Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016447.1 Corchorus olitorius cultivar O-4 contig16480, 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: 83711
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:665 original size:330 final size:329
Alignment explanation
Indices: 1--826 Score: 1324
Period size: 330 Copynumber: 2.5 Consensus size: 329
* * * * *
1 AAATTGATCCCAAA-TATTTTCCTCAATTTT-CGGCAAAATACTCATAAAATA-ATATAATTAAA
1 AAATTGACCCCAAATTTTTTTCCTCAATTTTAAGCCAAAATACTCATAAAATATATATATTTAAA
* * *
63 -G-CAAAAATATTTGAGGGCTTTTCACGCTTCTAAAATCATTTTTCTTATTTTTTGAAATATTTT
66 CGCCAAAAATATTTGAGGGATTTTCACGCTTCTAACATCATTTTTCTTATTTTCTGAAATATTTT
* *
126 CTAATAAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATTGTTAAATCCAATGCTGCACAG
131 CTAAT-AAATCGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATCCAACGCTGCACAG
*
191 AATTGTTTAGATGAATATAGATATTTCAAGGATTTTAGGCACCAAAAATCAAGCAAAACTGAGCC
195 AATTGGTTAGATGAATATAGATATTTCAAGGATTTTAGGCACCAAAAATCAAGCAAAACTGAGCC
*
256 GAGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGATGGTTTATAAATCATTTCGGCTAAAATTT
260 GAGGCCCCGAAACGCATTTTTAGCCAAAAACAGTGATGGTTTATAAATCATTTCGGCTAAAATTT
321 CGCAA
325 CGCAA
*
326 AAATTGACCCCAAATTTTTTTCCTCAATTTTAAGCCAAAATACTCATAAAATATATATGTTTAAA
1 AAATTGACCCCAAATTTTTTTCCTCAATTTTAAGCCAAAATACTCATAAAATATATATATTTAAA
391 CGCCAAAAATATTTGAGGGATTTTCACGCTTCTAACATCATTTTTCTTACTTTTCTGAAATATTT
66 CGCCAAAAATATTTGAGGGATTTTCACGCTTCTAACATCATTTTTCTTA-TTTTCTGAAATATTT
*
456 TCTAATAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATCCAACGTTGCACAG
130 TCTAATAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATCCAACGCTGCACAG
*
521 AGTTGGTTAGATGAATATAGATATTTCAAGGAGTTTT-GGCACCAAAAATCAAGCAAAACTGAGC
195 AATTGGTTAGATGAATATAGATATTTCAAGGA-TTTTAGGCACCAAAAATCAAGCAAAACTGAGC
* ** * *
585 TGAGGCCCCGAAACGTTTTTTTAGCCAGAAACAGTGATGG-TTAGTACATCATTTCGGCTAAAAT
259 CGAGGCCCCGAAACGCATTTTTAGCCAAAAACAGTGATGGTTTA-TAAATCATTTCGGCTAAAAT
*
649 TTTGCAA
323 TTCGCAA
* * *
656 AAATTGACCCAAAATATTTTTCCTAAATTTTAAGCCAAAATACTCATAAAATATATATATTTAAA
1 AAATTGACCCCAAATTTTTTTCCTCAATTTTAAGCCAAAATACTCATAAAATATATATATTTAAA
721 CGCCAAAAATATTTGAGGGATTTTCACGCTTCTAACATCATTTTTCTTATTTTTCTGAAATATTT
66 CGCCAAAAATATTTGAGGGATTTTCACGCTTCTAACATCATTTTTCTTA-TTTTCTGAAATATTT
* *
786 TCTATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAA
130 TCTAATAAATCGAAACAAGATTCAGATACTCGTAAAAACAA
827 TACGATTACC
Statistics
Matches: 465, Mismatches: 28, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
325 13 0.03
326 15 0.03
327 19 0.04
328 9 0.02
329 4 0.01
330 381 0.82
331 24 0.05
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (329 bp):
AAATTGACCCCAAATTTTTTTCCTCAATTTTAAGCCAAAATACTCATAAAATATATATATTTAAA
CGCCAAAAATATTTGAGGGATTTTCACGCTTCTAACATCATTTTTCTTATTTTCTGAAATATTTT
CTAATAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATCCAACGCTGCACAGA
ATTGGTTAGATGAATATAGATATTTCAAGGATTTTAGGCACCAAAAATCAAGCAAAACTGAGCCG
AGGCCCCGAAACGCATTTTTAGCCAAAAACAGTGATGGTTTATAAATCATTTCGGCTAAAATTTC
GCAA
Found at i:5448 original size:45 final size:45
Alignment explanation
Indices: 5398--5489 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
5388 ATCATCAGCT
5398 CCTACTAACCGAACCAAAACCTATAAAAAGACATCTTATATCAAA
1 CCTACTAACCGAACCAAAACCTATAAAAAGACATCTTATATCAAA
5443 CCTACTAACCGAACCAAAACCTATAAAAAGACATCTTATATCAAA
