Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018928.1 Corchorus olitorius cultivar O-4 contig18961, 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: 38117
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1224 original size:67 final size:65
Alignment explanation
Indices: 1113--1246 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 65
1103 AATATGTATG
* * *
1113 AACATAAATTAAAAATACATATGAGGTAATATATATGAAGGTAACTATATTGCTAATGAAGTACC
1 AACATAAATTAAAAATACATATGAGCTAATAAATATGAAGGTAAC--TATTGCCAATGAAGTACC
1178 AT
64 AT
*
1180 AACATAAATTAAAAATACATATGAGCTAATAAATATGAATGTAACTATTGCCAATGAAGTACCAT
1 AACATAAATTAAAAATACATATGAGCTAATAAATATGAAGGTAACTATTGCCAATGAAGTACCAT
1245 AA
1 AA
1247 AAGGGTCTCG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 21 0.33
67 42 0.67
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.28
Consensus pattern (65 bp):
AACATAAATTAAAAATACATATGAGCTAATAAATATGAAGGTAACTATTGCCAATGAAGTACCAT
Found at i:2071 original size:2 final size:2
Alignment explanation
Indices: 2064--2099 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2054 AATGACATAT
2064 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2100 TATATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2104 original size:2 final size:2
Alignment explanation
Indices: 2099--2128 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2089 ACACACACAC
2099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2129 TCCTTGCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3839 original size:60 final size:60
Alignment explanation
Indices: 3743--3873 Score: 217
Period size: 60 Copynumber: 2.2 Consensus size: 60
3733 TTAGGCTAAT
** * *
3743 TGCTCAAATAAGGGTCCGGTCTTTTAATTTGGCCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAAAGTCCGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTATCGAAAA
*
3803 TGCTCAAATAAAAGTCTGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAAAGTCCGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTATCGAAAA
3863 TGCTCAAATAA
1 TGCTCAAATAA
3874 GGGCCTGTCG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (60 bp):
TGCTCAAATAAAAGTCCGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:3874 original size:31 final size:31
Alignment explanation
Indices: 3776--3879 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
3766 TTAATTTGGC
3776 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
** * * * **
3807 CAAATAAAAGTCTGATC-TT-T-TAATTTGAC-
1 CAAATAAGGGCCT-AACGTTATCGAAAATG-CT
3836 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
3867 CAAATAAGGGCCT
1 CAAATAAGGGCCT
3880 GTCGTCAGTT
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
28 2 0.04
29 16 0.30
30 4 0.08
31 29 0.55
32 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:4015 original size:59 final size:60
Alignment explanation
Indices: 3921--4081 Score: 252
Period size: 60 Copynumber: 2.7 Consensus size: 60
3911 CGACGCCAGG
* * * *
3921 CCCTTATTTGATCATTTTGGCAAACGTTAGGCCCTTATTTGACC-AATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
* *
3980 CTCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
*
4040 CCCTTATTTGAGCATTTTGACAAATGTTAGGCCCTTATTTGA
1 CCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGA
4082 GTAATTAGCC
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 40 0.43
60 52 0.57
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
Found at i:4082 original size:31 final size:30
Alignment explanation
Indices: 3918--4082 Score: 126
Period size: 31 Copynumber: 5.5 Consensus size: 30
3908 TTTCGACGCC
* *
3918 AGGCCCTTATTTGATCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGACAAA-GTT
* * *
3949 AGGCCCTTATTTGACCA-ATT-A-AAAGATC
1 AGGCCCTTATTTGAGCATTTTGACAAAG-TT
* * *
3977 GGGCTCTTATTTGAGCATTTTGGCAAATGTT
1 AGGCCCTTATTTGAGCATTTTGACAAA-GTT
** *
4008 AGGCCCTTATTTG-GCCAAATT-A-AAAGATC
1 AGGCCCTTATTTGAG-CATTTTGACAAAG-TT
*
4037 AGACCCTTATTTGAGCATTTTGACAAATGTT
1 AGGCCCTTATTTGAGCATTTTGACAAA-GTT
4068 AGGCCCTTATTTGAG
