Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014873.1 Corchorus olitorius cultivar O-4 contig14906, 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: 58019
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:288 original size:12 final size:10
Alignment explanation
Indices: 261--291 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
251 AATTTGAAGG
261 TTGAGAGAAT
1 TTGAGAGAAT
271 TTGAGAGAAT
1 TTGAGAGAAT
281 TTGAGAGAAT
1 TTGAGAGAAT
291 T
1 T
292 GAAAATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
TTGAGAGAAT
Found at i:7177 original size:93 final size:96
Alignment explanation
Indices: 7056--7258 Score: 288
Period size: 95 Copynumber: 2.1 Consensus size: 96
7046 AAATTTTATG
*
7056 TTTTTCGATTATACCCTTTTTTACAAATATATTTCTAAATTG-CTAATATT-AAA-ATATTTTAA
1 TTTTTCGATTATACCATTTTTTACAAATATATTTCTAAATTGTC-AATATTAAAATATATTTTAA
*
7118 TTATGTCATTATTAAAATATAATTTTATGTAA
65 CTATGTCATTATTAAAATATAATTTTATGTAA
* * * *
7150 TTTTTCGATTGTACTATTTTTT-CAAATATATTTTTAAATTGTCATTATTAAAATATATTTTAAC
1 TTTTTCGATTATACCATTTTTTACAAATATATTTCTAAATTGTCAATATTAAAATATATTTTAAC
*
7214 TATGTCATTATTAAAATATAATTTTGTGTAA
66 TATGTCATTATTAAAATATAATTTTATGTAA
*
7245 TTTTTTCGAATATA
1 -TTTTTCGATTATA
7259 TTTCTAAATT
Statistics
Matches: 96, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
93 23 0.24
94 23 0.24
95 39 0.41
96 11 0.11
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.52
Consensus pattern (96 bp):
TTTTTCGATTATACCATTTTTTACAAATATATTTCTAAATTGTCAATATTAAAATATATTTTAAC
TATGTCATTATTAAAATATAATTTTATGTAA
Found at i:7210 original size:27 final size:27
Alignment explanation
Indices: 7173--7238 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
7163 CTATTTTTTC
7173 AAATATATTTTTAAAT-TGTCATTATTA
1 AAATATA-TTTTAAATATGTCATTATTA
*
7200 AAATATATTTTAACTATGTCATTATTA
1 AAATATATTTTAAATATGTCATTATTA
7227 AAATATAATTTT
1 AAATAT-ATTTT
7239 GTGTAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 7 0.19
27 24 0.67
28 5 0.14
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (27 bp):
AAATATATTTTAAATATGTCATTATTA
Found at i:9038 original size:335 final size:333
Alignment explanation
Indices: 8382--9265 Score: 1133
Period size: 333 Copynumber: 2.7 Consensus size: 333
8372 CGATTTCGAT
* * *
8382 TTGTTTTTACGAGCATATGAATCATGTTTCGATTCAATTAGGAATTAATTCGGAAAAAATAGGAA
1 TTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAA
* * * *
8447 AAACGATATTAGAAGCGTGAATAGCCTTTCAATCTTTTTGGTGATGAATTATCTATTTTTTATGA
66 AAACGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
* * *
8512 GTATCGTGACCAAAAATTGAGGAAAATTCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATC
131 GTATCGTGGCCAAAAATTGAGGAAAATTCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATC
** * * * * *
8577 GTGTACTAATTATTACG-ATTTTTAGCTAAAAACATGTTCCATGGCACCGGCTCAGTTATGCATG
196 GTGTACTAACCATCACGTTTTTTTAGCTAAAAACACGTTCCAGGGCACCGGCTCAGTTATACATG
* * *
8641 ATTTTTGGCGCCAAGACTCATTGAAATATCTATATTTATCTAACGAAATCTCAACTACATTGGAT
261 ATTGTTGGCGCCAAGACTCATTGAAATATCTATATCTATCTAACCAAATCTCAACTACATTGGAT
8706 TTAA-AAA
