Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014881.1 Corchorus capsularis cultivar CVL-1 contig14902, 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: 53430
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:527 original size:31 final size:31
Alignment explanation
Indices: 492--588 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
482 CAACTTCACA
* * * *
492 ATTTTGCGTGTTTGTGCACGAACCATTATTT
1 ATTTTGTGCGTTTGTGCGCGAAACATTATTT
*
523 ATTTTGTGCGTTTGTGCGCAAAACATTATTT
1 ATTTTGTGCGTTTGTGCGCGAAACATTATTT
* *
554 ATTTTATGCGTTTGTGTGCGAAACATTATTT
1 ATTTTGTGCGTTTGTGCGCGAAACATTATTT
585 ATTT
1 ATTT
589 GAAAATGATC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (31 bp):
ATTTTGTGCGTTTGTGCGCGAAACATTATTT
Found at i:5209 original size:14 final size:14
Alignment explanation
Indices: 5192--5218 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5182 GAGTGAAACT
5192 TTTTAATTTAGTCA
1 TTTTAATTTAGTCA
5206 TTTTAATTTAGTC
1 TTTTAATTTAGTC
5219 TTAATGTGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTTAATTTAGTCA
Found at i:11880 original size:12 final size:12
Alignment explanation
Indices: 11863--11902 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
11853 TTCTTCAAAG
*
11863 CATTTTTATTGC
1 CATTTTTCTTGC
*
11875 CATTTTTCTTAC
1 CATTTTTCTTGC
11887 C-TTTTTCTTGC
1 CATTTTTCTTGC
11898 CATTT
1 CATTT
11903 GTTTCCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.12, C:0.23, G:0.05, T:0.60
Consensus pattern (12 bp):
CATTTTTCTTGC
Found at i:11916 original size:22 final size:23
Alignment explanation
Indices: 11865--11918 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
11855 CTTCAAAGCA
* *
11865 TTTTTATTGCCATTTTTCTTACC
1 TTTTTCTTGCCATTTGTCTTACC
11888 TTTTTCTTGCCATTTGT-TT-CC
1 TTTTTCTTGCCATTTGTCTTACC
11909 TTTTTTCTTG
1 -TTTTTCTTG
11919 TCATAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 11 0.39
23 15 0.54
ACGTcount: A:0.07, C:0.20, G:0.07, T:0.65
Consensus pattern (23 bp):
TTTTTCTTGCCATTTGTCTTACC
Found at i:12129 original size:74 final size:73
Alignment explanation
Indices: 12008--12167 Score: 178
Period size: 73 Copynumber: 2.2 Consensus size: 73
11998 CTTTTCTGAA
* * * * ** ** *
12008 CTTGGCATAAATTTGGGCAAGATTTTTTATTTAGTGAATTTGAATTCTTGTAATAAATTTGGCCG
1 CTTGGAATAAATTTGGGCAAGATATTTAATTGAGTGAAAATGAATTCTTG-AATAAATTTAACCA
12073 AATTGAATT
65 AATTGAATT
* *
12082 CTTGGTATAAATTTGGGCAAGA-ATTTAATTGGATTGAAAATGAATTCTTGAATAAATTTAACCA
1 CTTGGAATAAATTTGGGCAAGATATTTAATT-GAGTGAAAATGAATTCTTGAATAAATTTAACCA
**
12146 AATTTCATT
65 AATTGAATT
12155 CTTGGAATAAATT
1 CTTGGAATAAATT
12168 CTTTCTTATA
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
73 36 0.50
74 36 0.50
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (73 bp):
CTTGGAATAAATTTGGGCAAGATATTTAATTGAGTGAAAATGAATTCTTGAATAAATTTAACCAA
ATTGAATT
Found at i:12336 original size:21 final size:20
Alignment explanation
Indices: 12310--12367 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
12300 TTTGAAACTT
*
12310 CATTACACCTAATTGTGATAC
1 CATTACACCTAATAGTGA-AC
*
12331 CATTACACCTAAAAG-GAAC
1 CATTACACCTAATAGTGAAC
*
12350 CATTACACCAAATAGTGA
