Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024532.1 Corchorus olitorius cultivar O-4 contig24565, 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: 134984
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:8247 original size:15 final size:15
Alignment explanation
Indices: 8227--8257 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8217 GAGAACATGA
8227 TTTGAAAAAACCTTT
1 TTTGAAAAAACCTTT
*
8242 TTTGAAAACACCTTT
1 TTTGAAAAAACCTTT
8257 T
1 T
8258 ATTGCTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (15 bp):
TTTGAAAAAACCTTT
Found at i:12653 original size:17 final size:17
Alignment explanation
Indices: 12633--12665 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12623 CAAATGCAAT
12633 TGTAGTACAAAGCTAAC
1 TGTAGTACAAAGCTAAC
12650 TGTAGTACAAAGCTAA
1 TGTAGTACAAAGCTAA
12666 GAAGAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (17 bp):
TGTAGTACAAAGCTAAC
Found at i:13520 original size:15 final size:15
Alignment explanation
Indices: 13500--13529 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13490 ATGATGAGAA
13500 AGTTGAAGAAGAAAG
1 AGTTGAAGAAGAAAG
*
13515 AGTTGAGGAAGAAAG
1 AGTTGAAGAAGAAAG
13530 GCAAACAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.37, T:0.13
Consensus pattern (15 bp):
AGTTGAAGAAGAAAG
Found at i:14560 original size:190 final size:190
Alignment explanation
Indices: 14230--14610 Score: 726
Period size: 190 Copynumber: 2.0 Consensus size: 190
14220 TTATGACAAA
14230 AAGGGGAAGAAGTATTGTGAATTGAGCTTATTGAATATCTGTTTTTTATATGCTATGGTATATAA
1 AAGGGGAAGAAGTATTGTGAATTGAGCTTATTGAATATCTGTTTTTTATATGCTATGGTATATAA
*
14295 TGCTTTATCTAAGTGTGTTCAGCATTAAACACCATCATGCTTAAAGGAAACTTTGGCATGCTTGG
66 TGCTTTATCTAAGTGTGTTCAGCATTAAACACCAGCATGCTTAAAGGAAACTTTGGCATGCTTGG
14360 ATGGGGTCGATGGGGAAAATGAATTGACTAACTCAAGGGGAGTTTAAAGACTTCAATGGT
131 ATGGGGTCGATGGGGAAAATGAATTGACTAACTCAAGGGGAGTTTAAAGACTTCAATGGT
*
14420 AAGGGGGAGAAGTATTGTGAATTGAGCTTATTGAATATCTGTTTTTTATATGCTATGGTATATAA
1 AAGGGGAAGAAGTATTGTGAATTGAGCTTATTGAATATCTGTTTTTTATATGCTATGGTATATAA
14485 TGCTTTATCTAAGTGTGTTCAGCATTAAACACCAGCATGCTTAAAGGAAACTTTGGCATGCTTGG
66 TGCTTTATCTAAGTGTGTTCAGCATTAAACACCAGCATGCTTAAAGGAAACTTTGGCATGCTTGG
* *
14550 ATGGGGTCGATGGGGAAGATGAATTGACTAACTCAGGGGGAGTTTAAAGACTTCAATGGT
131 ATGGGGTCGATGGGGAAAATGAATTGACTAACTCAAGGGGAGTTTAAAGACTTCAATGGT
14610 A
1 A
14611 TATCTTTTGT
Statistics
Matches: 187, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
190 187 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (190 bp):
AAGGGGAAGAAGTATTGTGAATTGAGCTTATTGAATATCTGTTTTTTATATGCTATGGTATATAA
TGCTTTATCTAAGTGTGTTCAGCATTAAACACCAGCATGCTTAAAGGAAACTTTGGCATGCTTGG
ATGGGGTCGATGGGGAAAATGAATTGACTAACTCAAGGGGAGTTTAAAGACTTCAATGGT
Found at i:16854 original size:30 final size:30
Alignment explanation
Indices: 16818--16884 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
16808 TACATCTAAA
16818 CCTCATGGATTGTATACACATTTACCTATT
1 CCTCATGGATTGTATACACATTTACCTATT
16848 CCTCATGGATTGTATACACATTTACCTATT
1 CCTCATGGATTGTATACACATTTACCTATT
16878 CCTCATG
1 CCTCATG
16885 AATCTTTGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.39
Consensus pattern (30 bp):
CCTCATGGATTGTATACACATTTACCTATT
Found at i:19282 original size:17 final size:17
Alignment explanation
Indices: 19251--19283 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19241 TCCAAATTTT
19251 CAATAAATCTCAAAATA
1 CAATAAATCTCAAAATA
19268 CAATACAATCT-AAAAT
1 CAATA-AATCTCAAAAT
19284 CCTAGATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
CAATAAATCTCAAAATA
Found at i:21247 original size:17 final size:16
Alignment explanation
