Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018282.1 Corchorus olitorius cultivar O-4 contig18315, 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: 47381
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1586 original size:332 final size:324
Alignment explanation
Indices: 9--1836 Score: 1013
Period size: 332 Copynumber: 5.5 Consensus size: 324
1 ATTGGATC
* * * *
9 TAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-TAGAAAA
1 TAAGGATTTGTTTTTATGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCGA-AAAA
* * * ** * *
73 ATATGAAAAACGATATTAAAAGCGTGAAAAGTCC-TCTAATCTTTTGGCATTAAATTATATATAT
65 ATAGGAAAAA-GATATTAGAAGCGTGAAAAGCCCTTC-AATCTTTT-TTATTGAATTATATATTT
* ** * * * * * *
137 TATATGAGTATTTAAGCCAAAAATCTACAGAAAAATTTTTCAGGTC-ATTTTTTGCGAAATTTTA
127 TTTATGAGTATTTTTGCAAAAAAT-GA-GGAAAAATCTTTC-GGTCAATTTTTTAC-AAAATTTA
* * * ** ** * * ** *
201 ACCGAAATCGTGTAA-TAATCATCACGGTTTT-TGGCTAAAAAGGCGTTTCGGGGCCCCGGCTAA
188 GCCGAAATCGTG-AACTAACCATCACGATTTTCT-GAAAAAAACACGTTACGAGG-ATCGGCTCA
* * * * * * * *
264 GTTTTGCATGATTTTTTG-CGCCAAGACTCTTTAAGATATCCAGATTCATCTAATCAAATCTCAG
250 TTTTTGCATGA-TTTTCGACGCAAAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAG
** *
328 ATATATTGGATT
314 CCACATT-GATT
* * * * * * * *
340 TAAGAATTTCTTTTTACGATCATCTGAATCTTGTTTTGATTTAATAAGAAATTAATT-TAGAAAA
1 TAAGGATTTGTTTTTATGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCGA-AAAA
* * * * * * * * *
404 ATATGAAAAACGATATTAAAAGCATGAAGAGTCCTCCAAT-TTTTTTGGCGTTTAATTATATATA
65 ATAGGAAAAA-GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTT---ATTGAATTATATATT
* * * * * * * * **
468 TTCTATGAGTATTGTGGTTAAAAATTGAGGAAAATTATTTTGAGTCAATTTTTTGTAAAATTTTA
126 TTTTATGAGTATTTTTG-CAAAAAATGAGGAAAAATCTTTCG-GTCAATTTTTTACAAAA-TTTA
* * * ** * * ** *
533 GCTGAAATCTTG---T-ACCATCACGGTTTT-TGGGCTAAAAACGCGTT-CTGGGGCCCCGGGTC
188 GCCGAAATCGTGAACTAACCATCACGATTTTCT--GAAAAAAACACGTTAC-GAGG-ATCGGCTC
* * ** * * * *
592 AGTTTTGCATGATTTTTGGTGGCAACAGTTTTCCTCTTTGAAATATCTACATTCATCTAACCAAA
249 ATTTTTGCATGA-TTTTCGACGCAA-AG----ACTCCTTAAAATATCTATATTCATCTAACCAAA
657 TCGT-AGCCACATTGGATT
308 TC-TCAGCCACATT-GATT
* * * *
675 TAAGGATTTGTTTTTATGAGCATTTGAATCATGTTTCAATTTAATTAGAAATTAATTTGAAAAAA
1 TAAGGATTTGTTTTTATGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCG--AAAA
* ***
740 AATAGGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTCTTGGCGTTGAATTATATATT
64 AATAGGAAAAA-GATATTAGAAGCGTGAAAAGCCCTTCAATCTT-TT-TTATTGAATTATATATT
* * * * *
805 TTGTATGAGTA-TTGTGGATAAAAATTGA-G-AAAATATTTCGGGTCAA-TTTTTGCAAAATTTT
126 TTTTATGAGTATTTTTGCA-AAAAA-TGAGGAAAAATCTTTC-GGTCAATTTTTTACAAAA-TTT
