Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011944.1 Corchorus olitorius cultivar O-4 contig11977, 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: 45725
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:6485 original size:16 final size:16
Alignment explanation
Indices: 6464--6569 Score: 126
Period size: 16 Copynumber: 6.6 Consensus size: 16
6454 CGGGCTCGGG
*
6464 CGGGTTTGGGTATTTT
1 CGGGTTCGGGTATTTT
6480 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* **
6496 CGGGCTCGGGT-TAAGT
1 CGGGTTCGGGTAT-TTT
6512 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
6528 CGGGCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
6544 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
6560 CGGGTTCGGG
1 CGGGTTCGGG
6570 CTCGGGTAGG
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
15 2 0.03
16 71 0.95
17 2 0.03
ACGTcount: A:0.07, C:0.14, G:0.42, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:6516 original size:32 final size:32
Alignment explanation
Indices: 6479--6569 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
6469 TTGGGTATTT
6479 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
*
6511 TCGGGTTCGGGTATTTTCGGGCTCGGGTTATG
1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
*
6543 TCGGGTTCGGGTATTTTCGGGTTCGGG
1 TCGGGTTCGGGTATTTTCGGGCTCGGG
6570 CTCGGGTAGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.07, C:0.15, G:0.42, T:0.36
Consensus pattern (32 bp):
TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
Found at i:6588 original size:23 final size:23
Alignment explanation
Indices: 6558--6606 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
6548 TTCGGGTATT
*
6558 TTCGGGTTCGGGCTCGGGTAGGG
1 TTCGGGTTCAGGCTCGGGTAGGG
*
6581 TTCGGGTTCAGGCTCGGGTCGGG
1 TTCGGGTTCAGGCTCGGGTAGGG
6604 TTC
1 TTC
6607 AGGCTTGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.04, C:0.20, G:0.47, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCAGGCTCGGGTAGGG
Found at i:6602 original size:17 final size:17
Alignment explanation
Indices: 6582--6616 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6572 CGGGTAGGGT
6582 TCGGGTTCAGGCTCGGG
1 TCGGGTTCAGGCTCGGG
*
6599 TCGGGTTCAGGCTTGGG
1 TCGGGTTCAGGCTCGGG
6616 T
1 T
6617 TTGATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.20, G:0.46, T:0.29
Consensus pattern (17 bp):
TCGGGTTCAGGCTCGGG
Found at i:9231 original size:146 final size:146
Alignment explanation
Indices: 8967--9239 Score: 537
Period size: 146 Copynumber: 1.9 Consensus size: 146
8957 CTTTGATTTG
*
8967 GTCTTCTACTGCAGGGTGGAAAACTCTGGCATGTTGCTTGACTGGCTTGGCATCAGGCCGAACAT
1 GTCTTCTACTGCAGGGTGGAAAACTCTGGCATGTTGCTTGACTGGCTTGACATCAGGCCGAACAT
9032 TCAATGAGTGGGCCACCATAGTAGGATCCAGGCCCGGCATGTCTTTGTAGCTCCACACAAAGTAA
66 TCAATGAGTGGGCCACCATAGTAGGATCCAGGCCCGGCATGTCTTTGTAGCTCCACACAAAGTAA
9097 GATCCAGGCCCGACAT
131 GATCCAGGCCCGACAT
9113 GTCTTCTACTGCAGGGTGGAAAACTCTGGCATGTTGCTTGACTGGCTTGACATCAGGCCGAACAT
