Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021774.1 Corchorus olitorius cultivar O-4 contig21807, 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: 56107
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:336 original size:93 final size:93
Alignment explanation
Indices: 178--414 Score: 377
Period size: 93 Copynumber: 2.5 Consensus size: 93
168 AATAGGTATA
178 TAAATAAAAAATAGAGTTTTT-TTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
1 TAAATAAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
242 AAGTATAATTAAATAGTTATAAGGATAT
66 AAGTATAATTAAATAGTTATAAGGATAT
270 TAAATAAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
1 TAAATAAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
335 AAGTATAATTAAATAGTTATAAGGATAT
66 AAGTATAATTAAATAGTTATAAGGATAT
*
363 TAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
1 T--A---AA-T--A-AAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGT
415 TTAAACAATG
Statistics
Matches: 134, Mismatches: 1, Indels: 10
0.92 0.01 0.07
Matches are distributed among these distances:
92 21 0.16
93 72 0.54
95 1 0.01
98 2 0.01
99 1 0.01
101 1 0.01
102 36 0.27
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37
Consensus pattern (93 bp):
TAAATAAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
AAGTATAATTAAATAGTTATAAGGATAT
Found at i:3024 original size:604 final size:609
Alignment explanation
Indices: 2011--3223 Score: 1843
Period size: 604 Copynumber: 2.0 Consensus size: 609
2001 CAAATATATT
* * **
2011 TCTAAATTGCCATTATTAAATCATATTTAATTATTCCATTATTAAAATAATGGAAATTTAGATTA
1 TCTAAATTGCCATTATTAAATAATATTTAATTAATCCACCATTAAAATAATGGAAATTTAGATTA
* **
2076 TCCTCATTAATTAGGATCCAATGTGACCAATAGGAATGCCCCACATCATCTTTAACATTTGAATT
66 TCCTCATTAATTAGGATCCAACGTGACCAATAGGAATGCCCCACATCATCTTTAACATCCGAATT
* * * *
2141 TTCGTCCAAAACATTCTTCAAGTCGGTTTAGGAGAAGATCAATTTTGTTCAGGAATTTCAAGGGT
131 TTCGTCCAAAACATTCTCCAACTCGGTTTAGGAGAAGATCAATTTTGTTCAGAAATTTCAAGGGC
* * *
2206 AAAATCTTCCACCGGAATGGCAGAATTAGATCTCGAGATAAACATAAAAAATGTAGACCTCAGAA
196 AAAATCATCCACCGAAATCGCAGAATTAGATCTCGAGATAAACATAAAAAATGTAGACCTCAGAA
* * * *
2271 TCCTCTTTCGAACGGTATCTCATTTGCATTTTTCTGAGATCTGGATCAAAAGTTATGGATTTTCT
261 TCCTCTTTCCAACAGTATCTCATTTGCATTTTTCTGAGATCTGGATCAAAAGTTAAGAATTTTCT
* * *
2336 TCCAAAACTGCTCTTGTGAAGTCCTCCATTAAATAGGATTTAACAATGTTGCATCTGGATTGAAT
326 TCCAAAACTACTCTTGTAAAGTCCTCCATTAAATAGGATTTAACAATGTTGCATCAGGATTGAAT
* * *
2401 CATTACTGCATCTTAATTACTGATTGGACTTGGACTCCTTCTTTGGGCTACCATATTAACAAATT
391 CATTACAGCATCATAATTACCGATTGGACTTGGACTCCTTCTTTGGGCTACCATATTAACAAATT
*
2466 AGGTCTAAAAATATCAGATTTATACTTCAAGACATTTGGCTTTACAATTTGGACTTCATGGACTC
456 AGGTCTAAAAATATCAGATTTATACTTCAAGACATTTGGCTTGACAATTTGGACTTCATGGACTC
* *
2531 AAACAAGCCTAATGGGCCTATTGGGCCGAAATGAGACAAAATC-ATAGTTTCTCCAAATCTATCT
521 AAACAAGCCTAATGGGCCTATTAGGCCGAAATGAGACAAAATCAATAGTTTCTCCAAATCTATCG
2595 ATACTATATATAAAAATACGAATA
586 ATACTATATATAAAAATACGAATA
*
2619 TCTAAATTGCCATTATTAAATAATATTTTAATTAATCCACCATTAAAATTATGGAAATTTAGATT
