Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3265
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: 41302
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4898 original size:40 final size:40
Alignment explanation
Indices: 4850--4975 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 40
4840 GGACTAAGAT
*
4850 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTT
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* * *
4890 TCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
4930 CCAAAGGCATTTGTG-TGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCT-AG-TGACTATATCCGGGCTAAGTC
4969 CCGAAGG
1 CCGAAGG
4976 TACTTGGGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
39 14 0.19
40 59 0.80
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:12992 original size:39 final size:39
Alignment explanation
Indices: 12867--12992 Score: 173
Period size: 40 Copynumber: 3.2 Consensus size: 39
12857 GGACTAAGAT
* *
12867 CCGAAGGCATTTGTGCTAG-TGACTATATCAGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTG-CTATATC-CGGCTAAGTC
* *
12907 CCGAAGGCTTTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAGTC
*
12947 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGCTAAATC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGCTAAGTC
12986 CCGAAGG
1 CCGAAGG
12993 TACTTGGGTT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
39 15 0.19
40 61 0.79
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGTTGCTATATCCGGCTAAGTC
Found at i:21263 original size:40 final size:40
Alignment explanation
Indices: 21209--21845 Score: 977
Period size: 40 Copynumber: 15.7 Consensus size: 40
21199 CAATTGACTT
* ** * * *
21209 CGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTT
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
* * *
21249 CGGGTCTTAGCCCGGATATATCAACTTGCACAATTGCCTT
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
21289 CGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTG
21331 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
* * * *
21371 CGGGTCTTAGCCCGGATATATCAACTTGCACAATTGCATT
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
21411 CGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTG
21453 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
** * *
21493 CGGGTCTTAGCCCGGATATATCAACTTTCACAATTGCCTT
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
21533 CGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTG
21575 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
*
21615 CGGGTCTTAGCTCGGATATATCAACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
* * *
21655 CGGGTCTTAGCCCGGATATATCAACTTGCACAATTGCCTT
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
*
21695 CGGGTCTTAGCCCGGATATATATCGACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTG
*
21737 CGGGTCTTAGCCCGGATATATATCGACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTG
21779 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
21819 CGGGTCTTAGCCCGGATATATCAACTC
1 CGGGTCTTAGCCCGGATATATCAACTC
21846 TCATGACACA
Statistics
Matches: 553, Mismatches: 36, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
40 366 0.66
42 187 0.34
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTG
Found at i:21347 original size:82 final size:80
Alignment explanation
Indices: 21209--21845 Score: 977
Period size: 82 Copynumber: 7.8 Consensus size: 80
21199 CAATTGACTT
* ** * * *
21209 CGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAAC
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
* * *
21274 TTGCACAATTGCCTT
66 TCGCACAAATGCCTG
21289 CGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCA
1 CGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCA
21354 ACTCGCACAAATGCCTG
64 ACTCGCACAAATGCCTG
* * * *
21371 CGGGTCTTAGCCCGGATATATCAACTTGCACAATTGCATTCGGGTCTTAGCCCGGATATATATCA
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCA
21436 ACTCGCACAAATGCCTG
64 ACTCGCACAAATGCCTG
21453 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
** * *
21518 TTTCACAATTGCCTT
66 TCGCACAAATGCCTG
21533 CGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCA
1 CGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCA
21598 ACTCGCACAAATGCCTG
64 ACTCGCACAAATGCCTG
*
21615 CGGGTCTTAGCTCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
* * *
21680 TTGCACAATTGCCTT
66 TCGCACAAATGCCTG
*
21695 CGGGTCTTAGCCCGGATATATATCGACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATAT
1 CGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGG--ATATAT
*
21760 CGACTCGCACAAATGCCTG
62 CAACTCGCACAAATGCCTG
21779 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
21844 TC
66 TC
21846 TCATGACACA
Statistics
Matches: 510, Mismatches: 37, Indels: 20
0.90 0.07 0.04
Matches are distributed among these distances:
80 173 0.34
82 301 0.59
84 36 0.07
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (80 bp):
CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
TCGCACAAATGCCTG
Found at i:21413 original size:122 final size:122
Alignment explanation
Indices: 21209--21845 Score: 1030
Period size: 122 Copynumber: 5.2 Consensus size: 122
21199 CAATTGACTT
* ** * * *
21209 CGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAAC
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
21274 TTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
66 TTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
21331 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
*
21396 TTGCACAATTGCATTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
66 TTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
21453 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
*
21518 TTTCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
66 TTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
*
21575 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCTCGGATATATCAAC
1 CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
* * * * * *
21640 TCGCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTTGCACAATTGCCTT
66 TTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
*
21695 CGGGTCTTAGCCCGGATATATATCGACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATAT
1 CGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGG--ATATAT
* * * *
21760 CGACTCGCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTG
62 CAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
21819 CGGGTCTTAGCCCGGATATATCAACTC
1 CGGGTCTTAGCCCGGATATATCAACTC
21846 TCATGACACA
Statistics
Matches: 487, Mismatches: 24, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
120 37 0.08
122 374 0.77
124 76 0.16
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (122 bp):
CGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAAC
TTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTG
Found at i:29037 original size:40 final size:40
Alignment explanation
Indices: 28985--29471 Score: 724
