Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020235.1 Corchorus olitorius cultivar O-4 contig20268, 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: 25093
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:41 original size:16 final size:17
Alignment explanation
Indices: 22--68 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
12 TATGCATTTG
22 TTTGTTTTAGTTTAGT-
1 TTTGTTTTAGTTTAGTC
*
38 TTTGTTTAAGTTTTTAGTC
1 TTTGTTTTAG--TTTAGTC
57 TTTGTTTT-GTTT
1 TTTGTTTTAGTTT
69 TCTAGCTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 12 0.46
18 7 0.27
19 7 0.27
ACGTcount: A:0.11, C:0.02, G:0.17, T:0.70
Consensus pattern (17 bp):
TTTGTTTTAGTTTAGTC
Found at i:4150 original size:1 final size:1
Alignment explanation
Indices: 4144--4176 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
4134 CTGCTAAAGA
4144 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4177 CTGTTTAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13319 original size:144 final size:143
Alignment explanation
Indices: 13144--13646 Score: 735
Period size: 144 Copynumber: 3.5 Consensus size: 143
13134 GGAATTTAAA
* *
13144 AGCACTCACTTCACTT-GACCTCTCTC-AAAACCAATTGAATGGAACTATCCCGCCTGAAATTGG
1 AGCACTCACTTCA-TTGGACCTCTC-CGGAAACCAATTGAATGGAACTATCCCACCTGAAATTGG
* *
13207 TAATTTGGAAAAACTCACTTCATTGGGTTTCTCTTTAAATCAATTGTCTGGATCCATTCCATCTA
64 TAATTTGGAAAAACTCACTTCATTGGATTTCTC-TCAAATCAATTGTCTGGATCCATTCCATCTA
13272 GAATTAAAGATTTGAG
128 GAATTAAAGATTTGAG
* * * *
13288 AGCACTCTCTTCATTGGATCTCTCCGGAAACCAATTGAATGGAACTATCCCGCATGAAATTGGTA
1 AGCACTCACTTCATTGGACCTCTCCGGAAACCAATTGAATGGAACTATCCCACCTGAAATTGGTA
* *
13353 ATTT-GAGAAAACTGACTTCATTGGATTTCTCCTCAAATCAATTGTCTGGATCCATTCCATCTAA
66 ATTTGGA-AAAACTCACTTCATTGGATTTCT-CTCAAATCAATTGTCTGGATCCATTCCATCTAG
13417 AATTAAAGATTTGAG
129 AATTAAAGATTTGAG
13432 AGCACTCACTTCATTGGACCTCTCCGGAAACCAATTGAATGGAACTATCCCACCTGAAATTGGTA
1 AGCACTCACTTCATTGGACCTCTCCGGAAACCAATTGAATGGAACTATCCCACCTGAAATTGGTA
* *
13497 ATTTGGGAAAACTCACTTCATTGGATTTATACTCAAATCAATTGTCTGGATCCATTCCATCTAGA
66 ATTTGGAAAAACTCACTTCATTGGATTTCT-CTCAAATCAATTGTCTGGATCCATTCCATCTAGA
*
13562 ATTAAAGATCTGAG
130 ATTAAAGATTTGAG
* * * * * *
13576 AGCACTCACTTCATTGGACCTCTCTGAAAACCAACTGAGTGG-ACATATTCCATCTGAAATTGGT
1 AGCACTCACTTCATTGGACCTCTCCGGAAACCAATTGAATGGAAC-TATCCCACCTGAAATTGGT
*
13640 AAGTTGG
65 AATTTGG
13647 GCCAACTCAT
Statistics
Matches: 328, Mismatches: 25, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
143 7 0.02
144 319 0.97
145 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (143 bp):
AGCACTCACTTCATTGGACCTCTCCGGAAACCAATTGAATGGAACTATCCCACCTGAAATTGGTA
ATTTGGAAAAACTCACTTCATTGGATTTCTCTCAAATCAATTGTCTGGATCCATTCCATCTAGAA
TTAAAGATTTGAG
Found at i:13539 original size:72 final size:72
Alignment explanation
Indices: 13175--13540 Score: 299
Period size: 72 Copynumber: 5.1 Consensus size: 72
13165 CTCTCAAAAC
* *
13175 CAATTGAATGGAACTATCCCGCCTGAAATTGGTAATTTG-GAAAAACTCACTTCATTGGGTTTCT