Indices: 21207--21257 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
21197 CATGTATTCT
*
21207 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
21223 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
21240 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
21257 T
1 T
21258 GAGGGTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:37188 original size:51 final size:53
Alignment explanation
Indices: 37133--37252 Score: 147
Period size: 54 Copynumber: 2.3 Consensus size: 53
37123 TTGATAATAC
* * *
37133 ATTGAAAGAGAAGTAAACCT-CGCAAAG-AATGTTTTAATGTCCGGAGACAAG
1 ATTGAAAGAGAAGAAAAACTGCGCAAAGTAATGTTTTAATGTCCAGAGACAAG
* * *
37184 ATTGAAAGAGAAGAAAAACTGGCGGAGAGTACTGTTTTAATGTCCAGAGACAAG
1 ATTGAAAGAGAAGAAAAACT-GCGCAAAGTAATGTTTTAATGTCCAGAGACAAG
*
37238 ATTGAAATAG-AGAAA
1 ATTGAAAGAGAAGAAA
37253 TGTTGAAGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 18 0.31
53 10 0.17
54 31 0.53
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (53 bp):
ATTGAAAGAGAAGAAAAACTGCGCAAAGTAATGTTTTAATGTCCAGAGACAAG
Found at i:38641 original size:38 final size:38
Alignment explanation
Indices: 38590--38667 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
38580 CCCTTTACTA
38590 TCATTAGTGGGCTTCCTTACCACTTTTTGCCATTTTGG
1 TCATTAGTGGGCTTCCTTACCACTTTTTGCCATTTTGG
*
38628 TCATTAGTGGGCTTCCTTACCACTTTTTGGCATTTTGG
1 TCATTAGTGGGCTTCCTTACCACTTTTTGCCATTTTGG
38666 TC
1 TC
38668 TAGGAATCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (38 bp):
TCATTAGTGGGCTTCCTTACCACTTTTTGCCATTTTGG
Found at i:40477 original size:19 final size:19
Alignment explanation
Indices: 40441--40477 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40431 GTTTTAGCAG
*
40441 CCAAAAAACAAGGGTTCTT
1 CCAAAAAACAAGGATTCTT
*
40460 CCAAAAAACTAGGATTCT
1 CCAAAAAACAAGGATTCT
40478 AGCTAACATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (19 bp):
CCAAAAAACAAGGATTCTT
Found at i:41014 original size:4 final size:4
Alignment explanation
Indices: 40995--41035 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
40985 TGTTAGGTGT
* *
40995 TTTA TTT- TTCA TTTA TTTA -TTA TTTA TTTA GTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
41036 GACTATGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
3 5 0.16
4 26 0.84
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:41031 original size:12 final size:11
Alignment explanation
Indices: 40995--41035 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
40985 TGTTAGGTGT
40995 TTTATTT-TTCA
1 TTTATTTATT-A
41006 TTTATTTATTA
1 TTTATTTATTA
41017 TTTATTTAGTTA
1 TTTATTTA-TTA
41029 TTTATTT
1 TTTATTT
41036 GACTATGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 16 0.57
12 12 0.43
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:42788 original size:69 final size:68
Alignment explanation
Indices: 42481--42967 Score: 529
Period size: 69 Copynumber: 7.3 Consensus size: 68
42471 TCTTTTTTTA
* *
42481 CAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTT-TTGCATTTAAGTTTAGTATTTTCTAT
1 CAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTATTTTCTAT
42545 TTC
66 TTC
* * * * * * *
42548 CAAAAATA-CCTTTCAGTCGAAGGGTCATTTTCGTC-CCTCTGCATTTGAGTTTA--CTTTT-GA
1 CAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCT-TGCATTTAAGTTTAGTATTTTCTA
42608 TTTC
65 TTTC
* * * *
42612 CAAAAATACCCTTTCGGTCGAGGGGCCGTTTTTGTCTTCTTGCATATAAGTTTGGTATTTTCTAT
1 CAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTATTTTCTAT
42677 TTC
66 TTC
* * *
42680 CAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTACATATAAGTTTGGTATTTTCTAT
1 CAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTATTTTCTAT
42745 TTC
66 TTC
*
42748 CAAAACATACCCTTTCGGTCGAAGGGTCGGTTTTGTCTTCTTGCATTTAAGTTTAGTATTTTCTA
1 CAAAA-ATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTATTTTCTA
*
42813 TTTT
65 TTTC
* * * * *
42817 C-AAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTT-TCCGCGTTTTAGTTTAG-------TG
1 CAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCT-TGCATTTAAGTTTAGTATTTTCTA
42873 TTTC
65 TTTC
* ** * ** *
42877 CAAAAATGCCCTTTCGGTCGAAGGGTCGTTTTCATCCTT-TTGTACCTAAGTTTAGTACTTTCTT
1 CAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGT-CTTCTTGCATTTAAGTTTAGTATTTTC-T
*
42941 TTTTC
64 ATTTC
*
42946 CAAAAATGCCCTTTCGGTCGAA
1 CAAAAATACCCTTTCGGTCGAA
42968 AGGCCAATTT
Statistics
Matches: 359, Mismatches: 42, Indels: 36
0.82 0.10 0.08
Matches are distributed among these distances:
60 5 0.01
61 38 0.11
62 4 0.01
64 13 0.04
65 37 0.10
66 30 0.08
67 68 0.19
68 78 0.22
69 86 0.24
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.43
Consensus pattern (68 bp):
CAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTATTTTCTAT
TTC
Found at i:44370 original size:18 final size:18
Alignment explanation
Indices: 44347--44384 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
44337 TAATAATTTC
44347 TCCTTCACCATGGACCGT
1 TCCTTCACCATGGACCGT
44365 TCCTTCACCATGGACCGT
1 TCCTTCACCATGGACCGT
44383 TC
1 TC
44385 AATGTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.39, G:0.16, T:0.29
Consensus pattern (18 bp):
TCCTTCACCATGGACCGT
Found at i:63188 original size:33 final size:33
Alignment explanation
Indices: 63146--63222 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
63136 AACTTTAATG
* *
63146 CAAAGAATGGACGCAATGTCTACTCAAGTTATT
1 CAAAGAATGGACGCAACGTCTACTCAACTTATT
63179 CAAAGAATGGACGCAACGTCTACTCAACTTATT
1 CAAAGAATGGACGCAACGTCTACTCAACTTATT
63212 CAAAGAATGGA
1 CAAAGAATGGA
63223 TACTATGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (33 bp):
CAAAGAATGGACGCAACGTCTACTCAACTTATT
Found at i:66941 original size:21 final size:21
Alignment explanation
Indices: 66915--66955 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
66905 TTAAAGCCCT
66915 ATTGGATAC-AAGTGGTACTAA
1 ATTGGAT-CTAAGTGGTACTAA
66936 ATTGGATCTAAGTGGTACTA
1 ATTGGATCTAAGTGGTACTA
66956 GGGTTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (21 bp):
ATTGGATCTAAGTGGTACTAA
Found at i:87382 original size:77 final size:77
Alignment explanation
Indices: 87216--87444 Score: 291
Period size: 77 Copynumber: 3.0 Consensus size: 77
87206 TTATGCTTAC
* * * * * * * *
87216 ACGGGGACGCCAATTTTGGCGTTCGGTCATTGTGGTGAAACGGTCTCTA-GGAGACGTTCGTTTC
1 ACGGGGACACCAGTTTAGGCGTTCGGCCGTTATGATGAAACGGTCTCGAGGGAGACGTTCGTTTC
* * *
87280 ATTTTTGTTTGT
66 ATTTCTGTTGGA
* * *
87292 ACGGGGACGCCAGTTTAGGTGTTCGGCCGTTATGATGAAACAGTCTCGAGGGAGACGTTCGTTTC
1 ACGGGGACACCAGTTTAGGCGTTCGGCCGTTATGATGAAACGGTCTCGAGGGAGACGTTCGTTTC
87357 ATTTCTGTTGGA
66 ATTTCTGTTGGA
* *
87369 ACGGGGACACCAGTTTGGGCGTTCGGCCGTTATGATGAAACGGTCTCGAGGGAGACACTT-GTTT
1 ACGGGGACACCAGTTTAGGCGTTCGGCCGTTATGATGAAACGGTCTCGAGGGAGAC-GTTCGTTT
87433 CATTTCTGTTGG
65 CATTTCTGTTGG
87445 GAAAATTTCA
Statistics
Matches: 134, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
76 40 0.30
77 92 0.69
78 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (77 bp):
ACGGGGACACCAGTTTAGGCGTTCGGCCGTTATGATGAAACGGTCTCGAGGGAGACGTTCGTTTC
ATTTCTGTTGGA
Found at i:89876 original size:50 final size:50
Alignment explanation
Indices: 89801--89922 Score: 199
Period size: 50 Copynumber: 2.4 Consensus size: 50
89791 TTAGAGTTGT
* * *
89801 CCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCTGTCTTTCAACAGA
1 CCAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGA
*
89851 CCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCAACAGA
1 CCAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGA
*
89901 CCAGGTCCTGGGCAGGAGTTGT
1 CCAAGTCCTGGGCAGGAGTTGT
89923 CAAGTCCTGG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.34
Consensus pattern (50 bp):
CCAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGA
Found at i:89931 original size:21 final size:21
Alignment explanation
Indices: 89905--89944 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
89895 AACAGACCAG
*
89905 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
89926 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
89945 CTGTTTTTAG
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:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:93313 original size:21 final size:21
Alignment explanation
Indices: 93287--93336 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
93277 AGGGGCTGAG
*
93287 CTGGGTGCTG-GGCCTTGTCGC
1 CTGGGTGCTGAGGCATT-TCGC
93308 CTGGGTGCTGAGGCATTTCGC
1 CTGGGTGCTGAGGCATTTCGC
93329 CTGGGTGC
1 CTGGGTGC
93337 CCAGCGGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.04, C:0.26, G:0.42, T:0.28
Consensus pattern (21 bp):
CTGGGTGCTGAGGCATTTCGC
Found at i:93617 original size:12 final size:14
Alignment explanation
Indices: 93595--93636 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
93585 GTTAGTAACA
93595 AAAATTTGAAAA-T
1 AAAATTTGAAAATT
93608 AAAA-TTGAAAATT
1 AAAATTTGAAAATT
93621 AAAAGTTTG-AAATT
1 AAAA-TTTGAAAATT
93635 AA
1 AA
93637 TTTGGGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.27
13 9 0.35
14 7 0.27
15 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (14 bp):
AAAATTTGAAAATT
Found at i:109484 original size:22 final size:22
Alignment explanation
Indices: 109453--109496 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
109443 TTCTTTCCGC
*
109453 AACAACTTCTGTCCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
* *
109475 AACAAGTTCTGGGCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
109497 TCCTGCGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTG
Found at i:109507 original size:52 final size:52
Alignment explanation
Indices: 109450--109566 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
109440 TTTTTCTTTC
109450 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
*
109502 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTTTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
*
109554 TGCAACAACTTCT
1 CGCAACAACTTCT
109567 CTTTTCGACA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.26
Consensus pattern (52 bp):
CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
Found at i:109694 original size:21 final size:21
Alignment explanation
Indices: 109670--109715 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
109660 TTTTCTTTGC
*
109670 TCAAATCATCTTCAAAGGTCT
1 TCAAATCAACTTCAAAGGTCT
* * *
109691 TCAATTGAACTTCAATGGTCT
1 TCAAATCAACTTCAAAGGTCT
109712 TCAA
1 TCAA
109716 GTCTTCAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (21 bp):
TCAAATCAACTTCAAAGGTCT
Found at i:111310 original size:66 final size:66
Alignment explanation
Indices: 111204--111366 Score: 263
Period size: 66 Copynumber: 2.5 Consensus size: 66
111194 AAGAGTAATT
* **
111204 CTAAATCTATTTTAGATGTTGTAAGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
111269 A
66 A
* * *
111270 CTAAATCTGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTTTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
111335 A
66 A
*