Period size: 40 Copynumber: 12.0 Consensus size: 40
28975 ATTACCACAA
* * * ** *
28985 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* * *
29025 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* *
29065 GCACAATTGCCTTCGGGTCTTA-CCCGGATATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTC
29106 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
*
29146 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* *
29186 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTC
*
29228 GCACAAATGCCTGCGGGTCTTATCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
*
29268 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* *
29308 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTC
*
29350 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATATCGACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTC
29392 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
29432 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
29472 TCATGACACA
Statistics
Matches: 412, Mismatches: 28, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
39 5 0.01
40 257 0.62
41 31 0.08
42 119 0.29
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
Found at i:29234 original size:82 final size:80
Alignment explanation
Indices: 28985--29471 Score: 724
Period size: 82 Copynumber: 6.0 Consensus size: 80
28975 ATTACCACAA
* * * ** * * *
28985 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
*
29050 CGGATATATCAACTT
66 CGGATATATCAACTC
* *
29065 GCACAATTGCCTTCGGGTCTTA-CCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
29129 CCCGGATATATCAACTC
64 CCCGGATATATCAACTC
* * *
29146 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
29211 CGGATATATATCAACTC
66 CGG--ATATATCAACTC
*
29228 GCACAAATGCCTGCGGGTCTTATCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
*
29293 CGGATATATCAACTT
66 CGGATATATCAACTC
* *
29308 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
*
29373 CCCGGATATATATCGACTC
64 CCCGG--ATATATCAACTC
29392 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
29457 CGGATATATCAACTC
66 CGGATATATCAACTC
29472 TCATGACACA
Statistics
Matches: 374, Mismatches: 24, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
79 5 0.01
80 106 0.28
81 66 0.18
82 161 0.43
84 36 0.10
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (80 bp):
GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
CGGATATATCAACTC
Found at i:29270 original size:122 final size:122
Alignment explanation
Indices: 28985--29465 Score: 820
Period size: 122 Copynumber: 3.9 Consensus size: 122
28975 ATTACCACAA
* * * ** * * *
28985 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
29050 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTA-CCCGGATATATATCAACTC
66 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
29106 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
29171 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
66 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
*
29228 GCACAAATGCCTGCGGGTCTTATCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
29293 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
66 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
*
29350 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATATCGACTCGCACAAATGCCTGCGGGTCTTAG
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
* * *
29415 CCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATAT
64 CCCGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATAT
29466 CAACTCTCAT
Statistics
Matches: 343, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
121 94 0.27
122 167 0.49
124 82 0.24
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (122 bp):
GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
Found at i:35412 original size:46 final size:46
Alignment explanation
Indices: 35362--35527 Score: 162
Period size: 46 Copynumber: 3.6 Consensus size: 46
35352 AGCATCCAAA
* *
35362 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAG
* * * * *
35408 CTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGGCATCTGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCCGAG
* *
35455 CTCGTTGAGTTG-GTCCGAGTTCATTTATGGATGCGAACG-CCTGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-GAG
*
35500 CTCGTTGAGTTGAGTCTGAGTTCACTTA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTA
35528 GGGGCGGGTT
Statistics
Matches: 96, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 18 0.19
46 47 0.49
47 19 0.20
49 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAG
Found at i:37006 original size:46 final size:46
Alignment explanation
Indices: 36956--37122 Score: 187
Period size: 46 Copynumber: 3.6 Consensus size: 46
36946 AGCATCCAAA
* *
36956 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAG
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCTGAG
* * * * * *
37002 CTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCTGAA
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAA--A--CGTCTGAG
* *
37049 CTCGTTGAGTTGAGTCTGAGTTCATTTATGGATGCGAACGTCTGAG
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCTGAG
37095 CTCGTTGAGTTGAGTCTGAGTTCACTTA
1 CTCGTTGAGTTGAGTCTGAGTTCACTTA
37123 GGGGCGGGTT
Statistics
Matches: 98, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 55 0.56
47 26 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.34
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCTGAG
Found at i:38683 original size:46 final size:46
Alignment explanation
Indices: 38542--38706 Score: 160
Period size: 46 Copynumber: 3.6 Consensus size: 46
38532 AGCATCCAAA
* *
38542 CTCGTTGAGTTGAGT-TGAGTTCACTTATGGATGCAAATGTCC-GAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG-CCTGAG
* * * * * *
38587 CTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ACGCCT-GAG
* *
38633 CTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCTGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCTGAG
*
38679 CTCGTTGAGTTGAGTCTGAGTTCACTTA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTA
38707 GGGGCGGGTT
Statistics
Matches: 96, Mismatches: 16, Indels: 15
0.76 0.13 0.12
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 19 0.20
46 59 0.61
47 6 0.06
49 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCTGAG
Found at i:40169 original size:46 final size:45
Alignment explanation
Indices: 40119--40288 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 45
40109 TGGTTGAGCA
*
40119 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCAAACG
* * * * *
40165 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCAA--A--CG
* *
40212 TCCGAACTCGTTGAGTTGAGTCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCAAACG
*
40257 -CCGAGCTCGTTGAGTTGAGTCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCGAGTTCACTTA
40289 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 6 0.06
44 30 0.29
45 4 0.04
46 35 0.34
47 23 0.22
49 5 0.05
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCAAACG
Done.