* * * * * * * * *
866 AGCCGAAATCGTG---T-ATCATCATGGTTTTTATTTACTAAAAACGCGTTCCG-GGACCCTAGG
187 AGCCGAAATCGTGAACTAACCATCA-CGATTTT-CTGA-AAAAAACACGTTACGAGGA---TCGG
* * * *
926 -TCAGTTTTGCATGATTTTTGGCGGC-AAGACT-C---------C----TTCATCTAAGCAAATC
246 CTCATTTTTGCATGATTTTCGAC-GCAAAGACTCCTTAAAATATCTATATTCATCTAACCAAATC
975 TCAGCCACATTGTATT
310 TCAGCCACATTG-ATT
* ** * * * * *
991 TAAGGATTTGTTTTTACGAGTTTCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTTGAAATA
1 TAAGGATTTGTTTTTATGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCGAAA-A
* *
1056 TAATAGGAAAAACGATATTAGAAGCGTGAAAAAGGCTTTCAAT-TTTTTTGGCATTGAATTATAT
64 -AATAGGAAAAA-GATATTAGAAGCGTG-AAAAGCCCTTCAATCTTTTTT---ATTGAATTATAT
* * *
1120 ATTTTTTATGAGTATTTTTGCTAGAAATCGAGGAAAAATCTTTCGGGCGAA--TTTTACAAAATT
123 ATTTTTTATGAGTATTTTTGCAAAAAAT-GAGGAAAAATCTTTCGGTC-AATTTTTTACAAAATT
* ** * * *
1183 TAGCCGAAATCGTGAACTAACCATCACGGTTTTCTGCTAAAAACGCGTTCCGAGGATCGGTTCAT
186 TAGCCGAAATCGTGAACTAACCATCACGATTTTCTGAAAAAAACACGTTACGAGGATCGGCTCAT
* * * *
1248 TTTTGCATGATTTTCGATGTAAAGACTCCTTAAAATATCTATATTCATCTAACCAATTCTTAGCC
251 TTTTGCATGATTTTCGACGCAAAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAGCC
1313 ACATTAGATT
316 ACATT-GATT
* *
1323 TAAGGATTTGTTTTTATGAGCATATGAATCTTGTTTCGGTTTAATTATAAATTAATTCGAAAAAA
1 TAAGGATTTGTTTTTATGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAA
*
1388 TAGGAAAAAGAATATTAGAAGCGT-AAAAGCCCTTCAATCTTTTTTATGTCGAATTATACA-TTT
66 TAGGAAAAAG-ATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTTAT-T-GAATTATATATTTT
* *
1451 TTATGAGTATTTTAGCAAAAAAATGAGGAAATATCTTTCGAGTCAATTTTTGTA-AAAATTTTAG
128 TTATGAGTATTTTTGC-AAAAAATGAGGAAAAATCTTTCG-GTCAATTTTT-TACAAAA-TTTAG
* * *
1515 CTGAAATCGTGTACTAACCATCACGATTTT-TGGAAAAAAAAACACGTTAC-AGTGCCA-CTGCT
189 CCGAAATCGTGAACTAACCATCACGATTTTCT-G--AAAAAAACACGTTACGAG-G--ATCGGCT
* * ** * * * * *
1577 C-TGTTTTGCATGATTTTTGGCGCCGATACTCCTTGAAATATCTTTATTAATCTAATCAAATCTC
248 CAT-TTTTGCATGATTTTCGACGCAAAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTC
* * *
1641 GGCTACTTTGGATT
312 AGCCACATT-GATT
* * * *
1655 TAAGGATTTGTTTTTATGTGCATTTGAATCTTATTTCGATTTAATTAGATATTAATTCAGAAAAA
1 TAAGGATTTGTTTTTATGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAA
* * * ** * **
1720 ATATGAAATACGATATTAAAAGCGTGAAAATTCCTCCAATCTTTTCGACATTGAATTATATATCT
65 ATAGGAAA-AAGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTT--TTATTGAATTATATAT-T
* *
1785 TTTTTTGAGTATTTTTGCTAAAAATTGAGGAAAAATCTTTCGGGTC-ATTTTT
126 TTTTATGAGTATTTTTGC-AAAAAATGAGGAAAAATCTTTC-GGTCAATTTTT
1837 ACCATCATGT
Statistics
