Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015821.1 Corchorus olitorius cultivar O-4 contig15854, 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: 139823
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1320 original size:74 final size:77
Alignment explanation
Indices: 1152--1307 Score: 219
Period size: 78 Copynumber: 2.1 Consensus size: 77
1142 GTATCTTTAA
** * * * *
1152 AATAAAATTAAAAATTTCATTTGGGGCTAAATTTAGTGACATTAGTTTTATATTTTATTATTTCT
1 AATAAAATTTTAATTTTAATTTGGGACTAAACTTAGTGACATTAGTTTTATA-TTTATTATTTCT
*
1217 AAAACCCTATAAT
65 AAAACCCTATAAC
1230 AATAAAATTTTAATTTTAATTTGGGACTAAACTTAGTGA-ATTAGTTTTATA-TT-TTATTTCTA
1 AATAAAATTTTAATTTTAATTTGGGACTAAACTTAGTGACATTAGTTTTATATTTATTATTTCTA
1292 AAACCCTATAAC
66 AAACCCTATAAC
1304 AATA
1 AATA
1308 TCTTATTAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
74 24 0.34
75 2 0.03
77 12 0.17
78 33 0.46
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (77 bp):
AATAAAATTTTAATTTTAATTTGGGACTAAACTTAGTGACATTAGTTTTATATTTATTATTTCTA
AAACCCTATAAC
Found at i:1501 original size:107 final size:104
Alignment explanation
Indices: 1220--1546 Score: 374
Period size: 103 Copynumber: 3.1 Consensus size: 104
1210 TATTTCTAAA
*
1220 ACCCTATAATAATAAAATTTTAATTTTAATTTGGGACTAAACTTAGTGAATTAGTTTTATATTTT
1 ACCCT-TAA-AATAAAA--TTAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTTTATATTTT
** *
1285 ATTTCTAAAACCCTATAACAATATCTTATTAATTTTGGAATTT
62 ATTTCTAAAACCCTATAACAATAAATTATTAATTTTAGAATTT
*
1328 ACCCTTAAAATAAAATT--TATTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATT
1 ACCCTTAAAATAAAATTAATTTTAATTTGGGGCTAAACTTAGTG-AATTAGTTTTATATTTTATT
* * *
1391 TCTAAAACTCTATACCAGTAAATTATTAATTTTAGAATTT
65 TCTAAAACCCTATAACAATAAATTATTAATTTTAGAATTT
* * ** *
1431 ACCCTTAAAATAAGATTAAAATTTTAATTTGGGGCTAAACTTAGTGACATCAGTTTTATAACTAA
1 ACCCTTAAAATAAAATT--AATTTTAATTTGGGGCTAAACTTAGTGA-ATTAGTTTTATATTTTA
* * * * *
1496 TTTCTAAAACCTTATAATAAAAAATCT-TTAATTTCA-TATTT
63 TTTCTAAAACCCTATAACAATAAAT-TATTAATTTTAGAATTT
*
1537 ACTCTTAAAA
1 ACCCTTAAAA
1547 ATTTTACCAA
Statistics
Matches: 189, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
102 23 0.12
103 70 0.37
104 2 0.01
106 21 0.11
107 67 0.35
108 6 0.03
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.43
Consensus pattern (104 bp):
ACCCTTAAAATAAAATTAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTTTATATTTTATTT
CTAAAACCCTATAACAATAAATTATTAATTTTAGAATTT
Found at i:3170 original size:15 final size:17
Alignment explanation
Indices: 3144--3176 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3134 ATCTACCTAC
3144 CAAATATACAAA-TAAA
1 CAAATATACAAACTAAA
3160 CAAAT-TACAAACTAAA
1 CAAATATACAAACTAAA
3176 C
1 C
3177 TCACATTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAATATACAAACTAAA
Found at i:4918 original size:15 final size:15
Alignment explanation
Indices: 4900--4928 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4890 CATGAAATGG
4900 CACTAACAAAAATTC
1 CACTAACAAAAATTC
4915 CACTAACAAAAATT
1 CACTAACAAAAATT
4929 GCATATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (15 bp):
CACTAACAAAAATTC
Found at i:8749 original size:5 final size:5
Alignment explanation
Indices: 8739--8766 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
8729 GAGGTGGGTA
8739 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
8767 TCTCGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:11927 original size:268 final size:267
Alignment explanation
Indices: 11448--11960 Score: 713
Period size: 268 Copynumber: 1.9 Consensus size: 267
11438 AAAATGACCC