1 CATTACACCTAATAGTGA
12368 CAACATTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.47
20 4 0.12
21 13 0.41
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (20 bp):
CATTACACCTAATAGTGAAC
Found at i:13937 original size:34 final size:34
Alignment explanation
Indices: 13893--13961 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
13883 GTGGGCTATT
13893 TGGCTATTGGACCTTCGGGCCCGATTTATATTTG
1 TGGCTATTGGACCTTCGGGCCCGATTTATATTTG
* * **
13927 TGGCTTTTGGACCTTTGGGTTCGATTTATATTTG
1 TGGCTATTGGACCTTCGGGCCCGATTTATATTTG
13961 T
1 T
13962 TCAACATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (34 bp):
TGGCTATTGGACCTTCGGGCCCGATTTATATTTG
Found at i:15960 original size:225 final size:220
Alignment explanation
Indices: 15477--16164 Score: 974
Period size: 219 Copynumber: 3.1 Consensus size: 220
15467 TCAATATGTT
15477 CATCGGACTCCATCATGGAAGCTTCTTCCTCCTCTCTATCAACCTTCTTCTTCAGAGCTTCTTCC
1 CATCGGACTCCATCATGGAAGCTTCTTCCTCCTCTCTATC-ACCTTCTTCTTCAGAGCTTCTTCC
* * * * *
15542 TCTGTTTGGATTCTTTAGAATGGTTCCTACGGCAAGTTGTCGCTACTTCCATTAGTTCTTTTTTT
65 TCTGTTTGGATTCTTTGGAATGGTTCCTTC-GCAAGTTGCCGCTACTTCCATTAGTTATTTTTTC
*
15607 TAATTTGTTGTTGACTAGAGA---TTCTTTGGCCGGAGGGTTGTGTAATGCACCTTCTTCGTTTT
129 TAATTTGTTGTTGACTAGAGATTCTTCTTTGGCCGGAGGGTTGTGTAATGCACCTTCTTCGTCTT
*
15669 CAGTCAGAGGAATCTTCGAAACTCTGC
194 CAGTCCGAGGAATCTTCGAAACTCTGC
* * *
15696 CATCGGACTCCATTATGGAAGCTTCTTTCTCCTCTCTATCGACCTTCTTCTTCAGAGGTTCTTCC
1 CATCGGACTCCATCATGGAAGCTTCTTCCTCCTCTCTATC-ACCTTCTTCTTCAGAGCTTCTTCC
15761 TCTGTTTGGATTCTTTGGAATGGTTCCTTCGCCAAGTTGCCGCTACTTCCATTAGTTATTTTTTC
65 TCTGTTTGGATTCTTTGGAATGGTTCCTTCG-CAAGTTGCCGCTACTTCCATTAGTTATTTTTTC
* * * ** *
15826 TAATTTGTTGTTCATTACTAGAGATTCTTCTTTGGCCAGAGGGTTGTGTTATGGTCTTTCTTCGT
129 TAATTTGTTG-T--TGACTAGAGATTCTTCTTTGGCCGGAGGGTTGTGTAATGCACCTTCTTCGT
*
15891 CTTCAGTCCGAGGAATCTTCGAAACTCAGC
191 CTTCAGTCCGAGGAATCTTCGAAACTCTGC
* * * *
15921 CATCGAACTACATCATGGAAGCTTCTTCCTCCTCTCTATCAAC--CTTCTTCAGAGCTTCTTCTT
1 CATCGGACTCCATCATGGAAGCTTCTTCCTCCTCTCTATCACCTTCTTCTTCAGAGCTTCTTCCT
* * * * *
15984 CTGTTAGGATTCTTTGGAATGGTTCCTTCAGCAAATTTCCGTTACTTCCATTAGTTCTTTTTTTC
66 CTGTTTGGATTCTTTGGAATGGTTCCTTC-GCAAGTTGCCGCTACTTCCATTAGTT-ATTTTTTC
* * *
16049 TAATTTGTTGTTGACCAGAGATTCTTCTTTGGCCGGAGGGTTGTATAATGCACCTTATTCGTCTT
129 TAATTTGTTGTTGACTAGAGATTCTTCTTTGGCCGGAGGGTTGTGTAATGCACCTTCTTCGTCTT
16114 CAG-CCTGAGGAATCTTCGAAACTCTGC
194 CAGTCC-GAGGAATCTTCGAAACTCTGC
*
16141 CATTGGACTCCATCATGGAAGCTT
1 CATCGGACTCCATCATGGAAGCTT
16165 TCCTTCTTCT
Statistics
Matches: 416, Mismatches: 43, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
218 1 0.00
219 131 0.31
220 90 0.22
222 78 0.19
223 18 0.04
224 2 0.00
225 96 0.23
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (220 bp):
CATCGGACTCCATCATGGAAGCTTCTTCCTCCTCTCTATCACCTTCTTCTTCAGAGCTTCTTCCT
CTGTTTGGATTCTTTGGAATGGTTCCTTCGCAAGTTGCCGCTACTTCCATTAGTTATTTTTTCTA
ATTTGTTGTTGACTAGAGATTCTTCTTTGGCCGGAGGGTTGTGTAATGCACCTTCTTCGTCTTCA
GTCCGAGGAATCTTCGAAACTCTGC
Found at i:16529 original size:31 final size:30
Alignment explanation
Indices: 16494--16566 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
16484 TTAAATTGAT
