Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009214.1 Corchorus capsularis cultivar CVL-1 contig09235, 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: 10326
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1723 original size:645 final size:643
Alignment explanation
Indices: 1--2215 Score: 3026
Period size: 645 Copynumber: 3.4 Consensus size: 643
* * * * *
1 GAAATCGTGTACTAACCATCATGGTTTTTAGCTAAAAACGCTTTTCGGGGCACCGGCTCCGTTTC
1 GAAATCGTGTACTAACCATCATGGTTTTTGGCTAAAAACGCGTTTCGAGGCACCAGCTCCGTTTT
* * * * *
66 GTATCATTTTTGGCAGAAAGACACCTTGAAATATCTATATTCATCTAACCAAATCTCAGGCATAT
66 GTATGATTTTTGGCATAAAGACACCATGAAATATCTATATTCATCTAACCAAATCTCAGCCACAT
* * * * *
131 TGGATTTAAGGATTTATTTTTACGAGTATCTGAATCTAGTTTGGATTTAATTAAAAATAAATTCG
131 TGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCG
* * * *
196 GAAAAAAGGGAAACGATATTAGAAGCGTGAAAAAACCCTTCAATTTTGCTGGCGTTGAATTATA-
196 AAAAAAAGGAAAACGATATTAGAAGCGTG-AAAAACCCTTCAATTTTGTTGGCGTTGAGTTATAT
* * * * * ** *
260 TATTTTTTCCATATATTATGGCAAAAAATTGAGGAAAAACTTATCTAGTTAGTTTTTCAAAATTT
260 TTTTTTTTCTATATATTGTGG-TAAATATTGAGGAAAAACTTATCGGGTCAGTTTTTC-AAATTT
* * * * *
325 TAGCCGAAATCGTGTGCTTACCATCACGATTTTTGGGTAAAATGCGTCCTGGAATCCCGGTTCAA
323 TAGCCGAAATCGTGTACTAACCATCATGATTTTTGGGTAAAATGCGTCC-GGAGTCCCGCTT-AA
* * * * *
390 TTTTGTATGATTTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCAAATCAAATTTCGGCG
386 TTTTGCAT-ATCTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATTTCAGCG
* * * *
455 ACATTGGATATAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATAAC
450 ACATTGGATATAAGGATTTATTTTTATGAGCATCTGAATCTTTTTTCGATTTAATTAGAAATTAC
* * *
520 TTCGAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAGCCCGTAAATCATTTTTGCATTGAAT
515 TTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTAAATCATTTTAGCATTGAAT
585 TAAATATTTTTTCAGAGTATTGTGGCAAAAAAATTGAGAAAAAAATTTTCGAGTCAGTTTTTAGC
580 TAAATA-TTTTTCAGAGTATTGTGGC-AAAAAATTGAGAAAAAAATTTTCGAGTCAGTTTTTAGC
650 C
643 C
* *
651 GAAATCGTGTACTTAACCATCATGGCTTTTGGCTAAAAACGCGTTTC-AGGGCCCCAGCTCCGTT
1 GAAATCGTGTAC-TAACCATCATGGTTTTTGGCTAAAAACGCGTTTCGA-GGCACCAGCTCCGTT
*
715 TTGTATGATTTTTGGCATAAAGACACCATGAAATATCTATATTCATCTAACTAAATCTCAGCCAC
64 TTGTATGATTTTTGGCATAAAGACACCATGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
780 ATTGGATTTAA-AGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAAT
129 ATTGGATTTAAGA-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAAT
*
844 TCAGAAAAAAAGGGAAAACGATATTAGAAACGTGAAAAACCCTTCAATTTTGTTGGCGTTGAGTT
193 TC-GAAAAAAA-GGAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTGTTGGCGTTGAGTT
* *
909 ATATTTTTTTTTCTATATATTGTGCTAAATATTGAGGAAAAACTTATCGGGTCAATTTTTACAAA
256 ATATTTTTTTTTCTATATATTGTGGTAAATATTGAGGAAAAACTTATCGGGTCAGTTTTT-CAAA
