Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021616.1 Corchorus olitorius cultivar O-4 contig21649, 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: 30048
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6439 original size:22 final size:22
Alignment explanation
Indices: 6414--6483 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
6404 TTCTGAGGCG
6414 TAATTGCAGGAATTTTTCGGAA
1 TAATTGCAGGAATTTTTCGGAA
* * ** **
6436 TAATAG--GGATAATTCTGAGGCG
1 TAATTGCAGG--AATTTTTCGGAA
6458 TAATTGCAGGAATTTTTCGGAA
1 TAATTGCAGGAATTTTTCGGAA
6480 TAAT
1 TAAT
6484 AGGGATAATT
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 2 0.06
22 28 0.88
24 2 0.06
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (22 bp):
TAATTGCAGGAATTTTTCGGAA
Found at i:6462 original size:44 final size:44
Alignment explanation
Indices: 6399--6495 Score: 194
Period size: 44 Copynumber: 2.2 Consensus size: 44
6389 CTTTATTCTT
6399 GATAATTCTGAGGCGTAATTGCAGGAATTTTTCGGAATAATAGG
1 GATAATTCTGAGGCGTAATTGCAGGAATTTTTCGGAATAATAGG
6443 GATAATTCTGAGGCGTAATTGCAGGAATTTTTCGGAATAATAGG
1 GATAATTCTGAGGCGTAATTGCAGGAATTTTTCGGAATAATAGG
6487 GATAATTCT
1 GATAATTCT
6496 AGGAATTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (44 bp):
GATAATTCTGAGGCGTAATTGCAGGAATTTTTCGGAATAATAGG
Found at i:6493 original size:22 final size:22
Alignment explanation
Indices: 6424--6493 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
6414 TAATTGCAGG
6424 AATTTTTCGGAATAATAGGGAT
1 AATTTTTCGGAATAATAGGGAT
* ** ** *
6446 AATTCTGAGGCGTAATTGCAGG--
1 AATTTTTCGGAATAATAG--GGAT
6468 AATTTTTCGGAATAATAGGGAT
1 AATTTTTCGGAATAATAGGGAT
6490 AATT
1 AATT
6494 CTAGGAATTT
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 2 0.06
22 28 0.88
24 2 0.06
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (22 bp):
AATTTTTCGGAATAATAGGGAT
Found at i:6493 original size:31 final size:32
Alignment explanation
Indices: 6465--6524 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
6455 GCGTAATTGC
*
6465 AGGAATTTTTCGGAATAATAGGG-ATAATTCT
1 AGGAATTTTTCAGAATAATAGGGAATAATTCT
6496 AGGAATTTTTCAGAATAATAGGGAATAAT
1 AGGAATTTTTCAGAATAATAGGGAATAAT
6525 AGGGACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (32 bp):
AGGAATTTTTCAGAATAATAGGGAATAATTCT
Found at i:7884 original size:20 final size:21
Alignment explanation
Indices: 7843--7885 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7833 AAGATCATAC
* *
7843 ATGGTTCCCCACATGTACTTG
1 ATGGTTCACAACATGTACTTG
7864 ATGGTTCACAACATG-ACTTG
1 ATGGTTCACAACATGTACTTG
7884 AT
1 AT
7886 TTCACCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGGTTCACAACATGTACTTG
Found at i:7889 original size:18 final size:20
Alignment explanation
Indices: 7853--7890 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7843 ATGGTTCCCC
7853 ACATGTACTTGATGGTTCACA
1 ACATGTACTTGAT-GTTCACA
