Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013053.1 Corchorus olitorius cultivar O-4 contig13086, 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: 22431
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--41 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42 CAAACACATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4385 original size:5 final size:5
Alignment explanation
Indices: 4375--4407 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
4365 CTATATGTTT
4375 AAATA AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
4408 CTAGTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:11860 original size:22 final size:22
Alignment explanation
Indices: 11786--12000 Score: 197
Period size: 22 Copynumber: 9.8 Consensus size: 22
11776 TCACAGGGAT
* *
11786 GTTATCAAAA-ATCATAGGAAG
1 GTTATCAAAATTTCATAGGTAG
* *
11807 ATTA-CAAAATTTCATAGGAAAG
1 GTTATCAAAATTTCATAGG-TAG
* * *
11829 TTTATTAAAATTTCATAGTTAG
1 GTTATCAAAATTTCATAGGTAG
*
11851 GTTATCAAAATTTCATATGGAAG
1 GTTATCAAAATTTCATA-GGTAG
* *
11874 GTTTATTAAAATTTCATAGTTAG
1 G-TTATCAAAATTTCATAGGTAG
11897 GTTATCAAAATTTCATATGG-AG
1 GTTATCAAAATTTCATA-GGTAG
* *
11919 TTTATCACAATTTCATAGGTA-
1 GTTATCAAAATTTCATAGGTAG
* * * *
11940 ATCATCAAAATTTCATATGTTG
1 GTTATCAAAATTTCATAGGTAG
*
11962 GTTATCAAAATTTTATAGGGTA-
1 GTTATCAAAATTTCATA-GGTAG
11984 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
12001 AAAATATTCA
Statistics
Matches: 157, Mismatches: 28, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.03
21 28 0.18
22 86 0.55
23 23 0.15
24 15 0.10
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGTAG
Found at i:11885 original size:46 final size:45
Alignment explanation
Indices: 11787--12000 Score: 226
Period size: 44 Copynumber: 4.8 Consensus size: 45
11777 CACAGGGATG
* * *
11787 TTATCAAAA-ATCATAGGAAGATTA-CAAAATTTCATA-GGAAAGT
1 TTATCAAAATTTCATAGGTAG-TTATCAAAATTTCATATGGAAGGT
* *
11830 TTATTAAAATTTCATAGTTAGGTTATCAAAATTTCATATGGAAGGT
1 TTATCAAAATTTCATAGGTA-GTTATCAAAATTTCATATGGAAGGT
* *
11876 TTATTAAAATTTCATAGTTAGGTTATCAAAATTTCATATGG-A-GT
1 TTATCAAAATTTCATAGGTA-GTTATCAAAATTTCATATGGAAGGT
* * * **
11920 TTATCACAATTTCATAGGTAATCATCAAAATTTCATAT-GTTGG-
1 TTATCAAAATTTCATAGGTAGTTATCAAAATTTCATATGGAAGGT
*
11963 TTATCAAAATTTTATAGGGTAGTTATCAAAATTTCATA
1 TTATCAAAATTTCATA-GGTAGTTATCAAAATTTCATA
12001 AAAATATTCA
Statistics
Matches: 149, Mismatches: 15, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
42 1 0.01
43 38 0.26
44 49 0.33
45 14 0.09
46 47 0.32
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (45 bp):
TTATCAAAATTTCATAGGTAGTTATCAAAATTTCATATGGAAGGT
Found at i:12065 original size:2 final size:2
Alignment explanation
Indices: 12058--12082 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12048 CTAAAACTAG
12058 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12083 TAAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13035 original size:400 final size:398
Alignment explanation
Indices: 12295--13036 Score: 908
Period size: 400 Copynumber: 1.9 Consensus size: 398
12285 TAATTTTTGG
* *** *
12295 TTGGATTATTTATCTAATGAACCTCATACTTTTATACTTTATGCTATTTAGTCCTTTACAATTAT