1 CAATTGAATGGAACTATCCCACCTGAAATTGGTAATTTGAG-AAAACTCACTTCATTGGATTTCT
* *
13239 CTTTAAAT
65 CCTCAAAT
** * * * * ** ** * *
13247 CAATTGTCTGGATCCATTCCATCT-AGAATT-AAAGATTTGAGAGCACTCTCTTCATTGGATCTC
1 CAATTGAATGGAACTATCCCACCTGA-AATTGGTA-ATTTGAGAAAACTCACTTCATTGGATTTC
** *
13310 TCCGGAAAC
64 TCCTCAAAT
* * *
13319 CAATTGAATGGAACTATCCCGCATGAAATTGGTAATTTGAGAAAACTGACTTCATTGGATTTCTC
1 CAATTGAATGGAACTATCCCACCTGAAATTGGTAATTTGAGAAAACTCACTTCATTGGATTTCTC
13384 CTCAAAT
66 CTCAAAT
** * * * * * ** ** **
13391 CAATTGTCTGGATCCATTCCATCTAAAATT-AAAGATTTGAGAGCACTCACTTCATTGGACCTCT
1 CAATTGAATGGAACTATCCCACCTGAAATTGGTA-ATTTGAGAAAACTCACTTCATTGGATTTCT
** *
13455 CCGGAAAC
65 CCTCAAAT
* * *
13463 CAATTGAATGGAACTATCCCACCTGAAATTGGTAATTTGGGAAAACTCACTTCATTGGATTTATA
1 CAATTGAATGGAACTATCCCACCTGAAATTGGTAATTTGAGAAAACTCACTTCATTGGATTTCTC
13528 CTCAAAT
66 CTCAAAT
13535 CAATTG
1 CAATTG
13541 TCTGGATCCA
Statistics
Matches: 213, Mismatches: 74, Indels: 14
0.71 0.25 0.05
Matches are distributed among these distances:
71 3 0.01
72 206 0.97
73 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (72 bp):
CAATTGAATGGAACTATCCCACCTGAAATTGGTAATTTGAGAAAACTCACTTCATTGGATTTCTC
CTCAAAT
Found at i:13583 original size:72 final size:72
Alignment explanation
Indices: 13219--13593 Score: 319
Period size: 72 Copynumber: 5.2 Consensus size: 72
13209 ATTTGGAAAA
* * *
13219 ACTCACTTCATTGGGTTTCTCTTTAAATCAATTGTCTGGATCCATTCCATCTAGAATTAAAGATT
1 ACTCACTTCATTGGATTTCTCCTCAAATCAATTGTCTGGATCCATTCCATCTAGAATTAAAGATT
13284 TGAGAGC
66 TGAGAGC
* * ** * ** * * ** **
13291 ACTCTCTTCATTGGATCTCTCCGGAAACCAATTGAATGGAACTA-TCCCGC-ATGAAATTGGTA-
1 ACTCACTTCATTGGATTTCTCCTCAAATCAATTGTCTGGATCCATTCCATCTA-G-AATT-AAAG
**
13353 ATTTGAGAAA
63 ATTTGAGAGC
* *
13363 ACTGACTTCATTGGATTTCTCCTCAAATCAATTGTCTGGATCCATTCCATCTAAAATTAAAGATT
1 ACTCACTTCATTGGATTTCTCCTCAAATCAATTGTCTGGATCCATTCCATCTAGAATTAAAGATT
13428 TGAGAGC
66 TGAGAGC
** ** * ** * * * * **
13435 ACTCACTTCATTGGACCTCTCCGGAAACCAATTGAATGGAACTATCCCACCT-GAAATTGGTA-A
1 ACTCACTTCATTGGATTTCTCCTCAAATCAATTGTCTGGATCCATTCCATCTAG-AATT-AAAGA
* **
13498 TTTGGGAAA
64 TTTGAGAGC
* * *
13507 ACTCACTTCATTGGATTTATACTCAAATCAATTGTCTGGATCCATTCCATCTAGAATTAAAGATC
1 ACTCACTTCATTGGATTTCTCCTCAAATCAATTGTCTGGATCCATTCCATCTAGAATTAAAGATT
13572 TGAGAGC
66 TGAGAGC
13579 ACTCACTTCATTGGA
1 ACTCACTTCATTGGA
13594 CCTCTCTGAA
Statistics
Matches: 222, Mismatches: 71, Indels: 20
0.71 0.23 0.06
Matches are distributed among these distances:
70 1 0.00
71 7 0.03
72 206 0.93
73 7 0.03
74 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (72 bp):
ACTCACTTCATTGGATTTCTCCTCAAATCAATTGTCTGGATCCATTCCATCTAGAATTAAAGATT
TGAGAGC
Found at i:13629 original size:72 final size:73
Alignment explanation
Indices: 13262--14069 Score: 296
Period size: 72 Copynumber: 11.2 Consensus size: 73
13252 GTCTGGATCC
* * * * *
13262 ATTCCATCT-AGAATT-AAAGATTTGAGAGCACTCTCTTCATTGGATCTCTCCGGAAACCAATTG
