Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020696.1 Corchorus olitorius cultivar O-4 contig20729, 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: 29046
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Found at i:11644 original size:75 final size:76
Alignment explanation
Indices: 11370--11668 Score: 519
Period size: 76 Copynumber: 3.9 Consensus size: 76
11360 CACCAGGTAG
* * * * *
11370 GACGGACGGGGGTGTCAGTCTCGGCGCTCAGCCGTTGGGTAAGCAGCATCTGCATGGACGCTTTG
1 GACGAACGGGGGTGCCAGTCTAGGCACTCAGCCGTTGGGTGAGCAGCATCTGCATGGACGCTTTG
11435 TCTCACTAATA
66 TCTCACTAATA
11446 GACGAACGGGGGTGCCAGTCTAGGCACTCAGCCGTTGGGTGAGCAGCATCTGCATGGACGCTTTG
1 GACGAACGGGGGTGCCAGTCTAGGCACTCAGCCGTTGGGTGAGCAGCATCTGCATGGACGCTTTG
11511 TCTCACTAATA
66 TCTCACTAATA
*
11522 GACGAACGGGGGTGCCAGTCTAGGCACTCAGCCGTTGGGTGAGCAGCGTCTGCATGGACGCTTTG
1 GACGAACGGGGGTGCCAGTCTAGGCACTCAGCCGTTGGGTGAGCAGCATCTGCATGGACGCTTTG
11587 TCTCACTAATA
66 TCTCACTAATA
* *
11598 GACGAAC-GGGGTGCCAGTCTAGGCACTCAGCCGTTGGGTGAGCAGCGTCTGCATGGACGCTTCG
1 GACGAACGGGGGTGCCAGTCTAGGCACTCAGCCGTTGGGTGAGCAGCATCTGCATGGACGCTTTG
11662 TCTCACT
66 TCTCACT
11669 GGTGTTCACA
Statistics
Matches: 216, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
75 63 0.29
76 153 0.71
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.22
Consensus pattern (76 bp):
GACGAACGGGGGTGCCAGTCTAGGCACTCAGCCGTTGGGTGAGCAGCATCTGCATGGACGCTTTG
TCTCACTAATA
Found at i:19176 original size:340 final size:326
Alignment explanation
Indices: 18539--19835 Score: 1150
Period size: 340 Copynumber: 3.9 Consensus size: 326
18529 ATTGAACTTA
* * *
18539 AAAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTTAGAAAAATA
1 AAAATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATA
* * * * * * *
18604 AGAAATACGATATTAAAAGTGTAAAAAGCCCTCCAATCTTTTTGGTGTTAAATTATATATTTTTA
66 TGAAAAACGATATTAAAAGCGTCAAAAGCCCTTCAATCTTTTT-GCGTTGAATTATATATTTTTA
* * **
18669 TGAGTATTTTAGCCAAAAATTGAGAAGAAATCTTTCGTGTCAATTTTTGCAAAATTTTAGTTGAA
130 TGAGTATTTTAGCCAAAAATTAAGAA-AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAA
*** * * * * * *
18734 ATTGTGTACTAACAAACCATCACG-GTTTTTGGCTAA-AAACGCGTTCCGGGGACCCGGCTCAAT
194 AACATG---TAA-TAACCATCACGATTTTTTTG--AATAAAAGCGTTCCGGGGACCCAGCTCAGT
* ** * * *
18797 TTTGCATGATTTCTGGCTTCGAGACTACTTGAAATATCTATATTTATCTAATCAAATCTCGCCCA
253 TTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTAGCCCA
*
18862 CCTTAGATTT
318 CATT-GATTT
* * **
18872 AAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAA-
1 AA-AATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAT
* * *
18936 ATAGAAAAAAATGATATTAGAAA-CGTCAAAAGCCCTTCAATGTTTTTGGCGTTGAGTTATATAT
65 AT-G--AAAAACGATATTA-AAAGCGTCAAAAGCCCTTCAATCTTTTT-GCGTTGAATTATATA-
* *
19000 TTTTTTTTTTGAGTATTTTAGCCAAAAATTAAGAAAATATCTTTCGGGTCAATTTTTACAAAAAC
124 ---TTTTTATGAGTATTTTAGCCAAAAATTAAGAAAA-ATCTTTCGGGTCAATTTTTGC-AAAA-
* * * * *
19065 TTTTAGCCGAAAACATGTAAATAATCATCACAATTTTTTTGAATAAAAGGCGTTCTGGGGCCCCG
183 TTTTAGCCGAAAACATGT-AATAACCATCACGATTTTTTTGAATAAAA-GCGTTCCGGGGACCCA
* * * * *
19130 GTTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGAGATATCTATATTTATCTAATCAAATC
246 GCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATC
19195 -AG-CCACATTGGATTT
311 TAGCCCACATT-GATTT
** * * *
19210 AAAAATTTGTTTTTACAAATATGTAAATCTTGTTTCGATTTAATTGGAAATTAATACAGAAAAAT
1 -AAAATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAT
* * * *
19275 ATGAAAAACGATATTAAAAGCGTGAAAAG-TCTTCCAATCTTTTTGC----CATTA-A-A-TTAT
65 ATGAAAAACGATATTAAAAGCGTCAAAAGCCCTT-CAATCTTTTTGCGTTGAATTATATATTTTT
* * * ** *
19332 AT-A-TATTTTATCCAAAAATTGAGGAAAAATTTTTCCAGTCATCTTTTTGCAAAATTTTAGCC-
129 ATGAGTATTTTAGCCAAAAATT-AAGAAAAATCTTTCGGGTCA-ATTTTTGCAAAATTTTAGCCG
* * * * ** * *
19394 AAAATCGTGTACTAACCATCATGATTTTTGGTT-AA-AAACGTATTTCGGGGAACCAGCTCAGTT
192 AAAA-CATGTAATAACCATCACGATTTTT--TTGAATAAAAGCGTTCCGGGGACCCAGCTCAGTT
* * * *
19457 TTGCATGATTTTTGGCGCCGATACTCTTTGAAATAACTATATTCATCTAATAAAATCTTA-CCCA
254 TTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATC-TAGCCCA
19521 CATTGCATTT
318 CATTG-ATTT
* * ** **
19531 AATATTT-TTTTTACGAGCATCCGAATCAGGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAT
1 AAAATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAT
*
19595 ATGAAAAACGATATTAAAAGCGTCAAAAGCCCTTCAATCTTTTTACTGTTGAATTATATATTTTT
65 ATGAAAAACGATATTAAAAGCGTCAAAAGCCCTTCAATCTTTTTGC-GTTGAATTATATA-TTTT
*** * * * *
19660 TATGAGTATTACGGCTAAAAATTGAGGAAATATCTTTCGGGTTAATTTTTGCAAAATTTTAGCCG
128 TATGAGTATTTTAGCCAAAAATT-AAGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
* ** * ** **
19725 AAATCATGTAATAATTATCACGGATTTTTGCT-AA-AAACA-CGTTCCAAGG-CCCATTTCAGTT
192 AAAACATGTAATAACCATCAC-GATTTTT-TTGAATAAA-AGCGTTCCGGGGACCCAGCTCAGTT
* *
19786 TTGAATGACTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAA
254 TTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAA
19836 CCTAATCCCA
Statistics
Matches: 783, Mismatches: 136, Indels: 94
0.77 0.13 0.09
Matches are distributed among these distances:
319 105 0.13
320 74 0.09
321 29 0.04
322 32 0.04
323 13 0.02
324 4 0.01
325 4 0.01
326 1 0.00
327 1 0.00
329 60 0.08
330 45 0.06
331 41 0.05
333 3 0.00
334 57 0.07
335 8 0.01
336 73 0.09
337 3 0.00
338 66 0.08
339 19 0.02
340 129 0.16
341 4 0.01
342 12 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (326 bp):
AAAATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATA
TGAAAAACGATATTAAAAGCGTCAAAAGCCCTTCAATCTTTTTGCGTTGAATTATATATTTTTAT
GAGTATTTTAGCCAAAAATTAAGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAA
CATGTAATAACCATCACGATTTTTTTGAATAAAAGCGTTCCGGGGACCCAGCTCAGTTTTGCATG
ATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTAGCCCACATTGATT
T
Found at i:21772 original size:326 final size:325
Alignment explanation
Indices: 20370--22325 Score: 1533
Period size: 326 Copynumber: 5.9 Consensus size: 325
20360 GTTCTAGGGC
* * *
20370 TCTAATCAAATCTCAGCCACATT-ACATTTAAAGATTTGTTTTTTACAAACATCTAAATCTTATT
1 TCTAATCAAATCTCAGCCACATTGA-ATTTAAGGATTTG-TTTTTACAAGCATCTAAATCTTGTT
* * * *
20434 TCTATTTAATAAGAAATTAATTC-------A-GAAAAA--ATATGAAAAGCGT-AAAATTCCTCC
64 TCGATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCC
* * * * *
20488 AATCTTTTTGGCGTTAAATAATATATATTTCATGACTATTTTAGCTAAAAATTGAGGAAAAAT-T
129 AATCTTTTTGACATTAAATTATATATATTTTATGAGTATTTT-GCTAAAAATTGAGGAAAAATAT
* *
20552 TTTGTGGTCATTTTTTGCAAAATTTTAGACGAAATCGTGTACTAACCATCACGGTTTTTTTTTTT
193 TTCG-GGTCATTTTTTGCAAAATTTTAGCCGAAATCGTG---T-ACCATCACGG---------TT
* *
20617 TTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGTCGA-ACGTC
244 TTTTGGCTAAAAACGCTTTTCGGGGCCCCG-CTCAGTTTTGCATGATTTTTGGCGTCGAGAC-TC
*
20681 CTTGAAATATATATATTCA
307 CTTGAAATATCTATATTCA
** *
20700 TCTAATGATCAAATCTCAGCCACATT-ACATTTAAAAATTTGTTTTTACGAGCATCTGAAA-CTT