* * *
974 TTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGGTAAAATGCATCCCGGTGTCCTGGCT
320 TTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGGTAAAATGCGT-CCGGAGTCC-CGCT
* * * * *
1039 TATTTTTGCATATCTTTGGCGCAAAGAATCCTAGAAATATTTATATTTATGGAACCAAATTTTAG
383 TAATTTTGCATATCTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATTTCAG
* * * *
1104 CGACATTGAATATAAGGATTTGTTTTTATGAG-TTCTGAATCTTTTTTCGATTTAATTAGAATTT
448 CGACATTGGATATAAGGATTTATTTTTATGAGCATCTGAATCTTTTTTCGATTTAATTAGAAATT
* * * *
1168 ACTTCGGAAAAAATGGGAAAACGATATTAGAAGCGTGACAAGCCCGTAAATCATTTTGGTATTGA
513 ACTTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTAAATCATTTTAGCATTGA
*
1233 ATTAAATATTTTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTCAGCTTTTAGC
578 ATTAAATATTTTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTCAGTTTTTAGC
1298 C
643 C
* *
1299 GAAATCGTGTACTAACCATCATGGTTTTTGGCTAAAAACGCGTTTCGATGCCCCAGCTCCGTTTT
1 GAAATCGTGTACTAACCATCATGGTTTTTGGCTAAAAACGCGTTTCGAGGCACCAGCTCCGTTTT
*
1364 GTATGATTTTTGGCATAAAGACACCATGAAATATCTATATTCATCTAACTAAATCTCAGCCACAT
66 GTATGATTTTTGGCATAAAGACACCATGAAATATCTATATTCATCTAACCAAATCTCAGCCACAT
* *
1429 TGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATAAATTCT
131 TGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCG
*
1494 AAAAAAAGGAAAACGATATTAGAAGTGTGAAAAACCCTTCAATTTTGTTGGCGTTGAGTTATATT
196 AAAAAAAGGAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTGTTGGCGTTGAGTTATATT
* *
1559 TTTTTTTCTATATATTGTGGTAAATACTGAGGAAAAATTTATCGGGTCAGTTTTTGCAAATTTTA
261 TTTTTTTCTATATATTGTGGTAAATATTGAGGAAAAACTTATCGGGTCAGTTTTT-CAAATTTTA
1624 GCCGAAATCGTGTACTAACCATCATGATTTTTGGGTAAAATGCGTGCCGGAGTCCCGACTTAATT
325 GCCGAAATCGTGTACTAACCATCATGATTTTTGGGTAAAATGCGT-CCGGAGTCCCG-CTTAATT
*
1689 TTGCATATCTTTGGTGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATTTCAGCGACA
388 TTGCATATCTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATTTCAGCGACA
* *
1754 TTGGATATGAGGATTTATTTTTATGAGCATCTGAATC-TTTTTCGGTTTAATTAGAAATTACTTC
453 TTGGATATAAGGATTTATTTTTATGAGCATCTGAATCTTTTTTCGATTTAATTAGAAATTACTTC
1818 GGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTAAATCATTTTAGCATTGAATTA
518 GG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTAAATCATTTTAGCATTGAATTA
* * * * *
1883 AATATTTTTCGGAATATTGTGGCAAAAAATGGAGGAAAAAATTTTCGAGTCAGTTTTTAGAC
582 AATATTTTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTCAGTTTTTAGCC
** * * ** ***
1945 GAAATCGTGTACTAAATATCATGGTTTTTGGCTAAAAAACAGTGTTCCG-GATTACCAGCTTAAT
1 GAAATCGTGTACTAACCATCATGGTTTTTGGCT-AAAAAC-GCGTTTCGAG-GCACCAGCTCCGT
* *** * * * * *
2009 TTTGCATGATTTTTGGTGCAAATACTCCTTGAAATATTTATATTTAT-TGAACCAAATCTCAGCC
63 TTTGTATGATTTTTGGCATAAAGACACCATGAAATATCTATATTCATCT-AACCAAATCTCAGCC
* * * * * * * * * *