1 GTCTTCTACTGCAGGGTGGAAAACTCTGGCATGTTGCTTGACTGGCTTGACATCAGGCCGAACAT
9178 TCAATGAGTGGGCCACCATAGTAGGATCCAGGCCCGGCATGTCTTTGTAGCTCCACACAAAG
66 TCAATGAGTGGGCCACCATAGTAGGATCCAGGCCCGGCATGTCTTTGTAGCTCCACACAAAG
9240 ACATCTTCAT
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 126 1.00
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.24
Consensus pattern (146 bp):
GTCTTCTACTGCAGGGTGGAAAACTCTGGCATGTTGCTTGACTGGCTTGACATCAGGCCGAACAT
TCAATGAGTGGGCCACCATAGTAGGATCCAGGCCCGGCATGTCTTTGTAGCTCCACACAAAGTAA
GATCCAGGCCCGACAT
Found at i:9801 original size:223 final size:223
Alignment explanation
Indices: 9413--9860 Score: 824
Period size: 223 Copynumber: 2.0 Consensus size: 223
9403 CCGCATGCTC
9413 GGGATTCACAAGATTGCAGTCATTACAGCTACTGGTGTTGGGATCTCCTTGAGGATCTTTAGGAG
1 GGGATTCACAAGATTGCAGTCATTACAGCTACTGGTGTTGGGATCTCCTTGAGGATCTTTAGGAG
* *
9478 ACCCCGTACACCTTCATAAGCGATAGACTACCTTCCCGCTAGGATAGACAGTCTTGCGGCATTGT
66 ACCCCGCACACCTTCATAAGCGATAGACTACCTTCCCGCTAGGACAGACAGTCTTGCGGCATTGT
* *
9543 GGTGAAGATTGTATCATTTTCTGCTTCTTGCGATCAAGCGCAGCTCGGAGATCCCAGTCTGTATC
131 GGTGAAAATTGTATCATTTTCTGCTTCTTGCGATCAAGCGCAGCTCGGAGATCCCAGTCTGGATC
9608 GTCTCGGATGTCTTCCAATCTGGGCAAA
196 GTCTCGGATGTCTTCCAATCTGGGCAAA
9636 GGGATTCACAAGATTGCAGTCATTACAGCTACTGGTGTTGGGATCTCCTTGAGGATCTTTAGGAG
1 GGGATTCACAAGATTGCAGTCATTACAGCTACTGGTGTTGGGATCTCCTTGAGGATCTTTAGGAG
*
9701 ACCCTGCACACCTTCATAAGCGATAGACTACCTTCCCGCTAGGACAGACAGTCTTGCGGCATTGT
66 ACCCCGCACACCTTCATAAGCGATAGACTACCTTCCCGCTAGGACAGACAGTCTTGCGGCATTGT
* *
9766 GGTGAAAATTGTGTCCTTTTCTGCTTCTTGCGATCAAGCGCAGCTCGGAGATCCCAGTCTGGATC
131 GGTGAAAATTGTATCATTTTCTGCTTCTTGCGATCAAGCGCAGCTCGGAGATCCCAGTCTGGATC
*
9831 GTCTCGGATGTCTTCCCATCTGGGCAAA
196 GTCTCGGATGTCTTCCAATCTGGGCAAA
9859 GG
1 GG
9861 AGTACCAGTC
Statistics
Matches: 217, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
223 217 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (223 bp):
GGGATTCACAAGATTGCAGTCATTACAGCTACTGGTGTTGGGATCTCCTTGAGGATCTTTAGGAG
ACCCCGCACACCTTCATAAGCGATAGACTACCTTCCCGCTAGGACAGACAGTCTTGCGGCATTGT
GGTGAAAATTGTATCATTTTCTGCTTCTTGCGATCAAGCGCAGCTCGGAGATCCCAGTCTGGATC
GTCTCGGATGTCTTCCAATCTGGGCAAA
Found at i:13510 original size:43 final size:42
Alignment explanation
Indices: 13463--13699 Score: 334
Period size: 43 Copynumber: 5.6 Consensus size: 42
13453 ATAAGGAGAA
*
13463 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
* *
13506 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
* *
13547 ATGCCTCTGTATTATATATGTGTTTGAGGACTTTGATATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGA-ATAGAG
* * *
13590 ATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGGATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
* * *
13631 ACGTCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGA-ATAGAG
13674 ATGCCCCTGTGTTATATATGTGTTTG
1 ATGCCCCTGTGTTATATATGTGTTTG
13700 GGGATTTTTG
Statistics
Matches: 169, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
41 69 0.41
42 6 0.04
43 94 0.56
