Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014399.1 Corchorus capsularis cultivar CVL-1 contig14420, 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: 46099
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4658 original size:32 final size:32
Alignment explanation
Indices: 4621--4690 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
4611 GAGGAAACTT
* *
4621 TATATTTTTCGATTGTACCCTTATTTTTAAAA
1 TATATTTTCCAATTGTACCCTTATTTTTAAAA
* *
4653 TATA-TTTCCAATTGTATCCTTTTTTTTAAAA
1 TATATTTTCCAATTGTACCCTTATTTTTAAAA
*
4684 CATATTT
1 TATATTT
4691 CTAAATTACC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (32 bp):
TATATTTTCCAATTGTACCCTTATTTTTAAAA
Found at i:4679 original size:31 final size:31
Alignment explanation
Indices: 4632--4691 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4622 ATATTTTTCG
*
4632 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCCA
* *
4663 ATTGTATCCTTTTTTTTAAAACATATTTC
1 ATTGTACCCTTATTTTTAAAACATATTTC
4692 TAAATTACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCCA
Found at i:4805 original size:59 final size:59
Alignment explanation
Indices: 4735--4853 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
4725 ACTCACTACG
4735 TGAGTGAATATATATGAAAATAAAATACTAATTATTATAAGGTAGTTTGTGACAGTTTT
1 TGAGTGAATATATATGAAAATAAAATACTAATTATTATAAGGTAGTTTGTGACAGTTTT
4794 TGAGTGAATATATATGAAAATAAAATACTAATTATTATAAGGTAGTTTGTGACAGTTTT
1 TGAGTGAATATATATGAAAATAAAATACTAATTATTATAAGGTAGTTTGTGACAGTTTT
4853 T
1 T
4854 TTTAAATGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.39
Consensus pattern (59 bp):
TGAGTGAATATATATGAAAATAAAATACTAATTATTATAAGGTAGTTTGTGACAGTTTT
Found at i:6251 original size:23 final size:23
Alignment explanation
Indices: 6225--6309 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
6215 ATAAAGAAAG
6225 TTATCAAAATTCTATAGGGAGGT
1 TTATCAAAATTCTATAGGGAGGT
* * *
6248 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTCTATAGGGAGGT
* *
6271 TTATCAAAATTTTATAGCGAGG-
1 TTATCAAAATTCTATAGGGAGGT
6293 TTATCACAAATTC-ATAG
1 TTATCA-AAATTCTATAG
6310 TGTGATTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 10 0.19
23 44 0.81
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTCTATAGGGAGGT
Found at i:6309 original size:22 final size:21
Alignment explanation
Indices: 6201--6328 Score: 80
Period size: 23 Copynumber: 5.7 Consensus size: 21
6191 AAAATTTGTA
* * *
6201 GTTATCAAGATTTCATAAAGAAA
1 GTTATCAAAATTTCAT--AGGAG
6224 GTTATCAAAA-TTCTATAGGGAG
1 GTTATCAAAATTTC-ATA-GGAG
*
6246 GTTTATCAAAATTTTATAGGAAG
1 G-TTATCAAAATTTCATAGG-AG
* *
6269 ATTTATCAAAATTTTATAGCGAG
1 -GTTATCAAAATTTCATAG-GAG
*
6292 GTTATCACAAA-TTCATAGTGTG
1 GTTATCA-AAATTTCATAG-GAG
*
6314 ATTATCAAAATTTCA