2073 ACATTCGATATAAGGATTTGCTTCTACGAGTATCTGAATCTGGTTTCGATGTAATTAGAAATTAA
127 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAA
* * * * * * * *
2138 TTCGGAAAAAATGTAAAATCAATATTGGAATCGT-TAAAAGCCTGTCAATCTTTTTTGGCGTTG-
192 TTC-GAAAAAAAGGAAAA-CGATATTAGAAGCGTGAAAAACCCT-TCAAT-TTTGTTGGCGTTGA
*
2201 GATTATATATTTTTT
253 G-TTATATTTTTTTT
2216 CTGAGTATTG
Statistics
Matches: 1396, Mismatches: 146, Indels: 45
0.88 0.09 0.03
Matches are distributed among these distances:
644 1 0.00
645 285 0.20
646 160 0.11
647 182 0.13
648 174 0.12
649 37 0.03
650 123 0.09
651 261 0.19
652 130 0.09
653 43 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (643 bp):
GAAATCGTGTACTAACCATCATGGTTTTTGGCTAAAAACGCGTTTCGAGGCACCAGCTCCGTTTT
GTATGATTTTTGGCATAAAGACACCATGAAATATCTATATTCATCTAACCAAATCTCAGCCACAT
TGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCG
AAAAAAAGGAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTGTTGGCGTTGAGTTATATT
TTTTTTTCTATATATTGTGGTAAATATTGAGGAAAAACTTATCGGGTCAGTTTTTCAAATTTTAG
CCGAAATCGTGTACTAACCATCATGATTTTTGGGTAAAATGCGTCCGGAGTCCCGCTTAATTTTG
CATATCTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATTTCAGCGACATTG
GATATAAGGATTTATTTTTATGAGCATCTGAATCTTTTTTCGATTTAATTAGAAATTACTTCGGA
AAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTAAATCATTTTAGCATTGAATTAAATA
TTTTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTCAGTTTTTAGCC
Found at i:1925 original size:328 final size:319
Alignment explanation
Indices: 71--2308 Score: 1891
Period size: 328 Copynumber: 6.9 Consensus size: 319
61 GTTTCGTATC
* * * * *
71 ATTTTTGGCAG-AAAGACACCTTGAAATATCTATATTCATCTAACCAAATCTCAG-GCATATTGG
1 ATTTTTGGC-GCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATCTCAGCG-ACATTGG
* * * * * *
134 ATTTAAGGATTTATTTTTACGAGTATCTGAATCTAGTTTGGATTTAATTAAAAATAAATTCGG-A
64 ATATAAGGATTTGTTTTTACGAGCATCTGAATCT-TTTTCGATTTAATTAGAAATAAATTCGGAA
* * * *
198 AAAAA-GG-GAAACGATATTAGAAGCGTGAAAAAACCCTTCAAT--TTTGCTGGCGTTGAATTAT
128 AAAAATGGAAAAACGATATTAGAAGCGTG-AAAAGCCCGTCAATCATTT--TGGCGTTGAATTAA
* * * * *
259 ATATTTTTTCCATATATTATGGCAAAAAATTGAGGAAAAACTTATCTAGTTAGTTTTTCAAAATT
190 ATA-TTTTTCGA-ATATTGTGGCAAAAAATTGAGGAAAAA-TTTTCGAGTCAG----TC----TT
* * * * *
324 TTAGCCGAAATCGTGTGCTTACCATCACGATTTTTGGGTAAAATGCGT-CCTGGAATCCCG-G-T
244 TTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAATGCGTGCC-GGAGTCCCGAGCT
*
386 TCAATTTTGTATG
308 T-AATTTTGCATG
* * * *
399 ATTTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCAAATCAAATTTCGGCGACATTGGAT
1 ATTTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATCTCAGCGACATTGGAT
* * *
464 ATAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATAACTTC-GAAAA
66 ATAAGGATTTGTTTTTACGAGCATCTGAATCTT-TTTCGATTTAATTAGAAATAAATTCGGAAAA