Matches: 1209, Mismatches: 192, Indels: 188
0.76 0.12 0.12
Matches are distributed among these distances:
315 5 0.00
316 76 0.06
317 38 0.03
318 81 0.07
319 33 0.03
320 16 0.01
321 6 0.00
322 6 0.00
325 2 0.00
326 36 0.03
327 28 0.02
328 31 0.03
329 103 0.09
330 13 0.01
331 131 0.11
332 236 0.20
333 32 0.03
334 61 0.05
335 122 0.10
336 80 0.07
337 68 0.06
338 3 0.00
339 2 0.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (324 bp):
TAAGGATTTGTTTTTATGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAA
TAGGAAAAAGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTTATTGAATTATATATTTTTTA
TGAGTATTTTTGCAAAAAATGAGGAAAAATCTTTCGGTCAATTTTTTACAAAATTTAGCCGAAAT
CGTGAACTAACCATCACGATTTTCTGAAAAAAACACGTTACGAGGATCGGCTCATTTTTGCATGA
TTTTCGACGCAAAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGATT
Found at i:6687 original size:17 final size:17
Alignment explanation
Indices: 6665--6703 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
6655 ATTTGATTAA
6665 TCAAGTTCAATGAATGC
1 TCAAGTTCAATGAATGC
6682 TCAAGTTCAATGAATGC
1 TCAAGTTCAATGAATGC
6699 TCAAG
1 TCAAG
6704 GCGTTAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (17 bp):
TCAAGTTCAATGAATGC
Found at i:8561 original size:43 final size:43
Alignment explanation
Indices: 8500--8587 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
8490 GTTTTATTAT
8500 CATAAAAAACATATGGAGTCAACAGGAATTAAATGACAGGCTA
1 CATAAAAAACATATGGAGTCAACAGGAATTAAATGACAGGCTA
8543 CATAAAAAACATATGGAGTCAACAGGAATTAAATGACAGGCTA
1 CATAAAAAACATATGGAGTCAACAGGAATTAAATGACAGGCTA
8586 CA
1 CA
8588 CAGAAGGAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (43 bp):
CATAAAAAACATATGGAGTCAACAGGAATTAAATGACAGGCTA
Found at i:12295 original size:19 final size:19
Alignment explanation
Indices: 12271--12308 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12261 TAATTTCCAA
*
12271 TATCAATCTGGAGTATAAC
1 TATCAATCTAGAGTATAAC
12290 TATCAATCTAGAGTATAAC
1 TATCAATCTAGAGTATAAC
12309 ACAACTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (19 bp):
TATCAATCTAGAGTATAAC
Found at i:14399 original size:25 final size:25
Alignment explanation
Indices: 14363--14421 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
14353 TTGCCTTTAA
*
14363 TTTTT-AATACATTTCAATCAATTT
1 TTTTTAAAGACATTTCAATCAATTT
14387 TTTTTAAAGACATTTCAATCAATTT
1 TTTTTAAAGACATTTCAATCAATTT
*
14412 TTTTAAAAGA
1 TTTTTAAAGA
14422 ATAAAACATC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.49
Consensus pattern (25 bp):
TTTTTAAAGACATTTCAATCAATTT
Found at i:16279 original size:19 final size:20
Alignment explanation
