Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011054.1 Corchorus olitorius cultivar O-4 contig11087, 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: 3065
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:281 original size:154 final size:153
Alignment explanation
Indices: 1--378 Score: 564
Period size: 154 Copynumber: 2.5 Consensus size: 153
* **
1 ACCAAAATGATTGTAGTTAGGCAATAAACAATGAAAAAAAAAGCATTGAGGTTTGCCAAATCGAA
1 ACCAAAATGATTATAGTTAGGCAATAAACAATGGGAAAAAAAGCATTGAGGTTTGCCAAATCGAA
* *
66 GACGATTCAAAACGTCACTAATGGGCGCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
66 GACGATTAAAAACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
* *
131 AAAACTTCAAAGTTGACTAATCTC
131 AAAACATCAAAGTGGACT-ATCTC
* *
155 ACCAAAATGATTATAGTTAGGTC-ATATAGAATGGGAAAAAAAGCATTGAGGTTTGCCAAATCGA
1 ACCAAAATGATTATAGTTAGG-CAATAAACAATGGGAAAAAAAGCATTGAGGTTTGCCAAATCGA
* *
219 AGGCGATTAAAAACGTCACTAATGGGCCCCGAA-ATGCCCAAAATAACAAGTGTTCCAAATGAGC
65 AGACGATTAAAAACGTCACTAATGGGCCCC-AATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
*
283 TAAAAACATCACAGTGGACTATCTC
129 TAAAAACATCAAAGTGGACTATCTC
* * *
308 ACCAAAAGGATTATAATTAGGCAATAAACAAT-GGAAAGAAAAGCATTGAGGTTTGGCAAATCGA
1 ACCAAAATGATTATAGTTAGGCAATAAACAATGGGAAA-AAAAGCATTGAGGTTTGCCAAATCGA
372 AGACGAT
65 AGACGAT
379 CCAAATGAGC
Statistics
Matches: 202, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
152 6 0.03
153 62 0.31
154 131 0.65
155 3 0.01
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (153 bp):
ACCAAAATGATTATAGTTAGGCAATAAACAATGGGAAAAAAAGCATTGAGGTTTGCCAAATCGAA
GACGATTAAAAACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
AAAACATCAAAGTGGACTATCTC
Found at i:457 original size:106 final size:105
Alignment explanation
Indices: 272--488 Score: 310
Period size: 106 Copynumber: 2.1 Consensus size: 105
262 TAACAAGTGT
*
272 TCCAAATGAGCTAAAAACATCACAGTGGACTATCTCACCAAAAGGATTATAATTAGGCAATAAAC
1 TCCAAATGAGCTAAAAACATCACAGTGGACTATATCACCAAAAGGATTATAATTAGGCAATAAAC
*
337 AATGGAAAGAAAAGCATTGAGGTTTGGCAAATCGAAGACGA
66 AATGGAAAGAAAAGCATTG-GGTTTGCCAAATCGAAGACGA
* * * * * *
378 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCTAAAGGTTTATAGTTATGCCATAAA
1 TCCAAATGAGCTAAAAACATCACAGTGGACT-ATATCACCAAAAGGATTATAATTAGGCAATAAA
**
443 -AATGGAAATTAAAGCATTGGGTTTGCCAAATCGAAGACGA
65 CAATGGAAAGAAAAGCATTGGGTTTGCCAAATCGAAGACGA
*
483 TTCAAA
1 TCCAAA
489 ACGTCTCTAA
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
105 25 0.25
106 47 0.47
107 27 0.27
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.23
Consensus pattern (105 bp):
TCCAAATGAGCTAAAAACATCACAGTGGACTATATCACCAAAAGGATTATAATTAGGCAATAAAC
AATGGAAAGAAAAGCATTGGGTTTGCCAAATCGAAGACGA
Found at i:628 original size:258 final size:260
Alignment explanation
Indices: 118--641 Score: 813
Period size: 258 Copynumber: 2.0 Consensus size: 260
108 TAACAAGTGT
* * * *
118 TCCAAATGAGCTAAAAACTTCAAAGTTGACTAATCTCACCAAAATGATTATAGTTAGGTCATATA
1 TCCAAATGAGCTAAAAACTTCAAAGTGGACTAATATCACCAAAAGGATTATAGTTAGGCCATATA
* * *
183 GAATGGGAAAAAAAGCATTGAGGTTTGCCAAATCGAAGGCGATTAAAAACGTCACTAATGGGCCC
66 AAATGGGAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTAAAAACGTCACTAACGGGCCC
*
248 CGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTATCTCACCAA
131 CGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTATCTCACCAA
*
313 AAGGATTATAATTAGGCAATAAACAATGGAAAGAAAAGCATTGAGGTTTGGCAAATCGAAGACGA
196 AAGGATTATAATTAGGCAATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
* * * *
378 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCTAAAGGTTTATAGTTATGCCATA-A
1 TCCAAATGAGCTAAAAACTTCAAAGTGGACTAATATCACCAAAAGGATTATAGTTAGGCCATATA
* * *
442 AAAT-GGAAATTAAAGCATTG-GGTTTGCCAAATCGAAGACGATTCAAAACGTCTCTAACGGGCC
66 AAATGGGAAA-AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTAAAAACGTCACTAACGGGCC
* *
505 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
130 CCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACT-ATCTCACC
* *
570 AAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-GGTTTGCCAAATCGAAGAC
194 AAAAGGATTATAATTAGGCAATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
634 GA
259 GA