111336 CTAAATCTGTTTTAGGTGTTGTTTGTGATGA
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGA
111367 AACAAATTCT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 89 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (66 bp):
CTAAATCTGTTTTAGATGTTGTTTGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
A
Found at i:111378 original size:33 final size:32
Alignment explanation
Indices: 111204--111417 Score: 153
Period size: 33 Copynumber: 6.5 Consensus size: 32
111194 AAGAGTAATT
* * ** *
111204 CTAAATCTATTTTAGATGTTGTAAGTGATGATA
1 CTAAATCTGTTTT-GGTGTTGTTTGTGATGAAA
* ** * *
111237 CTAAACCTAATTTGAGTATTGTTTGTGATGACA
1 CTAAATCTGTTTTG-GTGTTGTTTGTGATGAAA
* * *
111270 CTAAATCTGTTTTAGATGTTGTTTGCGATGATA
1 CTAAATCTGTTTT-GGTGTTGTTTGTGATGAAA
* ** * *
111303 CTAAACCTAATTTGAGTGTTGTTTTTGATGACA
1 CTAAATCTGTTTTG-GTGTTGTTTGTGATGAAA
111336 CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAA
1 CTAAATCTGTTTT-GGTGTTGTTTGTGATGAAA
* **
111369 C-AAATTCTGTTTTGGATGCTAATTGTGATGAAAA
1 CTAAA-TCTGTTTTGG-TGTTGTTTGTGATG-AAA
111403 C-AAATCTGTTTTGGT
1 CTAAATCTGTTTTGGT
111418 TGATCATAGC
Statistics
Matches: 145, Mismatches: 29, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
32 8 0.06
33 128 0.88
34 9 0.06
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (32 bp):
CTAAATCTGTTTTGGTGTTGTTTGTGATGAAA
Found at i:111398 original size:66 final size:66
Alignment explanation
Indices: 111204--111414 Score: 194
Period size: 66 Copynumber: 3.2 Consensus size: 66
111194 AAGAGTAATT
* ** * * ** **
111204 CTAAATCTATTTTAGATGTTGTAAGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
111269 A
66 A
* * ** *
111270 CTAAATCTGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTTTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
111335 A
66 A
* * * **
111336 CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGTTTTG-GATGCTAATTGTGATG
1 CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAA-CCTAATTTGAG-TGCTAATTGTGATG
*
111399 AAAA
64 -ACA
111403 C-AAATCTGTTTT
1 CTAAATCTGTTTT
111415 GGTTGATCAT
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
65 4 0.03
66 118 0.94
67 3 0.02
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (66 bp):
CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
A
Found at i:113251 original size:21 final size:20
Alignment explanation
Indices: 113225--113337 Score: 136
Period size: 21 Copynumber: 5.4 Consensus size: 20
113215 TGCTAGAAGT
113225 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAG-AAGTTCCAAGC
* *
113246 TCATTGGACCAGGTTCCAAGC
1 TCATTGGA-GAAGTTCCAAGC
*
113267 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAA-GTTCCAAGC
*
113288 TCATTGGAGAAGATTCCAAGA
1 TCATTGGAGAAG-TTCCAAGC
*
113309 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAA-GTTCCAAGC
113330 TCATTGGA
1 TCATTGGA
113338 ATTGCCTAAG
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.03
21 77 0.96
22 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (20 bp):
TCATTGGAGAAGTTCCAAGC
Found at i:113272 original size:42 final size:42
Alignment explanation
Indices: 113225--113337 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
113215 TGCTAGAAGT
* * *
113225 TCATTGGAGCAA-GTTCCAAGCTCATTGGACCAGGTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGCTCATTGGACAAGATTCCAAGA
* *
113267 TCATTGGAGAAGGTTCCAAGTTCATTGGAGAAGATTCCAAGA
1 TCATTGGAGAAGGTTCCAAGCTCATTGGACAAGATTCCAAGA
*
113309 TCATTGGAGAAGGTTTCAAGCTCATTGGA
1 TCATTGGAGAAGGTTCCAAGCTCATTGGA
113338 ATTGCCTAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
41 2 0.03
42 61 0.97
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (42 bp):