1 GTTATCAAAATTTCA
6329 GAGTGCGATT
Statistics
Matches: 86, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
21 4 0.05
22 32 0.37
23 47 0.55
24 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGAG
Found at i:6333 original size:22 final size:22
Alignment explanation
Indices: 6293--6340 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
6283 TATAGCGAGG
* *
6293 TTATCACAAATTCATAGTGTGA
1 TTATCACAAATTCAGAGTGCGA
6315 TTATCA-AAATTTCAGAGTGCGA
1 TTATCACAAA-TTCAGAGTGCGA
6337 TTAT
1 TTAT
6341 ATGGAGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCACAAATTCAGAGTGCGA
Found at i:15124 original size:5 final size:5
Alignment explanation
Indices: 15114--15148 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
15104 ACACAAATAT
15114 CATCC CATCC CATCC CATCC CATCC CATCC CATCC
1 CATCC CATCC CATCC CATCC CATCC CATCC CATCC
15149 GTCATCCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CATCC
Found at i:17587 original size:75 final size:75
Alignment explanation
Indices: 17464--17608 Score: 263
Period size: 75 Copynumber: 1.9 Consensus size: 75
17454 GCACATTTTG
* *
17464 TGTAATCTGTTACTAGCTGATTTGGATACAGCATATAAAGAAATATGTAAATCGATATGCAGACA
1 TGTAATCTGTTACCAGCTGATTTGGATACAGCATATAAAGAAATATGTAAATAGATATGCAGACA
17529 TCTGTATATA
66 TCTGTATATA
*
17539 TGTAATCTGTTACCAGCTGATTTGGATACAGCATATAAAGAAATATGTATATAGATATGCAGACA
1 TGTAATCTGTTACCAGCTGATTTGGATACAGCATATAAAGAAATATGTAAATAGATATGCAGACA
17604 TCTGT
66 TCTGT
17609 CCATTAAGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (75 bp):
TGTAATCTGTTACCAGCTGATTTGGATACAGCATATAAAGAAATATGTAAATAGATATGCAGACA
TCTGTATATA
Found at i:18796 original size:49 final size:49
Alignment explanation
Indices: 18742--18891 Score: 255
Period size: 49 Copynumber: 3.1 Consensus size: 49
18732 TGATAATATC
* *
18742 CCATATAGATGTAAAAATACCACTATATATCACATTCTTTTGCCAAAGA
1 CCATATAGATGTAAGAATACCACTATATATCACATTCTATTGCCAAAGA
* * *
18791 CCATATAAATGTAAGAACACCACTATAAATCACATTCTATTGCCAAAGA
1 CCATATAGATGTAAGAATACCACTATATATCACATTCTATTGCCAAAGA
18840 CCATATAGATGTAAGAATACCACTATATATCACATTCTATTGCCAAAGA
1 CCATATAGATGTAAGAATACCACTATATATCACATTCTATTGCCAAAGA
18889 CCA
1 CCA
18892 CATTAAGCTA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 93 1.00
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (49 bp):
CCATATAGATGTAAGAATACCACTATATATCACATTCTATTGCCAAAGA
Found at i:22089 original size:2 final size:2
Alignment explanation
Indices: 22084--22111 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22074 AAATATTTAG
22084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22112 CTAATTACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25182 original size:32 final size:32
Alignment explanation
