Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold438
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: 45560
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1518 original size:40 final size:40
Alignment explanation
Indices: 1474--1553 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
1464 CAAAATCTCA
*
1474 AAGTAAATCTTGGATCTCTATCTGACACAATAGACAATGG
1 AAGTAAATCTTGGATCTCTATCTGACACAATAAACAATGG
1514 AAGTAAATCTTGGATCTCTATCTGACACAATAAACAATGG
1 AAGTAAATCTTGGATCTCTATCTGACACAATAAACAATGG
1554 CACCCCGTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (40 bp):
AAGTAAATCTTGGATCTCTATCTGACACAATAAACAATGG
Found at i:7413 original size:22 final size:22
Alignment explanation
Indices: 7383--7425 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
7373 AGACTTCAAA
* * *
7383 TAAATTAAAGTAAAATCAAAGG
1 TAAAATAAAATAAAATAAAAGG
7405 TAAAATAAAATAAAATAAAAG
1 TAAAATAAAATAAAATAAAAG
7426 AGATAATCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.21
Consensus pattern (22 bp):
TAAAATAAAATAAAATAAAAGG
Found at i:9793 original size:40 final size:40
Alignment explanation
Indices: 9676--9859 Score: 234
Period size: 39 Copynumber: 4.7 Consensus size: 40
9666 GCTACTCGTT
*
9676 CAAATGCCTTCGGGACATAGCCC-G-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
9715 CAAATGCCTTCGGGACTTAACCC-GATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
9754 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
9794 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
9835 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9860 CATCATTCAA
Statistics
Matches: 131, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
39 60 0.46
40 60 0.46
41 11 0.08
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:27651 original size:47 final size:47
Alignment explanation
Indices: 27567--28254 Score: 1161
Period size: 47 Copynumber: 14.6 Consensus size: 47
27557 TATTTGAATA
27567 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
27616 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-ATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27662 AATGTGAAAGTGTATATATATGTGATAAGGCCTAAT-GCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
27710 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27757 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
27806 AATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27852 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27899 AATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27945 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
27994 AATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28040 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28087 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28134 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * * *
28181 AATGTGAAAGTGTATATATGCGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
28228 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
28255 TCCCGAAGGG
Statistics
Matches: 610, Mismatches: 18, Indels: 24
0.94 0.03 0.04
Matches are distributed among these distances:
46 157 0.26
47 309 0.51
48 63 0.10
49 81 0.13
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:27678 original size:95 final size:96
Alignment explanation
Indices: 27567--28254 Score: 1186
Period size: 95 Copynumber: 7.3 Consensus size: 96
27557 TATTTGAATA
27567 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
27632 TATGTGATAAGGCCGAATGGCC-ATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
27662 AATGTGAAAGTGTATATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* *
27726 TATGTGATAAGGCCGAATGGCCAATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
27757 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
27822 TATGTGATAAGGCCTAAT-GCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
27852 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
27915 TATGTGATAAGGCCTAAT-GCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
27945 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
28010 TATGTGATAAGGCCTAAT-GCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
28040 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
28103 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
28134 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * * * * * *
28197 TATGCGACAGGGCCGAGTGGCCAACGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
*
28228 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
28255 TCCCGAAGGG
Statistics
Matches: 576, Mismatches: 10, Indels: 15
0.96 0.02 0.02
Matches are distributed among these distances:
93 162 0.28
94 170 0.30
95 197 0.34
96 47 0.08
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (96 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
TATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:28423 original size:37 final size:35
Alignment explanation