1 ATTCCATCTGA-AATTGAAAGATTTGAGAGCACTCACTTCATTGGACCTCTCTGAAAACCAACTG
*
13325 AATGGA-ACT
65 AGTGGACA-T
** ** ** * ** * * *
13334 A-TCCCGCATGAAATTGGTA-ATTTGAGAAAACTGACTTCATTGGATTTCTCCT-CAAATCAATT
1 ATTCCATC-TGAAATTGAAAGATTTGAGAGCACTCACTTCATTGGACCTCT-CTGAAAACCAACT
** *
13396 GTCTGGATC-C
64 GAGTGGA-CAT
* * * *
13406 ATTCCATCTAAAATT-AAAGATTTGAGAGCACTCACTTCATTGGACCTCTCCGGAAACCAATTGA
1 ATTCCATCTGAAATTGAAAGATTTGAGAGCACTCACTTCATTGGACCTCTCTGAAAACCAACTGA
*
13470 ATGGA-ACT
66 GTGGACA-T
* * ** * ** ** * * * *
13478 ATCCCACCTGAAATTGGTA-ATTTGGGAAAACTCACTTCATTGGATTTATACT-CAAATCAATTG
1 ATTCCATCTGAAATTGAAAGATTTGAGAGCACTCACTTCATTGGACCTCT-CTGAAAACCAACTG
** *
13541 TCTGGATC-C
65 AGTGGA-CAT
*
13550 ATTCCATCT-AGAATT-AAAGATCTGAGAGCACTCACTTCATTGGACCTCTCTGAAAACCAACTG
1 ATTCCATCTGA-AATTGAAAGATTTGAGAGCACTCACTTCATTGGACCTCTCTGAAAACCAACTG
13613 AGTGGACAT
65 AGTGGACAT
* * * * *
13622 ATTCCATCTGAAATTGGTAAG--TTG-G-GCCAACTCA-TCTCATTGTATCTCTATCAAAACCAA
1 ATTCCATCTGAAATT-GAAAGATTTGAGAG-C-ACTCACT-TCATTGGACCTCTCTGAAAACCAA
13682 CTGAGTGGACAT
62 CTGAGTGGACAT
* * * * * *
13694 ATTCCATCTGAAATTGGTAAG--TTG-G-GCCAACTCACCT-ATTTGTATCTCTTTCAAAACCAA
1 ATTCCATCTGAAATT-GAAAGATTTGAGAG-C-ACTCACTTCA-TTGGACCTCTCTGAAAACCAA
*
13754 TTGAGTGGACAT
62 CTGAGTGGACAT
* * ** * *
13766 ATTCCATCTGAAATTGGTAAG--TTG-G-GCCAACTCACCT-ATTTGGTTCTTTCTCAAAACCAA
1 ATTCCATCTGAAATT-GAAAGATTTGAGAG-C-ACTCACTTCA-TTGGACCTCTCTGAAAACCAA
*
13826 TTGAGTGGACAT
62 CTGAGTGGACAT
* ** * *
13838 ATTCCATCTCAAATTGGTA-ATTT-AGGAGCACTC-CGTT-ACTTGGACCTCTCTCAAAACCAAT
1 ATTCCATCTGAAATTGAAAGATTTGA-GAGCACTCAC-TTCA-TTGGACCTCTCTGAAAACCAAC
13899 TGAGTGGACAT
63 TGAGTGGACAT
* * * * * * *
13910 ATTCCATCTGAAATTGGTAAG--TTG-G-GCCAACTCACCT-ATTTGATTCTTTCTCAAAACTAA
1 ATTCCATCTGAAATT-GAAAGATTTGAGAG-C-ACTCACTTCATTGGA-CCTCTCTGAAAACCAA
*
13970 TTGAGTGGACAT
62 CTGAGTGGACAT
* ** * *
13982 ATTCCATCTCAAATTGGTA-ATTT-AGGAGCACTC-CGTT-ACTTGGACCTCTCTCAAAACCAAT
1 ATTCCATCTGAAATTGAAAGATTTGA-GAGCACTCAC-TTCA-TTGGACCTCTCTGAAAACCAAC
*
14043 TGAGTGGACTT
63 TGAGTGGACAT
* *
14054 ATTCCACCTCAAATTG
1 ATTCCATCTGAAATTG
14070 GTAATTGCTC
Statistics
Matches: 585, Mismatches: 104, Indels: 94
0.75 0.13 0.12
Matches are distributed among these distances:
70 2 0.00
71 27 0.05
72 530 0.91
73 21 0.04
74 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (73 bp):
ATTCCATCTGAAATTGAAAGATTTGAGAGCACTCACTTCATTGGACCTCTCTGAAAACCAACTGA
GTGGACAT
Found at i:13647 original size:144 final size:144
Alignment explanation
Indices: 13144--14073 Score: 697
Period size: 144 Copynumber: 6.5 Consensus size: 144
13134 GGAATTTAAA
* **
13144 AGCACTCACTTCACTT-GACCTCTCTCAAAACCAATTGAATGGAACTATCCCGCCTGAAATTGGT
1 AGCACTCACTTCACTTGGACCTCTCTCAAAACCAATTGAATGGAACTATTCCATCTGAAATTGGT
* * * *
13208 AATTTGGAAAAACTCACTTCATTGGGTTTCT-CTTTAAATCAATTGTCTGGATCCATTCCATCTA
66 AAGTTGGGAAAACTCACTTCATTGGATTTCTAC-TCAAATCAATTGTCTGGATCCATTCCATCTA
13272 GAATTAAAGATTTGAG