1 TTGGATTATTTATCAAATGAACCTCATACTTTTATACTTTATAAAACTTAGTCCTTTACAATTAT
* * * * *
12360 AGGTTGGATGATTTAACGCATTGCCTTTTATTTTTGTATTTTTGTCTATTTGTCCGATTAACGTG
66 AGGTTGAATGATTTAACACATTGCCTTTAATTTTTATATTTTTGTATATTTGTCCGATTAACGTG
* *
12425 ATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAATTTTAATTAAGAACTCAAAAGCCAAT
131 ATTCAAGTGCCTATTAAAAGGTAATTTCATGATCTACAATTTCAATT-AGAACTCAAAAGCCAAT
** * * * * * *
12490 TTAAATGTTTTGATTCTAAAAAATGCTTCCGAAATTTTGTGGTTTTGATTGTTGGTCAATTTAAT
195 TTAAATGTTTCAATTCAAAAAAATGCTTCCCAAATTTGGTGGGTTCGATTGCTGGTCAATTTAAT
* * * * * *
12555 ATCGTATAATTTTTTGTCCACATGTCCGATTGAATTTATAGAAGTGTCGGTTAAAAGGTTATTGC
260 ACCATATAAGTTTTCGTCCACATGTCCGATTAAATTTATACAAGTGTCGGTTAAAAGGTTATTGC
12620 ATGATCTAAGACTTTCATGAATTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACGGTCA
325 ATGATCTAAGACTTTCATGAATTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACGGTCA
12685 TTTTCTTAA
390 TTTTCTTAA
* * * *
12694 TTGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATAAAACTTAGTCCTTTACTAATTC
1 TTGGATTATTTATCAAATGAACCTCATACTTTTATACTTTATAAAACTTAGTCCTTTAC-AATTA
* *
12759 TA-TTTTAATCGATTTAACAC-TT-CAACTTTAATTTTTAT-TTTTTGTTATATTTGTCCGATTA
65 TAGGTTGAAT-GATTTAACACATTGC--CTTTAATTTTTATATTTTTG-TATATTTGTCCGATTA
* * * * *
12820 AGGTGATTCAGGTGCCTATTACAAGGTAATTTCATTATTTACAACTTTCACAATT-G-ACTCAAA
126 ACGTGATTCAAGTGCCTATTAAAAGGTAATTTCATGATCTACAA-TTT--CAATTAGAACTCAAA
***
12883 AGCCAATTTTTGTGTTTCAATT-AAAGAAAATGCTTCCCAAATTTGGTGGGTTCGATTGCCT-GT
188 AGCCAATTTAAATGTTTCAATTCAAA-AAAATGCTTCCCAAATTTGGTGGGTTCGATTG-CTGGT
* * *
12946 CTATTTAATACCATAT-GGTTTTCGATCCACATGTCCGATTAAATTTATTCAAGTGTCGGTTAAA
251 CAATTTAATACCATATAAGTTTTCG-TCCACATGTCCGATTAAATTTATACAAGTGTCGGTTAAA
* *
13010 AGGTTATTGCATGATTTACGACTTTCA
315 AGGTTATTGCATGATCTAAGACTTTCA
13037 AGGACCTAAA
Statistics
Matches: 287, Mismatches: 45, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
398 1 0.00
399 70 0.24
400 207 0.72
401 5 0.02
403 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (398 bp):
TTGGATTATTTATCAAATGAACCTCATACTTTTATACTTTATAAAACTTAGTCCTTTACAATTAT
AGGTTGAATGATTTAACACATTGCCTTTAATTTTTATATTTTTGTATATTTGTCCGATTAACGTG
ATTCAAGTGCCTATTAAAAGGTAATTTCATGATCTACAATTTCAATTAGAACTCAAAAGCCAATT
TAAATGTTTCAATTCAAAAAAATGCTTCCCAAATTTGGTGGGTTCGATTGCTGGTCAATTTAATA
CCATATAAGTTTTCGTCCACATGTCCGATTAAATTTATACAAGTGTCGGTTAAAAGGTTATTGCA
TGATCTAAGACTTTCATGAATTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACGGTCAT
TTTCTTAA
Found at i:13443 original size:436 final size:433
Alignment explanation
Indices: 12621--13792 Score: 1398
Period size: 436 Copynumber: 2.7 Consensus size: 433
12611 GGTTATTGCA
* * * * **
12621 TGATCTAAGACTTTCATGAA---TTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACGGT
1 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAAC-AA
* * **
12683 CATTTTCTTAATTGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATAAAACTTAGTCC
65 CATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCC
* * **
12748 TTTACTAATTCTATTTTAA-TCGATTTAACACTTCAACTTTAATTTTTATTTTTTGTTATATTTG
130 TTTACAAATTCTATCTTAACTCGATTTAA-ACTTTTA--TT-ATTTTTATTTTTTGTTATA-TTG
* * * * * * * **
12812 TCCGATTAAGGTGATTCAGGTGCCTATTACAAGGTAATTTCATTATTTACAACTTTCACAATTGA