* *
16494 ATTAGAGTCTCATTTGAACCAATTTTGTAAC
1 ATTAGAGACTCA-TTGAACCAATTTTGCAAC
* * *
16525 ATTAGGGACTGATTGAGCCAATTTTGCAAC
1 ATTAGAGACTCATTGAACCAATTTTGCAAC
* *
16555 GTTAGAAACTCA
1 ATTAGAGACTCA
16567 ATTAACAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (30 bp):
ATTAGAGACTCATTGAACCAATTTTGCAAC
Found at i:18135 original size:12 final size:12
Alignment explanation
Indices: 18118--18143 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18108 GGAAAATTAA
18118 AAAATGTAAGCC
1 AAAATGTAAGCC
18130 AAAATGTAAGCC
1 AAAATGTAAGCC
18142 AA
1 AA
18144 CATTATTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAATGTAAGCC
Found at i:21382 original size:16 final size:17
Alignment explanation
Indices: 21363--21398 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
21353 GGTCTTATGC
21363 AGATTCTATCTTTTT-T
1 AGATTCTATCTTTTTCT
*
21379 AGATTCTGTCTTTTTCT
1 AGATTCTATCTTTTTCT
21396 AGA
1 AGA
21399 CCCTGTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (17 bp):
AGATTCTATCTTTTTCT
Found at i:27982 original size:147 final size:146
Alignment explanation
Indices: 27771--28212 Score: 616
Period size: 147 Copynumber: 3.0 Consensus size: 146
27761 TCCAACTCTA
* * * * *
27771 CCCTTTCATCACAACTCTTCTTAACCTCATTATTTGCATCCTCCACTTTCTCTTCCTCTGGCGGT
1 CCCTTTCATTACAACTCTTCTCAACCTCATTCTTCGCATCCTCCACTTTCTCTTCATCTGGCGGT
*
27836 GATGAATTTAGCTCCTCCTGCTCATTCACTTCATCCTTTCTTATGGGCTCGGCTTCTTTTTCCCC
66 GATGAATTTAGCTCCTCCTGCTCATTCACTTCATCCTTTC-TATGGGCTCGGCTTCTTTTTCCTC
27901 TGATTTCTTTTCCTGAT
130 TGATTTCTTTTCCTGAT
27918 CCCTTTCATTACAACTCTTCTCAACCTCATTCTTCGCATCCTCCACTTTCTCTTCATCTGGCGGT
1 CCCTTTCATTACAACTCTTCTCAACCTCATTCTTCGCATCCTCCACTTTCTCTTCATCTGGCGGT
27983 GATGAATTTAGCTCCTCCTGCTCATTCACTTCATCCCTTTCTATGGGCTCGGCTTCTTTTTCCTC
66 GATGAATTTAGCTCCTCCTGCTCATTCACTTCAT-CCTTTCTATGGGCTCGGCTTCTTTTTCCTC
*
28048 TGATTTCTTTTCCGGAT
130 TGATTTCTTTTCCTGAT
* * * * **
28065 CCCTTTCATTACAACTCTTCTCAACCTCATTATTCTTCGCATCCCCCAGTTTCACTTCATTTCTC
1 CCCTTTCATTACAACTCTTCTCAACCTC---ATTCTTCGCATCCTCCACTTTCTCTTCATCTGGC
* * ** * * ** *
28130 GATGATGAATTTGGCTCCTCCTGCTCAACCACTTCATCTTTTGGTATAAAG-TCGGTTTCTTTTT
63 GGTGATGAATTTAGCTCCTCCTGCTCATTCACTTCATCCTTT-CTAT-GGGCTCGGCTTCTTTTT
28194 CCTCTGATTTCTTTTCCTG
126 CCTCTGATTTCTTTTCCTG
28213 CTGATTCCTT
Statistics
Matches: 266, Mismatches: 23, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
147 161 0.61
148 6 0.02
149 4 0.02
150 94 0.35
151 1 0.00
ACGTcount: A:0.15, C:0.32, G:0.11, T:0.42
Consensus pattern (146 bp):
CCCTTTCATTACAACTCTTCTCAACCTCATTCTTCGCATCCTCCACTTTCTCTTCATCTGGCGGT
GATGAATTTAGCTCCTCCTGCTCATTCACTTCATCCTTTCTATGGGCTCGGCTTCTTTTTCCTCT
GATTTCTTTTCCTGAT
Found at i:28210 original size:15 final size:16
Alignment explanation
Indices: 28185--28227 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
28175 ATAAAGTCGG
28185 TTTCTTTTTCCT-CTGA
1 TTTC-TTTTCCTGCTGA
28201 TTTCTTTTCCTGCTGA
1 TTTCTTTTCCTGCTGA
*
28217 TTCCTTTTCCT
1 TTTCTTTTCCT
28228 TCCGGGAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.05, C:0.28, G:0.07, T:0.60
Consensus pattern (16 bp):
TTTCTTTTCCTGCTGA
Found at i:31578 original size:50 final size:50