* * * *
528 AAATGGAAAAACGATATTGGAAGCGTGAAAAGCCCGTAAATCATTTTTGCATTGAATTAAATATT
130 AAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCATTTTGGCGTTGAATTAAATA-T
* *
593 TTTTCAGAGTATTGTGGCAAAAAAATTGAGAAAAAAATTTTCGAGTCAGT-TTTTAGCCGAAATC
194 TTTTC-GAATATTGTGGC-AAAAAATTGAG-GAAAAATTTTCGAGTCAGTCTTTTAGCCGAAATC
** * * * * *** *
657 GTGTACTTAACCATCATGGCTTTTGGCTAAAAACGCGTTTCAGG-G-CCCCAGCTCCGTTTTGTA
256 GTGTAC-TAACCATCATGATTTTTGGCT-AAAATGCG-TGCCGGAGTCCCGAGCTTAATTTTGCA
720 TG
318 TG
** * * * * * * *
722 ATTTTTGGCATAAAGACACCATGAAATATCTATATTCATCTAACTAAATCTCAGCCACATTGGAT
1 ATTTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATCTCAGCGACATTGGAT
* * * *
787 TTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCAGAAAA
66 ATAAGGATTTGTTTTTACGAGCATCTGAATCTT-TTTCGATTTAATTAGAAATAAATTCGGAAAA
* * * * * * *
852 AAA-GGGAAAACGATATTAGAAACGTGAAAAACCCTTCAAT-TTTGTTGGCGTTGAGTTATATTT
130 AAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCATT-TTGGCGTTGAATTA-A-AT
* * * * * * *
915 TTTTTTCTATATATTGT-GCTAAATATTGAGGAAAAACTTATCGGGTCAATTTTTACAAATTTTA
192 ATTTTTCGA-ATATTGTGGCAAAAAATTGAGGAAAAA-TTTTCGAGTC-A---GT-C---TTTTA
* * * * * *
979 GCCGAAATCGTGTACTAACCATCATGATTTTTGGGTAAAATGCATCCCGGTGTCCTG-GCTTATT
247 GCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAATGCGTGCCGGAGTCCCGAGCTTAAT
1043 TTTGCAT-
312 TTTGCATG
* * * * * * *
1050 ATCTTTGGCGCAAAGAATCCTAGAAATATTTATATTTATGGAACCAAATTTTAGCGACATTGAAT
1 ATTTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATCTCAGCGACATTGGAT
* * * * *
1115 ATAAGGATTTGTTTTTATGAG-TTCTGAATCTTTTTTCGATTTAATTAGAATTTACTTCGG-AAA
66 ATAAGGATTTGTTTTTACGAGCATCTGAATC-TTTTTCGATTTAATTAGAAATAAATTCGGAAAA
* * * **
1178 AAATGGGAAAACGATATTAGAAGCGTGACAAGCCCGTAAATCATTTTGGTATTGAATTAAATATT
130 AAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCATTTTGGCGTTGAATTAAATATT
* *
1243 TTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTCAG-CTTTTAGCCGAAATCGT
195 TTTC-GAATATTGTGGCAAAAAATTGAG-GAAAAATTTTCGAGTCAGTCTTTTAGCCGAAATCGT
* * ** * *** *
1307 GTACTAACCATCATGGTTTTTGGCTAAAAACGCGTTTC-GA-TGCCCCAGCTCCGTTTTGTATG
258 GTACTAACCATCATGATTTTTGGCT-AAAATGCGTGCCGGAGT-CCCGAGCTTAATTTTGCATG
** * * * * * * *
1369 ATTTTTGGCATAAAGACACCATGAAATATCTATATTCATCTAACTAAATCTCAGCCACATTGGAT
1 ATTTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATCTCAGCGACATTGGAT
* * * * *
1434 TTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATAAATTC-TAAAA
66 ATAAGGATTTGTTTTTACGAGCATCTGAATCTT-TTTCGATTTAATTAGAAATAAATTCGGAAAA
* * * * * *
1498 AAA-GG-AAAACGATATTAGAAGTGTGAAAAACCCTTCAAT-TTTGTTGGCGTTGAGTTATATTT
130 AAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCATT-TTGGCGTTGAATTA-A-AT
* * * * * *
1560 TTTTTTCTATATATTGTGG-TAAATACTGAGGAAAAATTTATCGGGTCAGTTTTTGCAAATTTTA