Indices: 16245--16291 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
16235 ACTACCTTTC
*
16245 TAACTAACCATTTACAATAT
1 TAACTAATCATTTACAATAT
*
16265 TAACTAATC-TTTACAATTT
1 TAACTAATCATTTACAATAT
16284 TAACTAAT
1 TAACTAAT
16292 ATACAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (20 bp):
TAACTAATCATTTACAATAT
Found at i:18089 original size:20 final size:19
Alignment explanation
Indices: 18064--18109 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
18054 ACTACCTTTC
18064 TAACTAACCATTTACAATAT
1 TAACTAACC-TTTACAATAT
** *
18084 TAACTAGTCTTTACAATTT
1 TAACTAACCTTTACAATAT
18103 TAACTAA
1 TAACTAA
18110 TATACAAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.39
Consensus pattern (19 bp):
TAACTAACCTTTACAATAT
Found at i:25184 original size:17 final size:18
Alignment explanation
Indices: 25140--25209 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 18
25130 ATCCACTACA
*
25140 ATTT-TAATTATTAATTT
1 ATTTATAATTATTTATTT
25157 ACTTCTCATAATTATTTA-TT
1 A-TT-T-ATAATTATTTATTT
25177 ATTTATAATT-TTTATTT
1 ATTTATAATTATTTATTT
25194 ATTTATTAATTTATTT
1 ATTTA-TAA-TTATTT
25210 TACGTAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
16 4 0.09
17 14 0.32
18 6 0.14
19 5 0.11
20 6 0.14
21 9 0.20
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTATAATTATTTATTT
Found at i:27574 original size:22 final size:21
Alignment explanation
Indices: 27434--27721 Score: 147
Period size: 22 Copynumber: 13.0 Consensus size: 21
27424 AATTACAGAG
*
27434 GAAGGTTATTAAAATTTCATA
1 GAAGGTTATCAAAATTTCATA
* *
27455 CTGTAA--TTACCAAAACTTCATA
1 --G-AAGGTTATCAAAATTTCATA
*
27477 TGAAGGTTATCAAAACTTCATA
1 -GAAGGTTATCAAAATTTCATA
* *
27499 TTGTA-TTTATCAAAATTTCATA
1 --GAAGGTTATCAAAATTTCATA
* *
27521 CAAAGGTTACCAAAATTTCATAA
1 -GAAGGTTATCAAAATTTCAT-A
* **
27544 AAATTTTATCAAAATTTCATA
1 GAAGGTTATCAAAATTTCATA
** *
27565 CGAAGGTTATTGAAATTTTATA
1 -GAAGGTTATCAAAATTTCATA
* *
27587 G-TGTGATTATCAAAA-TTAATTA
1 GAAG-G-TTATCAAAATTTCA-TA
* *
27609 GAACGTTAACAAAATTTCATA
1 GAAGGTTATCAAAATTTCATA
27630 GGGAGGGAGGTTATCAAAATTTCATA
1 --GA---AGGTTATCAAAATTTCATA
*
27656 GGAAGGTTAACAAAATTTCATA
1 -GAAGGTTATCAAAATTTCATA
* *
27678 GAGAGGTTATGAAAATGTT-ATG
1 GA-AGGTTATCAAAAT-TTCATA
*
27700 GAGAGGTTATCAAAATTACATA
1 GA-AGGTTATCAAAATTTCATA
27722 TAGAGGATAT
Statistics
Matches: 207, Mismatches: 38, Indels: 41
0.72 0.13 0.14
Matches are distributed among these distances:
20 3 0.01
21 22 0.11
22 151 0.73
23 9 0.04
24 2 0.01
25 3 0.01
26 17 0.08
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.34
Consensus pattern (21 bp):
GAAGGTTATCAAAATTTCATA
Found at i:27707 original size:44 final size:44