1 CCTACTAACCGAACCAAAACCTATAAAAAGACATCTTATATCAAA
5488 CC
1 CC
5490 GTATAGCATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.48, C:0.28, G:0.04, T:0.20
Consensus pattern (45 bp):
CCTACTAACCGAACCAAAACCTATAAAAAGACATCTTATATCAAA
Found at i:8002 original size:18 final size:18
Alignment explanation
Indices: 7975--8016 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
7965 CAAAACCATT
* * *
7975 TTTATTTTATTTTTTTTA
1 TTTATGTTATTATGTTTA
7993 TTTATGTTATTATGTTTA
1 TTTATGTTATTATGTTTA
8011 TTTATG
1 TTTATG
8017 GCCAACACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTATGTTATTATGTTTA
Found at i:10888 original size:15 final size:15
Alignment explanation
Indices: 10868--10906 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
10858 TCTCAACTTC
**
10868 TTTTCTTTTTTTTCT
1 TTTTCTTTTTGGTCT
10883 TTTTCTTTTTGGTCT
1 TTTTCTTTTTGGTCT
*
10898 CTTTCTTTT
1 TTTTCTTTT
10907 AGATCTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTGGTCT
Found at i:14122 original size:22 final size:22
Alignment explanation
Indices: 14094--14291 Score: 179
Period size: 22 Copynumber: 8.9 Consensus size: 22
14084 TGTCTCTGTG
*
14094 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
14116 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
14139 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
14160 TGGTTACCAAAATTTTATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
14183 -GGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAGGA
*
14204 AGGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
14226 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
14248 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
** **
14272 AAGTTATTGAAATTTCATAG
1 TGGTTATCAAAATTTCATAG
14292 TACTACCACA
Statistics
Matches: 144, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
21 6 0.04
22 115 0.80
23 5 0.03
24 18 0.12
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:14197 original size:66 final size:65
Alignment explanation
Indices: 14091--15352 Score: 303
Period size: 66 Copynumber: 19.3 Consensus size: 65
14081 TCTTGTCTCT
* * * * *
14091 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCAT
1 GTGTGGTTACCAAAATTTCATAGGA-GGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCAT
14156 A
65 A
*
14157 GTGTGGTTACCAAAATTTTATATGGAGGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-GGAGGTTATCAAAATTTCATGAGG-AGGTTATCAAAATTTCA
14221 TA
64 TA
* * * **
14223 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TTAGGAAAGTTATTGAAATTT
1 GTGTGGTTACCAAAATTTCATAGG---AGGTTATCAAAATTTCATGAGG-AGGTTATCAAAATTT
14287 CATA
62 CATA
** * * *
14291 --GT-ACTACCACAATTTTATAGAAAGGTTATCAGAGAAATTATCAAAATGTCATAGCGAGGTTA
1 GTGTGGTTACCAAAATTTCATAG-GAGGTTATC--A-AAATT-TC---ATG----AG-GAGGTTA
14353 T-AAGAATTTCATA
53 TCAA-AATTTCATA
* * *
14366 GTGTGGTTAACAAAATTTCATAAGGAGGTTA-CTAATATTTCATTG-GGAGGTTATCAAAATTTT
1 GTGTGGTTACCAAAATTTCAT-AGGAGGTTATC-AAAATTTCA-TGAGGAGGTTATCAAAATTTC
14429 ATA
63 ATA
* ** * * *
14432 GTGTGGTTATCAAAATTTTTTAGTGTGATTATCAAAATTTCAATGA--AGGTTATAAAAGTCTCA
1 GTGTGGTTACCAAAATTTCATAG-GAGGTTATCAAAATTTC-ATGAGGAGGTTAT-CAA-----A
14495 ATTTCATAA
58 ATTTCAT-A
* * * * * * * * * **
14504 G-G-AG-TACCAAAATATGATAGAAGGTTATC-AAATCTCATAAAGTGATTATCGGAATTTCATA
1 GTGTGGTTACCAAAATTTCATAGGAGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATA
* * **