326 TTAAGAAA
* * *
8713 TTGTTTTTACGAGCATCTCAATC-CGATTTCGATTTGATTAGAAATTAATTCGGAAAAAATAGGA
1 TTGTTTTTACGAGCATCTGAATCATG-TTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGA
* * *
8777 AAAAAGATAATATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTCTGGCGTTGAGA-TATATAATTT
65 AAAACG---ATATTAGAAGCGTGAAAAGCCTTTCAATCTTTT-TGGCGTTGA-ATTATATATTTT
* * ** * ** *
8840 TTATGAATATGGTGGCCGGAAATTGAGGAGAAA-TGTTTCTTGTCAATTTTTGTAAAATTTTAGC
125 TTATGAGTATCGTGGCCAAAAATTGAGGA-AAATTCTTTCAGGTCAATTTTTGCAAAATTTTAGC
* * *
8904 CGAAATCGTGTACTAACCATCACAGTTTTTTTA-CTAAAAACGCGTTTC-GGG-ATCCCGGCTCT
189 CGAAATCGTGTACTAACCATCAC-GTTTTTTTAGCTAAAAACACGTTCCAGGGCA--CCGGCTCA
* *
8966 GTTTTACATGATTGTTGGCGCCAAGTCTCATTGAAATATCTATATCTATCTAACCAAATCTCAA-
251 GTTATACATGATTGTTGGCGCCAAGACTCATTGAAATATCTATATCTATCTAACCAAATCTCAAC
* *
9030 TAACATTGGATTTAAGGAT
316 T-ACATTGGATTTAAGAAA
9049 TTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATCTC-GAAAAAATAGGA
1 TTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAAT-TCGGAAAAAATAGGA
* *
9113 AAACCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATG
65 AAAACGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATG
* * * * *
9178 AGTATCATGGCAAAAAATTTAGGAAAATTCTTTCAGGTAAATTTTTGCAAAATTTTAACCGAAAT
130 AGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAAT
* *
9243 CGTGTATTAACCATCACGGTTTT
195 CGTGTACTAACCATCACGTTTTT
9266 GGTAACAAAG
Statistics
Matches: 472, Mismatches: 63, Indels: 35
0.83 0.11 0.06
Matches are distributed among these distances:
330 1 0.00
331 61 0.13
332 9 0.02
333 118 0.25
334 118 0.25
335 95 0.20
336 67 0.14
337 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (333 bp):
TTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAA
AAACGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
GTATCGTGGCCAAAAATTGAGGAAAATTCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATC
GTGTACTAACCATCACGTTTTTTTAGCTAAAAACACGTTCCAGGGCACCGGCTCAGTTATACATG
ATTGTTGGCGCCAAGACTCATTGAAATATCTATATCTATCTAACCAAATCTCAACTACATTGGAT
TTAAGAAA
Found at i:13525 original size:60 final size:60
Alignment explanation
Indices: 13458--13619 Score: 211
Period size: 60 Copynumber: 2.7 Consensus size: 60
13448 GTTAATTGCT
* * * *
13458 CAAATAAGGGTCTAACGTTTGTC-AAAATGTTCAAATAAGGGTTCGATTTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGTTCAAATAAGGGCTCGATCTTTTAATTTGGC
* *
13518 CAAATAAGGGCCTAACGTTATCGAAAATGCTT-AAATAAGAGCTCGATCTTTTGATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATG-TTCAAATAAGGGCTCGATCTTTTAATTTGGC
* * *
13578 CAAATAAAGGCCTAATGTTATCGAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGTTCAAATAAGGGC
13620 CTGATGTCAG
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
59 5 0.06
60 82 0.92
61 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGTTCAAATAAGGGCTCGATCTTTTAATTTGGC
Found at i:13621 original size:31 final size:31
Alignment explanation
Indices: 13518--13626 Score: 82
Period size: 31 Copynumber: 3.6 Consensus size: 31
13508 TTAATTTGGC
*
13518 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAATGTTATCGAAAATGCT
* * * * * **
13549 TAAATAAGAG-CTCGATCTT-TTG-ATTTGGC-
1 CAAATAAGGGCCT-AATGTTATCGAAAAT-GCT
*
13578 CAAATAAAGGCCTAATGTTATCGAAAATGCT
1 CAAATAAGGGCCTAATGTTATCGAAAATGCT
*
13609 CAAATAAGGGCCTGATGT
1 CAAATAAGGGCCTAATGT
13627 CAGTTTGGAT
Statistics
Matches: 54, Mismatches: 18, Indels: 12
0.64 0.21 0.14
Matches are distributed among these distances:
29 13 0.24
30 12 0.22
31 29 0.54
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (31 bp):
CAAATAAGGGCCTAATGTTATCGAAAATGCT
Found at i:13800 original size:60 final size:60
Alignment explanation
Indices: 13663--13824 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 60
13653 CGATGTCAGG
* ** * * *
13663 CTCTTATTTGAGCATTTTGGCAAACGTTAGATCCTTATTTGGCCAAATTAAAAGATCGGG
1 CTCTTATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCCGA
* * * *
13723 CTCTTAAATGAA-TATTTTGGCAAATGTTAGGCCCTTATTTGACCAAATTAAAAGATCCGA
1 CTCTT-ATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCCGA
* * *
13783 CTCTTATTTAAGCATTTTGACAAACATTAGGCTCTTATTTGA
1 CTCTTATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGA
13825 GCAATTAGCC
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 4 0.05
60 76 0.92
61 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (60 bp):
CTCTTATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCCGA
Found at i:17901 original size:315 final size:315
Alignment explanation
Indices: 17328--17947 Score: 1087
Period size: 315 Copynumber: 2.0 Consensus size: 315
17318 CTGGGAGTTA
17328 GAGTGAAAAAATACAAGAGATGCGAGACTTAAAATCTCACGCCTCCCTTGCAGAGATAAAGAAAT
1 GAGTGAAAAAATACAAGAGATGCGAGACTTAAAATCTCACGCCTCCCTTGCAGAGATAAAGAAAT
* *
17393 TACTCGCTGACAAATATTGACTTGCTAGCTCATAAAATACAAAAGACAGAAATACGACTCCTGAA
66 TACTCACTGACAAATATTGACTCGCTAGCTCATAAAATACAAAAGACAGAAATACGACTCCTGAA
* *
17458 AACAGGGAGGTGCCTCCTGGGCTATAGGAGGCGGCTTGTATTTATTAAATTCGGCCCATGAGACC
131 AACAAGGAGGTGCCTCCTGGGCTATAGGAGGCGGCTTGTATTTATTAAATTCAGCCCATGAGACC
*
17523 TCTCCTTATCTAATTATGAGGTGAGGTGTCATCAACTCCTTGATTCTTAATTTCTGCATTTGCTG
196 TCTCCTTATCTAATTATGAGGTGAGGTGTCATCAACTCCTTGATTCTTAATTTCTGAATTTGCTG
* * * *
17588 ACAACTTCATTAAATGAGTCAACTACTTGTGAAATTTTCGCCACAAGTAGTCAGC
261 AAAACTTCATTAAAGGAGTCAACTACTTGTGAAATATTCACCACAAGTAGTCAGC
* * *
17643 GAGTGAAAATATACAAGAGATGCGAGGCTTAAAATCTCACGCCTCTCTTGCAGAGATAAAGAAAT
1 GAGTGAAAAAATACAAGAGATGCGAGACTTAAAATCTCACGCCTCCCTTGCAGAGATAAAGAAAT
** *
17708 TACTCACTGACAAATATTGACTCGCTAGCTCATAAAATACAAAAGACAGGGATACGGCTCCTGAA
66 TACTCACTGACAAATATTGACTCGCTAGCTCATAAAATACAAAAGACAGAAATACGACTCCTGAA
17773 AACAAGGAGGTGCCTCCTGGGCTATAGGAGGCGGCTTGTATTTATTAAATTCAGCCCATGAGACC
131 AACAAGGAGGTGCCTCCTGGGCTATAGGAGGCGGCTTGTATTTATTAAATTCAGCCCATGAGACC
* *
17838 TCTCCTTATCTAATTATGAGGTGAGGTGTCATCAACTCCTTGCTTCTTAATTTTTGAATTTGCTG
196 TCTCCTTATCTAATTATGAGGTGAGGTGTCATCAACTCCTTGATTCTTAATTTCTGAATTTGCTG
17903 AAAACTTCATTAAAGGAGTCAACTACTTGTGAAATATTCACCACA
261 AAAACTTCATTAAAGGAGTCAACTACTTGTGAAATATTCACCACA
17948 TCTCCATGAA
Statistics
Matches: 288, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
