Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014712.1 Corchorus olitorius cultivar O-4 contig14745, 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: 217640
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:871 original size:335 final size:330
Alignment explanation
Indices: 11--1020 Score: 871
Period size: 335 Copynumber: 3.1 Consensus size: 330
1 TTTTTTTTTG
* * *
11 AGTATTATGGCGAAAAATTGAG-GAAAAACTTATCGAGTCAGTTTTTGCAAAATTTTAGCCGAAA
1 AGTATTGTGGCAAAAAATTGAGAGAAAAACTTTTC--GTCAGTTTTTGCAAAATTTTAGCCGAAA
* * *
75 TCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTCCGAAGCCCCAACTCAATTTTGCAT
64 TCGTGTACT-ACCATCACGGTTTTTAGCTAAAAACGTGTTCCG--GGCCCGACTCAATTTTGCAT
* * ** * * *
140 GATTTTTGGTGCAAAGATTGATTGAAATATCTATATATATATTCATCGAATCAAATCTCAGCTAC
126 GATTTTTGGCGAAAAGATTCCTTGAAATATC------TATATTCATTGAACCAAATCTCAGCCAC
* * * *
205 ATTGGATATAAGGATTTG-----TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
185 ATTGGATTTAAGGATTTGTTTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTGAAGTAAAAAT
* ** * *
265 TAATTCAGGAAAAAATGGAAAGACGATATTAGAAGCGTGAAAAGCCCGTTAATTTTGGCGTTGAA
250 AAATTCAAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTTAATTTTGGCGTTGAA
*
330 TTATATATTTTTTCTA
315 TTATATATTTATTCTA
* *
346 AGTATTGTGGCAAAAAATTGAGAATAAAAACTTTTCG--AG----T-C-AATTTTTAGCCGAAAT
1 AGTATTGTGGCAAAAAATTGAG-AGAAAAACTTTTCGTCAGTTTTTGCAAAATTTTAGCCGAAAT
* ** * * *
403 CGTGTACTAACCATCACGGTTTTGGAGCTAAAAAACGTGTTTTGGGGCCGCGGCTCAGTGTTGCA
65 CGTGTACT-ACCATCACGGTTTT-TAGCT-AAAAACGTG-TTCCGGGCC-CGACTCAATTTTGCA
* * ** * *
468 TGAATTTTGGCAAAAAGACGCCTTGAAATATCTGTATTCATCT-AACAAAATCTCAGCCACATTG
125 TGATTTTTGGCGAAAAGATTCCTTGAAATATCTATATTCAT-TGAACCAAATCTCAGCCACATTG
*
532 GATTTAAGGATTTGTTTTTTTTTTACGAGTATCTGAATCTTGTTTCGATTGAAGTAAAAATAAAT
189 GATTTAAGGATTTGTTTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTGAAGTAAAAATAAAT
* * **
597 TCGAAAAAATAAAAGGAAAAACGATATTTAGAAGCTTGGAAAA-TCC-TTCAATTTTTTTTCGTT
254 TC-AAAAAA-AAAAGGAAAAACGATA-TTAGAAGCGT-GAAAAGCCCGTT-AA--TTTTGGCGTT
660 GAATTATATATTTATTCTA
312 GAATTATATATTTATTCTA
** ** *
679 AGTATTGTGGCAAAGGATTGAG-GAAAAGTTTTTCGGATCAGTTTTTGCAAAATTTTAGCCAAAA
1 AGTATTGTGGCAAAAAATTGAGAGAAAAACTTTTC-G-TCAGTTTTTGCAAAATTTTAGCCGAAA
** *
743 TCGTGTA-T-TTATCACGGTTTTTTGCTAAAAACGTGTTCCGGGCCCTGACTCAATTTTGCATGA
64 TCGTGTACTACCATCACGGTTTTTAGCTAAAAACGTGTTCCGGGCCC-GACTCAATTTTGCATGA
* * * * * * *
806 TTTTTGGCGTATAGATTTCTTGAAATATCCATACTCATTGAACCAAATCCCAGCCGCATTGGATT
128 TTTTTGGCGAAAAGATTCCTTGAAATATCTATATTCATTGAACCAAATCTCAGCCACATTGGATT
* * ** **
871 TAAGGATTTG-----TTTTTACGAGCATCTTAATCTTG-TT-AATT--AG---AAATTGATTCGG
193 TAAGGATTTGTTTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTGAAGTAAAAATAAATTCAA
* * * *
924 AAAAAAATGGAAAAAGGATATTAGAAGCGTGAAAAACCC-TTCAATCTTTTTGGTGTTGAATTAT
258 AAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTT-AA---TTTTGGCGTTGAATTAT
* * *
988 ATATTTTTTATG
319 ATATTTATTCTA
1000 AGTATTGTGGCAAAAAATTGA
1 AGTATTGTGGCAAAAAATTGA
1021 TAAAAAAAAT
Statistics
Matches: 551, Mismatches: 91, Indels: 80
0.76 0.13 0.11
Matches are distributed among these distances:
319 5 0.01
320 16 0.03
321 57 0.10
322 4 0.01
323 47 0.09
326 2 0.00
327 38 0.07
328 53 0.10
329 51 0.09
330 40 0.07
331 22 0.04
332 6 0.01
333 48 0.09
334 2 0.00
335 104 0.19
336 9 0.02
337 13 0.02
338 11 0.02
339 1 0.00