1 TCTAAATTGCCATTATTAAATAATA-TTTAATTAATCCACCATTAAAATAATGGAAATTTAGATT
* ** *
2684 ATTCTCATTAATTAGGATCCAACGTGACCAATAGGGTTGCCCCACATCATCTTTAGCATCCGAAT
65 ATCCTCATTAATTAGGATCCAACGTGACCAATAGGAATGCCCCACATCATCTTTAACATCCGAAT
2749 TTTCGTCCAAAACATTCTCCAAACT-GGTTTA-G-G-A-ATCAA-TTTG-TCTAGAAATTTCAAG
130 TTTCGTCCAAAACATTCTCC-AACTCGGTTTAGGAGAAGATCAATTTTGTTC-AGAAATTTCAAG
* * * **
2807 GGCAAAATCATCCACTGAAATCGCAGAATTAGGTCTCGAGATAAACATAATAGTTGTAG-CTCTC
193 GGCAAAATCATCCACCGAAATCGCAGAATTAGATCTCGAGATAAACATAAAAAATGTAGAC-CTC
*
2871 GGAATCCAT-TTTCCAACAGTATCTCATTTGCATTTTTCTGAGATCTGGATCAAAAGTTAAGAAT
257 AGAATCC-TCTTTCCAACAGTATCTCATTTGCATTTTTCTGAGATCTGGATCAAAAGTTAAGAAT
* * * * *
2935 TTTCTTCTAAAACTACTCTTGTAAAGTCTTCCTTTAAATATGATTTAACAATGTTGCATCAGGGT
321 TTTCTTCCAAAACTACTCTTGTAAAGTCCTCCATTAAATAGGATTTAACAATGTTGCATCAGGAT
*
3000 TGAATCATTACAGCATCATAATTACCGATTGGACTTGGACTCCTTCTTTGGGCTTCCATATTAAC
386 TGAATCATTACAGCATCATAATTACCGATTGGACTTGGACTCCTTCTTTGGGCTACCATATTAAC
* * * *
3065 GAATTGGGTCTAAGAATATCATATTTATACTTCAAGACATTTGGCTTGACAATTTGGACTTCATG
451 AAATTAGGTCTAAAAATATCAGATTTATACTTCAAGACATTTGGCTTGACAATTTGGACTTCATG
* * *
3130 GGCTCAAACGAGTCTAATGGGCCTATTAGGCCGAAATGAGACAAAATCAATAGTTTCTCCAAATC
516 GACTCAAACAAGCCTAATGGGCCTATTAGGCCGAAATGAGACAAAATCAATAGTTTCTCCAAATC
*
3195 TATCGATACTATATATAAAAGTACGAATA
581 TATCGATACTATATATAAAAATACGAATA
3224 ATGCAAAACT
Statistics
Matches: 547, Mismatches: 52, Indels: 15
0.89 0.08 0.02
Matches are distributed among these distances:
603 3 0.01
604 347 0.63
605 49 0.09
606 1 0.00
607 1 0.00
608 25 0.05
609 118 0.22
610 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (609 bp):
TCTAAATTGCCATTATTAAATAATATTTAATTAATCCACCATTAAAATAATGGAAATTTAGATTA
TCCTCATTAATTAGGATCCAACGTGACCAATAGGAATGCCCCACATCATCTTTAACATCCGAATT
TTCGTCCAAAACATTCTCCAACTCGGTTTAGGAGAAGATCAATTTTGTTCAGAAATTTCAAGGGC
AAAATCATCCACCGAAATCGCAGAATTAGATCTCGAGATAAACATAAAAAATGTAGACCTCAGAA
TCCTCTTTCCAACAGTATCTCATTTGCATTTTTCTGAGATCTGGATCAAAAGTTAAGAATTTTCT
TCCAAAACTACTCTTGTAAAGTCCTCCATTAAATAGGATTTAACAATGTTGCATCAGGATTGAAT
CATTACAGCATCATAATTACCGATTGGACTTGGACTCCTTCTTTGGGCTACCATATTAACAAATT
AGGTCTAAAAATATCAGATTTATACTTCAAGACATTTGGCTTGACAATTTGGACTTCATGGACTC
AAACAAGCCTAATGGGCCTATTAGGCCGAAATGAGACAAAATCAATAGTTTCTCCAAATCTATCG
ATACTATATATAAAAATACGAATA
Found at i:3803 original size:22 final size:22
Alignment explanation
Indices: 3775--3924 Score: 94
Period size: 22 Copynumber: 6.9 Consensus size: 22
3765 TGTCTCTGTG
3775 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
3797 TGGTTATTATAACTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
3820 -GGGTATCAAAATTCCA-AAGTA
1 TGGTTATCAAAATTTCATAAG-A
* * *
3841 TTGTTACCAAAA-TTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* * *
3863 -AGTTAGCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* *
3884 AGGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
3906 TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
3925 GGATCAGCTT
Statistics
