Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014642.1 Corchorus olitorius cultivar O-4 contig14675, 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: 124724
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1563 original size:156 final size:159
Alignment explanation
Indices: 1259--1576 Score: 511
Period size: 156 Copynumber: 2.0 Consensus size: 159
1249 AATAGATATC
1259 GCAGCAACCATCAAAGGTAACTCTCTTTCCCTACATAATATACCCACAAAGAGTTATAAAAATGA
1 GCAGCAACCATCAAAGGTAACTCTCTTTCCCTACATAATATACCCACAAAGAGTTATAAAAA-GA
**
1324 AAAATATAAAGTATAAAGTACTGCTTTTTTATTTGTTAAGAAAAAACAATAAAGTATTTACCTCT
65 AAAATAT--A-TATAAAGTACTGCTTTTTTATTTGTTAAGAAAAAACAATAAAGTATAAACCTCT
1389 TGGTGAGAAGGAGTTAAGGAGAGCCAAATTATT
127 TGGTGAGAAGGAGTTAAGGAGAGCCAAATTATT
* *
1422 GCAGCAACCATCAAAGGTAACTCTCTTTCCCTACATAATATACCCACAGAGAGTTATAAAAA-AG
1 GCAGCAACCATCAAAGGTAACTCTCTTTCCCTACATAATATACCCACAAAGAGTTATAAAAAGAA
1486 AAA-AT-TATAAAGTACTG-TTGTTTTATTTGTTAA-AACAAAACAATAAAGTATAAACCTCTTG
66 AAATATATATAAAGTACTGCTT-TTTTATTTGTTAAGAA-AAAACAATAAAGTATAAACCTCTTG
1547 GTGAGAAGGAGTTAAGGAGAGCCAAATTAT
129 GTGAGAAGGAGTTAAGGAGAGCCAAATTAT
1577 GGTTCCAAGG
Statistics
Matches: 149, Mismatches: 4, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
155 4 0.03
156 78 0.52
160 2 0.01
161 4 0.03
163 61 0.41
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (159 bp):
GCAGCAACCATCAAAGGTAACTCTCTTTCCCTACATAATATACCCACAAAGAGTTATAAAAAGAA
AAATATATATAAAGTACTGCTTTTTTATTTGTTAAGAAAAAACAATAAAGTATAAACCTCTTGGT
GAGAAGGAGTTAAGGAGAGCCAAATTATT
Found at i:8498 original size:117 final size:116
Alignment explanation
Indices: 8291--8500 Score: 332
Period size: 117 Copynumber: 1.8 Consensus size: 116
8281 ACTTTAAATG
* * *
8291 ACAAAACTCCTCCTTTTCCTCTTCTAAGTCCAACTCAACCAATTTAAACACCTCATTTTCCTACC
1 ACAAAACTCCTACTTTTCCTCTTCTAAGTCCAACTCAACAAATTTAAACACCTCACTTTCCTACC
8356 CAAAGAGAATTGCTCAAAAGCAAATTACGGAATCAAATTGAATTCTTAATA
66 CAAAGAGAATTGCTCAAAAGCAAATTACGGAATCAAATTGAATTCTTAATA
* *
8407 ACAAAACTCCTACTTTTCCTCTTCTAAGTCCGACTCAAGCAAATTTAAACGTCC-CACTTTCCTA
1 ACAAAACTCCTACTTTTCCTCTTCTAAGTCCAACTCAA-CAAATTTAAAC-ACCTCACTTTCCTA
* *
8471 CCCAAAGAGATTTGCTCAAAATCAAATTAC
64 CCCAAAGAGAATTGCTCAAAAGCAAATTAC
8501 AGTTACAACA
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
116 36 0.42
117 47 0.55
118 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.07, T:0.29
Consensus pattern (116 bp):
ACAAAACTCCTACTTTTCCTCTTCTAAGTCCAACTCAACAAATTTAAACACCTCACTTTCCTACC
CAAAGAGAATTGCTCAAAAGCAAATTACGGAATCAAATTGAATTCTTAATA
Found at i:19568 original size:84 final size:84
Alignment explanation
Indices: 19422--19591 Score: 279
Period size: 84 Copynumber: 2.0 Consensus size: 84
19412 GCGTACACAG
*
19422 CTACCCCCGTTCGGAGACTCACCCACCAAAATCAGGTGCACGACGTGGATCGAATTCAGATTAAT
1 CTACCCCCGTTCGGAGACTCACCCACCAAAATCAGGTGCACGACGCGGATCGAATTCAGATTAAT
*
19487 CAGAACAAAGCTTTGAATA
66 CAGAACAAAACTTTGAATA
* *
19506 CTACCCCCGTT-GGAAGACTCACCCACCAAAATCAGGTGCACGACGCGGGTCGAATTCGGATTAA
1 CTACCCCCGTTCGG-AGACTCACCCACCAAAATCAGGTGCACGACGCGGATCGAATTCAGATTAA
*
19570 TCAGAACAAAATTTTGAATA
65 TCAGAACAAAACTTTGAATA
19590 CT
1 CT
19592 GGATGGGGTA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 2 0.03
84 78 0.98
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (84 bp):
CTACCCCCGTTCGGAGACTCACCCACCAAAATCAGGTGCACGACGCGGATCGAATTCAGATTAAT
CAGAACAAAACTTTGAATA
Found at i:21155 original size:52 final size:52
Alignment explanation
