Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012931.1 Corchorus olitorius cultivar O-4 contig12964, 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: 54121
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:8823 original size:31 final size:32
Alignment explanation
Indices: 8769--8830 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
8759 CATATGCACA
8769 TTTTTCGGTATTTTTTTTACAATATTTTTCGG
1 TTTTTCGGTATTTTTTTTACAATATTTTTCGG
8801 TTTTTCGGTATTTTTTTT-CAATATTTTTCG
1 TTTTTCGGTATTTTTTTTACAATATTTTTCG
8831 AGACCTTGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.15, C:0.10, G:0.11, T:0.65
Consensus pattern (32 bp):
TTTTTCGGTATTTTTTTTACAATATTTTTCGG
Found at i:9490 original size:20 final size:20
Alignment explanation
Indices: 9465--9504 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9455 TAGAAATTCA
9465 TAAGTGTTATGGAAATCATG
1 TAAGTGTTATGGAAATCATG
9485 TAAGTGTTATGGAAATCATG
1 TAAGTGTTATGGAAATCATG
9505 GAATGGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (20 bp):
TAAGTGTTATGGAAATCATG
Found at i:16652 original size:177 final size:177
Alignment explanation
Indices: 16304--16774 Score: 532
Period size: 177 Copynumber: 2.7 Consensus size: 177
16294 AATACAATCC
* * * * * * * * * *
16304 ACCGAAATAACAAATTTTTCAGAAGCATTTTTGGTATTTGAAATATCAAATTTAGCTTTCGAATC
1 ACCGAAACAACTAATTTTTCGGAAACATTTTT-ATACTTGAAACATTAAATTTAGCTTTTGAGTC
* * * * * *
16369 CTTCATGAAAATTGTAGATCACGGGACAACCTTTTAACAGATACTTGAATCACCTTAATCGGAAA
65 CTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGACACTTGAATCACCTCAATCAGAAA
* * * **
16434 TCTGGTGCAAAAATTATGTAATATTAAGTGAACGGTCCATTCCTAG-TA
130 TCTAGAGCAAAAATTATGTAATACTAAGTGAACCATCCATTCC-AGTTA
* * * *
16482 ACCGAAACAACTAATTTTTTGGAAGA-TTTTTTATTCTTGAGACATTAAATTTAGCTTTTGAGTC
1 ACCGAAACAACTAATTTTTCGGAA-ACATTTTTATACTTGAAACATTAAATTTAGCTTTTGAGTC
* * ** * *
16546 CTTTATGAAAGTTGTAGATCATGGAACAACCTTTTAAGAGACAAATGAATCACCTCAATTAGACA
65 CTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGACACTTGAATCACCTCAATCAGAAA
* * * *
16611 TCTAGAGTAAAAGTTATGTAATACTAAGTGGACCATCCATTCCCGTTA
130 TCTAGAGCAAAAATTATGTAATACTAAGTGAACCATCCATTCCAGTTA
* * * *
16659 ACTGAAATAACTAATTTTTCGGAAACATTTTTATACTTGAAACATTAAATTTAGTTTTTGAGTTC
1 ACCGAAACAACTAATTTTTCGGAAACATTTTTATACTTGAAACATTAAATTTAGCTTTTGAGTCC
* *
16724 TTCATGAAAGTTGTAGATCATGGAATAACCTTTTAATAGACACTTGAATCA
66 TTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGACACTTGAATCA
16775 TCTTGATAGA
Statistics
Matches: 242, Mismatches: 48, Indels: 7
0.81 0.16 0.02
Matches are distributed among these distances:
176 2 0.01
177 215 0.89
178 25 0.10
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (177 bp):
ACCGAAACAACTAATTTTTCGGAAACATTTTTATACTTGAAACATTAAATTTAGCTTTTGAGTCC
TTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGACACTTGAATCACCTCAATCAGAAAT
CTAGAGCAAAAATTATGTAATACTAAGTGAACCATCCATTCCAGTTA
Found at i:18154 original size:150 final size:151
Alignment explanation
Indices: 17983--18283 Score: 419
Period size: 151 Copynumber: 2.0 Consensus size: 151
17973 CGCGTTGTTT
*
17983 AGGTTTCCCTC-TCTTTTTTTTTCAGCACAAAATTGG-AAAATTATCTGAAAATTAACTATAACG
1 AGGTTTCCCTCTTCTTTTTTTTTCAGCACAAAATTGGAAAAATTAGCTGAAAATTAACTATAACG
* * * * * *
18046 GCGTTTGTTATATAGGACACGCCGTTATAGTTGTTAGTATTGCGGCATTTATAGT-TAAAAACGC
66 GCGTTTGTTAT-T-GGAAACGCCGTAATAGTCGTTAGTATGGCGGCATTTATACTAAAAAAACGC
18110 CACCATCCTTAAGGCAAAACTTA
129 CACCATCCTTAAGGCAAAACTTA