192 ATTTTTCGA-ATATTGTGGCAAAAAATTGAGGAAAAATTT-TCGAGTCAG----T-C---TTTTA
*
1624 GCCGAAATCGTGTACTAACCATCATGATTTTTGGGTAAAATGCGTGCCGGAGTCCCGA-CTTAAT
247 GCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAATGCGTGCCGGAGTCCCGAGCTTAAT
1688 TTTGCAT-
312 TTTGCATG
* * *
1695 ATCTTTGGTGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATTTCAGCGACATTGGAT
1 ATTTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATCTCAGCGACATTGGAT
* * * * * *
1760 ATGAGGATTTATTTTTATGAGCATCTGAATCTTTTTCGGTTTAATTAGAAATTACTTCGGAAAAA
66 ATAAGGATTTGTTTTTACGAGCATCTGAATCTTTTTCGATTTAATTAGAAATAAATTCGGAAAAA
* * *
1825 AATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTAAATCATTTTAGCATTGAATTAAATATTT
131 AATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCATTTTGGCGTTGAATTAAATATTT
* *
1890 TTCGGAATATTGTGGCAAAAAATGGAGGAAAAAATTTTCGAGTCAGT-TTTTAGACGAAATCGTG
196 TTC-GAATATTGTGGCAAAAAATTGAGG-AAAAATTTTCGAGTCAGTCTTTTAGCCGAAATCGTG
** * ** * *
1954 TACTAAATATCATGGTTTTTGGCTAAAAAACAGTGTTCCGGATTACC-AGCTTAATTTTGCATG
259 TACTAACCATCATGATTTTTGGCTAAAATGC-GTG--CCGGAGTCCCGAGCTTAATTTTGCATG
* * * * *
2017 ATTTTTGGTGCAAATACTCCTTGAAATATTTATATTTATTGAACCAAATCTCAGCCACATTCGAT
1 ATTTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATCTCAGCGACATTGGAT
* * * * * *
2082 ATAAGGATTTGCTTCTACGAGTATCTGAATCTGGTTTCGATGTAATTAGAAATTAATTCGG-AAA
66 ATAAGGATTTGTTTTTACGAGCATCTGAATCT-TTTTCGATTTAATTAGAAATAAATTCGGAAAA
* * * * * * * * * *
2146 AAATGTAAAATCAATATTGGAATCGTTAAAAGCCTGTCAATCTTTTTTGGCGTTGGATTATATAT
130 AAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATC-ATTTTGGCGTTGAATTAAATA-
* ** * * *
2211 TTTTTCTGAGTATTGTGGCAAAAAATTGATAAAAAAACTTTTCG-GATCAATTTTTTGGCCGAAA
193 TTTTTC-GAATATTGTGGCAAAAAATTGA-GGAAAAA-TTTTCGAG-TCAGTCTTTTAGCCGAAA
* * *
2275 TCGTGTACTAACCATCACGGTTTTTTGCTAAAAT
254 TCGTGTACTAACCATCATGATTTTTGGCTAAAAT
2309 TTGCAAAAAA
Statistics
Matches: 1533, Mismatches: 295, Indels: 166
0.77 0.15 0.08
Matches are distributed among these distances:
316 1 0.00
317 44 0.03
318 107 0.07
319 92 0.06
320 51 0.03
321 45 0.03
322 160 0.10
323 210 0.14
324 57 0.04
325 48 0.03
326 171 0.11
327 118 0.08
328 279 0.18
329 63 0.04
330 59 0.04
331 28 0.02
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (319 bp):
ATTTTTGGCGCAAAGACTCCTTGAAATATTTATATTTATCGAACCAAATCTCAGCGACATTGGAT
ATAAGGATTTGTTTTTACGAGCATCTGAATCTTTTTCGATTTAATTAGAAATAAATTCGGAAAAA
AATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCATTTTGGCGTTGAATTAAATATTT
TTCGAATATTGTGGCAAAAAATTGAGGAAAAATTTTCGAGTCAGTCTTTTAGCCGAAATCGTGTA
CTAACCATCATGATTTTTGGCTAAAATGCGTGCCGGAGTCCCGAGCTTAATTTTGCATG
Found at i:7252 original size:22 final size:22
Alignment explanation
Indices: 7226--7322 Score: 73
Period size: 22 Copynumber: 4.6 Consensus size: 22