Indices: 21077--21181 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
21067 AATGTTGCAG
21077 TTTGTTTGATGCTATCTAATGCTTTCATTACCTTTGCACCTAACATGTGCCA
1 TTTGTTTGATGCTATCTAATGCTTTCATTACCTTTGCACCTAACATGTGCCA
21129 TTTGTTTGATGCTATCTAATGCTTTCATTACCTTTGCACCTAACATGTGCCA
1 TTTGTTTGATGCTATCTAATGCTTTCATTACCTTTGCACCTAACATGTGCCA
21181 T
1 T
21182 CAACAGGTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (52 bp):
TTTGTTTGATGCTATCTAATGCTTTCATTACCTTTGCACCTAACATGTGCCA
Found at i:21164 original size:28 final size:28
Alignment explanation
Indices: 21081--21164 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
21071 TTGCAGTTTG
21081 TTTGATGCTATCTAATGCTTTCATTACC
1 TTTGATGCTATCTAATGCTTTCATTACC
* * ** **
21109 TTTGCA-CCTAAC--ATG-TGCCATT-TG
1 TTTG-ATGCTATCTAATGCTTTCATTACC
21133 TTTGATGCTATCTAATGCTTTCATTACC
1 TTTGATGCTATCTAATGCTTTCATTACC
21161 TTTG
1 TTTG
21165 CACCTAACAT
Statistics
Matches: 38, Mismatches: 12, Indels: 12
0.61 0.19 0.19
Matches are distributed among these distances:
23 1 0.03
24 8 0.21
25 5 0.13
26 6 0.16
27 5 0.13
28 12 0.32
29 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.45
Consensus pattern (28 bp):
TTTGATGCTATCTAATGCTTTCATTACC
Found at i:28802 original size:12 final size:12
Alignment explanation
Indices: 28785--28809 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28775 ATTCCTTCCA
28785 AATAATATATAT
1 AATAATATATAT
28797 AATAATATATAT
1 AATAATATATAT
28809 A
1 A
28810 GTTAATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAATATATAT
Found at i:29558 original size:76 final size:76
Alignment explanation
Indices: 29466--29606 Score: 210
Period size: 76 Copynumber: 1.9 Consensus size: 76
29456 GGTTACCAAT
* * ** * *
29466 CACATCGGTTTCGATTAAACTGAACTCAAGTTGTGTCAGATTTTATATAGTGTAAGATCTTAACT
1 CACATCGATTTCGATTAAACTGAACTCAAGTTATGTCAGATTCCATATAATGTAAGATCCTAACT
29531 CGAATGGTAAC
66 CGAATGGTAAC
* *
29542 CACATCGATTTCGATTAATCTGAACTCAAGTTATGTCAGATTCCATATAATGTAAGGTCCTAACT
1 CACATCGATTTCGATTAAACTGAACTCAAGTTATGTCAGATTCCATATAATGTAAGATCCTAACT
29607 TGAACCCGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 57 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (76 bp):
CACATCGATTTCGATTAAACTGAACTCAAGTTATGTCAGATTCCATATAATGTAAGATCCTAACT
CGAATGGTAAC
Found at i:30670 original size:6 final size:6
Alignment explanation
Indices: 30659--30683 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30649 TTGGTACAAG
30659 ATTATA ATTATA ATTATA ATTATA A
1 ATTATA ATTATA ATTATA ATTATA A
30684 AGATGGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:38546 original size:190 final size:189
Alignment explanation
Indices: 38038--38613 Score: 893
Period size: 190 Copynumber: 3.0 Consensus size: 189
38028 TATTTCTAAC
* * * *
38038 ATTGGGTGCCTCTATACACCTTAGAAAAAGGATATGTCAAAATTGAGATTCGAATCTCAGACTTC
1 ATTGGGTGCCTTTATACACCTTAGAAAAAGGATATGTCAAAATTGAGATTCGAAACTCAGACCTG
* * *
38103 TTACAATCTTCATCTTAAACGTGATCCGTCATTTTATTGCCTAATCAAGATAATTAACATT-AGT
66 TTAAAATC-T--TC-GAAACGTGATCCGTCATTTGATTGCCTAATCAAGATAATTAACATTGA-T
*
38167 CATCTGCATAAACAAAATTTTTAATTATTCTAGTATTGGATTTGAACCTTATGCAAATTCCCAA
126 CATTTGCATAAACAAAATTTTTAATTATTCTAGTATTGGATTTGAACCTTATGCAAATTCCCAA
* *
38231 ATTGGGTGCCTCTATATATACACCTTAGAAAAAGGATATGTCAGAATTGAGATTCGAAACTCAAA
1 ATTGGGTG-C-CT-T-TATACACCTTAGAAAAAGGATATGTCAAAATTGAGATTCGAAACTCAGA
* * *
38296 CCTGTTAAAATCTTAGAAACGTGATCCATCATTTGATTGCCTAATCAAGATAAATAACATTGATC
62 CCTGTTAAAATCTTCGAAACGTGATCCGTCATTTGATTGCCTAATCAAGATAATTAACATTGATC
*