Matches: 96, Mismatches: 23, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
20 2 0.02
21 17 0.18
22 73 0.76
23 4 0.04
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:3872 original size:21 final size:22
Alignment explanation
Indices: 3843--3957 Score: 110
Period size: 22 Copynumber: 5.2 Consensus size: 22
3833 CCAAAGTATT
3843 GTTACCAAAA-TTCATATGGAA-
1 GTTACCAAAATTTCATA-GGAAG
*
3864 GTTAGCAAAATTTCATAGGAAG
1 GTTACCAAAATTTCATAGGAAG
* *
3886 GTTATCAAAATTTCATAGTG-TG
1 GTTACCAAAATTTCATAG-GAAG
3908 GTTACCAAAATTTCATAGGATCAG
1 GTTACCAAAATTTCATAGGA--AG
* ** *
3932 CTTATTAAAATTTCTTAGGAAG
1 GTTACCAAAATTTCATAGGAAG
3954 GTTA
1 GTTA
3958 TTGGAATTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
21 14 0.18
22 46 0.59
23 1 0.01
24 17 0.22
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
GTTACCAAAATTTCATAGGAAG
Found at i:3892 original size:65 final size:67
Alignment explanation
Indices: 3810--3958 Score: 171
Period size: 65 Copynumber: 2.2 Consensus size: 67
3800 TTATTATAAC
* *
3810 TTCATGAGG-AGGGTATCAAAATTCCAAAGTATTGTTACCAAAA-TTCATATGGA-AG-TTAGCA
1 TTCAT-AGGAAGGTTATCAAAATTCCAAAGTATGGTTACCAAAATTTCATA-GGACAGCTTAGCA
3871 AAAT
64 AAAT
* * * **
3875 TTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAGCTTATTAA
1 TTCATAGGAAGGTTATCAAAATTCCAAAGTATGGTTACCAAAATTTCATAGGA-CAGCTTAGCAA
3940 AAT
65 AAT
*
3943 TTCTTAGGAAGGTTAT
1 TTCATAGGAAGGTTAT
3959 TGGAATTTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
64 3 0.04
65 37 0.52
66 6 0.08
67 2 0.03
68 23 0.32
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (67 bp):
TTCATAGGAAGGTTATCAAAATTCCAAAGTATGGTTACCAAAATTTCATAGGACAGCTTAGCAAA
AT
Found at i:4034 original size:22 final size:21
Alignment explanation
Indices: 4009--4329 Score: 170
Period size: 22 Copynumber: 14.4 Consensus size: 21
3999 ATCAAAGAGA
*
4009 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
4031 TTAT-AAGAATTTCATAGCATGG
1 TTATCAA-AATTTCATAGGA-GG
*
4053 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
4075 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
*
4097 TTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATAGGA-GG
** *
4119 TTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
*
4141 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
* *
4163 TTAT-AAAAGTCTCAATTTTATGAGG
1 TTATCAAAA-TTTC-A---TAGGAGG
** * * *
4188 AGAACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
4210 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
*
4230 ATTATCGAAATTTCATAGAGATCGG
1 -TTATCAAAATTTCATAG-GA--GG
*
4255 ATTATCAAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATAGG-AGG
*
4277 TTATCAAAATTTCATAGTAGTG
1 TTATCAAAATTTCATAGGAG-G
4299 TTATCAAAATTTCGA-AGCGAGG
1 TTATCAAAATTTC-ATAG-GAGG
*
4321 TTTTCAAAA
1 TTATCAAAA
4330 CTACATAATG
Statistics
Matches: 230, Mismatches: 41, Indels: 56
0.70 0.13 0.17
Matches are distributed among these distances:
19 2 0.01
20 9 0.04
21 31 0.13
22 142 0.62
23 12 0.05
24 7 0.03