* * *
11448 GAAAGATTTTTCCTCAATTCTTGACAAAAATACTCATAATATATATATAATTCAACGCCAAAAAG
1 GAAAGATATTTCCTCAATTCTTGACAAAAATACTCATAAAATATATATAATTCAACACCAAAAAG
* * * **
11513 ATTGAAGGATTTTTCACGCTTTCAATATCGTTTTTCATTTTTTTTCTGAATTAATTTCTAATTAA
66 ATTGAAGGACTTTTAACGCTTTCAATATCGTTTTTCATTTTCTTTCCAAATTAATTTCTAATTAA
* * * *
11578 ATCGATACAAGATTCAGATGCACATAAAAACAAATCGTTAAATCCAATGTGGCTGAGATTTTATT
131 ATCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATT
* * *
11643 AGATGAATACAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAATAGAGTCGTGGCCTT
196 AGATGAATACAGATATTTCAAGGAGTCTTGACACCAAAAATCATACAAAATAGAGTCGTGGCCTT
11708 AGAACCT
261 AGAACCT
* * * * ** * *
11715 GAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATGATTTGATATCAAAAAG
1 GAAAGATATTTCCTCAATTCTTGACAAAAATACTCATAAAATATATATAATTCAACACCAAAAAG
* * *
11780 ATTGAAGGGCTTTTAACGC-TTCTAATATTGTTTTTCCTATTTCTTTCCAAATTAATTTCTAATT
66 ATTGAAGGACTTTTAACGCTTTC-AATATCGTTTTTCAT-TTTCTTTCCAAATTAATTTCTAATT
* * * * *
11844 AAATCGAAATAAGATTCATATGCTCATAAAAACAAATCCTTAAATCTAATGTGGCTAAGATTTGG
129 AAATCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGA
*
11909 TTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATACAAAA
194 TTAGATGAATACAGATATTTCAAGGAGTCTTGACACCAAAAATCATACAAAA
11961 CTGAGCCGGA
Statistics
Matches: 212, Mismatches: 32, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
266 3 0.01
267 83 0.39
268 126 0.59
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (267 bp):
GAAAGATATTTCCTCAATTCTTGACAAAAATACTCATAAAATATATATAATTCAACACCAAAAAG
ATTGAAGGACTTTTAACGCTTTCAATATCGTTTTTCATTTTCTTTCCAAATTAATTTCTAATTAA
ATCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATT
AGATGAATACAGATATTTCAAGGAGTCTTGACACCAAAAATCATACAAAATAGAGTCGTGGCCTT
AGAACCT
Found at i:12575 original size:333 final size:328
Alignment explanation
Indices: 11727--13748 Score: 1895
Period size: 333 Copynumber: 6.2 Consensus size: 328
11717 AAGATATTTC
* * * ** ***
11727 CTCAATTTTTGGCTAAAATACTCATAAAATATATATGATTTGATATCAAAAAGATTGAAGGGCTT
1 CTCAATTTTTAGCCAAAATACTCATAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGGCTT
* * * * *
11792 TTAACGCTTCTAATATTGTTTTTCCTATTTCTTTCCAAATTAATTTCTAATTAAATCGAAATAAG
65 TTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAG
* * *
11857 ATTCATATGCTCATAAAAACAAATCCTTAAATCTAATGTGGCTAAGATTTGGTTAGATGAATATA
130 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATA
* * * *
11922 GATATTTCAAGGAGTCTTGACACCAAAAATCATACAAAACTGAGCC-GGACCCCGGAAGGCGTTT
195 GATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTT
** * * * *
11986 TTAGC-CGAAAACCGTGATGATTAGTACACGATTTCAGCTAAAATTTTCCAAAAATTGACTCGAA
260 TTAGCAAAAAAACC---ATGA-TGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG-A
* *
12050 AAAATTTTC
320 AATATTTTT
* * * * *
12059 CTCGATTTCTAGCAAAAATACTCATAAAAATATATAATTCAACGCCAAAAA-AGTGAAAGGCTTT
1 CTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGC-TT
* * * *
12123 TTCACGCTTCTAATATCGTTTTCCCTATTTTATTTCCAAATTAATTTCTGATTAAATCAAAACAA
65 TTCACGCTTCTAATATCGTTTTTCCTATTTT-TTTTCAAATTAATTTCTAATTAAATCGAAACAA
* *** * * *
12188 GATTTAGAAATTCCTAAAAACAAATCCTTAAATACAATGTGGCTGAGATTTGGTTAGATGAATAT
129 GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATAT
* * * *
12253 AGATATATTTTAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCCAGGACCCCGGAACACG
194 AG--ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCG
* *
12318 TTTTTAGCCAAAATTAAAAAACCATGATGGTACACGATTTTGGCTAAAATTTTGCAAAAATTAAC
257 TTTTTAG-C---A--AAAAAACCATGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
12383 CCGAAATATTTTT