Alignment explanation
Indices: 31503--31602 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
31493 TTTGATATCG
31503 CCATTTCAAGTATCAAATGTTTGGAATGTGTTTTTGTTATTATTCCTTTA
1 CCATTTCAAGTATCAAATGTTTGGAATGTGTTTTTGTTATTATTCCTTTA
* * *
31553 CCATTTTAAGTATCAAGTGTTTGGAATGTGTTTTTGTTATTCTTCCTTTA
1 CCATTTCAAGTATCAAATGTTTGGAATGTGTTTTTGTTATTATTCCTTTA
31603 TCTTATGATC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (50 bp):
CCATTTCAAGTATCAAATGTTTGGAATGTGTTTTTGTTATTATTCCTTTA
Found at i:37714 original size:45 final size:45
Alignment explanation
Indices: 37650--37739 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
37640 GCCCTGCCGG
37650 TTCCGTCTTATCTCAATCAATTTCGTTAAACTAAAAGAAAAAAAA
1 TTCCGTCTTATCTCAATCAATTTCGTTAAACTAAAAGAAAAAAAA
* *
37695 TTCCGTCTTTTCTCAATCAATTTCGTTAAATTAAAAGAAAAAAAA
1 TTCCGTCTTATCTCAATCAATTTCGTTAAACTAAAAGAAAAAAAA
37740 AGTAGGAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (45 bp):
TTCCGTCTTATCTCAATCAATTTCGTTAAACTAAAAGAAAAAAAA
Found at i:41865 original size:31 final size:32
Alignment explanation
Indices: 41794--41866 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 32
41784 GTTAGAGGGT
* ** **
41794 AAAATGTCTTGAATTTGAGAAATTTAGGGGGT
1 AAAATGTCTTGAATTTGAGAAATTCAAAGGAC
* *
41826 TAATTGTCTTGAATTTGA-AAATTCAAAGGAC
1 AAAATGTCTTGAATTTGAGAAATTCAAAGGAC
41857 AAAATGTCTT
1 AAAATGTCTT
41867 TGACATAATA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
31 16 0.50
32 16 0.50
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.36
Consensus pattern (32 bp):
AAAATGTCTTGAATTTGAGAAATTCAAAGGAC
Found at i:42097 original size:2 final size:2
Alignment explanation
Indices: 42090--42124 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
42080 TTATTTTAAA
42090 AT 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 AT A
42125 CTTTACACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46152 original size:22 final size:22
Alignment explanation
Indices: 46127--46753 Score: 223
Period size: 22 Copynumber: 29.0 Consensus size: 22
46117 ATAATCCCAT
46127 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
46149 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
46171 TATGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** * *
46193 TAT--AATTTTTTTAAACTTCT
1 TATGAAATTTTGATAACCTTCC
* *
46213 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
46235 TAAGGAATTTTGA-AGACC-TCAG
1 TATGAAATTTTGATA-ACCTTC-C
46257 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * *
46279 AATGAAATTTTGATAA-ATAACAC
1 TATGAAATTTTGATAACCT-TC-C
* * *
46302 CATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
46323 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
46346 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
46367 ATATG-AATTGTT-AGTAATCATAC
1 -TATGAAATT-TTGA-TAACCTTCC
* * *
46390 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
46412 TATGAAATTTTGATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
*
46434 TATGAAATTTTGATGAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
46457 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
46480 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
