Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020342.1 Corchorus olitorius cultivar O-4 contig20375, 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: 176117
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 6--71 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1 TGCTA
6 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
48 CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT
72 TTTAAATTCG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11204 original size:132 final size:132
Alignment explanation
Indices: 10959--11267 Score: 390
Period size: 132 Copynumber: 2.3 Consensus size: 132
10949 GACTTCTATT
* * * * *
10959 AGTCGTTGCGAATTCATAGTCTTCAT-GCAACGACTTCTGTTAGTCGTTGTTTAATATATTTTAC
1 AGTCGTTGCGAAATCTTACTCTT-ATCGCAACGACTTATGTTAGTCGTTGCTTAATATATTTTAC
* * * *
11023 AAATTGATTTTCGAAGTGACCTTGAAAGTCACTACAAAAAACATGATTACTTTTGAAACGACAGA
65 AAATTGATTTTCGAAGCGACCTTGAAAGTCACTACAAAAAACATAATTACTTTTGAAACCACAAA
11088 TTA
130 TTA
* * * *
11091 AGTCGTTGCGAAATCTTACTCTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAATTTATTTTTCA
1 AGTCGTTGCGAAATCTTACTCTTATCGCAACGACTTATGTTAGTCGTTGCTTAATATATTTTACA
* * *
11156 AATTGATTTTCGCAGCGACCTTGAAAGTCGCTAC-AAAAACAATAATTACTTTTGAAGCCACAAA
66 AATTGATTTTCGAAGCGACCTTGAAAGTCACTACAAAAAAC-ATAATTACTTTTGAAACCACAAA
11220 TTA
130 TTA
* * * *
11223 AGTCGCTGCGAAATCTTATTC-TAGTCGCAATGACTTATATTAGTC
1 AGTCGTTGCGAAATCTTACTCTTA-TCGCAACGACTTATGTTAGTC
11268 CTTTTCTAGG
Statistics
Matches: 153, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
131 8 0.05
132 145 0.95
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (132 bp):
AGTCGTTGCGAAATCTTACTCTTATCGCAACGACTTATGTTAGTCGTTGCTTAATATATTTTACA
AATTGATTTTCGAAGCGACCTTGAAAGTCACTACAAAAAACATAATTACTTTTGAAACCACAAAT
TA
Found at i:16982 original size:12 final size:12
Alignment explanation
Indices: 16967--16992 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16957 ACTTTTAAAC
16967 TTGATAATAATA
1 TTGATAATAATA
16979 TTGATAATAATA
1 TTGATAATAATA
16991 TT
1 TT
16993 TTAATTAGTT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
TTGATAATAATA
Found at i:17352 original size:93 final size:93
Alignment explanation
Indices: 17272--17453 Score: 301
Period size: 93 Copynumber: 2.0 Consensus size: 93
17262 TTAATTAAAT
*
17272 TAGTAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
1 TAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
*
17337 TTAGTTAAGTAAAACTATAAAAGTAATA
66 ATAGTTAAGTAAAACTATAAAAGTAATA
* *
17365 TAGTAAAATGGTAAATATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
1 TAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
* * *
17430 ATAGTTGACTAAAATTATAAAAGT
66 ATAGTTAAGTAAAACTATAAAAGT
17454 TTAAACAATG
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.34
Consensus pattern (93 bp):
TAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
ATAGTTAAGTAAAACTATAAAAGTAATA
Found at i:29122 original size:54 final size:54
Alignment explanation
Indices: 29040--29151 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
29030 TGAGACCATT
29040 GCATTGATTTTGCAAGATATTACTAACCTTGTCCTCGTAACAATTTATACCAGC
1 GCATTGATTTTGCAAGATATTACTAACCTTGTCCTCGTAACAATTTATACCAGC
29094 GCATTGATTTTGCAAGATATTACTAACCTTGTCCTCGTAACAATTTATACCAGC
1 GCATTGATTTTGCAAGATATTACTAACCTTGTCCTCGTAACAATTTATACCAGC
29148 GCAT
1 GCAT
29152 CACATTTTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (54 bp):
GCATTGATTTTGCAAGATATTACTAACCTTGTCCTCGTAACAATTTATACCAGC
Found at i:36849 original size:35 final size:35
Alignment explanation
Indices: 36795--37026 Score: 311
Period size: 35 Copynumber: 6.6 Consensus size: 35
36785 CATACTTTTC
* * * *
36795 ATTGGTTTTGATTGCTGGTAGTTGATATGAACATA
1 ATTGGTTTTGCTTGCTGCTAGTTGATAGGAGCATA
* * *
36830 ATTGGTTTTGCTTGTTGGTAGTTGATAGGAGGATA
1 ATTGGTTTTGCTTGCTGCTAGTTGATAGGAGCATA
* * *
36865 ATTGGTTTTGCTTGTTGGTAGTCGATAGGAGCATA
1 ATTGGTTTTGCTTGCTGCTAGTTGATAGGAGCATA
* *
36900 ATTGTTTTTGCTCGCTGCTAGTTGATAGGAGCATA
1 ATTGGTTTTGCTTGCTGCTAGTTGATAGGAGCATA
*
36935 CTTGGTTTTGCTTGCTGCTAGTTGATAGGAGCATA
1 ATTGGTTTTGCTTGCTGCTAGTTGATAGGAGCATA
* *
36970 CTTGGTTTTGCTCGCTGCTAGTTGATAGGAGCATA
1 ATTGGTTTTGCTTGCTGCTAGTTGATAGGAGCATA
