Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013836.1 Corchorus olitorius cultivar O-4 contig13869, 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: 72825
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:3257 original size:21 final size:21
Alignment explanation
Indices: 3231--3385 Score: 224
Period size: 21 Copynumber: 7.4 Consensus size: 21
3221 TGCTAGGAGT
3231 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
3252 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
3273 TCATTCGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
3294 TTATTGGAAAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
3315 TCATTGGAGAAGGTACCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
3336 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
3357 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
3378 TCATTGGA
1 TCATTGGA
3386 ATTGCCTAAG
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
20 2 0.02
21 120 0.98
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:11188 original size:35 final size:36
Alignment explanation
Indices: 11142--11520 Score: 553
Period size: 35 Copynumber: 10.7 Consensus size: 36
11132 ATTTTCAGGG
11142 ATTCAGATGACTCGGTGTAGCATCTTCAAA-ATTGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
11177 ATTCAGATGACTCGGTGTAGCATCTTCAAA-ATTGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
* *
11212 ATTCGGATGACTCGGTGTAGCATCTCCAAAG-TTGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
*
11247 ATTTAGATGACTCGGTGTAGCATCTTCAAAGA-TGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
*
11282 ATTCGGATGACTCGGTGTAGCATCTTCAAAGA-TGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
* *
11317 ATTCAGATAACTAGGTGTAGCATCTTCAAAGA-TGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
*
11352 ATTCGGATGACTCGGTGTAGCATCTTCAAAGA-TGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
11387 ATTCAGATGACTCGGTGTAGCATCTTCAAAGA-TGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
* *
11422 ATTCGGATGACTCGGTGTAGCATCTTTAAAG-TTGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
* * *
11457 ATTTAGATGACTCGGTGCAGCATCTCCAAAGACATTGGA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAG--ATT-GA
11496 A-TCAGATGACTCGGTGTAGCATCTT
1 ATTCAGATGACTCGGTGTAGCATCTT
11521 TAAAAGTTGA
Statistics
Matches: 313, Mismatches: 24, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
35 287 0.92
38 23 0.07
39 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (36 bp):
ATTCAGATGACTCGGTGTAGCATCTTCAAAGATTGA
Found at i:13498 original size:19 final size:18
Alignment explanation
Indices: 13465--13500 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13455 TTGAAATAAT
13465 TCTTCAATAATCTTCAAG
1 TCTTCAATAATCTTCAAG
*
13483 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
13501 ATAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAG
Found at i:13512 original size:11 final size:12
Alignment explanation
Indices: 13481--13512 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
13471 ATAATCTTCA
13481 AGTCTTCAAATT