316 CCGAAATATTTTT
* * * *
12396 CTCAATTTTTAGCCACAATACTGATAAAAAAATATAATTCAACGCCAAAAAGATTGAAGGGCTTC
1 CTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTT
*
12461 TCACGCTTCTAATATCG-TTTT-CT-TTTTTTTTCAAATTAATTTCTAATTAAATCGAAACATGA
66 TCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGA
* * *
12523 TTCAAATGCTCGCAAAAACAAATCCTTAAAT-CAAGTGTGGCTAAGGTTTGGTTAGATGAATATA
131 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA-TGTGGCTAAGATTTGGTTAGATGAATATA
* * * * * * *
12587 GATATTTCAAGGAGTTTTGTC-ACAAGAAATCATGCAAAACTGA-CATGGGGCCTCGGAACGCGA
195 GATATTTCAAGGAGTCTTGGCGCCAA-AAATCATGCAAAACTGAGC-CGGGACCCCGGAACGCGT
* **
12650 TTTTAACATAAAAAACTGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
258 TTTTAGCA-AAAAAACCATGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
12715 TATTTTGT
322 TATTTT-T
* * * * * *
12723 CTCAATTTTTAGCCACAACACTCATAAAATATATATAATTCAACACCAAAAAGACTGGAGGACTT
1 CTCAATTTTTAGCCAAAATACTCATAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGGCTT
* * * *
12788 TTCACGCTTTTAATATCGTTTTTCATA-TTTTCTT-AAATTAATTTCTAATTAAATCGAATCAAG
65 TTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAG
* ** * * *
12851 ATTCAGAGGCTCGTAAAAACAAATCCTTAAATTAAATGTGGGTGAGATTTGATTAGATGAATATA
130 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATA
* * * * * * *
12916 GATATTTCAAGAAGTCTCGGCGCAAAAAATCATGCAAAACTAAGTCTGGG-CCTCGAAACGCGTT
195 GATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG-CCGGGACCCCGGAACGCGTT
* * *
12980 TTTAGC-TAAAAACCATGA---TACA--ATTTCGGGTAAAATTTTGCAAAAATTGACCCGAAAAA
259 TTTAGCAAAAAAACCATGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATA
13039 TTTTT
324 TTTTT
* * *
13044 CCGACAATTTTTGGCTAAAATACTCAT--AAA-A-AT-ATT----G-------GA--GAA---CT
1 -C-TCAATTTTTAGCCAAAATACTCATAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCT
* * ** * * *
13088 TTTCACGCTTTTTAT-TCGTTTTTATTA-TTTTTTT-GAATTAATTTTTAATTAAATCGAAATAA
64 TTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAA
* * * * * *
13150 GATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATTTTGCTAATATTTGATTAGATGAATAT
129 GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATAT
* * * * * * *
13215 GGATATCTCAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGATCCCGAAACACGAT
194 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTT
* * * * * **
13280 TTTAGCCAAAAAACCGTGATGATTATCAAACGATTTCGGCTAGAATTTTACAAAAATTGACTTGA
259 TTTAGCAAAAAAACCATGATG-GTA-C--ACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGA
*
13345 AAGT-TATTTC
320 AA-TAT-TTTT
* * **
13355 CTCAATTTTTAGCCACAATACTCATTAAAATTATATAATTCAACGCCAATTAGATTGAAGGGCTT
1 CTCAATTTTTAGCCAAAATACTCA-TAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTT
* * * * * *
13420 TTCATGCTTCTAATATCGTTTTTCCTATTATTTTTCTAATTAATTTCTGATTAAATCGAAATATG
65 TTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAG
* ** * *
13485 ATTCAGATGCTTGTATTAA-AAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATA
130 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATA
** * * *
13549 GATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCAACACT-ATACCGGGATCCCGGAACGCGTT
195 GATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA-GCCGGGACCCCGGAACGCGTT
* * * * *
13613 TTTAGCAAAAAAAAAATCGTAATTTCGACTAACGTACACGATTTCAGCTAATATTTTGTAAAAAT
259 TTTAGC---AAAAAAA-C--CA--T-GA-T--GGTACACGATTTCGGCTAAAATTTTGCAAAAAT
* * *
13678 TAACCAGAAGTATTTTT
312 TGACCCGAAATATTTTT
** * *
13695 CCTCAATTTTTTTCTAAAATACTCAT-AAAATATATATTTCAACGCCAAAAAGAT
1 -CTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTCAACGCCAAAAAGAT
13749 CGCAAGACTG
Statistics
Matches: 1386, Mismatches: 224, Indels: 153
0.79 0.13 0.09
Matches are distributed among these distances:
299 4 0.00
300 149 0.11
301 26 0.02
304 2 0.00
305 2 0.00
306 3 0.00
308 1 0.00
309 19 0.01
310 33 0.02
311 3 0.00
312 2 0.00
313 1 0.00
314 2 0.00
315 3 0.00
317 3 0.00
318 2 0.00
319 2 0.00
320 1 0.00
321 3 0.00
322 40 0.03
323 19 0.01
324 4 0.00
326 61 0.04
327 38 0.03
328 49 0.04
329 135 0.10
330 28 0.02
331 111 0.08
332 127 0.09
333 185 0.13
334 84 0.06
335 22 0.02
336 10 0.01
337 73 0.05
338 43 0.03
339 28 0.02
340 5 0.00
341 51 0.04
342 8 0.01
343 2 0.00
344 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (328 bp):
CTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTT
TCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGA
TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAG
ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTT
TAGCAAAAAAACCATGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATT
TTT
Found at i:14819 original size:331 final size:326
Alignment explanation
Indices: 13764--15409 Score: 1372
Period size: 331 Copynumber: 5.0 Consensus size: 326
13754 GACTGTTCAG
* *
13764 ATGTGGCTGAGATTTGATTAGATAAATATAGATTTTTCAAGGAGTCTC-GACGCCAAAAATCATG
1 ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCTG-CGCCAAAAATCATG
* * * * * * * * *
13828 CAATACTAAGTCGGGGCCCGAAACACGTTTTTAGCAAAAAAAAAAAATCGTGACGG-T-GTACAC
65 CAAAACTGAGCCGGGCCCCGAAACGCGTTTTTAGC------CAAAAACCGTGATGGTTATTACAC
* * * * * * *
13891 GATTTCGGCTAAAATTTTGCAAAAAAT-A-CCTAAAAATTTTTCCCTCAATTTTGACTAAAATAC
124 GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTT-CCTCAATTTTTAGTATAATAC
* * * * * *
13954 TCGTGAAAATATATATAATTTAATGCCAAAAAGATTGGAGGAGGACTTTTCACGCTTTTCATATC
188 TCAT--AAA-ATATATAATTCAACGCCAAAAAGATT-GA--AGGGCTTTTCGCGCTTTTAATATC
** * * *
14019 GTTTTTCATATTTTTTTGAATTAATTTGTAATTAAATCGAAACAAGATACAGATACTCGTAAAAA
247 GTTTTTCATA-TTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* **
14084 TAAATCATTAAAAACA
311 CAAATCATTAAATCCA
* * * * * * * *
14100 ATTTGGATGAGATTTGTTTAGATTAATATGGATATCTCAAGGATTCT-TAACGCCAAAAATCATG
1 ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCT-GCGCCAAAAATCATG
* * * * * *
14164 CAAAACTGACCCGGGGCCCCGGAACTCGGTTTTGGCCAAAAAAAACTGTGAT-G---TTACACGA
65 CAAAACTGAGCC-GGGCCCCGAAACGCGTTTTTAGCC---AAAAACCGTGATGGTTATTACACGA
* * * * * * * * *
14225 TTTCGGCTAATATTTTGCAAAAATTTACCCAAAATATTTTTCCTTAACTTTTAGCCACAATACTC
126 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAG-TATAATACTC
* ** *
14290 ATAAAAAATATATAATTCGACGCCAAAAAGATTGAAGGGCTTTTTCATGCTTCTAATATCGTTTT
190 AT--AAAATATATAATTCAACGCCAAAAAGATTGAAGGGC-TTTTCGCGCTTTTAATATCGTTTT
* * * * **
14355 TCTTATTTTTTTTCGAATTAATTTCTAATTAAAACGAAACATGATTCAGATGCTTTTAAAAA-AA
252 TC--A-TATTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
**
14419 ATGGC-TGGAA--C-
314 AT--CATTAAATCCA
* * * *
14430 -T-TGGC-------T-A-T--ATGAATATAGATATTTCAAAGAGTTTCGGCGCCAAAAATCATTC
1 ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCATGC
** * *
14482 AAAACTGAATCGGGCCCCGGAACGCGTTTTTAGCCTAAAACCGTGATGTGATTATTACACGATTT
66 AAAACTGAGCCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATG-G-TTATTACACGATTT
* * * * *
14547 CGACTAAAATTTTGCAAAAGTTGACCTGAAAGATATTTCTTCAATTTTTAGCCATAATACTCAAT
129 CGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAG-TATAATACTC-AT
* *
14612 AAAATATATAATTCGACACCAAAAAGATTGAAGGGCTTTTCGCGCTTTTAATATCGTTTTTCATA
192 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCGCGCTTTTAATATCGTTTTTCATA
* *
