Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016311.1 Corchorus capsularis cultivar CVL-1 contig16332, 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: 4250
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Found at i:1662 original size:427 final size:427
Alignment explanation
Indices: 655--1631 Score: 1598
Period size: 427 Copynumber: 2.3 Consensus size: 427
645 GACACGATCA
* * *
655 GTATGCATAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCAC
1 GTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGGTGCATTTTTTGCGCAACGAGTGCTC
* *
720 AAATGTCATGCGTCGAATTGGGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACG
66 AAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACG
*
785 AAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGATAAACATAGTTCTTAGCAAAACTCTTTCTGG
131 AAGTCCAAAGCCTCAACTTTGCGCGTATTTGTGATAAACATAGTTCTTAGCAAAACTCTTTCTGG
* * * *
850 ATGTGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACC
196 ATGCGCTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAAACA
* *
915 GCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTTGTTTGCAAC
261 GCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGTATGCAAC
* *
980 ACATCGTTCTTAGTGGTGTGTTGGAGTGAGATGAACCTTTTGGACAGCCCTGAGCAGAAACAAAG
326 ACATCGTTCTTAGTGGTGTGTCGGAGTGAGATGAACCTTTTGAACAGCCCTGAGCAGAAACAAAG
*
1045 CTTTCGTAGAAGCCCAAAACCTCAACTCTAAGCGGTT
391 CTTTCCTAGAAGCCCAAAACCTCAACTCTAAGCGGTT
* *
1082 CTATG-AAAAGCATCATTTTTAGCGAAAGGCTCATTCCAGGTGCATTTTTTGTGCAACGAGTGCT
1 GTATGCAAAA-CATCATTTTTAGCGAAAGGCTCATTCCAGGTGCATTTTTTGCGCAACGAGTGCT
* * *
1146 CAAATGTCGTGTGTCGAATTGCTATGAGATTTTTGGACAGCCCTGTGCACAAACAAAGCTTTCAC
65 CAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCAC
* **
1211 GAAGTCCAAAGCCTCAACTTTGCGCGTATTTGTGCTATTCATAGTTCTTAGCAAAACTCTTTCTG
130 GAAGTCCAAAGCCTCAACTTTGCGCGTATTTGTGATAAACATAGTTCTTAGCAAAACTCTTTCTG
* *
1276 GATGCGCTTTTTCGCGTAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGGGCTTGTTAAAC
195 GATGCGCTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAAAC
* *
1341 AGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAGGCATGAACTTTGCGAGTTTGTATGCAA
260 AGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGTATGCAA
* * * * * *
1406 CACATCGTTTTTAGTGGTTTGTCGTAGTGAGATGAACTTTTTGAACAGCCCTGTGCAGAAACAAT
325 CACATCGTTCTTAGTGGTGTGTCGGAGTGAGATGAACCTTTTGAACAGCCCTGAGCAGAAACAAA
* * *
1471 GCTTTCCTAGAAGCTCAAAACCTCAACTTTGAGCGGTT
390 GCTTTCCTAGAAGCCCAAAACCTCAACTCTAAGCGGTT
1509 GTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGGTGCATTTTTTGCGCAACGA-TGCTC
1 GTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGGTGCATTTTTTGCGCAACGAGTGCTC
*
1573 AAATGTCGTGCGTCGAAGTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCT
66 AAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCT
1632 CTCCTTGATT
Statistics
Matches: 506, Mismatches: 42, Indels: 5
0.92 0.08 0.01
Matches are distributed among these distances:
426 63 0.12
427 439 0.87
428 4 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (427 bp):
GTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGGTGCATTTTTTGCGCAACGAGTGCTC
AAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACG
AAGTCCAAAGCCTCAACTTTGCGCGTATTTGTGATAAACATAGTTCTTAGCAAAACTCTTTCTGG
ATGCGCTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAAACA
GCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGTATGCAAC
ACATCGTTCTTAGTGGTGTGTCGGAGTGAGATGAACCTTTTGAACAGCCCTGAGCAGAAACAAAG
CTTTCCTAGAAGCCCAAAACCTCAACTCTAAGCGGTT
Found at i:1706 original size:269 final size:270
Alignment explanation
Indices: 1175--1901 Score: 835
Period size: 269 Copynumber: 2.7 Consensus size: 270
1165 TGCTATGAGA
* * * *
1175 TTTTTGGACAGCCCTGTGCACAAACAAAGCTTT-C-ACGAAGTCCAAAGCCTCAACTTTGCGC-G
1 TTTTTGAACAGCCCTGTGCACAAACAAAGCTTTCCTA-GAAGCCCAAAACCTCAACTTTGAGCGG
* * * ** * * * ** * * *
1237 TATTTGTGCTATTCAT-AGTTCTTAGC-AAA-ACTCTTTCTGGATGCGCTTTTTCGCGTAACGAG
65 T-TGTATGCAAAACATCA-TTTTTAGCGAAAGGCTCATTCCAGATGC-ATTTTTTGCGCAACGAG
* * * * ** * *
1299 TGCTCAAAAGTCGTGTGTCGGAA-TGAGATGGGCTTGTTAAACAGCGCTATGCACAAACAAAGCT
127 TGCTCAAATGTCGTGCGTC-GAAGTGAGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCT
* * **
1363 CTCCTCGAAGTCCAAGGCATGAACTTTGCGAGTTTGTATGCAACACATCGTTTTTAGTGGTTTGT
191 CTCCTCGAAGTCCAAAGCATGAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGCAGTTTGT
*
1428 CGTAGTGAGATGAAC
256 CGGAGTGAGATGAAC
* * *
1443 TTTTTGAACAGCCCTGTGCAGAAACAATGCTTTCCTAGAAGCTCAAAACCTCAACTTTGAGCGGT
1 TTTTTGAACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGT
*
1508 TGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGGTGCATTTTTTGCGCAACGA-TGCT
66 TGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCT
*
1572 CAAATGTCGTGCGTCGAAGTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTCTCCT
131 CAAATGTCGTGCGTCGAAGTGAGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTCTCCT
* ** * *
1637 TGATTTCCAAAGCATTAACTTTGCGCA-TTTGTATGCAACACATTGTTCTTAGCAGTTTGTCGGA
196 CGAAGTCCAAAGCATGAACTTTGCG-AGTTTGTATGCAACACATCGTTCTTAGCAGTTTGTCGGA
1701 GTGAGATGAAC
260 GTGAGATGAAC
* * * *
1712 TTTTTGGATAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCTAGTTTGAGCGGT
1 TTTTTGAACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGT
* * * *
1777 TTTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTCCCCTACGAGTGCT
66 TGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCT
* * * * * *
1842 CAAATGTCATGCGACGGAGTGAGTTGAGCA-TGTTGGACAGCCCTGTGCAAAAAAAAAGCT
131 CAAATGTCGTGCGTCGAAGTGAGATGAG-ATTGTTGGACAGCCCTGTGCACAAACAAAGCT
1902 TGTTAGGTAG
Statistics
Matches: 390, Mismatches: 59, Indels: 18
0.84 0.13 0.04
Matches are distributed among these distances:
268 33 0.08
269 270 0.69
270 76 0.19
271 11 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (270 bp):
TTTTTGAACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGT
TGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCT
CAAATGTCGTGCGTCGAAGTGAGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTCTCCT
CGAAGTCCAAAGCATGAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGCAGTTTGTCGGAG
TGAGATGAAC
Found at i:2369 original size:159 final size:157