38361 ATTTGCGTAAACAAAATTTTTAATTATTCTAGTATTGGATTTGAACCTTATGCAAATTCCCAA
127 ATTTGCATAAACAAAATTTTTAATTATTCTAGTATTGGATTTGAACCTTATGCAAATTCCCAA
* *
38424 ATTGGATGCCTTTATACACCTTAGAAAAAATGATATGTCAAAATTGAGATTCGAAACTCAGACCT
1 ATTGGGTGCCTTTATACACCTTAG-AAAAAGGATATGTCAAAATTGAGATTCGAAACTCAGACCT
*
38489 GTTAAAATCTTCGAAACGTGATCCGTCATTTGATTACCTAATCAAGATAATTAACATTGATCATT
65 GTTAAAATCTTCGAAACGTGATCCGTCATTTGATTGCCTAATCAAGATAATTAACATTGATCATT
*
38554 TGCATAAACAAAATTTTTAATTATTCTAGTATTGGATTTGAACCTTGTGCAAATTCCCAA
130 TGCATAAACAAAATTTTTAATTATTCTAGTATTGGATTTGAACCTTATGCAAATTCCCAA
38614 GTACTTGTCC
Statistics
Matches: 353, Mismatches: 24, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
189 12 0.03
190 157 0.44
191 2 0.01
192 1 0.00
193 120 0.34
194 3 0.01
195 2 0.01
196 1 0.00
197 55 0.16
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (189 bp):
ATTGGGTGCCTTTATACACCTTAGAAAAAGGATATGTCAAAATTGAGATTCGAAACTCAGACCTG
TTAAAATCTTCGAAACGTGATCCGTCATTTGATTGCCTAATCAAGATAATTAACATTGATCATTT
GCATAAACAAAATTTTTAATTATTCTAGTATTGGATTTGAACCTTATGCAAATTCCCAA
Found at i:56744 original size:15 final size:15
Alignment explanation
Indices: 56724--56754 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56714 ATAATACATT
56724 AACTATCAAATAGAA
1 AACTATCAAATAGAA
56739 AACTATCAAATAGAA
1 AACTATCAAATAGAA
56754 A
1 A
56755 CATGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:56801 original size:14 final size:14
Alignment explanation
Indices: 56782--56816 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
56772 CCTTTTAAAT
56782 TAAAATAGTAAAAA
1 TAAAATAGTAAAAA
*
56796 TAAAATGGTAAAAA
1 TAAAATAGTAAAAA
56810 TAAAATA
1 TAAAATA
56817 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
TAAAATAGTAAAAA
Found at i:57276 original size:15 final size:15
Alignment explanation
Indices: 57256--57286 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57246 ATAATACATT
57256 AACTATCAAATAGAA
1 AACTATCAAATAGAA
57271 AACTATCAAATAGAA
1 AACTATCAAATAGAA
57286 A
1 A
57287 CATGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:57336 original size:13 final size:13
Alignment explanation
Indices: 57310--57345 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
57300 ATAACCTTTT
57310 AAATAAAATAGTAA
1 AAAT-AAATAGTAA
*
57324 AAATAAATGGTAA
1 AAATAAATAGTAA
57337 AAATAAATA
1 AAATAAATA
57346 ATTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (13 bp):
AAATAAATAGTAA
Found at i:57517 original size:529 final size:535
Alignment explanation
Indices: 56513--57574 Score: 2055
Period size: 529 Copynumber: 2.0 Consensus size: 535
56503 GACCATATGA
56513 CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAACCTGACCTCCCATTTGCATATA
1 CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAACCTGACCTCCCATTTGCATATA
56578 CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
66 CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
56643 AAAATATAACGTACTTTATCTAGCAATAATTGAAATTAATTATAAGTTAAATAAAATAATAAATT
131 AAAATATAACGTACTTTATCTAGCAATAATTGAAATTAATTATAAGTTAAATAAAATAATAAATT
56708 ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACATGTTAATCACAATAAC
196 ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACATGTTAATCACAATAAC
*
56773 CTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAATAATTATAAAAATATTTAATTTA
261 CTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAATAATTATAAAAATATTTAATCTA
56838 ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