* * ** *
18133 AGGTTTCCCTCTTTTTTTTTTTTCGGTGCAAAATTGGAAAAATTAGCTGAAAATTAACTATAATG
1 AGGTTTCCCTCTTCTTTTTTTTTCAGCACAAAATTGGAAAAATTAGCTGAAAATTAACTATAACG
* * * *
18198 GCGTTTGTTATTGGAAACGCCGTAATAGTCGTTAGTGTGGCGGCTTTTGTACTAAAAAAACGCCG
66 GCGTTTGTTATTGGAAACGCCGTAATAGTCGTTAGTATGGCGGCATTTATACTAAAAAAACGCCA
18263 CCATCCTTAAGGCAAAACTTA
131 CCATCCTTAAGGCAAAACTTA
18284 TGGTGCAAAA
Statistics
Matches: 132, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
150 44 0.33
151 52 0.39
152 36 0.27
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (151 bp):
AGGTTTCCCTCTTCTTTTTTTTTCAGCACAAAATTGGAAAAATTAGCTGAAAATTAACTATAACG
GCGTTTGTTATTGGAAACGCCGTAATAGTCGTTAGTATGGCGGCATTTATACTAAAAAAACGCCA
CCATCCTTAAGGCAAAACTTA
Found at i:18314 original size:127 final size:127
Alignment explanation
Indices: 18157--18398 Score: 371
Period size: 127 Copynumber: 1.9 Consensus size: 127
18147 TTTTTTTTTC
* *
18157 GGTGCAAAATTGGAAAAATTAGCTGAAAATTAACTATAATGGCGTTTGTTATTGG-AAACGCCGT
1 GGTGCAAAATTGGAAAAATTAGCTGAAAATTAACTATAACGGCGTTTGGTA-TGGCAAACGCCGT
* * *
18221 AATAGTCGTTAGTGTGGCGGCTTTTGTACTAAAAAAACGCCGCCATCCTTAAGGCAAAACTTAT
65 AAAAGTCGTTAGTGTGGCGGCGTTTGTA-TAAAAAAACGCCACCATCCTTAAGGCAAAACTTAT
*
18285 GGTGCAAAATT-GAAAAATTAGCTGAAAATTAACTATAACGGCGTTTGGTATGGCAAATGCCGTA
1 GGTGCAAAATTGGAAAAATTAGCTGAAAATTAACTATAACGGCGTTTGGTATGGCAAACGCCGTA
* **
18349 AAAGTTGTTAGTGTGGCGGCGTTTGTATTTAAAAACGCCACCATCCTTAA
66 AAAGTCGTTAGTGTGGCGGCGTTTGTATAAAAAAACGCCACCATCCTTAA
18399 AAAAAATAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
126 23 0.22
127 70 0.67
128 11 0.11
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (127 bp):
GGTGCAAAATTGGAAAAATTAGCTGAAAATTAACTATAACGGCGTTTGGTATGGCAAACGCCGTA
AAAGTCGTTAGTGTGGCGGCGTTTGTATAAAAAAACGCCACCATCCTTAAGGCAAAACTTAT
Found at i:23095 original size:5 final size:5
Alignment explanation
Indices: 23085--23109 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
23075 TTTAAATGTT
23085 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
23110 TTAGTATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:23237 original size:22 final size:22
Alignment explanation
Indices: 23212--23311 Score: 114
Period size: 22 Copynumber: 4.6 Consensus size: 22
23202 TATTTTTATC
*
23212 AAATTTTGATAACTACCCTATT
1 AAATTTTGATAACTACCCTATG
* *
23234 AAATTTTGATAACCACGCTATG
1 AAATTTTGATAACTACCCTATG
*
23256 AAATTTTGATAATTA-CCTATG
1 AAATTTTGATAACTACCCTATG
* *
23277 AAATTGTGATAAACT-CCATATG
1 AAATTTTGAT-AACTACCCTATG
*
23299 AAACTTTGATAAC
1 AAATTTTGATAAC
23312 CTAAATATGA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
21 17 0.26
22 48 0.74
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACTACCCTATG
Found at i:23287 original size:43 final size:44
Alignment explanation
Indices: 23212--23311 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 44
23202 TATTTTTATC
* * *
23212 AAATTTTGATAACTACCCTATTAAATTTTGATAACCACGC-TATG
1 AAATTTTGATAACTACCCTATGAAATTGTGATAAACAC-CATATG
* *
23256 AAATTTTGATAATTA-CCTATGAAATTGTGATAAACTCCATATG
1 AAATTTTGATAACTACCCTATGAAATTGTGATAAACACCATATG
*
23299 AAACTTTGATAAC
1 AAATTTTGATAAC
23312 CTAAATATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.02
43 33 0.69
44 14 0.29
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAACTACCCTATGAAATTGTGATAAACACCATATG
Found at i:24387 original size:28 final size:28
Alignment explanation