Indices: 28373--28470 Score: 135
Period size: 37 Copynumber: 2.8 Consensus size: 35
28363 CCGAGCTCTA
28373 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGT-C-GGT
*
28410 AAGACCCGATGACTACGTGTGGAGATTTTGTCGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCGGT
* * *
28445 AAGACCC-ATAACTTCATGTGGAGATT
1 AAGACCCGATGACTACGTGTGGAGATT
28471 TCGTCTGAGC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
34 16 0.28
35 10 0.18
36 1 0.02
37 30 0.53
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (35 bp):
AAGACCCGATGACTACGTGTGGAGATTATGTCGGT
Found at i:29868 original size:79 final size:79
Alignment explanation
Indices: 29759--30006 Score: 379
Period size: 79 Copynumber: 3.1 Consensus size: 79
29749 GGGCTAAATC
29759 CCGAAGAGCATTCGTGCTAGTGATGTATCCGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
29824 ATCCGGACTAAGTT
66 ATCCGGACTAAGTT
29838 CCGAAGAGCATTCGTGCTAGTGATGTATCCGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
29903 ATCCGGACTAAGTT
66 ATCCGGACTAAGTT
* * *** * * * *
29917 CCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTA
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCG-ACTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* * *
29982 TATCCGGGCTAGGTC
65 TATCCGGACTAAGTT
29997 CCGAAGAGCA
1 CCGAAGAGCA
30007 ATCATGCTGG
Statistics
Matches: 156, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 109 0.70
80 47 0.30
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGAGCATTCGTGCTAGTGATGTATCCGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
ATCCGGACTAAGTT
Found at i:30018 original size:40 final size:40
Alignment explanation
Indices: 29759--30006 Score: 367
Period size: 40 Copynumber: 6.2 Consensus size: 40
29749 GGGCTAAATC
29759 CCGAAGAGCATTCGTGCTAGTGATGTATCC-GACTAAGTT
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
29798 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
29838 CCGAAGAGCATTCGTGCTAGTGATGTATCC-GACTAAGTT
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
29877 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
* ***
29917 CCGAAGAGCATTCGTGCTAGTGATATATCCGTG-CTAAACC
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCG-GACTAAGTT
* * * * * * *
29957 CCGAAGAGCATTTGTGCTGGTGTTATATCCGGGCTAGGTC
1 CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
29997 CCGAAGAGCA
1 CCGAAGAGCA
30007 ATCATGCTGG
Statistics
Matches: 195, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
39 70 0.36
40 124 0.64
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTT
Found at i:34102 original size:47 final size:47
Alignment explanation
Indices: 34018--34753 Score: 1260
Period size: 47 Copynumber: 15.6 Consensus size: 47
34008 TATTTGAATA
34018 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
34067 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
34114 AATGTGAAAGTTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAG-TGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34162 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
34209 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-ATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
34255 AATGTGAAAGTTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAG-TGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34303 AATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34349 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
34396 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34443 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
34492 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34539 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34586 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
34633 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * * *
34680 AATGTGAAAGTGTATATATGCGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
34727 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
34754 TCCCGAAGGG
Statistics
Matches: 655, Mismatches: 26, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
46 64 0.10
47 471 0.72
48 62 0.09
49 58 0.09
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:34973 original size:37 final size:37
Alignment explanation
Indices: 34872--34973 Score: 152
Period size: 37 Copynumber: 2.8 Consensus size: 37
34862 CCGAGCTCTA
*
34872 AAGACCCGATGACTAT-GTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACT-TCGTGTGGAGATTTTGTCCGGGT
*
34909 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTTCGTGTGGAGATTTTGTCCGGGT
* *
34946 AAGACCCGATAACTTCATGTGGAGATTT
1 AAGACCCGATGACTTCGTGTGGAGATTT
34974 CGTCTGAGCT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (37 bp):
AAGACCCGATGACTTCGTGTGGAGATTTTGTCCGGGT
Found at i:36039 original size:16 final size:16
Alignment explanation
Indices: 36014--36045 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36004 ACTAAATCAT
36014 GCTCTAATACCAACCA
1 GCTCTAATACCAACCA