340 2 0.00
341 20 0.04
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (330 bp):
AGTATTGTGGCAAAAAATTGAGAGAAAAACTTTTCGTCAGTTTTTGCAAAATTTTAGCCGAAATC
GTGTACTACCATCACGGTTTTTAGCTAAAAACGTGTTCCGGGCCCGACTCAATTTTGCATGATTT
TTGGCGAAAAGATTCCTTGAAATATCTATATTCATTGAACCAAATCTCAGCCACATTGGATTTAA
GGATTTGTTTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTGAAGTAAAAATAAATTCAAAAA
AAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTTAATTTTGGCGTTGAATTATATATTTA
TTCTA
Found at i:1270 original size:270 final size:264
Alignment explanation
Indices: 796--1301 Score: 721
Period size: 263 Copynumber: 1.9 Consensus size: 264
786 CCTGACTCAA
* * * * * *
796 TTTTGCATGATTTTTGGCGTATAGATTTCTTGAAATATCCATACTCATTGAACCAAATCCCAGCC
1 TTTTGCATGATTTTTAGCGTAAAGACTCCTTAAAATATCCATACTCATCGAACCAAATCCCAGCC
* ** * * *
861 GCATTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTAATTAGAAATTGATTCGGAA
66 ACATTCCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTAATTAGAAATTAATTCGAAA
* * *
926 AAAAATGGAAAAAGGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGTGTTGAATTATATA
131 AAAAATGGAAAAACGATATTAAAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATA
*
991 TTTTTTATGAGTATTGTGGC-AAAAAATTGATAAAAAAAATTACAGGTCATTTTTTAACCCCGGT
196 TTTTTTATGAGTATTGTGGCAAAAAAATTGAGAAAAAAAATTACAGGTCATTTTTTAACCCCGGT
1055 TCAG
261 TCAG
* * *
1059 TTTTGCATGATTTTTAGCGTAAAGACTCCTTAAAATATCTATATTCATCGAAGCAAATCCCAGCC
1 TTTTGCATGATTTTTAGCGTAAAGACTCCTTAAAATATCCATACTCATCGAACCAAATCCCAGCC
1124 ACATTCCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAA
66 ACATTCCATTTAAGGATTTGTTTTTACGAGCATCTGAATC----TT-G--TTAATTAGAAATTAA
1189 TTC-AAAAAAAATGGGAAAAAACGATATTAAAAGCGTG-AAAACCCTTCAATCTTTTTGGCGTTG
124 TTCGAAAAAAAAT-GG-AAAAACGATATTAAAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTG
*
1252 AATTATATATTTTTTATGAGTTTTGTGGCAAAAAAAATTGAGAAAAAAAA
187 AATTATATATTTTTTATGAGTATTGTGGC-AAAAAAATTGAGAAAAAAAA
1302 AATCGGTTCA
Statistics
Matches: 212, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
263 92 0.43
267 2 0.01
268 1 0.00
269 8 0.04
270 72 0.34
271 19 0.09
272 18 0.08
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (264 bp):
TTTTGCATGATTTTTAGCGTAAAGACTCCTTAAAATATCCATACTCATCGAACCAAATCCCAGCC
ACATTCCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTAATTAGAAATTAATTCGAAA
AAAAATGGAAAAACGATATTAAAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATA
TTTTTTATGAGTATTGTGGCAAAAAAATTGAGAAAAAAAATTACAGGTCATTTTTTAACCCCGGT
TCAG
Found at i:9875 original size:63 final size:63
Alignment explanation
Indices: 9797--9923 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
9787 TACCATTCTC
9797 AGAAGCATCTGCAGACTCAGTACTCAACTTAGATCCATCACTTATCTCACTGAGACTTTTGTA
1 AGAAGCATCTGCAGACTCAGTACTCAACTTAGATCCATCACTTATCTCACTGAGACTTTTGTA
* *
9860 AGAAGCATCTGCAGACTCTGTACTTAACTTAGATCCATCACTTATCTCACTGAGACTTTTGTA
1 AGAAGCATCTGCAGACTCAGTACTCAACTTAGATCCATCACTTATCTCACTGAGACTTTTGTA
9923 A
1 A
9924 CTTTCACATG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (63 bp):
AGAAGCATCTGCAGACTCAGTACTCAACTTAGATCCATCACTTATCTCACTGAGACTTTTGTA
Found at i:22106 original size:29 final size:29
Alignment explanation
Indices: 22073--22138 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
22063 TTTCCTTTAA
22073 TTATATTTCATTCTGATTTAATTATATTT
1 TTATATTTCATTCTGATTTAATTATATTT
* *
22102 TTATATGTCATTTTGATTTAATTATATTT
