Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_28 ID=scaffold_28-JGI_221_v2.0
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: 64497
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.27
Warning! 11096 characters in sequence are not A, C, G, or T
Found at i:1257 original size:19 final size:20
Alignment explanation
Indices: 1233--1270 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1223 AAATTTCAAT
1233 ATTTTTATAACTTT-TTTTC
1 ATTTTTATAACTTTATTTTC
*
1252 ATTTTTATATCTTTATTTT
1 ATTTTTATAACTTTATTTT
1271 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTATAACTTTATTTTC
Found at i:3658 original size:41 final size:41
Alignment explanation
Indices: 3601--3686 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
3591 ATTGAAAAGG
*
3601 AAACCATATATCTCAAAATAATTAGACTTCATAGAAAGTTT
1 AAACCATATATCTCAAAAGAATTAGACTTCATAGAAAGTTT
*
3642 AAACCATATATCTCAAAAGAATTAGACTTCATATAAAGTTT
1 AAACCATATATCTCAAAAGAATTAGACTTCATAGAAAGTTT
3683 AAAC
1 AAAC
3687 TTTAAGTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (41 bp):
AAACCATATATCTCAAAAGAATTAGACTTCATAGAAAGTTT
Found at i:5671 original size:14 final size:15
Alignment explanation
Indices: 5652--5682 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5642 TTTTCTCAAT
5652 TTGATTCTA-TTTCA
1 TTGATTCTATTTTCA
5666 TTGATTCTATTTTCA
1 TTGATTCTATTTTCA
5681 TT
1 TT
5683 TTCTTCCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
TTGATTCTATTTTCA
Found at i:8234 original size:21 final size:21
Alignment explanation
Indices: 8191--8234 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
8181 AGGATCCAAC
*
8191 ATTTTGAAATCTACGAAGTTTT
1 ATTTTGAAATATACG-AGTTTT
8213 ATTTTGAAATTATACG-GTTTT
1 ATTTTGAAA-TATACGAGTTTT
8234 A
1 A
8235 ACAAAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.48
Consensus pattern (21 bp):
ATTTTGAAATATACGAGTTTT
Found at i:8960 original size:65 final size:64
Alignment explanation
Indices: 8869--9007 Score: 251
Period size: 65 Copynumber: 2.2 Consensus size: 64
8859 AATTGCTAAT
* *
8869 ATATTATTATATACATACATACGCATACTAAGAAAACAATATTATATAAACATAAAAAAAATGAG
1 ATATCATTATATACATACATACGCATACTAAGAAAACAATAGTATATAAACAT-AAAAAAATGAG
8934 ATATCATTATATACATACATACGCATACTAAGAAAACAATAGTATATAAACATAAAAAAATGAG
1 ATATCATTATATACATACATACGCATACTAAGAAAACAATAGTATATAAACATAAAAAAATGAG
8998 ATATCATTAT
1 ATATCATTAT
9008 GAAAAAAAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 21 0.29
65 51 0.71
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (64 bp):
ATATCATTATATACATACATACGCATACTAAGAAAACAATAGTATATAAACATAAAAAAATGAG
Found at i:10036 original size:16 final size:15
Alignment explanation
Indices: 10015--10044 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10005 TTCAATTTTT
10015 TGTATTGATCTTTCTG
1 TGTATTGAT-TTTCTG
10031 TGTATTGATTTTCT
1 TGTATTGATTTTCT
10045 CTTGATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (15 bp):
TGTATTGATTTTCTG
Found at i:11118 original size:13 final size:13
Alignment explanation
Indices: 11100--11131 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
11090 TGTATAACAA
11100 AAATTTAGTTAAG
1 AAATTTAGTTAAG
11113 AAATTTAGTTAAG
1 AAATTTAGTTAAG
11126 AAATTT
1 AAATTT
11132 TACTGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (13 bp):
AAATTTAGTTAAG
Found at i:12242 original size:25 final size:25
Alignment explanation
Indices: 12213--12280 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
12203 CGACTCACCA
12213 CAGCTCGCATGAGCTTCCCATTATT
1 CAGCTCGCATGAGCTTCCCATTATT
* * *
12238 CAGCTCACATGAGCTCCCCGTTATT
1 CAGCTCGCATGAGCTTCCCATTATT
*
12263 TAGCTCAG-ATGAGCTTCC
1 CAGCTC-GCATGAGCTTCC
12281 TGTTTACAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (25 bp):
CAGCTCGCATGAGCTTCCCATTATT
Found at i:21304 original size:8 final size:8
