Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023049.1 Corchorus olitorius cultivar O-4 contig23082, 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: 42257
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2039 original size:51 final size:50
Alignment explanation
Indices: 1984--2131 Score: 145
Period size: 50 Copynumber: 2.9 Consensus size: 50
1974 TTTTTGATCG
* * *
1984 ATTTGTAAATGAAGA-TGTAACCTTTGAGTAAAAGATTGGATCTTTTAAGTA
1 ATTTGTAAATAAAGATTG-AACCTTTAAGTAAAAGATT-AATCTTTTAAGTA
* ** *
2035 ATTTGTAAATAAAGATTGGATTTTTAAGTGAAAGATTAATCTTTTAAGTA
1 ATTTGTAAATAAAGATTGAACCTTTAAGTAAAAGATTAATCTTTTAAGTA
* * * ** *
2085 ATTTGTAGATAAAGATCGGAGTTTTAAGTGAAAGATTGAATCTTTTA
1 ATTTGTAAATAAAGATTGAACCTTTAAGTAAAAGATT-AATCTTTTA
2132 TCTAAAGTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
50 46 0.54
51 37 0.44
52 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (50 bp):
ATTTGTAAATAAAGATTGAACCTTTAAGTAAAAGATTAATCTTTTAAGTA
Found at i:2097 original size:50 final size:51
Alignment explanation
Indices: 2014--2131 Score: 193
Period size: 50 Copynumber: 2.3 Consensus size: 51
2004 CCTTTGAGTA
* * *
2014 AAAGATTGGATCTTTTAAGTAATTTGTAAATAAAGATTGGATTTTTAAGTG
1 AAAGATTGAATCTTTTAAGTAATTTGTAAATAAAGATCGGAGTTTTAAGTG
*
2065 AAAGATT-AATCTTTTAAGTAATTTGTAGATAAAGATCGGAGTTTTAAGTG
1 AAAGATTGAATCTTTTAAGTAATTTGTAAATAAAGATCGGAGTTTTAAGTG
2115 AAAGATTGAATCTTTTA
1 AAAGATTGAATCTTTTA
2132 TCTAAAGTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 46 0.74
51 16 0.26
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (51 bp):
AAAGATTGAATCTTTTAAGTAATTTGTAAATAAAGATCGGAGTTTTAAGTG
Found at i:4676 original size:41 final size:40
Alignment explanation
Indices: 4613--4691 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
4603 AGGCCGCATA
4613 AATTAAAAATAAAATCTTAAATCAGGGGCAAAATTGAATC
1 AATTAAAAATAAAATCTTAAATCAGGGGCAAAATTGAATC
* *
4653 AATTAACAAATGAAATAC-TAAATCAGGGGCAACATTGAA
1 AATTAA-AAATAAAAT-CTTAAATCAGGGGCAAAATTGAA
4692 AACGGAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 6 0.17
41 28 0.80
42 1 0.03
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (40 bp):
AATTAAAAATAAAATCTTAAATCAGGGGCAAAATTGAATC
Found at i:7854 original size:27 final size:27
Alignment explanation
Indices: 7824--7878 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
7814 AAATTAAATG
**
7824 TGAATCTGTAAATGACCAAAATACCCC
1 TGAATCTAAAAATGACCAAAATACCCC
* *
7851 TGAATGTAAAAATGACCAAAATGCCCC
1 TGAATCTAAAAATGACCAAAATACCCC
7878 T
1 T
7879 ATATGACCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.22
Consensus pattern (27 bp):
TGAATCTAAAAATGACCAAAATACCCC
Found at i:8359 original size:46 final size:46
Alignment explanation
Indices: 8294--8466 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
8284 TCTTACCTCT
* *
8294 TTCCAACAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTCTA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTCTA
* * * * *
8340 TTCCAAAAATACCCTTTCCTGGTTGGAAGGTCCCTATTTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTCTA
* * * *
8386 TACCAAAAATGCCCATTCCCGGTCGGAAGGTCCCAGTTTTCGATATCTCA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC--T-TCT-A
*
8436 TCCCAAAAATGCCCCTTCCTGGTCGGAAGGT
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGT
8467 GTTGTCCAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
46 75 0.70
48 1 0.01
49 2 0.02
50 29 0.27
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.32
Consensus pattern (46 bp):
TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTCTTCTA
Found at i:8578 original size:41 final size:40
Alignment explanation
Indices: 8493--9322 Score: 843
Period size: 41 Copynumber: 20.4 Consensus size: 40
8483 TACTTCCTGT
* * **
8493 TTTGCCC-TCTCTTATCGGAAGGTGTCGTCAACATTT-CCAA
1 TTTGCCCTTC-CTCATCGGAAGGTGTTGT-TGCATTTACCAA
* * * * * *
8533 TTTGCCGTTCCTCATCGGGAGGTATTGTTGCCTTTGTCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTT-ACCAA
** * **
8574 TTTGCTTTTCCTCATCGGATGGTGTTGTCAACATTT-CCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTACCAA
* * *
8614 TCTGCCCTTCCTCATCGGGAGGTGTTGTTGCCATTGT-CCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTG-CATT-TACCAA
* * ** *
8655 TTTGTCTTTCCTCATCGGATTGTGTTGTCAGCATTT-CCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTACCAA
* * * **
8695 TTTACCCTTCCTCATCGGGAGGTGTTGTTGCCTTGGT-CCTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATT--TACCAA
8736 TTTGCCCTTCCTCATCGGAAGGTGTT-TTCAGCATTTACCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTT--GCATTTACCAA
*
8777 TTTGCCCTTCCTCACCGGAAGGTGTTGTTGCATTTACCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAA
*
8817 TTTGCCCTTCCTCATCGGAAGGT-TTGTCAGCATTTACCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTACCAA
* * *
8857 TTTGCCTTTCCTCACCGGAAGGTGTTGTTGCACTTACCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAA
8897 TTTGCCCTTCCTCATCGGAAGGTGTTGTTAGCATTTACCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTT-GCATTTACCAA
* * *
8938 TTTGCTCTTCCTCACCGGAAGGTGTTGTTGCATTTACTAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAA
* *
8978 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTATTTACCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTACCAA
* * *
9019 TTTTCTCTTCCTCACCGGAAGGTGTTGTTGCATTTACCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAA
* *
9059 TTTGCCCTTCCTCACCGGAAGGTGTTGTTGCATTTAACAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAA
* *
9099 TTTGCCCTTCCTCATACGGAAGGTGTTGTCAGGATTTACCAA
1 TTTGCCCTTCCTCAT-CGGAAGGTGTTGT-TGCATTTACCAA
* * * * *
9141 TTTGCCCTTCCTCATCGGGAGGTGTAGTTGCCTTTGTCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTT-ACCAA
* *
9182 TTTGCCCGTCCTCATCGGAAGGTGTTGTCTGCATTTTCCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTACCAA
* * * * * *
9223 TTTGCCCTTACTCATCGCAAGATGTTGTTTAG-GTTCACCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTG-TT-GCATTTACCAA