14677 TTTTGTCAGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGT-AAAACAAATCCTT
257 TTTT-TCA-AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATT
* *
14741 AAATGCT
320 AAATCCA
* * *
14748 ATGTTGCT-ATGATTTTATTAGATGAATATAGATATTTCAAGGAGTGTCTGCGCCAAAAATCATG
1 ATGTGGCTGA-GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCATG
* *
14812 CAAAACTGAGCCGGGCCCCGAAACGCGTTTTCAGCCAAAAAACCGTGA-GG---GTACACGATTT
65 CAAAACTGAGCCGGGCCCCGAAACGCGTTTTTAGCC-AAAAACCGTGATGGTTATTACACGATTT
* * * * * *
14873 TGGCTAAAATTCTGCAAAAAAATGACCCGAAAAATTTTTCCTC-ATTTTT-GTATAAAATACTTA
129 CGGCTAAAATTTTGC-AAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGTAT--AATACTCA
* * * * * * *
14936 TAAAATATTTATAATTTAACGCCAAAAAAATTGGAGGACTTTTCACGCTTTTAATATCATTTTTT
191 TAAAATA--TATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCGCGCTTTTAATATCGTTTTTC
* * * *
15001 ATATTTTTCTCAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTTGTAAAAACAAATTA
254 ATATTTTTC-AAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCA
15066 TTAAATCCA
318 TTAAATCCA
* * ** * *
15075 ATGTGGTTGAGATTTGATTAGATGAATATGGATATCCCAAGGAGTCT-TGACACCAAAAATCAGG
1 ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCTG-CGCCAAAAATCATG
* * ** * *
15139 CAAAACTGAGGCGGGGTCCTAAAACGCATTTTTAGCCAAAAACTGTGATGGTTATTACACGATTT
65 CAAAACTGA-GCCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTT
* * * *
15204 CGGCTAAAATTTTGTAAAAATTGACCCGAAAGATATTTCCTCAATTTTGATTAAAATACTCATAA
129 CGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGTATAATACTCAT-A
* * * * *
15269 AAACTATATAATTCAACGCCAAAAAGATTGAATGGCTTTT-GAGGTTTCTAACATCGTTTTTCCT
193 AAA-TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCGCGCTTT-TAATATCGTTTTTCAT
** *
15333 ATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTGGATGCTCGTAAAAACAAAT-TT
256 A-TTTTT-CAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCAT
15397 ATAAATCCA
319 -TAAATCCA
15406 ATGT
1 ATGT
15410 TGCTAATGTT
Statistics
Matches: 1064, Mismatches: 180, Indels: 137
0.77 0.13 0.10
Matches are distributed among these distances:
313 10 0.01
314 6 0.01
315 11 0.01
316 62 0.06
317 67 0.06
318 35 0.03
319 63 0.06
320 5 0.00
321 1 0.00
324 2 0.00
325 9 0.01
326 77 0.07
327 161 0.15
328 28 0.03
329 6 0.01
330 80 0.08
331 192 0.18
332 51 0.05
333 84 0.08
334 35 0.03
336 61 0.06
337 18 0.02
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (326 bp):
ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCATGC
AAAACTGAGCCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCG
GCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGTATAATACTCATAAAA
TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCGCGCTTTTAATATCGTTTTTCATATTTT
TCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCC
A
Found at i:15812 original size:15 final size:16
Alignment explanation
Indices: 15794--15823 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15784 ATAAATAATA
15794 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
15809 ATATTATAATCTAAA
1 ATATTATAATCTAAA
15824 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:16114 original size:2 final size:2
Alignment explanation
Indices: 16109--16142 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
16099 TTCGTGATTT
* *
16109 TA TA TA TA TA TA TA TA TA TA TA TA AA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16143 AAGGGTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:16746 original size:3 final size:3
Alignment explanation
Indices: 16740--16775 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