7216 ATATTCATAC
7226 GAAATTATGATAACCTTCCTAT
1 GAAATTATGATAACCTTCCTAT
*
7248 TAAATTATGATAA--TTACACTAT
1 GAAATTATGATAACCTT-C-CTAT
** *
7270 --TTTTGATGATATCC-T--TAT
1 GAAATT-ATGATAACCTTCCTAT
*
7288 GAAATTTTGATAACCTTCCTAT
1 GAAATTATGATAACCTTCCTAT
7310 GAAATTATGATAA
1 GAAATTATGATAA
7323 TTACACTATT
Statistics
Matches: 56, Mismatches: 9, Indels: 20
0.66 0.11 0.24
Matches are distributed among these distances:
18 3 0.05
19 7 0.12
20 7 0.12
21 7 0.12
22 32 0.57
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (22 bp):
GAAATTATGATAACCTTCCTAT
Found at i:7372 original size:22 final size:21
Alignment explanation
Indices: 7347--7994 Score: 263
Period size: 22 Copynumber: 30.0 Consensus size: 21
7337 ATGACGTCCT
7347 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
** * *
7369 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAAC-CTCC
* *
7391 TATGAAATTTCGAGAACCT--
1 TATGAAATTTTGATAACCTCC
* * ** *
7410 TTTTATAATTTTTTTAAACCTTCT
1 TATGA-AATTTTGAT-AACC-TCC
*
7434 TATGAAATTTTGTTAACCTCTC
1 TATGAAATTTTGATAACCTC-C
* * * *
7456 TAAGGAATTTTGA-AGATCTCAT
1 TATGAAATTTTGATA-ACCTC-C
*
7478 TATGAAATTTTGATAACTTCC
1 TATGAAATTTTGATAACCTCC
* **
7499 AAATGAAATTTTGATAATCAACAC
1 -TATGAAATTTTGATAA-CCTC-C
*
7523 TAT-AAGATGTTGATAACCTCC
1 TATGAA-ATTTTGATAACCTCC
* * * * *
7544 ATATGATATATTGATAATCACGT
1 -TATGAAATTTTGATAACCTC-C
* * *
7567 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
7588 ATATG-AATTGTT-AGTAATCGCAC
1 -TATGAAATT-TTGA-TAACCTC-C
* * *
7611 TTTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTC-C
*
7633 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
7655 TATGAAATTTTGATAATCCTTCC
1 TATGAAATTTTGATAA-CC-TCC
* *
7678 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCT-CC
*
7701 TATAAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
7722 TTATGAAATCTTAATAA----C
1 -TATGAAATTTTGATAACCTCC
*
7740 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
** *
7761 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTC-C
* *
7783 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
7805 TATGAAATTTTGATCTACATAC
1 TATGAAATTTTGAT-AACCTCC
*
7827 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CCTCC
* * *
7849 TCTGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
*
7871 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACC-TCC
* *
7893 TATGAAATTGTGATATCCTCC
1 TATGAAATTTTGATAACCTCC
* *
7914 -ATTAAATTTTGATTA-CTCC
1 TATGAAATTTTGATAACCTCC
* * *
7933 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACC-TCC
* *
7957 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACC-TCC
7974 TATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
7995 CCAAAAATAC
Statistics
Matches: 463, Mismatches: 112, Indels: 103
0.68 0.17 0.15