130 GAATTAAAGA-TTGAG
* * * **
13288 AGCACTCTCTTCA-TTGGATCTCTC-CGGAAACCAATTGAATGGAACTA-TCCCGCATGAAATTG
1 AGCACTCACTTCACTTGGACCTCTCTC-AAAACCAATTGAATGGAACTATTCCATC-TGAAATTG
* * * *
13350 GTAATTTGAGAAAACTGACTTCATTGGATTTCTCCTCAAATCAATTGTCTGGATCCATTCCATCT
64 GTAAGTTGGGAAAACTCACTTCATTGGATTTCTACTCAAATCAATTGTCTGGATCCATTCCATCT
*
13415 AAAATTAAAGATTTGAG
129 AGAATTAAAGA-TTGAG
* * *
13432 AGCACTCACTTCA-TTGGACCTCTC-CGGAAACCAATTGAATGGAACTATCCCACCTGAAATTGG
1 AGCACTCACTTCACTTGGACCTCTCTC-AAAACCAATTGAATGGAACTATTCCATCTGAAATTGG
* *
13495 TAATTTGGGAAAACTCACTTCATTGGATTTATACTCAAATCAATTGTCTGGATCCATTCCATCTA
65 TAAGTTGGGAAAACTCACTTCATTGGATTTCTACTCAAATCAATTGTCTGGATCCATTCCATCTA
13560 GAATTAAAGATCTGAG
130 GAATTAAAGAT-TGAG
* * *
13576 AGCACTCACTTCA-TTGGACCTCTCTGAAAACCAACTGAGTGG-ACATATTCCATCTGAAATTGG
1 AGCACTCACTTCACTTGGACCTCTCTCAAAACCAATTGAATGGAAC-TATTCCATCTGAAATTGG
** * * * * ** *
13639 TAAGTTGGGCCAACTCA-TCTCATTGTATCTCTA-TCAAAACCAACTGAGTGGA-CATATTCCAT
65 TAAGTTGGGAAAACTCACT-TCATTGGATTTCTACTC-AAATCAATTGTCTGGATC-CATTCCAT
*
13701 CT-GAAATTGGTAAG-TTG-G
127 CTAG-AATT--AAAGATTGAG
* * * * * *
13719 -GCCAACTCACCT-ATTTGTATCTCTTTCAAAACCAATTGAGTGG-ACATATTCCATCTGAAATT
1 AG-C-ACTCACTTCACTTGGACCTCTCTCAAAACCAATTGAATGGAAC-TATTCCATCTGAAATT
** * * * ** *
13781 GGTAAGTTGGGCCAACTCACCT-ATTTGG--TTCTTTCTCAAAACCAATTGAGTGGA-CATATTC
63 GGTAAGTTGGGAAAACTCACTTCA-TTGGATTTC-TACTC-AAATCAATTGTCTGGATC-CATTC
** *
13842 CATCTCA-AATTGGTA-ATTTAGG
124 CATCT-AGAATT-AAAGATTGA-G
*
13864 AGCACTC-CGTT-ACTTGGACCTCTCTCAAAACCAATTGAGTGG-ACATATTCCATCTGAAATTG
1 AGCACTCAC-TTCACTTGGACCTCTCTCAAAACCAATTGAATGGAAC-TATTCCATCTGAAATTG
** * * * * ** *
13926 GTAAGTTGGGCCAACTCACCT-ATTTGA-TTCTTTCTCAAAACTAATTGAGTGGA-CATATTCCA
64 GTAAGTTGGGAAAACTCACTTCATTGGATTTC-TACTCAAATC-AATTGTCTGGATC-CATTCCA
** *
13988 TCTCA-AATTGGTA-ATTTAGG
126 TCT-AGAATT-AAAGATTGA-G
* * *
14008 AGCACTC-CGTT-ACTTGGACCTCTCTCAAAACCAATTGAGTGG-ACTTATTCCACCTCAAATTG
1 AGCACTCAC-TTCACTTGGACCTCTCTCAAAACCAATTGAATGGAAC-TATTCCATCTGAAATTG
14070 GTAA
64 GTAA
14074 TTGCTCCTAT
Statistics
Matches: 692, Mismatches: 64, Indels: 60
0.85 0.08 0.07
Matches are distributed among these distances:
142 3 0.00
143 31 0.04
144 647 0.93
145 7 0.01
146 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (144 bp):
AGCACTCACTTCACTTGGACCTCTCTCAAAACCAATTGAATGGAACTATTCCATCTGAAATTGGT
AAGTTGGGAAAACTCACTTCATTGGATTTCTACTCAAATCAATTGTCTGGATCCATTCCATCTAG
AATTAAAGATTGAG
Found at i:13700 original size:288 final size:283
Alignment explanation
Indices: 13144--14075 Score: 850
Period size: 288 Copynumber: 3.2 Consensus size: 283
13134 GGAATTTAAA
*
13144 AGCACTCACTTCACTT-GACCTCTCTCAAAACCAATTGAATGGA-ACTATCCCGCCTGAAATTGG
1 AGCACTCACTT-ACTTGGACCTCTCTCAAAACCAATTGAATGGACA-TATCCCACCTGAAATTGG
* *
13207 TAATTTGGAAAAACTCACTTCATTGGGTTTCTCTTTAAATCAATTGTCTGGATCCATTCCATCTA
64 TAATTTGGGAAAACTCACTTCATT-GGTTT-TC-TCAAATCAATTGTCTGGATCCATTCCATCTA
* * * *