Alignment explanation
Indices: 27421--28074 Score: 179
Period size: 44 Copynumber: 14.8 Consensus size: 44
27411 ACAATCAAAC
* * ** ** * *
27421 CAAAATTACAGAGGAAGGTTATTAAAATTTCATACTGTA-ATTAC
1 CAAAATTTCATAGGAAGGTTAACAAAATTTCATAGAG-AGGTTAT
* * * * ** *
27465 CAAAACTTCATATGAAGGTTATCAAAACTTCATATTGTA-TTTAT
1 CAAAATTTCATAGGAAGGTTAACAAAATTTCATAGAG-AGGTTAT
** * * * **
27509 CAAAATTTCATACAAAGGTTACCAAAATTTCATAAAAATTTTAT
1 CAAAATTTCATAGGAAGGTTAACAAAATTTCATAGAGAGGTTAT
* *** * * * *
27553 CAAAATTTCATACGAAGGTTATTGAAATTTTATAGTGTGATTAT
1 CAAAATTTCATAGGAAGGTTAACAAAATTTCATAGAGAGGTTAT
* *
27597 CAAAA-TTAATTA-GAACGTTAACAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCA-TAGGAAGGTTAACAAAATTTCATA--GA--GAGGTTAT
27644 CAAAATTTCATAGGAAGGTTAACAAAATTTCATAGAGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAACAAAATTTCATAGAGAGGTTAT
* * * * *
27688 GAAAATGTT-AT-GGAGAGGTTATCAAAATTACATATAGAGGATAT
1 CAAAAT-TTCATAGGA-AGGTTAACAAAATTTCATAGAGAGGTTAT
* * * * * * *
27732 CACAGTTTCATTCCTATGGGGAA-GTTAGCGAAATTTCATGGTGTGGTTAT
1 CAAAATTTCA----TA---GGAAGGTTAACAAAATTTCATAGAGAGGTTAT
* * * ** * *
27782 CAAAATTTTCATAGTG-TGATT-AC-CAATTTTTTA-ATGTGATTAT
1 CAAAA-TTTCATAG-GAAGGTTAACAAAATTTCATAGA-GAGGTTAT
* * * * * *
27825 GAAAATTTCACACTG-AGG--ACCAAAATTTCATAGGGAGGTTAC
1 CAAAATTTCATA-GGAAGGTTAACAAAATTTCATAGAGAGGTTAT
* * * * * *
27867 CAAAATATAATAGTG-GGGTTAAGAAAATTTCATCG-GGGGTTA-
1 CAAAATTTCATAG-GAAGGTTAACAAAATTTCATAGAGAGGTTAT
* *
27909 CGAAAATTTCATAAGG-AGGTTAACAAAATTTCAT-GGGAAGGTTAC
1 C-AAAATTTCAT-AGGAAGGTTAACAAAATTTCATAGAG-AGGTTAT
* * * * * * *
27954 CAAAATTCCATAGTCAA-GTTACCGAAATTTCATAGTGAGGTCAC
1 CAAAATTTCATAG-GAAGGTTAACAAAATTTCATAGAGAGGTTAT
* * * *
27998 CAAAA-TTCATAGTCAA-GTTACCGAAATTTCATAGTGAGGTT-T
1 CAAAATTTCATAG-GAAGGTTAACAAAATTTCATAGAGAGGTTAT
* *
28040 CCAAAA-TTCATAGTCAA-GTTACCAAAATTTCATAG
1 -CAAAATTTCATAG-GAAGGTTAACAAAATTTCATAG
28075 TAATTAAGAA
Statistics
Matches: 467, Mismatches: 104, Indels: 79
0.72 0.16 0.12
Matches are distributed among these distances:
41 1 0.00
42 33 0.07
43 143 0.31
44 208 0.45
45 10 0.02
46 2 0.00
47 15 0.03
48 24 0.05
50 22 0.05
51 6 0.01
52 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (44 bp):
CAAAATTTCATAGGAAGGTTAACAAAATTTCATAGAGAGGTTAT
Found at i:27726 original size:22 final size:22
Alignment explanation
Indices: 27465--28074 Score: 160
Period size: 22 Copynumber: 27.6 Consensus size: 22
27455 CTGTAATTAC
*
27465 CAAAACTTCATATGA-AGGTTAT
1 CAAAATTTCATA-GAGAGGTTAT
* ** *
27487 CAAAACTTCATATTGTA-TTTAT
1 CAAAATTTCATAGAG-AGGTTAT
* * *
27509 CAAAATTTCATACAAAGGTTAC
