Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2057
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: 76733
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6888 original size:119 final size:120
Alignment explanation
Indices: 6704--6928 Score: 305
Period size: 119 Copynumber: 1.9 Consensus size: 120
6694 GCTCCTCGTT
*
6704 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
6769 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
6824 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
6886 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
6929 CATCATTCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
118 4 0.04
119 66 0.72
120 22 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:6928 original size:40 final size:40
Alignment explanation
Indices: 6704--6928 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
6694 GCTCCTCGTT
* *
6704 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
6744 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
6784 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
6824 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
6863 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
6904 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6929 CATCATTCAA
Statistics
Matches: 166, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 32 0.19
40 120 0.72
41 12 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:25297 original size:40 final size:39
Alignment explanation
Indices: 25110--25290 Score: 185
Period size: 40 Copynumber: 4.6 Consensus size: 39
25100 CGAATGATGT
* * * *
25110 CCGGGCTAAGT-CCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* *
25149 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
25189 CCGGGCTAAG-CCCGAAGGCA-TTG-GTGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
25225 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
25266 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
25291 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
37 20 0.16
38 13 0.11
39 22 0.18
40 58 0.48
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31790 original size:96 final size:97
Alignment explanation
Indices: 31604--31787 Score: 216
Period size: 96 Copynumber: 1.9 Consensus size: 97
31594 TTTTAGTTTA
*
31604 AAGAATGATAATTATTAATATATAATTATATCCATTATAATATATATTAATTATTATCAAATTTT
1 AAGAATGATAATTATTAATATATAATTATATCCATTAAAATATATATTAATTATTATCAAATTTT
* *** *
31669 AGGATTTTATTTGATAAGTTTTTAATGATAAT
66 AGCATAGAATTGGATAAGTTTTTAATGATAAT
*
31701 AAGAA-GATAATCT-TTAATATATAATTATATCTATTAAAAAATATATATTAATCT-TTATC-AA
1 AAGAATGATAAT-TATTAATATATAATTATATCCATT--AAAATATATATTAAT-TATTATCAAA
*
31762 -TTTAGCATAGAATTAGGATTAGTTTT
62 TTTTAGCATAGAATT-GGATAAGTTTT
31788 AATCATATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
96 37 0.50
97 17 0.23
98 19 0.26
99 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (97 bp):
AAGAATGATAATTATTAATATATAATTATATCCATTAAAATATATATTAATTATTATCAAATTTT
AGCATAGAATTGGATAAGTTTTTAATGATAAT
Found at i:49328 original size:40 final size:41
Alignment explanation
Indices: 49284--49430 Score: 156
Period size: 41 Copynumber: 3.6 Consensus size: 41
49274 AATTATACAT
*
49284 TAGCGGTGATTTC-AAT-AAAACGCCACTAAAAACTGAGCAA
1 TAGCGGCG-TTTCTAATCAAAACGCCACTAAAAACTGAGCAA
* *
49324 TAGCGGCGTTTCTAGTCCAAACGCCACTAAAAACTGAGCAA
1 TAGCGGCGTTTCTAATCAAAACGCCACTAAAAACTGAGCAA