315 288 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (315 bp):
GAGTGAAAAAATACAAGAGATGCGAGACTTAAAATCTCACGCCTCCCTTGCAGAGATAAAGAAAT
TACTCACTGACAAATATTGACTCGCTAGCTCATAAAATACAAAAGACAGAAATACGACTCCTGAA
AACAAGGAGGTGCCTCCTGGGCTATAGGAGGCGGCTTGTATTTATTAAATTCAGCCCATGAGACC
TCTCCTTATCTAATTATGAGGTGAGGTGTCATCAACTCCTTGATTCTTAATTTCTGAATTTGCTG
AAAACTTCATTAAAGGAGTCAACTACTTGTGAAATATTCACCACAAGTAGTCAGC
Found at i:39946 original size:198 final size:198
Alignment explanation
Indices: 39608--39996 Score: 595
Period size: 198 Copynumber: 2.0 Consensus size: 198
39598 AATGCTACAA
*
39608 CCACATACCTAAACTTAGTCAAACTTTCCATTCCAAAGGTTCTAAGATTCTAATTTGAAACCAAA
1 CCACATACCTAAACTTAGTCAAACTTTCCATTCCAAAGGTACTAAGATTCTAATTTGAAACCAAA
* * * *
39673 ACATCTCTAAATGTCCTTCATAGGAAATTTTGTACCTCTGATTGGCATAGCCACTTTCTTCATTT
66 ACATCTCTAAACGCCCTCCATAGGAAATTTTGTACCTCTAATTGGCATAGCCACTTTCTTCATTT
*
39738 ACAACATGAGATTTTGAAGGATTTGTGGATCCCTTTC-TTTGCT-CTTTGCTCTTAATAGTGTTA
131 ACAACATGAGATTTTGAAGGATTTGTGGATCCC-CTCGTTTGCTACTTT-CTCTTAATAGTGTTA
39801 GTCAG
194 GTCAG
* * * *
39806 CCACATACCTAAAGTTAGTCAACCTTTCCATTCCAAA-GTAACTAAGATTCTGATTTTAAACCAA
1 CCACATACCTAAACTTAGTCAAACTTTCCATTCCAAAGGT-ACTAAGATTCTAATTTGAAACCAA
* *
39870 AGCATCTCTAAACGCCCTCCATAGGAAATTTTGTACCTCTAATTGGCCTAGCCACTTTCTTCATT
65 AACATCTCTAAACGCCCTCCATAGGAAATTTTGTACCTCTAATTGGCATAGCCACTTTCTTCATT
* * *
39935 TACCACATGAGATTTTGACGGATTTGTGGATCCCCTCGTTTGCTAGTTTCTCTTAATAGTGT
130 TACAACATGAGATTTTGAAGGATTTGTGGATCCCCTCGTTTGCTACTTTCTCTTAATAGTGT
39997 ACTAGCGTCC
Statistics
Matches: 173, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
197 4 0.02
198 166 0.96
199 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (198 bp):
CCACATACCTAAACTTAGTCAAACTTTCCATTCCAAAGGTACTAAGATTCTAATTTGAAACCAAA
ACATCTCTAAACGCCCTCCATAGGAAATTTTGTACCTCTAATTGGCATAGCCACTTTCTTCATTT
ACAACATGAGATTTTGAAGGATTTGTGGATCCCCTCGTTTGCTACTTTCTCTTAATAGTGTTAGT
CAG
Found at i:41848 original size:12 final size:12
Alignment explanation
Indices: 41831--41859 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
41821 TTTGTATATA
41831 TATGTTTGTATG
1 TATGTTTGTATG
41843 TATGTTTGTATG
1 TATGTTTGTATG
41855 TATGT
1 TATGT
41860 ATATAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (12 bp):
TATGTTTGTATG
Found at i:44587 original size:80 final size:80
Alignment explanation
Indices: 44454--44607 Score: 281
Period size: 80 Copynumber: 1.9 Consensus size: 80
44444 TTAAGATATC
* *
44454 TATAAGAATATATAAAATGAGAAGTAAAAGTACCAAAAAACCAGTTGAGAAACCTCACCACATTT
1 TATAACAATATATAAAATGAGAAGTAAAAGTACCAAAAAACCAGTTGAGAAACCTCACCACATTC
44519 ATCCAAGAATAAAAA
66 ATCCAAGAATAAAAA
*
44534 TATAACAATATATAAAATGAGAAGTAAAAGTACCAAAAAACCAGTTGAGAAACCTCACCTCATTC
1 TATAACAATATATAAAATGAGAAGTAAAAGTACCAAAAAACCAGTTGAGAAACCTCACCACATTC
44599 ATCCAAGAA
66 ATCCAAGAA
44608 CAAATTGTCA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (80 bp):
TATAACAATATATAAAATGAGAAGTAAAAGTACCAAAAAACCAGTTGAGAAACCTCACCACATTC
ATCCAAGAATAAAAA
Found at i:45548 original size:61 final size:61
Alignment explanation
Indices: 45436--45611 Score: 203