**
9264 TTTGCCCTTCCTCATCGGAAGGTGTTGTCTGCATTT-CTCGG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTAC-CAA
*
9305 TTTGCCCTCCCTCATCGG
1 TTTGCCCTTCCTCATCGG
9323 TAGAACTGGC
Statistics
Matches: 658, Mismatches: 106, Indels: 51
0.81 0.13 0.06
Matches are distributed among these distances:
39 12 0.02
40 285 0.43
41 318 0.48
42 43 0.07
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (40 bp):
TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAA
Found at i:8628 original size:81 final size:81
Alignment explanation
Indices: 8493--9322 Score: 856
Period size: 81 Copynumber: 10.2 Consensus size: 81
8483 TACTTCCTGT
* * * * * *
8493 TTTGCCC-TCTCTTATCGGAAGGTGTCGTCAACATTT-CCAATTTGCCGTTCCTCATCGGGAGGT
1 TTTGCCCTTC-CTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGT
* * *
8556 ATTGTTGCCTTTGTCCAG
65 GTTGTTGCCTTT-ACCAA
** * * * * *
8574 TTTGCTTTTCCTCATCGGATGGTGTTGTCAACATTT-CCAATCTGCCCTTCCTCATCGGGAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTG
*
8638 TTGTTGCCATTGT-CCAG
66 TTGTTGCC-TT-TACCAA
* * ** * * *
8655 TTTGTCTTTCCTCATCGGATTGTGTTGTCAGCATTT-CCAATTTACCCTTCCTCATCGGGAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTG
**
8719 TTGTTGCCTTGGT-CCTG
66 TTGTTGCCTT--TACCAA
*
8736 TTTGCCCTTCCTCATCGGAAGGTGTTTTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTG
*
8801 TTGTTGCATTTACCAA
66 TTGTTGCCTTTACCAA
*
8817 TTTGCCCTTCCTCATCGGAAGGT-TTGTCAGCATTTACCAATTTGCCTTTCCTCACCGGAAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTG
8881 TTGTTGCAC-TTACCAA
66 TTGTTGC-CTTTACCAA
* *
8897 TTTGCCCTTCCTCATCGGAAGGTGTTGTTAGCATTTACCAATTTGCTCTTCCTCACCGGAAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTG
* *
8962 TTGTTGCATTTACTAA
66 TTGTTGCCTTTACCAA
* * *
8978 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTATTTACCAATTTTCTCTTCCTCACCGGAAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTG
*
9043 TTGTTGCATTTACCAA
66 TTGTTGCCTTTACCAA
* * * *
9059 TTTGCCCTTCCTCACCGGAAGGTGTTGT-TGCATTTAACAATTTGCCCTTCCTCATACGGAAGGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCA-CCGGAAGGT
* **
9123 GTTGTCAGGATTTACCAA
65 GTTGT-TGCCTTTACCAA
* * * * * * * *
9141 TTTGCCCTTCCTCATCGGGAGGTGTAGT-TGCCTTTGTCCAGTTTGCCCGTCCTCATCGGAAGGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTT-ACCAATTTGCCCTTCCTCACCGGAAGGT
* *
9205 GTTGTCTGCATTTTCCAA
65 GTTGT-TGCCTTTACCAA
* * * * * * * *
9223 TTTGCCCTTACTCATCGCAAGATGTTGTTTAG-GTTCACCAGTTTGCCCTTCCTCATCGGAAGGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTG-TCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGT
* **
9287 GTTGTCTGCATTT-CTCGG
65 GTTGT-TGCCTTTAC-CAA
*
9305 TTTGCCCTCCCTCATCGG
1 TTTGCCCTTCCTCATCGG
9323 TAGAACTGGC
Statistics
Matches: 660, Mismatches: 74, Indels: 29
0.87 0.10 0.04
Matches are distributed among these distances:
80 100 0.15
81 361 0.55
82 179 0.27
83 19 0.03
84 1 0.00