190 TCCGATTAAGGTGATTCAAGTGTCTATTAAAAGTTAATTTCATGATCTACAACTTTCATAAAAGA
* * * * * ** * *
12877 CTCAAAAGCCAATTTTTGTGTTTCAATTAAAGAAAATGCTTCCCAAATTTGGTGGGTTCGATTGC
255 CT-AAAAACAAATTTTTATGTTTCAATTAAAAAAAATGCTTCACAAATTTAATCGGTTCAATTGC
** * *
12942 CTGTCTATTTAATACCATATGGTTTTCGATCCACATGTCCGATTAAATTTATTCAAGTGTCGGTT
319 CTGTCTATTTAATACCATATAATTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTT
* * * *
13007 AAAAGGTTATTGCATGATTTACGACTTT-C-AAGGACCTAAAAGCTAAATT
384 AAAAGGTTATTGCATGATATAAGACTTTACGAAGAACCCAAAAG-TAAATT
*
13056 TGATTTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAAC-AC
1 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACAAC
13120 ATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTA-TGTAGTCC
66 ATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACT-TAGTCC
* *
13184 TTTACAAATTCTATCTTAACCTAACG-TTTAAACTTTTATTATTATTATTTTTTGTTCTATTAGT
130 TTTACAAATTCTATCTTAA-CT--CGATTTAAACTTTTATTATTTTTATTTTTTGTTATATT-GT
* * * *
13248 CCGATTAAGTTGATTCATGTGTCTATTAAAAGTTAATTTCATGATCTACAACTTTCATGAAGGAC
191 CCGATTAAGGTGATTCAAGTGTCTATTAAAAGTTAATTTCATGATCTACAACTTTCATAAAAGAC
* * * *
13313 TTAAAACAAATTTTTATGTTTCAATTAAAAAAAATGCTTCATAAATTTAATCGTTTCAATTG-TT
256 TAAAAACAAATTTTTATGTTTCAATTAAAAAAAATGCTTCACAAATTTAATCGGTTCAATTGCCT
13377 AGTCTATTTAATACCATATATAATTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGGT
321 -GTCTATTTAATACC--ATATAATTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGGT
* * *
13442 TAAAAGGTTATTGTATGATATAAGACTTTCACGAAGAACCCGAAAGTTAATT
383 TAAAAGGTTATTGCATGATATAAGACTTT-ACGAAGAACCCAAAAGTAAATT
*
13494 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTTAAGATCTCCATTAACAAA
1 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAAC-AA
* * * * * *
13559 TATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTATTTTATGCTACTTAATCC
65 CATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCC
* * *
13624 TTTACAAATTCTATCTT-ACTCGATTTAAAGTTTCGT-TTTTTTTATATTTCTTTGTTTTAATTG
130 TTTACAAATTCTATCTTAACTCGATTTAAACTTT--TATTATTTT-TATTT-TTTGTTAT-ATTG
* * *
13687 TCCAATTAAGGTAATTCAAGTGTCTATTAAAA-TGTAATTTTATGATCTACAACTTTCATAAAAG
190 TCCGATTAAGGTGATTCAAGTGTCTATTAAAAGT-TAATTTCATGATCTACAACTTTCATAAAAG
* **
13751 ACTCAAAAACTAATTTTTATGTTTCAATTCTAAAAAATGCTT
254 ACT-AAAAACAAATTTTTATGTTTCAATTAAAAAAAATGCTT
13793 TTAAAATTTT
Statistics
Matches: 637, Mismatches: 74, Indels: 46
0.84 0.10 0.06
Matches are distributed among these distances:
433 1 0.00
434 65 0.10
435 92 0.14
436 150 0.24
437 9 0.01
438 116 0.18
439 23 0.04
440 143 0.22
441 38 0.06
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (433 bp):
TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACAAC
ATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCCT
TTACAAATTCTATCTTAACTCGATTTAAACTTTTATTATTTTTATTTTTTGTTATATTGTCCGAT
TAAGGTGATTCAAGTGTCTATTAAAAGTTAATTTCATGATCTACAACTTTCATAAAAGACTAAAA
ACAAATTTTTATGTTTCAATTAAAAAAAATGCTTCACAAATTTAATCGGTTCAATTGCCTGTCTA
TTTAATACCATATAATTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGT
TATTGCATGATATAAGACTTTACGAAGAACCCAAAAGTAAATT
Found at i:13712 original size:440 final size:431
Alignment explanation