Alignment explanation
Indices: 2016--2386 Score: 379
Period size: 159 Copynumber: 2.3 Consensus size: 157
2006 ATGAACTTTT
* * * * * *
2016 TGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGTTTGTG
1 TGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAACATCAACTTTCACCATTTGTG
* * * * *
2081 TGCAAAACATGTTTTGAGGAATAGGCTCATTCCAGATGCGTTTTTTGCGCAATGAGTGCTCAAAT
66 TGCAAAACATGTTTTGAGCAAAACGCTCATTCCAGATGCGTTTTTTGCGCAATGACTGCTCAAAA
* * * *
2146 GTCATGAATCGGAGCGAGTTGAGCATCT
131 GTCATG-ATCAGAGCGAGATGAGCAACA
* * * * *
2174 TAGACAGCCGTGTGCACAAACAAAGTTTTCCCCGAAGTCCAAAACTTCAACTTATCACCATTT-T
1 TGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAACATCAACTT-TCACCATTTGT
* ** * *
2238 GTGCAAAACATCGTTCTT-AGCAAAACTCTTTTTCCGGATGCGATTTTTTGTGCAATGACTGCTC
65 GTGCAAAACAT-GTT-TTGAGCAAAACGCTCATTCCAGATGCG-TTTTTTGCGCAATGACTGCTC
* * *
2302 AAAAGTCGTTG-TCAGAGTGAGATGAGCAAGA
127 AAAAGTC-ATGATCAGAGCGAGATGAGCAACA
* * * *
2333 TGGACAGCCCTATGCACAAAGAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTT
1 TGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAACATCAACTTT
2387 GCGCGTATGT
Statistics
Matches: 172, Mismatches: 36, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
158 59 0.34
159 84 0.49
160 27 0.16
161 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (157 bp):
TGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAACATCAACTTTCACCATTTGTG
TGCAAAACATGTTTTGAGCAAAACGCTCATTCCAGATGCGTTTTTTGCGCAATGACTGCTCAAAA
GTCATGATCAGAGCGAGATGAGCAACA
Found at i:2431 original size:569 final size:568
Alignment explanation
Indices: 1856--3040 Score: 1564
Period size: 569 Copynumber: 2.1 Consensus size: 568
1846 TGTCATGCGA
* * * *
1856 CGGAGTGAGTTGAGCATGTTGGACAGCCCTGTGCAAAAAAAAAGCTTGTTAGGTAGCGCTATGCA
1 CGGAGTGAGATGAGCAT-TTGGACAGCCCTGTGCACAAACAAAGCTTGTTAGGGAGCGCTATGCA
*
1921 CAAACAAAGCTCTCCTCGAAGTCCAAAGAATCAACTTTGCGCGTTTGTATGCAAAACATCGTTCT
65 CAAACAAAGCTCTCCTCGAAGTCCAAAGAATCAACTTTGCGCATTTGTATGCAAAACATCGTTCT
* *
1986 TAGCGGTTTGTCGGAATGAGATGAACTTTTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGA
130 TAGCAGTTTGTCGGAATGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGA
* * *
2051 AGCCCAAAACCTCAACTTTGAGCGTTTGTGTGCAAAACAT-GTTTTGAG-GAATAGGCTCATTCC
195 AGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTGAGCGAA-AGGCTCATTCC
* * * *
2114 AGATGCGTTTTTTGCGCA-ATGAGTGCTCAAATGTCATGAATCGGAGCG-AGTTGAGCA-TCTTA
259 AGATGCATTTTTTGCG-ATACGAGTGCTCAAATGTCATGAATCGAAGCGCA-ATGAG-ATTCTTA
* * * *
2176 GACAGCCGTGTGCACAAACAAAGTTTTCCC-CGAAGTCCAAAACTTCAACTTAT-CACCATTT-T
321 GACAGCCCTCTGCACAAACAAAG-CTTCCCTCGAAGTCCAAAACATCAA-TTATGCA-CATTTCT
* * *
2238 GTGCAAAACAT-CGTTCTTAGCAAAACTCTTTTTCCGGATGCGATTTTTT-GTGCAATGACTGCT
383 GTGCAAAACATAC-TTCTTAGCAAAACAC--TTTCCAGATGC-ATTTTTTCGTGCAACGACTGCT
* * *
2301 CAAAAGTCGT-TGTCAGAGTGAGATGAGCAAGATGGACAGCCCTATGCACAAAGAAAGCTCTCCT
444 CAAAAGACGTGTGTCAGAGTGAGATGAGCAAGATAGACAGCCCTATGCACAAACAAAGCTCTCCT
*
2365 CGAAGTCCAAAGCATCAACTTTGCGCGTATGTATGCAAAACATCATTCTTAGCGGTGTGT
509 CGAAGACCAAAGCATCAACTTTGCGCGTATGTATGCAAAACATCATTCTTAGCGGTGTGT
