTAATCCTGTTTGAGGATCATTACTTCATTTTAATCCTGTTTGAGGATCATTACTTC
1 GCTTCATTTTAATCCTGTTTGAGGATCATTACTTCATTTTAATCCTGTTTGAGGATCATTACTTC
4282 ATTTTAATCCTGTTTGAGGATCATT
66 ATTTTAATCCTGTTTGAGGATCATT
* * * * * * *
4307 ACTTTATTTTAAATCCTGTTCGAGGATCATTGCTTTATTTTAAATCCTATTT-AGGATCATTGCT
1 GCTTCATTTT-AATCCTGTTTGAGGATCATTACTTCATTTT-AATCCTGTTTGAGGATCATTACT
*
4371 TTATTTTAAATCCTGTTTGAGGATCATT
64 TCATTTT-AATCCTGTTTGAGGATCATT
* * * * * * * * * * *
4399 GCTTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAGTCCTGGTCGAGGATCATTATTTT
1 GCTTCATTTTAATCCTGTTTGAGGATCATTACTTCATTTTAATCCTGTTTGAGGATCATTACTTC
* *
4464 ATTTCAATCCTGGTTT-AAGATCATT
66 ATTTTAATCCT-GTTTGAGGATCATT
* ** * **
4489 GCTTTATTTTAACTCCTGTTTGAGGATCATGGCTTCATTTTAATCCTGGTTGAGGATCATGGCTT
1 GCTTCATTTTAA-TCCTGTTTGAGGATCATTACTTCATTTTAATCCTGTTTGAGGATCATTACTT
*
4554 CATTTTAATCCTGGTTGAGGATCATT
65 CATTTTAATCCTGTTTGAGGATCATT
* * * ** *
4580 GCTTCATTTTAATCCTGGTTAAGGA-CATTGCGTTTTTTTTTTTAATCCTGGTTGAGGATCATTG
1 GCTTCATTTTAATCCTGTTTGAGGATCATTAC----TTCATTTTAATCCTGTTTGAGGATCATT-
* * *
4644 A-TTTATTTTAATCTTGGTTGAGGATCATT
61 ACTTCATTTTAATCCTGTTTGAGGATCATT
* * * *
4673 AC-TCTATTTTAATCCTGGTTGAGGATCATTGA-TTTATTTTAATCCTGGTTT-AGGATCATT-G
1 GCTTC-ATTTTAATCCTGTTTGAGGATCATT-ACTTCATTTTAATCCT-GTTTGAGGATCATTAC
* *
4734 TTTATTTTAATCCTGGTT----A--ATT
63 TTCATTTTAATCCTGTTTGAGGATCATT
* ** * * * * * * * * *
4756 GCTTCATTCTAATCCTGGCTGAAGATCAATGCTTTATTTTAATCATGGTTGAGGATCAGTGCTTT
1 GCTTCATTTTAATCCTGTTTGAGGATCATTACTTCATTTTAATCCTGTTTGAGGATCATTACTTC
*
4821 ATTTCAATCCTG
66 ATTTTAATCCTG
4833 ATTTAGGGTT
Statistics
Matches: 610, Mismatches: 73, Indels: 53
0.83 0.10 0.07
Matches are distributed among these distances:
82 3 0.00
83 46 0.08
84 16 0.03
85 1 0.00
89 50 0.08
90 151 0.25
91 229 0.38
92 39 0.06
93 71 0.12
94 4 0.01
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (90 bp):
GCTTCATTTTAATCCTGTTTGAGGATCATTACTTCATTTTAATCCTGTTTGAGGATCATTACTTC
ATTTTAATCCTGTTTGAGGATCATT
Found at i:4316 original size:121 final size:119
Alignment explanation
Indices: 4037--4839 Score: 842
Period size: 121 Copynumber: 6.7 Consensus size: 119
4027 GCTTTATCAG
* *
4037 CTTCATTTTAATCCT-GTTCGAGGATCATTACTTCATTTTTAATCTTGTTTGAGGATCATTACTT
1 CTTCATTTTAATCCTGGTT-GAGGATCATTACTTCA-TTTTAATCCTGGTTGAGGATCATTACTT
* * * * *
4101 CGTTTTAATCCTGTTTGAGGAGCACTGC-TAATTTTAATCTTGTTTGAGGATCATTA
64 CATTTTAATCCTGTTT-AGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTA
* * *
4157 CTTCATTTTAATCCTGTTTGAGGATCATTACTTCATTTTTAATCCTGTTTAAGGATCATTACTTC
1 CTTCATTTTAATCCTGGTTGAGGATCATTACTTCA-TTTTAATCCTGGTTGAGGATCATTACTTC
* *
4222 ATTTTAATCCTGTTTGAGGATCATTACTTCATTTTAATCCTGTTTGAGGATCATTA
65 ATTTTAATCCTGTTT-AGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTA
* * *
4278 CTTCATTTTAATCCTGTTTGAGGATCATTACTTTATTTTAAATCCT-GTTCGAGGATCATTGCTT
1 CTTCATTTTAATCCTGGTTGAGGATCATTACTTCATTTT-AATCCTGGTT-GAGGATCATTACTT
* * *
4342 TATTTTAAATCCTATTTAGGATCATTGCTTTATTTTAAATCCTGTTTGAGGATCATTG
64 CATTTT-AATCCTGTTTAGGATCATTGCTTTATTTT-AATCCTGTTTGAGGATCATTA
* * * * * * * * *