1 AGTCTTCAAATT
13493 A-TCTTCAAA-T
1 AGTCTTCAAATT
13503 AGTCTTCAAA
1 AGTCTTCAAA
13513 CACGAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (12 bp):
AGTCTTCAAATT
Found at i:18511 original size:30 final size:29
Alignment explanation
Indices: 18447--18526 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
18437 GAAAATATTT
* * *
18447 TTTTTCTTTTTGAGAACGCAGAAACAAATT
1 TTTTTCTTTTT-AAAACGCAAAAACAAATA
18477 TTTTTCTTTTTAAAACGCAAAAACGCAAA-A
1 TTTTTCTTTTTAAAACGCAAAAA--CAAATA
* *
18507 TTTTT-TTTCTAAAACACAAA
1 TTTTTCTTTTTAAAACGCAAA
18527 GAATAAAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 23 0.53
30 16 0.37
31 4 0.09
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (29 bp):
TTTTTCTTTTTAAAACGCAAAAACAAATA
Found at i:20626 original size:27 final size:27
Alignment explanation
Indices: 20588--20675 Score: 135
Period size: 27 Copynumber: 3.3 Consensus size: 27
20578 TTACTTCTTG
20588 TTTTGGTCATTTACATGTCCAGGGGCA
1 TTTTGGTCATTTACATGTCCAGGGGCA
*
20615 TTTTGGTCATTTGCATGTCCAGGGGCA
1 TTTTGGTCATTTACATGTCCAGGGGCA
20642 TTTTGGTCATTTGGACA--TCCAGGGGCA
1 TTTTGGTCATTT--ACATGTCCAGGGGCA
20669 TTTTGGT
1 TTTTGGT
20676 AACTTCAAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
27 55 0.96
29 2 0.04
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.39
Consensus pattern (27 bp):
TTTTGGTCATTTACATGTCCAGGGGCA
Found at i:25090 original size:30 final size:31
Alignment explanation
Indices: 25020--25104 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
25010 TTTCTTAAGC
* *
25020 AAATCCAAAAGAAGATTTTGGAAAATAAGGT
1 AAATCCAAAAGAAGATTTTGGAAAACAAAGT
*
25051 AATTCCAAAAGAAGATTTTGGAAAACAAAG-
1 AAATCCAAAAGAAGATTTTGGAAAACAAAGT
25081 AAATCCAAAAGAAGATTTTGGAAA
1 AAATCCAAAAGAAGATTTTGGAAA
25105 TTAATTGGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 23 0.46
31 27 0.54
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.21
Consensus pattern (31 bp):
AAATCCAAAAGAAGATTTTGGAAAACAAAGT
Found at i:28386 original size:36 final size:35
Alignment explanation
Indices: 28328--28552 Score: 310
Period size: 36 Copynumber: 6.3 Consensus size: 35
28318 GCATCCATGC
28328 ATTAAGTAAAAATCAGTCAAAGACTTAATTCATGGTA
1 ATTAAGT-AAAATCAGTCAAAGACTTAATTCA-GGTA
*
28365 ATTAAGTAAAATCAGTAAAAGACTTAATTCAGGTA
1 ATTAAGTAAAATCAGTCAAAGACTTAATTCAGGTA
*
28400 ATTACGTAAAATCAGTCAAAGACTTAATTCATGGTA
1 ATTAAGTAAAATCAGTCAAAGACTTAATTCA-GGTA
*
28436 ATTAAGTAAAATCAGTCAAAGACTTAATTCAGGATG
1 ATTAAGTAAAATCAGTCAAAGACTTAATTCAGG-TA
*
28472 ATTAAGTAAACTCAG-CAAAGAACTTAATTCAAGGTA
1 ATTAAGTAAAATCAGTCAAAG-ACTTAATTC-AGGTA
* *
28508 ATTAAGTAAAATCAGT-AAACAACTTAGTTCAGGGTA
1 ATTAAGTAAAATCAGTCAAA-GACTTAATTCA-GGTA
28544 ATTAAGTAA
1 ATTAAGTAA
28553 GTAACTTAAT
Statistics
Matches: 171, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
35 41 0.24
36 120 0.70
37 10 0.06
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (35 bp):
ATTAAGTAAAATCAGTCAAAGACTTAATTCAGGTA
Found at i:28522 original size:72 final size:70
Alignment explanation
Indices: 28328--28552 Score: 326