13272 GAATTAAAGATTTGAGAGCACTCTCTTCATTGGATCTCTCCGGAAACCAATTGAATGGA-ACTA-
126 GAATTAAAGA-TTGAGAGCACTC-CTTCATTGGACCTCTCTGAAAACCAATTGAGTGGACA-TAT
** * * ** * * * * **
13335 TCCCGCATGAAATTGGTAATTTGAGAAAACTGACTTCATTGGATTTCTCCTC-AAATCAATTGTC
188 TCCATC-TGAAATTGGTAAGTTGGGCCAACTCAC-TCATTGTATCTCT-CTCAAAACCAATTGAG
*
13399 TGGATC-CATTCCATCTAAAATT-AAAGATTTGAG
250 TGGA-CATATTCCATCTAAAATTGAAAGATTTGAG
*
13432 AGCACTCACTT-CATTGGACCTCTC-CGGAAACCAATTGAATGGA-ACTATCCCACCTGAAATTG
1 AGCACTCACTTAC-TTGGACCTCTCTC-AAAACCAATTGAATGGACA-TATCCCACCTGAAATTG
13494 GTAATTTGGGAAAACTCACTTCATTGGATTTATACTCAAATCAATTGTCTGGATCCATTCCATCT
63 GTAATTTGGGAAAACTCACTTCATTGG-TTT-T-CTCAAATCAATTGTCTGGATCCATTCCATCT
*
13559 AGAATTAAAGATCTGAGAGCACTCACTTCATTGGACCTCTCTGAAAACCAACTGAGTGGACATAT
125 AGAATTAAAGAT-TGAGAGCACTC-CTTCATTGGACCTCTCTGAAAACCAATTGAGTGGACATAT
* *
13624 TCCATCTGAAATTGGTAAGTTGGGCCAACTCATCTCATTGTATCTCTATCAAAACCAACTGAGTG
188 TCCATCTGAAATTGGTAAGTTGGGCCAACTCA-CTCATTGTATCTCTCTCAAAACCAATTGAGTG
* *
13689 GACATATTCCATCTGAAATTGGTAAG--TTG-G
252 GACATATTCCATCTAAAATT-GAAAGATTTGAG
* * * * * * * *
13719 -GCCAACTCACCTATTTGTATCTCTTTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGG
1 AG-C-ACTCACTTACTTGGACCTCTCTCAAAACCAATTGAATGGACATATCCCACCTGAAATTGG
* ** * * ** *
13783 TAAGTTGGGCCAACTCACCT-ATTTGGTTCTTTCTCAAAACCAATTGAGTGGA-CATATTCCATC
64 TAATTTGGGAAAACTCACTTCA-TTGG-T-TTTCTC-AAATCAATTGTCTGGATC-CATTCCATC
** * *
13846 TCA-AATTGGTA-ATTTAGGAGCACTCCGTT-ACTTGGACCTCTCTCAAAACCAATTGAGTGGAC
124 T-AGAATT-AAAGATTGA-GAGCACTCC-TTCA-TTGGACCTCTCTGAAAACCAATTGAGTGGAC
* *
13908 ATATTCCATCTGAAATTGGTAAGTTGGGCCAACTCAC-CTATT-TGATTCTTTCTCAAAACTAAT
184 ATATTCCATCTGAAATTGGTAAGTTGGGCCAACTCACTC-ATTGT-A-TCTCTCTCAAAACCAAT
* **
13971 TGAGTGGACATATTCCATCTCAAATTGGTA-ATTT-AGG
246 TGAGTGGACATATTCCATCTAAAATTGAAAGATTTGA-G
* * * *
14008 AGCACTC-CGTTACTTGGACCTCTCTCAAAACCAATTGAGTGGACTTATTCCACCTCAAATTGGT
1 AGCACTCAC-TTACTTGGACCTCTCTCAAAACCAATTGAATGGACATATCCCACCTGAAATTGGT
14072 AATT
65 AATT
14076 GCTCCTATTT
Statistics
Matches: 541, Mismatches: 67, Indels: 72
0.80 0.10 0.11
Matches are distributed among these distances:
286 4 0.01
287 28 0.05
288 490 0.91
289 15 0.03
290 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (283 bp):
AGCACTCACTTACTTGGACCTCTCTCAAAACCAATTGAATGGACATATCCCACCTGAAATTGGTA
ATTTGGGAAAACTCACTTCATTGGTTTTCTCAAATCAATTGTCTGGATCCATTCCATCTAGAATT
AAAGATTGAGAGCACTCCTTCATTGGACCTCTCTGAAAACCAATTGAGTGGACATATTCCATCTG
AAATTGGTAAGTTGGGCCAACTCACTCATTGTATCTCTCTCAAAACCAATTGAGTGGACATATTC
CATCTAAAATTGAAAGATTTGAG
Found at i:14074 original size:216 final size:216
Alignment explanation
Indices: 13589--14075 Score: 659
Period size: 216 Copynumber: 2.3 Consensus size: 216
13579 ACTCACTTCA
* * * *
13589 TTGGACCTCTCTGAAAACCAACTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAACT
1 TTGGACCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTCAAATTGGTAATTTGGGCCAACT
* *