326 ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
56903 TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
391 TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
56968 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGCATTTAAGAAATATAT
456 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGCATTTAAGAAATATAT
57033 TCGAAAAATAAGGGT
521 TCGAAAAATAAGGGT
*
57048 CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAATCTGACCTCCCATTTGCATATA
1 CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAACCTGACCTCCCATTTGCATATA
57113 CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
66 CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
57178 AAAATATAACGTACTTTATCTAGCAATAATTGAAATT-A-TATAAGTTAAAT-AAATAATAAATT
131 AAAATATAACGTACTTTATCTAGCAATAATTGAAATTAATTATAAGTTAAATAAAATAATAAATT
57240 ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACATGTTAATCACAATAAC
196 ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACATGTTAATCACAATAAC
57305 CTTTTAAA-TAAAATAGTAAAAAT-AAATGGTAAAAAT-AAATAATTATAAAAATATTTAATCTA
261 CTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAATAATTATAAAAATATTTAATCTA
57367 ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
326 ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
57432 TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
391 TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
*
57497 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAATATAT
456 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGCATTTAAGAAATATAT
57562 TCGAAAAATAAGG
521 TCGAAAAATAAGG
57575 ATATAATGGG
Statistics
Matches: 524, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
529 232 0.44
530 13 0.02
531 15 0.03
532 85 0.16
533 12 0.02
534 1 0.00
535 166 0.32
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (535 bp):
CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAACCTGACCTCCCATTTGCATATA
CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
AAAATATAACGTACTTTATCTAGCAATAATTGAAATTAATTATAAGTTAAATAAAATAATAAATT
ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACATGTTAATCACAATAAC
CTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAATAATTATAAAAATATTTAATCTA
ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGCATTTAAGAAATATAT
TCGAAAAATAAGGGT
Found at i:57695 original size:15 final size:16
Alignment explanation
Indices: 57667--57698 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
57657 ATAATACATT
57667 AACTATCAAAATAGAA
1 AACTATCAAAATAGAA
57683 AACTATC-AAATAGAA
1 AACTATCAAAATAGAA
57698 A
1 A
57699 CAGGTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (16 bp):
AACTATCAAAATAGAA
Found at i:57747 original size:14 final size:14
Alignment explanation
Indices: 57728--57762 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
57718 CCTTTTAAAT
57728 TAAAATAGTAAAAA
1 TAAAATAGTAAAAA
*
57742 TAAAATGGTAAAAA
1 TAAAATAGTAAAAA
57756 TAAAATA
1 TAAAATA
57763 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
TAAAATAGTAAAAA
Found at i:57788 original size:417 final size:409
Alignment explanation
Indices: 57223--58049 Score: 1555
Period size: 417 Copynumber: 2.0 Consensus size: 409
57213 TTATATAAGT
57223 TAAATAAATAATAAATTATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAAC
1 TAAATAAATAATAAATTATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAAC
*
57288 ATGTTAATCACAATAACCTTTTAAATAAAATAGTAAAAATAAATGGTAAAAATAAATAATTATAA
66 AGGTTAATCACAATAACCTTTTAAATAAAATAGTAAAAATAAATGGTAAAAATAAATAATTATAA
