Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014221.1 Corchorus olitorius cultivar O-4 contig14254, 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: 27848
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1194 original size:332 final size:334
Alignment explanation
Indices: 1--1964 Score: 2993
Period size: 332 Copynumber: 5.9 Consensus size: 334
*
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAAATAAATCGAAA
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
* *
66 CAAGATTTAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCATAGAGAATTGATTAGAT-
66 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCATAGAGATTTGATTAGATG
* *
130 ATATATAGATATTTCGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCGCCTGAA
131 A-ATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGC-CCCGAA
* *
195 ACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAATTTTGAAAAAAACTG
194 ACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGAAAAAAACTG
* *
260 ACCCGAAAAGTTTTTCCCCAATTTTTTGCTACAATACTCAGAAAAATCATATAATTCAACACCAA
259 ACCCGAAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAA
325 AAATATTTTAG
324 AAATATTTTAG
* *
336 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATGAAATTGAAA
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
* * * * * *
401 CACGATTTAGATACTTGTAAAAATAAATCTGTAAATCCATTGTGGCTTACAGATTTGATTAGATG
66 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCATAGAGATTTGATTAGATG
* * * * * *
466 AATATAGATATTTCGAGAAATCTTACTTCAAAAAATCATGC-AAACGGAGTCAGGGCACCGAAAC
131 AATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAAC
* * * * *
530 GCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTGTAAAAACCTGAT
196 GCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGAAAAAAACTGAC
* * *
595 GCGAAAAGTTTTTCCACAATTTTTTCCCACAATACTCAGAAAAATCATATAATTCAACGCCAAAA
261 CCGAAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAAAA
660 ATATTTTAG
326 ATATTTTAG
*
669 GGTGTTTCACACTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
* *
734 CAAGATTCAGATACTCGTAAAATTAAATCCGTAAATCCATTGTGGCTTAGAGATTTGATTAGATG
66 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCATAGAGATTTGATTAGATG
799 AATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAAC
131 AATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAAC
*
864 GCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGAAAAAACTGAC
196 GCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGAAAAAAACTGAC
*
929 CCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAATTCAACGCCAAAA
261 CCGAAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAAAA
994 ATATTTTAG
326 ATATTTTAG
1003 GGT-TTTCACGCTTCTAATATCGTTTTTCCATTTT-TTCTGAATTTATTTCTAATTAAATCGAAA
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
* *
1066 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGAATAGAGATTTCATTAGATG
66 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCATAGAGATTTGATTAGATG
* * * * **
1131 AGTATAGATATTTTGAGAAGTCTTTCTGCCAAAAAT-ATTGGAAAACTGAGCCAGGATCCCGAAA
131 AATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCA-TGCAAAACTGAGTCAGGGCCCCGAAA
* *
1195 CGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAACTG
195 CGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA-TTTGAAAAAAACTG
** *
1260 ATGCGAAAAGTTTTTCCACAA-----T---AC--T--TCAGAAAAATCATATAATTCAACGCCAA
259 ACCCGAAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAA
1313 AAATATTTTAG
324 AAATATTTTAG
1324 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
* *
1389 CAAGATTCAGATACTTGTAAAAATAAATCTGTAAATCCATTGTGGC-TGAGAGATTTGATTAGAT