13654 CATCTCATTGTATCTCTATCAAAACCAACTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGG
66 CATCTCATTGGACCTCTATCAAAACCAACTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGG
*
13719 GCCAACTCACCTATTTGTATCTCTTTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGT
131 GCCAACTCACCTATTTGTATCTCTTTCAAAACCAATTGAGTGGACATATTCCATCTCAAATTGGT
*
13784 AAGTTGGGCCAACTCACCTAT
196 AAGTTGGGCCAACTCACCTAC
** *
13805 TTGGTTCTTTCTCAAAACCAATTGAGTGGACATATTCCATCTCAAATTGGTAATTTAGGAG-C-A
1 TTGGACCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTCAAATTGGTAATTT-GG-GCCAA
* * *
13868 CTC--CGTTACTTGGACCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAG
64 CTCATC-TCA-TTGGACCTCTATCAAAACCAACTGAGTGGACATATTCCATCTGAAATTGGTAAG
*
13931 TTGGGCCAACTCACCTATTTG-AT-TCTTTCTCAAAACTAATTGAGTGGACATATTCCATCTCAA
127 TTGGGCCAACTCACCTATTTGTATCTC-TT-TCAAAACCAATTGAGTGGACATATTCCATCTCAA
* *
13994 ATTGGTAATTTAGGAG-C-ACTC-CGTTAC
190 ATTGGTAAGTT-GG-GCCAACTCAC-CTAC
* *
14021 TTGGACCTCTCTCAAAACCAATTGAGTGGACTTATTCCACCTCAAATTGGTAATT
1 TTGGACCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTCAAATTGGTAATT
14076 GCTCCTATTT
Statistics
Matches: 240, Mismatches: 22, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
214 3 0.01
215 7 0.03
216 222 0.93
217 6 0.03
218 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (216 bp):
TTGGACCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTCAAATTGGTAATTTGGGCCAACT
CATCTCATTGGACCTCTATCAAAACCAACTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGG
GCCAACTCACCTATTTGTATCTCTTTCAAAACCAATTGAGTGGACATATTCCATCTCAAATTGGT
AAGTTGGGCCAACTCACCTAC
Found at i:14075 original size:72 final size:72
Alignment explanation
Indices: 13589--14073 Score: 599
Period size: 72 Copynumber: 6.7 Consensus size: 72
13579 ACTCACTTCA
* * *
13589 TTGGACCTCTCTGAAAACCAACTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAACT
1 TTGGATCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAACT
*
13654 CATCT-C
66 CACCTAC
* * *
13660 ATTGTATCTCTATCAAAACCAACTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAAC
1 -TTGGATCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAAC
*
13725 TCACCTAT
65 TCACCTAC
* *
13733 TTGTATCTCTTTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAACT
1 TTGGATCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAACT
*
13798 CACCTAT
66 CACCTAC
* * * *
13805 TTGGTTCTTTCTCAAAACCAATTGAGTGGACATATTCCATCTCAAATTGGTAATTTAGGAG-C-A
1 TTGGATCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAGTT-GG-GCCAA
*
13868 CTC-CGTTAC
64 CTCAC-CTAC
*
13877 TTGGACCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAACT
1 TTGGATCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAACT
13942 CACCTA-
66 CACCTAC
* * * * *
13948 TTTGATTCTTTCTCAAAACTAATTGAGTGGACATATTCCATCTCAAATTGGTAATTTAGGAG-C-
1 TTGGA-TCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAGTT-GG-GCCA
*
14011 ACTC-CGTTAC
63 ACTCAC-CTAC
* * * *
14021 TTGGACCTCTCTCAAAACCAATTGAGTGGACTTATTCCACCTCAAATTGGTAA