57353 AAATATTTAATCTAATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTT
131 AAATATTTAATCTAATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTT
57418 TTAATATATCCAAGTTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATAT
196 TTAATATATCCAAGTTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATAT
*
57483 TAGATTTCATTAAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTA
261 TAGATTTCATTAAATAAAAATAGAGTTTGTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTA
57548 TTTAAGAAATATATTCGAAAAATAAGGATATAATGGGCGATTCAAAAGTTTTACAGGTGAACGTA
326 TTTAAGAAATATATTCGAAAAATAAGGATATAATGGGCGATTCAAAAGTTTTACAGGTGAACGTA
57613 CTTTTTAATATAGTATAGA
391 CTTTTTAATATAGTATAGA
57632 TAAATAAAATAATAAATTATAATCAATAATACATTAACTATCAAAATAGAAAACTATCAAATAGA
1 TAAAT-AAATAATAAATTATAATC-ATAATACATTAACTATC-AAATAGAAAACTATCAAATAGA
57697 AACAGGTTAATTCTACAATAACCTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAAT
63 AACAGGTTAA-TC-ACAATAACCTTTTAAA-TAAAATAGTAAAAAT-AAATGGTAAAAAT-AAAT
*
57762 AATTATAAAAATATTTAATTTAATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATT
123 AATTATAAAAATATTTAATCTAATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATT
57827 AAAAGTTTTTAATATATCCAAGTTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTAT
188 AAAAGTTTTTAATATATCCAAGTTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTAT
57892 AAAGATATTAGATTTCATTAAATAAAAATAGAGTTTGTAGTAGAATAAAACTATAATAGTTTAAG
253 AAAGATATTAGATTTCATTAAATAAAAATAGAGTTTGTAGTAGAATAAAACTATAATAGTTTAAG
57957 TAATGGTATTTAAGAAATATATTCGAAAAATAAGGATATAATGGGCGATTCAAAAGTTTTACAGG
318 TAATGGTATTTAAGAAATATATTCGAAAAATAAGGATATAATGGGCGATTCAAAAGTTTTACAGG
58022 TGAACGTACTTTTTAATATAGTATAGA
383 TGAACGTACTTTTTAATATAGTATAGA
58049 T
1 T
58050 TATTAAAAAT
Statistics
Matches: 407, Mismatches: 3, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
409 5 0.01
410 18 0.04
411 17 0.04
412 31 0.08
413 2 0.00
414 16 0.04
415 15 0.04
416 13 0.03
417 290 0.71
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.34
Consensus pattern (409 bp):
TAAATAAATAATAAATTATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAAC
AGGTTAATCACAATAACCTTTTAAATAAAATAGTAAAAATAAATGGTAAAAATAAATAATTATAA
AAATATTTAATCTAATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTT
TTAATATATCCAAGTTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATAT
TAGATTTCATTAAATAAAAATAGAGTTTGTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTA
TTTAAGAAATATATTCGAAAAATAAGGATATAATGGGCGATTCAAAAGTTTTACAGGTGAACGTA
CTTTTTAATATAGTATAGA
Found at i:58107 original size:27 final size:28
Alignment explanation
Indices: 58054--58113 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
58044 ATAGATTATT
*** *
58054 AAAAATATGTTTCAAATTTTTACCAAAA
1 AAAAATATGTTTCAAATTGGAAACAAAA
58082 AAAAATATGTTTCAAA-TGGAAACAAAA
1 AAAAATATGTTTCAAATTGGAAACAAAA
58109 AAAAA
1 AAAAA
58114 GTTTCAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.58, C:0.08, G:0.07, T:0.27
Consensus pattern (28 bp):
AAAAATATGTTTCAAATTGGAAACAAAA
Found at i:61464 original size:14 final size:13
Alignment explanation
Indices: 61445--61483 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
61435 ACTCAACACT
61445 AACTGACTCGAAAA
1 AACTGACTC-AAAA
*
61459 AACTGACTCAACA
1 AACTGACTCAAAA
61472 AACTGACT-AAAA
1 AACTGACTCAAAA
61484 CCCGATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (13 bp):
AACTGACTCAAAA
Found at i:61476 original size:13 final size:13
Alignment explanation