*
636 TTCAAA
1 TCCAAA
642 ACGTCACTAG
Statistics
Matches: 241, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
258 122 0.51
259 64 0.27
260 55 0.23
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (260 bp):
TCCAAATGAGCTAAAAACTTCAAAGTGGACTAATATCACCAAAAGGATTATAGTTAGGCCATATA
AAATGGGAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTAAAAACGTCACTAACGGGCCC
CGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTATCTCACCAA
AAGGATTATAATTAGGCAATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
Found at i:859 original size:154 final size:154
Alignment explanation
Indices: 378--1407 Score: 1585
Period size: 154 Copynumber: 6.7 Consensus size: 154
368 TCGAAGACGA
* * * * *
378 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCTAAAGGTTTATAGTTATGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
** * * *
443 -AATGGAAATTAAAGCATTG-GGTTTGCCAAATCGAAGACGATTCAAAACGTCTCTAACGGGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGAGCCC
506 CGATAGGCCCAAAATAACAAGTGT
131 CGATAGGCCCAAAATAACAAGTGT
*
530 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
** *
595 CAATGGAAAGAAAAGCATTG-GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAGCGGGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGAGCCC
659 CGATAGGCCCAAAATAACAAGTGT
131 CGATAGGCCCAAAATAACAAGTGT
*
683 TCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * * **
748 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGGATATGATTGAAAACGGAACTAATGAGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGAGCCC
*
813 AGATAGGCCCAAAATAACAAGTGT
131 CGATAGGCCCAAAATAACAAGTGT
* *
837 TCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATTAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* **
902 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGGAA-ACGATTGAAAACGGAACTAATGAGCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC-GAAGACGATTCAAAACGTCACTAATGAGCC
* *
966 CAGATAAGCCCAAAATAACAAGTGT
130 CCGATAGGCCCAAAATAACAAGTGT
*
991 TCCAAATGAGCTAAAAACTTCACCGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * *
1056 CAATCGAAAAAAAAGCATTGAGATTTGCCAAATCGAAGACGATTCAAAACGTCACTAAT-AGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGAG-CC
*
1120 CCGAAAGGCCCAAAATAACAAGTGT
130 CCGATAGGCCCAAAATAACAAGTGT
* *
1145 TCAAAATGAGATAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * *
1210 CAATCGAAA-AAAAGCATTGCGATTTGCCAAATCGAAGACGATTCAAAACGTCACTAAT-AGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGAG-CC
*
1273 CCGAAAGGCCCAAAATAACAAGTGT
130 CCGATAGGCCCAAAATAACAAGTGT
*
1298 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCAATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
*
1363 -AATGG-AA-AAAAGCATTGAGGTTTGCCAAATCGAAGACGATCCAAA
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
1408 TGAGCTAAAA
Statistics
Matches: 826, Mismatches: 47, Indels: 11
0.93 0.05 0.01
Matches are distributed among these distances:
151 37 0.04
152 65 0.08
153 311 0.38
154 411 0.50
155 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGAGCCC
CGATAGGCCCAAAATAACAAGTGT
Found at i:1863 original size:154 final size:154
Alignment explanation
Indices: 1402--3058 Score: 2347
Period size: 154 Copynumber: 10.7 Consensus size: 154
1392 TCGAAGACGA
* * * * *
1402 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCTAAAGGTTTATAGTTATGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
** * *
1467 -AATGGAAATTAAAGCATTG-GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGTAACTAATGGGCCC
*
1530 CGATAGGCCCAAAATAACAAATGT
131 CGATAGGCCCAAAATAACAAGTGT
1554 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTATAGTTAGGCCAT
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG---ATTATAGTTAGGCCAT
* * * * * *
1619 AAACAATGGAAAAAAAAGCATTGGGGTTTGCCAAATTGACGACGATTCAAAACATAACTAATGGG
63 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGTAACTAATGGG
*** * *
1684 CAAAGAAAGGCCCAAAATAATAAGTGT
128 CCCCGATAGGCCCAAAATAACAAGTGT
* * * *
1711 TCCGAATGAGCTAAAAACTTCCCAGTGGACAAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * * * *
1776 CAAAT-GAAAGAAAAACATTGGGGTTTGCCAAATCGAAGGTGATTCAAAACGGAACGAATGTGCC