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.42
Consensus pattern (42 bp):
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
Found at i:13575 original size:84 final size:84
Alignment explanation
Indices: 13463--13703 Score: 430
Period size: 84 Copynumber: 2.9 Consensus size: 84
13453 ATAAGGAGAA
13463 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAATAGAGATGCCCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAT-ATAGAGATGCCCCTGTGTTATATATGT
*
13527 GTTTGGGGACTTTGATATAG
65 GTTTGGGGACTTGGATATAG
*
13547 ATGCCTCTGTATTATATATGTGTTTGAGGACTTTGATATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAGAGATGCCCCTGTGTTATATATGTG
13612 TTTGGGGACTTGGATATAG
66 TTTGGGGACTTGGATATAG
* *
13631 ACGTCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAGAGATGCCCCTGTGTTATATATGTG
13696 TTTGGGGA
66 TTTGGGGA
13704 TTTTTGGTTA
Statistics
Matches: 151, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
84 150 0.99
85 1 0.01
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.41
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAGAGATGCCCCTGTGTTATATATGTG
TTTGGGGACTTGGATATAG
Found at i:16409 original size:22 final size:22
Alignment explanation
Indices: 16366--16404 Score: 57
Period size: 19 Copynumber: 1.9 Consensus size: 22
16356 TCGTTTTCGT
16366 TTTTCTGTTTTTTGTTTTTGCG
1 TTTTCTGTTTTTTGTTTTTGCG
16388 TTTTC-G--TTTTGTTTTTG
1 TTTTCTGTTTTTTGTTTTTG
16405 TTGCGCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.00, C:0.08, G:0.18, T:0.74
Consensus pattern (22 bp):
TTTTCTGTTTTTTGTTTTTGCG
Found at i:18674 original size:29 final size:28
Alignment explanation
Indices: 18629--18705 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
18619 AATCCTCTTC
* *
18629 TAGGGGCAAAGTCGTAATTGTACC-AATTA
1 TAGGGGAAAAATCGTAATT-T-CCTAATTA
* *
18658 TAGGGGAAAAATGGTAATTTCCTCATTA
1 TAGGGGAAAAATCGTAATTTCCTAATTA
*
18686 TAGGGGTAAAATCGTAATTT
1 TAGGGGAAAAATCGTAATTT
18706 TATCAATCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.05
28 23 0.56
29 16 0.39
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.31
Consensus pattern (28 bp):
TAGGGGAAAAATCGTAATTTCCTAATTA
Found at i:20094 original size:2 final size:2
Alignment explanation
Indices: 20087--20111 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20077 TGTGGCCAGT
20087 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
20112 TGTGTAAAAG
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:26458 original size:14 final size:15
Alignment explanation
Indices: 26430--26458 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
26420 AAAATTCTCA
26430 TGAAATCCTTTTTTT
1 TGAAATCCTTTTTTT
26445 TGAAATCCTTTTTT
1 TGAAATCCTTTTTT
26459 AAAAATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (15 bp):
TGAAATCCTTTTTTT
Found at i:27290 original size:13 final size:13
Alignment explanation
Indices: 27272--27298 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27262 TAGAAATTGG
27272 ATGGGAGATGTCC
1 ATGGGAGATGTCC