Matches are distributed among these distances:
16 10 0.02
17 12 0.03
18 3 0.01
19 8 0.02
20 19 0.04
21 28 0.06
22 302 0.65
23 69 0.15
24 12 0.03
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:7393 original size:62 final size:62
Alignment explanation
Indices: 7226--7377 Score: 259
Period size: 62 Copynumber: 2.5 Consensus size: 62
7216 ATATTCATAC
* * *
7226 GAAATTATGATAACCTTCCTATTAAATTATGATAATTACACTATTTTTGATGATATCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACATCCTTAT
* *
7288 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACATCCTTAT
7350 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACCTTCCTATGAAATT
7378 TCAATAACGA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 85 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACATCCTTAT
Found at i:7716 original size:46 final size:44
Alignment explanation
Indices: 7615--7716 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 44
7605 TCGCACTTTG
* * *
7615 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTATG
1 AAATTTTGATAATCACACTATAAAATTGTGATAACCTCCCTATA
* * *
7659 AAATTTTGATAATC-CTTCCTATAAAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAATCAC--ACTATAAAATTGTGAT-AACCTCCCTATA
7705 AAATTTTGATAA
1 AAATTTTGATAA
7717 CCTCCTTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 1 0.02
44 14 0.29
45 13 0.27
46 21 0.43
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAATCACACTATAAAATTGTGATAACCTCCCTATA
Found at i:8057 original size:22 final size:22
Alignment explanation
Indices: 8032--8137 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
8022 AATCACATTT
* *
8032 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
8054 TGAAA-TTTGAATAACCTCTCTA
1 TGAAATTTTG-ATAACCTCTCTA
* * * *
8076 TCAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
** *
8098 TGAAATTTTGATAGTCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
*
8120 TGTAATTTTGATAACCTC
1 TGAAATTTTGATAACCTC
8138 GTTTTATGCT
Statistics
Matches: 66, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
21 4 0.06
22 57 0.86
23 5 0.08
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:8937 original size:37 final size:36
Alignment explanation
Indices: 8845--8941 Score: 95
Period size: 38 Copynumber: 2.6 Consensus size: 36
8835 ATCTAAGCCC
* *
8845 AAATAGGACGTTGGAGACGAAAATAAAAAGCAAAATT
1 AAATAGGAAGTTGGAAAC-AAAATAAAAAGCAAAATT
** * * *
8882 AAATACAACAATTAGAAACAAAGATAAAAGGCAAAATT
1 AAATAGGA-AGTTGGAAACAAA-ATAAAAAGCAAAATT
*
8920 AAATAGGATGTTGGAAACAAAA
1 AAATAGGAAGTTGGAAACAAAA
8942 AGTCAAATTG
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
36 1 0.02
37 19 0.41
38 26 0.57
ACGTcount: A:0.58, C:0.08, G:0.18, T:0.16
Consensus pattern (36 bp):
AAATAGGAAGTTGGAAACAAAATAAAAAGCAAAATT
Done.