1 CAAAATTTCATAGAGAGGTTAT
* * **
27531 CAAAATTTCATAAAAATTTTAT
1 CAAAATTTCATAGAGAGGTTAT
27553 CAAAATTTCATACGA-AGGTTAT
1 CAAAATTTCATA-GAGAGGTTAT
** * * * *
27575 TGAAATTTTATAGTGTGATTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
27597 CAAAA-TTAATTAGA-ACGTTAA
1 CAAAATTTCA-TAGAGAGGTTAT
27618 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCATA--GA--GAGGTTAT
*
27644 CAAAATTTCATAG-GAAGGTTAA
1 CAAAATTTCATAGAG-AGGTTAT
27666 CAAAATTTCATAGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
27688 GAAAATGTT-ATGGAGAGGTTAT
1 CAAAAT-TTCATAGAGAGGTTAT
* * *
27710 CAAAATTACATATAGAGGATAT
1 CAAAATTTCATAGAGAGGTTAT
* * * * *
27732 CACAGTTTCATTCCTATGGGGAAGTTAG
1 CAAAATTTCA----TA--GAGAGGTTAT
* * * *
27760 CGAAATTTCATGGTGTGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
27782 CAAAATTTTCATAGTGTGATTA-
1 CAAAA-TTTCATAGAGAGGTTAT
* ** * *
27804 C-CAATTTTTTA-ATGTGATTAT
1 CAAAATTTCATAGA-GAGGTTAT
* * ** *
27825 GAAAATTTCACACTGAGG--AC
1 CAAAATTTCATAGAGAGGTTAT
* *
27845 CAAAATTTCATAGGGAGGTTAC
1 CAAAATTTCATAGAGAGGTTAT
* * * * *
27867 CAAAATATAATAGTGGGGTTAA
1 CAAAATTTCATAGAGAGGTTAT
* * *
27889 GAAAATTTCATCG-GGGGTTA-
1 CAAAATTTCATAGAGAGGTTAT
*
27909 CGAAAATTTCATA-AGGAGGTTAA
1 C-AAAATTTCATAGA-GAGGTTAT
* *
27932 CAAAATTTCAT-GGGAAGGTTAC
1 CAAAATTTCATAGAG-AGGTTAT
* ** * *
27954 CAAAATTCCATAGTCAAGTTAC
1 CAAAATTTCATAGAGAGGTTAT
* * * *
27976 CGAAATTTCATAGTGAGGTCAC
1 CAAAATTTCATAGAGAGGTTAT
** * *
27998 CAAAA-TTCATAGTCAAGTTAC
1 CAAAATTTCATAGAGAGGTTAT
* *
28019 CGAAATTTCATAGTGAGGTT-T
1 CAAAATTTCATAGAGAGGTTAT
** * *
28040 CCAAAA-TTCATAGTCAAGTTAC
1 -CAAAATTTCATAGAGAGGTTAT
28062 CAAAATTTCATAG
1 CAAAATTTCATAG
28075 TAATTAAGAA
Statistics
Matches: 435, Mismatches: 113, Indels: 80
0.69 0.18 0.13
Matches are distributed among these distances:
20 27 0.06
21 71 0.16
22 281 0.65
23 23 0.05
24 2 0.00
26 19 0.04
28 12 0.03
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTTAT
Found at i:28023 original size:43 final size:43
Alignment explanation
Indices: 27847--28075 Score: 223
Period size: 43 Copynumber: 5.3 Consensus size: 43
27837 CTGAGGACCA
* * *** *
27847 AAATTTCATAGGGAGGTTACCAAAATATAATAGTGGGGTTA-AG
1 AAATTTCATAGTGAGGTTACCAAAAT-TCATAGTCAAGTTACCG
* * * * * * *
27890 AAAATTTCATCG-GGGGTTACGAAAATTTCATAAG-GAGGTTAACA
1 -AAATTTCATAGTGAGGTTACCAAAA-TTCAT-AGTCAAGTTACCG
*
27934 AAATTTCAT-GGGAAGGTTACCAAAATTCCATAGTCAAGTTACCG
1 AAATTTCATAGTG-AGGTTACCAAAATT-CATAGTCAAGTTACCG
*
27978 AAATTTCATAGTGAGGTCACCAAAATTCATAGTCAAGTTACCG
1 AAATTTCATAGTGAGGTTACCAAAATTCATAGTCAAGTTACCG
* *
28021 AAATTTCATAGTGAGGTTTCCAAAATTCATAGTCAAGTTACCA