14565 GAGATCGGGATTACCAAAATTT-ATAGGAAGATTATCAAAATTTCAT-AGTGTTGTTATCAAAAT
1 GTG-T--GG-TTACCAAAATTTCATAGG-AGGTTATCAAAATTTCATGAG-GAGGTTATCAAAAT
*
14628 TTCAAA
60 TTCATA
* * * * * * * * * *
14634 GCGAGTTTATC-AAATTTACATAATGTGATTATCAAAATTTCATAGAGG-GGTCAACAAAATTTT
1 GTGTGGTTACCAAAATTT-CAT-AGGAGGTTATCAAAATTTCAT-GAGGAGGTTATCAAAATTTC
14697 ATA
63 ATA
* * * * * * ** * * * *
14700 GAGAGATTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTACCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCAT-AGGAGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCAT
14765 A
65 A
* *
14766 --GTGG-T------ATTTC-TGAGGAGGTTATCAAAATTTCAT-AGTATGGTTA-CCAAA--T--
1 GTGTGGTTACCAAAATTTCAT-AGGAGGTTATCAAAATTTCATGAGGA-GGTTATCAAAATTTCA
14815 TA
64 TA
* ** * * * * * *
14817 G-GAAGGTTATTAAACTTTTATTATGGA-GTAATGAAAATTTCA-G-GGAGGATGTCAAAATTTC
1 GTG-TGGTTACCAAAATTTCA-TA-GGAGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTC
14878 ATA
63 ATA
* * * * * * *
14881 -TGAAGGTTATCAAAATTTCTTAGTATAGTTTTCAAAATTTCAT-AAGAGGGTTATCAAAATTTC
1 GTG-TGGTTACCAAAATTTCATAGGA-GGTTATCAAAATTTCATGAGGA-GGTTATCAAAATTTC
14944 ATA
63 ATA
* * * * * * * * **
14947 GGGAGATTAACAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTATCAAAAAATCAT
1 GTGTGGTTACCAAAATTTCATA-GGAGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCAT
15012 A
65 A
* * * * * * *
15013 GGGAGGTTATCAAAA---C-TTGTA-GTTATCAAAATTTCATAAGGAAGTTATCAAAATTTCATA
1 GTGTGGTTACCAAAATTTCATAGGAGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATA
* *
15073 -------T--CAAAATTTCATAGGGAGGTTTATTAAAATTT--TGTATGAAGGTTTATCAAAATT
1 GTGTGGTTACCAAAATTTCATA-GGAGG-TTATCAAAATTTCATG-A-GGAGG-TTATCAAAATT
15127 TCATA
61 TCATA
* * * * * * * * * *
15132 GCGAGGTTATCACAATTTCATAGTGTGATTATTAAAATTTCA-GAGTGTGATTA-CTACCAA-TT
1 GTGTGGTTACCAAAATTTCATAG-GAGGTTATCAAAATTTCATGAG-GAGGTTATC-A-AAATTT
15194 CATA
62 CATA
* *** * * * * * *
15198 -TGAAGGTT-TTTAAATTCTCATAATGTGGTTATCAATATATCAT-ATGGAGGTTATCAATATCT
1 GTG-TGGTTACCAAAATT-TCAT-AGGAGGTTATCAAAATTTCATGA-GGAGGTTATCAAAATTT
15260 CATA
62 CATA
* * * *
15264 GTGTTGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCAT-AGCGAGGTCT-TCAAAATTC
1 GTG-TGGTTACCAAAATTTCA-TAGGAGGTTATCAAAATTTCATGAG-GAGGT-TATCAAAATTT
*
15327 CTTA
62 CATA
* * *
15331 GAGAGGTTAACAAAATTTCATA
1 GTGTGGTTACCAAAATTTCATA
15353 AGAATGTTAC
Statistics
Matches: 888, Mismatches: 186, Indels: 245
0.67 0.14 0.19
Matches are distributed among these distances:
51 7 0.01
52 1 0.00
53 4 0.00
54 2 0.00
55 6 0.01
56 26 0.03
57 7 0.01
58 14 0.02
59 19 0.02
60 42 0.05
61 18 0.02
62 17 0.02
63 11 0.01
64 37 0.04
65 45 0.05
66 349 0.39
67 96 0.11
68 87 0.10
69 37 0.04
70 1 0.00
71 10 0.01
72 4 0.00
74 3 0.00
75 21 0.02
76 2 0.00
77 3 0.00
78 17 0.02
79 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (65 bp):
GTGTGGTTACCAAAATTTCATAGGAGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATA
Found at i:14353 original size:22 final size:22
Alignment explanation
Indices: 14328--14768 Score: 181
Period size: 22 Copynumber: 19.9 Consensus size: 22
14318 ATCAGAGAAA
* *
14328 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
14350 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
14372 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
14394 TTA-CTAATATTTCATTGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