46502 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
46519 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* ** *
46540 TAGGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
46562 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
*** * *
46584 TATGAAATTTTGATCTGCATAC
1 TATGAAATTTTGATAACCTTCC
* *
46606 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
46628 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
46650 TATAAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
46671 -CTGAAATTTTGAT-ATCTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
46691 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
46715 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
46732 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
46754 CAGAAATACC
Statistics
Matches: 437, Mismatches: 127, Indels: 82
0.68 0.20 0.13
Matches are distributed among these distances:
16 11 0.03
17 12 0.03
18 2 0.00
19 2 0.00
20 30 0.07
21 18 0.04
22 283 0.65
23 71 0.16
24 8 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:46468 original size:23 final size:23
Alignment explanation
Indices: 46394--46495 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
46384 TCATACTCTG
* * * *
46394 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
** *
46416 AAATTTTGAT-AACCTCGTTATG
1 AAATTTTGATAAACCTCCCTATA
* * *
46438 AAATTTTGATGAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
46461 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
46484 AAATTTTGATAA
1 AAATTTTGATAA
46496 CTTTCTTATG
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
22 28 0.42
23 39 0.58
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:46842 original size:22 final size:22
Alignment explanation
Indices: 46790--47188 Score: 113
Period size: 22 Copynumber: 18.0 Consensus size: 22
46780 AATCACATTC
* *
46790 TGAAAATTTGATAACCTCTTTC
1 TGAAATTTTGATAACCTCTTTA
46812 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * *
46834 TAAAATTTTGTTGATCC-CTTTA
1 TGAAATTTTGAT-AACCTCTTTA
* * * *
46856 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
46878 TGTAATTTTGATAACATCGCTTT-
1 TGAAATTTTGATAAC--CTCTTTA
* ** *
46901 CG-AATTTTGATAACAACATTA
1 TGAAATTTTGATAACCTCTTTA
46922 TGAAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
* *
46944 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTTTA
* * * * *
46968 TGGAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
46990 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
47010 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
* *
47030 TGAAATTAAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCT-TTA
* **
47058 TGAAATTTTGATAACCACGCTA
1 TGAAATTTTGATAACCTCTTTA
* ***
47080 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTTTA
* * *
47102 TGAAATATT-ACTAACCTCCTAA
1 TGAAATTTTGA-TAACCTCTTTA
* * * * **
47124 TGAAATTTTGTTGAGCACACTA
1 TGAAATTTTGATAACCTCTTTA
**
47146 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTTTA
* *
47168 TGACATTTTGATAATCTCTTT
1 TGAAATTTTGATAACCTCTTT
47189 GATAACCTTT
Statistics
Matches: 274, Mismatches: 73, Indels: 60