Indices: 61434--61479 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
61424 GCCAGACTCA
61434 GACTCAACACTAACT
1 GACTCAACA--AACT
*
61449 GACTCGAAAAAACT
1 GACTC-AACAAACT
61463 GACTCAACAAACT
1 GACTCAACAAACT
61476 GACT
1 GACT
61480 AAAACCCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (13 bp):
GACTCAACAAACT
Found at i:66530 original size:18 final size:18
Alignment explanation
Indices: 66509--66562 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
66499 TTCTGGAGGC
*
66509 TATGGTGGTGGCGGCGGA
1 TATGGAGGTGGCGGCGGA
* * *
66527 TATGGAGGTGACAGCGGT
1 TATGGAGGTGGCGGCGGA
*
66545 TATGGAGGCGGCGGCGGA
1 TATGGAGGTGGCGGCGGA
66563 GGTGGACGTG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.13, G:0.52, T:0.19
Consensus pattern (18 bp):
TATGGAGGTGGCGGCGGA
Found at i:67216 original size:3 final size:3
Alignment explanation
Indices: 67162--67196 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
67152 GCTGGTGACC
67162 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GT
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GT
67197 TATAACAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
GTG
Found at i:85675 original size:2 final size:2
Alignment explanation
Indices: 85668--85694 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
85658 CAAAGTCATG
85668 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 A
85695 GTATTTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94997 original size:197 final size:197
Alignment explanation
Indices: 94656--95011 Score: 676
Period size: 197 Copynumber: 1.8 Consensus size: 197
94646 AATACTAAGG
*
94656 GTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGTTAACACA
1 GTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAATTAACACA
*
94721 TGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCAC
66 TGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATGTCAC
*
94786 CCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGGTGTATTGTATAATTTGCCTTAT
131 CCTTCAGAACCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGGTGTATTGTATAATTTGCCTTAT
94851 GA
196 GA
*
94853 GTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAATTGACACA
1 GTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAATTAACACA
94918 TGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATGTCAC
66 TGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATGTCAC
94983 CCTTCAGAACCCGCTTGTGTAGTCTGCTA
131 CCTTCAGAACCCGCTTGTGTAGTCTGCTA
95012 TACTAATATT
Statistics
Matches: 155, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
197 155 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (197 bp):
GTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAATTAACACA
TGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATGTCAC
CCTTCAGAACCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGGTGTATTGTATAATTTGCCTTAT
GA
Found at i:116521 original size:102 final size:101
Alignment explanation
Indices: 116346--116536 Score: 346
Period size: 102 Copynumber: 1.9 Consensus size: 101
116336 ACAAATAACC
* *
116346 AACGAAATTTAACCAATTCCGTCCTAATTAATTTGTCACTTTTTACAAATTTAGGCGTGTAAATT
1 AACGAAATTTAACCAATTCCGTCCTAATTAATTTGTCACCTTTTACAAATGTAGGCGTGTAAATT
116411 GGTAATTTTAGAAAAGGAGAGGGGATTGTGATAAAT
66 GGTAATTTTAGAAAAGGAGAGGGGATTGTGATAAAT
116447 AACGAAATTTAACCAATTTCCGTCCTAATTAATTTGTCACCTTTTACAAATGTAGGCGTGTAAAT
1 AACGAAATTTAACCAA-TTCCGTCCTAATTAATTTGTCACCTTTTACAAATGTAGGCGTGTAAAT
*
116512 TGGTAATTTTAGAAAAGGAGGGGGG