1 TTATATTTCATTCTGATTTAATTATATTT
22131 TTATATTT
1 TTATATTT
22139 TATGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (29 bp):
TTATATTTCATTCTGATTTAATTATATTT
Found at i:28170 original size:13 final size:13
Alignment explanation
Indices: 28154--28179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28144 TATAGCAAGA
28154 TCTTTCCTTTTGT
1 TCTTTCCTTTTGT
28167 TCTTTCCTTTTGT
1 TCTTTCCTTTTGT
28180 CAGAAGCAGC
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:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (13 bp):
TCTTTCCTTTTGT
Found at i:30031 original size:18 final size:19
Alignment explanation
Indices: 29997--30037 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
29987 GCTTTTTTTC
*
29997 CTTC-TCTTTCTCTTTCAA
1 CTTCTTCTTTATCTTTCAA
30015 CTTCTTCTTTATC-TTCAA
1 CTTCTTCTTTATCTTTCAA
30033 -TTCTT
1 CTTCTT
30038 GCAGCAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 9 0.43
19 7 0.33
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (19 bp):
CTTCTTCTTTATCTTTCAA
Found at i:42522 original size:2 final size:2
Alignment explanation
Indices: 42515--42557 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
42505 AATATTTGGA
42515 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
42557 A
1 A
42558 CAAGTTTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43608 original size:22 final size:23
Alignment explanation
Indices: 43583--43628 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
43573 TAATATCCAC
43583 ACACAATTAAT-ATATAAT-TAAA
1 ACACAATTAATCATA-AATATAAA
*
43605 ACACACTTAATCATAAATATAAA
1 ACACAATTAATCATAAATATAAA
43628 A
1 A
43629 ATAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATAAATATAAA
Found at i:61331 original size:28 final size:28
Alignment explanation
Indices: 61277--61331 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
61267 GATTTCTATT
**
61277 ATATTAAATTAAATGTTTTTTTGAAAAC
1 ATATTAAATTAAATGTTTTTTAAAAAAC
61305 ATATTAAATTAAATGTTTTTTAAAAAA
1 ATATTAAATTAAATGTTTTTTAAAAAA
61332 TTACTATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (28 bp):
ATATTAAATTAAATGTTTTTTAAAAAAC
Found at i:61796 original size:126 final size:121
Alignment explanation
Indices: 61585--61832 Score: 302
Period size: 126 Copynumber: 2.0 Consensus size: 121
61575 TCATCTTCAG
* *
61585 AAGATGGTAGGAAAAAGTGTTAAGAAATTAAGGAACAAATGCTTATTTATTTTCCTTAATTAATG
1 AAGATGGTAGGAAAAAGTGTTAAAAAATTAAGGAACAAATGCCTATTTATTTTCCTTAATTAATG
* * *
61650 GAATTCAATAAGAGAATAATTCATAGCTTAATTAAAAACTATTCCCTCTCTTTTCAATTTA
66 GAATGCAATAAGAGAATAATT-A-A--TT-ACTAAAAACTATTCCCTCTCTCTTCAATTTA
*
61711 AAGATGGTAGG-AAAAGTGTTAAAAACATTAAGGAAGAAATGCCTATTTATTTTCCTTAATTAAT
1 AAGATGGTAGGAAAAAGTGTTAAAAA-ATTAAGGAACAAATGCCTATTTATTTTCCTTAATTAAT
* * * * ** *
61775 -TAATGGAATTCATAGCTTAATTAATTACTACAAACTATTCCCTCTCTCTTCAATTTA
65 GGAATGCAA-TAAGAGAATAATTAATTACTAAAAACTATTCCCTCTCTCTTCAATTTA
61832 A
1 A
61833 TTCTACAAAG
Statistics
Matches: 107, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
121 29 0.27
122 2 0.02
124 1 0.01
125 19 0.18
126 56 0.52
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (121 bp):
AAGATGGTAGGAAAAAGTGTTAAAAAATTAAGGAACAAATGCCTATTTATTTTCCTTAATTAATG
GAATGCAATAAGAGAATAATTAATTACTAAAAACTATTCCCTCTCTCTTCAATTTA
Found at i:71172 original size:29 final size:30
Alignment explanation
Indices: 71139--71210 Score: 137