66 C-AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGTAACTAATGGGCC
* *
1840 CCAAAAGGCCCAAAATAACAAGTGT
130 CCGATAGGCCCAAAATAACAAGTGT
* *
1865 TCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAATTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * * * **
1930 CAATTGAAAGAAAAACCATTTAGGGTTGCCAAATCGAAGATGATTCAAAACGGAACTAATGCTCC
66 CAATGGAAAG-AAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGTAACTAATGGGCC
*
1995 CCGAAAGGCCCAAAATAACAAGTGT
130 CCGATAGGCCCAAAATAACAAGTGT
* * *
2020 TCCAAATGAGCTAAAAACTTCCCAATGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * *
2085 CAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
66 CAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGTAACTAATGGGCC
* *
2149 CCGATAGGCCCAAAATAAGAAATGT
130 CCGATAGGCCCAAAATAACAAGTGT
* * *
2174 TCCAAATGAGCTAAAAGCTTCACAATGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * *
2239 CAATGGAGAGAAAAGCATTGAGGTTTGCTAAATCGAAG-TCGATTCAAAACGTCACTAATGGGCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAT-GATTCAAAACGTAACTAATGGGCC
* *
2303 CTGATAGGCCCAAAATAACAAATGT
130 CCGATAGGCCCAAAATAACAAGTGT
* *
2328 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCTATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
*
2393 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG-TCGATTCAAAACGGAACTAAATGGGC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAT-GATTCAAAACGTAACT-AATGGGC
2457 CCCGATAGGCCCAAAATAACAAGTGT
129 CCCGATAGGCCCAAAATAACAAGTGT
* *
2483 TCCAAATGAGCTAAAATCTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * * *
2548 CACTGGAAAGAAAAGCAATGAGGTATGCCAAATCGAAGATGATTTAAAACGTCACTAATGGGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGTAACTAATGGGCCC
2613 CGATAGGCCCAAAATAACAAGTGT
131 CGATAGGCCCAAAATAACAAGTGT
*
2637 TCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * *
2702 CAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGACGATGATTCAAAACGTCACTAATGAGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGTAACTAATGGGCCC
2767 CGATAGGCCCAAAATAACAAGTGT
131 CGATAGGCCCAAAATAACAAGTGT
* * *
2791 TGCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAATTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
** * * * *
2856 CAATGGAAAGAAAATTATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGTAACTAATGGGCCC
* *
2921 CGAAAGACCCAAAATAACAAGTGT
131 CGATAGGCCCAAAATAACAAGTGT
* *
2945 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCTATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * *
3010 CAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTGAAAA
66 CAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAA
3059 ACGTCAC
Statistics
Matches: 1359, Mismatches: 132, Indels: 26
0.90 0.09 0.02
Matches are distributed among these distances:
152 43 0.03
153 4 0.00
154 895 0.66
155 298 0.22
156 19 0.01
157 100 0.07
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGTAACTAATGGGCCC
CGATAGGCCCAAAATAACAAGTGT
Found at i:2274 original size:463 final size:463
Alignment explanation
Indices: 1402--3065 Score: 2426
Period size: 463 Copynumber: 3.6 Consensus size: 463
1392 TCGAAGACGA
* * * * * *
1402 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCTAAAGGTTTATAGTTATGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAATTAGGCCATAAA
** * **
1467 -AATGGAAATTAAAGCATTG-GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
66 CAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCC
* * *
1530 CGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
131 CGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCA
* * * * *
1595 AAATGATTATTATAGTTAGGCCATAAACAA-TGGAAAAAAAAGCATTGGGGTTTGCCAAATTGAC
196 AAA-G--GATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA
* * *** * * *
1659 GACGATTCAAAACATAACTAATGGGCAAAGAAAGGCCCAAAATAATAAGTGTTCCGAATGAGCTA
258 GACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
* * * *
1724 AAAACTTCCCAGTGGACAAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAAAT-GAAAGAA
323 AAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-AATGGAAAGAA
* * ** * * * *
1788 AAACATTGGGGTTTGCCAAATCGAAGGTGATTCAAAACGGAACGAATGTGCCCCAAAAGGCCCAA