* * * * * *
49365 TAGCGGCATTTTTAGTGAAAACGCTGA-TAAAAACTAAGCAA
1 TAGCGGCGTTTCTAATCAAAACGC-CACTAAAAACTGAGCAA
**
49406 TAGCGGCGTTTCTGCTCAAAACGCC
1 TAGCGGCGTTTCTAATCAAAACGCC
49431 GCAAAAAGAT
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
39 4 0.04
40 9 0.10
41 75 0.84
42 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (41 bp):
TAGCGGCGTTTCTAATCAAAACGCCACTAAAAACTGAGCAA
Found at i:49352 original size:41 final size:41
Alignment explanation
Indices: 49300--49430 Score: 176
Period size: 41 Copynumber: 3.2 Consensus size: 41
49290 TGATTTCAAT
49300 AAAACGCCACTAAAAACTGAGCAATAGCGGCGTTTCTAGTC
1 AAAACGCCACTAAAAACTGAGCAATAGCGGCGTTTCTAGTC
* * * *
49341 CAAACGCCACTAAAAACTGAGCAATAGCGGCATTTTTAGTG
1 AAAACGCCACTAAAAACTGAGCAATAGCGGCGTTTCTAGTC
* *
49382 AAAACGCTGA-TAAAAACTAAGCAATAGCGGCGTTTCT-GCTC
1 AAAACGC-CACTAAAAACTGAGCAATAGCGGCGTTTCTAG-TC
49423 AAAACGCC
1 AAAACGCC
49431 GCAAAAAGAT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.01
41 75 0.97
42 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
AAAACGCCACTAAAAACTGAGCAATAGCGGCGTTTCTAGTC
Found at i:49469 original size:82 final size:82
Alignment explanation
Indices: 49310--49470 Score: 191
Period size: 82 Copynumber: 2.0 Consensus size: 82
49300 AAAACGCCAC
* * * *
49310 TAAAAACTGAGCAATAGCGGCGTTTCTAGTCCAAACGCCACTAAAAACTGAGCAATAGCGGCATT
1 TAAAAACTAAGCAATAGCGGCGTTTCTAGTCAAAACGCCACTAAAAAATGAGCAATAGCAGCATT
*
49375 TTTAGTGAAAACGCTGA
66 TTTAGTCAAAACGCTGA
* * * *
49392 TAAAAACTAAGCAATAGCGGCGTTTCT-GCTCAAAACGCCGC-AAAAAGATTATCTATAGCAGCA
1 TAAAAACTAAGCAATAGCGGCGTTTCTAG-TCAAAACGCCACTAAAAA-ATGAGCAATAGCAGCA
* *
49455 TTTTTGGTCCAAACGC
64 TTTTTAGTCAAAACGC
49471 CGCAAAAAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
81 6 0.09
82 60 0.91
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (82 bp):
TAAAAACTAAGCAATAGCGGCGTTTCTAGTCAAAACGCCACTAAAAAATGAGCAATAGCAGCATT
TTTAGTCAAAACGCTGA
Found at i:49479 original size:82 final size:82
Alignment explanation
Indices: 49300--49479 Score: 186
Period size: 82 Copynumber: 2.2 Consensus size: 82
49290 TGATTTCAAT
* * * * *
49300 AAAACGCCACTAAAAACTGAGCAATAGCGGCGTTTCTAGTCCAAACGCCACTAAAAACTGAGCAA
1 AAAACGCCGCAAAAAACTAAGCAATAGCGGCGTTTCTAGTCAAAACGCCACTAAAAAATGAGCAA
* *
49365 TAGCGGCATTTTTAGTG
66 TAGCAGCATTTTTAGTC
* * * *
49382 AAAACGCTG-ATAAAAACTAAGCAATAGCGGCGTTTCT-GCTCAAAACGCCGC-AAAAAGATTAT
1 AAAACGCCGCA-AAAAACTAAGCAATAGCGGCGTTTCTAG-TCAAAACGCCACTAAAAA-ATGAG
* *
49444 CTATAGCAGCATTTTTGGTC
63 CAATAGCAGCATTTTTAGTC
*
49464 CAAACGCCGCAAAAAA
1 AAAACGCCGCAAAAAA
49480 GTTGAGCAGC
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
81 6 0.08
82 72 0.91
83 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (82 bp):
AAAACGCCGCAAAAAACTAAGCAATAGCGGCGTTTCTAGTCAAAACGCCACTAAAAAATGAGCAA
TAGCAGCATTTTTAGTC
Found at i:49768 original size:8 final size:7
Alignment explanation
Indices: 49754--49818 Score: 60
Period size: 7 Copynumber: 9.1 Consensus size: 7
49744 ATGGCTTTCT
49754 CTAAACC
1 CTAAACC
49761 CTTAAACC
1 C-TAAACC
49769 CTAAA-C
1 CTAAACC
* *
49775 ATAGACC
1 CTAAACC
*
49782 CTAAACA
1 CTAAACC
*
49789 CTAATCC
1 CTAAACC
*
49796 ATAAACC
1 CTAAACC
49803 CTAAGACC
1 CTAA-ACC
49811 CTAAACC
1 CTAAACC
49818 C
1 C
49819 CAAAAAAATT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
6 4 0.09
7 27 0.60
8 14 0.31
ACGTcount: A:0.43, C:0.37, G:0.03, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:49956 original size:7 final size:7