Indices: 12621--13792 Score: 1385
Period size: 440 Copynumber: 2.7 Consensus size: 431
12611 GGTTATTGCA
* * * * *
12621 TGATCTAAGACTTTCATGAA---TTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACGGT
1 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAAC-AT
* * **
12683 CATTTTCTTAATTGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATAAAACTTAGTCC
65 -ATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCC
* * * * *
12748 TTTACTAATTCTATTTTAATCGATTTAACACTTCAACTTTAATTTT-TATTTTTTGTTATATTTG
129 TTTACAAATTCTATCTTACTCGATTTAA-ACTT---CTTT-TTTTTATATTTTTTGTTATAATTG
* * * * * * * **
12812 TCCGATTAAGGTGATTCAGGTGCCTATTACAAGGTAATTTCATTATTTACAACTTTCACAATTGA
189 TCCGATTAAGGTGATTCAAGTGTCTATTAAAAGTTAATTTCATGATCTACAACTTTCATAAAAGA
* * * * * ** * *
12877 CTCAAAAGCCAATTTTTGTGTTTCAATTAAAGAAAATGCTTCCCAAATTTGGTGGGTTCGATTGC
254 CT-AAAAACAAATTTTTATGTTTCAATTAAAAAAAATGCTTCACAAATTTAATCGGTTCAATTGC
** * *
12942 CTGTCTATTTAATACCATATGGTTTTCGATCCACATGTCCGATTAAATTTATTCAAGTGTCGGTT
318 CTGTCTATTTAATACCATATAATTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTT
* * * *
13007 AAAAGGTTATTGCATGATTTACGACTTTCAAGGACCTAAAAGCTAAATT
383 AAAAGGTTATTGCATGATATAAGACTTTCAAGAACCCAAAAGCTAAATT
* *
13056 TGATTTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACACA
1 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACATA
13121 TTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTA-TGTAGTCCT
66 TTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACT-TAGTCCT
* * *
13185 TTACAAATTCTATCTTAACCTAACG-TTTAAACTT-TTATTATTATTATTTTTTGTTCT-ATTAG
130 TTACAAATTCTATCTT-A-CT--CGATTTAAACTTCTTTTTTTTA-TATTTTTTGTTATAATT-G
* * * *
13247 TCCGATTAAGTTGATTCATGTGTCTATTAAAAGTTAATTTCATGATCTACAACTTTCATGAAGGA
189 TCCGATTAAGGTGATTCAAGTGTCTATTAAAAGTTAATTTCATGATCTACAACTTTCATAAAAGA
* * * *
13312 CTTAAAACAAATTTTTATGTTTCAATTAAAAAAAATGCTTCATAAATTTAATCGTTTCAATTG-T
254 CTAAAAACAAATTTTTATGTTTCAATTAAAAAAAATGCTTCACAAATTTAATCGGTTCAATTGCC
13376 TAGTCTATTTAATACCATATATAATTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGG
319 T-GTCTATTTAATACC--ATATAATTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGG
* * *
13441 TTAAAAGGTTATTGTATGATATAAGACTTTCACGAAGAACCCGAAAG-TTAATT
381 TTAAAAGGTTATTGCATGATATAAGACTTT--C-AAGAACCCAAAAGCTAAATT
*
13494 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTTAAGATCTCCATTAACAAA
1 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAAC--A
* * * * *
13559 TATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTATTTTATGCTACTTAATCC
64 TATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCC
* *
13624 TTTACAAATTCTATCTTACTCGATTTAAAGTTTCGTTTTTTTTATATTTCTTTGTTTTAATTGTC
129 TTTACAAATTCTATCTTACTCGATTTAAA-CTTC-TTTTTTTTATATTT-TTTGTTATAATTGTC
* * *
13689 CAATTAAGGTAATTCAAGTGTCTATTAAAA-TGTAATTTTATGATCTACAACTTTCATAAAAGAC
191 CGATTAAGGTGATTCAAGTGTCTATTAAAAGT-TAATTTCATGATCTACAACTTTCATAAAAGAC
* **
13753 TCAAAAACTAATTTTTATGTTTCAATTCTAAAAAATGCTT
255 T-AAAAACAAATTTTTATGTTTCAATTAAAAAAAATGCTT
13793 TTAAAATTTT
Statistics
Matches: 632, Mismatches: 77, Indels: 50
0.83 0.10 0.07
Matches are distributed among these distances:
433 4 0.01
434 67 0.11
435 87 0.14
436 145 0.23
437 7 0.01