Indices: 25141--25205 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
25131 GCACCTTGAG
*
25141 CCCGTGAAAAAACTTGCACAAAGTGAGGGGAT
1 CCCGTGAAAAAAATTGCACAAAGTGAGGGGAT
*
25173 CCCGTGAAAAAAATTGCACAAATTGAGGGGAT
1 CCCGTGAAAAAAATTGCACAAAGTGAGGGGAT
25205 C
1 C
25206 AGCTCCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.17
Consensus pattern (32 bp):
CCCGTGAAAAAAATTGCACAAAGTGAGGGGAT
Found at i:27444 original size:17 final size:16
Alignment explanation
Indices: 27422--27459 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
27412 TCTTGGTATA
27422 ATTATTATTATAATAAT
1 ATTATTATTATAAT-AT
*
27439 ATTATTATTATTATAT
1 ATTATTATTATAATAT
27455 ATTAT
1 ATTAT
27460 CATCATCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATTATTATAATAT
Found at i:30837 original size:144 final size:144
Alignment explanation
Indices: 30577--31155 Score: 899
Period size: 144 Copynumber: 4.0 Consensus size: 144
30567 GATGCTCAGT
*
30577 TTCACTATGAAGCA-TTTGTGCTGAACTCAAAGGGAACCACAACCCTACGATAAAAAATAAACTG
1 TTCACTATGAAGCACTGTGTGCTGAACTCAAAGGGAACCACAACCCTACGAT-AAAAATAAACTG
* *
30641 GATAAGCTGAAGAAAAGGGATCATGTCTTCTTCACGTTGAGTCCGGAAGTCCAAGCTGCCGCATT
65 GATAAGCTGAAGAAGAGGGATCATGTCTTCTTCATGTTGAGTCCGGAAGTCCAAGCTGCCGCATT
30706 CATCCGCGAGGGAGC
130 CATCCGCGAGGGAGC
* * * ***
30721 TTCACTATGAAGCATTATGTGCTGAACTCAAAGGGAACCACAACCTTACGATAAAAATAAACCAA
1 TTCACTATGAAGCACTGTGTGCTGAACTCAAAGGGAACCACAACCCTACGATAAAAATAAACTGG
30786 ATAAGCTGAAGAAGAGGGATCATGTCTTCTTCATGTTGAGTCCGGAAGTCCAAGCTGCCGCATTC
66 ATAAGCTGAAGAAGAGGGATCATGTCTTCTTCATGTTGAGTCCGGAAGTCCAAGCTGCCGCATTC
* **
30851 ATCTGCGAATGAGC
131 ATCCGCGAGGGAGC
* *
30865 TTCACTATGAAGCACTGTGTGCTGAACACAAAGGGAACCACAACCCTACGACAAAAATAAACTGG
1 TTCACTATGAAGCACTGTGTGCTGAACTCAAAGGGAACCACAACCCTACGATAAAAATAAACTGG
* *
30930 ATAAGCTGAAGAAGAGGGATCATGTCTTATTCATGTTGAGTCCGGAAGTCCAAGCTGCCACATTC
66 ATAAGCTGAAGAAGAGGGATCATGTCTTCTTCATGTTGAGTCCGGAAGTCCAAGCTGCCGCATTC
* *
30995 GTCCGCGAGAGAGC
131 ATCCGCGAGGGAGC
** * *
31009 TTCACTATGAAGCACTGTGTGCTGAACTCAAAAAGAACCACAACCCTACGACAAAAAATAAATTG
1 TTCACTATGAAGCACTGTGTGCTGAACTCAAAGGGAACCACAACCCTACGA-TAAAAATAAACTG
* * * *
31074 GATAAGCTGAATAAGAGGGATCATGTCTTCTTCATGTTGAGTCTGGAAGTCCAAGCTGTCGTATT
65 GATAAGCTGAAGAAGAGGGATCATGTCTTCTTCATGTTGAGTCCGGAAGTCCAAGCTGCCGCATT
31139 CATCCGCGAGGGAGC
130 CATCCGCGAGGGAGC
31154 TT
1 TT
31156 TCATTTGTTG
Statistics
Matches: 396, Mismatches: 37, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
144 276 0.70
145 120 0.30
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (144 bp):
TTCACTATGAAGCACTGTGTGCTGAACTCAAAGGGAACCACAACCCTACGATAAAAATAAACTGG
ATAAGCTGAAGAAGAGGGATCATGTCTTCTTCATGTTGAGTCCGGAAGTCCAAGCTGCCGCATTC
ATCCGCGAGGGAGC
Found at i:35306 original size:53 final size:50