25 17 0.07
26 6 0.03
27 4 0.02
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:7439 original size:22 final size:22
Alignment explanation
Indices: 7411--7971 Score: 116
Period size: 22 Copynumber: 25.7 Consensus size: 22
7401 TCAGGGAGGA
7411 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
7433 TATCAAATTTTCACAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
7455 TTTCAAAATTTTATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
7477 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
7498 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
7521 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
7543 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
7565 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * * *
7581 TATCAAGATTTCATAAGGATGT
1 TATCAAAATTTCATATGAAGGT
* * * * *
7603 TATGAAAATTTTATAGGGAGACT
1 TATCAAAATTTCATATGAAG-GT
* * *
7626 TATCAAAATTTTATAGGATGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
7649 TATCAAAATTTTATA-GCGATGT
1 TATCAAAATTTCATATG-AAGGT
* * * * *
7671 TGTCACAATTTTATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
** * *
7693 TATCAAAATTTCAGGGTG-TGAT
1 TATCAAAATTTCA-TATGAAGGT
*** *
7715 TACTTTCAA-TTCATATGGAGGT
1 TA-TCAAAATTTCATATGAAGGT
* * * ** *
7737 TTTTAAATTTTCATAACATGGT
1 TATCAAAATTTCATATGAAGGT
* * *
7759 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
** * **
7781 TATCACCATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
7804 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
7826 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
7848 CT-TCAAAATTTCTTAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
** *
7870 TAAAAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** * **
7892 TAAAAAAAATT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
7913 TCTCGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* **
7935 TATTAAAATTTCATGGGAAGGT
1 TATCAAAATTTCATATGAAGGT
7957 TATCAAAATTTCATA
1 TATCAAAATTTCATA
7972 AGAATATCAT
Statistics
Matches: 386, Mismatches: 120, Indels: 66
0.67 0.21 0.12
Matches are distributed among these distances:
16 9 0.02
17 2 0.01
18 2 0.01
20 2 0.01
21 30 0.08
22 275 0.71
23 64 0.17
24 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:7840 original size:45 final size:44
Alignment explanation
Indices: 7755--7884 Score: 106
Period size: 45 Copynumber: 2.9 Consensus size: 44
7745 TTTCATAACA
* * * ** *
7755 TGGTTATCAATATATCATAT-GGAGGTTATCACCATCTCATAGTG
1 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
7799 TTGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATAGTG
1 -TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATAGTG
* **
7844 AGGTCT-TCAAAATTTC-TTAGGG-AGATTAAAAAAATTTCATA
1 TGGT-TATCAAAATTTCATT-GGGAAG-TTATCAAAATTTCATA
7885 AGAAGGTTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.06
44 31 0.43
45 37 0.51
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (44 bp):
TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATAGTG
Found at i:9614 original size:44 final size:43
Alignment explanation
Indices: 9432--9711 Score: 224
Period size: 41 Copynumber: 6.6 Consensus size: 43
9422 AAATTGCCCT
* * * *
9432 TGTGTTATGATTGTGTTT-AGGACTTTAGTATG-G-ATGT-CTC
1 TGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAAT-TCCTC
* *
9472 TGTGTTATTAATGTGTTTGAGGACTTTTAG--AGAGAATTGCCTA
1 TGTGTTATAAATGTGTTTGAGGAC-TTTAGAAAGAGAATT-CCTC
* * ** ** *
9515 TGTGTTATAATTGTGTTTGGGGACTTT-GGTA-TTAATGT-CTT
1 TGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAAT-TCCTC
*
9556 TGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAATTACCCC
1 TGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAATT-CCTC
* ** *
9600 TGTGTTATAAATGTGTTTGGGGACTTT-GGTATAG-ATGT-CTC
1 TGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAAT-TCCTC
*
9641 TGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAATTGCCCC
1 TGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAATT-CCTC
* *
9685 TGTATTATAAATGTGTTTGGGGACTTT
1 TGTGTTATAAATGTGTTTGAGGACTTT
9712 GGTTATTTGG
Statistics
Matches: 192, Mismatches: 30, Indels: 32
0.76 0.12 0.13
Matches are distributed among these distances:
40 17 0.09
41 63 0.33
42 23 0.12
43 35 0.18
44 54 0.28
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (43 bp):
TGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAATTCCTC
Found at i:9625 original size:85 final size:85
Alignment explanation
Indices: 9423--9714 Score: 412
Period size: 85 Copynumber: 3.5 Consensus size: 85
9413 GCCATATAGA
* * * * * ** *
9423 AATTGCCCTTGTGTTATGATTGTGTTT-AGGACTTTAGTATGGATGTCTCTGTGTTATTAATGTG
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGGTATTAATGTCTCTGTGTTATAAATGTG
9487 TTTGAGGACTTTTAG--AGAG
66 TTTGAGGAC-TTTAGAAAGAG
** * *
9506 AATTGCCTATGTGTTATAATTGTGTTTGGGGACTTTGGTATTAATGTCTTTGTGTTATAAATGTG
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGGTATTAATGTCTCTGTGTTATAAATGTG
9571 TTTGAGGACTTTAGAAAGAG
66 TTTGAGGACTTTAGAAAGAG
*
9591 AATTACCCCTGTGTTATAAATGTGTTTGGGGACTTTGGTA-TAGATGTCTCTGTGTTATAAATGT
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGGTATTA-ATGTCTCTGTGTTATAAATGT
9655 GTTTGAGGACTTTAGAAAGAG
65 GTTTGAGGACTTTAGAAAGAG
*
9676 AATTGCCCCTGTATTATAAATGTGTTTGGGGACTTTGGT
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGGT
9715 TATTTGGGTA
Statistics
Matches: 189, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
83 29 0.15
84 42 0.22
85 118 0.62
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (85 bp):
AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGGTATTAATGTCTCTGTGTTATAAATGTG
TTTGAGGACTTTAGAAAGAG
Found at i:13103 original size:30 final size:30
Alignment explanation
Indices: 13069--13132 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
13059 TCATACTAAC
* * *
13069 AAAAGAAATTTGTTTATGATCCTCTTTGAA
1 AAAAGAAATTTGCTTATGAACCTCTTTAAA
*
13099 AAAAGATATTTGCTTATGAACCTCTTTAAA
1 AAAAGAAATTTGCTTATGAACCTCTTTAAA
13129 AAAA
1 AAAA
