Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022452.1 Corchorus olitorius cultivar O-4 contig22485, 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: 15144
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:166 original size:25 final size:24
Alignment explanation
Indices: 132--178 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
122 ACGTTTGCAC
132 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
157 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
179 TATAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:4387 original size:16 final size:16
Alignment explanation
Indices: 4352--4383 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4342 AATAAAAAAG
4352 ATTTTATTTACTTTTT
1 ATTTTATTTACTTTTT
4368 ATTTTATTTA-TTTTT
1 ATTTTATTTACTTTTT
4383 A
1 A
4384 ATTTCAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTATTTACTTTTT
Found at i:4470 original size:20 final size:21
Alignment explanation
Indices: 4439--4479 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
4429 CACATAGGCA
4439 AAAAAATGGGTTTAACGGCGC
1 AAAAAATGGGTTTAACGGCGC
4460 AAAAAAT-GGTTTAACGGCGC
1 AAAAAATGGGTTTAACGGCGC
4480 GTGTTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (21 bp):
AAAAAATGGGTTTAACGGCGC
Found at i:8353 original size:29 final size:29
Alignment explanation
Indices: 8320--8403 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
8310 TCAAGGGCTA
* *
8320 AAAACAGCACCGAAAGGTCAATCAGGCAG
1 AAAACAGGACCGAAAGGTCAAACAGGCAG
*
8349 AAAACAGGACC-AAGAGGTCAAACATGCAG
1 AAAACAGGACCGAA-AGGTCAAACAGGCAG
8378 AAAACAGGACCGAAAGGTCAAACAGG
1 AAAACAGGACCGAAAGGTCAAACAGG
8404 ACCAAGAGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.04
29 45 0.92
30 2 0.04
ACGTcount: A:0.48, C:0.21, G:0.25, T:0.06
Consensus pattern (29 bp):
AAAACAGGACCGAAAGGTCAAACAGGCAG
Found at i:8402 original size:18 final size:17
Alignment explanation
Indices: 8379--8515 Score: 91
Period size: 18 Copynumber: 8.4 Consensus size: 17
8369 AACATGCAGA
8379 AAACAGGACCGAAAGGTC
1 AAACAGGACC-AAAGGTC
8397 AAACAGGACCAAGAGGTC
1 AAACAGGACCAA-AGGTC
* *
8415 AACCAGG--C--A-G-A
1 AAACAGGACCAAAGGTC
8426 AAACAGGACCAAAGGGTC
1 AAACAGGACCAAA-GGTC
8444 AAACAGGACCAAGAGGTC
1 AAACAGGACCAA-AGGTC
* *
8462 AAACATG--C--A-G-A
1 AAACAGGACCAAAGGTC
8473 AAACAGGACCGAAAGGTC
1 AAACAGGACC-AAAGGTC
*
8491 AAACAGAACCAAGAGGTC
1 AAACAGGACCAA-AGGTC
8509 AAACAGG
1 AAACAGG
8516 CAGAAAACAG
Statistics
Matches: 92, Mismatches: 10, Indels: 34
0.68 0.07 0.25
Matches are distributed among these distances:
11 12 0.13
12 2 0.02
13 4 0.04
15 1 0.01
16 3 0.03
17 6 0.07
18 63 0.68
19 1 0.01
ACGTcount: A:0.47, C:0.22, G:0.26, T:0.05
Consensus pattern (17 bp):
AAACAGGACCAAAGGTC
Found at i:8404 original size:47 final size:47
Alignment explanation
Indices: 8350--8542 Score: 334
Period size: 47 Copynumber: 4.1 Consensus size: 47
8340 ATCAGGCAGA
*
8350 AAACAGGACCAAGAGGTCAAACATGCAGAAAACAGGACCGAAAGGTC
1 AAACAGGACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAAAGGTC
*
8397 AAACAGGACCAAGAGGTCAACCAGGCAGAAAACAGGACC-AAAGGGTC