14416 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
** * *
14438 TTATCAAAATTTTTTAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
14460 TTATCAAAATTTCA-A-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
14481 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * * *
14506 AGTACCAAAATATGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
*
14528 TTATC-AAATCTCATAAAGTGA--
1 TTATCAAAATTTCAT--AGTGAGG
** *
14549 TTATCGGAATTTCATAGAGATCGGG
1 TTATCAAAATTTCATAGTGA---GG
* *
14574 ATTACCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
**
14596 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* * *
14618 TTATCAAAATTTCAAAGCGAGT
1 TTATCAAAATTTCATAGTGAGG
* * *
14640 TTATC-AAATTTACATAATGTGA
1 TTATCAAAATTT-CATAGTGAGG
* *
14662 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
14684 TCAACAAAATTTTATAGAGAGA
1 TTATCAAAATTTCATAGTGAGG
**
14706 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
14728 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
14750 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
14769 GTATTTCTGA
Statistics
Matches: 315, Mismatches: 73, Indels: 62
0.70 0.16 0.14
Matches are distributed among these distances:
20 17 0.05
21 38 0.12
22 217 0.69
23 14 0.04
24 1 0.00
25 9 0.03
26 15 0.05
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:14387 original size:44 final size:42
Alignment explanation
Indices: 14328--15352 Score: 161
Period size: 44 Copynumber: 23.9 Consensus size: 42
14318 ATCAGAGAAA
*
14328 TTATCAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTATAA-AATTTCATAGTGTGG
* * * * *
14372 TTAACAAAATTTCATAAGGAGGTTACTAATATTTCATTGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTA-TAAAATTTCATAGTGTGG
* * ** *
14416 TTATCAAAATTTTATAGTGTGGTTATCAAAATTTTTTAGTGTGA
1 TTATCAAAATTTCATAG-GAGGTTAT-AAAATTTCATAGTGTGG
* * **
14460 TTATCAAAATTTCA-ATGAAGGTTATAAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAATTTCATA-GGAGGTTATAAAA-TTTC-A--T-AGTGTGG
* * * * * * * ** *
14506 AGTACCAAAATATGATAGAAGGTTATCAAATCTCATAAAGTGA
1 -TTATCAAAATTTCATAGGAGGTTATAAAATTTCATAGTGTGG
** * * *
14549 TTATCGGAATTTCATAGAGATCGGGATTACCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAG-GA---GG-TTA-TAAAATTTCATAGTG-TGG
** * * * *
14596 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGT
1 TTATCAAAATTTCATAG-GAGGTTAT-AAAATTTCATAGTGTGG
* * * * *
14640 TTATC-AAATTTACATAATGTGATTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTT-CAT-AGGAGGTTAT-AAAATTTCATAGTGTGG
* * * * ** *
14684 TCAACAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAG-GAGGTTAT-AAAATTTCATAGTGTGG
* * * * * *
14728 TTATCAAATTTTCAAAATGTGATTACCAAAATTTCATA--GTGG
1 TTATCAAAATTTC-ATAGGAGGTTA-TAAAATTTCATAGTGTGG
*
14770 ---T----ATTTC-TGAGGAGGTTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCAT-AGGAGGTTAT-AAAATTTCATAGTGTGG
* * *
14806 TTA-CCAAA--T--TAGGAAGGTTATTAAACTTTTATTA-TG-GAG
1 TTATCAAAATTTCATAGG-AGGTTA-TAAAATTTCA-TAGTGTG-G
* * * * * *
14845 TAATGAAAATTTCA-GGGAGGATGTCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGGAGGTTAT-AAAATTTCATAGTG-TGG
* * * * *
14887 TTATCAAAATTTCTTAGTATAGTTTTCAAAATTTCATAAGAG-GG
1 TTATCAAAATTTCATAGGA-GGTTAT-AAAATTTCAT-AGTGTGG
* * * * *
14931 TTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATA-GGAGGTT-ATAAAATTTCATAGTGTGG
* * ** * *
14975 TTAACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTAT-AAAATTTCATAGTGTGG
