Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014527.1 Corchorus olitorius cultivar O-4 contig14560, 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: 57382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3245 original size:31 final size:31
Alignment explanation
Indices: 3208--3318 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
3198 ACGGTGTCTG
3208 ACGTGACATGCCACGTGTACCAAAAAATGAC
1 ACGTGACATGCCACGTGTACCAAAAAATGAC
* * * *
3239 ATGTGACACGCCACGTGTACCAAAGAGTGAC
1 ACGTGACATGCCACGTGTACCAAAAAATGAC
* * ** *
3270 ACATGACATGCCATGTGTTTCAAAAAAGTGAA
1 ACGTGACATGCCACGTGTACCAAAAAA-TGAC
* *
3302 ACGTGGCATGTCACGTG
1 ACGTGACATGCCACGTG
3319 CACAAAAGGA
Statistics
Matches: 62, Mismatches: 17, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
31 46 0.74
32 16 0.26
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (31 bp):
ACGTGACATGCCACGTGTACCAAAAAATGAC
Found at i:21045 original size:2 final size:2
Alignment explanation
Indices: 21040--21067 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21030 TCTCTCTAAG
21040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21068 TTCTTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26293 original size:11 final size:11
Alignment explanation
Indices: 26268--26309 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
26258 GTTTTTCTGT
26268 TTTTTGTTTTTG
1 TTTTTG-TTTTG
*
26280 TTTTTGTTTCG
1 TTTTTGTTTTG
*
26291 TTTTCGTTTTG
1 TTTTTGTTTTG
26302 TTTTTGTT
1 TTTTTGTT
26310 GCGCTGTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 20 0.77
12 6 0.23
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.79
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:26306 original size:6 final size:6
Alignment explanation
Indices: 26268--26309 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
26258 GTTTTTCTGT
* *
26268 TTTTTG TTTTTG TTTTTG -TTTCG TTTTCG -TTTTG TTTTTG TT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
26310 GCGCTGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 8 0.25
6 24 0.75
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.79
Consensus pattern (6 bp):
TTTTTG
Found at i:27274 original size:17 final size:17
Alignment explanation
Indices: 27248--27280 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27238 TAATATGAAA
27248 ATCAATGATA-AAATTT
1 ATCAATGATAGAAATTT
27264 ATCAGATGATAGAAATT
1 ATCA-ATGATAGAAATT
27281 GAAAATAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
ATCAATGATAGAAATTT
Found at i:28003 original size:17 final size:17
Alignment explanation
Indices: 27980--28028 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
27970 AAATTCTGAT
27980 TTTTTTTATTTTAAT-A
1 TTTTTTTATTTTAATAA
27996 TTTCTTTTAACTTTTAATAA
1 TTT-TTTT-A-TTTTAATAA
28016 TTTTTATTATTTT
1 TTTTT-TTATTTT
28029 TATTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 5 0.18
19 10 0.36
20 6 0.21
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTTATTTTAATAA
Found at i:41231 original size:2 final size:2
Alignment explanation
Indices: 41211--41248 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
41201 AGCATTTTAT
41211 TA TA T- TA TA T- TA CTA 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 T
41249 CTTTGGGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 29 0.88
3 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:46690 original size:32 final size:31
Alignment explanation
Indices: 46625--46696 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
46615 TAACGTGACC
* * *
46625 TTGTCACGTGGTATTTTGGTCCAACATATCA
1 TTGTCACGTGGCATTTTGCTCCAACATAGCA
* *
46656 TTGTCACGTGGCAGTTTTGCTCCGACATGGCA
1 TTGTCACGTGGCA-TTTTGCTCCAACATAGCA
*
46688 TTGCCACGT
1 TTGTCACGT
46697 CAGCAATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (31 bp):
TTGTCACGTGGCATTTTGCTCCAACATAGCA
Found at i:48691 original size:15 final size:16
Alignment explanation
Indices: 48665--48741 Score: 52
Period size: 17 Copynumber: 4.6 Consensus size: 16
48655 GGTTCAATTT
*
48665 TAATTATATATAATATA
1 TAATTATATA-ACTATA
*
48682 TAATTATATATATTAAATA
1 TAATTATATA-ACT--ATA
*
48701 TAATTATATTA-TATA
1 TAATTATATAACTATA
48716 TAATT-T-TGAACTATA
1 TAATTATAT-AACTATA
48731 TATATTATATA
1 TA-ATTATATA
48742 TAATTTCAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
13 1 0.02
14 2 0.04
15 14 0.28
16 3 0.06
17 16 0.32
18 2 0.04