Indices: 24330--24404 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
24320 AGGGTCACCT
** **
24330 AGGGGCATTTTAATCA-TTTGCATGTCC
1 AGGGGCATTTTGGTCATTTTGCACATCC
*
24357 AGGGGCATTTTGGTCATTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTGCACATCC
24385 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
24405 AAGTTCACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 14 0.33
28 28 0.67
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGCACATCC
Found at i:32184 original size:13 final size:12
Alignment explanation
Indices: 32140--32186 Score: 60
Period size: 11 Copynumber: 3.9 Consensus size: 12
32130 AAATTCCCAT
32140 AAAAAAATGAA-
1 AAAAAAATGAAG
32151 AAAAAAATGAAG
1 AAAAAAATGAAG
*
32163 AAAAGAATGAATG
1 AAAAAAATGAA-G
*
32176 AAAACAATGAA
1 AAAAAAATGAA
32187 AGAATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 11 0.34
12 10 0.31
13 11 0.34
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (12 bp):
AAAAAAATGAAG
Found at i:32610 original size:15 final size:14
Alignment explanation
Indices: 32591--32617 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32581 TCCACTCCAA
32591 AAAAAAAATCAAAT
1 AAAAAAAATCAAAT
32605 AAAAAAAATCAAA
1 AAAAAAAATCAAA
32618 AAATTGAAAG
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:0.81, C:0.07, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAAATCAAAT
Found at i:33696 original size:169 final size:169
Alignment explanation
Indices: 33406--33804 Score: 521
Period size: 169 Copynumber: 2.4 Consensus size: 169
33396 TTCCATATAA
* * * * * **
33406 GTTAAG-TTAAAATCCTTGTTTAAGGCCTCTATTTAGAGTCTGCATTGTTAAGACCTCCGAACAC
1 GTTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGACCTCCGGGCAC
*
33470 AAAGTCAGAAACCTCTGGGTATTAATTCTGATAAGACCTCCGGGCAATTAATAAAACCTCCGGGT
66 AAAGTCAGAAACCTCCGGGTATTAATTCTGATAAGACCTCCGGGCAATTAATAAAACCTCCGGGT
*
33535 ACCATGTCATTTCACCAAGTTTTTAATCAAAGATTCATG
131 ACCATGTCATTTCACCAAGTTTTTAATCAAAAATTCATG
* * * * *
33574 TTTAAGTTTAAAATCCTTGGTCAAGGTCTCTGTTCAGAGTTTACATTGGTAAGACCTTCGGGCAC
1 GTTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGACCTCCGGGCAC
* * * **
33639 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCTGGGCAATTGGTAAAACCTCCGGGT
66 AAAGTCAGAAACCTCCGGGTATTAATTCTGATAAGACCTCCGGGCAATTAATAAAACCTCCGGGT
* * * * *
33704 ACCATTTCATTTCATCGAGTTTTTCATTAAAAATTCATG
131 ACCATGTCATTTCACCAAGTTTTTAATCAAAAATTCATG
* * * * * *
33743 GTTAAGTTTTAAATACTTGTTCAAGGTCTCAATTCAAAGCTTGCATTGGTAAGTCCTCCGGG
1 GTTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGACCTCCGGG
33805 TATTAATTCG
Statistics
Matches: 195, Mismatches: 35, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
168 5 0.03
169 190 0.97
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (169 bp):
GTTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGACCTCCGGGCAC
AAAGTCAGAAACCTCCGGGTATTAATTCTGATAAGACCTCCGGGCAATTAATAAAACCTCCGGGT
ACCATGTCATTTCACCAAGTTTTTAATCAAAAATTCATG
Found at i:33840 original size:20 final size:20
Alignment explanation
Indices: 33815--33854 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
33805 TATTAATTCG
* *
33815 GATAAGTCCTCCGGGCATTT
1 GATAAGACCTCCAGGCATTT
33835 GATAAGACCTCCAGGCATTT
1 GATAAGACCTCCAGGCATTT
33855 CATATCTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (20 bp):
GATAAGACCTCCAGGCATTT
Found at i:34018 original size:63 final size:63
Alignment explanation
Indices: 33898--34019 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 63