66 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCAT-AGAGATTTGATTAGAT
*
1453 GAGA-ATAGATATTTTGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAA
130 GA-ATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAA
* * * * *
1517 ACGCATTTTTAGCCAAAATCTGTGATGGTTAGTACACTATTTCGGCTAAAATTTGGAAAAAACTA
194 ACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGAAAAAAACTG
* * *
1582 ACCCGAAAAGTTTTTCCCCAATTTTTTTCGACAATACTCAGAAAAATCATATAATTCAATGCCAA
259 ACCCGAAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAA
*
1647 AAATATTTGAG
324 AAATATTTTAG
* * *
1658 GGTTTTTCACGCTTCTAATATCGTTTTTCC-TTTT-TTCTAAATTTATTTTTAATTAAATCGAAA
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
* * *
1721 CAAGATTTAGATACTCGTAAAAATAAATTCGTAAATCCATTGATGG--TGAGAGATTTAATTAGA
66 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTG-TGGCAT-AGAGATTTGATTAGA
* * * * *
1784 TTAATATAAATATTTGGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTTAGGGCCCCGAA
129 TGAATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAA
*
1849 ACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTCTGCAAAAAAAT
194 ACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATT-TG-AAAAAAAC
* * *
1914 TGACCAGAAAAGTTTTTGCCCAATTTTTTGCCATAATACTCAGAAAAATCA
257 TGACCCGAAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCA
1965 CATATTATAA
Statistics
Matches: 1494, Mismatches: 110, Indels: 51
0.90 0.07 0.03
Matches are distributed among these distances:
321 42 0.03
322 62 0.04
323 191 0.13
324 1 0.00
325 2 0.00
327 1 0.00
328 1 0.00
330 2 0.00
331 2 0.00
332 386 0.26
333 361 0.24
334 285 0.19
335 157 0.11
336 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (334 bp):
GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCATAGAGATTTGATTAGATG
AATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAAC
GCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGAAAAAAACTGAC
CCGAAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAAAA
ATATTTTAG
Found at i:1463 original size:655 final size:654
Alignment explanation
Indices: 1--1911 Score: 2996
Period size: 655 Copynumber: 2.9 Consensus size: 654
*
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAAATAAATCGAAA
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
* *
66 CAAGATTTAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCATAGAGAATTGATTAGAT-
66 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGC-TAGAGATTTGATTAGATG
* *
130 ATATATAGATATTTCGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCGCCTGAA
130 A-ATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGC-CCCGAA
* * *
195 ACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAATTTTGAAAAAAACTG
193 ACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGAAAAAACTG
* *
260 ACCCGAAAAGTTTTTCCCCAATTTTTTGCTACAATACTCAGAAAAATCATATAATTCAACACCAA
258 ACCCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAATTCAACGCCAA
325 AAATATTTTAGGGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAA
323 AAATATTTTAGGGT-TTTCACGCTTCTAATATCGTTTTTCCATTTT-TTCTGAATTTATTTCTAA
* * * * * *
390 TGAAATTGAAACACGATTTAGATACTTGTAAAAATAAATCTGTAAATCCATTGTGGCTTACAGAT
386 TTAAATCGAAACAAGATTTAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGG--TAGAGAT
* * * * * * *
455 TTGATTAGATGAATATAGATATTTCGAGAAATCTTACTTCAAAAAATCAT-GCAAACGGAGTCAG
449 TTAATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGGAAAACTGAGTCA-
* *
519 GGCACCGAAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA-TTTG
513 GGCCCCGAAACGCATTTTTAGCCAAAAAC-GTGATGGTTAGTACACGATTTCGGCTAAAATTTTG
* *
583 TAAAAACCTGATGCGAAAAGTTTTTCCACAATTTTTTCCCACAATACTCAGAAAAATCATATAAT