* *
37005 TTTGGTTTTGCTTGCTGTTAGT
1 ATTGGTTTTGCTTGCTGCTAGT
37027 GCACTTTTTA
Statistics
Matches: 178, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 178 1.00
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (35 bp):
ATTGGTTTTGCTTGCTGCTAGTTGATAGGAGCATA
Found at i:39128 original size:13 final size:13
Alignment explanation
Indices: 39110--39134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39100 TTTTTGACTT
39110 GATGATTCTGTTG
1 GATGATTCTGTTG
39123 GATGATTCTGTT
1 GATGATTCTGTT
39135 CTCTGTTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (13 bp):
GATGATTCTGTTG
Found at i:40172 original size:828 final size:831
Alignment explanation
Indices: 38641--40232 Score: 2504
Period size: 828 Copynumber: 1.9 Consensus size: 831
38631 CATGTTACTT
* *
38641 TTTCTGTTTCGATCTATTTGTCGTTTCGATCCGTTTGCCCATAACTGAATTTTCCCGACCTCCAA
1 TTTCTGTTTCGATATATCTGTCGTTTCGATCCGTTTGCCCATAACTGAATTTTCCCGACCTCCAA
* *
38706 TTTCGACACTGCCAACACCGATGGATAGCATGTGCTCCGCTCTGCCACCCAACAAAATTTCAGTC
66 TTTCGACACCGCCAACACCGATGGATAGCATGTGCTCCGCTCTGCCACCCAACAAAATTTCAATC
* * **
38771 CAATCCGATCACCATGGGGCTCACACACGCCGGTCAAAATTGTTGCTCCAGTGTTGACCAGATCT
131 CAATCCGATCACCATGGGGCTCACACACGCCGGTCAAAATTGCTACTCCAACGTTGACCAGATCT
38836 AAACCTATTGACCAATCAGCTTCTGCCACGTCAATGTTGACTTTGACAGTTGACCCTTGACTTTG
196 AAACCTATTGACCAATCAGCTTCTGCCACGTCAATGTTGACTTTGACAGTTGACCC-T-AC-TTG
*
38901 ACTATGACCTCCTTGAGTAAGACCTCCTTTCTGCATATTTTCAATCCTCTGATCTCATTTTTGGG
258 ACTATGACCTCCGTGAGTAAGACCTCCTTTCTGCATATTTTCAATCCTCTGATCTCATTTTTGGG
* *
38966 CTCTATTTCAGCAAATCTTGTTTGTAAGATGAATAAATTTGCGTATTGCACTCCATTTGACCTTT
323 CTCTATTTCAGCAAATCTTGTTTGTAAGATGAAGAAATTTGCGTATTCCACTCCATTTGACCTTT
* * *
39031 ATGTCCCATTTTCTGCTCTTGATCTGTTGATCTCGTATTTCGTTTGACCTTTTGGGTCCCGTATT
388 ATGTCCCATTTTCTGCTCTTGATCTGTTGATCCCGTATTCCGTTTGACCTTTTGGATCCCGTATT
* *
39096 CTGCTTTTTGACTTGATGATTCTGTTGGATGATTCTGTTCTCTGTTATCCGATCCCCGATGTCCG
453 CTGCTTTTTGACTTGATGATTCTGTTGCATGATTCTGTTATCTGTTATCCGATCCCCGATGTCCG
* *
39161 TTGTTTTGATCCGTTATACACTCCATTTTGGTTTTCAAACTCAAGTTAGCATCTTGAGTTTGAGG
518 CTGTTTTGATCCGTTATACACTCCATTTTGGTTTTCAAACTCAAGTTAGCATCTTAAGTTTGAGG
* *
39226 AAGGGTGTTAAAATAATTTAGTATATTATATTTTTCTAGATTCAGTTTCCTAATTTCAGTTCATT
583 AAGGGTGTTAAAATAATTTAGTATATTATATTTTCCTAGATTCAGTTTCCTAATTTCAATTCATT
* * * *
39291 TAGGTTTTTTAGGCCTTAAGTTTAGGAGTATGTTATAGTATAAAAGGCCTCGTATTGTACTTAGT
648 TAGGTTTCTTAGGCCTTAAGTTTAGGAGTATATTATAGTATAAAAGACCTCGTATTATACTTAGT
* * *
39356 TTTTTTGTGGTTTCTAAATAAGATTTC-TCAGTTTTCTGTTTTGTTATTTTCTCTTGCATTATGT
713 TTTTTCGTGGTTTCTAAATAAGAGTTCTTC-GTCTTCTGTTTTGTTATTTTCTCTTGCATTATGT
39420 TAACTTGGTATCCATAGCTAGGTTCTAATTTTTTTTCTAAAAAATTGTATTTCTC
777 TAACTTGGTATCCATAGCTAGGTTCTAATTTTTTTTCTAAAAAATTGTATTTCTC
39475 TTTCTGTTTCGATATATCTGTCGTTTCGATCCGTTTGCCCA-AATCTGAATTTTTCCCGACCTCC
1 TTTCTGTTTCGATATATCTGTCGTTTCGATCCGTTTGCCCATAA-CTGAA-TTTTCCCGACCTCC
* *
39539 -ATTTCCGGCACCGCCAACACCGATGGATAGCATGTGCTCCGCTCTGCCACCCAGCAAAATTTCA
64 AATTT-CGACACCGCCAACACCGATGGATAGCATGTGCTCCGCTCTGCCACCCAACAAAATTTCA
** *
39603 ATCCAATCCGATCACCATGGGGCTCACACGTGCCGGTCAAAGTTGCTACTCCAACGTTGACCAGA
128 ATCCAATCCGATCACCATGGGGCTCACACACGCCGGTCAAAATTGCTACTCCAACGTTGACCAGA
* * * * *
39668 TCTGAACCTGTTGACCAGTCAGTTTCTGCCACGTCAATGTTGACTTTGATAGTTGA-CC-A-TTG
193 TCTAAACCTATTGACCAATCAGCTTCTGCCACGTCAATGTTGACTTTGACAGTTGACCCTACTTG
* * ** *
39730 ACTTTGACCTCCGTGAGTAAGACCTCTTTTCTGCATATTTTTGATCCTCTGATCTCGTTTTTGGG
258 ACTATGACCTCCGTGAGTAAGACCTCCTTTCTGCATATTTTCAATCCTCTGATCTCATTTTTGGG
* * *
39795 CTTTGTTTTAGCAAATCTTGTTTGTAAGATGAAGGAAA-TTGCGTATTCCACTCCATTTGACCTT
323 CTCTATTTCAGCAAATCTTGTTTGTAAGATGAA-GAAATTTGCGTATTCCACTCCATTTGACCTT
* *
39859 TATGTCCCGTTTTCTGCTTTTGATCTGTTGATCCCGTATTCCGTTTGACCTTTTGGATCCCGTAT
387 TATGTCCCATTTTCTGCTCTTGATCTGTTGATCCCGTATTCCGTTTGACCTTTTGGATCCCGTAT
*
39924 TCTGC-TTTTGA-TCTGATGATTCTGTTGTCA-GATT-TCGTTATCTGTTATCTGATCCCCGATG
452 TCTGCTTTTTGACT-TGATGATTCTGTTG-CATGATTCT-GTTATCTGTTATCCGATCCCCGATG
* * *
39985 TCCGCTGTTTTGATCTGTTATCCACTGCATTTTGGTTTTCAAACTCAAGTTAGCATCTTAAGTTT
514 TCCGCTGTTTTGATCCGTTATACACTCCATTTTGGTTTTCAAACTCAAGTTAGCATCTTAAGTTT
* * *
40050 GAGGGAGGGTGTTAAAATAATTTAGTATTTTATATTTTCCTAGATTCAGTTTCCTAGTTTCAATT