13133 ATTGATACCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (30 bp):
AAAAGAAATTTGCTTATGAACCTCTTTAAA
Found at i:14525 original size:2 final size:2
Alignment explanation
Indices: 14518--14546 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14508 GCAGGTGTAC
14518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14547 AAATTAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27257 original size:2 final size:2
Alignment explanation
Indices: 27250--27274 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27240 TCCTCGATCG
27250 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27275 GCTAGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27583 original size:2 final size:2
Alignment explanation
Indices: 27543--27567 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27533 TTATAGAGAT
27543 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
27568 TTCTACTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30827 original size:3 final size:3
Alignment explanation
Indices: 30819--30847 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30809 ATTGCATGAC
30819 ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30848 TACAAGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:37450 original size:21 final size:21
Alignment explanation
Indices: 37426--37466 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
37416 TATCTTAGAT
*
37426 ATAATATATACTA-TTAAATAA
1 ATAATAAATA-TATTTAAATAA
37447 ATAATAAATATATTTAAATA
1 ATAATAAATATATTTAAATA
37467 GTAAATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATAAATATATTTAAATAA
Found at i:53637 original size:80 final size:80
Alignment explanation
Indices: 53516--53676 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
53506 CAAAATATTT
53516 CAGCATAGAACTTGATCACGCTTGTATAACTAGCTCAGATGATCCATAGGCAGTCTCATAGAGTA
1 CAGCATAGAACTTGATCACGCTTGTATAACTAGCTCAGATGATCCATAGGCAGTCTCATAGAGTA
53581 GCAAACAAAAGAACC
66 GCAAACAAAAGAACC
53596 CAGCATAGAACTTGATCACGCTTGTATAACTAGCTCAGATGATCCATAGGCAGTCTCATAGAGTA
1 CAGCATAGAACTTGATCACGCTTGTATAACTAGCTCAGATGATCCATAGGCAGTCTCATAGAGTA
53661 GCAAACAAAAGAACC
66 GCAAACAAAAGAACC
53676 C
1 C
53677 TAAAATGAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (80 bp):
CAGCATAGAACTTGATCACGCTTGTATAACTAGCTCAGATGATCCATAGGCAGTCTCATAGAGTA
GCAAACAAAAGAACC
Found at i:55388 original size:169 final size:160
Alignment explanation
Indices: 54993--56100 Score: 738
Period size: 160 Copynumber: 6.7 Consensus size: 160
54983 ACATTTAGCA
* *
54993 ACATAATCTTTTATGTTTTGACCTCATTAGTC-TTTC--AGCCACGTGTGAGTAATGGTTGTTAC
1 ACATAATCTTTTATATTTTGACCTCATTAGTCTTTTCATAGCCACGCGTGAGTAATGGTTGTTAC
* * * *
55055 ATGCAACTTACATGTATGTTCCACGTTGAATTATGCTGTCACGTGGACGTAAAATCCATAAATTT
66 ATGCAACTTACATGTACGTTCTACGTTGAATGATGTTGTCACGTGGACGTAAAATCCATAAATTT
* *
55120 TTGTTTCACTCAAATCAGATAAAGTAATG-T
131 TTGTTTTACTCAAAACAGATAAAGTAA-GAT
* * * * *
55150 ACGTAATCTTTTATGTTTTGACCTTATTAGTC-TTTCTGTAGCCACGCGTGAGCAATGGTTGTTA
1 ACATAATCTTTTATATTTTGACCTCATTAGTCTTTTC-ATAGCCACGCGTGAGTAATGGTTGTTA