65 TGGTAATTTTAGAAAAGGAGAGGGG
116537 GAAGGGGGGG
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
101 16 0.19
102 70 0.81
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (101 bp):
AACGAAATTTAACCAATTCCGTCCTAATTAATTTGTCACCTTTTACAAATGTAGGCGTGTAAATT
GGTAATTTTAGAAAAGGAGAGGGGATTGTGATAAAT
Found at i:118962 original size:17 final size:17
Alignment explanation
Indices: 118940--118973 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
118930 GAACCCGATA
118940 AAAAACTTGAATATTTT
1 AAAAACTTGAATATTTT
118957 AAAAACTTGAATATTTT
1 AAAAACTTGAATATTTT
118974 TTTCATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
AAAAACTTGAATATTTT
Found at i:119157 original size:19 final size:18
Alignment explanation
Indices: 119115--119157 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
119105 TGAGTAATTT
*
119115 TTAAGTAAAAATATAATA
1 TTAAATAAAAATATAATA
*
119133 TATAAATAAAAATTTAATAA
1 T-TAAATAAAAATATAAT-A
119153 TTAAA
1 TTAAA
119158 ACAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 18 0.86
20 2 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:121950 original size:2 final size:2
Alignment explanation
Indices: 121945--121983 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
121935 TATATAGGAA
* *
121945 AT AT AT AT AT AT AT AT AGG AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
121984 TTAAATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 32 0.97
3 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:121958 original size:21 final size:21
Alignment explanation
Indices: 121928--121982 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
121918 CTTTTTTTGT
121928 TATA-ATATATATAGGAAATA
1 TATATATATATATAGGAAATA
121948 TATATATATATATAGGAAATA
1 TATATATATATATAGGAAATA
121969 TATATATATATATA
1 TATATATATATATA
121983 TTTAAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TATATATATATATAGGAAATA
Found at i:122949 original size:155 final size:153
Alignment explanation
Indices: 122740--123041 Score: 480
Period size: 155 Copynumber: 2.0 Consensus size: 153
122730 CACAATAACC
* *
122740 TTTTAAATTAAAGTGGTAAAAATAAAATTATTATAAAAATATTGAATTTAATTAAATGAAAATAG
1 TTTTAAATTAAAATAGTAAAAATAAAATTATTATAAAAATATTGAATTTAATTAAATGAAAATAG
*
122805 AGTTTTTAGTATAATAAAACTGTATATTAAA-AAACTTTAATATATCCAAGTTTTTAATGAAAAA
66 AGTTTTTAGTAGAATAAAACTGTATATTAAATAAACTTTAATATATCCAAGTTTTTAATGAAAAA
122869 TAGTAAAATGGTAAAAATACATT
131 TAGTAAAATGGTAAAAATACATT
122892 TTTTAAATTAAAATAGTAAAAATAAAATAATTATTATAAAAATATTGAATTTAATTAAATGAAAA
1 TTTTAAATTAAAATAGTAAAAAT--AA-AATTATTATAAAAATATTGAATTTAATTAAATGAAAA
**** * *
122957 TAGAGTTTTTAGTAGAATAAAACTGTATATTAAATTTTTTTTAATATATCCTAGTTTTTAATTAA
63 TAGAGTTTTTAGTAGAATAAAACTGTATATTAAATAAACTTTAATATATCCAAGTTTTTAATGAA
*
123022 AAATGGTAAAATGGTAAAAA
128 AAATAGTAAAATGGTAAAAA
123042 ATAAGGTAAT
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
152 21 0.15
154 2 0.01
155 70 0.51
156 43 0.32
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (153 bp):
TTTTAAATTAAAATAGTAAAAATAAAATTATTATAAAAATATTGAATTTAATTAAATGAAAATAG
AGTTTTTAGTAGAATAAAACTGTATATTAAATAAACTTTAATATATCCAAGTTTTTAATGAAAAA
TAGTAAAATGGTAAAAATACATT
Found at i:124437 original size:2 final size:2
Alignment explanation
Indices: 124432--124472 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
124422 GTGAGAGATC
124432 AT AT AT 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 AT AT AT A
124473 CAACAGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.