1 AAATTTCATAGTGAGGTTACCAAAATTCATAGTCAAGTTACCG
28064 AAATTTCATAGT
1 AAATTTCATAGT
28076 AATTAAGAAA
Statistics
Matches: 159, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.01
43 102 0.64
44 54 0.34
45 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (43 bp):
AAATTTCATAGTGAGGTTACCAAAATTCATAGTCAAGTTACCG
Found at i:28047 original size:65 final size:66
Alignment explanation
Indices: 27752--28075 Score: 213
Period size: 65 Copynumber: 5.0 Consensus size: 66
27742 TTCCTATGGG
* * * * * * ** *
27752 GAAGTTAGCGAAATTTCATGGTGTGGTTATCAAAATTTTCATAGTGTGATTACCAATTTTTTA-A
1 GAAGTTACCGAAATTTCATAGTGAGGTTACCAAAA-TTTCATAGTGAGGTTACCAAAATTTCATA
27816 TGT
65 -GT
* * * * * *
27819 G-A-TTA-TGAAAATTTCACACTGAGG--ACCAAAATTTCATAGGGAGGTTACCAAAATATAATA
1 GAAGTTACCG-AAATTTCATAGTGAGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATA
27879 GT
65 GT
** * * * * *
27881 GGGGTTA-AGAAAATTTCATCG-GGGGTTACGAAAATTTCATAAG-GAGGTTAACAAAATTTCAT
1 GAAGTTACCG-AAATTTCATAGTGAGGTTACCAAAATTTCAT-AGTGAGGTTACCAAAATTTCAT
*
27943 -GG
64 AGT
* * * * * *
27945 GAAGGTTACCAAAATTCCATAGTCAAGTTACCGAAATTTCATAGTGAGGTCACCAAAA-TTCATA
1 GAA-GTTACCGAAATTTCATAGTGAGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATA
28009 GT
65 GT
* * * *
28011 CAAGTTACCGAAATTTCATAGTGAGGTTTCCAAAA-TTCATAGTCAAGTTACCAAAATTTCATAG
1 GAAGTTACCGAAATTTCATAGTGAGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAG
28075 T
66 T
28076 AATTAAGAAA
Statistics
Matches: 196, Mismatches: 48, Indels: 28
0.72 0.18 0.10
Matches are distributed among these distances:
62 23 0.12
63 10 0.05
64 34 0.17
65 97 0.49
66 31 0.16
67 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.31
Consensus pattern (66 bp):
GAAGTTACCGAAATTTCATAGTGAGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAG
T
Found at i:28075 original size:22 final size:22
Alignment explanation
Indices: 27843--28075 Score: 188
Period size: 22 Copynumber: 10.7 Consensus size: 22
27833 CACACTGAGG
* *
27843 ACCAAAATTTCATAGGGAGGTT
1 ACCAAAATTTCATAGTGAAGTT
* * **
27865 ACCAAAATATAATAGTGGGGTT
1 ACCAAAATTTCATAGTGAAGTT
** * **
27887 AAGAAAATTTCATCG-GGGGTT
1 ACCAAAATTTCATAGTGAAGTT
* *
27908 ACGAAAATTTCATAAG-GAGGTT
1 ACCAAAATTTCAT-AGTGAAGTT
* *
27930 AACAAAATTTCAT-GGGAAGGTT
1 ACCAAAATTTCATAGTGAA-GTT
* *
27952 ACCAAAATTCCATAGTCAAGTT
1 ACCAAAATTTCATAGTGAAGTT
* * *
27974 ACCGAAATTTCATAGTGAGGTC
1 ACCAAAATTTCATAGTGAAGTT
*
27996 ACCAAAA-TTCATAGTCAAGTT
1 ACCAAAATTTCATAGTGAAGTT
* *
28017 ACCGAAATTTCATAGTGAGGTT
1 ACCAAAATTTCATAGTGAAGTT
* *
28039 TCCAAAA-TTCATAGTCAAGTT
1 ACCAAAATTTCATAGTGAAGTT
28060 ACCAAAATTTCATAGT
1 ACCAAAATTTCATAGT