19 12 0.24
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
TAATTATATAACTATA
Found at i:48731 original size:41 final size:41
Alignment explanation
Indices: 48667--48746 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
48657 TTCAATTTTA
*
48667 ATTATATATAATATATAATTATATATATTAAATATAATTAT
1 ATTATATATAATATATAACTATATATATTAAATATAATTAT
* *
48708 ATTATATATAAT-TTTGAACTATATATATTATATATAATT
1 ATTATATATAATATAT-AACTATATATATTAAATATAATT
48747 TCAGAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 33 0.94
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (41 bp):
ATTATATATAATATATAACTATATATATTAAATATAATTAT
Found at i:55490 original size:335 final size:333
Alignment explanation
Indices: 54848--56859 Score: 3004
Period size: 335 Copynumber: 6.1 Consensus size: 333
54838 TATATGCACG
*
54848 TATATTTTTATGAGCTTCTGATTCTTGTTTCGA--TAATCAGAAATTAATTAGTAAAAAACATTG
1 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAACATTG
54911 GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATATTTTTTT
66 GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATATTTTTTT
* *
54976 AGAGTAATTTGGCCAAAAATTGAGGAAAATTATTTCGGGTCAATTTTTACAAAATTTTAGCCGAA
131 AGAGT-ATTTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAGCCGAA
55041 ATCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTCT
195 ATCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTCT
*
55106 TCTTTTTTGGCGCCGAGACTCCTTGAAATATCCATATTCATCAAATCAAATCTCAGCCACTTTGG
260 TCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCACTTTGG
55171 ATTTAAGGA
325 ATTTAAGGA
*
55180 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATCAGAAATTAATTAGTAAAAAACATTG
1 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAACATTG
55245 GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATATTTTTTT
66 GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATATTTTTTT
**
55310 AAGAGTATCGCGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAGCCGA
131 -AGAGTAT-TTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAGCCGA
* *
55375 AATCGTGTACCAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTC
194 AATCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTC
*
55440 TTCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATGTCAGCCACTTTG
259 TTCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCACTTTG
55505 GATTTAAGGA
324 GATTTAAGGA
*
55515 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTTATTAGTAAAAAACATTG
1 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAACATTG
*
55580 G-AAAATGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATAT-TTTTTTT
66 GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATATTTTTTT
* *
55643 AGAGTAATTTGGCCAAAAATTGAGGAAAATTAATTCGGGACAATTTTTGGAAAATTTTAGCCGAA
131 AGAGT-ATTTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAGCCGAA
* * *
55708 ATCGTG---T---CATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCACGACTCAATTTTCCT
195 ATCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTCT
* * * * * * *
55767 TATTTCTTGGCGCCGAGACTCATTGAAATATTTGTATTCATCAAATCAAATGTGAGCCACTTTGG
260 TCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCACTTTGG
55832 ATTT-AGGTA
325 ATTTAAGG-A
55841 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAACATTG
1 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAACATTG
* * * ** *
55906 GAAAAACGATATTAGAAACGCTAAAAGCCCTTCAAACTTTTTGGCGTAAAATTTTATATTTTTTT
66 GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATATTTTTTT
* * *
55971 ACGAGTATCGTGGCAAAAAATTGAGGAAAAATAATTCGGGTCAATTTTTGCAAAATTTTAGCCGA
131 A-GAGTAT-TTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAGCCGA
* * * *
56036 AATCGTGTACTAACCATCACGGTTTTTTGCTAAAACCGCGTTCCGGGGTCACGGCTCAGTTTTTC
194 AATCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTC
** * ** *
56101 CCCTTTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGATACATTG
259 TTCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCACTTTG
56166 GATTTAAGGA
324 GATTTAAGGA
* * ** *
56176 TATATTTTTACGAGCTTCTGATTCTTGTTTCGATTTAATCAGAAATTTTTTAGTAAAAAACATTA
1 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAACATTG
*
56241 GAAAAACGATATTAGAAACGTTAAAA--CC--C---C----TGTCATTGAATTATATATATTTTT
66 GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATAT-TTTTT
* *
56295 TAGAGTATTTCGGCCAAAAATTGAGGAAAATTATTTCGGGTCAATTTTTACAAAATTTTAGCCGA