Period size: 29 Copynumber: 2.4 Consensus size: 30
71129 TGAAGGCAAT
71139 AGCTTTTATAAGCTTTACCAAG-AAAAAAA
1 AGCTTTTATAAGCTTTACCAAGAAAAAAAA
71168 AGCTTTTATAAGCTTTACCAAGAAAAAAAA
1 AGCTTTTATAAGCTTTACCAAGAAAAAAAA
71198 AGCTTTTATAAGC
1 AGCTTTTATAAGC
71211 AATTAAGTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 22 0.52
30 20 0.48
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (30 bp):
AGCTTTTATAAGCTTTACCAAGAAAAAAAA
Found at i:75303 original size:84 final size:84
Alignment explanation
Indices: 75162--75331 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
75152 CAATAAGCAA
*
75162 CTCCGCTACTATCCACCTGTAATGCTTCCTTCAACTCCGAAGGTGGCTGCCTGAACACAACATAA
1 CTCCGCTACTATCCACCTGTAATACTTCCTTCAACTCCGAAGGTGGCTGCCTGAACACAACATAA
75227 TCTTCCTTAAATAGCATGT
66 TCTTCCTTAAATAGCATGT
*
75246 CTCCGCTACTATCCACCTGTAATACTTCCTTCACCTCCGAAGGTGGCTGCCTGAACACAACATAA
1 CTCCGCTACTATCCACCTGTAATACTTCCTTCAACTCCGAAGGTGGCTGCCTGAACACAACATAA
75311 TCTTCCTTAAATAGCATGT
66 TCTTCCTTAAATAGCATGT
75330 CT
1 CT
75332 ACACTAAACT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.29
Consensus pattern (84 bp):
CTCCGCTACTATCCACCTGTAATACTTCCTTCAACTCCGAAGGTGGCTGCCTGAACACAACATAA
TCTTCCTTAAATAGCATGT
Found at i:76022 original size:21 final size:20
Alignment explanation
Indices: 75996--76051 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
75986 TCTCCGTCTT
75996 TCCCCTGGTTACAGCCCATCA
1 TCCCCTGGTTACAGCCCA-CA
* * *
76017 TCCCCTGGCTATGATCCCACA
1 TCCCCTGGTTA-CAGCCCACA
*
76038 TCTCCTGGTTACAG
1 TCCCCTGGTTACAG
76052 TCCAACAAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.04
21 21 0.78
22 5 0.19
ACGTcount: A:0.18, C:0.39, G:0.16, T:0.27
Consensus pattern (20 bp):
TCCCCTGGTTACAGCCCACA
Found at i:94837 original size:10 final size:10
Alignment explanation
Indices: 94824--94849 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
94814 TATTATCAAG
94824 TTTGATTAGT
1 TTTGATTAGT
94834 TTTGATTAGT
1 TTTGATTAGT
94844 TTTGAT
1 TTTGAT
94850 ATCCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (10 bp):
TTTGATTAGT
Found at i:97992 original size:12 final size:12
Alignment explanation
Indices: 97975--98008 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
97965 ACTTTATGAC
97975 TACTGAATTTAA
1 TACTGAATTTAA
97987 TACTGAATTTAA
1 TACTGAATTTAA
97999 TACTGAATTT
1 TACTGAATTT
98009 GTAGTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (12 bp):
TACTGAATTTAA
Found at i:104025 original size:29 final size:29
Alignment explanation
Indices: 103956--104027 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
103946 CCTGAGGGGG
* * *
103956 CAAAACGTTCAAAAATTGAAGTTCAGGGGA
1 CAAAACG-TCCAAAATTGAAGTTCAAGAGA
* **
103986 TAAAATATCCAAAATTGAAGTTCAAGAGA
1 CAAAACGTCCAAAATTGAAGTTCAAGAGA
104015 CAAAACGTCCAAA
1 CAAAACGTCCAAA
104028 CTATACAAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (29 bp):
CAAAACGTCCAAAATTGAAGTTCAAGAGA
Found at i:107941 original size:2 final size:2
Alignment explanation
Indices: 107936--107961 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
107926 AAAAAAAATA
107936 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
107962 TTGCAGCCAA
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
Found at i:111495 original size:18 final size:17
Alignment explanation
Indices: 111469--111502 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