33888 TAATTTTCGA
** * * *
33898 TCCTGGTTTAGGATCATTACTTTATCAGTTTAATCTTGATTTAGGATCATTGGTTTATTTCAT
1 TCCTGGTTTAGGATCATTACTTTATCAGGATAATCCTGATTCAGGATCATTGCTTTATTTCAT
* * *
33961 TCCTGGTTTAGGATCTTTGCTTTAT-TGGATAATCCTG-TTCAGGATCATTTTGCTTTATT
1 TCCTGGTTTAGGATCATTACTTTATCAGGATAATCCTGATTCAGGATCA--TTGCTTTATT
34020 AGTTAATATC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
61 9 0.18
62 8 0.16
63 32 0.65
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (63 bp):
TCCTGGTTTAGGATCATTACTTTATCAGGATAATCCTGATTCAGGATCATTGCTTTATTTCAT
Found at i:34514 original size:21 final size:21
Alignment explanation
Indices: 34488--34529 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
34478 ACGCAAAGAA
*
34488 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCGCATCGGAGTTG
34509 GTTTCAAGCGCATCGGAGTTG
1 GTTTCAAGCGCATCGGAGTTG
34530 CCTAAGGTGC
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:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (21 bp):
GTTTCAAGCGCATCGGAGTTG
Found at i:35429 original size:25 final size:24
Alignment explanation
Indices: 35393--35439 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
35383 TCCTTCTATT
35393 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
35416 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
35440 AATTTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:35465 original size:9 final size:8
Alignment explanation
Indices: 35450--35487 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
35440 AATTTTTAAG
35450 ATTCAAAA
1 ATTCAAAA
35458 ATTCCAAAA
1 ATT-CAAAA
35467 ATTCAAAA
1 ATTCAAAA
35475 ATTCAAAA
1 ATTCAAAA
35483 ATTCA
1 ATTCA
35488 TTGTGGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (8 bp):
ATTCAAAA
Found at i:35470 original size:17 final size:16
Alignment explanation
Indices: 35450--35487 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
35440 AATTTTTAAG
35450 ATTCAAAAATTCCAAAA
1 ATTCAAAAATT-CAAAA
35467 ATTCAAAAATTCAAAA
1 ATTCAAAAATTCAAAA
35483 ATTCA
1 ATTCA
35488 TTGTGGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTCAAAAATTCAAAA
Found at i:36413 original size:15 final size:15
Alignment explanation
Indices: 36393--36421 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36383 TGGAGGTTCG
36393 AAATCAACAAGCTCA
1 AAATCAACAAGCTCA
36408 AAATCAACAAGCTC
1 AAATCAACAAGCTC
36422 CACTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATCAACAAGCTCA
Found at i:37061 original size:33 final size:33
Alignment explanation
Indices: 37008--37088 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
36998 GTGTTTTAGA
** *
37008 TGTTGTTTGCAATGATACTAAACCTAATTTGA-G
1 TGTTGTTTGTGATGACACTAAACCT-ATTTGAGG
* * *
37041 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
1 TGTTGTTTGTGATGACACTAAACCTATTTGAGG
37074 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
37089 AACAAATTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 4 0.10
33 37 0.90
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAACCTATTTGAGG
Found at i:37100 original size:33 final size:31
Alignment explanation
Indices: 37035--37138 Score: 127
Period size: 33 Copynumber: 3.2 Consensus size: 31
37025 CTAAACCTAA
*
37035 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT
1 TTTG-GTGTTGTTTGTGATGAAAC-AAATCTGT
37068 TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
1 TTT-GGTGTTGTTTGTGATGAAACAAA-TCTGT
* **