130 TAGAGTATTT-GGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAGCCGA
* *
56360 AATCGTGTACTAACCATCACGGGTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCA-ATTTTC
194 AATCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTC
** *
56424 TTTCTTTTTTTGGCGCTAAGACTCCTTGAAATATCTATATTCATCAAATCAAATGTCAGCCACTT
259 -TTC-TTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCACTT
56489 TGGATTTAAGGA
322 TGGATTTAAGGA
* * * *
56501 AATATTTTTATGAGCTTCTGATCCTTGTTTTGATTTAATAAGAAATTAATTA-TTAAAAACATTG
1 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAACATTG
*
56565 G-AAAACGATATTAGAAACGTTAAAACCCCTTCAAATTTTTTGGCATTGAA-T-TATATTTTTTT
66 GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATATTTTTTT
* * * *
56627 AGCGTATTTTGGCCAATAATTGAGGAAAATTATTTCGGGCCAATTTTTGCAAAATTTTAGCCGAA
131 AGAGTA-TTTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAGCCGAA
* * * * * * *
56692 ATCGTGTAC---CTATCACGGTTTTTGGCTAAAAACACGTTCCGAGGCTACGGCTCAGTTTTTCC
195 ATCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTCT
* * * *
56754 TCTTTTTTTTGCGCCGAGACTCCTTGAAATATCCATATTCATCAAATAAAATCTCAGCCACATTG
260 TC-TTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCACTTTG
56819 GATTTAAGGA
324 GATTTAAGGA
*
56829 TATATTTTTACGAGCTTCTGATTCTTGTTTC
1 TATATTTTTATGAGCTTCTGATTCTTGTTTC
56860 AAGGAGTCTC
Statistics
Matches: 1524, Mismatches: 122, Indels: 72
0.89 0.07 0.04
Matches are distributed among these distances:
323 30 0.02
324 134 0.09
325 122 0.08
326 178 0.12
327 49 0.03
328 144 0.09
329 67 0.04
331 73 0.05
332 106 0.07
333 12 0.01
334 160 0.10
335 446 0.29
336 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (333 bp):
TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAACATTG
GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATATTTTTTT
AGAGTATTTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA
TCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTCTT
CTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCACTTTGGA
TTTAAGGA
Found at i:56120 original size:661 final size:660
Alignment explanation
Indices: 54848--56859 Score: 3060
Period size: 661 Copynumber: 3.0 Consensus size: 660
54838 TATATGCACG
* *
54848 TATATTTTTATGAGCTTCTGATTCTTGTTTCGA--TAATCAGAAATTAATTAGTAAAAAACATTG
1 TATATTTTTACGAGCTTCTGATTCTTGTTTCGATTTAATCAGAAATTTATTAGTAAAAAACATTG
54911 GAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATATTTTTTT
66 G-AAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATAT-TTTTTTT
54976 AGAGTAATTTGGCCAAAAATTGAGGAAAATTATTTCGGGTCAATTTTTACAAAATTTTAGCCGAA
129 AGAGTAATTTGGCCAAAAATTGAGGAAAATTATTTCGGGTCAATTTTTACAAAATTTTAGCCGAA
* *
55041 ATCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTCT
194 ATCGTG-A-T-A-CATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAATTTTCCT
* * *
55106 TCTTTTTTGGCGCCGAGACTCCTTGAAATATCCATATTCATCAAATCAAATCTCAGCCACTTTGG
255 TATTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATGTCAGCCACTTTGG
*
55171 ATTTAAGGATATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATCAGAAATTAATTAGTAA
320 ATTTAAGGATATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAA
*
55236 AAAACATTGGAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATA
385 AAAACATTGGAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTTTA
*
55301 TATTTTTTTAAGAGTATCGCGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAAT
450 TATTTTTTT-AGAGTATCGTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAAT
*
55366 TTTAGCCGAAATCGTGTACCAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGACT
514 TTTAGCCGAAATCGTGTA-CAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGG-CACGGCT
** *
55431 CAGTTTTTCTTCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATGTCA
577 CAGTTTTTCCCCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCA
*
55496 GCCACTTTGGATTTAAGGA
642 GCCACATTGGATTTAAGGA
* *
55515 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTTATTAGTAAAAAACATTG
1 TATATTTTTACGAGCTTCTGATTCTTGTTTCGATTTAATCAGAAATTTATTAGTAAAAAACATTG
*
55580 GAAAATGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATTTTTTTTAG
66 GAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATTTTTTTTAG
* * **
55645 AGTAATTTGGCCAAAAATTGAGGAAAATTAATTCGGGACAATTTTTGGAAAATTTTAGCCGAAAT
131 AGTAATTTGGCCAAAAATTGAGGAAAATTATTTCGGGTCAATTTTTACAAAATTTTAGCCGAAAT