579 GAGGAAGGGTGTTAAAATAATTTAGTATATTATATTTTCCTAGATTCAGTTTCCTAATTTCAATT
*
40115 CATTTAGGTTTCTTAGGCCTTAAGTTTAGGAGTATATTATAGTGTAAAAGACCTCGTATTATACT
644 CATTTAGGTTTCTTAGGCCTTAAGTTTAGGAGTATATTATAGTATAAAAGACCTCGTATTATACT
*
40180 TAGTTTTTTCGTGGTTTCTGAATAAGAGTTCTTCGTCTTCTGTTTTGTTATTT
709 TAGTTTTTTCGTGGTTTCTAAATAAGAGTTCTTCGTCTTCTGTTTTGTTATTT
40233 CTTTCTCACA
Statistics
Matches: 694, Mismatches: 56, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
827 2 0.00
828 273 0.39
829 185 0.27
830 3 0.00
831 1 0.00
833 2 0.00
834 50 0.07
835 178 0.26
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (831 bp):
TTTCTGTTTCGATATATCTGTCGTTTCGATCCGTTTGCCCATAACTGAATTTTCCCGACCTCCAA
TTTCGACACCGCCAACACCGATGGATAGCATGTGCTCCGCTCTGCCACCCAACAAAATTTCAATC
CAATCCGATCACCATGGGGCTCACACACGCCGGTCAAAATTGCTACTCCAACGTTGACCAGATCT
AAACCTATTGACCAATCAGCTTCTGCCACGTCAATGTTGACTTTGACAGTTGACCCTACTTGACT
ATGACCTCCGTGAGTAAGACCTCCTTTCTGCATATTTTCAATCCTCTGATCTCATTTTTGGGCTC
TATTTCAGCAAATCTTGTTTGTAAGATGAAGAAATTTGCGTATTCCACTCCATTTGACCTTTATG
TCCCATTTTCTGCTCTTGATCTGTTGATCCCGTATTCCGTTTGACCTTTTGGATCCCGTATTCTG
CTTTTTGACTTGATGATTCTGTTGCATGATTCTGTTATCTGTTATCCGATCCCCGATGTCCGCTG
TTTTGATCCGTTATACACTCCATTTTGGTTTTCAAACTCAAGTTAGCATCTTAAGTTTGAGGAAG
GGTGTTAAAATAATTTAGTATATTATATTTTCCTAGATTCAGTTTCCTAATTTCAATTCATTTAG
GTTTCTTAGGCCTTAAGTTTAGGAGTATATTATAGTATAAAAGACCTCGTATTATACTTAGTTTT
TTCGTGGTTTCTAAATAAGAGTTCTTCGTCTTCTGTTTTGTTATTTTCTCTTGCATTATGTTAAC
TTGGTATCCATAGCTAGGTTCTAATTTTTTTTCTAAAAAATTGTATTTCTC
Found at i:41257 original size:113 final size:114
Alignment explanation
Indices: 41136--41341 Score: 333
Period size: 113 Copynumber: 1.8 Consensus size: 114
41126 ATAAGCTCAT
* * * *
41136 ATGGTTTTTGAAGTTTATGAAATTTAAATTGATGGACATTACAAATATGGGTAAGTT-ACATATA
1 ATGGTTTTTAAAGTTTATGAAATTTAAATTGATGGAAATTACAAATATGAGTAAATTAACATATA
41200 TACCCAGTGGTTTTGAGTGAAACAAATGACCCCTGAATTTTGAATTTTG
66 TACCCAGTGGTTTTGAGTGAAACAAATGACCCCTGAATTTTGAATTTTG
*
41249 ATGGTTTTTAAAGTTTATGAAATTTAAATTGATGGAAATTACAAATATGAGTAAATTAAATATAT
1 ATGGTTTTTAAAGTTTATGAAATTTAAATTGATGGAAATTACAAATATGAGTAAATT-AACATAT
**
41314 ATACCTTGTGGTTTTGAGTGAAACAAAT
65 ATACCCAGTGGTTTTGAGTGAAACAAAT
41342 ATGACTCCTG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 53 0.63
115 31 0.37
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (114 bp):
ATGGTTTTTAAAGTTTATGAAATTTAAATTGATGGAAATTACAAATATGAGTAAATTAACATATA
TACCCAGTGGTTTTGAGTGAAACAAATGACCCCTGAATTTTGAATTTTG
Found at i:44345 original size:23 final size:23
Alignment explanation
Indices: 44317--44363 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
44307 TACTTTATTA
44317 TCTACAACCATGCACTTATTAAT
1 TCTACAACCATGCACTTATTAAT
44340 TCTACAACCATGCACTTATTAAT
1 TCTACAACCATGCACTTATTAAT
44363 T
1 T
44364 TTCCAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (23 bp):
TCTACAACCATGCACTTATTAAT
Found at i:53759 original size:33 final size:33
Alignment explanation
Indices: 53717--53797 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 33
53707 AATTACATAT
**
53717 TATTTCTAATAATATTTATTGTATATTAAATAAA
1 TATTTCTAATAATATTTATTACATATT-AATAAA
53751 TA-TTC---TAATATTTATTACATATTAATAAA
1 TATTTCTAATAATATTTATTACATATTAATAAA
*
53780 TATTTCTAATAAAATTTA
1 TATTTCTAATAATATTTA
53798 AATATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
29 8 0.20
30 19 0.47
33 11 0.28
34 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (33 bp):
TATTTCTAATAATATTTATTACATATTAATAAA
Found at i:53803 original size:30 final size:29
Alignment explanation
Indices: 53739--53804 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
53729 TATTTATTGT
** *
53739 ATATTAAATAAATATTCTAATATTTATTAC
1 ATATT-AATAAATATTCTAATAAATATTAA
53769 ATATTAATAAATATTTCTAATAAA-ATTTAA
1 ATATTAATAAATA-TTCTAATAAATA-TTAA
53799 ATATTA
1 ATATTA
53805 TTTGAAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATTAATAAATATTCTAATAAATATTAA
Found at i:56869 original size:11 final size:11
Alignment explanation
Indices: 56853--56877 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56843 TTAAAAATTA
56853 AAATAAATAAT
1 AAATAAATAAT
56864 AAATAAATAAT
1 AAATAAATAAT
56875 AAA
1 AAA