27285 ATGGGAGATGTCC
1 ATGGGAGATGTCC
27298 A
1 A
27299 ATGTATGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (13 bp):
ATGGGAGATGTCC
Found at i:28880 original size:27 final size:27
Alignment explanation
Indices: 28850--28942 Score: 75
Period size: 27 Copynumber: 3.4 Consensus size: 27
28840 GAAAGTTGTA
28850 TTTGCAGTGTTCCTTATCATGTGTTAG
1 TTTGCAGTGTTCCTTATCATGTGTTAG
* ** **
28877 TTTGCACTGTTCC--GCCATGAAACTTA-
1 TTTGCAGTGTTCCTTATCATG--TGTTAG
28903 TAATTGCAGTGTTCCTTATCATGTGTTAG
1 T--TTGCAGTGTTCCTTATCATGTGTTAG
*
28932 TTTGCATTGTT
1 TTTGCAGTGTT
28943 ATCTCTCGTT
Statistics
Matches: 48, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
25 4 0.08
26 1 0.02
27 24 0.50
28 14 0.29
29 1 0.02
30 4 0.08
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.45
Consensus pattern (27 bp):
TTTGCAGTGTTCCTTATCATGTGTTAG
Found at i:28919 original size:55 final size:55
Alignment explanation
Indices: 28835--28942 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
28825 TGATTTGTTT
* * *
28835 GCCATGAAAGTTGTATTTGCAGTGTTCCTTATCATGTGTTAGTTTGCACTGTTCC
1 GCCATGAAACTTATAATTGCAGTGTTCCTTATCATGTGTTAGTTTGCACTGTTCC
*
28890 GCCATGAAACTTATAATTGCAGTGTTCCTTATCATGTGTTAGTTTGCATTGTT
1 GCCATGAAACTTATAATTGCAGTGTTCCTTATCATGTGTTAGTTTGCACTGTT
28943 ATCTCTCGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (55 bp):
GCCATGAAACTTATAATTGCAGTGTTCCTTATCATGTGTTAGTTTGCACTGTTCC
Found at i:37633 original size:22 final size:22
Alignment explanation
Indices: 37603--37667 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
37593 GTTGTCTCGA
*
37603 TGTGGTTATCAAAATTTCATAG
1 TGTGATTATCAAAATTTCATAG
37625 TGTGATTATCAAAATTTCATAG
1 TGTGATTATCAAAATTTCATAG
*
37647 TGTGATTATCAAAATTCCATA
1 TGTGATTATCAAAATTTCATA
37668 ATGAGGATCG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (22 bp):
TGTGATTATCAAAATTTCATAG
Found at i:37794 original size:65 final size:66
Alignment explanation
Indices: 37710--37848 Score: 165
Period size: 65 Copynumber: 2.1 Consensus size: 66
37700 GTACGGAAAC
*
37710 CAAAATTTCATAAGGGAGGTTACCAAAATTTCAT-GGGAGATTACCAAAATTTCATAGAGAGGTT
1 CAAAATTTCATAAGAGAGGTTACC-AAATTTCATAGGGAGATTACCAAAATTTCATAGAGAGGTT
37774 AA
65 AA
* * * * * * * *
37776 CAAAATTTCATAA-AGAGGTTATCGATTTTTATAGGGAGATTATCGAAATTTCATAGTGTGGTTA
1 CAAAATTTCATAAGAGAGGTTACCAAATTTCATAGGGAGATTACCAAAATTTCATAGAGAGGTTA
*
37840 T
66 A
37841 CAAAATTT
1 CAAAATTT
37849 TATAGTGTGG
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
64 6 0.10
65 43 0.69
66 13 0.21
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (66 bp):
CAAAATTTCATAAGAGAGGTTACCAAATTTCATAGGGAGATTACCAAAATTTCATAGAGAGGTTA
A
Found at i:37840 original size:22 final size:22
Alignment explanation
Indices: 37680--38324 Score: 197
Period size: 22 Copynumber: 29.5 Consensus size: 22
37670 GAGGATCGTA
37680 TGAGGTTATCAAAATTTCA-AG
1 TGAGGTTATCAAAATTTCATAG
** *
37701 T-ACGGAAACCAAAATTTCATAAG
1 TGA-GGTTATCAAAATTTCAT-AG
* *
37724 GGAGGTTACCAAAATTTCAT-G
1 TGAGGTTATCAAAATTTCATAG