1 AGGCCCTTATTTGAG
4083 TAATTAGCCC
Statistics
Matches: 102, Mismatches: 21, Indels: 22
0.70 0.14 0.15
Matches are distributed among these distances:
27 1 0.01
28 19 0.19
29 22 0.22
30 5 0.05
31 53 0.52
32 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGACAAAGTT
Found at i:11193 original size:60 final size:60
Alignment explanation
Indices: 11123--11985 Score: 1380
Period size: 60 Copynumber: 14.5 Consensus size: 60
11113 AATCAGATTA
*
11123 CCTTATCTTGTTTTAAAAATCCAGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
*
11183 CCTTATCTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* * *
11243 -CTTATCTTGCTTTAAAAATTCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTGAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* *
11302 CCTTATCTTGGTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* *
11362 -CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATATCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
*
11421 CCTTATCTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* * *
11481 -CTTATCTTGCTTTAAAAATCCAGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
*
11540 CCTTATCTTGTTTTAAAAATTCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* *
11600 -CTTATCTTGTTTTAAAAATCCAGGTCGAGGTCTCTGTTAGAGAATTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
*
11659 -CTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCACTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* *
11718 CCTTATCTTGTTTTAAAAATCCTGTTCGAGGTCTTTGTTAGAGAGTTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
*
11778 -CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* * * * *
11837 CCTTATCCTGTTTTAAGAATCCTGTTCAAGGTCTCTGTTAGAAAGTTTTCATTTCAAAAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* * *
11897 CCTTATCTTGTTTTAAAAATCCCGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAGAT
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* * * * *
11957 -CTTATCATGCTTCAAAAATCATGTTCGAG
1 CCTTATCTTGTTTTAAAAATCCTGGTCGAG
11986 AGTTTTCAAT
Statistics
Matches: 747, Mismatches: 51, Indels: 11
0.92 0.06 0.01
Matches are distributed among these distances:
59 360 0.48
60 387 0.52
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (60 bp):
CCTTATCTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
Found at i:11283 original size:119 final size:119
Alignment explanation
Indices: 11124--11985 Score: 1404
Period size: 119 Copynumber: 7.2 Consensus size: 119
11114 ATCAGATTAC
* *
11124 CTTATCTTGTTTTAAAAATCCAGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTAT
1 CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTAT
11189 CTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
66 CTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* *
11243 CTTATCTTGCTTTAAAAATTCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTGAAAATCCTTAT
1 CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTAT
*
11308 CTTGGTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
66 CTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
*
11362 CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATATCAAAATCCTTAT
1 CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTAT
11427 CTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
66 CTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* *
11481 CTTATCTTGCTTTAAAAATCCAGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTAT
1 CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTAT
* *
11546 CTTGTTTTAAAAATTCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
66 CTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* * *
11600 CTTATCTTGTTTTAAAAATCCAGGTCGAGGTCTCTGTTAGAGAATTTTCATTTCAAAAT-CTTAT
1 CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTAT
* *
11664 CTTGTTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCACTTCAAAAT
66 CTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* * *
11718 CCTTATCTTGTTTTAAAAATCCTGTTCGAGGTCTTTGTTAGAGAGTTTTCATTTCAAAAT-CTTA