56878 AGAAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:62519 original size:83 final size:83
Alignment explanation
Indices: 62380--62541 Score: 315
Period size: 83 Copynumber: 2.0 Consensus size: 83
62370 ACTGTGGGTA
*
62380 CCATGGGCCATCAAAGATAAGTGTTTCTATATATTGAGATTTCTTTCGAATTATTATTAATGCTA
1 CCATGGGCCATCAAAGATAAGTGTTTCTATATATTGAGATTTCTTTCGAATTATTATTAACGCTA
62445 ATATATGTTGACACTTCT
66 ATATATGTTGACACTTCT
62463 CCATGGGCCATCAAAGATAAGTGTTTCTATATATTGAGATTTCTTTCGAATTATTATTAACGCTA
1 CCATGGGCCATCAAAGATAAGTGTTTCTATATATTGAGATTTCTTTCGAATTATTATTAACGCTA
62528 ATATATGTTGACAC
66 ATATATGTTGACAC
62542 CAGAAGTGTC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (83 bp):
CCATGGGCCATCAAAGATAAGTGTTTCTATATATTGAGATTTCTTTCGAATTATTATTAACGCTA
ATATATGTTGACACTTCT
Found at i:62616 original size:30 final size:30
Alignment explanation
Indices: 62580--63141 Score: 694
Period size: 30 Copynumber: 18.5 Consensus size: 30
62570 TAAATGATAT
62580 CAGAAGTTGTCATGATCTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
62610 CAGAAGTTGTCATGATCTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
*
62640 CAGAAGTTGTCATGATCTTGCAATTGGCAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
62670 CAGAAGTTGTCATGATCTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
* *
62700 CAGAAGTTGTCATGGTCTTGCAATTGACAT
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
**
62730 CAGAAGTTGTCATGGCCTTGC-ATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
**
62759 CAGAAGTTGTCATGGCCTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
* *
62789 CAGAAGCTGTCATGGTCTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
** *
62819 CAGAAACTGTCATGATGTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
**
62849 CAGAAGTTGTCATGGCCTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
* *
62879 CAGAAGCTGTCATGGTCTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
** *
62909 CAGAAACTGTCATGATGTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
*
62939 CAGAAGTTGTCATGATGTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
* *
62969 CAGAAGCTGTCATGATCTTGCAATTGACAT
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
** * * * * *
62999 TTGAAGATGTCATAATTTTATTCAATTGGCAC
1 CAGAAGTTGTCATGA-TCT-TGCAATTGACAC
* * *
63031 CAGAAGTTGTCATGATAAATTTCCAATAGACAC
1 CAGAAGTTGTCATGAT---CTTGCAATTGACAC
** * * * *
63064 TTGAAGATGTCATAATTTTACTCAATTGACAC
1 CAGAAGTTGTCATGATCTT--GCAATTGACAC
*
63096 CAGAAGTTGTCGTGATCTTGCAATTGACAC
1 CAGAAGTTGTCATGATCTTGCAATTGACAC
*
63126 TAGAAGTTGTCATGAT
1 CAGAAGTTGTCATGAT
63142 TTTACCTTTT
Statistics
Matches: 468, Mismatches: 56, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
29 28 0.06
30 372 0.79
31 3 0.01
32 42 0.09
33 21 0.04
34 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (30 bp):
CAGAAGTTGTCATGATCTTGCAATTGACAC
Found at i:76925 original size:13 final size:13
Alignment explanation
Indices: 76907--76932 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76897 TTTGAATCTA
76907 TACATGATCCCTC
1 TACATGATCCCTC
76920 TACATGATCCCTC
1 TACATGATCCCTC
76933 GCTCAAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.08, T:0.31
Consensus pattern (13 bp):
TACATGATCCCTC
Found at i:80983 original size:131 final size:130
Alignment explanation
Indices: 80824--81073 Score: 378
Period size: 131 Copynumber: 1.9 Consensus size: 130
80814 TCATTTATCC
*
80824 AAATTCTAATATATCTAAGTTTTTAATTA-AATTAGTAAAATGAT-AAAAATAAATTAGGTATAA
1 AAATTCTAATATATATAAGTTTTTAATTAGAA-TAGTAAAATGATGAAAAATAAA-TAGGTATAA
* *
80887 GGATATAAGATTTAATTAAACAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTT
64 AGATATAAGATTTAAATAAA-AAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTT
80952 AAA
128 AAA
* * *
80955 AAATTCTAATATATATAAGTTTTTAATTAGAATAGTAAAATGATGAACATTAAATAGTTATAAAG
1 AAATTCTAATATATATAAGTTTTTAATTAGAATAGTAAAATGATGAAAAATAAATAGGTATAAAG
* * *
81020 ATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAA
66 ATATAAGATTTAAATAAAAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
81074 TTTTAAACAA
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
130 34 0.31
131 65 0.60
132 9 0.08
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (130 bp):