28076 AATTAAGAAA
Statistics
Matches: 169, Mismatches: 36, Indels: 12
0.78 0.17 0.06
Matches are distributed among these distances:
20 1 0.01
21 55 0.33
22 110 0.65
23 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (22 bp):
ACCAAAATTTCATAGTGAAGTT
Found at i:30445 original size:22 final size:22
Alignment explanation
Indices: 30420--30585 Score: 165
Period size: 22 Copynumber: 7.5 Consensus size: 22
30410 TTTAATGTGA
*
30420 TTATCAAAATTTCACATTGAGG
1 TTATCAAAATTTCACAGTGAGG
* *
30442 TTATCAAAACTTCATC-GTGTGG
1 TTATCAAAATTTCA-CAGTGAGG
30464 TTATCAAAATTTCACAGT-ATGG
1 TTATCAAAATTTCACAGTGA-GG
* * *
30486 TTATCCAAATTTCACATTGTGG
1 TTATCAAAATTTCACAGTGAGG
* * *
30508 TTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCACAGTGAGG
* *
30530 TTATCGAAATTTCACAATGAGG
1 TTATCAAAATTTCACAGTGAGG
* **
30552 TTATCAAATTTTCACAGTGTTG
1 TTATCAAAATTTCACAGTGAGG
*
30574 TTATCAATATTT
1 TTATCAAAATTT
30586 TTACGTTGGA
Statistics
Matches: 114, Mismatches: 26, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
21 1 0.01
22 112 0.98
23 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCACAGTGAGG
Found at i:30577 original size:66 final size:65
Alignment explanation
Indices: 30420--30586 Score: 192
Period size: 66 Copynumber: 2.5 Consensus size: 65
30410 TTTAATGTGA
* ** * * * *
30420 TTATCAAAATTTCACATTGAGGTTATCAAAACTTCATCGTGTGGTTATCAAAATTTCACAGTATG
1 TTATC-AAATTTCACATTGTGGTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCACAATATG
30485 G
65 G
*
30486 TTATCCAAATTTCACATTGTGGTTATCAAATTTTCATAGGGAGGTTATCGAAATTTCACAATGA-
1 TTAT-CAAATTTCACATTGTGGTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCACAAT-AT
30550 GG
64 GG
* *
30552 TTATCAAATTTTCACAGTGTTGTTATCAATATTTT
1 TTATCAAA-TTTCACATTGTGGTTATCAA-ATTTT
30587 TACGTTGGAG
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
65 4 0.05
66 76 0.87
67 7 0.08
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (65 bp):
TTATCAAATTTCACATTGTGGTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCACAATATGG
Found at i:41742 original size:29 final size:31
Alignment explanation
Indices: 41684--41753 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
41674 ATACTGTACA
* *
41684 GGTACCTCTATTTACAAAAAGTGATCAATTT
1 GGTACCTCTATTAACAAAAACTGATCAATTT
41715 GGTACCTCTA-TAACAAAAACT-ATCAATTT
1 GGTACCTCTATTAACAAAAACTGATCAATTT
*
41744 GGTCCCTCTA
1 GGTACCTCTA
41754 CCTACAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 17 0.47
30 9 0.25
31 10 0.28
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.33
Consensus pattern (31 bp):
GGTACCTCTATTAACAAAAACTGATCAATTT
Done.