Alignment explanation
Indices: 35237--35519 Score: 216
Period size: 49 Copynumber: 5.6 Consensus size: 50
35227 TTTCGTGCTA
* *
35237 TTTCCCAAAACACCCTTCCCGGACGGAAGGCGCTATTTAATTTTTACTCGCTT
1 TTTCCCAAAACACCCTTCCCGGACGGAAGACGC---TTAATTTTTACTCACTT
* * ** * * * *
35290 TTTCCCAGAACGCCCTTCCCAAATGGAAGACG-TTAGTTTTTGCTTACTT
1 TTTCCCAAAACACCCTTCCCGGACGGAAGACGCTTAATTTTTACTCACTT
* * ** * ** *
35339 TTTGCAAAAATGCCCTTCCCAGACGGAAGACGCTT-ATTTTCGCACACTT
1 TTTCCCAAAACACCCTTCCCGGACGGAAGACGCTTAATTTTTACTCACTT
* * *
35388 TTTCCCAAAACACCCTTCCCGGATGGAAGGCGCTATTTAATTTTTACTCGCTT
1 TTTCCCAAAACACCCTTCCCGGACGGAAGACGC---TTAATTTTTACTCACTT
* * * *
35441 TTTCCCAGAACTCCCTTCCCGGACGGAAGACACTT-ATTTTTACCTGA--T
1 TTTCCCAAAACACCCTTCCCGGACGGAAGACGCTTAATTTTTA-CTCACTT
* **
35489 TTTCCTAAAATGCCCTTCCCGGACGGAAGAC
1 TTTCCCAAAACACCCTTCCCGGACGGAAGAC
35520 ACTGATTTTT
Statistics
Matches: 182, Mismatches: 42, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
48 28 0.15
49 82 0.45
50 6 0.03
52 2 0.01
53 64 0.35
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (50 bp):
TTTCCCAAAACACCCTTCCCGGACGGAAGACGCTTAATTTTTACTCACTT
Found at i:35510 original size:48 final size:49
Alignment explanation
Indices: 35453--35874 Score: 237
Period size: 48 Copynumber: 8.4 Consensus size: 49
35443 TCCCAGAACT
*
35453 CCCTTCCCGGACGGAAGACACTTATTTTTACCTG-ATTTTCCTAAAATG
1 CCCTTCCCGGACGGAAGACACTTATTTTTACCTGTTTTTTCCTAAAATG
* ** *
35501 CCCTTCCCGGACGGAAGACACTGATTTTTACCTGTTTTTTTTTTTAAAAAAACG
1 CCCTTCCCGGACGGAAGACACTTATTTTTACCTG--TTTTTTCCT---AAAATG
* * * * *
35555 CCATTCCCAGACGGAAGACACTGATTTTTACCATTTTTTTTTTTCTTTTCCTAAAACG
1 CCCTTCCCGGACGGAAGACACTTATTTTTACC--------TGTT-TTTTCCTAAAATG
* * * ** * * *
35613 CTCTTCTCGGACGGAAGGCACCAATCTTTACC-GGTTTTTCCCAAAATG
1 CCCTTCCCGGACGGAAGACACTTATTTTTACCTGTTTTTTCCTAAAATG
* * * *
35661 -CCTTCCCGGACGGAAGGCACTTA-TTTTACTTGCTATTTTCCAAAAATG
1 CCCTTCCCGGACGGAAGACACTTATTTTTACCTG-TTTTTTCCTAAAATG
* * * ** * * *
35709 CCCTTCCCGGATGGGAGACGCTTATTTTTACCTACTTTTCCCCAAAGTG
1 CCCTTCCCGGACGGAAGACACTTATTTTTACCTGTTTTTTCCTAAAATG
* * * * **
35758 CCCTTCCCGGACAGAAGGCACTAATTTTTACTTGCTTTTTT-CTAAAACA
1 CCCTTCCCGGACGGAAGACACTTATTTTTACCTG-TTTTTTCCTAAAATG
* * * * * * *
35807 CCCATCCCGGATGGAAGGC-GTTAGTTTTA-CTCGCTTTTTCTTAAAATG
1 CCCTTCCCGGACGGAAGACACTTATTTTTACCT-GTTTTTTCCTAAAATG
* *
35855 CCCTTTCCGGACGAAAGACA
1 CCCTTCCCGGACGGAAGACA
35875 AGTTCGCTTT
Statistics
Matches: 279, Mismatches: 72, Indels: 45
0.70 0.18 0.11
Matches are distributed among these distances:
46 5 0.02
47 26 0.09
48 83 0.30
49 76 0.27
50 11 0.04
51 5 0.02
54 35 0.13
58 30 0.11
60 2 0.01
61 5 0.02
62 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (49 bp):