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (81 bp):
TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTG
TTGTTGCCTTTACCAA
Found at i:8709 original size:121 final size:120
Alignment explanation
Indices: 8493--9322 Score: 780
Period size: 121 Copynumber: 6.8 Consensus size: 120
8483 TACTTCCTGT
* * ** * * *
8493 TTTGCCC-TCTCTTATCGGAAGGTGTCGTCAACATTT-CCAATTTGCCGTTCCTCATCGGGAGGT
1 TTTGCCCTTC-CTCATCGGAAGGTGTTGT-TGCATTTACCAATTTGCCCTTCCTCACCGGAAGGT
* * * * * ** * **
8556 ATTGTTGCCTTTGTCCAGTTTGCTTTTCCTCATCGGATGGTGTTGTCAACATTT-CCAA
64 GTTGTAGCATTT-ACCAATTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTACCAA
* * * * * * **
8614 TCTGCCCTTCCTCATCGGGAGGTGTTGTTGCCATTGT-CCAGTTTGTCTTTCCTCATCGGATTGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTG-CATT-TACCAATTTGCCCTTCCTCACCGGAAGGT
* * * **
8678 GTTGTCAGCATTT-CCAATTTACCCTTCCTCATCGGGAGGTGTTGTTGCCTTGGT-CCTG
64 GTTGT-AGCATTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATT--TACCAA
8736 TTTGCCCTTCCTCATCGGAAGGTGTT-TTCAGCATTTACCAATTTGCCCTTCCTCACCGGAAGGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTT--GCATTTACCAATTTGCCCTTCCTCACCGGAAGGT
* *
8800 GTTGTTGCATTTACCAATTTGCCCTTCCTCATCGGAAGGT-TTGTCAGCATTTACCAA
64 GTTGTAGCATTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTACCAA
* * * *
8857 TTTGCCTTTCCTCACCGGAAGGTGTTGTTGCACTTACCAATTTGCCCTTCCTCATCGGAAGGTGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTGT
* * *
8922 TGTTAGCATTTACCAATTTGCTCTTCCTCACCGGAAGGTGTTGTTGCATTTACTAA
66 TG-TAGCATTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAA
* * * *
8978 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTATTTACCAATTTTCTCTTCCTCACCGGAAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTG
* * *
9043 TTGTTGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTGTTGTTGCATTTAACAA
65 TTGTAGCATTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAA
* * * *
9099 TTTGCCCTTCCTCATACGGAAGGTGTTGTCAGGATTTACCAATTTGCCCTTCCTCATCGGGAGGT
1 TTTGCCCTTCCTCAT-CGGAAGGTGTTGT-TGCATTTACCAATTTGCCCTTCCTCACCGGAAGGT
* * * * * * *
9164 GTAGTTGCCTTTGTCCAGTTTGCCCGTCCTCATCGGAAGGTGTTGTCTGCATTTTCCAA
64 GTTGTAGCATTT-ACCAATTTGCCCTTCCTCATCGGAAGGTGTTGT-TGCATTTACCAA
* * * * * * *
9223 TTTGCCCTTACTCATCGCAAGATGTTGTTTAG-GTTCACCAGTTTGCCCTTCCTCATCGGAAGGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTG-TT-GCATTTACCAATTTGCCCTTCCTCACCGGAAGGT
* ** *
9287 GTTGTCTGCATTT-CTCGGTTTGCCCTCCCTCATCGG
64 GTTGT-AGCATTTAC-CAATTTGCCCTTCCTCATCGG
9323 TAGAACTGGC
Statistics
Matches: 598, Mismatches: 88, Indels: 44
0.82 0.12 0.06
Matches are distributed among these distances:
120 40 0.07
121 223 0.37
122 208 0.35
123 95 0.16
124 32 0.05
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (120 bp):
TTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAATTTGCCCTTCCTCACCGGAAGGTGT
TGTAGCATTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTGCATTTACCAA
Found at i:9485 original size:15 final size:16