1 AAACAGGACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAAA-GGTC
*
8444 AAACAGGACCAAGAGGTCAAACATGCAGAAAACAGGACCGAAAGGTC
1 AAACAGGACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAAAGGTC
*
8491 AAACAGAACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAAAGGTC
1 AAACAGGACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAAAGGTC
8538 AAACA
1 AAACA
8543 AAGCGGAATA
Statistics
Matches: 138, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
46 3 0.02
47 132 0.96
48 3 0.02
ACGTcount: A:0.48, C:0.22, G:0.25, T:0.05
Consensus pattern (47 bp):
AAACAGGACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAAAGGTC
Found at i:8822 original size:28 final size:29
Alignment explanation
Indices: 8790--8858 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
8780 GATGTGGCAA
* *
8790 AATGACGTGGCAGGTTGA-TTGGTCAACG
1 AATGACGTGGCAGGTTGACTCGATCAACG
*
8818 AATGATGTGGCAGGTTGACTCGATCAACG
1 AATGACGTGGCAGGTTGACTCGATCAACG
*
8847 GATGACGTGGCA
1 AATGACGTGGCA
8859 ATTTAAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.26, C:0.16, G:0.35, T:0.23
Consensus pattern (29 bp):
AATGACGTGGCAGGTTGACTCGATCAACG
Found at i:11396 original size:667 final size:658
Alignment explanation
Indices: 10192--12616 Score: 2394
Period size: 667 Copynumber: 3.7 Consensus size: 658
10182 CCCGGGTCAG
* * *
10192 TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAATTATCTATATTTATCTAATCAATTCTCAGCC
1 TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
* * * *
10257 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTTC-ATTTAATTATAAATTA
66 ACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTT-GTTTCGATTTAATTAGAAATTA
* * * * * * * * * *
10321 ATTCTGAAAAAGTAGGAAAAACAATATTAGAAGCATAAAAAATTCTTCAAA-ATTTTTGGCATTG
130 ATTCAGAAAAAATATGAAAAACAATATTAAAAGCGT-GAAAAGTCCTCAAATATTTTTGACGTTG
* * * * * *
10385 AATTATATATTTTTTTTGAGTA-TTTAGCCAAAAATCGA-GGAAATATCTTTCAGGTCAATTTTT
194 AATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTTTCTGGTCAATTTTT
* * **
10448 GCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGGTTTTGAATAAAAACGCGTTACAGGAC
259 GCAAAATTTTAGCCGAAATCGTGTACT-ATCATCACGGGTTTTGGCTAAAAACGCGTTACAGGA-
* * * * * * *
10513 CCCTAG-TCAGTGTTGCATTATTTTTGGTGCTAAGACTCCTTGAGATGT-TCGTATTCATCTAAT
322 CCCTGGTTCAGTGTTGCATTA-TTTTGTTGCCAAGACTCCTTGAAATATCT-ATATTCATCTAAC
* * * * * *
10576 CAGATCTCAGCCGCATTGCATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTTTTTCGATTTA
385 CAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
* * *
10641 ATTAG-AATTCAATTCA-AAAAAAAATGTGAAAAACCGATATGAAAAGCGTGAAAAATTCTC-T-
450 ATTAGAAATT-AATTCAGAAAAAATA-G-G-AAAA-CGATATTAAAAGCGTG--AAATGCTCTTC
* * * *
10702 AATCTTTTTGGCGTTAAATTATATATATTTTAAGAGTATTTTCACCAAAAATCGTGGGAAAACTT
508 AATCTTTTTGACATTAAATTATATAT-TTTTAAGAGTATTTT-ACCAAAAATTGTGGAAAAACTT
* * * * * *
10767 TTCAGGTCATTTTTTTCCAAAATTTTGGTCGATATCGTGTACAAACCATCACGGTTTTTTTGCTA
571 TTCAGGTCA-TTTTTTGCAAAATTTTAGCCGAAATCGTGTACAAACTATCACGG-TTTTTGGCTA
* *
10832 AAAACGCCTTTTGGGGCCCGGACTCAA
634 AAAACGCGTTTCGGGGCCC-GACT-AA
** * * *
10859 TTTTGCATGATTTTTTCCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCC
1 TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
* * *
10924 ACATTGCATTTAAGGATTTGTTTTTACTAGCATCTGAATCTTCTTTCGATTTAATTAGAAATTAA
66 ACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * *
10989 TTTAGAAAAAATATG-AAAACAATTTTAAAAGCGTGAAAAGTCCTCAAATCTTTTTGGA-GTTGA
131 TTCAGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCCTCAAATATTTTT-GACGTTGA
* * * * *
11052 ATTATATATATCTTATGAGTATTTTAGACAAAAACTGA-GGAAAAATATCTCTGGTCAATTTTTG
195 ATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTTTCTGGTCAATTTTTG
* * * * * *
11116 CAAAATATTAGGCGAAATTGTGTACGTTATTCGAAGTCACGGGTTTTGGCTAAAAAAGCATTCCA
260 CAAAATTTTAGCCGAAATCGTGTAC--TA-TC--A-TCACGGGTTTTGGCTAAAAACGCGTTACA
* *
11181 GGACCCTGGTTCAGTGTTGCATTCTTTTGTTGCCGAGACTCCTTGAAATATCTATATTCATCTAA
319 GGACCCTGGTTCAGTGTTGCATTATTTTGTTGCCAAGACTCCTTGAAATATCTATATTCATCTAA
* *** *
11246 CCAAATCTCAGCCACATTGGATTTAAGGATTTG-TAAAACAAGCATCTGAATCATGTTTCGATTT
384 CCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTT
* * *
11310 AATTAGAAATTAATT-AGGAAAATAATAGGAAAAGCGATATTAGAAGCATGAAATGCCCTTCAAT
449 AATTAGAAATTAATTCA-GAAAA-AATAGGAAAA-CGATATTAAAAGCGTGAAATGCTCTTCAAT
* * ** * * *
11374 CTTTTTGACATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGTAAATAAC-TTT
511 CTTTTTGACATTAAATTATATA-TTTTTAAGAGTATT-TTACCAAAAATTGTGGAAA-AACTTTT
** * *
11438 CAATTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-ATAATTATCACGGTTTTTGGCTAAAA
573 CAGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACA-AACTATCACGGTTTTTGGCTAAAA
* ***
11502 ACGCGTTCCAGAACCCCGACTAA
637 ACGCGTTTC-GGGGCCCGACTAA
** * * * * * *
11525 GTTTTGCATGATTTTTAACGCCAAGCCTCTTTGAGATATCCATATTCATATAATCAAATCTCTGC
1 -TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
* *
11590 TACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
65 CACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * *
11655 ATTCAG-AAAAATATGAAAAAAAGATATTAAAAGCGTGAAAAGTACC-CCAATCTTTTTGACATT
130 ATTCAGAAAAAATATGAAAAACA-ATATTAAAAGCGTGAAAAGT-CCTCAAATATTTTTGACGTT
* ** * *
11718 CAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGATTGAAAAATTTTTCGGGTCATTTTT
193 GAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTTTCTGGTCAATTTT
** * * ***
11783 TGCAAAATTTTAGATGAAATCGTGTACTAACCATCA-GAGTTTTTGGCTAAAAACGCGTTTTTGG
258 TGCAAAATTTTAGCCGAAATCGTGTACT-ATCATCACG-GGTTTTGGCTAAAAACGCGTTACAGG
* * * * *
11847 TTCCC-GGCTT-AGTTTTGCATGATTTT-TGGCTCTAAGACTCCATGAAATATCTATATTCATCT
321 -ACCCTGG-TTCAGTGTTGCATTATTTTGTTGC-C-AAGACTCCTTGAAATATCTATATTCATCT
* *
11909 AACCAAATCTCAACCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTGAAT-ATTGTTTCGA
382 AACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCA-TGTTTCGA
* * *
11973 TTTAATTAGAAATTAATTCAG-AAAAATATGATAAACGATATTAAAAGCGTGAAAAG-TATTCAA
446 TTTAATTAGAAATTAATTCAGAAAAAATAGGA-AAACGATATTAAAAGCGTGAAATGCTCTTCAA
* *
12036 TCTTTTCTTGA-AGTTAAATTATATAAATTTTTAATAATATTTTATCCAAAAATTGATGGAAAAA
510 TC-TTT-TTGACA-TTAAATTATAT--ATTTTTAAGAGTATTTTA-CCAAAAATTG-TGGAAAAA
* ** * *
12100 ATTTTTGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACTATCACGGTTTTTGGCT
568 CTTTTCAGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACAAACTATCACGGTTTTTGGCT
* * *
12165 AAAAAAGCGTTTCGGGGCATCGACTTAG
633 AAAAACGCGTTTCGGGGC-CCGAC-TAA
* * * ** * *
12193 TTTTGCATGATTTTTGGCACCAAGACTCCATAAAATATCTATATTTGTCTAATCAAATATCAACC
1 TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
* *
12258 ACATTGAATTTAAGGATTTGTTTTTACAAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAA
66 ACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
12323 TTCA-AAAAAATATGAATAACTATATTAAAAGTGTGAAAAGTCCTCCAATATTTTTGACGTT-AC
131 TTCAGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCCTCAAATATTTTTGACGTTGA-
* * *
12386 TATTATATGTATTTTATGAGTATTTTAGGCAAAAATTGACGGAAAAATTTTTCTGGTCACTTTTT
195 -ATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTTTCTGGTCAATTTTT
* ***
12451 ACAAAATTTTAGCCGAAATCGTG--------TCA-GGGTTTTTGGCTAAAAACGCGTTTTGGGAC
259 GCAAAATTTTAGCCGAAATCGTGTACTATCATCACGGG-TTTTGGCTAAAAACGCGTTACAGGAC
* * * * * * *
12507 CCCGGCTT-AGTTTTGCATGATTTT-TGGCGGCGAGACTCCATGAAATATCTATATTCATCTAAT
323 CCTGG-TTCAGTGTTGCATTATTTTGTTGC--CAAGACTCCTTGAAATATCTATATTCATCTAAC
* ** **
12570 CAAATTTTTGCCACATTGAATTTAACTATTT-TTTATTACGAGCATCT
385 CAAATCTCAGCCACATTGAATTTAAGGATTTGTTT-TTACGAGCATCT
12617 TGTCGCAACG
Statistics
Matches: 1469, Mismatches: 231, Indels: 125
0.80 0.13 0.07
Matches are distributed among these distances:
657 7 0.00
658 119 0.08
659 1 0.00
663 11 0.01
664 67 0.05
665 101 0.07
666 157 0.11
667 617 0.42
668 111 0.08
669 118 0.08
670 40 0.03
671 77 0.05
672 43 0.03
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (658 bp):
TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
ACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCAGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCCTCAAATATTTTTGACGTTGAA
TTATATATATTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTTTCTGGTCAATTTTTGC
AAAATTTTAGCCGAAATCGTGTACTATCATCACGGGTTTTGGCTAAAAACGCGTTACAGGACCCT
GGTTCAGTGTTGCATTATTTTGTTGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATC
TCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGA
AATTAATTCAGAAAAAATAGGAAAACGATATTAAAAGCGTGAAATGCTCTTCAATCTTTTTGACA
TTAAATTATATATTTTTAAGAGTATTTTACCAAAAATTGTGGAAAAACTTTTCAGGTCATTTTTT
GCAAAATTTTAGCCGAAATCGTGTACAAACTATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGC
CCGACTAA
Found at i:11839 original size:333 final size:331
Alignment explanation
Indices: 10190--12616 Score: 2303
Period size: 333 Copynumber: 7.3 Consensus size: 331
10180 GCCCCGGGTC
* * *
10190 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAATTATCTATATTTATCTAATCAATTCTCAG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* * * *
10255 CCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTTC-ATTTAATTATAAAT
66 CCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTT-GTTTCGATTTAATTAGAAAT
* * * * * * * ** ** *
10319 TAATTCTGAAAAAGTAGGAAAAACAATATTAGAAGCATAAAAAATTCTTCAAAATTTTTGGCATT
130 TAATTCAGAAAAA-TATGAAAAACGATATTAAAAGCGT-GAAAAGTCCCCAATCTTTTTGACATT
* * * * *