CCCTTCCCGGACGGAAGACACTTATTTTTACCTGTTTTTTCCTAAAATG
Found at i:35541 original size:151 final size:150
Alignment explanation
Indices: 35237--35528 Score: 426
Period size: 151 Copynumber: 1.9 Consensus size: 150
35227 TTTCGTGCTA
35237 TTTCCCAAAACACCCTTCCCGGACGGAAGGCGCTATTTAATTTTTACTCGCTTTTTCCCAGAACG
1 TTTCCCAAAACACCCTTCCCGGACGGAAGGCGCTATTTAATTTTTACTCGCTTTTTCCCAGAACG
* * * * *
35302 CCCTTCCCAAATGGAAGACGTTAGTTTTTGCTTACTTTTTGCAAAAATGCCCTTCCCAGACGGAA
66 CCCTTCCCAAACGGAAGACCTTAGTTTTTCCTGAC-TTTTCCAAAAATGCCCTTCCCAGACGGAA
* *
35367 GACGCTTATTTTCGCACACTT
130 GACACTGATTTTCGCACACTT
* *
35388 TTTCCCAAAACACCCTTCCCGGATGGAAGGCGCTATTTAATTTTTACTCGCTTTTTCCCAGAACT
1 TTTCCCAAAACACCCTTCCCGGACGGAAGGCGCTATTTAATTTTTACTCGCTTTTTCCCAGAACG
** * *
35453 CCCTTCCCGGACGGAAGACACTTA-TTTTTACCTGA-TTTTCCTAAAATGCCCTTCCCGGACGGA
66 CCCTTCCCAAACGGAAGAC-CTTAGTTTTT-CCTGACTTTTCCAAAAATGCCCTTCCCAGACGGA
35516 AGACACTGATTTT
129 AGACACTGATTTT
35529 TACCTGTTTT
Statistics
Matches: 126, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
150 36 0.29
151 84 0.67
152 6 0.05
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (150 bp):
TTTCCCAAAACACCCTTCCCGGACGGAAGGCGCTATTTAATTTTTACTCGCTTTTTCCCAGAACG
CCCTTCCCAAACGGAAGACCTTAGTTTTTCCTGACTTTTCCAAAAATGCCCTTCCCAGACGGAAG
ACACTGATTTTCGCACACTT
Found at i:35568 original size:54 final size:53
Alignment explanation
Indices: 35495--35598 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 53
35485 TGATTTTCCT
* * * *
35495 AAAATGCCCTTCCCGGACGGAAGACACTGATTTTTACCTGTTTTTTTTTTTAAA
1 AAAACGCCATTCCCAGACGGAAGACACTGATTTTTACC-ATTTTTTTTTTTAAA
35549 AAAACGCCATTCCCAGACGGAAGACACTGATTTTTACCATTTTTTTTTTT
1 AAAACGCCATTCCCAGACGGAAGACACTGATTTTTACCATTTTTTTTTTT
35599 CTTTTCCTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 11 0.24
54 35 0.76
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (53 bp):
AAAACGCCATTCCCAGACGGAAGACACTGATTTTTACCATTTTTTTTTTTAAA
Found at i:35733 original size:49 final size:49
Alignment explanation
Indices: 35600--35867 Score: 202
Period size: 49 Copynumber: 5.5 Consensus size: 49
35590 TTTTTTTTTC
* * * * ** * * *
35600 TTTTCCTAAAACGCTCTTCTCGGACGGAAGGCACCAATCTTTAC-CGGT
1 TTTTCCAAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCT
*
35648 TTTTCCCAAAATG-CCTTCCCGGACGGAAGGCACTTA-TTTTACTTGCT
1 TTTTCCAAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCT
* * * * * *
35695 ATTTTCCAAAAATGCCCTTCCCGGATGGGAGACGCTTATTTTTACCTACT
1 -TTTTCCAAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCT
* * * * *
35745 TTTCCCCAAAGTGCCCTTCCCGGACAGAAGGCACTAATTTTTACTTGCT
1 TTTTCCAAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCT
* * ** * * * * *
35794 TTTTTCTAAAACACCCATCCCGGATGGAAGGC-GTTAGTTTTACTCGCT