AAATTCTAATATATATAAGTTTTTAATTAGAATAGTAAAATGATGAAAAATAAATAGGTATAAAG
ATATAAGATTTAAATAAAAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAA
Found at i:81602 original size:19 final size:18
Alignment explanation
Indices: 81580--81615 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
81570 CCATGTCAAA
81580 ATTATATATATAAATAAAT
1 ATTATATATAT-AATAAAT
81599 ATTATATATATAATAAA
1 ATTATATATATAATAAA
81616 CACTTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATATATATAATAAAT
Found at i:90859 original size:15 final size:15
Alignment explanation
Indices: 90839--90871 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
90829 CTCAAGCATT
90839 GAAAAA-AAAAAGAGA
1 GAAAAAGAAAAAGA-A
90854 GAAAAAGAAAAAGAA
1 GAAAAAGAAAAAGAA
90869 GAA
1 GAA
90872 GCAAGGAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAAAGAA
Found at i:100909 original size:11 final size:11
Alignment explanation
Indices: 100875--100922 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
100865 TTGAAATAAT
100875 TCTTC-AATAG
1 TCTTCAAATAG
100885 TCTTC--A-AG
1 TCTTCAAATAG
100893 TCTTCAAATTA-
1 TCTTCAAA-TAG
100904 TCTTCAAATAG
1 TCTTCAAATAG
100915 TCTTCAAA
1 TCTTCAAA
100923 CACGAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 8 0.24
11 16 0.48
12 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAG
Found at i:101070 original size:17 final size:18
Alignment explanation
Indices: 101048--101081 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
101038 ACTTAAAGAC
101048 TCAAAACA-CATATATTA
1 TCAAAACAGCATATATTA
*
101065 TCAAAATAGCATATATT
1 TCAAAACAGCATATATT
101082 TAAGCATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (18 bp):
TCAAAACAGCATATATTA
Found at i:108053 original size:7 final size:7
Alignment explanation
Indices: 108041--108067 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
108031 TTGATCGATG
108041 CCTCCCT
1 CCTCCCT
108048 CCTCCCT
1 CCTCCCT
108055 CCTCCCT
1 CCTCCCT
108062 CCTCCC
1 CCTCCC
108068 AAACTCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (7 bp):
CCTCCCT
Found at i:109466 original size:16 final size:16
Alignment explanation
Indices: 109447--109497 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
109437 GTGATTATCC
109447 TTGTTTTTTATTAACT
1 TTGTTTTTTATTAACT
** * * *
109463 TTG-TAGTGATTATCC
1 TTGTTTTTTATTAACT
109478 TTGTTTTTTATTAACT
1 TTGTTTTTTATTAACT
109494 TTGT
1 TTGT
109498 ATTCAGATGA
Statistics
Matches: 24, Mismatches: 10, Indels: 2
0.67 0.28 0.06
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.18, C:0.08, G:0.12, T:0.63
Consensus pattern (16 bp):
TTGTTTTTTATTAACT
Found at i:109474 original size:31 final size:31
Alignment explanation
Indices: 109436--109498 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
109426 GTAAGAAAAA
109436 AGTGATTATCCTTGTTTTTTATTAACTTTGT
1 AGTGATTATCCTTGTTTTTTATTAACTTTGT
109467 AGTGATTATCCTTGTTTTTTATTAACTTTGT
1 AGTGATTATCCTTGTTTTTTATTAACTTTGT
109498 A
1 A
109499 TTCAGATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.57
Consensus pattern (31 bp):
AGTGATTATCCTTGTTTTTTATTAACTTTGT
Found at i:116703 original size:5 final size:5
Alignment explanation
Indices: 116695--116735 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
116685 GATCAAAGAT
* *
116695 TTTTC TTTTT TTCTTC TTTTC TTTTC TTTTC CTTTC TTTTC
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC
116736 CTTCCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:116730 original size:15 final size:16
Alignment explanation
Indices: 116696--116743 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
116686 ATCAAAGATT
* *
116696 TTTCTTTTTTTCTTCT
1 TTTCTTTTCTTCTTCC
116712 TTTCTTTTCTT-TTCC
1 TTTCTTTTCTTCTTCC
116727 TTTCTTTTC--CTTCC
1 TTTCTTTTCTTCTTCC
116741 TTT
1 TTT
116744 TTCTATGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.24
15 12 0.41
16 10 0.34
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTCTTTTCTTCTTCC
Found at i:116736 original size:10 final size:10
Alignment explanation
Indices: 116708--116744 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
116698 TCTTTTTTTC
*
116708 TTCTTTTCTT
1 TTCTTTTCCT
116718 TTCTTTTCCT