Period size: 71 Copynumber: 3.1 Consensus size: 70
28318 GCATCCATGC
28328 ATTAAGTAAAAATCAGTCAAAGACTTAATTCATGGTAATTAAGTAAAATCAGTAAAAGACTTAAT
1 ATTAAGT-AAAATCAGTCAAAGACTTAATTCATGGTAATTAAGTAAAATCAGT-AAAGACTTAAT
28393 TCAGGTA
64 TCAGGTA
*
28400 ATTACGTAAAATCAGTCAAAGACTTAATTCATGGTAATTAAGTAAAATCAGTCAAAGACTTAATT
1 ATTAAGTAAAATCAGTCAAAGACTTAATTCATGGTAATTAAGTAAAATCAGT-AAAGACTTAATT
*
28465 CAGGATG
65 CAGG-TA
* * * *
28472 ATTAAGTAAACTCAG-CAAAGAACTTAATTCAAGGTAATTAAGTAAAATCAGTAAACAACTTAGT
1 ATTAAGTAAAATCAGTCAAAG-ACTTAATTCATGGTAATTAAGTAAAATCAGTAAA-GACTTAAT
28536 TCAGGGTA
64 TCA-GGTA
28544 ATTAAGTAA
1 ATTAAGTAA
28553 GTAACTTAAT
Statistics
Matches: 140, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
71 69 0.49
72 69 0.49
73 2 0.01
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (70 bp):
ATTAAGTAAAATCAGTCAAAGACTTAATTCATGGTAATTAAGTAAAATCAGTAAAGACTTAATTC
AGGTA
Found at i:28552 original size:27 final size:27
Alignment explanation
Indices: 28521--28579 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
28511 AAGTAAAATC
* *
28521 AGTAAACAACTTAGTTCAGGGTAATTA
1 AGTAAACAACTTAATTCAGGGTAACTA
**
28548 AGTAAGTAACTTAATTCAGGGTAACTA
1 AGTAAACAACTTAATTCAGGGTAACTA
28575 AGTAA
1 AGTAA
28580 TTCAATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (27 bp):
AGTAAACAACTTAATTCAGGGTAACTA
Found at i:28589 original size:35 final size:35
Alignment explanation
Indices: 28541--28614 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
28531 TTAGTTCAGG
* *
28541 GTAATTAAGTAAGTAACTTAATTCAGGGTAACTAA
1 GTAATTAAGTAAGTAACTTAATTCAAGATAACTAA
*
28576 GTAATTCAA-TAAGTAACTTAATTCAAGATAATTAA
1 GTAATT-AAGTAAGTAACTTAATTCAAGATAACTAA
28611 GTAA
1 GTAA
28615 ATAAAATGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 33 0.94
36 2 0.06
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (35 bp):
GTAATTAAGTAAGTAACTTAATTCAAGATAACTAA
Found at i:29945 original size:14 final size:14
Alignment explanation
Indices: 29926--29954 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29916 ATTACATGGG
29926 CATGTGCCTAATTT
1 CATGTGCCTAATTT
29940 CATGTGCCTAATTT
1 CATGTGCCTAATTT
29954 C
1 C
29955 TTCACTGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (14 bp):
CATGTGCCTAATTT
Found at i:37996 original size:36 final size:36
Alignment explanation
Indices: 37956--38037 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
37946 TAATGTCCCC
**
37956 ACTTAATTACCCTGAA-CTAAGTTCTTTATTGACTTT
1 ACTTAATTACCCCAAATC-AAGTTCTTTATTGACTTT
*
37992 ACTTAATTACCCCAAATCAAGTTCTTTATTGCCTTT
1 ACTTAATTACCCCAAATCAAGTTCTTTATTGACTTT
*
38028 GCTTAATTAC
1 ACTTAATTAC
38038 TGATACGGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 40 0.98
37 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (36 bp):
ACTTAATTACCCCAAATCAAGTTCTTTATTGACTTT
Found at i:44451 original size:35 final size:35
Alignment explanation
Indices: 44381--44478 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
44371 CTCCCGGGTC
* * * *
44381 AATTACCCCGAATTAATTTCTTT-ATTGACTCTACTT
1 AATTACCCTGAATTAA-CTCTTTGACTG-CTTTACTT
* *