Alignment explanation
Indices: 9465--9502 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
9455 CGTTCAAATG
9465 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
9480 TCGGGTCAATTCTGGGT
1 TCGGGTCAATT-TGGGT
9497 T-GGGTC
1 TCGGGTC
9503 GTTTTTGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:11169 original size:16 final size:17
Alignment explanation
Indices: 11141--11185 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
11131 GTCGTTTTGA
*
11141 TCGGGTTCAGGTCATTT
1 TCGGGTTCGGGTCATTT
*
11158 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCATTT
11174 TCGGGTTCGGGT
1 TCGGGTTCGGGT
11186 ACCCAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.07, C:0.13, G:0.38, T:0.42
Consensus pattern (17 bp):
TCGGGTTCGGGTCATTT
Found at i:12842 original size:22 final size:22
Alignment explanation
Indices: 12814--12860 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
12804 TAATAGTTGA
12814 ATTTTTGCATGGCACCTTTTGC
1 ATTTTTGCATGGCACCTTTTGC
*
12836 ATTTTTGCATGGCATCTTTTGC
1 ATTTTTGCATGGCACCTTTTGC
12858 ATT
1 ATT
12861 CATCCTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.49
Consensus pattern (22 bp):
ATTTTTGCATGGCACCTTTTGC
Found at i:17503 original size:7 final size:7
Alignment explanation
Indices: 17491--17603 Score: 51
Period size: 7 Copynumber: 16.3 Consensus size: 7
17481 ATGGTAATGT
17491 TAAAGAG
1 TAAAGAG
17498 TAAAGAG
1 TAAAGAG
*
17505 T-AATAG
1 TAAAGAG
**
17511 TAATCAG
1 TAAAGAG
17518 TAAAGAG
1 TAAAGAG
*
17525 TGAAGAG
1 TAAAGAG
**
17532 TAATCAG
1 TAAAGAG
17539 TAAA-ATGG
1 TAAAGA--G
*
17547 T-AATAG
1 TAAAGAG
*
17553 TAATCG-G
1 TAA-AGAG
17560 TAAAGAG
1 TAAAGAG
17567 TAAAAGAG
1 T-AAAGAG
17575 TAATAGTAG
1 TAA-AG-AG
17584 T--A-AG
1 TAAAGAG
17588 TAAAGAG
1 TAAAGAG
17595 TAAAGAG
1 TAAAGAG
17602 TA
1 TA
17604 GTCAAGAAAG
Statistics
Matches: 80, Mismatches: 13, Indels: 26
0.67 0.11 0.22
Matches are distributed among these distances:
4 3 0.04
6 11 0.14
7 51 0.64
8 12 0.15
9 3 0.04
ACGTcount: A:0.50, C:0.03, G:0.25, T:0.22
Consensus pattern (7 bp):
TAAAGAG
Found at i:17535 original size:21 final size:22
Alignment explanation
Indices: 17496--17582 Score: 78
Period size: 21 Copynumber: 4.2 Consensus size: 22
17486 AATGTTAAAG
*
17496 AGTAAAGAGT--AATAGTAATC
1 AGTAAAGAGTAGAAGAGTAATC
17516 AGTAAAGAGT-GAAGAGTAATC
1 AGTAAAGAGTAGAAGAGTAATC
* *
17537 AGTAAA-A-TGGTAATAGTAATC
1 AGTAAAGAGTAG-AAGAGTAATC
* *
17558 GGTAAAGAGTAAAAGAGTAAT-
1 AGTAAAGAGTAGAAGAGTAATC
17579 AGTA
1 AGTA
17583 GTAAGTAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.02
20 12 0.22
21 32 0.58
22 9 0.16
23 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.23
Consensus pattern (22 bp):
AGTAAAGAGTAGAAGAGTAATC
Found at i:17590 original size:28 final size:28
Alignment explanation
Indices: 17537--17603 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
17527 AAGAGTAATC
**
17537 AGTAAAATG-GTAATAGTAATCGGTAAAG