*
36030 GCTCTGATACCAACCA
1 GCTCTAATACCAACCA
36046 AATGTAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.38, G:0.09, T:0.19
Consensus pattern (16 bp):
GCTCTAATACCAACCA
Found at i:37675 original size:19 final size:20
Alignment explanation
Indices: 37651--37688 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
37641 GGTACCACCA
37651 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
37670 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
37689 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:38057 original size:46 final size:46
Alignment explanation
Indices: 37913--38038 Score: 189
Period size: 46 Copynumber: 2.7 Consensus size: 46
37903 AACCCGCCCC
* * *
37913 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCA
* * *
37959 TAAATGAACTCGGACTCAACTCAACGACTTCGGACATTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCA
*
38005 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
38039 TGCTCAACCA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCA
Found at i:40398 original size:43 final size:44
Alignment explanation
Indices: 40337--40486 Score: 152
Period size: 43 Copynumber: 3.5 Consensus size: 44
40327 CTAGACGTGA
*
40337 TCTTACATGTAATCAAATATCGATGCC-ACTGTCCCAGACAGGG
1 TCTTACATGAAATCAAATATCGATGCCAACTGTCCCAGACAGGG
* * *
40380 TCTTACATGAAATCAAATA-CGATACCGA-TGTCCCAGACATGG
1 TCTTACATGAAATCAAATATCGATGCCAACTGTCCCAGACAGGG
40422 TCTTACATGTAAATCATAAGT-T-GATGCCAAC-GTCCCAGAC-GTGG
1 TCTTACATG-AAATCA-AA-TATCGATGCCAACTGTCCCAGACAG-GG
** *
40466 TCTTACACAAAATCACATATC
1 TCTTACATGAAATCAAATATC
40487 AAAAATCCTA
Statistics
Matches: 89, Mismatches: 9, Indels: 18
0.77 0.08 0.16
Matches are distributed among these distances:
41 1 0.01
42 30 0.34
43 31 0.35
44 26 0.29
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (44 bp):
TCTTACATGAAATCAAATATCGATGCCAACTGTCCCAGACAGGG
Found at i:40425 original size:42 final size:41
Alignment explanation
Indices: 40337--40472 Score: 148
Period size: 42 Copynumber: 3.2 Consensus size: 41
40327 CTAGACGTGA
* *
40337 TCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGG
1 TCTTACATGAAATCAAATA-CGATGCCA-TGTCCCAGACATGG
*
40380 TCTTACATGAAATCAAATACGATACCGATGTCCCAGACATGG
1 TCTTACATGAAATCAAATACGATGCC-ATGTCCCAGACATGG
* * *
40422 TCTTACATGTAAATCATAAGT-TGATGCCAACGTCCCAGACGTGG
1 TCTTACATG-AAATCA-AA-TACGATGCC-ATGTCCCAGACATGG
40466 TCTTACA
1 TCTTACA
40473 CAAAATCACA
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
42 28 0.35
43 25 0.31
44 27 0.33
45 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (41 bp):
TCTTACATGAAATCAAATACGATGCCATGTCCCAGACATGG
Found at i:42463 original size:14 final size:16
Alignment explanation
Indices: 42444--42482 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
42434 AATAAACTGA
42444 TGATATATGACA-A-G
1 TGATATATGACATATG
*
42458 TGATATATGATATATG
1 TGATATATGACATATG
42474 TGATATATG
1 TGATATATG
42483 TTACGTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (16 bp):
TGATATATGACATATG
Found at i:42760 original size:45 final size:45
Alignment explanation
Indices: 42696--42786 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
42686 CTTGGAATTA
* * *
42696 AGAAATTTGAGCTTGTTGAGTTGGTCCGAGTTCGTGATATATGTG
1 AGAAATCTGAACTTGTTGAGTTGGTCCAAGTTCGTGATATATGTG
*
42741 AGAAATCTGAACTTGTTGAGTTGGTCCAAGTTCGTGGTATATGTG
1 AGAAATCTGAACTTGTTGAGTTGGTCCAAGTTCGTGATATATGTG
42786 A
1 A
42787 AGTATCCGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.24, C:0.10, G:0.30, T:0.36
Consensus pattern (45 bp):
AGAAATCTGAACTTGTTGAGTTGGTCCAAGTTCGTGATATATGTG
Found at i:42818 original size:45 final size:45
Alignment explanation
Indices: 42704--42806 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
42694 TAAGAAATTT
*
42704 GAGCTTGTTGAGTTGGTCCGAGTTCGTGATATATGTGAGAAATCT
1 GAGCTTGTTGAGTTGGTCCGAGTTCGTGATATATGTGAGAAATCC
* * * *
42749 GAACTTGTTGAGTTGGTCCAAGTTCGTGGTATATGTGA-AGTATCC
1 GAGCTTGTTGAGTTGGTCCGAGTTCGTGATATATGTGAGA-AATCC
42794 GAGCTTGTTGAGT
1 GAGCTTGTTGAGT
42807 CGGTTTGAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
44 1 0.02
45 50 0.98
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (45 bp):
GAGCTTGTTGAGTTGGTCCGAGTTCGTGATATATGTGAGAAATCC
Found at i:44834 original size:76 final size:76
Alignment explanation
Indices: 44708--44861 Score: 254
Period size: 76 Copynumber: 2.0 Consensus size: 76
44698 GCACACGGGT
* *
44708 GTGTGGCCTGGCTGTGTGGTTCAATTTATTTTGCAGGCATCATAAATAGAGAGTTACACGGCCTA
1 GTGTGGCCTGGCTGTGTGGTTCAATTTATTTTGCAGACATCATAAATAGAGAGTTACACGACCTA
*
44773 AGGACACAGGC
66 AAGACACAGGC
* *
44784 GTGTGGCCTGGCTGTGTGGTTCAATTTATTTTGCAGACGTCATTAATAGAGAGTTACACGACCTA
1 GTGTGGCCTGGCTGTGTGGTTCAATTTATTTTGCAGACATCATAAATAGAGAGTTACACGACCTA
*
44849 AAGACACGGGC
66 AAGACACAGGC
44860 GT
1 GT
44862 ATCCCCCTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (76 bp):
GTGTGGCCTGGCTGTGTGGTTCAATTTATTTTGCAGACATCATAAATAGAGAGTTACACGACCTA
AAGACACAGGC
Done.