111459 GTCACGGTGC
111469 AAGTAAAAAAATAAAAAG
1 AAGT-AAAAAATAAAAAG
*
111487 AAGTTAAAAATAAAAA
1 AAGTAAAAAATAAAAA
111503 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (17 bp):
AAGTAAAAAATAAAAAG
Found at i:116669 original size:14 final size:14
Alignment explanation
Indices: 116627--116671 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
116617 TGAAGAAGAG
*
116627 TATAAGAAGAATC-
1 TATAAGGAGAATCA
*
116640 TA-AAGGA-AAGCA
1 TATAAGGAGAATCA
116652 TATAAGGAGAATCA
1 TATAAGGAGAATCA
116666 TATAAG
1 TATAAG
116672 TTAAGGAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
11 3 0.12
12 6 0.23
13 7 0.27
14 10 0.38
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (14 bp):
TATAAGGAGAATCA
Found at i:124231 original size:24 final size:24
Alignment explanation
Indices: 124195--124251 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
124185 GATTCAATTC
* *
124195 GGGAAGTTACTGATACGGATACTA
1 GGGAGGTTGCTGATACGGATACTA
* *
124219 GGGAGGTTGCTGATGCGGATGCTA
1 GGGAGGTTGCTGATACGGATACTA
*
124243 GGGGGGTTG
1 GGGAGGTTG
124252 GGTTCCCCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.44, T:0.25
Consensus pattern (24 bp):
GGGAGGTTGCTGATACGGATACTA
Found at i:130440 original size:31 final size:31
Alignment explanation
Indices: 130402--130463 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
130392 GAGTTTTGTA
130402 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
130433 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
130464 TTTTAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCACCTATTATACCCTTATT
Found at i:131755 original size:57 final size:57
Alignment explanation
Indices: 131667--131779 Score: 181
Period size: 57 Copynumber: 2.0 Consensus size: 57
131657 AAAAAAAGAT
* * *
131667 TGAGAGTTAGTCCATTATATAGAGTTAAATCTCTCGCAAAAACAATGAGACTTGTGG
1 TGAGAGTCAGTCCATTATATAGAGTTAAATCTCCCACAAAAACAATGAGACTTGTGG
* *
131724 TGAGAGTCGGTCCATTATATAGAGTTAAATCTCCCATAAAAACAATGAGACTTGTG
1 TGAGAGTCAGTCCATTATATAGAGTTAAATCTCCCACAAAAACAATGAGACTTGTG
131780 ACACGACCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (57 bp):
TGAGAGTCAGTCCATTATATAGAGTTAAATCTCCCACAAAAACAATGAGACTTGTGG
Found at i:136198 original size:23 final size:23
Alignment explanation
Indices: 136154--136198 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
136144 TCTCATTCAT
136154 TTAGCTGAACCAAGGCTACAATC
1 TTAGCTGAACCAAGGCTACAATC
* *
136177 TTAGACTGAGCCATGGCT-CAAT
1 TTAG-CTGAACCAAGGCTACAAT
136199 ATGGTGCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
TTAGCTGAACCAAGGCTACAATC
Found at i:142408 original size:29 final size:29
Alignment explanation
Indices: 142376--142442 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
142366 AACGTTGACG
142376 TTTTGCCCTTTGAACTTCAATTTT-GGACA
1 TTTTGCCC-TTGAACTTCAATTTTAGGACA
**
142405 TTTTGCTCCTTGAACTTCAATTTTAGGATG
1 TTTTGC-CCTTGAACTTCAATTTTAGGACA
142435 TTTTGCCC
1 TTTTGCCC
142443 CCTCAACCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (29 bp):
TTTTGCCCTTGAACTTCAATTTTAGGACA
Found at i:142581 original size:28 final size:29
Alignment explanation
Indices: 142542--142611 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
142532 TTGAGGGGGC
* *
142542 AAAACGTCCCAAAATTGAAGTTC-ATGGAA
1 AAAACGT-CCAAAATTGAAATTCAAGGGAA
* * *
142571 AAAATGTCCAAGATTGAAATTCAAGGGAC
1 AAAACGTCCAAAATTGAAATTCAAGGGAA