* * **
15019 TTATCAAAA---C-TTGTA-GTTATCAAAATTTCATAAG-GAAG
1 TTATCAAAATTTCATAGGAGGTTAT-AAAATTTCAT-AGTGTGG
* * *
15057 TTATCAAAATTTCAT---A---T-CAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGGAGGTTATAAAATTTCATAGTGTGG
* ** * * *
15092 TTTATTAAAATTTTGTATGAAGGTTTATCAAAATTTCATAGCGAGG
1 -TTATCAAAATTTCATA-GGAGG-TTAT-AAAATTTCATAGTGTGG
* * * * *
15138 TTATCACAATTTCATAGTGTGATTATTAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGGTTA-TAAAATTTCATAGTGTGG
* * * * *
15182 TTA-CTACCAA-TTCATATGAAGGTTTTTAAATTCTCATAATGTGG
1 TTATC-A-AAATTTCATA-GGAGGTTATAAAATT-TCATAGTGTGG
* * * *
15226 TTATCAATATATCATATGGAGGTTATCAATATCTCATAGTGTTGG
1 TTATCAAAATTTCATA-GGAGGTTAT-AAAATTTCATAGTG-TGG
* * * *
15271 TTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCA-TAGGAGGTTAT-AAAATTTCATAGTGTGG
* * *
15315 TCT-TCAAAATTCCTTAGAGAGGTTAACAAAATTTCATA
1 T-TATCAAAATTTCATAG-GAGGTT-ATAAAATTTCATA
15353 AGAATGTTAC
Statistics
Matches: 715, Mismatches: 174, Indels: 184
0.67 0.16 0.17
Matches are distributed among these distances:
34 19 0.03
35 17 0.02
36 15 0.02
37 1 0.00
38 30 0.04
39 23 0.03
40 9 0.01
41 7 0.01
42 45 0.06
43 51 0.07
44 338 0.47
45 79 0.11
46 28 0.04
47 47 0.07
48 6 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (42 bp):
TTATCAAAATTTCATAGGAGGTTATAAAATTTCATAGTGTGG
Found at i:14896 original size:22 final size:22
Alignment explanation
Indices: 14868--15072 Score: 158
Period size: 22 Copynumber: 9.6 Consensus size: 22
14858 AGGGAGGATG
*
14868 TCAAAATTTCATATGAAGGTTA
1 TCAAAATTTCATAGGAAGGTTA
* * *
14890 TCAAAATTTCTTAGTATA-GTTT
1 TCAAAATTTCATAGGA-AGGTTA
* *
14912 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAGGAAGGTTA
* *
14934 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAGGAAGGTTA
* * *
14956 ACAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAGGAAGGTTA
* *
14978 ACAAAATTTCATAATG-AGGTTA
1 TCAAAATTTCAT-AGGAAGGTTA
** *
15000 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAGGAAGGTTA
* *
15022 TCAAAA---C-T-TGTA-GTTA
1 TCAAAATTTCATAGGAAGGTTA
15038 TCAAAATTTCATAAGGAA-GTTA
1 TCAAAATTTCAT-AGGAAGGTTA
15060 TCAAAATTTCATA
1 TCAAAATTTCATA
15073 TCAAAATTTC
Statistics
Matches: 149, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
16 10 0.07
17 2 0.01
18 1 0.01
19 2 0.01
20 1 0.01
21 3 0.02
22 127 0.85
23 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
TCAAAATTTCATAGGAAGGTTA
Found at i:15050 original size:38 final size:38
Alignment explanation
Indices: 14996--15148 Score: 125
Period size: 38 Copynumber: 3.9 Consensus size: 38
14986 TCATAATGAG
**
14996 GTTATCAAAAAATCATAGGGAGGTTATCAAAACTTGT-A
1 GTTATCAAAATTTCATAGGGAGGTTATCAAAA-TTGTAA
* * *
15034 GTTATCAAAATTTCATAAGGAAGTTATCAAAATT-TCA
1 GTTATCAAAATTTCATAGGGAGGTTATCAAAATTGTAA
*
15071 --TATCAAAATTTCATAGGGAGGTTTATTAAAATTTTGTATGAA
1 GTTATCAAAATTTCATAGGGAGG-TTATCAAAA--TTG--T-AA
* *
15113 GGTTTATCAAAATTTCATAGCGAGGTTATCACAATT
1 -G-TTATCAAAATTTCATAGGGAGGTTATCAAAATT
15149 TCATAGTGTG
Statistics
Matches: 92, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
35 19 0.21
36 9 0.10
37 3 0.03
38 30 0.33
41 1 0.01
42 1 0.01
43 2 0.02
45 7 0.08
46 20 0.22
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GTTATCAAAATTTCATAGGGAGGTTATCAAAATTGTAA
Found at i:15076 original size:13 final size:13
Alignment explanation