*
2425 CGGAGTGAGATGAGCTATTTGGACAGCCCTGTGCACAAACAAAGCTTTTTAGGGAGCGCTATGCA
1 CGGAGTGAGATGAGC-ATTTGGACAGCCCTGTGCACAAACAAAGCTTGTTAGGGAGCGCTATGCA
* * **
2490 TAAACAAAGCTCTCCTCGATGTCCAAAGCTTCAACTTTGCGCATTTGTATGCAAAACATCGTTCT
65 CAAACAAAGCTCTCCTCGAAGTCCAAAGAATCAACTTTGCGCATTTGTATGCAAAACATCGTTCT
* * *
2555 TAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAGCCCTATGCACAAACAATGCTTTCCTAGA
130 TAGCAGTTTGTCGGAATGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGA
** * *
2620 AGCCTGAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCTA
195 AGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTGAGCGAAAGGCTCATTCCA
* ** * * *
2685 GATGCATTTTTTGCGATACGAGTGCTCAAATGTCGTGTGTCGAAGTGCAATGAGATTGTTGGACA
260 GATGCATTTTTTGCGATACGAGTGCTCAAATGTCATGAATCGAAGCGCAATGAGATTCTTAGACA
* * *
2750 GCCCTCTGCACAAACAAAGCTTCCCTCGAAGTCCAAAGCATCAATTTTGCACATTTCTGTGCTAA
325 GCCCTCTGCACAAACAAAGCTTCCCTCGAAGTCCAAAACATCAATTATGCACATTTCTGTGCAAA
* * *
2815 ACATACTTCTTAGCAGAACACTTTCTAGATGCATTTTTTCGTGCAACGAGTGCTCAAAAGACGTG
390 ACATACTTCTTAGCAAAACACTTTCCAGATGCATTTTTTCGTGCAACGACTGCTCAAAAGACGTG
* ** * **
2880 TGTCGGAGTGAGATGAGCTTGTTAGACAGCGTTATGCACAAACAAAGCTCTCCTCGAAGACCAAA
455 TGTCAGAGTGAGATGAGCAAGATAGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGACCAAA
* * * * * * *
2945 GCATCAACTTTGCGTGTTTGTTTGCAACACATCGTTTTTAGCGGTTTGT
520 GCATCAACTTTGCGCGTATGTATGCAAAACATCATTCTTAGCGGTGTGT
* * * * *
2994 CGGAATGAGATGAACTTTTTAGATAGCCCTGTGCACAAACAAAGCTT
1 CGGAGTGAGATGAGC-ATTTGGACAGCCCTGTGCACAAACAAAGCTT
3041 TCCTAGAAGC
Statistics
Matches: 537, Mismatches: 67, Indels: 24
0.86 0.11 0.04
Matches are distributed among these distances:
567 7 0.01
568 30 0.06
569 368 0.69
570 127 0.24
571 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (568 bp):
CGGAGTGAGATGAGCATTTGGACAGCCCTGTGCACAAACAAAGCTTGTTAGGGAGCGCTATGCAC
AAACAAAGCTCTCCTCGAAGTCCAAAGAATCAACTTTGCGCATTTGTATGCAAAACATCGTTCTT
AGCAGTTTGTCGGAATGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGAA
GCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTGAGCGAAAGGCTCATTCCAG
ATGCATTTTTTGCGATACGAGTGCTCAAATGTCATGAATCGAAGCGCAATGAGATTCTTAGACAG
CCCTCTGCACAAACAAAGCTTCCCTCGAAGTCCAAAACATCAATTATGCACATTTCTGTGCAAAA
CATACTTCTTAGCAAAACACTTTCCAGATGCATTTTTTCGTGCAACGACTGCTCAAAAGACGTGT
GTCAGAGTGAGATGAGCAAGATAGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGACCAAAG
CATCAACTTTGCGCGTATGTATGCAAAACATCATTCTTAGCGGTGTGT
Found at i:2601 original size:141 final size:141
Alignment explanation
Indices: 2342--2613 Score: 418
Period size: 141 Copynumber: 1.9 Consensus size: 141
2332 ATGGACAGCC
* *
2342 CTATGCACAAAGAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTATGTATGCAAAACA
1 CTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCATATGTATGCAAAACA
* * *
2407 TCATTCTTAGCGGTGTGTCGGAGTGAGATGAGCTATTTGGACAGCCCTGTGCACAAACAAAGCTT
66 TCATTCTTAGCAGTGTGTCGGAGTGAGATGAACTATTTGGACAGCCCTATGCACAAACAAAGCTT
2472 TTTAGGGAGCG
131 TTTAGGGAGCG
* * * *
2483 CTATGCATAAACAAAGCTCTCCTCGATGTCCAAAGCTTCAACTTTGCGCATTTGTATGCAAAACA