4400 CTTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAGTCCTGGTCGAGGATCATTATTTTA
1 CTTCATTTTAATCCTGGTTGAGGATCATTACTTCATTTTAATCCTGGTTGAGGATCATTACTTCA
* * **
4465 TTTCAATCCTGGTTTAAGATCATTGCTTTATTTTAACTCCTGTTTGAGGATCATGG
66 TTTTAATCCT-GTTTAGGATCATTGCTTTATTTTAA-TCCTGTTTGAGGATCATTA
** *
4521 CTTCATTTTAATCCTGGTTGAGGATCATGGCTTCATTTTAATCCTGGTTGAGGATCATTGCTTCA
1 CTTCATTTTAATCCTGGTTGAGGATCATTACTTCATTTTAATCCTGGTTGAGGATCATTACTTCA
* * *
4586 TTTTAATCCTGGTTAAGGA-CATTGCGTTTTTTTTTTTAATCCTGGTTGAGGATCATTGA
66 TTTTAATCCT-GTTTAGGATCATTGC----TTTATTTTAATCCTGTTTGAGGATCATT-A
* *
4645 -TTTATTTTAATCTTGGTTGAGGATCATTAC-TCTATTTTAATCCTGGTTGAGGATCATTGA-TT
1 CTTCATTTTAATCCTGGTTGAGGATCATTACTTC-ATTTTAATCCTGGTTGAGGATCATT-ACTT
* * *
4707 TATTTTAATCCTGGTTTAGGATCATTG-TTTATTTTAATCCTGGTT----A--ATTG
64 CATTTTAATCCT-GTTTAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTA
* * * * * * * * * *
4757 CTTCATTCTAATCCTGGCTGAAGATCAATGCTTTATTTTAATCATGGTTGAGGATCAGTGCTTTA
1 CTTCATTTTAATCCTGGTTGAGGATCATTACTTCATTTTAATCCTGGTTGAGGATCATTACTTCA
*
4822 TTTCAATCCTGATTTAGG
66 TTTTAATCCTG-TTTAGG
4840 GTTATCATTC
Statistics
Matches: 593, Mismatches: 69, Indels: 49
0.83 0.10 0.07
Matches are distributed among these distances:
112 1 0.00
113 68 0.11
114 1 0.00
115 1 0.00
119 17 0.03
120 102 0.17
121 234 0.39
122 67 0.11
123 88 0.15
124 14 0.02
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (119 bp):
CTTCATTTTAATCCTGGTTGAGGATCATTACTTCATTTTAATCCTGGTTGAGGATCATTACTTCA
TTTTAATCCTGTTTAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTA
Found at i:4789 original size:30 final size:29
Alignment explanation
Indices: 4361--4832 Score: 140
Period size: 30 Copynumber: 15.8 Consensus size: 29
4351 TCCTATTTAG
* ** *
4361 GATCATTGCTTTATTTTAAATCCTGTTTGAG
1 GATCAATGCTTTA-TTT-AATCCTGGCTGAA
* * *
4392 GATCATTGCTTTATGTTAATCCTGGTTGAG
1 GATCAATGCTTTAT-TTAATCCTGGCTGAA
* * *
4422 GATCATTGCTTTATGTTAGTCCTGG-TCGAG
1 GATCAATGCTTTAT-TTAATCCTGGCT-GAA
* ** * *
4452 GATCATTATTTTATTTCAATCCTGGTTTAA
1 GATCAATGCTTTATTT-AATCCTGGCTGAA
* ** *
4482 GATCATTGCTTTATTTTAACTCCTGTTTGAG
1 GATCAATGCTTTA-TTTAA-TCCTGGCTGAA
* * *
4513 GATC-ATGGCTTCATTTTAATCCTGGTTGAG
1 GATCAAT-GCTTTA-TTTAATCCTGGCTGAA
* * *
4543 GATC-ATGGCTTCATTTTAATCCTGGTTGAG
1 GATCAAT-GCTTTA-TTTAATCCTGGCTGAA
* * *
4573 GATCATTGCTTCATTTTAATCCTGG-TTAA
1 GATCAATGCTTTA-TTTAATCCTGGCTGAA
* * * *
4602 GGA-CATTGCGTTTTTTTTTTTAATCCTGGTTGAG
1 -GATCAATGC-----TTTATTTAATCCTGGCTGAA
* * * * *
4636 GATCATTGATTTATTTTAATCTTGGTTGAG
1 GATCAATGCTTTA-TTTAATCCTGGCTGAA
* * * * *
4666 GATCATTACTCTATTTTAATCCTGGTTGAG
1 GATCAATGCTTTA-TTTAATCCTGGCTGAA
* * * * *
4696 GATCATTGATTTATTTTAATCCTGGTTTAG
1 GATCAATGCTTTA-TTTAATCCTGGCTGAA
* *
4726 GATCATTG-TTTATTTTAATCCTGG-T-TA
1 GATCAATGCTTTA-TTTAATCCTGGCTGAA
*
4753 -AT---TGCTTCATTCTAATCCTGGCTGAA
1 GATCAATGCTTTATT-TAATCCTGGCTGAA
* * *
4779 GATCAATGCTTTATTTTAATCATGGTTGAG
1 GATCAATGCTTTA-TTTAATCCTGGCTGAA
*
4809 GATCAGTGCTTTATTTCAATCCTG
1 GATCAATGCTTTATTT-AATCCTG
4833 ATTTAGGGTT
Statistics
Matches: 371, Mismatches: 43, Indels: 55