1 TTCTTTTCCT
116728 TTCTTTTCCT
1 TTCTTTTCCT
*
116738 TCCTTTT
1 TTCTTTT
116745 TCTATGCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTCTTTTCCT
Found at i:117624 original size:28 final size:29
Alignment explanation
Indices: 117592--117646 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
117582 AGCAAATATT
* *
117592 TCATGTTTTATTCTTGTGAAC-AAAAATC
1 TCATGTTTTAGTCTTATGAACGAAAAATC
117620 TCATGTTTTAGTCTTATGAACGAAAAA
1 TCATGTTTTAGTCTTATGAACGAAAAA
117647 AAAAAGCGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (29 bp):
TCATGTTTTAGTCTTATGAACGAAAAATC
Found at i:117695 original size:77 final size:77
Alignment explanation
Indices: 117533--117694 Score: 279
Period size: 78 Copynumber: 2.1 Consensus size: 77
117523 ATTCGCCTTA
* *
117533 AACAAAGATCTCATGTTTTAGTCTTATGAACGAAAAAAAAAGCCACTTAAGCAAATATTTCATGT
1 AACAAAAATCTCATGTTTTAGTCTTATGAACGAAAAAAAAAGCCACTTAAGCAAAGATTTCATGT
117598 TTTATTCTTGTG
66 TTTATTCTTGTG
*
117610 AACAAAAATCTCATGTTTTAGTCTTATGAACGAAAAAAAAAAGCGACTTAAGCAAAGATTTCATG
1 AACAAAAATCTCATGTTTTAGTCTTATGAACG-AAAAAAAAAGCCACTTAAGCAAAGATTTCATG
117675 TTTTATTCTTGTG
65 TTTTATTCTTGTG
*
117688 AAGAAAA
1 AACAAAA
117695 TATACATAGG
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 31 0.39
78 49 0.61
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (77 bp):
AACAAAAATCTCATGTTTTAGTCTTATGAACGAAAAAAAAAGCCACTTAAGCAAAGATTTCATGT
TTTATTCTTGTG
Found at i:118371 original size:12 final size:13
Alignment explanation
Indices: 118340--118369 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
118330 TTGAATATGT
*
118340 TTTTTCATAATTA
1 TTTTTAATAATTA
118353 TTTTTAATAATTA
1 TTTTTAATAATTA
118366 TTTT
1 TTTT
118370 AAGACTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTAATAATTA
Found at i:118460 original size:22 final size:21
Alignment explanation
Indices: 118430--118478 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
118420 CAATATTTTT
* *
118430 ATTAATAATTTTTTTTAATAA
1 ATTAATAATTTTTATGAATAA
118451 ATTAATTAATTTTTATGAATAA
1 ATTAA-TAATTTTTATGAATAA
118473 A-TAATA
1 ATTAATA
118479 GGGTTAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 8 0.32
22 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTAATAATTTTTATGAATAA
Found at i:118965 original size:45 final size:46
Alignment explanation
Indices: 118878--119014 Score: 249
Period size: 45 Copynumber: 3.0 Consensus size: 46
118868 AAAAAAAATC
*
118878 ATATAAATTTCTATCAAAATAAAAAAGAATGCATATAAATAAATTA
1 ATATAAATTTCTACCAAAATAAAAAAGAATGCATATAAATAAATTA
*
118924 ATATAAATTTCTACCAAAATAAAAAA-AATGCATATACATAAATTA
1 ATATAAATTTCTACCAAAATAAAAAAGAATGCATATAAATAAATTA
118969 ATATAAATTTCTACCAAAATAAAAAAGAATGCATATAAATAAATTA
1 ATATAAATTTCTACCAAAATAAAAAAGAATGCATATAAATAAATTA
119015 TTATCTATGA
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
45 44 0.51
46 43 0.49
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (46 bp):
ATATAAATTTCTACCAAAATAAAAAAGAATGCATATAAATAAATTA
Found at i:120137 original size:12 final size:13
Alignment explanation
Indices: 120120--120177 Score: 56
Period size: 14 Copynumber: 4.8 Consensus size: 13
120110 CCGTTTAATA
120120 ATTATATATAT-T
1 ATTATATATATCT
*
120132 ATTATATATATGT
1 ATTATATATATCT
120145 AATTATATATATCT
1 -ATTATATATATCT
120159 A--ATAT-TAT-T
1 ATTATATATATCT
120168 -TTATATATAT
1 ATTATATATAT
120178 AATATATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
9 1 0.03
10 7 0.17
11 7 0.17
12 11 0.28
13 2 0.05
14 12 0.30
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
ATTATATATATCT
Found at i:120141 original size:14 final size:14
Alignment explanation
Indices: 120117--120161 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
120107 AAACCGTTTA
120117 ATAATTATATATAT
1 ATAATTATATATAT
120131 -T-ATTATATATAT
1 ATAATTATATATAT
*
120143 GTAATTATATATAT
1 ATAATTATATATAT
*
120157 CTAAT
1 ATAAT
120162 ATTATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 11 0.39
13 2 0.07
14 15 0.54
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATAATTATATATAT
Found at i:120165 original size:16 final size:15
Alignment explanation
Indices: 120122--120184 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 15