16730 TATTATTATT
16740 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
16776 CGGCAATCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:17974 original size:3 final size:3
Alignment explanation
Indices: 17966--17992 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17956 CTTTGTAGTT
17966 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
17993 CCTAATTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:20915 original size:57 final size:57
Alignment explanation
Indices: 20827--20938 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 57
20817 CTTTTCCTTT
*
20827 CACACAATAAATGTTATAATAAATCAAATCCCCCCTATCTCTACTTAATTATTCTTC
1 CACACAATAAATGTTATAATAAATCAAATCCCCCATATCTCTACTTAATTATTCTTC
**
20884 CACACAATAAATGTTATAATAAATCCCATCCCCCATATCTCTACTTAATTATTCT
1 CACACAATAAATGTTATAATAAATCAAATCCCCCATATCTCTACTTAATTATTCT
20939 ACAAAATAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (57 bp):
CACACAATAAATGTTATAATAAATCAAATCCCCCATATCTCTACTTAATTATTCTTC
Found at i:20979 original size:11 final size:11
Alignment explanation
Indices: 20963--20989 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20953 ATTTTCTTTT
20963 AAGTTAGAACA
1 AAGTTAGAACA
20974 AAGTTAGAACA
1 AAGTTAGAACA
20985 AAGTT
1 AAGTT
20990 TTTAGATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (11 bp):
AAGTTAGAACA
Found at i:21076 original size:42 final size:42
Alignment explanation
Indices: 21017--21097 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
21007 TAAGGATTAG
*
21017 GATTTGAGTTGAATATTTCTTAAT-TTACAAAGAATTTTCTAT
1 GATTTGAATTGAATATTTCTT-ATCTTACAAAGAATTTTCTAT
* *
21059 GATTTGAATTGAGTATTTCTTATCTTACAGAGAATTTTC
1 GATTTGAATTGAATATTTCTTATCTTACAAAGAATTTTC
21098 AAGACTTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.47
Consensus pattern (42 bp):
GATTTGAATTGAATATTTCTTATCTTACAAAGAATTTTCTAT
Found at i:21430 original size:13 final size:13
Alignment explanation
Indices: 21412--21437 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21402 GAACCGGACG
21412 TTTTACCGGTTTT
1 TTTTACCGGTTTT
21425 TTTTACCGGTTTT
1 TTTTACCGGTTTT
21438 GGACTTGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (13 bp):
TTTTACCGGTTTT
Found at i:22888 original size:82 final size:80
Alignment explanation
Indices: 22773--22921 Score: 217
Period size: 82 Copynumber: 1.8 Consensus size: 80
22763 ATTTCCTGTT
*
22773 ATCTCATTGATCTTCCCTCTTTCAAATCGTTTCTCTTTCATTTAAGTCAAAATTTTCTGATTTTA
1 ATCTCATTGATCTTCCCTCTTTCAAATCGTTTCTCTTTCATTTAAATCAAAATTTTCTGATTTTA
22838 TTTATGTTAGGAACC
66 TTTATGTTAGGAACC
* ** * * *
22853 ATCTCGTTGATCTTTTCCCTCTTTTGAATTGTTTCTGTTTTATTTAAATCAAAATTTTCTGATTT
1 ATCTCATTGATC--TTCCCTCTTTCAAATCGTTTCTCTTTCATTTAAATCAAAATTTTCTGATTT
22918 TATT
64 TATT
22922 GCAACAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 11 0.18
82 49 0.82
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (80 bp):
ATCTCATTGATCTTCCCTCTTTCAAATCGTTTCTCTTTCATTTAAATCAAAATTTTCTGATTTTA
TTTATGTTAGGAACC
Found at i:24668 original size:19 final size:20
Alignment explanation
Indices: 24621--24668 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 20
24611 TTTAATGTGG
24621 GTATACTTGTTTATACATGT
1 GTATACTTGTTTATACATGT
*
24641 -TAT--TTGTTT-TGCATGT
1 GTATACTTGTTTATACATGT
24657 GTATACTTGTTT
1 GTATACTTGTTT
24669 CCATACCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
19 9 0.38
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.56
Consensus pattern (20 bp):
GTATACTTGTTTATACATGT
Found at i:25240 original size:24 final size:24
Alignment explanation