577 CAAAAAACTGATGCGAAAAGTTTTTCCACAA----TT--CAC-ATA-TCAGAAAAATCATATAAT
648 TCAACGCCAAAAATATTTTAG
634 TCAACGCCAAAAATATTTTAG
*
669 GGTGTTTCACACTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
*
734 CAAGATTCAGATACTCGTAAAATTAAATCCGTAAATCCATTGTGGCTTAGAGATTTGATTAGATG
66 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGC-TAGAGATTTGATTAGATG
799 AATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAAC
130 AATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAAC
864 GCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGAAAAAACTGAC
195 GCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGAAAAAACTGAC
929 CCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAATTCAACGCCAAAA
260 CCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAATTCAACGCCAAAA
994 ATATTTTAGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTTATTTCTAATTAA
325 ATATTTTAGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTTATTTCTAATTAA
* *
1059 ATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGAATAGAGATTTCA
390 ATCGAAACAAGATTTAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGG--TAGAGATTTAA
* * * *
1124 TTAGATGAGTATAGATATTTTGAGAAGTCTTTCTGCCAAAAAT-ATTGGAAAACTGAGCCAGGAT
453 TTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCA-TGGAAAACTGAGTCAGG-C
1188 CCCGAAACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
516 CCCGAAACGCATTTTTAGCCAAAAA-CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
1253 AAAACTGATGCGAAAAGTTTTTCCACAA-T-AC-T-TCAGAAAAATCATATAATTCAACGCCAAA
580 AAAACTGATGCGAAAAGTTTTTCCACAATTCACATATCAGAAAAATCATATAATTCAACGCCAAA
1314 AATATTTTAG
645 AATATTTTAG
1324 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
1 GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
* *
1389 CAAGATTCAGATACTTGTAAAAATAAATCTGTAAATCCATTGTGGCTGAGAGATTTGATTAGATG
66 CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCT-AGAGATTTGATTAGATG
*
1454 AGA-ATAGATATTTTGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAA
130 A-ATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAA
* * * *
1518 CGCATTTTTAGCCAAAATCTGTGATGGTTAGTACACTATTTCGGCTAAAATTTGGAAAAAACTAA
194 CGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGAAAAAACTGA
* *
1583 CCCGAAAAGTTTTTCCCCAATTTTTTTCGACAATACTCAGAAAAATCATATAATTCAATGCCAAA
259 CCCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAATTCAACGCCAAA
* * *
1648 AATATTTGAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-TTTTTTCTAAATTTATTTTTAATT
324 AATATTTTAGGG-TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTTATTTCTAATT
*
1712 AAATCGAAACAAGATTTAGATACTCGTAAAAATAAATTCGTAAATCCATTGATGGTGAGAGATTT
388 AAATCGAAACAAGATTTAGATACTCGTAAAAATAAATCCGTAAATCCATTG-TGGT-AGAGATTT
* * * * *
1777 AATTAGATTAATATAAATATTTGGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTTAGGG
451 AATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGGAAAACTGAGTCA-GG
*
1842 CCCCGAAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTCTGCA
515 CCCCGAAACGCATTTTTAGCCAAAAA-CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
1907 AAAAA
579 AAAAA
1912 ATTGACCAGA
Statistics
Matches: 1166, Mismatches: 64, Indels: 39
0.92 0.05 0.03
Matches are distributed among these distances:
654 2 0.00
655 557 0.48
656 34 0.03
657 1 0.00
659 2 0.00
662 1 0.00
664 1 0.00
665 117 0.10
666 94 0.08
667 178 0.15
668 178 0.15
669 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (654 bp):
GGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAATTTATTTCTAATTAAATCGAAA
CAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGCTAGAGATTTGATTAGATGA
ATATAGATATTTTGAGAAGTCTTACTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACG
CATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGAAAAAACTGACC
CGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAATTCAACGCCAAAAA
TATTTTAGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTTATTTCTAATTAAA
TCGAAACAAGATTTAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGTAGAGATTTAATTA
GATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGGAAAACTGAGTCAGGCCCCGA
AACGCATTTTTAGCCAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAACT
GATGCGAAAAGTTTTTCCACAATTCACATATCAGAAAAATCATATAATTCAACGCCAAAAATATT
TTAG
Found at i:2246 original size:17 final size:17
Alignment explanation
Indices: 2224--2278 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
2214 GATCACCCCC
*
2224 AGATCACTAGTGATCCA
1 AGATCACCAGTGATCCA
*
2241 AGATCACCAGTGATGCA
1 AGATCACCAGTGATCCA
* *
2258 AGATCACCGGTGATCAA
1 AGATCACCAGTGATCCA
2275 AGAT
1 AGAT
2279 TATATGGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (17 bp):
AGATCACCAGTGATCCA
Found at i:6265 original size:30 final size:30
Alignment explanation
Indices: 6231--6429 Score: 193
Period size: 30 Copynumber: 6.6 Consensus size: 30
6221 GTTCTGATAA
* * * *
6231 GGGCTATGCTGAGCATTTACGTTTTGGTAG
1 GGGCTATGCTGAGCATTCATGCTATGGTAG
*
6261 GGGCTATGCTGAGCATTCATGCTCTGGTAG
1 GGGCTATGCTGAGCATTCATGCTATGGTAG
*
6291 GGGCTATGCTGAGCATTCATGCTAGGGTAG
1 GGGCTATGCTGAGCATTCATGCTATGGTAG
6321 GGGCTATGCTGAGCATTCATGCT-TGTGTAG
1 GGGCTATGCTGAGCATTCATGCTATG-GTAG
** * * **
6351 GAACTCTGCTGAGCATTCATACTCGGGTAG
1 GGGCTATGCTGAGCATTCATGCTATGGTAG
** ** *
6381 GAACCCTGCTGAGCATTCATGCTAGGGTAG
1 GGGCTATGCTGAGCATTCATGCTATGGTAG
** * *
6411 GAACTCTGCTGAACATTCA
1 GGGCTATGCTGAGCATTCA
6430 AATTTTGATA
Statistics
Matches: 150, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
29 1 0.01
30 148 0.99
31 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (30 bp):
GGGCTATGCTGAGCATTCATGCTATGGTAG
Found at i:6337 original size:90 final size:90
Alignment explanation
Indices: 6231--6429 Score: 238
Period size: 90 Copynumber: 2.2 Consensus size: 90
6221 GTTCTGATAA
* * ** * * **
6231 GGGCTATGCTGAGCATTTACG-TTTTGGTAGGGGCTATGCTGAGCATTCATGCTCTGGTAGGGGC
1 GGGCTATGCTGAGCATTCACGCTTGT-GTAGGAACTATGCTGAGCATTCATACTCGGGTAGGAAC
*
6295 TATGCTGAGCATTCATGCTAGGGTAG
65 CATGCTGAGCATTCATGCTAGGGTAG
* *
6321 GGGCTATGCTGAGCATTCATGCTTGTGTAGGAACTCTGCTGAGCATTCATACTCGGGTAGGAACC
1 GGGCTATGCTGAGCATTCACGCTTGTGTAGGAACTATGCTGAGCATTCATACTCGGGTAGGAACC
*
6386 CTGCTGAGCATTCATGCTAGGGTAG
66 ATGCTGAGCATTCATGCTAGGGTAG
** * *
6411 GAACTCTGCTGAACATTCA
1 GGGCTATGCTGAGCATTCA
6430 AATTTTGATA
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
90 89 0.97
91 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (90 bp):
GGGCTATGCTGAGCATTCACGCTTGTGTAGGAACTATGCTGAGCATTCATACTCGGGTAGGAACC
ATGCTGAGCATTCATGCTAGGGTAG
Found at i:6442 original size:60 final size:60
Alignment explanation
Indices: 6327--6463 Score: 166
Period size: 60 Copynumber: 2.3 Consensus size: 60
6317 GTAGGGGCTA
* * * * *
6327 TGCTGAGCATTCATGCTTGTGTAGGAACTCTGCTGAGCATTCATACTCGGGTAGGAACCC
1 TGCTGAGCATTCATGCTAGGGTAGGAACTCTGCTGAACATTCAAACTCGGATAGGAACCC
* ** **
6387 TGCTGAGCATTCATGCTAGGGTAGGAACTCTGCTGAACATTCAAATTTTGATAGGAACTG
1 TGCTGAGCATTCATGCTAGGGTAGGAACTCTGCTGAACATTCAAACTCGGATAGGAACCC
* *
6447 TGTTGTGCATTCATGCT
1 TGCTGAGCATTCATGCT
6464 TTGTCCGGAA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (60 bp):
TGCTGAGCATTCATGCTAGGGTAGGAACTCTGCTGAACATTCAAACTCGGATAGGAACCC
Found at i:6442 original size:90 final size:90
Alignment explanation
Indices: 6267--6460 Score: 228
Period size: 90 Copynumber: 2.2 Consensus size: 90
6257 GTAGGGGCTA
* * ** * **