120112 GTTTAATAAT
*
120122 TATATATAT-TATTA
1 TATATATCTATATTA
*
120136 TATATATGTA-ATTA
1 TATATATCTATATTA
120150 TATATATCTAATATTA
1 TATATATCT-ATATTA
* * *
120166 T-TTTATATATATAA
1 TATATATCTATATTA
120180 TATAT
1 TATAT
120185 TTAATTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
14 26 0.67
15 8 0.21
16 5 0.13
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
TATATATCTATATTA
Found at i:120174 original size:19 final size:18
Alignment explanation
Indices: 120125--120186 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
120115 TAATAATTAT
120125 ATATATTATTATATATAT-
1 ATATATT-TTATATATATA
* * *
120143 GTA-ATTATATATATCTA
1 ATATATTTTATATATATA
120160 ATATTATTTTATATATATA
1 ATA-TATTTTATATATATA
120179 ATATATTT
1 ATATATTT
120187 AATTATAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.23
17 5 0.14
18 7 0.20
19 15 0.43
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATATATTTTATATATATA
Found at i:120192 original size:21 final size:23
Alignment explanation
Indices: 120118--120193 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 23
120108 AACCGTTTAA
120118 TAATTATATATATTATTATATATAT
1 TAATTATATATATTA--ATATATAT
120143 GTAATTATATATATCTAATAT-TAT
1 -TAATTATATATAT-TAATATATAT
120167 T--TTATATATA-TAATATAT-T
1 TAATTATATATATTAATATATAT
120186 TAATTATA
1 TAATTATA
120194 AAAATTACTA
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
19 8 0.17
20 1 0.02
21 14 0.30
23 1 0.02
24 3 0.07
25 4 0.09
26 13 0.28
27 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
TAATTATATATATTAATATATAT
Found at i:127503 original size:4 final size:4
Alignment explanation
Indices: 127494--127520 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
127484 AGATTTGTGT
127494 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
127521 TAATCAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:136716 original size:14 final size:13
Alignment explanation
Indices: 136685--136729 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
136675 ATCGGGTTTT
136685 AGTCAGTTTGTTG
1 AGTCAGTTTGTTG
*
136698 AGTCAGTTTTTTCG
1 AGTCAGTTTGTT-G
136712 AGTCAGTTAGTGTTG
1 AGTCAGTT--TGTTG
136727 AGT
1 AGT
136730 TTGAGTCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.41
14 9 0.33
15 4 0.15
16 3 0.11
ACGTcount: A:0.18, C:0.09, G:0.29, T:0.44
Consensus pattern (13 bp):
AGTCAGTTTGTTG
Found at i:137237 original size:10 final size:9
Alignment explanation
Indices: 137211--137263 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 9
137201 CCTTTCCTCA
*
137211 AAAGAAAAA
1 AAAGAAAAG
137220 AAATGAAAATG
1 AAA-GAAAA-G
137231 AAAGAAAAG
1 AAAGAAAAG
137240 AAAAGAAAAG
1 -AAAGAAAAG
137250 AAA-AAGAAG
1 AAAGAA-AAG
137259 AAAGA
1 AAAGA
137264 GATTAGATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
8 2 0.05
9 13 0.34
10 20 0.53
11 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:137241 original size:5 final size:5
Alignment explanation
Indices: 137210--137253 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
137200 CCCTTTCCTC
137210 AAAAG AAAA- AAAATG AAAATG -AAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAA-G AAAA-G AAAAG AAAAG AAAAG AAAAG AAAA
137254 AGAAGAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 5 0.14
5 25 0.69
6 6 0.17
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:137252 original size:25 final size:24
Alignment explanation
Indices: 137210--137261 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
137200 CCCTTTCCTC
*
137210 AAAAGAAAAAAAATGAAAATGAAAG
1 AAAAGAAAAAAAATGAAAAAG-AAG
137235 AAAAGAAAAGAAAA-GAAAAAGAAG
1 AAAAGAAAA-AAAATGAAAAAGAAG
137259 AAA
1 AAA
137262 GAGATTAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 15 0.60
26 4 0.16
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAAGAAAAAAAATGAAAAAGAAG
Found at i:151809 original size:4 final size:4
Alignment explanation
Indices: 151795--151829 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
151785 TTACTTAAAG
*
151795 GTTT TTTT GTTT GTTT GTTT GTTT GTTT GTGTT GT
1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GT-TT GT
151830 GGCAATAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (4 bp):