1 -CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTA
* *
11782 TCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
65 TCTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* * * * * *
11837 CCTTATCCTGTTTTAAGAATCCTGTTCAAGGTCTCTGTTAGAAAGTTTTCATTTCAAAATCCTTA
1 -CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTA
* *
11902 TCTTGTTTTAAAAATCCCGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAGAT
65 TCTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
* * * *
11957 CTTATCATGCTTCAAAAATCATGTTCGAG
1 CTTATCTTGCTTTAAAAATCCTGGTCGAG
11986 AGTTTTCAAT
Statistics
Matches: 701, Mismatches: 40, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
118 57 0.08
119 589 0.84
120 55 0.08
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (119 bp):
CTTATCTTGCTTTAAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATCCTTAT
CTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAAT
Found at i:12344 original size:29 final size:29
Alignment explanation
Indices: 12300--12567 Score: 311
Period size: 29 Copynumber: 9.2 Consensus size: 29
12290 CCTAGGGGCA
* *
12300 TTTTGCACATCTAGGGGCATTTCGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* * * *
12329 TTTTACATATCCAGGGGCACTCTGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
*
12358 TTTTGCACATCCAAGGGCATTTTGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* *
12387 ATTTGCACATCCAGGGGTATTTTGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* * *
12416 TTTTACACATCCAAGGGCATTATGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* *
12445 TTTTGCGCATCTAGGGGCATTTTGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* **
12474 ATTTGCACATTTAGGGGCATTTTGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* ** * *
12503 TTTTGCATATTTAGGGGTATTTTGGTCTT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* *
12532 TTTTGCGCATCCAGGGGCATTATGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
*
12561 CTTTGCA
1 TTTTGCA
12568 TACTCTAGGT
Statistics
Matches: 199, Mismatches: 40, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 199 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (29 bp):
TTTTGCACATCCAGGGGCATTTTGGTCAT
Found at i:12447 original size:87 final size:87
Alignment explanation
Indices: 12301--12590 Score: 364
Period size: 87 Copynumber: 3.3 Consensus size: 87
12291 CTAGGGGCAT
* * * *
12301 TTTGCACATCTAGGGGCATTTCGGTCATTTTTACATATCCAGGGGCACTCTGGTCATTTTTGCAC
1 TTTGCACATCTAGGGGCATTTTGGTCATTTTTACATATCCAGGGGCATTATGGTCATTTTTGCGC
*
12366 ATCCAAGGGCATTTTGGTCATA
66 ATCCAGGGGCATTTTGGTCATA
* * * *
12388 TTTGCACATCCAGGGGTATTTTGGTCATTTTTACACATCCAAGGGCATTATGGTCATTTTTGCGC
1 TTTGCACATCTAGGGGCATTTTGGTCATTTTTACATATCCAGGGGCATTATGGTCATTTTTGCGC
*
12453 ATCTAGGGGCATTTTGGTCATA
66 ATCCAGGGGCATTTTGGTCATA
* * ** * * *
12475 TTTGCACATTTAGGGGCATTTTGGTCATTTTTGCATATTTAGGGGTATTTTGGTCTTTTTTGCGC
1 TTTGCACATCTAGGGGCATTTTGGTCATTTTTACATATCCAGGGGCATTATGGTCATTTTTGCGC
* *
12540 ATCCAGGGGCATTATGGTCATC
66 ATCCAGGGGCATTTTGGTCATA
* ** *
12562 TTTGCATACTCTAGGTTCTTTTTGGTCAT
1 TTTGCACA-TCTAGGGGCATTTTGGTCAT
12591 CTTAATTATA
Statistics
Matches: 173, Mismatches: 29, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
87 157 0.91
88 16 0.09
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (87 bp):
TTTGCACATCTAGGGGCATTTTGGTCATTTTTACATATCCAGGGGCATTATGGTCATTTTTGCGC
ATCCAGGGGCATTTTGGTCATA
Found at i:17614 original size:23 final size:22
Alignment explanation
Indices: 17570--17614 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
17560 ACAAAATGGG
*
17570 ATTCATATGAAAAGAAAGATTA
1 ATTCATATGAAAAGAAAAATTA
17592 ATTCATTATGAAAA-AAGAAATTA
1 ATTCA-TATGAAAAGAA-AAATTA
17615 TTTTCAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (22 bp):
ATTCATATGAAAAGAAAAATTA
Found at i:20320 original size:27 final size:28
Alignment explanation
Indices: 20254--20327 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
20244 AGTGAATTTA
* *
20254 AAATGATCAAAATGCCCCTCTAAATGCTC
1 AAATGACCAAAATGCCCCTCGAAATGC-C