0.67 0.18 0.15
Matches are distributed among these distances:
19 2 0.01
20 19 0.07
21 32 0.12
22 180 0.66
23 6 0.02
24 7 0.03
25 10 0.04
26 7 0.03
27 2 0.01
28 9 0.03
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:46928 original size:88 final size:88
Alignment explanation
Indices: 46766--46931 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
46756 GAAATACCAC
* * * ** *
46766 TATGAAATTTTTGTAATCACATTCTGAAAATTTGATAACCTCTTTCTGAAATTTTGATAACCTCT
1 TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCGCTTTCTGAAATTTTGATAACAACA
46831 TTATAAAATTTTGTTGATCCCTT
66 TTATAAAATTTTGTTGATCCCTT
* *
46854 TATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACATCGCTTTC-G-AATTTTGATAACA
1 TATGAAATTTCTG-TAATCACATTATGAAAATTTGATAAC--CGCTTTCTGAAATTTTGATAACA
*
46916 ACATTATGAAATTTTG
63 ACATTATAAAATTTTG
46932 ATAATCTTCC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
87 4 0.06
88 55 0.83
89 1 0.02
90 6 0.09
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (88 bp):
TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCGCTTTCTGAAATTTTGATAACAACA
TTATAAAATTTTGTTGATCCCTT
Found at i:46974 original size:25 final size:22
Alignment explanation
Indices: 46920--47019 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 22
46910 ATAACAACAT
46920 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATCTTCC
46942 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATCT--TC-C
* * *
46966 TATGGAATTTCGATAATC-ACTC
1 TATGAAATTTTGATAATCTTC-C
* *
46988 TATGAGA-TTTGATAACCTT-C
1 TATGAAATTTTGATAATCTTCC
*
47008 TATCAAATTTTG
1 TATGAAATTTTG
47020 GTACTCCTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
20 6 0.10
21 27 0.44
22 11 0.18
23 2 0.03
24 4 0.06
25 12 0.19
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCC
Found at i:47105 original size:44 final size:43
Alignment explanation
Indices: 47042--47399 Score: 166
Period size: 44 Copynumber: 8.3 Consensus size: 43
47032 AAATTAAGAC
* * *
47042 TTTT-ATAACCTTCATATGAAATTTTGATAACCACGCTATAAAA
1 TTTTGATAACCTCCCTATGAAATTTTGATAACCAC-CTATGAAA
* * *
47085 TTTTGATAACCTCCCCATGAAATATT-ACTAACCTCCTAATGAAA
1 TTTTGATAACCTCCCTATGAAATTTTGA-TAACCACCT-ATGAAA
* * * * * * *
47129 TTTTGTTGAGCACACTATGAAATTCTT-ATAACCTCGCTATGACA
1 TTTTGATAACCTCCCTATGAAATT-TTGATAACCAC-CTATGAAA
* * ** *
47173 TTTTGATAA--TCTCTTTGATAACCTTTCT-ATAA--AATTGTGAAA
1 TTTTGATAACCTCCCTATGA-AA--TTT-TGATAACCACCTATGAAA
* * ** * *
47215 --AT--TAACCACCCTATGAAATTTCAATAATCAACCTAAGAAA
1 TTTTGATAACCTCCCTATGAAATTTTGATAA-CCACCTATGAAA
* * *
47255 TTTTAATAACCTGATCCTATGAAATTTTGGTAACCACACTATGAAA
1 TTTTGATAACCT--CCCTATGAAATTTTGATAACCAC-CTATGAAA
** * * *
47301 TTTTGATAAGTTCCATATGAAATTTTGGTAACCACGCTATGGAA
1 TTTTGATAACCTCCCTATGAAATTTTGATAACCAC-CTATGAAA
* * *
47345 TTTTGATAACCT-CCTCATGAAATTATAATAACCATCTTATGAAA
1 TTTTGATAACCTCCCT-ATGAAATTTTGATAACCA-CCTATGAAA
47389 TTTTGATAACC
1 TTTTGATAACC
47400 ACATAGAGAC
Statistics
Matches: 235, Mismatches: 56, Indels: 47
0.70 0.17 0.14
Matches are distributed among these distances:
37 7 0.03
38 3 0.01
39 2 0.01
40 13 0.06
42 12 0.05
43 11 0.05
44 140 0.60
45 16 0.07
46 31 0.13