* * * *
55214 CATGCAACTTACATGCACATT-TACGTTGAATGATGTTGTCATGTGGATGTAAAATCCATAAAAT
65 CATGCAACTTACATGTACGTTCTACGTTGAATGATGTTGTCACGTGGACGTAAAATCCAT-AAAT
55278 TTTTGTTTTACTCAAAACAGATAAAGTAAGAT
129 TTTTGTTTTACTCAAAACAGATAAAGTAAGAT
*
55310 ACATAATTGTTTTATATTTTGATCTCATTAGTTCATTAGTCTTTTCATAGCCACGCGTGAGTAAT
1 ACATAA-TCTTTTATATTTTGA-C-C------TCATTAGTCTTTTCATAGCCACGCGTGAGTAAT
* * * * *
55375 GGTTGTTACATGCAACTTACGTGTACGTTCCACGTTGAATGTTATTGTTACAG-GGACGTAAAAT
57 GGTTGTTACATGCAACTTACATGTACGTTCTACGTTGAATGATGTTGTCAC-GTGGACGTAAAAT
* *
55439 CCATAAAATTTTTGTTTTACTCAAAACAAATAAAGTAATAT
121 CCAT-AAATTTTTGTTTTACTCAAAACAGATAAAGTAAGAT
** * * * * * * * ** ** *
55480 ATGTAATCTTTAATGTTTTGACCTCATTTGTCTTTTCACAGTCACACGTGAATAATACTTAATAT
1 ACATAATCTTTTATATTTTGACCTCATTAGTCTTTTCATAGCCACGCGTGAGTAATGGTTGTTAC
* * * * ** ***
55545 ATG-TACATTACGTGTACATTCTACGTTGAATCATGTTGTCACGTGGATATATTCTCCATAAATT
66 ATGCAAC-TTACATGTACGTTCTACGTTGAATGATGTTGTCACGTGGACGTAAAATCCATAAATT
* * * * *
55609 TTTGTTTTA-TCCAAAAAAAATACGATATTTACAAAA
130 TTTGTTTTACT-CAAAACAGATA--A-A-GTA-AGAT
* * **** * ** * * * *
55645 ATATTAAACAAAAAAATAGGTTTGCTACACAAATTAGCCCTTAAACTTGACAAAAG-AATGACAA
1 ACA-TAATC--TTTTATA-TTTTG--AC-CTCATTAG-TCTT----TT--C-ATAGCCACG-C--
* * * ** * * *
55709 ATTA-TATACCTTAGTAATGGTTGTTACATGCAACTTACATGAACGTT-TCACGTTGAAT--T-A
48 GTGAGTA-A---TGGT--T-GTT-ACA-T-GCAACTTACATGTACGTTCT-ACGTTGAATGATGT
* *
55769 TGTCACGTGGACGTAAAATCCATAAATTTTTGTTTCACTCAAAACAGATAAAGTAAGGT
102 TGTCACGTGGACGTAAAATCCATAAATTTTTGTTTTACTCAAAACAGATAAAGTAAGAT
* * * *
55828 ACGTAAAT-TTTTATGTTTTGACCTCATTAGTCTTTCCGTAGCCACGCGTGAGTAATGGTTGTTA
1 ACAT-AATCTTTTATATTTTGACCTCATTAGTCTTTTCATAGCCACGCGTGAGTAATGGTTGTTA
* * * * * *
55892 CATGCAACTTACATGCACATT-TACGTTGAATGATGTTGTCATGTAGAAGTAAAATCTATAAAAT
65 CATGCAACTTACATGTACGTTCTACGTTGAATGATGTTGTCACGTGGACGTAAAATCCAT-AAAT
55956 TTTTGTTTTACTCAAAACAGATAAAGTAAGAT
129 TTTTGTTTTACTCAAAACAGATAAAGTAAGAT
* *
55988 ACATAATTGTTTTATATTTTGATCTCATTAGTTCATTAGTCTTTTCATAGCCACGCGTGGGTAAT
1 ACATAA-TCTTTTATATTTTGA-C-C------TCATTAGTCTTTTCATAGCCACGCGTGAGTAAT
* *
56053 GGTTGTTACATGCAACTTACGTGTACGTTCCACGTTGAATGATGTTGT
57 GGTTGTTACATGCAACTTACATGTACGTTCTACGTTGAATGATGTTGT
56101 TACAAGG
Statistics
Matches: 735, Mismatches: 142, Indels: 135
0.73 0.14 0.13
Matches are distributed among these distances:
156 9 0.01
157 51 0.07
158 1 0.00
159 57 0.08
160 146 0.20
161 100 0.14
162 3 0.00
163 6 0.01
164 2 0.00
165 4 0.01
166 7 0.01
167 3 0.00
168 7 0.01
169 126 0.17
170 90 0.12
171 4 0.01
172 5 0.01
173 3 0.00
175 3 0.00
176 6 0.01
177 4 0.01
179 6 0.01
180 6 0.01
181 2 0.00
182 4 0.01
183 4 0.01
184 2 0.00
185 4 0.01
186 1 0.00
187 1 0.00
188 41 0.06
189 4 0.01
190 1 0.00
191 20 0.03
192 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (160 bp):
ACATAATCTTTTATATTTTGACCTCATTAGTCTTTTCATAGCCACGCGTGAGTAATGGTTGTTAC
ATGCAACTTACATGTACGTTCTACGTTGAATGATGTTGTCACGTGGACGTAAAATCCATAAATTT
TTGTTTTACTCAAAACAGATAAAGTAAGAT
Done.