142600 AAAACGTCCAAA
1 AAAACGTCCAAA
142612 CGTTACAAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (29 bp):
AAAACGTCCAAAATTGAAATTCAAGGGAA
Found at i:144212 original size:17 final size:14
Alignment explanation
Indices: 144175--144207 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
144165 TTCTTGCTGG
144175 CATTGTTGTACCTC
1 CATTGTTGTACCTC
144189 CATTGTTGTACCTC
1 CATTGTTGTACCTC
144203 CATTG
1 CATTG
144208 ATGTTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.15, T:0.42
Consensus pattern (14 bp):
CATTGTTGTACCTC
Found at i:149948 original size:11 final size:11
Alignment explanation
Indices: 149932--149959 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
149922 ATATATATAT
149932 ATAAAATAAAA
1 ATAAAATAAAA
149943 ATAAAATAAAA
1 ATAAAATAAAA
149954 ATAAAA
1 ATAAAA
149960 CACTCTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:153775 original size:3 final size:3
Alignment explanation
Indices: 153767--153797 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
153757 GGGATTTTAA
153767 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
153798 TATAGATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:155595 original size:2 final size:2
Alignment explanation
Indices: 155588--155620 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
155578 ATTTGACATC
155588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
155621 CTTACAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:156552 original size:2 final size:2
Alignment explanation
Indices: 156545--156569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
156535 CATGTCTATG
156545 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
156570 ATTAAAGTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:158842 original size:3 final size:3
Alignment explanation
Indices: 158824--158866 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
158814 AAAACAATTC
*
158824 ATT ACT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
158867 AGTAATGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:159412 original size:34 final size:37
Alignment explanation
Indices: 159325--159403 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 37
159315 TTGAACAAAG
159325 TTTAGAAAAGATTTGATTGAAAAAAAAAAAACGAATTT
1 TTTAGAAAAGATTTGATTG-AAAAAAAAAAACGAATTT
159363 TTTAGAAAAGATTTGATTG-AAAAAAAAAA-GAA-TT
1 TTTAGAAAAGATTTGATTGAAAAAAAAAAACGAATTT
159397 TTTAGAA
1 TTTAGAA
159404 TTTATTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
34 9 0.22
35 3 0.07
36 10 0.24
38 19 0.46
ACGTcount: A:0.54, C:0.01, G:0.14, T:0.30
Consensus pattern (37 bp):
TTTAGAAAAGATTTGATTGAAAAAAAAAAACGAATTT
Found at i:165472 original size:103 final size:101
Alignment explanation
Indices: 165344--165548 Score: 245
Period size: 103 Copynumber: 2.0 Consensus size: 101
165334 TCATGCATCA
* * ** * * *
165344 ATTATTAAGTCAAATATTCAGATATTAAACGTGATATATTTCGTTACTTAACTAATACAATGCTA
1 ATTATTAAGTCAAATATTCAAATATTAAACGTGATAAATACCGTTAATTAACAAATACAAT-ATA
* *
165409 CTAATGATTGAATA-CAGAGTGATCGATCGTGTATTAATT
65 --AATGATTGAATAGCA-AGTGATCGACCGTGTATCAATT
*
165448 ATTA-TAAGTCAAATCATT-AAATATTAAATGTGATAAATACCGTTAATTAACAAATACAATATA
1 ATTATTAAGTCAAAT-ATTCAAATATTAAACGTGATAAATACCGTTAATTAACAAATACAATATA
*
165511 AATGATTGATTAGCAAGTGATCGACCGTGTATCAATT
65 AATGATTGAATAGCAAGTGATCGACCGTGTATCAATT
165548 A
1 A