1 TTGGATCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAA
14074 TTGCTCCTAT
Statistics
Matches: 366, Mismatches: 35, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
70 1 0.00
71 9 0.02
72 343 0.94
73 11 0.03
74 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (72 bp):
TTGGATCTCTCTCAAAACCAATTGAGTGGACATATTCCATCTGAAATTGGTAAGTTGGGCCAACT
CACCTAC
Found at i:16533 original size:15 final size:15
Alignment explanation
Indices: 16513--16543 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16503 TATCGGCCAT
16513 GTTGTTAAAGTTCCA
1 GTTGTTAAAGTTCCA
16528 GTTGTTAAAGTTCCA
1 GTTGTTAAAGTTCCA
16543 G
1 G
16544 CCATTTCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (15 bp):
GTTGTTAAAGTTCCA
Found at i:19742 original size:22 final size:21
Alignment explanation
Indices: 19717--19791 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 21
19707 TTGAATATTT
19717 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAA-TACC
*
19739 TTATTG-AATTTTGATAATCACG
1 TTA-TGAAATTTTGATAAT-ACC
*
19761 TTATGGAATTTTGATAATTTACC
1 TTATGAAATTTTGATAA--TACC
19784 -TATGAAAT
1 TTATGAAAT
19792 ATGAAACTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
21 3 0.07
22 37 0.82
23 4 0.09
24 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (21 bp):
TTATGAAATTTTGATAATACC
Found at i:19839 original size:23 final size:23
Alignment explanation
Indices: 19812--19884 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
19802 GATAACCTAA
*
19812 CTATGAAATTTTAATAAACCTTT
1 CTATGAAATTTTAATAAACCTTC
*
19835 TTATGAAATTTTAATAAACCTTC
1 CTATGAAATTTTAATAAACCTTC
*
19858 CTATGAAATTTT-GT-AACCTTC
1 CTATGAAATTTTAATAAACCTTC
19879 CTATGA
1 CTATGA
19885 TTTTTGATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.28
22 1 0.02
23 32 0.70
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACCTTC
Found at i:21433 original size:27 final size:25
Alignment explanation
Indices: 21384--21439 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 25
21374 AATCTAAATT
21384 TTTAATAATGAAATAATTAAAATATTA
1 TTTAATAATGAAAT-ATTAAAATA-TA
21411 TTTAATAATGACAAT-TTAGAAATATA
1 TTTAATAATGA-AATATTA-AAATATA
21437 TTT
1 TTT
21440 GAAAAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.30
27 16 0.59
28 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (25 bp):
TTTAATAATGAAATATTAAAATATA
Found at i:21651 original size:22 final size:22
Alignment explanation
Indices: 21560--21702 Score: 118
Period size: 21 Copynumber: 6.7 Consensus size: 22
21550 GAATTTTTTC
21560 ATGAAATTTTGATAA-CTACCT
1 ATGAAATTTTGATAACCTACCT
* *
21581 ATTAAATTTTGATAA-TTACCT
1 ATGAAATTTTGATAACCTACCT
* * *
21602 ATAAAATTGTGATAAACT-CCAT
1 ATGAAATTTTGATAACCTACC-T
* *
21624 AAGAAATTTTGATAACCTAACT
1 ATGAAATTTTGATAACCTACCT
* * *
21646 ATGAAATTTTAATAAACTTTCCT
1 ATGAAATTTTGAT-AACCTACCT
*
21669 ATG-AATTTTG-TAACCTTCCT
1 ATGAAATTTTGATAACCTACCT
*
21689 ATG-ATTTTTGATAA
1 ATGAAATTTTGATAA