* * *
37745 GGAGATTACCAAAATTTCATAG
1 TGAGGTTATCAAAATTTCATAG
* * *
37767 AGAGGTTAACAAAATTTCATAA
1 TGAGGTTATCAAAATTTCATAG
* * * *
37789 AGAGGTTATC-GATTTTTATAG
1 TGAGGTTATCAAAATTTCATAG
* * *
37810 GGAGATTATCGAAATTTCATAG
1 TGAGGTTATCAAAATTTCATAG
* *
37832 TGTGGTTATCAAAATTTTATAG
1 TGAGGTTATCAAAATTTCATAG
* *
37854 TGTGG---T----ATTTCAGAG
1 TGAGGTTATCAAAATTTCATAG
* *
37869 GGAGGTTATCAAAATTTCATTG
1 TGAGGTTATCAAAATTTCATAG
*
37891 TGCGG-TATCAAAATTTCATTA-
1 TGAGGTTATCAAAATTTCA-TAG
* * *
37912 TGGGGTAATCTAAATTTC-TAAG
1 TGAGGTTATCAAAATTTCAT-AG
* ** *
37934 TGTGGTTAAAAAAAATTTGATAG
1 TGAGGTT-ATCAAAATTTCATAG
** * *
37957 TCTGGTTATCGAAATTACATAG
1 TGAGGTTATCAAAATTTCATAG
* *
37979 -GAAGATTAACAAAATTTCATAG
1 TG-AGGTTATCAAAATTTCATAG
* ** *
38001 GGAGGTTATCGTAATTTCATAT
1 TGAGGTTATCAAAATTTCATAG
38023 TGTA-GTTATCAAAATTTCATAG
1 TG-AGGTTATCAAAATTTCATAG
* * **
38045 T-ATGGTTTTCACAATTTTGTAG
1 TGA-GGTTATCAAAATTTCATAG
* * * * * *
38067 GGAGATGAACAGAATTTCGTAAG
1 TGAGGTTATCAAAATTTCAT-AG
* *
38090 -GAGGACGTTATAAAAAATTCATAG
1 TGA-G--GTTATCAAAATTTCATAG
* * *
38114 GGTA-ATTATTAAAATTTCATGAG
1 TG-AGGTTATCAAAATTTCAT-AG
* * * *
38137 -GTGGTTATCGAAATTCCGTGAG
1 TGAGGTTATCAAAATTTCAT-AG
* *
38159 -GAGATTATCAAAATTTCAAACG
1 TGAGGTTATCAAAATTTCATA-G
* * *
38181 -G-GGATTAGCAAACATTTTTACAG
1 TGAGG-TTATCAAA-A-TTTCATAG
*
38204 GGAGGTTTATCAAAATTTCATAG
1 TGAGG-TTATCAAAATTTCATAG
*
38227 TGAGGTTATCAAAATTTTATAAG
1 TGAGGTTATCAAAATTTCAT-AG
** * *
38250 -GAAATTATCACAATTTGATAG
1 TGAGGTTATCAAAATTTCATAG
* *
38271 TGTA-GTTATCAAATTTTCATAA
1 TG-AGGTTATCAAAATTTCATAG
* * * * *
38293 TGTGATTATCAATATTTTACAG
1 TGAGGTTATCAAAATTTCATAG
*
38315 GGAGGTTATC
1 TGAGGTTATC
38325 TGTCACGCCC
Statistics
Matches: 454, Mismatches: 127, Indels: 85
0.68 0.19 0.13
Matches are distributed among these distances:
15 10 0.02
18 1 0.00
19 1 0.00
20 3 0.01
21 71 0.16
22 282 0.62
23 55 0.12
24 11 0.02
25 19 0.04
26 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (22 bp):
TGAGGTTATCAAAATTTCATAG
Found at i:37901 original size:21 final size:21
Alignment explanation
Indices: 37875--37929 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
37865 AGAGGGAGGT
*
37875 TATCAAAATTTCATTGTGCGG
1 TATCAAAATTTCATTATGCGG
*
37896 TATCAAAATTTCATTATGGGG
1 TATCAAAATTTCATTATGCGG
*
37917 TAATCTAAATTTC
1 T-ATCAAAATTTC
37930 TAAGTGTGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (21 bp):
TATCAAAATTTCATTATGCGG
Found at i:39500 original size:179 final size:179
Alignment explanation
Indices: 39200--39556 Score: 705
Period size: 179 Copynumber: 2.0 Consensus size: 179
39190 TGAGTCCAAC
39200 TACTAGCTAGTATACCAAGCCATACATACTCCCTGGACTGTGTCCAGTCCACGAGTCCCTGTATG
1 TACTAGCTAGTATACCAAGCCATACATACTCCCTGGACTGTGTCCAGTCCACGAGTCCCTGTATG
39265 ATTTCTAATCGTGTCATAATCAAAACCAAGAGTCATTCATGCACCCAAAACATTCATCAAAACAT
66 ATTTCTAATCGTGTCATAATCAAAACCAAGAGTCATTCATGCACCCAAAACATTCATCAAAACAT
39330 TTTATAAATCATTTATATAAAAACAGTAACAAAACATTTCCTCAACGGA