7874 ACATG-ACTTGAT-TTCAC
1 ACATGTACTTGATGTTCAC
7891 CTTAATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (20 bp):
ACATGTACTTGATGTTCACA
Found at i:13981 original size:22 final size:22
Alignment explanation
Indices: 13956--14014 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
13946 CCCCACAATA
* *
13956 AAATTTTAATAACCTTCTTATG
1 AAATTTTGATAACCTTATTATG
* *
13978 AAATTTTGGTAACCATATTATG
1 AAATTTTGATAACCTTATTATG
*
14000 AAATTTCGATAACCT
1 AAATTTTGATAACCT
14015 CCCCCTGAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTTATTATG
Found at i:14142 original size:21 final size:20
Alignment explanation
Indices: 14083--14164 Score: 85
Period size: 22 Copynumber: 4.0 Consensus size: 20
14073 ATTATCCTCC
*
14083 CTATGAAATTTTGGTAACCAT
1 CTATGAAATTTTGATAACC-T
*
14104 ACTATGAAATTGTGATAACCT
1 -CTATGAAATTTTGATAACCT
* *
14125 CCTTATG-GATTTTGATAATCT
1 -C-TATGAAATTTTGATAACCT
14146 CTATGAAATTTTGATAACC
1 CTATGAAATTTTGATAACC
14165 ACGCATTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
19 4 0.08
20 12 0.24
21 13 0.26
22 21 0.42
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
CTATGAAATTTTGATAACCT
Found at i:14360 original size:22 final size:21
Alignment explanation
Indices: 14323--14422 Score: 105
Period size: 22 Copynumber: 4.7 Consensus size: 21
14313 ACTTTTATAG
* * *
14323 GGAGATTATCAGAATTTCGTA
1 GGAGGTTATCAAAATTTCATA
*
14344 GTATGGTTATCAAAATTTCATAA
1 GGA-GGTTATCAAAATTTCAT-A
*
14367 GGAGGTTATCAAAATTTTATA
1 GGAGGTTATCAAAATTTCATA
14388 GGGAGGTTATCAAAATTTCATA
1 -GGAGGTTATCAAAATTTCATA
*
14410 -GTGGTTA-CAAAAT
1 GGAGGTTATCAAAAT
14423 GATCGTAAGA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.09
20 6 0.09
21 3 0.04
22 50 0.74
23 3 0.04
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (21 bp):
GGAGGTTATCAAAATTTCATA
Found at i:14396 original size:44 final size:43
Alignment explanation
Indices: 14348--15331 Score: 345
Period size: 44 Copynumber: 22.8 Consensus size: 43
14338 TTCGTAGTAT
*
14348 GGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTTATAGGGA
1 GGTTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGGGA
* * * * *
14392 GGTTATCAAAATTTCATA-GTGGTTA-CAAAATGATCGTAAGAA
1 GGTTATCAAAATTTCATAGGAGGTTATCAAAAT-TTCATAGGGA
** * * * * * *
14434 GGATATAAAAATCTCAATTTTATAAGGATGTTATCATAATTTTATAGTGT
1 GG-T-T----ATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGGGA
* * *
14484 GTTTATCAAAATTTCATAAAGAGCTTATCAAAA--TC-T----A
1 GGTTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGGGA
* * *
14521 --TTATCAAAATTTCATAGAGATCAGATTATCAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAG-G---AGGTTATCAAAATTTCATAGGGA
* * * *
14566 AGTTATCAAAATTTTATAAGGAGGTTATCAAAATTTCAAAGCGA
1 GGTTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGGGA
* * * *
14610 GGTTATCAAAACTTCATAGCGTGGTTATCAAAATCTCATAGTGA
1 GGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGGGA
* * * * *
14654 GGTCATCACAATTTCATGGTGTGGTTTTCAAAATTTCAT-GTGGA
1 GGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAG-GGA
* * * *
14698 GGTTA-CAAAATTTTATAGGATGGTTATGAAAATTTCATCGAGA
1 GGTTATCAAAATTTCATAGGA-GGTTATCAAAATTTCATAGGGA
* * * *
14741 CGTTAACAAAATTTCATA-GA-G-TATCAAATTTTCATATGGA
1 GGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGGGA
* * *
14781 GGTTATCAAAATTTCAGAGTGTGGTTATCAAAATTT--TAGGGT
1 GGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGGGA
* ** *
14823 GTGGTAT-ATCA--T-ATA-AAGGTTATCAAAATTTCAT-GGTGTA
1 G-GTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGG-G-A
* * * * * *
14863 -GTTA-CCAAA-TT-A-CGAAGGTTATTAAAATTTTATTGTGGA
1 GGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAG-GGA
* *
14902 -GTTATCAAAATTTCATAGGCAGGTTATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAGG-AGGTTATCAAAATTTCATAGGGA
* * * * ***
14945 TGTTACCAAAATGTT-ATAAGGAGGTTATCTAAATGTCATAATTTA
1 GGTTATCAAAAT-TTCAT-AGGAGGTTATCAAAATTTCAT-AGGGA
** ** *
14990 AATT-TCAAAATTTCATA-G-TTTTGTTCAAAATTTCATA-GGA
1 GGTTATCAAAATTTCATAGGAGGTT-ATCAAAATTTCATAGGGA
** * * *
15030 GGTTATCAAAAAATCATAGGTGGTTATCAAAACTTCATAAGGA
1 GGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGGGA
* * * * * ** *
15073 GGTTATCGAAATTTTATAATGTGTTTTATCAAAATTTTGTAGGAA
1 GGTTATCAAAATTTCAT-AGGAG-GTTATCAAAATTTCATAGGGA
* ** * * ** *
15118 TGTTTATCACGATTTTATAGTGAGATTATCAAAATTTCATACTGT
1 -GGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGGGA
* * * * *
15163 GATTATCAAAATTTCACAGTGTGATTA-CTAACATTTCATAGGGA
1 GGTTATCAAAATTTCATAG-GAGGTTATC-AAAATTTCATAGGGA
* * * * * *
15207 GGTT-TCCAAAAGTTT-ATAGTGTGCTTACCAACATTTCACAAGGA
1 GGTTAT-CAAAA-TTTCATAG-GAGGTTATCAAAATTTCATAGGGA
** *** * *
15251 CATTATCAAAATTTCATAGCGTTCTTATCAAAATTTCATTGAGA
1 GGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGGGA
* *
15295 GGTTATCAAAATTTTATATTGG-GGTTTTCAAAATTTC
1 GGTTATCAAAATTTCATA--GGAGGTTATCAAAATTTC
15332 TTAGACATGT
Statistics
Matches: 696, Mismatches: 174, Indels: 140
0.69 0.17 0.14
Matches are distributed among these distances:
34 1 0.00
35 16 0.02
37 14 0.02
38 17 0.02
39 28 0.04
40 41 0.06
41 26 0.04
42 48 0.07
43 72 0.10
44 326 0.47
45 47 0.07
46 16 0.02
47 15 0.02
48 13 0.02
49 2 0.00
50 9 0.01
51 5 0.01
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGGGA
Found at i:14630 original size:22 final size:21
Alignment explanation
Indices: 14521--15331 Score: 256
Period size: 22 Copynumber: 37.6 Consensus size: 21
14511 TCAAAATCTA
*
14521 TTATCAAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCATAG-G---AGG
* *
14546 TTATCAAAATTTCATAAGAAAG
1 TTATCAAAATTTCAT-AGGAGG
*
14568 TTATCAAAATTTTATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
14590 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* *
14612 TTATCAAAACTTCATAGCGTGG
1 TTATCAAAATTTCATAG-GAGG