20283 AAATGACCAAAATGCCCCT-GAATATG-C
1 AAATGACCAAAATGCCCCTCGAA-ATGCC
20310 AAATGACCAAAATGCCCC
1 AAATGACCAAAATGCCCC
20328 CTAGGTGACC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 19 0.45
28 2 0.05
29 21 0.50
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTCGAAATGCC
Found at i:22479 original size:39 final size:40
Alignment explanation
Indices: 22423--22503 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
22413 TTTAATTCCT
22423 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
22463 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
22502 AT
1 AT
22504 TCTTAGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:22986 original size:204 final size:204
Alignment explanation
Indices: 22639--23209 Score: 1062
Period size: 204 Copynumber: 2.8 Consensus size: 204
22629 TCTTAATATC
*
22639 TTTTGAAATTTTGTTTGACATTGATC---CTTAATTTAATAAATCAACCACTAATGTTCAACTAA
1 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
22701 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
66 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
22766 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATAT
131 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATAT
22831 CTTTTATAA
196 CTTTTATAA
22840 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
1 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
22905 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
66 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
*
22970 TAGTAATCTTAGACTTAAAAAATTAATAACATTTACCATTGATAAATAAATCGGATCTTTAATAT
131 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATAT
23035 CTTTTATAA
196 CTTTTATAA
*
23044 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAC
1 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
* *
23109 TTTTTTTTTGTATAGTT-T-TATATATAATAATAATGTGTTGTATCTTATTCACTACAACTTTGT
66 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
23172 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCA
131 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCA
23210 AAGTTATTAA
Statistics
Matches: 361, Mismatches: 6, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
201 26 0.07
202 81 0.22
203 1 0.00
204 253 0.70
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (204 bp):
TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATAT
CTTTTATAA
Found at i:28501 original size:16 final size:14
Alignment explanation
Indices: 28480--28532 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
28470 TTGAGGTTAA
28480 GTTTTGAAAAAGCTTG
1 GTTTTGAAAAAG--TG
*
28496 GTTTTGAAGAAGTG
1 GTTTTGAAAAAGTG
28510 GTTTTG-AAAAGTG
1 GTTTTGAAAAAGTG
* *
28523 CTTTTTAAAA
1 GTTTTGAAAA
28533 TTAGGGTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 10 0.31
14 11 0.34
16 11 0.34
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.40
Consensus pattern (14 bp):
GTTTTGAAAAAGTG
Found at i:28513 original size:14 final size:13
Alignment explanation
Indices: 28480--28532 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
28470 TTGAGGTTAA
28480 GTTTTGAAAAAGCTTG
1 GTTTTG-AAAAG--TG
28496 GTTTTGAAGAAGTG
1 GTTTTGAA-AAGTG
28510 GTTTTGAAAAGTG
1 GTTTTGAAAAGTG
* *
28523 CTTTTTAAAA
1 GTTTTGAAAA
28533 TTAGGGTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 13 0.38
14 10 0.29
15 2 0.06
16 9 0.26
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.40
Consensus pattern (13 bp):
GTTTTGAAAAGTG
Found at i:34371 original size:28 final size:28
Alignment explanation
Indices: 34328--34402 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
34318 ACAAGGTTAA
* *
34328 AAGGGTAAAACT-GTAACTTTATC-CCTCT
1 AAGGGTAAAA-TGGTAA-TTTATCAACTCC
34356 AAGGGTAAAATGGTAATTTATCAACTCC
1 AAGGGTAAAATGGTAATTTATCAACTCC
34384 AAGGGT-AAATCGGTAATTT
1 AAGGGTAAAAT-GGTAATTT
34403 TATATCCCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 11 0.26
28 31 0.74
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (28 bp):
AAGGGTAAAATGGTAATTTATCAACTCC
Done.