1 AGTAAAA-GAGTAATAGTAATAAGTAAAG
*
17565 AGTAAAAGAGTAATAGTAGTAAGTAAAG
1 AGTAAAAGAGTAATAGTAATAAGTAAAG
17593 AGT-AAAGAGTA
1 AGTAAAAGAGTA
17604 GTCAAGAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.26
28 26 0.74
ACGTcount: A:0.51, C:0.01, G:0.25, T:0.22
Consensus pattern (28 bp):
AGTAAAAGAGTAATAGTAATAAGTAAAG
Found at i:17618 original size:41 final size:41
Alignment explanation
Indices: 17569--17679 Score: 186
Period size: 41 Copynumber: 2.7 Consensus size: 41
17559 GTAAAGAGTA
* *
17569 AAAGAGTAATAGTAGTAAGTAAAGAGTAAAGAGTAGTCAAG
1 AAAGAGTAATAATAGTAAGTAAAGAGTAAAGAGTAATCAAG
*
17610 AAAGAGTAATAATAGTCAGTAAAGAGTAAAGAGTAATCAAG
1 AAAGAGTAATAATAGTAAGTAAAGAGTAAAGAGTAATCAAG
*
17651 AAAGAGTAATAATAGTTAGTAAAGAGTAA
1 AAAGAGTAATAATAGTAAGTAAAGAGTAA
17680 TCAAGAAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.21
Consensus pattern (41 bp):
AAAGAGTAATAATAGTAAGTAAAGAGTAAAGAGTAATCAAG
Found at i:17636 original size:34 final size:34
Alignment explanation
Indices: 17593--17707 Score: 131
Period size: 34 Copynumber: 3.2 Consensus size: 34
17583 GTAAGTAAAG
17593 AGTAAAGAGTAGTCAAGAAAGAGTAATAATAGTC
1 AGTAAAGAGTAGTCAAGAAAGAGTAATAATAGTC
*
17627 AGTAAAGAGTAAAGAGTAATCAAGAAAGAGTAATAATAGTT
1 AGTAAAGAGT----AG---TCAAGAAAGAGTAATAATAGTC
* * *
17668 AGTAAAGAGTAATCAAGAAAGAGTAATAGTAATC
1 AGTAAAGAGTAGTCAAGAAAGAGTAATAATAGTC
17702 AGTAAA
1 AGTAAA
17708 ATGGTAATGT
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
34 35 0.51
37 1 0.01
38 2 0.03
41 31 0.45
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (34 bp):
AGTAAAGAGTAGTCAAGAAAGAGTAATAATAGTC
Found at i:17654 original size:14 final size:14
Alignment explanation
Indices: 17637--17694 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
17627 AGTAAAGAGT
17637 AAAGAGTAATCAAG
1 AAAGAGTAATCAAG
*
17651 AAAGAGTAATAATAGTTAG
1 AAAGAGTAAT--CA---AG
17670 TAAAGAGTAATCAAG
1 -AAAGAGTAATCAAG
17685 AAAGAGTAAT
1 AAAGAGTAAT
17695 AGTAATCAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 20 0.56
15 2 0.06
16 1 0.03
18 1 0.03
19 2 0.06
20 10 0.28
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (14 bp):
AAAGAGTAATCAAG
Found at i:17730 original size:7 final size:7
Alignment explanation
Indices: 17718--17742 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17708 ATGGTAATGT
17718 TAAAGAG
1 TAAAGAG
17725 TAAAGAG
1 TAAAGAG
17732 TAAAGAG
1 TAAAGAG
17739 TAAA
1 TAAA
17743 ATGGTCATAG
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:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (7 bp):
TAAAGAG
Found at i:17730 original size:75 final size:73
Alignment explanation
Indices: 17559--17741 Score: 183
Period size: 75 Copynumber: 2.3 Consensus size: 73
17549 ATAGTAATCG
*
17559 GTAAAGAGTAAAAGAGTAATAGTAGTAAGTAAAGAGTAAAGAGTAGTCAAGAAAGAGTAATAATA
1 GTAAAGAGT-AAAGAGTAA-AG-AGTAAGTAAAGAGTAAAGAGTAATCAAGAAAGAGTAATAATA
*
17624 GTCAGTAAAGA
63 ATCAGTAAAGA
*