Period size: 61 Copynumber: 2.9 Consensus size: 61
45426 GGTGGTATGC
** * * *
45436 ATTCGAATAAAATATACAGTAAGTTGGAAATTTTTTATTTTCTTTTATGTGTTGGGTATTGT
1 ATTCGAATAAAATATATGGAAAGTTGGTAA-TTTTTATTTTCTTTTATGTGTTGGCTATTGT
* * * *
45498 ATTCGAATAGAATATATGGAAAGTTGGTAATTTTTGTTTTGTTTTATGTGTTGGCTTTTGT
1 ATTCGAATAAAATATATGGAAAGTTGGTAATTTTTATTTTCTTTTATGTGTTGGCTATTGT
* * * *
45559 ATTCGAATATAATATATGGGAAGTTGGTCAA-TTTT-CTTTCTTTAATGTGTTGG
1 ATTCGAATAAAATATATGGAAAGTTGGT-AATTTTTATTTTCTTTTATGTGTTGG
45612 GTTTCTGACT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
60 15 0.15
61 57 0.58
62 27 0.27
ACGTcount: A:0.26, C:0.05, G:0.20, T:0.48
Consensus pattern (61 bp):
ATTCGAATAAAATATATGGAAAGTTGGTAATTTTTATTTTCTTTTATGTGTTGGCTATTGT
Found at i:46249 original size:21 final size:21
Alignment explanation
Indices: 46225--46295 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
46215 GTTGTGCAAC
46225 AGAGGGTTGAAGAAGATGAAG
1 AGAGGGTTGAAGAAGATGAAG
* * *
46246 AGAGGGTTCAGGTAGATGAAG
1 AGAGGGTTGAAGAAGATGAAG
46267 AGAGGGTTGAAGAAGATGAAG
1 AGAGGGTTGAAGAAGATGAAG
46288 AGAGGGTT
1 AGAGGGTT
46296 CAGGTAGACG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.38, C:0.01, G:0.44, T:0.17
Consensus pattern (21 bp):
AGAGGGTTGAAGAAGATGAAG
Found at i:46272 original size:42 final size:42
Alignment explanation
Indices: 46225--46309 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
46215 GTTGTGCAAC
*
46225 AGAGGGTTGAAGAAGATGAAGAGAGGGTTCAGGTAGATGAAG
1 AGAGGGTTGAAGAAGATGAAGAGAGGGTTCAGGTAGACGAAG
46267 AGAGGGTTGAAGAAGATGAAGAGAGGGTTCAGGTAGACGAAG
1 AGAGGGTTGAAGAAGATGAAGAGAGGGTTCAGGTAGACGAAG
46309 A
1 A
46310 TGATTCTGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.39, C:0.04, G:0.42, T:0.15
Consensus pattern (42 bp):
AGAGGGTTGAAGAAGATGAAGAGAGGGTTCAGGTAGACGAAG
Found at i:46308 original size:21 final size:21
Alignment explanation
Indices: 46238--46309 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
46228 GGGTTGAAGA
46238 AGATGAAGAGAGGGTTCAGGT
1 AGATGAAGAGAGGGTTCAGGT
* * *
46259 AGATGAAGAGAGGGTTGAAGA
1 AGATGAAGAGAGGGTTCAGGT
46280 AGATGAAGAGAGGGTTCAGGT
1 AGATGAAGAGAGGGTTCAGGT
*
46301 AGACGAAGA
1 AGATGAAGA
46310 TGATTCTGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.39, C:0.04, G:0.42, T:0.15
Consensus pattern (21 bp):
AGATGAAGAGAGGGTTCAGGT
Found at i:49303 original size:18 final size:18
Alignment explanation
Indices: 49280--49314 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49270 TCTTGTTGTT
49280 CTGACATTTTCTGATGTA
1 CTGACATTTTCTGATGTA
*
49298 CTGACATTTTGTGATGT
1 CTGACATTTTCTGATGT
49315 TCACAGCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (18 bp):
CTGACATTTTCTGATGTA
Found at i:55970 original size:20 final size:21
Alignment explanation
Indices: 55945--55985 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
55935 TTTTACTTTC
55945 CTATTT-TCTTTTTC-TTTTTT
1 CTATTTAT-TTTTTCATTTTTT
55965 CTATTTATTTTTTCATTTTTT
1 CTATTTATTTTTTCATTTTTT
55986 TTTCAGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (21 bp):
CTATTTATTTTTTCATTTTTT
Done.