1 CTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCATATGTATGCAAAACA
* * * * *
2548 TCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAGCCCTATGCACAAACAATGCTT
66 TCATTCTTAGCAGTGTGTCGGAGTGAGATGAACTATTTGGACAGCCCTATGCACAAACAAAGCTT
2613 T
131 T
2614 CCTAGAAGCC
Statistics
Matches: 117, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
141 117 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (141 bp):
CTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCATATGTATGCAAAACA
TCATTCTTAGCAGTGTGTCGGAGTGAGATGAACTATTTGGACAGCCCTATGCACAAACAAAGCTT
TTTAGGGAGCG
Found at i:2986 original size:158 final size:153
Alignment explanation
Indices: 2563--2987 Score: 410
Period size: 158 Copynumber: 2.7 Consensus size: 153
2553 CTTAGCAGTT
* * * * *
2563 TGTCGGAGTGAGATGAACTTTTTGGATAGCCCTATGCACAAACAATGCTTTCCTAGAAGCCTGAA
1 TGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTATGCACAAACAAAGC-TTCCTCGAAGCC--AA
* * *
2628 A-CCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCTAGATGCAT
63 AGCATCAACTTTGCGCGTTTGTATGC-AAACATC-TTTTTAGCGAAA-GCT-ATTCTAGATGCAT
* *
2692 TTTTTGCGATACGAGTGCTCAAATGTCGTG
124 TTTTTGCGATACGAGTGCTCAAAAGACGTG
* * *
2722 TGTCGAAGTGCA-ATGAGATTGTTGGACAGCCCTCTGCACAAACAAAGCTTCCCTCGAAGTCCAA
1 TGTCGGAGTG-AGATGAGCTTGTTGGACAGCCCTATGCACAAACAAAGCTT-CCTCGAAG-CCAA
* * * * * *
2786 AGCATCAATTTTGCACATTTCTGTGCTAAACATACTTCTTAGCAGAACA-CT-TTCTAGATGCAT
63 AGCATCAACTTTGCGCGTTTGTATGC-AAACAT-CTTTTTAGC-GAA-AGCTATTCTAGATGCAT
*
2849 TTTTTCGTGCA-ACGAGTGCTCAAAAGACGTG
124 TTTTT-GCG-ATACGAGTGCTCAAAAGACGTG
* **
2880 TGTCGGAGTGAGATGAGCTTGTTAGACAGCGTTATGCACAAACAAAGCTCTCCTCGAAGACCAAA
1 TGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTATGCACAAACAAAGCT-TCCTCGAAG-CCAAA
* *
2945 GCATCAACTTTGCGTGTTTGTTTGCAACACATCGTTTTTAGCG
64 GCATCAACTTTGCGCGTTTGTATGCAA-ACATC-TTTTTAGCG
2988 GTTTGTCGGA
Statistics
Matches: 218, Mismatches: 35, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
157 22 0.10
158 109 0.50
159 79 0.36
160 7 0.03
161 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (153 bp):
TGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTATGCACAAACAAAGCTTCCTCGAAGCCAAAGC
ATCAACTTTGCGCGTTTGTATGCAAACATCTTTTTAGCGAAAGCTATTCTAGATGCATTTTTTGC
GATACGAGTGCTCAAAAGACGTG
Found at i:3031 original size:111 final size:111
Alignment explanation
Indices: 2880--3093 Score: 275
Period size: 111 Copynumber: 1.9 Consensus size: 111
2870 AAAAGACGTG
* * ** *
2880 TGTCGGAGTGAGATGAGCTTGTTAGACAGCGTTATGCACAAACAAAGCTCTCCTCGAAGACCAAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGACCAAA
* * * * * *
2945 GCATCAACTTTGCGTGTTTGTTTGCAACACATCGTTTTTAGCGGTT
66 ACATCAACTTTGAGCGTTTGTGTGCAAAACATCATTTTTAGCGGTT
* * * * *
2991 TGTCGGAATGAGATGAACTTTTTAGATAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGACCAAA
*
3056 ACCTCAACTTTGAGCGTTTGTGTGCAAAACATCATTTT
66 ACATCAACTTTGAGCGTTTGTGTGCAAAACATCATTTT
3094 CAGGAACAGG
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
111 86 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (111 bp):
TGTCGGAATGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGACCAAA
ACATCAACTTTGAGCGTTTGTGTGCAAAACATCATTTTTAGCGGTT
Found at i:3454 original size:300 final size:300
Alignment explanation
Indices: 2895--3500 Score: 991
Period size: 300 Copynumber: 2.0 Consensus size: 300
2885 GAGTGAGATG
* * *
2895 AGCTTGTTAGACAGCGTTATGCACAAACAAAGCTCTCCTCGAAGACCAAAGCATCAACTTTGCGT
1 AGCTTTTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGACCAAAGCATCAACTTTGCGC
* * * *
2960 GTTTGTTTGCAACACATCGTTTTTAGCGGTTTGTCGGAATGAGATGAACTTTTTAGATAGCCCTG
66 GTTTGTATGCAAAACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACTTTTTAGACAGCCCTG
3025 TGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGTTTGTGTGCAAAACATCA
131 TGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGTTTGTGTGCAAAACATCA
* * **
3090 TTTTCAGGAACAGGCTCATTCCAGATGTGTTTTTTGCGCAATGAGTGCTCAAATGTCATGCGACG
196 TTTTCAGGAACAAGCTCATTCCAGATGCGTTTTTTGCGCAATGAGTGCTCAAATGAAATGCGACG
*
3155 GAGTGACTTGAGCATGTTGGACAGCCCTGTGCACAAAAAA
261 GAGTGACTTGAGCATGTTGGACAGCCCTATGCACAAAAAA
* *
3195 AGCTTTTTAGGCAGCGCTATGCACAAACAAAGCTCTCCTC-AATGTCCAAAGCATCAACTTTGCG
1 AGCTTTTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAA-GACCAAAGCATCAACTTTGCG
*
3259 CGTTTGTATGCAAAACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACTTTTTGGACAGCCCT
65 CGTTTGTATGCAAAACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACTTTTTAGACAGCCCT
* *
3324 GTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGTTTGTGTGGAAAACATT
130 GTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGTTTGTGTGCAAAACATC
* * *
3389 GTTTTGAGGAACAAGTTCATTCCAGATGCGTTTTTTGCGCAATGAGTGCTCAAATGAAATGCGAC
195 ATTTTCAGGAACAAGCTCATTCCAGATGCGTTTTTTGCGCAATGAGTGCTCAAATGAAATGCGAC
* *
3454 GGAGTGAGTTGAGCATGTTGGACAGCCCTATGCACAAACAA
260 GGAGTGACTTGAGCATGTTGGACAGCCCTATGCACAAAAAA
3495 AG-TTTT
1 AGCTTTT
3501 CCACGAAGTC
Statistics
Matches: 283, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
299 6 0.02
300 277 0.98
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (300 bp):
AGCTTTTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGACCAAAGCATCAACTTTGCGC
GTTTGTATGCAAAACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACTTTTTAGACAGCCCTG
TGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGTTTGTGTGCAAAACATCA
TTTTCAGGAACAAGCTCATTCCAGATGCGTTTTTTGCGCAATGAGTGCTCAAATGAAATGCGACG
GAGTGACTTGAGCATGTTGGACAGCCCTATGCACAAAAAA
Found at i:3942 original size:270 final size:269
Alignment explanation
Indices: 3453--4250 Score: 1034
Period size: 270 Copynumber: 2.9 Consensus size: 269
3443 TGAAATGCGA
* * * *
3453 CGGAGTGAGTTGAGC-ATGTTGGACAGCCCTATGCACAAACAAAGTTTTCC-ACGAAGTCAAAAA
1 CGGAGTGAGATGAGCTAT-TTGGACAGCCCTGTGCACAAACAAAGCTTTCCTA-GAAGCCAAAAA
* * * * * * * * *
3516 CCTCAACTTATCACCAG-TTTGTGCAAAACATCATTCTTAGC-AAAA-CTCTTTTTCCGGATGCG
64 CCTCAACTT-TGAGCGGTTTTATGTAAAACATCATTTTTGGCGAAAAGCTC--ATTCCAGATGC-
* * * * * ** *
3578 ATTTTTTTGTGCAATGAGTGCTCAAAAGTCGTTTGTCAGAGTGAGATGAGAAAGATGGACAGCCC
125 A-TTTTTTGCGCAACGAGTGCTCAAATGTCGTGTGTC-GAATGAGATGAGATTGTTGGACAGCCC
* * * * *
3643 TATGCACAAAGAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGTGCGTATGTTTGCCAA-ACA
188 TATGCACAAACAAAGCTCTCCTTGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATG-CAACACA
3707 TCGTTCTTAGCGGTGTGT
252 TCGTTCTTAGCGGTGTGT
* * *
3725 CGGAGTGAGATGAGCTATTTGGACAGCCCTGTACACAAACACAGCTTTCCTAGAAGCCTAAAACC
1 CGGAGTGAGATGAGCTATTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCAAAAACC
3790 TCAACTTTGAGCGGTTTTATGTAAAACATCATTTTTGGCGAAAAGCTCATTCCAGATGCATTTTT
66 TCAACTTTGAGCGGTTTTATGTAAAACATCATTTTTGGCGAAAAGCTCATTCCAGATGCATTTTT
* * * **
3855 TGCGCTACGAGTGCTCAAATGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGGGCTATGCAC
131 TGCGCAACGAGTGCTCAAATGTCGTGTGTC-GAATGAGATGAGATTGTTGGACAGCCCTATGCAC
3920 AAACAAAGCTCTCCTTGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCGTTCTT
195 AAACAAAGCTCTCCTTGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCGTTCTT
*
3985 AGCGGTTTGT
260 AGCGGTGTGT
* * * *
3995 CGGAATGAGATGAAG-TTTTTTGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAAC
1 CGGAGTGAGATG-AGCTATTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCAAAAAC
* *
4059 CTCAACTCTGAGCGGTTGTATGTAAAACATCATTTTTGGCGAAAAGCTCATTCCAGATGCATTTT
65 CTCAACTTTGAGCGGTTTTATGTAAAACATCATTTTTGGCGAAAAGCTCATTCCAGATGCATTTT
* * * *
4124 TTGCGCAACGAGTGCTCAAATGTTGTGCGTCGAAGTGCGATGAGATTGTTGGACAGCCCTGTGCA
130 TTGCGCAACGAGTGCTCAAATGTCGTGTGTCGAA-TGAGATGAGATTGTTGGACAGCCCTATGCA
4189 CAAACAAAGCTCTCCTTGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCGT
194 CAAACAAAGCTCTCCTTGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCGT
Statistics
Matches: 465, Mismatches: 53, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
269 6 0.01
270 353 0.76
271 7 0.02
272 89 0.19
273 7 0.02
274 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (269 bp):
CGGAGTGAGATGAGCTATTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCAAAAACC
TCAACTTTGAGCGGTTTTATGTAAAACATCATTTTTGGCGAAAAGCTCATTCCAGATGCATTTTT
TGCGCAACGAGTGCTCAAATGTCGTGTGTCGAATGAGATGAGATTGTTGGACAGCCCTATGCACA
AACAAAGCTCTCCTTGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCGTTCTTA
GCGGTGTGT
Found at i:4078 original size:111 final size:111
Alignment explanation
Indices: 3881--4089 Score: 267
Period size: 111 Copynumber: 1.9 Consensus size: 111
3871 AAATGTCGTG
** * *
3881 TGTCGGAATGAGATGAGCTTGTTAGACAGGGCTATGCACAAACAAAGCTCTCCTTGAAGTCCAAA
1 TGTCGGAATGAGATGAGCTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
* * * * *
3946 GCATCAACTTTGCGCGTTTGTATGCAACACATCGTTCTTAGCGGTT
66 ACATCAACTCTGAGCGGTTGTATGCAAAACATCGTTCTTAGCGGTT
* * * *
3992 TGTCGGAATGAGATGAAG-TTTTTTGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAA
1 TGTCGGAATGAGATG-AGCTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAA
* *
4056 AACCTCAACTCTGAGCGGTTGTATGTAAAACATC
65 AACATCAACTCTGAGCGGTTGTATGCAAAACATC
4090 ATTTTTGGCG
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
111 80 0.98
112 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (111 bp):
TGTCGGAATGAGATGAGCTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
ACATCAACTCTGAGCGGTTGTATGCAAAACATCGTTCTTAGCGGTT
Done.