17635 GTAAAGAGTAATCA-AG-AAAGAGTAA-TAATAGTTAGTAAAGAGTAATCAAGAAAGAGTAATAG
1 GTAAAGAGTAA--AGAGTAAAGAGTAAGTAA-AG--AGTAAAGAGTAATCAAGAAAGAGTAATAA
17697 TAATCAGTAAAATGGTAA
61 TAATCAGT-AAA--G--A
17715 TGTTAAAGAGTAAAGAGTAAAGAGTAA
1 -G-TAAAGAGTAAAGAGTAAAGAGTAA
17742 AATGGTCATA
Statistics
Matches: 90, Mismatches: 3, Indels: 22
0.78 0.03 0.19
Matches are distributed among these distances:
72 3 0.03
73 7 0.08
74 2 0.02
75 38 0.42
76 14 0.16
77 1 0.01
78 1 0.01
80 2 0.02
81 3 0.03
82 19 0.21
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.21
Consensus pattern (73 bp):
GTAAAGAGTAAAGAGTAAAGAGTAAGTAAAGAGTAAAGAGTAATCAAGAAAGAGTAATAATAATC
AGTAAAGA
Found at i:17734 original size:35 final size:38
Alignment explanation
Indices: 17685--17793 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 38
17675 AGTAATCAAG
*
17685 AAAGAGT-AATAGTAATCAGTAAAATGGTAAT-G-T-T
1 AAAGAGTAAAGAGTAATCAGTAAAATGGTAATAGATAT
** *
17719 AAAGAGTAAAGAGTAAAGAGTAAAATGGTCATAGCAATCAGT
1 AAAGAGTAAAGAGTAATCAGTAAAATGGTAATAG--AT-A-T
17761 AAAGAGTAAAGAGTAATCAGTAAAATGGTAATA
1 AAAGAGTAAAGAGTAATCAGTAAAATGGTAATA
17794 ATAATCAGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
34 7 0.12
35 20 0.33
36 1 0.02
39 1 0.02
42 31 0.52
ACGTcount: A:0.50, C:0.05, G:0.22, T:0.23
Consensus pattern (38 bp):
AAAGAGTAAAGAGTAATCAGTAAAATGGTAATAGATAT
Found at i:17764 original size:42 final size:42
Alignment explanation
Indices: 17718--17804 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
17708 ATGGTAATGT
* * *
17718 TAAAGAGTAAAGAGTAAAGAGTAAAATGGTCATAGCAATCAG
1 TAAAGAGTAAAGAGTAAACAGTAAAATGGTAATAACAATCAG
* *
17760 TAAAGAGTAAAGAGTAATCAGTAAAATGGTAATAATAATCAG
1 TAAAGAGTAAAGAGTAAACAGTAAAATGGTAATAACAATCAG
17802 TAA
1 TAA
17805 TTAAAATTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.22
Consensus pattern (42 bp):
TAAAGAGTAAAGAGTAAACAGTAAAATGGTAATAACAATCAG
Found at i:17883 original size:35 final size:35
Alignment explanation
Indices: 17839--17914 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
17829 TAAAAAGATT
*
17839 AAAAAGAGTAAAAATGGTATTCAATAATTAAAGTA
1 AAAAAGAGTAAAAATGGTACTCAATAATTAAAGTA
*
17874 AAAAAGAGTAAAAATGGTACTCAGTAATTAAAGTA
1 AAAAAGAGTAAAAATGGTACTCAATAATTAAAGTA
17909 AAAAAG
1 AAAAAG
17915 GCAAAAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (35 bp):
AAAAAGAGTAAAAATGGTACTCAATAATTAAAGTA
Found at i:17922 original size:35 final size:35
Alignment explanation
Indices: 17839--17935 Score: 126
Period size: 35 Copynumber: 2.8 Consensus size: 35
17829 TAAAAAGATT
* * *
17839 AAAAAGAGTAAAAATGGTATTCAATAATTAAAGTA
1 AAAAAGAGAAAAAATGGTACTCAGTAATTAAAGTA
*
17874 AAAAAGAGTAAAAATGGTACTCAGTAATTAAAGTA
1 AAAAAGAGAAAAAATGGTACTCAGTAATTAAAGTA
17909 AAAAAG-GCAAAAAATGGATAC-CAGTAA
1 AAAAAGAG-AAAAAATGG-TACTCAGTAA
17936 AAAAGGAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
34 1 0.02
35 53 0.93
36 3 0.05
ACGTcount: A:0.57, C:0.06, G:0.16, T:0.21
Consensus pattern (35 bp):