6267 TGCTGAGCATTCATGCTCTGGTAGGGGCTATGCTGAGCATTCATGCTAGGGTAGGGGCTATGCTG
1 TGCTGAGCATTCATACTCGGGTAGGAACCATGCTGAGCATTCATGCTAGGGTAGGAACTATGCTG
* **
6332 AGCATTCATGCTTGTGTAGGAACTC
66 AACATTCATAATTGTGTAGGAACTC
* *
6357 TGCTGAGCATTCATACTCGGGTAGGAACCCTGCTGAGCATTCATGCTAGGGTAGGAACTCTGCTG
1 TGCTGAGCATTCATACTCGGGTAGGAACCATGCTGAGCATTCATGCTAGGGTAGGAACTATGCTG
* *
6422 AACATTCA-AATTTTGATAGGAACTG
66 AACATTCATAATTGTG-TAGGAACTC
* *
6447 TGTTGTGCATTCAT
1 TGCTGAGCATTCAT
6461 GCTTTGTCCG
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 4 0.05
90 83 0.95
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (90 bp):
TGCTGAGCATTCATACTCGGGTAGGAACCATGCTGAGCATTCATGCTAGGGTAGGAACTATGCTG
AACATTCATAATTGTGTAGGAACTC
Found at i:14023 original size:13 final size:13
Alignment explanation
Indices: 13998--14035 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
13988 AAAGAAACCC
13998 AAAAAGAAGAAAAA
1 AAAAAGAA-AAAAA
14012 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
*
14025 AGAAAGAAAAA
1 AAAAAGAAAAA
14036 GCCCAACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:18063 original size:30 final size:29
Alignment explanation
Indices: 17983--18065 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
17973 AAATGGCTTT
* **
17983 AAATTGCAAGTTCAAGGGGCAAAATGTCCA
1 AAATTACAAGTTC-AGGGGCAAAACATCCA
*
18013 AAATTA-AAGTTTATGGGGCAAAACAT-CA
1 AAATTACAAGTTCA-GGGGCAAAACATCCA
18041 AAATCATACAAGTTCAGGGGCAAAA
1 AAAT--TACAAGTTCAGGGGCAAAA
18066 AGGACATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 7 0.16
29 15 0.34
30 16 0.36
31 6 0.14
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (29 bp):
AAATTACAAGTTCAGGGGCAAAACATCCA
Found at i:19872 original size:2 final size:2
Alignment explanation
Indices: 19865--19893 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19855 CATAATGTAT
19865 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19894 GAGGATTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:19884 original size:13 final size:13
Alignment explanation
Indices: 19866--19891 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19856 ATAATGTATT
19866 ATATATATATATA
1 ATATATATATATA
19879 ATATATATATATA
1 ATATATATATATA
19892 TAGAGGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:19885 original size:15 final size:15
Alignment explanation
Indices: 19865--19893 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19855 CATAATGTAT
19865 TATATATATATATAA
1 TATATATATATATAA
19880 TATATATATATATA
1 TATATATATATATA
19894 GAGGATTTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:20602 original size:18 final size:19
Alignment explanation
Indices: 20571--20609 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
20561 TTTCCTATAT
20571 AAAACTAGTAAAGTACAAA
1 AAAACTAGTAAAGTACAAA
20590 AAAACTAGT-AAGTACAAA
1 AAAACTAGTAAAGTACAAA
20608 AA
1 AA
20610 TAGTGCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAACTAGTAAAGTACAAA
Found at i:20771 original size:12 final size:12
Alignment explanation
Indices: 20754--20779 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20744 TCTCATTCAT
20754 TATTCATTCAAA
1 TATTCATTCAAA
20766 TATTCATTCAAA
1 TATTCATTCAAA
20778 TA
1 TA
20780 AAATTACATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (12 bp):
TATTCATTCAAA
Found at i:26592 original size:21 final size:21
Alignment explanation
Indices: 26566--26605 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
26556 CTGTTTAGCA
*
26566 ACTGTACAAATTAGATTATGT
1 ACTGTACAAATGAGATTATGT
26587 ACTGTACAAATGAGATTAT
1 ACTGTACAAATGAGATTAT
26606 TAGAGCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
ACTGTACAAATGAGATTATGT
Done.