Indices: 15058--15085 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15048 ATAAGGAAGT
15058 TATCAAAATTTCA
1 TATCAAAATTTCA
15071 TATCAAAATTTCA
1 TATCAAAATTTCA
15084 TA
1 TA
15086 GGGAGGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (13 bp):
TATCAAAATTTCA
Found at i:15082 original size:35 final size:36
Alignment explanation
Indices: 15036--15104 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
15026 AACTTGTAGT
15036 TATCAAAATTTCATAAGGAAG-TTATCAAAATTTCA
1 TATCAAAATTTCATAAGGAAGTTTATCAAAATTTCA
* * *
15071 TATCAAAATTTCATAGGGAGGTTTATTAAAATTT
1 TATCAAAATTTCATAAGGAAGTTTATCAAAATTT
15105 TGTATGAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38
Consensus pattern (36 bp):
TATCAAAATTTCATAAGGAAGTTTATCAAAATTTCA
Found at i:15138 original size:23 final size:22
Alignment explanation
Indices: 15071--15154 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 22
15061 CAAAATTTCA
15071 TATCAAAATTTCATAGGGAGGTT
1 TATCAAAATTTCATA-GGAGGTT
* ** *
15094 TATTAAAATTTTGTATGAAGGTT
1 TATCAAAATTTCATA-GGAGGTT
15117 TATCAAAATTTCATAGCGAGG-T
1 TATCAAAATTTCATAG-GAGGTT
*
15139 TATCACAATTTCATAG
1 TATCAAAATTTCATAG
15155 TGTGATTATT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 17 0.34
23 33 0.66
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAGGTT
Found at i:15296 original size:45 final size:44
Alignment explanation
Indices: 15213--15309 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
15203 GTTTTTAAAT
* * * *
15213 TCTCATAATGTGGTTATCAATATATCATATGGAGGTTATCAATA
1 TCTCATAGTGTGGTTATCAAAATATCATATGGAAGTTATCAAAA
*
15257 TCTCATAGTGTTGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAA
1 TCTCATAGTG-TGGTTATCAAAATATCATAT-GGAAGTTATCAAAA
*
15302 TTTCATAG
1 TCTCATAG
15310 CGAGGTCTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
44 10 0.22
45 35 0.78
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.39
Consensus pattern (44 bp):
TCTCATAGTGTGGTTATCAAAATATCATATGGAAGTTATCAAAA
Found at i:15321 original size:22 final size:22
Alignment explanation
Indices: 15071--15352 Score: 130
Period size: 22 Copynumber: 12.7 Consensus size: 22
15061 CAAAATTTCA
*
15071 TATCAAAATTTCATAGGGAGGTT
1 TATCAAAATTTCATAGAGAGG-T
* **
15094 TATTAAAATTTTGTATGA-AGGTT
1 TATCAAAATTTCATA-GAGAGG-T
*
15117 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGAGAGGT
* * * *
15139 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGAGAGGT
* * * * *
15161 TATTAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGAGAGGT
*
15183 TA-CTACCAA-TTCATATGA-AGGT
1 TATC-A-AAATTTCATA-GAGAGGT
** *
15205 T-TTTAAATTCTCATA-ATGTGGT
1 TATCAAAATT-TCATAGA-GAGGT
* *
15227 TATCAATATATCATATG-GAGGT
1 TATCAAAATTTCATA-GAGAGGT
* * * *
15249 TATCAATATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGAG-AGGT
* * *
15272 TATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCATAGAGAGGT
*
15294 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGAGAGGT
* *
15316 CT-TCAAAATTCCTTAGAGAGGT
1 -TATCAAAATTTCATAGAGAGGT
*
15338 TAACAAAATTTCATA
1 TATCAAAATTTCATA
15353 AGAATGTTAC
Statistics
Matches: 195, Mismatches: 47, Indels: 35
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.02
21 3 0.02
22 131 0.67
23 57 0.29
24 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATAGAGAGGT
Found at i:17540 original size:9 final size:8
Alignment explanation