AAAAAGAGAAAAAATGGTACTCAGTAATTAAAGTA
Found at i:17958 original size:24 final size:24
Alignment explanation
Indices: 17904--17988 Score: 75
Period size: 26 Copynumber: 3.4 Consensus size: 24
17894 TCAGTAATTA
17904 AAGTAAAAAAGGCAAAAAATGG--AT
1 AAGTAAAAAAGG--AAAAATGGTAAT
17928 ACCAGTAAAAAAGGAAAAATGGTAAT
1 A--AGTAAAAAAGGAAAAATGGTAAT
* *
17954 AAGTAAAAAGAGTGAAAATTGATAAT
1 AAGTAAAAA-AG-GAAAAATGGTAAT
*
17980 CAGTAAAAA
1 AAGTAAAAA
17989 TAGTAAGGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
24 17 0.33
25 2 0.04
26 33 0.63
ACGTcount: A:0.60, C:0.05, G:0.19, T:0.16
Consensus pattern (24 bp):
AAGTAAAAAAGGAAAAATGGTAAT
Found at i:30423 original size:5 final size:5
Alignment explanation
Indices: 30413--30438 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30403 TTCGGGTCTT
30413 GACAC GACAC GACAC GACAC GACAC G
1 GACAC GACAC GACAC GACAC GACAC G
30439 GAACGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.38, G:0.23, T:0.00
Consensus pattern (5 bp):
GACAC
Found at i:30953 original size:12 final size:12
Alignment explanation
Indices: 30936--30967 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
30926 TACCCTATGT
30936 AAACACGACACG
1 AAACACGACACG
30948 AAACACGACACG
1 AAACACGACACG
30960 AAACACGA
1 AAACACGA
30968 ATTGTCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:38531 original size:34 final size:34
Alignment explanation
Indices: 38488--38558 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
38478 AAACACTGAC
* *
38488 ATATTTTGTATATGTTGTTTAGATGGGATACCTG
1 ATATTTTGTATATGTTGTGTAGATGGGAAACCTG
* *
38522 ATATTTTGTATATGTTGTGTAGTTGGGAAATCTG
1 ATATTTTGTATATGTTGTGTAGATGGGAAACCTG
38556 ATA
1 ATA
38559 GTTTAGGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.25, C:0.04, G:0.24, T:0.46
Consensus pattern (34 bp):
ATATTTTGTATATGTTGTGTAGATGGGAAACCTG
Found at i:38578 original size:21 final size:22
Alignment explanation
Indices: 38549--38594 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
38539 TGTAGTTGGG
*
38549 AAATCTGATAGTTTAGGGTACC
1 AAATCTGATAGTTCAGGGTACC
*
38571 AAAT-TGATGGTTCAGGGTACC
1 AAATCTGATAGTTCAGGGTACC
38592 AAA
1 AAA
38595 ACAATGATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (22 bp):
AAATCTGATAGTTCAGGGTACC
Found at i:41086 original size:16 final size:16
Alignment explanation
Indices: 41061--41092 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41051 AAAATGCTAA
41061 AAAATAATAATTGAAT
1 AAAATAATAATTGAAT
*
41077 AAAATTATAATTGAAT
1 AAAATAATAATTGAAT
41093 GGTTTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
AAAATAATAATTGAAT
Found at i:41456 original size:14 final size:15
Alignment explanation
Indices: 41429--41461 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
41419 TTACTAAAAA
41429 TAATATTAATTAAAT
1 TAATATTAATTAAAT
*
41444 TAATATTCA-TAAAT
1 TAATATTAATTAAAT
41458 TAAT
1 TAAT
41462 TCTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATTAATTAAAT
Done.