10384 GAATTATATATTTTTTTTGAGTA-TTTAGCCAAAAATCGA-GGAAATATCTTTCAGGTCAATTTT
193 GAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGATGGAAAAATTTTTCAGGTCAATTTT
* * ** *
10447 TGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGG-TTTTGAATAAAAACGCGTTACAGG
258 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GGTTTTTGGCTAAAAACGCGTTTCAGG
* * *
10511 ACCCCTAGTC
322 ACCCCGACTA
* * * * * * * *
10521 AGTGTTGCATTATTTTTGGTGCTAAGACTCCTTGAGATGT-TCGTATTCATCTAATCAGATCTCA
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCT-ATATTCATCTAATCAAATCTCA
* * * * *
10585 GCCGCATTGCATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTTTTTCGATTTAATTAG-AAT
65 GCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * * * * *
10649 TCAATTCAAAAAAAAATGTGAAAAACCGATATGAAAAGCGTGAAAAATTCTCTAATCTTTTTGGC
130 T-AATTC--AGAAAAATATGAAAAA-CGATATTAAAAGCGTG-AAAAGTCCCCAATCTTTTTGAC
* * * * * *
10714 GTTAAATTATATATATTTTAAGAGTATTTTCA-CCAAAAATCG-TGGGAAAACTTTTCAGGTCAT
190 ATTGAATTATATATATTTTATGAGTATTTT-AGCCAAAAATTGATGGAAAAATTTTTCAGGTCA-
* * * * * * * *
10777 TTTTTTCCAAAATTTTGGTCGATATCGTGTACAAACCATCACGGTTTTTTTGCTAAAAACGCCTT
253 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGGCTAAAAACGCGTT
** * *
10842 TTGGGGCCCGGACTCA
317 TCAGGACCCCGACT-A
** * * *
10858 A-TTTTGCATGATTTTTTCCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* * *
10922 CCACATTGCATTTAAGGATTTGTTTTTACTAGCATCTGAATCTTCTTTCGATTTAATTAGAAATT
66 CCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * *
10987 AATTTAGAAAAAATATG-AAAACAATTTTAAAAGCGTGAAAAGTCCTCAAATCTTTTTGGA-GTT
131 AATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC-CCAATCTTTTT-GACATT
* * * * * *
11050 GAATTATATATATCTTATGAGTATTTTAGACAAAAACTGA-GGAAAAATATCTCTGGTCAATTTT
193 GAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGATGGAAAAATTTTTCAGGTCAATTTT
* * * * * * * * *
11114 TGCAAAATATTAGGCGAAATTGTGTACGTTATTCGAAGTCACGGGTTTTGGCTAAAAAAGCATTC
258 TGCAAAATTTTAGCCGAAATCGTGTAC--TA-AC-CA-TCACGGTTTTTGGCTAAAAACGCGTTT
* ** *
11179 CAGGACCCTGGTTC
318 CAGGACCCCGACTA
* ** * *
11193 AGTGTTGCAT--TCTTTTGTTGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCA
1 AGTTTTGCATGAT-TTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
*** *
11256 GCCACATTGGATTTAAGGATTTG-TAAAACAAGCATCTGAATCATGTTTCGATTTAATTAGAAAT
65 GCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * * *
11320 TAATT-AGGAAAATAATAGGAAAAGCGATATTAGAAGCATGAAATG-CCCTTCAATCTTTTTGAC
130 TAATTCA-G-AAA-AATATGAAAAACGATATTAAAAGCGTGAAAAGTCCC--CAATCTTTTTGAC
* * * * * * **
11383 ATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGA-GTAAATAA-CTTTCAATTCAA
190 ATTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGATGGAAA-AATTTTTCAGGTCAA
* ** *
11446 TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATTATCACGGTTTTTGGCTAAAAACGCGTTCC
254 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC
*
11511 AGAACCCCGACTA
319 AGGACCCCGACTA
** * * * * * *
11524 AGTTTTGCATGATTTTTAACGCCAAGCCTCTTTGAGATATCCATATTCATATAATCAAATCTCTG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* *
11589 CTACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