1 TTTTCCAAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCT
** *
35842 TTTTCTTAAAATGCCCTTTCCGGACG
1 TTTTCCAAAAATGCCCTTCCCGGACG
35868 AAAGACAAGT
Statistics
Matches: 169, Mismatches: 47, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
46 5 0.03
47 21 0.12
48 54 0.32
49 80 0.47
50 9 0.05
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (49 bp):
TTTTCCAAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCT
Found at i:35846 original size:98 final size:96
Alignment explanation
Indices: 35639--35846 Score: 235
Period size: 98 Copynumber: 2.1 Consensus size: 96
35629 GGCACCAATC
* * *
35639 TTTACCGGTTTTT-CCCAAAATGCCTTCCCGGACGGAAGGCACTTATTTTACTTGCTATTTTCCA
1 TTTACCGCTTTTTCCCCAAAATGCCTTCCCGGACAGAAGGCACTAATTTTACTTGCTATTTTCCA
* * *
35703 AAAATGCCCTTCCCGGATGGGAGACGCTTATT
66 AAAA-GCCCATCCCGGATGGAAGACGCTTAGT
* * *
35735 TTTACCTAC-TTTTCCCCAAAGTGCCCTTCCCGGACAGAAGGCACTAATTTTTACTTGCTTTTTT
1 TTTACC-GCTTTTTCCCCAAAATG-CCTTCCCGGACAGAAGGCACTAA-TTTTACTTGCTATTTT
* *
35799 CTAAAACA-CCCATCCCGGATGGAAGGCG-TTAGT
63 CCAAAA-AGCCCATCCCGGATGGAAGACGCTTAGT
35832 TTTACTCGCTTTTTC
1 TTTAC-CGCTTTTTC
35847 TTAAAATGCC
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
96 10 0.11
97 18 0.19
98 44 0.47
99 20 0.22
100 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.35
Consensus pattern (96 bp):
TTTACCGCTTTTTCCCCAAAATGCCTTCCCGGACAGAAGGCACTAATTTTACTTGCTATTTTCCA
AAAAGCCCATCCCGGATGGAAGACGCTTAGT
Found at i:37451 original size:19 final size:19
Alignment explanation
Indices: 37422--37458 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
37412 ATTGAAAACA
37422 AAATAAAAACTACCTAATTT
1 AAATAAAAACTACC-AATTT
37442 AAAT-AAAACTACCAATT
1 AAATAAAAACTACCAATT
37459 AAAGGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATAAAAACTACCAATTT
Found at i:37534 original size:41 final size:41
Alignment explanation
Indices: 37479--37563 Score: 120
Period size: 43 Copynumber: 2.1 Consensus size: 41
37469 TATAATATTT
* *
37479 AAATTGTATTTATATCAT-TTAAAA-AACTACCTATTTAAA
1 AAATTGTATTTATATCATCTTAAAATAACTACCAATTAAAA
37518 AAATTGTCATTTTATATCATCTTAAAATAACTACCAATTAAAA
1 AAATTGT-A-TTTATATCATCTTAAAATAACTACCAATTAAAA
37561 AAA
1 AAA
37564 ACTGTCACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 7 0.17
40 1 0.03
41 10 0.25
42 6 0.15
43 16 0.40
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (41 bp):
AAATTGTATTTATATCATCTTAAAATAACTACCAATTAAAA
Found at i:42652 original size:6 final size:6
Alignment explanation
Indices: 42643--42672 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
42633 AAATGGAGAC
42643 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
42673 AAATACCCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
GAAAAT
Done.