131 TTTATAAATCATTTATATAAAAACAGTAACAAAACATTTCCTCAACGGA
39379 TACTAGCTAGTATACCAAGCCATACATACTCCCTGGACTGTGTCCAGTCCACGAGTCCCTGTATG
1 TACTAGCTAGTATACCAAGCCATACATACTCCCTGGACTGTGTCCAGTCCACGAGTCCCTGTATG
*
39444 ATTTCTAATTGTGTCATAATCAAAACCAAGAGTCATTCATGCACCCAAAACATTCATCAAAACAT
66 ATTTCTAATCGTGTCATAATCAAAACCAAGAGTCATTCATGCACCCAAAACATTCATCAAAACAT
39509 TTTATAAATCATTTATATAAAAACAGTAACAAAACATTTCCTCAACGG
131 TTTATAAATCATTTATATAAAAACAGTAACAAAACATTTCCTCAACGG
39557 GTTCTCCGTT
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 177 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (179 bp):
TACTAGCTAGTATACCAAGCCATACATACTCCCTGGACTGTGTCCAGTCCACGAGTCCCTGTATG
ATTTCTAATCGTGTCATAATCAAAACCAAGAGTCATTCATGCACCCAAAACATTCATCAAAACAT
TTTATAAATCATTTATATAAAAACAGTAACAAAACATTTCCTCAACGGA
Found at i:40888 original size:36 final size:34
Alignment explanation
Indices: 40847--40927 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 34
40837 GCTGGTCCGT
* * *
40847 GCGCTTGGGTCGTGCTGGCCCGTGAGCCTGGCCTA
1 GCGCTTGGGCCGCGCTGGCCCG-GAGCCTAGCCTA
*
40882 GGCGCTTGGGCCGCGCTGGCCCGGCGCCTAGCCTA
1 -GCGCTTGGGCCGCGCTGGCCCGGAGCCTAGCCTA
*
40917 GCGTTTGGGCC
1 GCGCTTGGGCC
40928 ACGCCAGGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 10 0.25
35 10 0.25
36 20 0.50
ACGTcount: A:0.05, C:0.35, G:0.41, T:0.20
Consensus pattern (34 bp):
GCGCTTGGGCCGCGCTGGCCCGGAGCCTAGCCTA
Found at i:41845 original size:22 final size:21
Alignment explanation
Indices: 41819--42139 Score: 150
Period size: 22 Copynumber: 14.8 Consensus size: 21
41809 ATCAGTGTAA
41819 TTATCAAAATTTCATAGGCAGG
1 TTATCAAAATTTCATAGG-AGG
** *
41841 TTATCAAAATTTCATAACCAGC
1 TTATCAAAATTTCAT-AGGAGG
* * ***
41863 TTATTAAATTTTCATAGTTTTG
1 TTATCAAAATTTCATAG-GAGG
*
41885 TTATCAAAATTTCATAGAGTGG
1 TTATCAAAATTTCATAG-GAGG
*
41907 TTAT-AATAATTTTCGTAGGAGG
1 TTATCAA-AA-TTTCATAGGAGG
* *
41929 TTATCAAAATTTCATATTGAGA
1 TTATCAAAATTTCATA-GGAGG
* * *
41951 TTTTCACAATTTCAGAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
* * *
41973 CTAAC-AAA-TTCATAGGGAAG
1 TTATCAAAATTTCATA-GGAGG
*
41993 TTAACAAAATTT-ATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
42014 TTCTCAAAATTCCATAGG-GTTG
1 TTATCAAAATTTCATAGGAG--G
* * *
42036 TTATCAGAATTTCATAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
*
42058 TTATCAAAATTTCATATGGATG
1 TTATCAAAATTTCATA-GGAGG
* * * *
42080 TCATTAAAATTTCATGTGGATG
1 TTATCAAAATTTCAT-AGGAGG
* * * *
42102 TCATTAAAATTTCAT-GGTTTGA
1 TTATCAAAATTTCATAGG--AGG
42124 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
42140 AGAATATTTA
Statistics
Matches: 228, Mismatches: 53, Indels: 35
0.72 0.17 0.11
Matches are distributed among these distances:
20 17 0.07
21 33 0.14
22 165 0.72
23 12 0.05
24 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:41984 original size:20 final size:20
Alignment explanation
Indices: 41956--42000 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
41946 TGAGATTTTC
* *
41956 ACAATTTCAGAGGGAGGCTA
1 ACAAATTCAGAGGGAAGCTA