TCATTGGAGAAGGTTCCAAGCTCATTGGACAAGATTCCAAGA
Found at i:118487 original size:18 final size:19
Alignment explanation
Indices: 118464--118501 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
118454 AGGTTTTTTT
118464 TTTTTTAAGAT-TAATTTG
1 TTTTTTAAGATGTAATTTG
*
118482 TTTTTTTAGATGTAATTTG
1 TTTTTTAAGATGTAATTTG
118501 T
1 T
118502 CTCAATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (19 bp):
TTTTTTAAGATGTAATTTG
Found at i:118487 original size:19 final size:19
Alignment explanation
Indices: 118463--118501 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
118453 CAGGTTTTTT
118463 TTTTTTTAAGAT-TAATTTG
1 TTTTTTT-AGATGTAATTTG
118482 TTTTTTTAGATGTAATTTG
1 TTTTTTTAGATGTAATTTG
118501 T
1 T
118502 CTCAATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (19 bp):
TTTTTTTAGATGTAATTTG
Found at i:120904 original size:20 final size:19
Alignment explanation
Indices: 120875--120912 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
120865 ACCCAACATC
120875 AAAACCCAAATAAATAAAT
1 AAAACCCAAATAAATAAAT
*
120894 AAAAGCCCAAATGAATAAA
1 AAAA-CCCAAATAAATAAA
120913 GCTGAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.66, C:0.16, G:0.05, T:0.13
Consensus pattern (19 bp):
AAAACCCAAATAAATAAAT
Found at i:123816 original size:51 final size:51
Alignment explanation
Indices: 123703--124028 Score: 414
Period size: 51 Copynumber: 6.5 Consensus size: 51
123693 CGATCAACTT
* *** * * *
123703 CTTTGAATTGTCTTCCAATTCAATCTT--CGGGGTAGCGTCTTCCACTTACC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGG-ACCGTCTTCCGCTTATC
* ** *
123753 CTTTGAACTGTCTTCCACTTCAATCTTAAAAAGGGTCGTCTTTCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
* * ** *
123804 CTTCGAACTGTCTTCTAATTCAATCTT-AAAAGGATTGTCTT-C-C-AATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
*
123851 GTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
*
123902 CTTTGAACTATCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
*
123952 CTTTGACCTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
*
124003 CTTTGAACTATCTTCCAATTCAATCT
1 CTTTGAACTGTCTTCCAATTCAATCT
124029 CGAGAAAACC
Statistics
Matches: 241, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
47 27 0.11
48 13 0.05
49 2 0.01
50 86 0.36
51 111 0.46
52 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (51 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
Found at i:123999 original size:101 final size:100
Alignment explanation
Indices: 123703--124028 Score: 433
Period size: 101 Copynumber: 3.3 Consensus size: 100
123693 CGATCAACTT
* * *** * *
123703 CTTTGAATTGTCTTCCAATTCAATCTT-CGGGGTAGCGTCTTCCACTTACCCTTTGAACTGTCTT
1 CTTTGAACTATCTTCCAATTCAATCTTAAAAGG-ACCGTCTTCC-CTTATCCTTTGAACTGTCTT
* ** *
123767 CCACTTCAATCTTAAAAAGGGTCGTCTTTCGCTTATC
64 CCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
* * * ** * *
123804 CTTCGAACTGTCTTCTAATTCAATCTTAAAAGGATTGTCTT-CC-AATCGTTTGAACTGTCTTCC
1 CTTTGAACTATCTTCCAATTCAATCTTAAAAGGACCGTCTTCCCTTATCCTTTGAACTGTCTTCC
123867 AATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
66 AATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
*
123902 CTTTGAACTATCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGACCTGTCTTC
1 CTTTGAACTATCTTCCAATTCAATCTTAAAAGGACCGTCTTCC-CTTATCCTTTGAACTGTCTTC
123967 CAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
65 CAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
124003 CTTTGAACTATCTTCCAATTCAATCT
1 CTTTGAACTATCTTCCAATTCAATCT
124029 CGAGAAAACC
Statistics
Matches: 198, Mismatches: 23, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
98 84 0.42