* *
55710 CGTG-T-CATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCACGACTCAATTTTCCTTATTTC
196 CGTGATACATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAATTTTCCTTATTTT
* * * *
55773 TTGGCGCCGAGACTCATTGAAATATTTGTATTCATCAAATCAAATGTGAGCCACTTTGGATTT-A
261 TTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATGTCAGCCACTTTGGATTTAA
55837 GGTATATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAAC
326 GG-ATATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAAC
* * * **
55902 ATTGGAAAAACGATATTAGAAACGCTAAAAGCCCTTCAAACTTTTTGGCGTAAAATTTTATATTT
390 ATTGGAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTTTATATTT
* *
55967 TTTTACGAGTATCGTGGCAAAAAATTGAGGAAAAATAATTCGGGTCAATTTTTGCAAAATTTTAG
455 TTTTA-GAGTATCGTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAG
* *
56032 CCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAACCGCGTTCCGGGGTCACGGCTCAGTT
519 CCGAAATCGTGTAC-AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGG-CACGGCTCAGTT
* **
56097 TTTCCCCTTTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGATAC
582 TTTCCCCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCAC
56162 ATTGGATTTAAGGA
647 ATTGGATTTAAGGA
*
56176 TATATTTTTACGAGCTTCTGATTCTTGTTTCGATTTAATCAGAAATTTTTTAGTAAAAAACATTA
1 TATATTTTTACGAGCTTCTGATTCTTGTTTCGATTTAATCAGAAATTTATTAGTAAAAAACATT-
* * *
56241 GAAAAACGATATTAGAAACGTTAAAACCCCTGTC--A----TT-GAATT--A-TATATATTTTTT
65 GGAAAACGATATTAGAAACGTTAAAACCCCT-TCAAACTTTTTGGCATTGAATTATATTTTTTTT
56296 AGAGT-ATTTCGGCCAAAAATTGAGGAAAATTATTTCGGGTCAATTTTTACAAAATTTTAGCCGA
129 AGAGTAATTT-GGCCAAAAATTGAGGAAAATTATTTCGGGTCAATTTTTACAAAATTTTAGCCGA
* *
56360 AATCGTGTACTAACCATCACGGGTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAATTTTCT
193 AATCGTG-A-T-A-CATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAATTTTCC
* **
56425 TTCTTTTTTTGGCGCTAAGACTCCTTGAAATATCTATATTCATCAAATCAAATGTCAGCCACTTT
254 TT-ATTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATGTCAGCCACTTT
* * *
56490 GGATTTAAGGAAATATTTTTATGAGCTTCTGATCCTTGTTTTGATTTAATAAGAAATTAATTA-T
318 GGATTTAAGGATATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGT
* *
56554 TAAAAACATTGG-AAAACGATATTAGAAACGTTAAAACCCCTTCAAATTTTTTGGCATTGAA--T
383 AAAAAACATTGGAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTT
* ** * * *
56616 TATATTTTTTTAGCGTATTTTGGCCAATAATTGAGGAAAATTATTTCGGGCCAATTTTTGCAAAA
448 TATATTTTTTTAGAGTATCGTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAA
* * *
56681 TTTTAGCCGAAATCGTGTAC--CTATCACGGTTTTTGGCTAAAAACACGTTCCGAGGCTACGGCT
513 TTTTAGCCGAAATCGTGTACAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGC-ACGGCT
* * * *
56744 CAGTTTTTCCTCTTTTTTTTGCGCCGAGACTCCTTGAAATATCCATATTCATCAAATAAAATCTC
577 CAGTTTTTCC-CCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTC
56809 AGCCACATTGGATTTAAGGA
641 AGCCACATTGGATTTAAGGA
56829 TATATTTTTACGAGCTTCTGATTCTTGTTTC
1 TATATTTTTACGAGCTTCTGATTCTTGTTTC
56860 AAGGAGTCTC
Statistics
Matches: 1236, Mismatches: 91, Indels: 50
0.90 0.07 0.04
Matches are distributed among these distances:
651 1 0.00
652 50 0.04
653 171 0.14
654 1 0.00
655 65 0.05
656 18 0.01
657 2 0.00
658 43 0.03
659 62 0.05
660 115 0.09
661 486 0.39
662 29 0.02
663 2 0.00
664 1 0.00
667 107 0.09
668 54 0.04
669 29 0.02
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (660 bp):
TATATTTTTACGAGCTTCTGATTCTTGTTTCGATTTAATCAGAAATTTATTAGTAAAAAACATTG
GAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTATATTTTTTTTAG
AGTAATTTGGCCAAAAATTGAGGAAAATTATTTCGGGTCAATTTTTACAAAATTTTAGCCGAAAT
CGTGATACATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCACGACTCAATTTTCCTTATTTT
TTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATGTCAGCCACTTTGGATTTAA
GGATATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATAAGAAATTAATTAGTAAAAAACA
TTGGAAAAACGATATTAGAAACGTTAAAACCCCTTCAAACTTTTTGGCATTGAATTTTATATTTT
TTTAGAGTATCGTGGCCAAAAATTGAGGAAAATTAATTCGGGTCAATTTTTGCAAAATTTTAGCC
GAAATCGTGTACAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCACGGCTCAGTTTTTC
CCCTTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCACATTG
GATTTAAGGA
Found at i:57364 original size:2 final size:2
Alignment explanation
Indices: 57357--57382 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57347 TATACTCATA
57357 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.