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.01
24 12 0.03
25 1 0.00
26 3 0.01
27 2 0.01
28 1 0.00
29 33 0.09
30 248 0.67
31 45 0.12
33 13 0.04
34 9 0.02
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (29 bp):
GATCAATGCTTTATTTAATCCTGGCTGAA
Found at i:5332 original size:27 final size:27
Alignment explanation
Indices: 5302--5353 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5292 GCACATCGGT
5302 CATTCAGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTA
5329 CATTCAGGGGCATTTTGGTCATTTT
1 CATTCAGGGGCATTTTGGTCATTTT
5354 AACTTCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.44
Consensus pattern (27 bp):
CATTCAGGGGCATTTTGGTCATTTTTA
Found at i:5360 original size:26 final size:27
Alignment explanation
Indices: 5302--5360 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
5292 GCACATCGGT
*
5302 CATTCAGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTAA
5329 CATTCAGGGGCATTTTGGTCATTTTAA
1 CATTCAGGGGCATTTTGGTCATTTTAA
5356 C-TTCA
1 CATTCA
5361 CATTATTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
CATTCAGGGGCATTTTGGTCATTTTAA
Found at i:9505 original size:123 final size:124
Alignment explanation
Indices: 9286--9523 Score: 442
Period size: 123 Copynumber: 1.9 Consensus size: 124
9276 CGGAAATTTG
*
9286 TACCCGAGTACACTTATCCGAGAGGCCCTTCATCTCGGTAAAAGATAAATGTTAATACATTTTTA
1 TACCCGAGTACACTTATCCGAGAGGCCCTTCATCTCGGTAAAAGACAAATGTTAATACATTTTTA
*
9351 GCATGATCAAAGTGACATACTATATAAATGGCATGGATGCA-TGATTATTCATTGATTC
66 GCATGATCAAAGTGACATACTATATAAATGGCATGGATGCACTAATTATTCATTGATTC
*
9409 TACCCTAGTACACTTATCCGAGAGGCCCTTCATCTCGGTAAAAGACAAATGTTAATACATTTTTA
1 TACCCGAGTACACTTATCCGAGAGGCCCTTCATCTCGGTAAAAGACAAATGTTAATACATTTTTA
9474 GCATGATCAAAGTGACATACTATATAAATGGCATGGATGCACTAATTATT
66 GCATGATCAAAGTGACATACTATATAAATGGCATGGATGCACTAATTATT
9524 ACAAATTCAA
Statistics
Matches: 111, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
123 104 0.94
124 7 0.06
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (124 bp):
TACCCGAGTACACTTATCCGAGAGGCCCTTCATCTCGGTAAAAGACAAATGTTAATACATTTTTA
GCATGATCAAAGTGACATACTATATAAATGGCATGGATGCACTAATTATTCATTGATTC
Found at i:11091 original size:22 final size:22
Alignment explanation
Indices: 11066--11118 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
11056 AAATCAAACT
**
11066 AACAATTAAGACTATCT-AAGAA
1 AACAATTAAGAAAAT-TAAAGAA
*
11088 AACAATCAAGAAAATTAAAGAA
1 AACAATTAAGAAAATTAAAGAA
11110 AACAATTAA
1 AACAATTAA
11119 TTAGAAAGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.62, C:0.11, G:0.08, T:0.19
Consensus pattern (22 bp):
AACAATTAAGAAAATTAAAGAA
Found at i:18180 original size:36 final size:37
Alignment explanation
Indices: 18133--18207 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 37
18123 TTAGCATGTG
*
18133 CACCTTTAGTATTTTTGCATATTTCAT-GTTTAGTTT
1 CACCTTTAGTATTTTTGCATATTTCATGGCTTAGTTT
*
18169 CACCTTTAGTATTTTTGCATATTTGATGGCTTAGTTT
1 CACCTTTAGTATTTTTGCATATTTCATGGCTTAGTTT
18206 CA
1 CA
18208 TTCAGTGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (37 bp):
CACCTTTAGTATTTTTGCATATTTCATGGCTTAGTTT
Done.