99 2 0.01
100 2 0.01
101 108 0.55
102 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (100 bp):
CTTTGAACTATCTTCCAATTCAATCTTAAAAGGACCGTCTTCCCTTATCCTTTGAACTGTCTTCC
AATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
Found at i:124377 original size:232 final size:232
Alignment explanation
Indices: 123971--124428 Score: 898
Period size: 232 Copynumber: 2.0 Consensus size: 232
123961 GTCTTCCAAT
123971 TCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTATCTTCCAATTCAATCTCGAGAAA
1 TCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTATCTTCCAATTCAATCTCGAGAAA
124036 ACCATCTTTTGATACTCTTTGAAAAGATCCTTTTCAGGAATTTCATTTGAGAAAAGTCGTCTCCC
66 ACCATCTTTTGATACTCTTTGAAAAGATCCTTTTCAGGAATTTCATTTGAGAAAAGTCGTCTCCC
124101 AATGCATTTGAGGAGATTGTCTTCCAATCAATTTCTAATTCCGAAAATCTTCTTGAAAAATCGTC
131 AATGCATTTGAGGAGATTGTCTTCCAATCAATTTCTAATTCCGAAAATCTTCTTGAAAAATCGTC
*
124166 TTCCGATTGGCTTCTAGATATCTAAATCTGAAATGGA
196 TTCCGAATGGCTTCTAGATATCTAAATCTGAAATGGA
*
124203 TCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTCGAGAAA
1 TCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTATCTTCCAATTCAATCTCGAGAAA
124268 ACCATCTTTTGATACTCTTTGAAAAGATCCTTTTCAGGAATTTCATTTGAGAAAAGTCGTCTCCC
66 ACCATCTTTTGATACTCTTTGAAAAGATCCTTTTCAGGAATTTCATTTGAGAAAAGTCGTCTCCC
124333 AATGCATTTGAGGAGATTGTCTTCCAATCAATTTCTAATTCCGAAAATCTTCTTGAAAAATCGTC
131 AATGCATTTGAGGAGATTGTCTTCCAATCAATTTCTAATTCCGAAAATCTTCTTGAAAAATCGTC
124398 TTCCGAATGGCTTCTAGATATCTAAATCTGA
196 TTCCGAATGGCTTCTAGATATCTAAATCTGA
124429 TAAACCTTCT
Statistics
Matches: 224, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
232 224 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (232 bp):
TCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTATCTTCCAATTCAATCTCGAGAAA
ACCATCTTTTGATACTCTTTGAAAAGATCCTTTTCAGGAATTTCATTTGAGAAAAGTCGTCTCCC
AATGCATTTGAGGAGATTGTCTTCCAATCAATTTCTAATTCCGAAAATCTTCTTGAAAAATCGTC
TTCCGAATGGCTTCTAGATATCTAAATCTGAAATGGA
Found at i:124715 original size:64 final size:64
Alignment explanation
Indices: 124614--124821 Score: 326
Period size: 64 Copynumber: 3.2 Consensus size: 64
124604 TCGTCTTCCG
*
124614 ACCATCTTCTGCTGTACATCTTGATGAGATCGTCTTCCGCTCAACTTCTGAAAACTTTTGAGAA
1 ACCATCTTCTGGTGTACATCTTGATGAGATCGTCTTCCGCTCAACTTCTGAAAACTTTTGAGAA
* * * *
124678 ACCATCTTCTGGTGTACATCTTGATGAGACCGTCTTCCGATCAACTTCTGAAACCTTTTGAGTA
1 ACCATCTTCTGGTGTACATCTTGATGAGATCGTCTTCCGCTCAACTTCTGAAAACTTTTGAGAA
* * ** *
124742 GCCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGCTCAACTTCTGAAAACTCTTGAGAA
1 ACCATCTTCTGGTGTACATCTTGATGAGATCGTCTTCCGCTCAACTTCTGAAAACTTTTGAGAA
124806 ACCATCTTCTGGTGTA
1 ACCATCTTCTGGTGTA
124822 GACCTGAAAA
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 129 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (64 bp):
ACCATCTTCTGGTGTACATCTTGATGAGATCGTCTTCCGCTCAACTTCTGAAAACTTTTGAGAA
Found at i:126915 original size:21 final size:21
Alignment explanation
Indices: 126885--126926 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
126875 TGCATGTATA
*
126885 TAGCAGTCCTGTTTTAGAATT
1 TAGCAATCCTGTTTTAGAATT
126906 TAGCAATCCTGTTTTAGAATT
1 TAGCAATCCTGTTTTAGAATT
126927 GTAGAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (21 bp):
TAGCAATCCTGTTTTAGAATT
Found at i:126965 original size:18 final size:18
Alignment explanation
Indices: 126921--126957 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
126911 ATCCTGTTTT
126921 AGAATTGTAGAATTTAGC
1 AGAATTGTAGAATTTAGC
126939 AGAATTGTAGAATTTAGC
1 AGAATTGTAGAATTTAGC
126957 A
1 A
126958 ATTCTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (18 bp):
AGAATTGTAGAATTTAGC
Done.