Alignment explanation
Indices: 49932--49993 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
49922 TATTTTTGGA
*
49932 TTTAGGG
1 TTTAAGG
**
49939 TTTAATA
1 TTTAAGG
49946 TTTAAGG
1 TTTAAGG
49953 TTTAAGG
1 TTTAAGG
* *
49960 TCTATGG
1 TTTAAGG
*
49967 TTTAGGG
1 TTTAAGG
*
49974 TTCTATGG
1 TT-TAAGG
49982 TTTAAGG
1 TTTAAGG
49989 TTTAA
1 TTTAA
49994 TGGCCATGGG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
7 37 0.86
8 6 0.14
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (7 bp):
TTTAAGG
Found at i:49980 original size:15 final size:15
Alignment explanation
Indices: 49951--49990 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
49941 TAATATTTAA
49951 GGTTTAAGG-TCTAT
1 GGTTTAAGGTTCTAT
*
49965 GGTTTAGGGTTCTAT
1 GGTTTAAGGTTCTAT
49980 GGTTTAAGGTT
1 GGTTTAAGGTT
49991 TAATGGCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.17, C:0.05, G:0.33, T:0.45
Consensus pattern (15 bp):
GGTTTAAGGTTCTAT
Found at i:49996 original size:15 final size:14
Alignment explanation
Indices: 49932--49992 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
49922 TATTTTTGGA
* **
49932 TTTAGGGTTTAATA
1 TTTATGGTTTAAGG
*
49946 TTTAAGGTTTAAGG
1 TTTATGGTTTAAGG
* *
49960 TCTATGGTTTAGGG
1 TTTATGGTTTAAGG
49974 TTCTATGGTTTAAGG
1 TT-TATGGTTTAAGG
49989 TTTA
1 TTTA
49993 ATGGCCATGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.48
Consensus pattern (14 bp):
TTTATGGTTTAAGG
Found at i:50358 original size:21 final size:21
Alignment explanation
Indices: 50306--50359 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
50296 TTAAGTTTAT
50306 GGTTTAAGGTTTGTTATTTTG
1 GGTTTAAGGTTTGTTATTTTG
* **
50327 GGCTTGGGGTTTGTTATTTTG
1 GGTTTAAGGTTTGTTATTTTG
50348 GGTTTAAGGTTT
1 GGTTTAAGGTTT
50360 AAGGTATATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.11, C:0.02, G:0.33, T:0.54
Consensus pattern (21 bp):
GGTTTAAGGTTTGTTATTTTG
Found at i:51043 original size:40 final size:40
Alignment explanation
Indices: 50983--51066 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
50973 CTTCAGTGGC
50983 ATTAGCGGCACTTTTAGAAAAACGCCGCTATAGATTAAGT
1 ATTAGCGGCACTTTTAGAAAAACGCCGCTATAGATTAAGT
* * * *
51023 ATTAGCGGCGCTTTTTGAAAAATGCCGCTATAGATTGAGT
1 ATTAGCGGCACTTTTAGAAAAACGCCGCTATAGATTAAGT
51063 ATTA
1 ATTA
51067 CTCAAAAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (40 bp):
ATTAGCGGCACTTTTAGAAAAACGCCGCTATAGATTAAGT
Found at i:51383 original size:22 final size:22
Alignment explanation
Indices: 51341--51383 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
51331 ACCTGATTTG
**
51341 AAATCCCCAAATCTGTTTCCCA
1 AAATCCCCAAATCTGAATCCCA
51363 AAATCCCCAAATC-GAAATCCC
1 AAATCCCCAAATCTG-AATCCC
51384 TTTTACTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.37, C:0.37, G:0.05, T:0.21
Consensus pattern (22 bp):
AAATCCCCAAATCTGAATCCCA
Found at i:55177 original size:43 final size:43
Alignment explanation
Indices: 55130--55229 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
55120 CTTACGTAAT
*
55130 TTACATAACTTACAGAATACATAAATATATATCATATTACAAC
1 TTACATAACTTACAGAATACATAAATATATATCATATCACAAC
* * * * *
55173 TTACATAACTTACATAATACTTAAATATTTATCATATCATATC
1 TTACATAACTTACAGAATACATAAATATATATCATATCACAAC
*
55216 ATACATAACTTACA
1 TTACATAACTTACA
55230 AAACTTACTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.36
Consensus pattern (43 bp):