Indices: 25208--25255 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
25198 ACCTGTCGAA
25208 AGAGAAAATTAAGGAAGCAATATT
1 AGAGAAAATTAAGGAAGCAATATT
25232 AGAGAAAATTAAGGAAGCAATATT
1 AGAGAAAATTAAGGAAGCAATATT
25256 TTGGACAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (24 bp):
AGAGAAAATTAAGGAAGCAATATT
Found at i:25472 original size:24 final size:24
Alignment explanation
Indices: 25444--25490 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
25434 TTGATGCATT
25444 GTATTGGTATCTAACTAATTCAAG
1 GTATTGGTATCTAACTAATTCAAG
25468 GTATTGGTATCTAACTAATTCAA
1 GTATTGGTATCTAACTAATTCAA
25491 TTGATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (24 bp):
GTATTGGTATCTAACTAATTCAAG
Found at i:25966 original size:2 final size:2
Alignment explanation
Indices: 25959--25983 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25949 AGTCACTACT
25959 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
25984 TATGAACTGA
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:29093 original size:2 final size:2
Alignment explanation
Indices: 29086--29126 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
29076 TGCCTAAAAC
*
29086 TA TA TA TA TA TA TA TA TA TA TA TC 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
29127 GTATTCTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41952 original size:6 final size:6
Alignment explanation
Indices: 41941--41996 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
41931 ACTGGCTTTC
* * *
41941 CTTTTT CTTTTT C-TTTT C-TTTT CTTTTT -TTTTC CTTTTG GTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
41986 CTTTTT CTTTT
1 CTTTTT CTTTT
41997 AATTTTAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
5 14 0.33
6 29 0.67
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:43116 original size:21 final size:23
Alignment explanation
Indices: 43054--43120 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 23
43044 TTTGAGATAA
43054 TATAATATTCCATCAAACAATTG
1 TATAATATTCCATCAAACAATTG
* *
43077 TAATACACAATTTCATCAAACAA-T-
1 T-ATA-A-TATTCCATCAAACAATTG
43101 TATAATATTCCATCAAACAA
1 TATAATATTCCATCAAACAA
43121 GTGAAACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 13 0.35
22 1 0.03
23 4 0.11
24 4 0.11
25 2 0.05
26 13 0.35
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.31
Consensus pattern (23 bp):
TATAATATTCCATCAAACAATTG
Found at i:51084 original size:13 final size:13
Alignment explanation
Indices: 51066--51091 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51056 TCTAAAAATA
51066 AAATAATTAATTT
1 AAATAATTAATTT
51079 AAATAATTAATTT
1 AAATAATTAATTT
51092 TAGGCTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATAATTAATTT
Found at i:77523 original size:16 final size:16
Alignment explanation
Indices: 77504--77535 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
77494 TTGAGAAGGG
77504 GTTAAAGTGAGGGAGA
1 GTTAAAGTGAGGGAGA
77520 GTTAAAGTGAGGGAGA
1 GTTAAAGTGAGGGAGA
77536 CATAGCTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.44, T:0.19
Consensus pattern (16 bp):
GTTAAAGTGAGGGAGA
Found at i:79084 original size:10 final size:10
Alignment explanation
Indices: 79071--79108 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
79061 TTCTTGACAG
79071 AGAGAAAAGA
1 AGAGAAAAGA
79081 AGAGAAAAGA
1 AGAGAAAAGA
*
79091 GAGAGAAGAGA
1 -AGAGAAAAGA
79102 AGAGAAA
1 AGAGAAA
79109 TCAGAAGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (10 bp):
AGAGAAAAGA
Found at i:79095 original size:21 final size:21
Alignment explanation
Indices: 79069--79108 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