GTTT
Found at i:152680 original size:59 final size:60
Alignment explanation
Indices: 152613--152774 Score: 258
Period size: 60 Copynumber: 2.7 Consensus size: 60
152603 GCTAATTGTT
*
152613 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATC-TTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
*
152672 CAAATAAGGGCCTAACGTTATTG--AAAATGCTCAAATAAGGACCCGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACG-T-TTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
*
152732 CAAATAAGGGCCTAACGTTTGCCAAATTGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
152775 TGACATCAGT
Statistics
Matches: 94, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
58 3 0.03
59 42 0.45
60 46 0.49
61 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:152915 original size:31 final size:31
Alignment explanation
Indices: 152877--152977 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 31
152867 AGAGATCAGA
152877 CCCTTATTTAAGCATTTTGACAAACGTTAGG
1 CCCTTATTTAAGCATTTTGACAAACGTTAGG
* ** **
152908 CCCTTATTT-GGTCAAATT-A-AAA-GATCGGG
1 CCCTTATTTAAG-CATTTTGACAAACG-TTAGG
* *
152937 CCCTT-TTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTAAGCATTTTGACAAACGTTAGG
152967 CCCTTATTTAA
1 CCCTTATTTAA
152978 AAAAAGGGTA
Statistics
Matches: 51, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
28 8 0.16
29 12 0.24
30 13 0.25
31 18 0.35
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (31 bp):
CCCTTATTTAAGCATTTTGACAAACGTTAGG
Found at i:152973 original size:59 final size:60
Alignment explanation
Indices: 152813--152975 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
152803 TTTTCGATGC
* *
152813 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCTCTTATTTGGCCAAATTAAGAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* * * *
152873 CAGACCCTTATTTAAGCATTTTGACAAACGTTAGGCCCTTATTTGGTCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
*
152933 CGGGCCCTT-TTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
152976 AAAAAAAGGG
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 32 0.34
60 61 0.66
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:153108 original size:4 final size:4
Alignment explanation
Indices: 153099--153141 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
153089 CGTACTTCTC
*
153099 TAGA TAGA TAGA TAGA T--A TAGA TAGA TATA TAGA TAGA TAGA T
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA T
153142 TCATTGATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
4 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.30
Consensus pattern (4 bp):
TAGA
Found at i:153122 original size:18 final size:18
Alignment explanation
Indices: 153099--153134 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
153089 CGTACTTCTC
153099 TAGATAGATAGATAGATA
1 TAGATAGATAGATAGATA
*
153117 TAGATAGATATATAGATA
1 TAGATAGATAGATAGATA
153135 GATAGATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (18 bp):
TAGATAGATAGATAGATA
Found at i:169092 original size:21 final size:21
Alignment explanation
Indices: 169054--169096 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
169044 TTGTTCTTTG
169054 CTTCTCCCGCCATCTCTTCTTC
1 CTTCTCCCGCCATCTCTT-TTC
* *
169076 CTTC-CCCTCCATTTCTTTTC
1 CTTCTCCCGCCATCTCTTTTC
169096 C
1 C
169097 GCCGTCGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.05, C:0.49, G:0.02, T:0.44
Consensus pattern (21 bp):
CTTCTCCCGCCATCTCTTTTC
Found at i:172071 original size:5 final size:5
Alignment explanation
Indices: 172061--172104 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
172051 CATAAAAGAT
*
172061 AAAAG AAAAG AAAAG AAAAG ACAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
172105 ATACAGTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:173176 original size:23 final size:23
Alignment explanation
Indices: 173146--173191 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
173136 TATCTATTGC
* * *
173146 ACAAATTGTAACGGATTTTTTTG
1 ACAAATTGCAACGAATTATTTTG
173169 ACAAATTGCAACGAATTATTTTG
1 ACAAATTGCAACGAATTATTTTG
173192 GCTCTCTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (23 bp):
ACAAATTGCAACGAATTATTTTG
Done.