37101 TATGGATGTTAATTGTGATGAAACAAATCTGT
1 TTTGG-TGTTGTTTGTGATGAAACAAATCTGT
37133 TTTGGT
1 TTTGGT
37139 TGATCATAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
31 1 0.02
32 14 0.22
33 47 0.75
34 1 0.02
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (31 bp):
TTTGGTGTTGTTTGTGATGAAACAAATCTGT
Found at i:37648 original size:15 final size:15
Alignment explanation
Indices: 37628--37665 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
37618 AATTATATGC
37628 TAGTGATGCTTACTT
1 TAGTGATGCTTACTT
37643 TAGTGATGCTTACTT
1 TAGTGATGCTTACTT
37658 TAGTGATG
1 TAGTGATG
37666 TGTTTAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.45
Consensus pattern (15 bp):
TAGTGATGCTTACTT
Found at i:38981 original size:21 final size:21
Alignment explanation
Indices: 38955--38996 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
38945 GATTGAAGAA
38955 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
38976 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
38997 CCTAAGGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:41435 original size:14 final size:14
Alignment explanation
Indices: 41418--41498 Score: 72
Period size: 14 Copynumber: 5.5 Consensus size: 14
41408 AAAATGTTTC
41418 TTCTGAAATATGGA
1 TTCTGAAATATGGA
* * **
41432 TTCTCAATGTATATA
1 TTCTGAA-ATATGGA
*
41447 TACTGAAATATGGA
1 TTCTGAAATATGGA
*
41461 CTGTTTTGAAATATGGA
1 ---TTCTGAAATATGGA
41478 TTCTGAAATATGGA
1 TTCTGAAATATGGA
41492 TTCTGAA
1 TTCTGAA
41499 TTCTGAAGTT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
14 30 0.59
15 9 0.18
17 12 0.24
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (14 bp):
TTCTGAAATATGGA
Found at i:49802 original size:133 final size:133
Alignment explanation
Indices: 49564--49815 Score: 468
Period size: 133 Copynumber: 1.9 Consensus size: 133
49554 TAATAATCAA
49564 GGATTAGGATTAAAAGCAACCATATTTTTCTTCTGGACCCACTAGATTTAGTTAGACTAGAGGCA
1 GGATTAGGATTAAAAGCAACCATATTTTTCTTCTGGACCCACTAGATTTAGTTAGACTAGAGGCA
*
49629 CCATCATTTGACAGGCGACTCGGGGGTGCTAATCCTTCCCCGGGCGTGATCAACCATATTTTTCT
66 CCATCATTTGACAGGCGACTCGGGGGTGCTAATCCTTCCCCGGGCGTAATCAACCATATTTTTCT
49694 TCT
131 TCT
*
49697 GGATTAGGATTAAAAGCAACCATATTTTTCTTCTGGACCCACTAGATTTAGTTAGACTAGAGGTA
1 GGATTAGGATTAAAAGCAACCATATTTTTCTTCTGGACCCACTAGATTTAGTTAGACTAGAGGCA
* *
49762 CCATCATTTGACGGGCGACTCGGGGGTGTTAATCCTTCCCCGGGCGTAATCAAC
66 CCATCATTTGACAGGCGACTCGGGGGTGCTAATCCTTCCCCGGGCGTAATCAAC
49816 TCCCGAACCT
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 115 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (133 bp):
GGATTAGGATTAAAAGCAACCATATTTTTCTTCTGGACCCACTAGATTTAGTTAGACTAGAGGCA
CCATCATTTGACAGGCGACTCGGGGGTGCTAATCCTTCCCCGGGCGTAATCAACCATATTTTTCT
TCT
Found at i:51689 original size:11 final size:12
Alignment explanation
Indices: 51663--51689 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
51653 AGATAATTTC
51663 TTTTCTTCTAGT
1 TTTTCTTCTAGT
51675 TTTTCTTCTAGT
1 TTTTCTTCTAGT
51687 TTT
1 TTT
51690 AGGCTAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTCTTCTAGT
Found at i:52479 original size:15 final size:16
Alignment explanation
Indices: 52449--52488 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
52439 TTACTTTGCT
52449 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
52465 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
52480 TTGCTTTCT
1 TTGTTTTCT
52489 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Done.