79059 AGTTCTTGAC
79069 AGAGAGAAAAGAAGAGAAAAG
1 AGAGAGAAAAGAAGAGAAAAG
*
79090 AGAGAGAAGAGAAGAGAAA
1 AGAGAGAAAAGAAGAGAAA
79109 TCAGAAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (21 bp):
AGAGAGAAAAGAAGAGAAAAG
Found at i:85838 original size:15 final size:15
Alignment explanation
Indices: 85812--85855 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
85802 GCAGCAACTA
*
85812 GAAGAAGAAGAAGAT
1 GAAGAGGAAGAAGAT
* * *
85827 GATGATGAAGAAAAT
1 GAAGAGGAAGAAGAT
85842 GAAGAGGAAGAAGA
1 GAAGAGGAAGAAGA
85856 AGAGAGGATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.34, T:0.09
Consensus pattern (15 bp):
GAAGAGGAAGAAGAT
Found at i:86961 original size:16 final size:16
Alignment explanation
Indices: 86940--86971 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
86930 AGTAATATAA
86940 GTGTCTTTTTTTTTTG
1 GTGTCTTTTTTTTTTG
86956 GTGTCTTTTTTTTTTG
1 GTGTCTTTTTTTTTTG
86972 ACATAGTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.19, T:0.75
Consensus pattern (16 bp):
GTGTCTTTTTTTTTTG
Found at i:87085 original size:57 final size:58
Alignment explanation
Indices: 86976--87095 Score: 208
Period size: 57 Copynumber: 2.1 Consensus size: 58
86966 TTTTTGACAT
86976 AGTGTCTTGCATATGCAAATTTAAAGAACTTAAAAGAGGTAAATTATGAAAAGTTTGAA
1 AGTGTCTTGCATATGCAAATTTAAAGAACTTAAAAGAGGTAAATTATGAAAAGTTTG-A
*
87035 AGTGTCTTGCATA-GCAAATTTAAAGAACTT-AAAGAGGTAAATTGTGAAAAGTTTGA
1 AGTGTCTTGCATATGCAAATTTAAAGAACTTAAAAGAGGTAAATTATGAAAAGTTTGA
87091 AGTGT
1 AGTGT
87096 GAAGGTCCTA
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
56 6 0.10
57 24 0.40
58 17 0.28
59 13 0.22
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.31
Consensus pattern (58 bp):
AGTGTCTTGCATATGCAAATTTAAAGAACTTAAAAGAGGTAAATTATGAAAAGTTTGA
Found at i:118652 original size:55 final size:55
Alignment explanation
Indices: 118566--118678 Score: 199
Period size: 55 Copynumber: 2.1 Consensus size: 55
118556 CTCTGTATAC
*
118566 TTATTATCCCATCTCTTTGATCAAATCTCCTTAAAGAATAAAAGATTCAAATAAA
1 TTATTATCCCATCTCTTTGATCAAATCTCCTTAAAGAATAAAAGATTCAAAGAAA
* *
118621 TTATTATCCCATCTCTTTGATCAAATGTCCTTAAAGAATACAAGATTCAAAGAAA
1 TTATTATCCCATCTCTTTGATCAAATCTCCTTAAAGAATAAAAGATTCAAAGAAA
118676 TTA
1 TTA
118679 AAAAATTTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.35
Consensus pattern (55 bp):
TTATTATCCCATCTCTTTGATCAAATCTCCTTAAAGAATAAAAGATTCAAAGAAA
Found at i:125204 original size:33 final size:34
Alignment explanation
Indices: 125162--125228 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
125152 TTGCTACTCA
125162 CTTGTGGAAGA-TTGCTACCTAGAGATAGAGGAT
1 CTTGTGGAAGATTTGCTACCTAGAGATAGAGGAT
125195 CTTGTGGAAGATTTGCTACCTAGAGATAGAGGAT
1 CTTGTGGAAGATTTGCTACCTAGAGATAGAGGAT
125229 AGGATATTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (34 bp):
CTTGTGGAAGATTTGCTACCTAGAGATAGAGGAT
Found at i:131531 original size:51 final size:52
Alignment explanation
Indices: 131430--131531 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
131420 GTTCATCAAA
* **
131430 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
131482 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
131532 CTTCATTCGG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Found at i:139389 original size:36 final size:36
Alignment explanation
Indices: 139342--139411 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
139332 TTTGATAACC
* *
139342 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
139378 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
139412 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.