TTACATAACTTACAGAATACATAAATATATATCATATCACAAC
Found at i:55229 original size:9 final size:9
Alignment explanation
Indices: 55217--55250 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
55207 TATCATATCA
55217 TACATAACT
1 TACATAACT
*
55226 TACAAAACT
1 TACATAACT
*
55235 TACTTAACT
1 TACATAACT
55244 TACATAA
1 TACATAA
55251 TACATAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:58832 original size:79 final size:79
Alignment explanation
Indices: 58734--58916 Score: 192
Period size: 79 Copynumber: 2.3 Consensus size: 79
58724 TATTCGTTCA
* * *
58734 AATGCCTTCGAGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCG-GGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
58797 ATTTAGTAAC-TCGCACC
63 ATATAGTAACTTAGCA-C
* * **
58814 AATGCCTTCGGGCTTAGCCCAGAATTAGTAACTCGCATAAATGCCTTCGGATCTTAGTCCGGATA
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
* *
58879 TGGTCACTTAGCAC
66 TAGTAACTTAGCAC
*
58893 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGG-CTTAGCCCGGA
58917 CATCATTCGA
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.67
80 25 0.29
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
TAGTAACTTAGCAC
Found at i:58857 original size:39 final size:40
Alignment explanation
Indices: 58760--58863 Score: 156
Period size: 39 Copynumber: 2.6 Consensus size: 40
58750 AGCCCGGTTA
* *
58760 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAAT
* *
58800 TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCAGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAAT
*
58839 TAGTAACTCGCATAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
58864 ATCTTAGTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 33 0.57
40 25 0.43
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAAT
Found at i:58916 original size:40 final size:40
Alignment explanation
Indices: 58732--58916 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
58722 GCTATTCGTT
* * *
58732 CAAATGCCTTCGAGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
58772 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
58812 CCAATGCCTTCGGG-CTTAGCCCAGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
58851 TAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
58892 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58917 CATCATTCGA
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 78 0.64
41 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:60118 original size:56 final size:56
Alignment explanation
Indices: 60051--60170 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
60041 TATTAGTTTA
60051 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
60107 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
60163 TTGCCCAT
1 TTGCCCAT
60171 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:63401 original size:13 final size:14
Alignment explanation
Indices: 63385--63413 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
63375 TTATAAATAT
63385 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
63398 TTATAATGGTTTAA
1 TTATAATGGTTTAA
63412 TT
1 TT
63414 CGTTGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:65844 original size:41 final size:41
Alignment explanation
Indices: 65782--65969 Score: 258
Period size: 41 Copynumber: 4.7 Consensus size: 41
65772 TTGGGGTTTA
*
65782 AATCCGAGCTTGGTCTGGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