1 TCT-A--ATCAAATCTCAGCCACATTGA-ATTTAAGGATTTGTTTTTACAAGCATCT-AAATCTT
* *
20763 GTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATCAAAAGCGTGACAAGTC
61 GTTTCGATTTAATTAGAAATTAATTCAG-AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTC
* * * * *
20828 CTCTAATATTTTTGGA-GTTGAATTATATATATTTTATGAGTATTTTAGAC-AAGAATTGAGGAA
125 CTCCAATCTTTTT-GACATTAAATTATATATATTTTATGAGTATTTT-G-CTAAAAATTGAGGAA
* * * * * *
20891 AACTATATCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACGTTAGTAGAAATCACGTT
187 AAATATTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAC---------CATCACG--
* * * * * * * * * * * *
20956 TTTTTTTTGTTAAAACCG-TGTTTCGGGGTCCTGTTTCAATGTTGCATGATTTTTTGCGTCGGGT
241 GTTTTTTGGCTAAAAACGCT-TTTCGGGGCCCCG-CTCAGTTTTGCATGATTTTTGGCGTCGAGA
* *
21020 CTCATTGAAATATCTATATTAA
304 CTCCTTGAAATATCTATATTCA
* ** * * * *** * *
21042 TCTAACCAAATCTCATACACAATGGATTTAAGGATTT-ATAAAACAAGCATCTGAATCATGTTTC
1 TCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTC
* * ** * * *
21106 GATTTAATAAGAAATTAATTCGGAAAATAATAGGAAAAACGATATTGGAAGCATGAAAAGCCCTT
66 GATTTAATTAGAAATTAATTCAGAAAAT-AT--GAAAAACGATATTAAAAGCGTGAAAAGTCCTC
* * *
21171 CAATCTTTTTGGCATTGAATTATATA-ATTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATAA
128 CAATCTTTTTGACATTAAATTATATATA-TTTTATGAGTATT-TTGCTAAAAATTGAGGAAA-AA
* * * * * * * *
21235 -ATTTCGAGTCAATTTTTGTAAAATTCTAGCCGAAATCTTGTAATAATCATCATGG-TTTTTGCC
190 TATTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATC--GT-GT-ACCATCACGGTTTTTTGGC
* * * ** * * *
21298 TAAAAATG-TGTTTCGGGGCCCCGGCTAAGTTTTGCATAATTTTTTACGTCAAGACTCTTTGAGA
251 TAAAAACGCT-TTTCGGGGCCCC-GCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAA
*
21362 TATCCATATTCA
314 TATCTATATTCA
* * *
21374 TCTAATCAAATCTCAGCTACATTGGAA-TTAAGAATTTATTTTTACGAA-CATCTAAATCTTGTT
1 TCTAATCAAATCTCAGCCACATT-GAATTTAAGGATTTGTTTTTAC-AAGCATCTAAATCTTGTT
* * *
21437 TCAATTTAATTAGAAATTAATTCCGAAAATATGAAAAACGATATTAAAAACGTGAAAAGTCCTCC
64 TCGATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCC
* * * *
21502 AATATTTTTTACATTAAATTATATATATTTTATGAGTATTTATGCCAAAAATTGACGGAAAAATT
129 AATCTTTTTGACATTAAATTATATATATTTTATGAGTATTT-TGCTAAAAATTGA-GGAAAAATA
* * *
21567 TTTCGGGTCATTTTTTGTAAAATTTTAGCCAAAATCGTGTACCATCACCG-TTTTTGGCT-AAAA
192 TTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACCATCACGGTTTTTTGGCTAAAAA
* * * *
21630 CGCTTTTCGGGACCCCTGCTTAGTTTTACATGATTTTTGGCGCCGAGACTCCTTGAAATATCTAT
257 CGCTTTTCGGGGCCCC-GCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTAT
21695 ATTCA
321 ATTCA
*
21700 TCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTATTTC
1 TCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTC
* * *
21765 GATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACAATATTAAAAGCGTGAAGAGTCCTCCA
66 GATTTAATTAGAAATTAATTCAG-AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCA
* * * * * * *
21830 ATCTTCTTGGA-TTTTAATTATATATATTCTACGAGTATTGTGGCTAAAAATTGAGGGAAAATAT
130 ATCTT-TTTGACATTAAATTATATATATTTTATGAGTATT-TTGCTAAAAATTGAGGAAAAATAT
** *
21894 TTCAAGTTATTTTTTGCAAAATTTTAGCCGAAATC--G--CCATCACGGTTTTTTGGCTAAAAAA
193 TTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACCATCACGGTTTTTTGGCT--AAAA
* * * * *
21955 ACG-TTTT-GGGGCCCCGGTCAGTTTTGCATAATTTTTGGTG-CAAGACTTCTTGAAATATCTAT
256 ACGCTTTTCGGGGCCCCGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTAT
22017 A-TCAA
321 ATTC-A
* * * * * * * * *
22022 TCTAATCAAATATTAGCCACATTGGATTTAAGGATTTATTTTTACGAGTATTTGAATCATGTTTC
1 TCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTC
* * * * * * * * *
22087 AATTTAATTAGAAATTATTTTGAAAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAGAAGCCCT
66 GATTTAATTAGAAATTA-ATT---CAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * * * * *
22152 TCGATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAATTTGA-GAAAAAT
127 CCAATCTTTTTGACATTAAATTATATATATTTTATGAGTATT-TTGCTAAAAATTGAGGAAAAAT
* * * * * * * *
22216 ATTTCGGGTCAATTTTTACAAAATTATAGCCGAAGTCATGCAGCATCATGGTTTTTTTTTGGCTA
191 ATTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACCATCACGG---TTTTTTGGCTA
* * * ** *
22281 AAAATGC-ATTCTGGGGTTCTAGGTCAGTTTTGCATGATTTTTGGC
253 AAAACGCTTTTC-GGGG-CCCCGCTCAGTTTTGCATGATTTTTGGC
22326 AACAAGAATC
Statistics
Matches: 1309, Mismatches: 236, Indels: 160
0.77 0.14 0.09
Matches are distributed among these distances:
321 2 0.00
322 101 0.08
323 31 0.02
324 47 0.04
325 83 0.06
326 179 0.14
327 93 0.07
328 12 0.01
329 11 0.01
330 77 0.06
331 53 0.04
332 153 0.12
333 82 0.06
334 2 0.00
335 5 0.00
337 7 0.01
338 40 0.03
339 28 0.02
340 106 0.08
341 10 0.01
342 72 0.06
343 14 0.01
344 91 0.07
345 4 0.00
349 6 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (325 bp):
TCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTC
GATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAA
TCTTTTTGACATTAAATTATATATATTTTATGAGTATTTTGCTAAAAATTGAGGAAAAATATTTC
GGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACCATCACGGTTTTTTGGCTAAAAACGCT
TTTCGGGGCCCCGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCA
Found at i:22347 original size:2 final size:2
Alignment explanation
Indices: 22340--22379 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
22330 AGAATCCTTA
*
22340 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22380 TTATTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:22384 original size:4 final size:4
Alignment explanation
Indices: 22377--22405 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
22367 TATATATATA
22377 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
22406 CTCTAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:23206 original size:9 final size:9
Alignment explanation
Indices: 23192--23259 Score: 56
Period size: 9 Copynumber: 8.1 Consensus size: 9
23182 CTAATTACTA
23192 ATATATAAT
1 ATATATAAT
23201 ATATATAA-
1 ATATATAAT
*
23209 CT-TA-AAT
1 ATATATAAT
*
23216 ATATTTAAT
1 ATATATAAT
*
23225 ATTTATAAT
1 ATATATAAT
*
23234 AAATAT-AT
1 ATATATAAT
*
23242 ATTTAT-AT
1 ATATATAAT
23250 ATATATAAT
1 ATATATAAT
23259 A
1 A
23260 AAAACTTATT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
6 2 0.04
7 3 0.07
8 15 0.33
9 25 0.56
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATATAAT
Found at i:23219 original size:24 final size:22
Alignment explanation
Indices: 23192--23261 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 22
23182 CTAATTACTA
23192 ATATATAATATATATAACTTAAAT
1 ATATATAATATATATAA--TAAAT
* *
23216 ATATTTAATATTTATAATAAAT
1 ATATATAATATATATAATAAAT
23238 ATATATTTATATATATATAATAAA
1 ATATA--TA-ATATATATAATAAA
23262 AACTTATTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
22 9 0.23
24 17 0.44
25 13 0.33
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATATAATATATATAATAAAT
Found at i:23293 original size:80 final size:82
Alignment explanation
Indices: 23163--23323 Score: 281
Period size: 82 Copynumber: 2.0 Consensus size: 82
23153 TTATCTTTAA
*
23163 TATATATATATAGTAAAAACTAATTACTAATATATAATATATATAACTTAAATATATTTAATATT
1 TATATATATATAATAAAAACTAATTACTAATATATAATATATAT-ACTTAAATATATTTAATATT
23228 TATAAT-AAATATATATT
65 TATAATAAAATATATATT
*
23245 TATATATATATAATAAAAACTTATTACTAATATATAATATATAT-CTTAAATATATTTAATATTT
1 TATATATATATAATAAAAACTAATTACTAATATATAATATATATACTTAAATATATTTAATATTT
23309 ATAATAAAATATATA
66 ATAATAAAATATATA
23324 CTCGGGTTCT
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
80 25 0.33
81 9 0.12
82 42 0.55
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (82 bp):
TATATATATATAATAAAAACTAATTACTAATATATAATATATATACTTAAATATATTTAATATTT
ATAATAAAATATATATT
Found at i:24642 original size:40 final size:40
Alignment explanation
Indices: 24578--24654 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
24568 CACATAAATA
*
24578 TTATAATAAATCTCATCCCCCTTAATTATCTAGAATTATG
1 TTATAATAAATCTCATCCACCTTAATTATCTAGAATTATG
*
24618 TTATAATAAATC-CTATCCATCTTAATTATCTAGAATT
1 TTATAATAAATCTC-ATCCACCTTAATTATCTAGAATT
24655 GTAACCTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (40 bp):
TTATAATAAATCTCATCCACCTTAATTATCTAGAATTATG
Found at i:28413 original size:31 final size:29
Alignment explanation
Indices: 28373--28445 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
28363 TACCCAGAAA
* *
28373 AATCTCTTATGTTTTACTTTTGGGACAAAAT
1 AATCCCTTATGTTTT--TTTGGGGACAAAAT
*
28404 AATCCCTTATG-TTTTTTGGGGACAAATT
1 AATCCCTTATGTTTTTTTGGGGACAAAAT
*
28432 AATCCCTTACGTTT
1 AATCCCTTATGTTT
28446 CAAAAATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 22 0.59
29 2 0.05
30 3 0.08
31 10 0.27
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (29 bp):
AATCCCTTATGTTTTTTTGGGGACAAAAT
Found at i:28421 original size:27 final size:28
Alignment explanation
Indices: 28390--28445 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
28380 TATGTTTTAC
*
28390 TTTT-GGGACAAAATAATCCCTTATGTT
1 TTTTGGGGACAAAATAATCCCTTACGTT
*
28417 TTTTGGGGACAAATTAATCCCTTACGTT
1 TTTTGGGGACAAAATAATCCCTTACGTT
28445 T
1 T
28446 CAAAAATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (28 bp):
TTTTGGGGACAAAATAATCCCTTACGTT
Found at i:28645 original size:32 final size:32
Alignment explanation
Indices: 28584--28678 Score: 160
Period size: 32 Copynumber: 3.1 Consensus size: 32
28574 AAGGGACTAA
28584 TTTGTCCC-AAA-AAAAACATAAGGGA-TTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTTT
28613 TTTGTCCCAAAAGAAAAACATAAGGGATTTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTTT
*
28645 TTTGTCCCAAAAGAAAAACATTAGGGATTTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTTT
28677 TT
1 TT
28679 AGTATTTAGT
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
29 8 0.13
30 3 0.05
31 14 0.23
32 37 0.60
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (32 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTTT
Found at i:28733 original size:8 final size:8
Alignment explanation
Indices: 28720--28750 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
28710 AAAAAGTTGA
28720 TTTTTTCT
1 TTTTTTCT
28728 TTTTTTCT
1 TTTTTTCT
28736 TTTTTTCT
1 TTTTTTCT
28744 TTTTTTC
1 TTTTTTC
28751 CTTCTCCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTCT
Done.