*
14634 TTATCAAAATCTCATAGTGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
14656 TCATCACAATTTCATGGTGTGG
1 TTATCAAAATTTCATAG-GAGG
* *
14678 TTTTCAAAATTTCATGTGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
14700 TTA-CAAAATTTTATAGGATGG
1 TTATCAAAATTTCATAGGA-GG
* * *
14721 TTATGAAAATTTCATCGAGACG
1 TTATCAAAATTTCATAG-GAGG
*
14743 TTAACAAAATTTCATA-GA-G
1 TTATCAAAATTTCATAGGAGG
*
14762 -TATCAAATTTTCATATGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
14783 TTATCAAAATTTCAGAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
14805 TTATCAAAATTT--TAGG-GTG
1 TTATCAAAATTTCATAGGAG-G
** *
14824 TGGTAT-ATCA--T-ATA-AAGG
1 T--TATCAAAATTTCATAGGAGG
*
14842 TTATCAAAATTTCAT-GGTGTAG
1 TTATCAAAATTTCATAGGAG--G
* * *
14864 TTA-CCAAA-TT-A-CGAAGG
1 TTATCAAAATTTCATAGGAGG
* * *
14881 TTATTAAAATTTTATTGTG-GAG
1 TTATCAAAATTTCATAG-GAG-G
14903 TTATCAAAATTTCATAGGCAGG
1 TTATCAAAATTTCATAGG-AGG
* *
14925 TTATCAAAATTTCATATGAATG
1 TTATCAAAATTTCATA-GGAGG
*
14947 TTACCAAAATGTT-ATAAGGAGG
1 TTATCAAAAT-TTCAT-AGGAGG
* * ** **
14969 TTATCTAAATGTCATAATTTAAA
1 TTATCAAAATTTCAT-A-GGAGG
* * *
14992 TT-TC-AAAATT--TCA-TAGTT
1 TTATCAAAATTTCAT-AGGAG-G
*
15010 TTGTTCAAAATTTCATAGGAGG
1 TT-ATCAAAATTTCATAGGAGG
** *
15032 TTATCAAAAAATCATAGGTGG
1 TTATCAAAATTTCATAGGAGG
*
15053 TTATCAAAACTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* * * * *
15075 TTATCGAAATTTTATAATGTGTT
1 TTATCAAAATTTCAT-AGGAG-G
** *
15098 TTATCAAAATTTTGTAGGAATGT
1 TTATCAAAATTTCATAGG-A-GG
** * *
15121 TTATCACGATTTTATAGTGAGA
1 TTATCAAAATTTCATAG-GAGG
* * *
15143 TTATCAAAATTTCATACTGTGA
1 TTATCAAAATTTCATA-GGAGG
* * *
15165 TTATCAAAATTTCACAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
*
15187 TTA-CTAACATTTCATAGGGAGG
1 TTATC-AAAATTTCATA-GGAGG
* *
15209 TT-TCCAAAAGTTT-ATAGTGTGC
1 TTAT-CAAAA-TTTCATAG-GAGG
* * * **
15231 TTACCAACATTTCACAAGGACA
1 TTATCAAAATTTCA-TAGGAGG
***
15253 TTATCAAAATTTCATAGCGTTC
1 TTATCAAAATTTCATAG-GAGG
*
15275 TTATCAAAATTTCATTGAGAGG
1 TTATCAAAATTTCATAG-GAGG
*
15297 TTATCAAAATTTTATATTGG-GG
1 TTATCAAAATTTCATA--GGAGG
*
15319 TTTTCAAAATTTC
1 TTATCAAAATTTC
15332 TTAGACATGT
Statistics
Matches: 589, Mismatches: 134, Indels: 129
0.69 0.16 0.15
Matches are distributed among these distances:
16 3 0.01
17 8 0.01
18 22 0.04
19 15 0.03
20 19 0.03
21 74 0.13
22 377 0.64
23 51 0.09
24 3 0.01
25 15 0.03
26 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:14637 original size:66 final size:63
Alignment explanation
Indices: 14521--15331 Score: 291
Period size: 66 Copynumber: 12.6 Consensus size: 63
14511 TCAAAATCTA
* * **
14521 TTATCAAAATTTCATAGAGATCAGATTATCAAAATTTCATAAGAAAGTTATCAAAATTTTATAAG
1 TTATCAAAATTTCAT--AG-TGAGGTTATCAAAATTTCAT-AG-GGGTTATCAAAATTTTAT-AG
14586 GAGG
60 GAGG
* * * * *
14590 TTATCAAAATTTCAAAGCGAGGTTATCAAAACTTCATAGCGTGGTTATCAAAATCTCATAGTGAG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAG-G-GGTTATCAAAATTTTATAG-GAG