*
65823 AATCTGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
65864 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCA-TGTC--
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * * *
65902 AA-CCGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
65942 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
65970 TGAGTCAGCG
Statistics
Matches: 127, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
37 24 0.19
38 6 0.05
40 6 0.05
41 91 0.72
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:65959 original size:78 final size:81
Alignment explanation
Indices: 65782--65969 Score: 256
Period size: 78 Copynumber: 2.3 Consensus size: 81
65772 TTGGGGTTTA
* * * * *
65782 AATCCGAGCTTGGTCTGGAAGGGCTTTTGAGCCAGTGTCATAATCTGAGCTTGGTCTCGAAGGGC
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCA-AATCCGAACCTAGTCTCGAAGGGC
* * *
65847 TTTTGAGCCAGTGTCAT
65 CTTCGAGCCAATGTCAT
*
65864 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCA-TGTC-AA-CCGAACCTAGTTTCGAAGGGCC
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAAATCCGAACCTAGTCTCGAAGGGCC
*
65926 TTCGGGCCAATGTCAT
66 TTCGAGCCAATGTCAT
65942 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
65970 TGAGTCAGCG
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 57 0.59
79 2 0.02
81 4 0.04
82 33 0.34
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (81 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAAATCCGAACCTAGTCTCGAAGGGCC
TTCGAGCCAATGTCAT
Found at i:74192 original size:39 final size:41
Alignment explanation
Indices: 74063--74292 Score: 314
Period size: 40 Copynumber: 5.8 Consensus size: 41
74053 TTGGGGTTTA
74063 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
74104 AATCCGAGCTT-GTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
*
74144 AATCCGAGCTT-GTCTCGAAGGGCTTTTG-GCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* *
74183 AATCCGAGCTTGGTCTCGAAGGGTTTTTGAGCGAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * *
74224 AA-CCGAAC-TAGT-TACGAA-GGCCTTCGAGCCAATGTCAT
1 AATCCGAGCTTGGTCT-CGAAGGGCTTTTGAGCCAGTGTCAT
74262 AATCCGAGCTTGGTC-CGAAGGGCTTGTTGAG
1 AATCCGAGCTTGGTCTCGAAGGGCTT-TTGAG
74293 TCAGCGCTAA
Statistics
Matches: 166, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
38 18 0.11
39 37 0.22
40 85 0.51
41 26 0.16
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:74255 original size:79 final size:81
Alignment explanation
Indices: 74075--74292 Score: 286
Period size: 79 Copynumber: 2.7 Consensus size: 81
74065 TCCGAGCTTG
* * * *
74075 GTCTCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAGCTT-GTCTCGAAGGGCTTTTGAGCCAGT
1 GTCTCGAAGGGCCTTCGAGCCAATGTCATAATCCGAGCTTGGTCTCGAAGGGTTTTTGAGCCAGT
* *
74139 GTCATAATCCGAGCTT
66 GTCATAATCCGAACTA
* * *
74155 GTCTCGAAGGGCTTTTG-GCCAATGTCATAATCCGAGCTTGGTCTCGAAGGGTTTTTGAGCGAGT
1 GTCTCGAAGGGCCTTCGAGCCAATGTCATAATCCGAGCTTGGTCTCGAAGGGTTTTTGAGCCAGT
74219 GTCATAA-CCGAACTA
66 GTCATAATCCGAACTA
*
74234 GT-TACGAA-GGCCTTCGAGCCAATGTCATAATCCGAGCTTGGTC-CGAAGGGCTTGTTGAG
1 GTCT-CGAAGGGCCTTCGAGCCAATGTCATAATCCGAGCTTGGTCTCGAAGGG-TTTTTGAG
74293 TCAGCGCTAA
Statistics
Matches: 126, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
78 14 0.11
79 66 0.52
80 46 0.37
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (81 bp):
GTCTCGAAGGGCCTTCGAGCCAATGTCATAATCCGAGCTTGGTCTCGAAGGGTTTTTGAGCCAGT
GTCATAATCCGAACTA
Done.