* *
41976 ACAAATTCATAGGGAAGTTA
1 ACAAATTCAGAGGGAAGCTA
41996 ACAAA
1 ACAAA
42001 ATTTATAGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.20
Consensus pattern (20 bp):
ACAAATTCAGAGGGAAGCTA
Found at i:42002 original size:21 final size:21
Alignment explanation
Indices: 41974--42032 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
41964 AGAGGGAGGC
41974 TAAC-AAATTCATAGGGAAGT
1 TAACAAAATTCATAGGGAAGT
* *
41994 TAACAAAATTTATAGGGAGGT
1 TAACAAAATTCATAGGGAAGT
**
42015 TCTCAAAATTCCATAGGG
1 TAACAAAATT-CATAGGG
42033 TTGTTATCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 4 0.12
21 22 0.69
22 6 0.19
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (21 bp):
TAACAAAATTCATAGGGAAGT
Found at i:42964 original size:29 final size:30
Alignment explanation
Indices: 42908--42971 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
42898 GCCCGTATTA
**
42908 TATATATATAATATAATCTAATTAAATAAT
1 TATATATATAATATAATAAAATTAAATAAT
* *
42938 TATATTTAT-ATATAATAAAATTGAATAAT
1 TATATATATAATATAATAAAATTAAATAAT
42967 T-TATA
1 TATATA
42972 AGTATACAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 3 0.10
29 18 0.62
30 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
TATATATATAATATAATAAAATTAAATAAT
Found at i:44339 original size:20 final size:20
Alignment explanation
Indices: 44314--44354 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44304 AACCTCCCTA
*
44314 TGAAATGTTAATATTCACAC
1 TGAAATGTTAATAATCACAC
* *
44334 TGAAATTTTGATAATCACAC
1 TGAAATGTTAATAATCACAC
44354 T
1 T
44355 ATGAGATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (20 bp):
TGAAATGTTAATAATCACAC
Found at i:44450 original size:21 final size:21
Alignment explanation
Indices: 44273--44577 Score: 144
Period size: 22 Copynumber: 14.2 Consensus size: 21
44263 GTATAGATGG
*
44273 AATTTTGATAACCATACTATGA
1 AATTTTGATAACC-TCCTATGA
*
44295 AGTTTTGATAACCTCCCTATGA
1 AATTTTGATAACCT-CCTATGA
* * *
44317 AATGTTAAT-A-TTCAC-ACTGA
1 AATTTTGATAACCTC-CTA-TGA
* *
44337 AATTTTGATAATCACACTATGA
1 AATTTTGATAACCTC-CTATGA
* *
44359 GATTGTGATAACCTCACTATGA
1 AATTTTGATAACCTC-CTATGA
* * *
44381 AATTATGACAAATCTTCCTAT-A
1 AATTTTGA-TAA-CCTCCTATGA
44403 TAATTTTGATAACCT-C----A
1 -AATTTTGATAACCTCCTATGA
*
44420 AATGTTGATAACCTCCTATGA
1 AATTTTGATAACCTCCTATGA
** *
44441 TTTTTTGATAACCTCATCATGA
1 AATTTTGATAACCTCCT-ATGA
* *
44463 AATTTTGTTAACCTCTCTATGG
1 AATTTTGATAACCTC-CTATGA
* * *
44485 AATTTTTATAATCACACTATGA
1 AATTTTGATAACCTC-CTATGA
* * *
44507 AATTTTGATGACTTCTTATGA
1 AATTTTGATAACCTCCTATGA
* **
44528 AATTTTGA-AAACTAAATTATGA
1 AATTTTGATAACCT--CCTATGA
*
44550 AATTTTGATAAACTCCCTATGA
1 AATTTTGATAACCT-CCTATGA
44572 ACATTT
1 A-ATTT
44578 GTTCACCTCC
Statistics
Matches: 213, Mismatches: 50, Indels: 39
0.71 0.17 0.13
Matches are distributed among these distances:
16 13 0.06
17 2 0.01
19 2 0.01
20 15 0.07
21 32 0.15
22 122 0.57
23 24 0.11
24 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (21 bp):
AATTTTGATAACCTCCTATGA
Done.