Indices: 17521--17563 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
17511 TGTTGTCTTG
17521 TAATAATA
1 TAATAATA
17529 TAATATATA
1 TAATA-ATA
*
17538 TAATAATT
1 TAATAATA
*
17546 TAATAATT
1 TAATAATA
17554 TAATAA-A
1 TAATAATA
17561 TAA
1 TAA
17564 ATTTGGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 3 0.09
8 21 0.66
9 8 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TAATAATA
Found at i:28615 original size:13 final size:15
Alignment explanation
Indices: 28581--28617 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28571 CTGCCCAGTA
*
28581 AAAAAGAAAAGAAAT
1 AAAAGGAAAAGAAAT
28596 AAAAGGAAAA-AAAT
1 AAAAGGAAAAGAAAT
28610 -AAAGGAAA
1 AAAAGGAAA
28618 GGACTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.38
14 4 0.19
15 9 0.43
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (15 bp):
AAAAGGAAAAGAAAT
Found at i:44377 original size:17 final size:17
Alignment explanation
Indices: 44355--44388 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44345 GAAGAAAGAT
44355 GAAGAGAAAAAACAAAA
1 GAAGAGAAAAAACAAAA
*
44372 GAAGAGAAAAAATAAAA
1 GAAGAGAAAAAACAAAA
44389 AGGAAAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (17 bp):
GAAGAGAAAAAACAAAA
Found at i:56665 original size:13 final size:13
Alignment explanation
Indices: 56647--56678 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56637 TATTATTCAC
56647 TCATAATCTTTAA
1 TCATAATCTTTAA
56660 TCATAATCTTTAA
1 TCATAATCTTTAA
*
56673 TTATAA
1 TCATAA
56679 CATGAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (13 bp):
TCATAATCTTTAA
Found at i:59136 original size:19 final size:19
Alignment explanation
Indices: 59099--59137 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
59089 CCCAATTGCA
59099 AAACTTATCCCGACATATCC
1 AAACTTATCCC-ACATATCC
59119 AAACTTATCTCC-CATATCC
1 AAACTTATC-CCACATATCC
59138 TTATCCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 9 0.50
21 2 0.11
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (19 bp):
AAACTTATCCCACATATCC
Found at i:66522 original size:22 final size:22
Alignment explanation
Indices: 66473--66515 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
66463 AAATCTATTG
**
66473 AATTGTGATTTTTTTTGGTGAAA
1 AATTGTGA-TTTTTTTGGCCAAA
66496 AATTGTGATTTTTTTGGCCA
1 AATTGTGATTTTTTTGGCCA
66516 CATATTGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (22 bp):
AATTGTGATTTTTTTGGCCAAA
Found at i:74086 original size:2 final size:2
Alignment explanation
Indices: 74079--74128 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
74069 AGAATTGGCA
* *
74079 AT AT AT AT AT -T AT GT -T AT AT -T AT AT -T TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74117 AT AT AT AT AT AT
1 AT AT AT AT AT AT
74129 TACATCATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:75590 original size:2 final size:2
Alignment explanation
Indices: 75585--75616 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
75575 GCACACACAC
75585 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
75617 AATAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:83672 original size:2 final size:2
Alignment explanation
Indices: 83667--83711 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
83657 AGTGGGAAAT
83667 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83708 TA TA
1 TA TA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.