14655 G
63 G
* * * * * *
14656 TCATCACAATTTCATGGTGTGGTTTTCAAAATTTCATGTGGAGGTTA-CAAAATTTTATAGGATG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT-AGG-GGTTATCAAAATTTTATAGGA-G
14720 G
63 G
* * * * * *
14721 TTATGAAAATTTCATCGAGACGTTAACAAAATTTCATA-GAG-TATC-AAATTTTCATATGGAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGGTTATCAAAATTTT-ATA-GGAGG
* * ** * ** *
14783 TTATCAAAATTTCAGAGTGTGGTTATCAAAATTT--TAGGGTGTGGT--ATATCATATA-AAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGG-GTTATCAAAATTTTATAGGAGG
* * * * *
14842 TTATCAAAATTTCATGGTGTA-GTTA-CCAAATTACGA-A--GGTTATTAAAATTTTATTGTG-G
1 TTATCAAAATTTCATAGTG-AGGTTATCAAAATTTC-ATAGGGGTTATCAAAATTTTATAG-GAG
14901 AG
63 -G
** * *
14903 TTATCAAAATTTCATAG-GCAGGTTATCAAAATTTCATATGAATGTTACCAAAATGTTATAAGGA
1 TTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATA-G-GGGTTATCAAAATTTTAT-AGGA
14967 GG
62 GG
* * * * ** ** * *
14969 TTATCTAAATGTCATAATTTAAATT-TCAAAATTTCATA-GTTTTGTTCAAAATTTCATAGGAGG
1 TTATCAAAATTTCAT-AGTGAGGTTATCAAAATTTCATAGGGGTT-ATCAAAATTTTATAGGAGG
** * * * * *
15032 TTATCAAAAAATCATAG-GTGGTTATCAAAACTTCATAAGGAGGTTATCGAAATTTTATAATGTG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT-AGG-GGTTATCAAAATTTTAT-AGGAG
*
15096 TT
63 -G
** * ** * * * *
15098 TTATCAAAATTTTGTAG-GAATGTTTATCACGATTTTATAGTGAGATTATCAAAATTTCATACTG
1 TTATCAAAATTTCATAGTG-A-GGTTATCAAAATTTCATAG-G-GGTTATCAAAATTTTATA-GG
* *
15162 TGA
61 AGG
* * * * *
15165 TTATCAAAATTTCACAGTGTGATTA-CTAACATTTCATAGGGAGGTT-TCCAAAAGTTTATAGTG
1 TTATCAAAATTTCATAGTGAGGTTATC-AAAATTTCATA-GG-GGTTAT-CAAAATTTTATAG-G
* *
15228 TGC
61 AGG
* * * ** ** * *
15231 TTACCAACATTTCACAAG-GACATTATCAAAATTTCATAGCGTTCTTATCAAAATTTCATTGAGA
1 TTATCAAAATTTCA-TAGTGAGGTTATCAAAATTTCATAG-G-GGTTATCAAAATTTTATAG-GA
15295 GG
62 GG
* * * *
15297 TTATCAAAATTTTATATTGGGGTTTTCAAAATTTC
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTC
15332 TTAGACATGT
Statistics
Matches: 543, Mismatches: 148, Indels: 105
0.68 0.19 0.13
Matches are distributed among these distances:
57 3 0.01
58 7 0.01
59 30 0.06
60 6 0.01
61 37 0.07
62 59 0.11
63 27 0.05
64 22 0.04
65 54 0.10
66 220 0.41
67 31 0.06
68 33 0.06
69 14 0.03
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (63 bp):
TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGGTTATCAAAATTTTATAGGAGG
Found at i:15478 original size:22 final size:22
Alignment explanation
Indices: 15453--15512 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
15443 AATAGTATAA
15453 TTATCATAATTTCATAGGGAGG
1 TTATCATAATTTCATAGGGAGG
* * * *
15475 TTATTATAATTTCATAGTGTGT
1 TTATCATAATTTCATAGGGAGG
*
15497 TTATCAAAATTTCATA
1 TTATCATAATTTCATA
15513 TGAATATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (22 bp):
TTATCATAATTTCATAGGGAGG
Found at i:17949 original size:21 final size:21