66 CCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* *
11654 AATTCAGAAAAATATGAAAAAAAGATATTAAAAGCGTGAAAAGTACCCCAATCTTTTTGACATTC
131 AATTCAGAAAAATATG-AAAAACGATATTAAAAGCGTGAAAAGT-CCCCAATCTTTTTGACATTG
* * *
11719 AATTATATATATTTTATGAGTATTTTAGCCAAAAATTGATTGAAAAATTTTTCGGGTCATTTTTT
194 AATTATATATATTTTATGAGTATTTTAGCCAAAAATTGATGGAAAAATTTTTCAGGTCAATTTTT
** ** *
11784 GCAAAATTTTAGATGAAATCGTGTACTAACCATCA-GAGTTTTTGGCTAAAAACGCGTTTTTGGT
259 GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACG-GTTTTTGGCTAAAAACGCGTTTCAGGA
* * *
11848 TCCCGGCTT
323 CCCCGACTA
* * * * *
11857 AGTTTTGCATGATTTTTGGCTCTAAGACTCCATGAAATATCTATATTCATCTAACCAAATCTCAA
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* * * *
11922 CCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATT
66 CCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* ***
11987 AATTCAGAAAAATATGATAAACGATATTAAAAGCGTGAAAAGTATTCAATCTTTTCTTGA-AGTT
131 AATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCCCAATC-TTT-TTGACA-TT
* * * * * *
12051 AAATTATATAAATTTTTAAT-AATATTTTATCCAAAAATTGATGGAAAAAATTTTT-GGGTCATT
193 GAATTATATATA-TTTT-ATGAGTATTTTAGCCAAAAATTGATGG-AAAAATTTTTCAGGTCAAT
* * * *
12114 TTTTGCAAAATTTTAGCCAAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAAAAGCGTTTCG
255 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCA
* ** *
12179 GGGCATCGACTT
320 GGACCCCGACTA
* * * ** * *
12191 AGTTTTGCATGATTTTTGGCACCAAGACTCCATAAAATATCTATATTTGTCTAATCAAATATCAA
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* *
12256 CCACATTGAATTTAAGGATTTGTTTTTACAAGCATCCGAATCTTGTTTCGATTTAATTAGAAATT
66 CCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * * *
12321 AATTCAAAAAAATATGAATAACTATATTAAAAGTGTGAAAAGTCCTCCAATATTTTTGACGTT-A
131 AATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC-CCAATCTTTTTGACATTGA
* * * * *
12385 CTATTATATGTATTTTATGAGTATTTTAGGCAAAAATTGACGGAAAAATTTTTCTGGTCACTTTT
195 --ATTATATATATTTTATGAGTATTTTAGCCAAAAATTGATGGAAAAATTTTTCAGGTCAATTTT
* * **
12450 TACAAAATTTTAGCCGAAATCGTG---------TCAGGGTTTTTGGCTAAAAACGCGTTTTGGGA
258 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCAGGA
* *
12506 CCCCGGCTT
323 CCCCGACTA
* * * * **
12515 AGTTTTGCATGATTTTTGGCGGCGAGACTCCATGAAATATCTATATTCATCTAATCAAATTTTTG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* ** *
12580 CCACATTGAATTTAACTATTT-TTTATTACGAGCATCT
66 CCACATTGGATTTAAGGATTTGTTT-TTACAAGCATCT
12617 TGTCGCAACG
Statistics
Matches: 1728, Mismatches: 309, Indels: 125
0.80 0.14 0.06
Matches are distributed among these distances:
323 3 0.00
324 118 0.07
330 10 0.01
331 158 0.09
332 221 0.13
333 450 0.26
334 354 0.20
335 138 0.08
336 262 0.15
337 14 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (331 bp):
AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
CCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
AATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCCCAATCTTTTTGACATTGAA
TTATATATATTTTATGAGTATTTTAGCCAAAAATTGATGGAAAAATTTTTCAGGTCAATTTTTGC
AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCAGGACCC
CGACTA
Done.