44417 AATTACCTTGAATTAAGTCTTTGACTGCTTTACTT
1 AATTACCCTGAATTAACTCTTTGACTGCTTTACTT
44452 AATTACCCTGAATTAACTCTTTGACTG
1 AATTACCCTGAATTAACTCTTTGACTG
44479 ATTTTGATAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 37 0.69
36 17 0.31
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (35 bp):
AATTACCCTGAATTAACTCTTTGACTGCTTTACTT
Found at i:45299 original size:21 final size:21
Alignment explanation
Indices: 45273--45314 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
45263 GAACCTTAGA
* *
45273 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTGGAAAC
45294 CAACTCCGATGAGCTGGAAAC
1 CAACTCCGATGAGCTGGAAAC
45315 TTCTTTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTGGAAAC
Found at i:45480 original size:36 final size:35
Alignment explanation
Indices: 45433--46195 Score: 810
Period size: 36 Copynumber: 21.4 Consensus size: 35
45423 TGGCGCATCA
* *
45433 GATTTTACTTAATTACCTTGAATTGAGTCTTTGGCT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTT-GCT
*
45469 GATTTTACTTAATTTCCTTGAATTAAGTCTTTCACT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTT-GCT
*
45505 GA-TGTACTTAATTTCCTTGAATTAAGTCTTTGGCT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTT-GCT
* *
45540 GATTTTACTTGATTTCCCTGAATTAAGTCTTTGCT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTTGCT
* *
45575 GATTTTACTTAAATTACCCTGAATTAAGTTCTTTGCT
1 GATTTTACTT-AATTTCCTTGAATTAAG-TCTTTGCT
* * *
45612 AATTTTACCTAATTACCTTGAATTAAGTCTTTGCT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTTGCT
* *
45647 GATTTTACCTAATTTCCTTTAAATTAAGTCTTTGCT
1 GATTTTACTTAATTTCC-TTGAATTAAGTCTTTGCT
* *
45683 GATTTTACTTAATTACCTTGAATTAAGTCTTTGATT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTTG-CT
* *
45719 GAGTTTACTTAATTACCTTGAATTAAGTCTTTGACT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTTG-CT
* *
45755 AATTTTACCTAATTTCCTTGAAATTAAGTCTTTGCTT
1 GATTTTACTTAATTTCCTTG-AATTAAGTCTTTGC-T
* * *
45792 GAATTTACTTAATTACATTGAATTAAGTCTTTGACT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTTG-CT
* *
45828 -AATTTACTTAATTACCTTGAATTAAGTCTTTGCCT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTTG-CT
* *
45863 GAGTTTACTTAATGTCCTTGAAATTAAGTCTTTGCTT
1 GATTTTACTTAATTTCCTTG-AATTAAGTCTTTGC-T
* * *
45900 GGTTTTACCTAATTTCCTTGAAATTAAGTCTTTGTTT
1 GATTTTACTTAATTTCCTTG-AATTAAGTCTTTG-CT
* *
45937 GATTTTACCTAATTTCCGTGAAATTAAGTCTTTGC-
1 GATTTTACTTAATTTCCTTG-AATTAAGTCTTTGCT
* *
45972 ---TTGA--T--TTTCCTTGAAATTAAGTCTTTGAT
1 GATTTTACTTAATTTCCTTG-AATTAAGTCTTTGCT
* *
46001 GATTTTACCTAATTTCCTTGAAATTAAGTCTTTGAT
1 GATTTTACTTAATTTCCTTG-AATTAAGTCTTTGCT
46037 GATTTTAAC-TAATTTCCTTGAAATTAAGTCTTTGCTT
1 GATTTT-ACTTAATTTCCTTG-AATTAAGTCTTTGC-T
* * *
46074 GATTTTACCTAATTTCCTTGAAATTAAGTCTTCGAT
1 GATTTTACTTAATTTCCTTG-AATTAAGTCTTTGCT
* *
46110 GATTTTACCTAATTTCCTTGAAATTAATTCTTTGCTT
1 GATTTTACTTAATTTCCTTG-AATTAAGTCTTTGC-T
* * ** *
46147 GAGTTTACTTAATTACCTCAAATTAAGTCTTTGGTT
1 GATTTTACTTAATTTCCTTGAATTAAGTCTTT-GCT
46183 GATTTTACTTAAT
1 GATTTTACTTAAT
46196 ACATGGATGC
Statistics
Matches: 638, Mismatches: 64, Indels: 50