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (43 bp):
TTTTGATAACCTCCCTATGAAATTTTGATAACCACCTATGAAA
Found at i:47299 original size:22 final size:22
Alignment explanation
Indices: 47217--47402 Score: 123
Period size: 22 Copynumber: 8.4 Consensus size: 22
47207 TTGTGAAAAT
* **
47217 TAACCACCCTATGAAATTTCAA
1 TAACCACACTATGAAATTTTGA
* * *
47239 TAATCA-ACCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
*
47261 TAACCTGATC-CTATGAAATTTTGG
1 TAACC--A-CACTATGAAATTTTGA
47285 TAACCACACTATGAAATTTTGA
1 TAACCACACTATGAAATTTTGA
* *
47307 TAAGTTC-CA-TATGAAATTTTGG
1 TAA--CCACACTATGAAATTTTGA
* *
47329 TAACCACGCTATGGAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * *
47351 TAACCTC-CTCATGAAATTATAA
1 TAACCACACT-ATGAAATTTTGA
*
47373 TAACCATC-TTATGAAATTTTGA
1 TAACCA-CACTATGAAATTTTGA
47395 TAACCACA
1 TAACCACA
47403 TAGAGACAAG
Statistics
Matches: 128, Mismatches: 23, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
20 1 0.01
21 5 0.04
22 100 0.78
23 4 0.03
24 18 0.14
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:47597 original size:19 final size:20
Alignment explanation
Indices: 47566--47603 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
47556 TATTGACATT
47566 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
47585 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
47604 ACTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:47793 original size:19 final size:18
Alignment explanation
Indices: 47744--47793 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
47734 TAATAATGGG
47744 ATAATTTATAATTAAAAA
1 ATAATTTATAATTAAAAA
* *
47762 ATAATTGAATAATTAAAAT
1 ATAATT-TATAATTAAAAA
*
47781 ATTATTTAGTAAT
1 ATAATTTA-TAAT
47794 GGCAATTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
ATAATTTATAATTAAAAA
Found at i:47832 original size:32 final size:32
Alignment explanation
Indices: 47796--47862 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
47786 TTAGTAATGG
*
47796 CAATTTAGAAATATGTTTTTAAAAA-AGGGGTA
1 CAATTTAGAAATATG-TTTTAAAAATAAGGGTA
*
47828 CAA-TTGGAAATATGTTTTAAAAATAAGGGTA
1 CAATTTAGAAATATGTTTTAAAAATAAGGGTA
47859 CAAT
1 CAAT
47863 CGGAAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 9 0.29
31 19 0.61
32 3 0.10
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (32 bp):
CAATTTAGAAATATGTTTTAAAAATAAGGGTA
Found at i:47848 original size:30 final size:32
Alignment explanation
Indices: 47803--47868 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
47793 TGGCAATTTA
* *
47803 GAAATATGTTTTTAAAAA-AGGGGTACAATTG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
47834 GAAATATG-TTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
47865 GAAA
1 GAAA
47869 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (32 bp):
GAAATATGTTTTTAAAAATAAGGGTACAATCG
Found at i:48710 original size:148 final size:145
Alignment explanation
Indices: 48472--48906 Score: 600
Period size: 145 Copynumber: 3.0 Consensus size: 145
48462 TTCAAACACG
* * * *
48472 TACACTTTCTCTTTTGGAATATGATAAATAAGGGAAAAA-AAAGA-ATGATGTTGTC--T-AATG
1 TACACTTTTTCTTTTGGAATATGATGAATAA--GAAAAATAATGATAT--TGTTGCCAATCAATG
* * *