Alignment explanation
Indices: 17917--18081 Score: 197
Period size: 21 Copynumber: 7.9 Consensus size: 21
17907 TATATGAAAC
* *
17917 TTTGGGGTTTGACTAGCAAAA
1 TTTGGGGGTTGACTATCAAAA
* * *
17938 TTCGGGGGTTGACCATCAAAC
1 TTTGGGGGTTGACTATCAAAA
*
17959 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGGTTGACTATCAAAA
* * *
17980 TTAGGGGTTTGACAATCAAAA
1 TTTGGGGGTTGACTATCAAAA
*
18001 TTTGGGTGTTGACTATCAAAA
1 TTTGGGGGTTGACTATCAAAA
* *
18022 TTTGGGGGTTGACCATCAAAC
1 TTTGGGGGTTGACTATCAAAA
*
18043 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGGTTGACTATCAAAA
*
18064 TTT-GGGGTTGACCATCAA
1 TTTGGGGGTTGACTATCAA
18082 TGAGATTTGA
Statistics
Matches: 121, Mismatches: 23, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
20 13 0.11
21 108 0.89
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (21 bp):
TTTGGGGGTTGACTATCAAAA
Found at i:17972 original size:42 final size:41
Alignment explanation
Indices: 17913--18081 Score: 250
Period size: 42 Copynumber: 4.0 Consensus size: 41
17903 GAAATATATG
*
17913 AAACTTTGGGGTTTGACTAGCAAAATTCGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATT-GGGGGTTGACCATC
* *
17955 AAACTTTGGGGTTTGACTATCAAAATTAGGGGTTTGACAATC
1 AAACTTTGGGGTTTGACTATCAAAATT-GGGGGTTGACCATC
*
17997 AAAATTT-GGGTGTTGACTATCAAAATTTGGGGGTTGACCATC
1 AAACTTTGGGGT-TTGACTATCAAAA-TTGGGGGTTGACCATC
*
18039 AAACTTTGGGGTTTGACTATCAAAATTTGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTGGGGGTTGACCATC
18080 AA
1 AA
18082 TGAGATTTGA
Statistics
Matches: 115, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
41 21 0.18
42 88 0.77
43 6 0.05
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (41 bp):
AAACTTTGGGGTTTGACTATCAAAATTGGGGGTTGACCATC
Found at i:19860 original size:178 final size:176
Alignment explanation
Indices: 19541--20003 Score: 486
Period size: 178 Copynumber: 2.6 Consensus size: 176
19531 ATACCTATCA
** * * * *
19541 AGGTGATTTAAGTGTCTATTAAAAGGTTGTTTCATGATTTACAACTTTCATGAAGACTCGAAAAC
1 AGGTGATCCAAGTGTCTA-TAAAAGGTTGTTTCATGATCTACAACTTTCATGAGGATTCGAAAGC
* *
19606 TAAATTTAATATTTCAAGTATCAAAAAA-GCTTCCGAATAATTAGTTGTTTCGGTTAGCGGGAAT
65 TAAATTTAATATTTCAAGTAT-AAAAAATGCTTCCGAAAAATTAATTGTTTCGGTTAGCGGGAAT
* * * ***
19670 GGACGATCCACTTAGT-ATAACATTACTTTTGCTCCAGATGTCTTCTTG
129 GAACGATCCACTTAATAAT-ACATAACTTTTGCTCCAGATGTCCGATTG
* * * *
19718 AGTTGATCCAAGTGTCTCATAAAAGATTATTTTATGATCTACAACTTTCATGCAGGATTCGAAAG
1 AGGTGATCCAAGTGTCT-ATAAAAGGTTGTTTCATGATCTACAACTTTCATG-AGGATTCGAAAG
* * * *
19783 TTAAATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAATTTTTTCGGTTAG-GGAGAA
64 CTAAATTTAATATTTCAAGTATAAAAAATGCTTCCGAAAAATTAATTGTTTCGGTTAGCGG-GAA
* *
19847 TGAAC-AGTCCACTTAATAATACATAATTTTTGCTTCAGATGTCCGATTG
128 TGAACGA-TCCACTTAATAATACATAACTTTTGCTCCAGATGTCCGATTG
** * * *
19896 AGGTGATTTAAGTGTCTGTTAAAAGGTTGTTTCATGATCTTCAGCTTTCATGTAGGACTT-GAAA