438 112 0.18
439 22 0.03
440 150 0.24
441 38 0.06
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (431 bp):
TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACATA
TTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCCTT
TACAAATTCTATCTTACTCGATTTAAACTTCTTTTTTTTATATTTTTTGTTATAATTGTCCGATT
AAGGTGATTCAAGTGTCTATTAAAAGTTAATTTCATGATCTACAACTTTCATAAAAGACTAAAAA
CAAATTTTTATGTTTCAATTAAAAAAAATGCTTCACAAATTTAATCGGTTCAATTGCCTGTCTAT
TTAATACCATATAATTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTT
ATTGCATGATATAAGACTTTCAAGAACCCAAAAGCTAAATT
Found at i:15321 original size:2 final size:2
Alignment explanation
Indices: 15309--15344 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
15299 TATCCCTGGG
15309 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15345 TACATGGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16329 original size:16 final size:16
Alignment explanation
Indices: 16310--16353 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
16300 ACTTTTTACA
*
16310 GAGAATGCTTTCCTAG
1 GAGAATGCTTTCCCAG
*
16326 GAGAATG-ATTCCCAG
1 GAGAATGCTTTCCCAG
*
16341 GAGAGTGCTTTCC
1 GAGAATGCTTTCC
16354 ATAAAAAGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (16 bp):
GAGAATGCTTTCCCAG
Found at i:16391 original size:31 final size:31
Alignment explanation
Indices: 16333--16391 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
16323 TAGGAGAATG
* * *
16333 ATTCCCAGGAGAGTGCTTTCCATAAAAAGTC
1 ATTCCAAGGAGAGTACTTTCCAGAAAAAGTC
*
16364 ATTCCAAGGAGAGTACTTTCCCGAAAAA
1 ATTCCAAGGAGAGTACTTTCCAGAAAAA
16392 ATCTTTCCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (31 bp):
ATTCCAAGGAGAGTACTTTCCAGAAAAAGTC
Found at i:17956 original size:15 final size:16
Alignment explanation
Indices: 17936--17974 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
17926 CCAATTATGG
*
17936 AAATGTTT-AGGCTTA
1 AAATGTTTCACGCTTA
17951 AAATGTTTCACGCTTA
1 AAATGTTTCACGCTTA
*
17967 AAAAGTTT
1 AAATGTTT
17975 TAGACTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (16 bp):
AAATGTTTCACGCTTA
Found at i:18445 original size:39 final size:39
Alignment explanation
Indices: 18327--18462 Score: 141
Period size: 39 Copynumber: 3.5 Consensus size: 39
18317 TTAGTTTTTG
** *
18327 TTTGGAGTAGATAGACTATGTTAAGTAAGTAGTAGTTAAT
1 TTTGGAGTAGATAGAAGATGTTAAGTAA-TAGTGGTTAAT
* * **
18367 TTTGGAGTAGATAGAAGACT-TTAGGTAATAATGACTAAT
1 TTTGGAGTAGATAGAAGA-TGTTAAGTAATAGTGGTTAAT
*
18406 TTTGGAGT-GAATAGCAGATGTTAAGTAATAGTGGTTAAT
1 TTTGGAGTAG-ATAGAAGATGTTAAGTAATAGTGGTTAAT
* *
18445 TTTAGAATAGATAGAAGA
1 TTTGGAGTAGATAGAAGA
18463 CTTTAATTAT
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.03
39 50 0.65
40 24 0.31
41 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (39 bp):
TTTGGAGTAGATAGAAGATGTTAAGTAATAGTGGTTAAT
Found at i:19244 original size:25 final size:25
Alignment explanation
Indices: 19198--19245 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
19188 GTAGAATATA
**
19198 ATTGTAAAAGTTTATTTCTAAAAAT
1 ATTGTAAAAGAATATTTCTAAAAAT
19223 ATTGTAAAAGAATATATT-TAAAA
1 ATTGTAAAAGAATAT-TTCTAAAA
19246 TTCTAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (25 bp):
ATTGTAAAAGAATATTTCTAAAAAT
Done.