48532 TTTTCAG--TCTTCCTTTGCTGTTCTTCTATATTTGTGCAGCCTTAAAATGATTTAACCTTTCTG
62 TGTTCAGTTTCTTCCCTTGCTATTCTTCTATATTTGTGCAGCCTTAAAATGATTTAACCTTTCTG
48595 TTTAGAAGGATCTCATGCT
127 TTTAGAAGGATCTCATGCT
*
48614 TACACTTTTT-TTTTGGTATATGATGAATAAGAAAAATAATTAATGATATTGTTGCCAATCAATG
1 TACACTTTTTCTTTTGGAATATGATGAATAAG--AAA-AA-TAATGATATTGTTGCCAATCAATG
* *
48678 TGTTCAGTTTCTTCCCTTGCTATTATTGTATATTTGTGCAGCCTTAAAATGATTTAACCTTTCTG
62 TGTTCAGTTTCTTCCCTTGCTATTCTTCTATATTTGTGCAGCCTTAAAATGATTTAACCTTTCTG
*
48743 TTTACAAGGATCTCATGCT
127 TTTAGAAGGATCTCATGCT
*
48762 TACACTTTTTCTTTTGGAATATGATGAATAAGAAAAATAATGATATTGTTGCCGATCAATGTGTT
1 TACACTTTTTCTTTTGGAATATGATGAATAAGAAAAATAATGATATTGTTGCCAATCAATGTGTT
* *
48827 CAGTTTCTTCCCTTGTTATTCTTCTATATTTGTGCAGCCTTAAAATGATTTACCCTTT-TCGTTT
66 CAGTTTCTTCCCTTGCTATTCTTCTATATTTGTGCAGCCTTAAAATGATTTAACCTTTCT-GTTT
48891 AGAAGGATCTCATGCT
130 AGAAGGATCTCATGCT
48907 CGTCTGAGTC
Statistics
Matches: 262, Mismatches: 18, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
139 1 0.00
141 21 0.08
142 11 0.04
143 6 0.02
144 5 0.02
145 103 0.39
146 12 0.05
147 3 0.01
148 80 0.31
149 20 0.08
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (145 bp):
TACACTTTTTCTTTTGGAATATGATGAATAAGAAAAATAATGATATTGTTGCCAATCAATGTGTT
CAGTTTCTTCCCTTGCTATTCTTCTATATTTGTGCAGCCTTAAAATGATTTAACCTTTCTGTTTA
GAAGGATCTCATGCT
Found at i:49693 original size:18 final size:18
Alignment explanation
Indices: 49670--49704 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49660 AGCTCAGGAT
49670 GGCATGACTGAAATGTTA
1 GGCATGACTGAAATGTTA
*
49688 GGCATGACTGGAATGTT
1 GGCATGACTGAAATGTT
49705 CTCCTAAATT
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:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (18 bp):
GGCATGACTGAAATGTTA
Found at i:51010 original size:59 final size:59
Alignment explanation
Indices: 50851--51110 Score: 280
Period size: 59 Copynumber: 4.4 Consensus size: 59
50841 TGCGCGCGTC
* * * *
50851 TTCTGTTTATAACAATAATTTGAAAAAAATGTATAACGGTTTTCTTATT-C-CACACA-
1 TTCTCTTTATAACTATAATTTGAAAAAATTGTATAACGGTTTTCTTATTGCGCACATAT
* * *
50907 -TATCTTTATAACTATAATAATTTGAAAAAATTATGTAACGGTTTTCTTATTGCGCACATAT
1 TTCTCTTTATAAC--T-ATAATTTGAAAAAATTGTATAACGGTTTTCTTATTGCGCACATAT
* * * **
50968 TTCTCTTTATAACTATAATTTGAAAAAATTGTGTAACGGTTTTCTTAATGTGCGTATAT
1 TTCTCTTTATAACTATAATTTGAAAAAATTGTATAACGGTTTTCTTATTGCGCACATAT
* * ** * *
51027 TTCTCTTTATAACTATAATTTAAAAAAATTGTATAACGGTTTTCCTT-TTACGTGCTTGT
1 TTCTCTTTATAACTATAATTTGAAAAAATTGTATAACGGTTTT-CTTATTGCGCACATAT
51086 TTCTCTTTATAACTATAATTT-AAAA
1 TTCTCTTTATAACTATAATTTGAAAA
51111 TTTTCACTCC
Statistics
Matches: 174, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
55 10 0.06
58 36 0.21
59 108 0.62
60 9 0.05
62 11 0.06
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (59 bp):
TTCTCTTTATAACTATAATTTGAAAAAATTGTATAACGGTTTTCTTATTGCGCACATAT
Found at i:53344 original size:2 final size:2
Alignment explanation
Indices: 53337--53367 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53327 TTGCCTCTAC
53337 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 A
53368 ATAGTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.