0.85 0.09 0.07
Matches are distributed among these distances:
28 21 0.03
30 1 0.00
32 6 0.01
34 1 0.00
35 116 0.18
36 320 0.50
37 173 0.27
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (35 bp):
GATTTTACTTAATTTCCTTGAATTAAGTCTTTGCT
Found at i:46003 original size:27 final size:28
Alignment explanation
Indices: 45949--46006 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
45939 TTTTACCTAA
*
45949 TTTCCGTGAAATTAAGTCTTTGCTTGAT
1 TTTCCGTGAAATTAAGTCTTTGCATGAT
*
45977 TTTCCTTGAAATTAAGTCTTTG-ATGAT
1 TTTCCGTGAAATTAAGTCTTTGCATGAT
46004 TTT
1 TTT
46007 ACCTAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (28 bp):
TTTCCGTGAAATTAAGTCTTTGCATGAT
Found at i:46186 original size:73 final size:73
Alignment explanation
Indices: 45977--46195 Score: 325
Period size: 73 Copynumber: 3.0 Consensus size: 73
45967 TTTGCTTGAT
*
45977 TTTCCTTGAAATTAAGTCTTTG-ATGATTTTACCTAATTTCCTTGAAATTAAGTCTTTGATGATT
1 TTTCCTTGAAATTAAGTCTTTGCTTGATTTTACCTAATTTCCTTGAAATTAAGTCTTTGATGATT
*
46041 TTAACTAA
66 TTACCTAA
*
46049 TTTCCTTGAAATTAAGTCTTTGCTTGATTTTACCTAATTTCCTTGAAATTAAGTCTTCGATGATT
1 TTTCCTTGAAATTAAGTCTTTGCTTGATTTTACCTAATTTCCTTGAAATTAAGTCTTTGATGATT
46114 TTACCTAA
66 TTACCTAA
* * * * * *
46122 TTTCCTTGAAATTAATTCTTTGCTTGAGTTTACTTAATTACC-TCAAATTAAGTCTTTGGTTGAT
1 TTTCCTTGAAATTAAGTCTTTGCTTGATTTTACCTAATTTCCTTGAAATTAAGTCTTT-GATGAT
*
46186 TTTACTTAA
65 TTTACCTAA
46195 T
1 T
46196 ACATGGATGC
Statistics
Matches: 134, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
72 35 0.26
73 99 0.74
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (73 bp):
TTTCCTTGAAATTAAGTCTTTGCTTGATTTTACCTAATTTCCTTGAAATTAAGTCTTTGATGATT
TTACCTAA
Found at i:50092 original size:46 final size:46
Alignment explanation
Indices: 50035--50130 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
50025 GAGTTCCCCT
* *
50035 TTATAATTACTTCTTCCTTCTTCCAAGAAACTAAATGGTGATTGGC
1 TTATAAGTACTTCTTCCTTCTTCCAAGAAACTAAATGATGATTGGC
* *
50081 TTATAAGTACTTCTTCTTTCTTCCAAGATACTAAATGATGATTGGC
1 TTATAAGTACTTCTTCCTTCTTCCAAGAAACTAAATGATGATTGGC
50127 TTAT
1 TTAT
50131 TTGATGAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (46 bp):
TTATAAGTACTTCTTCCTTCTTCCAAGAAACTAAATGATGATTGGC
Found at i:69535 original size:9 final size:9
Alignment explanation
Indices: 69521--69546 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
69511 GGTGCGACTG
69521 AGCTAGGGC
1 AGCTAGGGC
69530 AGCTAGGGC
1 AGCTAGGGC
69539 AGCTAGGG
1 AGCTAGGG
69547 TTTCTCCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.46, T:0.12
Consensus pattern (9 bp):
AGCTAGGGC
Found at i:69579 original size:17 final size:16
Alignment explanation
Indices: 69557--69599 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
69547 TTTCTCCAGC
69557 GGAGGAAGATGAGTCGA
1 GGAGGAAGATGAG-CGA
*
69574 GGAGGAGAGATGTGCGA
1 GGAGGA-AGATGAGCGA
*
69591 GGAAGAAGA
1 GGAGGAAGA
69600 AGGCTTAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 14 0.61
18 6 0.26
ACGTcount: A:0.37, C:0.05, G:0.49, T:0.09
Consensus pattern (16 bp):
GGAGGAAGATGAGCGA
Done.