387 AAGCATTGAGGTTTGCCAAATCGAAGGTGATTCAAAACGTCACTAATGAGCCCCGATAGGCCCAA
1853 AATAACAAGTGT
452 AATAACAAGTGT
*
1865 TCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAATTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAATTAGGCCATAAA
* * * * **
1930 CAATTGAAAGAAAAACCATTTAGGGTTGCCAAATCGAAGATGATTCAAAACGGAACTAATGCTCC
66 CAATGGAAAG-AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
*
1995 CCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCCCAATGGACTAATCTCACC
130 CCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACC
* *
2060 AAAAGGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGA
195 AAAAGGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
* *
2124 CGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAGAAATGTTCCAAATGAGCTAAA
260 CGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* * *
2189 AGCTTCACAATGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAGAGAAAAG
325 AACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
2254 CATTGAGGTTTGCTAAATCGAA-GTCGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAA
390 CATTGAGGTTTGCCAAATCGAAGGT-GATTCAAAACGTCACTAATGAGCCCCGATAGGCCCAAAA
*
2318 TAACAAATGT
454 TAACAAGTGT
* * *
2328 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCTATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAATTAGGCCATAAA
* *
2393 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAAATGGGCC
66 CAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACT-AATGGGCC
* *
2458 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAATCTTCACAATGGACTAATCTCACC
130 CCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACC
* * *
2523 AAAATGATTATAGTTAGGCCATAAAC-ACTGGAAAGAAAAGCAATGAGGTATGCCAAATCGAAGA
195 AAAAGGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
* *
2587 TGATTTAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
260 CGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
2652 AACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
325 AACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
2717 CAATGAGGTTTGCCAAATCGACGATGATTCAAAACGTCACTAATGAGCCCCGATAGGCCCAAAAT
390 CATTGAGGTTTGCCAAATCGAAGGTGATTCAAAACGTCACTAATGAGCCCCGATAGGCCCAAAAT
2782 AACAAGTGT
455 AACAAGTGT
* *
2791 TGCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAATTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAATTAGGCCATAAA
** *
2856 CAATGGAAAGAAAATTATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCC
66 CAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCC
* * *
2921 CGAAAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTA
131 CGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCA
* * * *
2986 AAATGATTATAGTTAGGCTATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGAC
196 AAAGGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
*
3050 GATTGAAAAACGTCAC
261 GATT-CAAAACGTCAC
Statistics
Matches: 1078, Mismatches: 112, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
462 175 0.16
463 784 0.73
464 9 0.01
465 8 0.01
466 102 0.09
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (463 bp):
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAATTAGGCCATAAA
CAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCC
CGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCA
AAAGGATTATAGTTAGGCCATAAACAACTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
GATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
ATTGAGGTTTGCCAAATCGAAGGTGATTCAAAACGTCACTAATGAGCCCCGATAGGCCCAAAATA
ACAAGTGT
Found at i:2579 original size:617 final size:616
Alignment explanation
Indices: 1402--3058 Score: 2489
Period size: 617 Copynumber: 2.7 Consensus size: 616
1392 TCGAAGACGA
* * * * *
1402 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCTAAAGGTTTATAGTTATGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
**
1467 -AATGGAAATTAAAGCATTG-GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
1530 CGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
131 CGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-
* * * *
1595 AAATGATTATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGGGGTTTGCCAAATTGACG
195 AAA--ATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* ** * *
1660 ACGATTCAAAACATAACTAATGGGCAAAGAAAGGCCCAAAATAATAAGTGTTCCGAATGAGCTAA
258 ACGATTCAAAACGTAACTAATGGGCCCAGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* * * *
1725 AAACTTCCCAGTGGACAAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAAATGAAAGAAAA
323 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAAC-AATGAAAGAAAA
* * * *
1790 ACATTGGGGTTTGCCAAATCGAAGGT-GATTCAAAACGGAACGAATGTGCCCCAAAAGGCCCAAA
387 GCATTGAGGTTTGCCAAATCGAA-GTCGATTCAAAACGGAACAAATGGGCCCCAAAAGGCCCAAA
* *
1854 ATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAAT
451 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAAT
* * *
1919 TAGGCCATAAACAATTGAAAGAAAAACCATTTAGGGTTGCCAAATCGAAGATGATTCAAAACGGA
516 TAGGCCATAAACAATGGAAAGAAAAACCAATGAGGGTTGCCAAATCGAAGATGATTCAAAACGGA
*
1984 ACTAATGCTCCCCGAAAGGCCCAAAATAACAAGTGT
581 ACTAATGCGCCCCGAAAGGCCCAAAATAACAAGTGT
*
2020 TCCAAATGAGCTAAAAACTTCCCAATGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
* *
2085 CAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
66 CAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
* * *
2149 CCGATAGGCCCAAAATAAGAAATGTTCCAAATGAGCTAAAAGCTTCACAATGGACTAATCTCACC
130 CCGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
* * *
2214 AAAATTATTATAGTTAGGCCATAAACAATGGAGAGAAAAGCATTGAGGTTTGCTAAATCGAAGTC
195 AAAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* * * *
2279 GATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAA
260 GATTCAAAACGTAACTAATGGGCCCAGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
2344 ACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCTATAAACAATGGAAAGAAAAGC
325 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAAT-GAAAGAAAAGC
* *
2409 ATTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAAATGGGCCCCGATAGGCCCAAAAT
389 ATTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAAC-AAATGGGCCCCAAAAGGCCCAAAAT
* *
2474 AACAAGTGTTCCAAATGAGCTAAAATCTTCACAATGGACTAATCTCACCAAAATGATTATAGTTA
453 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAATTA
* * * **
2539 GGCCATAAACACTGGAAAG-AAAAGCAATGA-GGTATGCCAAATCGAAGATGATTTAAAACGTCA
518 GGCCATAAACAATGGAAAGAAAAACCAATGAGGGT-TGCCAAATCGAAGATGATTCAAAACGGAA
* *
2602 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
582 CTAATGCGCCCCGAAAGGCCCAAAATAACAAGTGT
*
2637 TCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
* * * *
2702 CAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGACGATGATTCAAAACGTCACTAATGAGCCC
66 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
* * *
2767 CGATAGGCCCAAAATAACAAGTGTTGCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCA
131 CGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
* * ** *
2832 AAATGATTATAATTAGGCCATAAACAATGGAAAGAAAATTATTGAGGGTTGCCAAATCGAAGACG
196 AAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
* * * *
2897 ATTCAAAACGGAACTAATGGTCCCCGAAAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
261 ATTCAAAACGTAACTAATGGGCCCAGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
* * *
2962 CTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCTATAAACAACTTAAAGAAAAGCT
326 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAA-TGAAAGAAAAGCA
* *
3027 TTGAGGTTTGCCAAATCGAAGACGATTGAAAA
390 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAA
3059 ACGTCAC
Statistics
Matches: 940, Mismatches: 90, Indels: 19
0.90 0.09 0.02
Matches are distributed among these distances:
616 9 0.01
617 650 0.69
618 159 0.17
619 16 0.02
620 106 0.11
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (616 bp):
TCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
CGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
AAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
ATTCAAAACGTAACTAATGGGCCCAGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAATGAAAGAAAAGCAT
TGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACAAATGGGCCCCAAAAGGCCCAAAATAAC
AAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAATTAGGC
CATAAACAATGGAAAGAAAAACCAATGAGGGTTGCCAAATCGAAGATGATTCAAAACGGAACTAA
TGCGCCCCGAAAGGCCCAAAATAACAAGTGT
Done.