1 AGGTGATCCAAGTGTCT-ATAAAAGGTTGTTTCATGATCTACAACTTTCATG-AGGA-TTCGAAA
* * * ** *
19960 GCTAAATTTTATTTTTCAAATACCAAAAATGCTTCTGAAAAATT
63 GCTAAATTTAATATTTCAAGTATAAAAAATGCTTCCGAAAAATT
20004 TATATTTCGG
Statistics
Matches: 236, Mismatches: 43, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
177 52 0.22
178 180 0.76
179 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (176 bp):
AGGTGATCCAAGTGTCTATAAAAGGTTGTTTCATGATCTACAACTTTCATGAGGATTCGAAAGCT
AAATTTAATATTTCAAGTATAAAAAATGCTTCCGAAAAATTAATTGTTTCGGTTAGCGGGAATGA
ACGATCCACTTAATAATACATAACTTTTGCTCCAGATGTCCGATTG
Found at i:28024 original size:18 final size:18
Alignment explanation
Indices: 28001--28103 Score: 98
Period size: 18 Copynumber: 5.1 Consensus size: 18
27991 ACAAGTGGTT
28001 ATGATTTAGATAAAAGTA
1 ATGATTTAGATAAAAGTA
28019 ATGATTTAGATGAAAGTTATGATA
1 ATGATTTAGAT-AAA---A-G-TA
28043 ATGATTTAGATAAAAGTA
1 ATGATTTAGATAAAAGTA
28061 ATGATTTAGATGAAAGTTATGATA
1 ATGATTTAGAT-AAA---A-G-TA
28085 ATGATTTAGATAAAAGTA
1 ATGATTTAGATAAAAGTA
28103 A
1 A
28104 GTAGTTCAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 24
0.75 0.00 0.25
Matches are distributed among these distances:
18 27 0.37
19 8 0.11
20 2 0.03
22 2 0.03
23 8 0.11
24 26 0.36
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (18 bp):
ATGATTTAGATAAAAGTA
Found at i:28044 original size:24 final size:24
Alignment explanation
Indices: 28017--28101 Score: 119
Period size: 24 Copynumber: 3.8 Consensus size: 24
28007 TAGATAAAAG
28017 TAATGATTTAGATGAAAGTTATGA
1 TAATGATTTAGATGAAAGTTATGA
28041 TAATGATTTAGAT-AAA---A-G-
1 TAATGATTTAGATGAAAGTTATGA
28059 TAATGATTTAGATGAAAGTTATGA
1 TAATGATTTAGATGAAAGTTATGA
*
28083 TAATGATTTAGATAAAAGT
1 TAATGATTTAGATGAAAGT
28102 AAGTAGTTCA
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
18 13 0.24
19 4 0.07
20 1 0.02
22 1 0.02
23 4 0.07
24 31 0.57
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (24 bp):
TAATGATTTAGATGAAAGTTATGA
Found at i:28060 original size:42 final size:42
Alignment explanation
Indices: 28001--28103 Score: 206
Period size: 42 Copynumber: 2.5 Consensus size: 42
27991 ACAAGTGGTT
28001 ATGATTTAGATAAAAGTAATGATTTAGATGAAAGTTATGATA
1 ATGATTTAGATAAAAGTAATGATTTAGATGAAAGTTATGATA
28043 ATGATTTAGATAAAAGTAATGATTTAGATGAAAGTTATGATA
1 ATGATTTAGATAAAAGTAATGATTTAGATGAAAGTTATGATA
28085 ATGATTTAGATAAAAGTAA
1 ATGATTTAGATAAAAGTAA
28104 GTAGTTCAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (42 bp):
ATGATTTAGATAAAAGTAATGATTTAGATGAAAGTTATGATA
Found at i:29309 original size:21 final size:21
Alignment explanation
Indices: 29283--29324 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29273 TAAGGAAGAA
29283 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
29304 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
29325 TCTAAGATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Done.