21703 TCTCTCTGTG
Statistics
Matches: 99, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
20 17 0.17
21 38 0.38
22 34 0.34
23 10 0.10
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTACCT
Found at i:23754 original size:27 final size:26
Alignment explanation
Indices: 23700--23760 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
23690 ATAAATTTCC
23700 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
23728 ATTATTTAATAATGGCAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
23755 A-TATTT
1 ATTATTT
23761 GAAAAAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:23935 original size:44 final size:45
Alignment explanation
Indices: 23885--24002 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 45
23875 TGAATATTTT
* * *
23885 TATGAAATTTTGATAACTAT-CTTATTAAATTTTGAT-AACTACA
1 TATGAAATTTTGATAACTATACCTATGAAATTGTGATAAACTACA
* * *
23928 CTATGAAATTATGATAA-TTTACCTATGAAATTGTGATAAACTTCA
1 -TATGAAATTTTGATAACTATACCTATGAAATTGTGATAAACTACA
* *
23973 TATGAAACTTTGATAACT-TAACTATGAAAT
1 TATGAAATTTTGATAACTATACCTATGAAAT
24003 ATTAATAAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
43 2 0.03
44 53 0.85
45 7 0.11
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (45 bp):
TATGAAATTTTGATAACTATACCTATGAAATTGTGATAAACTACA
Found at i:23998 original size:22 final size:21
Alignment explanation
Indices: 23885--24002 Score: 98
Period size: 22 Copynumber: 5.4 Consensus size: 21
23875 TGAATATTTT
*
23885 TATGAAATTTTGATAAC-TATC
1 TATGAAA-TTTGATAACTTAAC
*
23906 TTATTAAATTTTGATAAC-TACAC
1 -TATGAAA-TTTGATAACTTA-AC
* *
23929 TATGAAATTATGATAATTTACC
1 TATGAAATT-TGATAACTTAAC
*
23951 TATGAAATTGTGATAAACTTCA-
1 TATGAAATT-TGAT-AACTTAAC
23973 TATGAAACTTTGATAACTTAAC
1 TATGAAA-TTTGATAACTTAAC
23995 TATGAAAT
1 TATGAAAT
24003 ATTAATAAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 13
0.78 0.10 0.13
Matches are distributed among these distances:
21 9 0.11
22 62 0.77
23 9 0.11
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (21 bp):
TATGAAATTTGATAACTTAAC
Found at i:24011 original size:44 final size:42
Alignment explanation
Indices: 23885--24047 Score: 118
Period size: 44 Copynumber: 3.7 Consensus size: 42
23875 TGAATATTTT
* * *
23885 TATGAAATTTTGATAAC-TATCTTATTAAATTTTGAT-AACTACA
1 TATGAAA-TTTGATAACTTAAC-TATGAAA-TTTGATAAACTTCA
* *
23928 CTATGAAATTATGATAATTTACCTATGAAATTGTGATAAACTTCA
1 -TATGAAATT-TGATAACTTAACTATGAAATT-TGATAAACTTCA
* *
23973 TATGAAACTTTGATAACTTAACTATGAAATATTAATAAACCTTCC
1 TATGAAA-TTTGATAACTTAACTATGAAAT-TTGATAAA-CTTCA
** *
24018 TATGATTTTTGAT-AC-TATAGTATGAAATTT
1 TATGAAATTTGATAACTTA-ACTATGAAATTT
24048 CGAAAATTTC
Statistics
Matches: 100, Mismatches: 11, Indels: 18
0.78 0.09 0.14
Matches are distributed among these distances:
42 4 0.04
43 15 0.15
44 60 0.60
45 21 0.21
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.41
Consensus pattern (42 bp):
TATGAAATTTGATAACTTAACTATGAAATTTGATAAACTTCA
Done.