165549 CTGAATCAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
100 32 0.36
101 2 0.02
102 2 0.02
103 45 0.51
104 7 0.08
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (101 bp):
ATTATTAAGTCAAATATTCAAATATTAAACGTGATAAATACCGTTAATTAACAAATACAATATAA
ATGATTGAATAGCAAGTGATCGACCGTGTATCAATT
Found at i:179763 original size:3 final size:3
Alignment explanation
Indices: 179755--179803 Score: 53
Period size: 3 Copynumber: 14.7 Consensus size: 3
179745 GTTCATGTTT
179755 ATG ATG ATG ATG ATG AATG ATG AATG ATG AATG ATG AATG ATG AATG
1 ATG ATG ATG ATG ATG -ATG ATG -ATG ATG -ATG ATG -ATG ATG -ATG
179802 AT
1 AT
179804 TCCCCTCTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
3 26 0.63
4 15 0.37
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:179776 original size:7 final size:7
Alignment explanation
Indices: 179758--179803 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
179748 CATGTTTATG
179758 ATGATG-
1 ATGATGA
179764 ATGATGA
1 ATGATGA
179771 ATGATGA
1 ATGATGA
179778 ATGATGA
1 ATGATGA
179785 ATGATGA
1 ATGATGA
179792 ATGATGA
1 ATGATGA
179799 ATGAT
1 ATGAT
179804 TCCCCTCTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.30
Consensus pattern (7 bp):
ATGATGA
Found at i:190158 original size:99 final size:99
Alignment explanation
Indices: 189987--190185 Score: 355
Period size: 99 Copynumber: 2.0 Consensus size: 99
189977 CAAAAGATGA
189987 AGAAGAATCAAAAGAACCCACATTTTGACATGAAAAAAGGAAACATTTTTGGAAAACTACTACTA
1 AGAAGAATCAAAAGAACCCACATTTTGACATGAAAAAAGGAAACATTTTTGGAAAACTACTACTA
*
190052 TCAAGTTTAAGGTTTTAAACATTATAACTCTTTT
66 TCAAGTTTAAGGTTTTAAACATTACAACTCTTTT
*
190086 AGAAGAATCAAAAGAACCCACATTTTGACATGAAAAAAGGAAACATTTTTTGAAAACTAAC-ACT
1 AGAAGAATCAAAAGAACCCACATTTTGACATGAAAAAAGGAAACATTTTTGGAAAACT-ACTACT
*
190150 ATCAAGTTTAAGGTTTTAAACATTGCAACTCTTTT
65 ATCAAGTTTAAGGTTTTAAACATTACAACTCTTTT
190185 A
1 A
190186 CTTACCAGTA
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
99 94 0.98
100 2 0.02
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.30
Consensus pattern (99 bp):
AGAAGAATCAAAAGAACCCACATTTTGACATGAAAAAAGGAAACATTTTTGGAAAACTACTACTA
TCAAGTTTAAGGTTTTAAACATTACAACTCTTTT
Found at i:195751 original size:13 final size:12
Alignment explanation
Indices: 195730--195766 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
195720 CATGTATCAC
195730 TTTTTCTTTTTT
1 TTTTTCTTTTTT
195742 TTTTTAC--TTTT
1 TTTTT-CTTTTTT
195753 TTTTTCTTTTTT
1 TTTTTCTTTTTT
195765 TT
1 TT
195767 GGTTAATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.05
11 9 0.41
12 11 0.50
13 1 0.05
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:195752 original size:11 final size:10
Alignment explanation
Indices: 195729--195766 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
195719 TCATGTATCA
*
195729 CTTTTTCTTT
1 CTTTTTTTTT
*
195739 -TTTTTTTTA
1 CTTTTTTTTT
195748 CTTTTTTTTT
1 CTTTTTTTTT
195758 CTTTTTTTT
1 CTTTTTTTT
195767 GGTTAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:195752 original size:19 final size:19
Alignment explanation
Indices: 195728--195765 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
195718 CTCATGTATC
195728 ACTTTTTCTTTT-TTTTTTT
1 ACTTTTT-TTTTCTTTTTTT
195747 ACTTTTTTTTTCTTTTTTT
1 ACTTTTTTTTTCTTTTTTT
195766 TGGTTAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (19 bp):
ACTTTTTTTTTCTTTTTTT
Done.