Alignment explanation
Indices: 21291--21316 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
21281 TTTATGTTAA
21291 AAATTGTG
1 AAATTGTG
21299 AAATTGTG
1 AAATTGTG
21307 AAATTGTG
1 AAATTGTG
21315 AA
1 AA
21317 TTATGTGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (8 bp):
AAATTGTG
Found at i:28482 original size:9 final size:9
Alignment explanation
Indices: 28408--28482 Score: 53
Period size: 9 Copynumber: 8.0 Consensus size: 9
28398 ACCCATTCTT
*
28408 TAAAAAATA
1 TAAAAATTA
28417 TACAAAATTA
1 TA-AAAATTA
*
28427 GTAAATATTTA
1 -TAAA-AATTA
**
28438 TAAAAACGA
1 TAAAAATTA
28447 TAAAAATT-
1 TAAAAATTA
* *
28455 TTAAAATAA
1 TAAAAATTA
28464 TTAAAAATTA
1 -TAAAAATTA
28474 TAAAAATTA
1 TAAAAATTA
28483 ATATCTAACT
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
8 6 0.12
9 19 0.38
10 19 0.38
11 6 0.12
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:29086 original size:41 final size:41
Alignment explanation
Indices: 28979--29258 Score: 172
Period size: 41 Copynumber: 6.8 Consensus size: 41
28969 ATTTTTAAAC
* * * * * *
28979 CTTTAGCGGTGTTTTTATTTTAGCGCCGCTAAT-TCTCCGAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGT-TCTGGT
* ** * ** *
29020 CTTTAGTGATGTTTTTAACCGAGCGCCACTAATGTTCTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGTTCTGGT
* * * * *
29061 CTTTAGCGGTGTTTTTGTCTAAGCGCCGCTAATGCTC-GTAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGTTCTG-GT
* * * * * *
29102 CATTAGTGGCGTTATTGTCTGAGCGCCACTAAT-TCTCTGTT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGT-TCTGGT
* * *
29143 CTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTC-GTGT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGTTCTG-GT
* * * ** *
29184 TTTTAGTGGCGTTTTTATCTGAGCGCCACTAATACTCTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGTTCTGGT
* *
29225 CTTTAGCGGCGTTTTATATGTAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTT-TATCTAAGCGCCACTAAT
29259 AGTAACAAAA
Statistics
Matches: 181, Mismatches: 50, Indels: 15
0.74 0.20 0.06
Matches are distributed among these distances:
40 2 0.01
41 160 0.88
42 19 0.10
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.39
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGTTCTGGT
Found at i:29126 original size:82 final size:81
Alignment explanation
Indices: 28978--29258 Score: 312
Period size: 82 Copynumber: 3.4 Consensus size: 81
28968 GATTTTTAAA
* * * * ** * *
28978 CCTTTAGCGGTGTTTTTATTTTAGCGCCGCTAATTCTCCG-ATCTTTAGTGATGTTTTTAACCGA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGA
29042 GCGCCACTAATGTTCTGG
65 GCGCCACTAAT-TTCTGG
* * * * *
29060 CCTTTAGCGGTGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTATTGTCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
*
29125 CGCCACTAATTCTCTGT
66 CGCCACTAATT-TCTGG
* * * * * *
29142 TCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTCGTGTTTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
*
29207 CGCCACTAATACTCTGG
66 CGCCACTAAT-TTCTGG
*
29224 CCTTTAGCGGCGTTTTATATGTAAGCGCCGCTAAT
1 CCTTTAGCGGCGTTTT-TATCTAAGCGCCGCTAAT
29259 AGTAACAAAA
Statistics
Matches: 167, Mismatches: 28, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
81 3 0.02
82 149 0.89
83 15 0.09
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (81 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATTTCTGG
Found at i:30573 original size:43 final size:43
Alignment explanation
Indices: 30473--30813 Score: 472
Period size: 43 Copynumber: 7.9 Consensus size: 43
30463 TATTGTCAAT
*
30473 GCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTTCCAAAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAAC
*
30515 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTATAAAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAAC
* * *
30558 GCAGCTATAGGTCAGGACCTTTAGCGGCGCTTTTTATAAAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAAC
*
30601 GCCGCTATAGGTCAGGACCTTTAGCGGCGCTTTTTACAAAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAAC
30644 GCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTTACAAAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAAC
* * *
30686 GCCGCTATAGATCAGGACCTTTAGCGACGCATCTTT-CACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTTTACAAAAAC
* * * *
30729 GCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTTCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAAC
* * * * *
30772 GTCGCTATAGCTCAAGACATTTAGCGACGCTTTGATTACAAA
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTT--TTACAAA
30814 TGGCGCTAAA
Statistics
Matches: 274, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
42 75 0.27
43 191 0.70
44 3 0.01
45 5 0.02
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (43 bp):
GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAAC
Found at i:30632 original size:128 final size:129
Alignment explanation
Indices: 30473--30813 Score: 472
Period size: 128 Copynumber: 2.6 Consensus size: 129
30463 TATTGTCAAT
*
30473 GCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTTCCAAAAACGCCGCTATAGATCAGGACCTTT
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAACGCCGCTATAGATCAGGACCTTT
* * * * *
30537 AGCGGCGCTTTTTATAAAAACGCAGCTATAGGTCAGGACCTTTAGCGGCGC-TTTTTATAAAAAC
66 AGCGGCGCTTTTTACAAAAACGCAGCTATAGATCAGGACCTTTAGCGACGCATCTTT-CAAAAAC
*
30601 GCCGCTATAGGTCAGGACCTTTAGCGGCGCTTTTTACAAAAACGCCGCTATAGATCAGGACCTTT
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAACGCCGCTATAGATCAGGACCTTT
* *
30666 AGCGGCGC-TTTTACAAAAACGCCGCTATAGATCAGGACCTTTAGCGACGCATCTTTCACAAAC
66 AGCGGCGCTTTTTACAAAAACGCAGCTATAGATCAGGACCTTTAGCGACGCATCTTTCAAAAAC
* * * * * * * *
30729 GCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTTCACAAACGTCGCTATAGCTCAAGACATTT
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAACGCCGCTATAGATCAGGACCTTT
*
30794 AGCGACGCTTTGATTACAAA
66 AGCGGCGCTTT--TTACAAA
30814 TGGCGCTAAA
Statistics
Matches: 190, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
128 136 0.72
129 47 0.25
131 7 0.04
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (129 bp):
GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAAAACGCCGCTATAGATCAGGACCTTT
AGCGGCGCTTTTTACAAAAACGCAGCTATAGATCAGGACCTTTAGCGACGCATCTTTCAAAAAC
Found at i:30758 original size:171 final size:172
Alignment explanation
Indices: 30473--30813 Score: 508
Period size: 171 Copynumber: 2.0 Consensus size: 172
30463 TATTGTCAAT
*
30473 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCAAAAACGCCGCTATAGATCAGGACCTTTA
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTATAGATCAGGACCTTTA
* * * * *
30538 GCGGCGCTTTTTATAAAAACGCAGCTATAGGTCAGGACCTTTAGCGGCGCTTTTTAT-AAAAACG
66 GCGACGCTCTTTACAAAAACGCAGCTATAGCTCAAGACCTTTAGCGGCGCTTTTT-TCAAAAACG
* * * *
30602 CCGCTATAGGTCAGGACCTTTAGCGGCGCTTT-TTACAAAAAC
130 CCGCTATAGCTCAAGACATTTAGCGACGCTTTATTACAAAAAC
30644 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTATAGATCAGGACCTTTA
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTATAGATCAGGACCTTTA
* * *
30709 GCGACGCATCTTT-CACAAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTTCACAAACG
66 GCGACGC-TCTTTACAAAAACGCAGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTTCAAAAACG
*
30773 TCGCTATAGCTCAAGACATTTAGCGACGCTTTGATTACAAA
130 CCGCTATAGCTCAAGACATTTAGCGACGCTTT-ATTACAAA
30814 TGGCGCTAAA
Statistics
Matches: 152, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
170 1 0.01
171 140 0.92
172 4 0.03
173 7 0.05
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (172 bp):
GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTATAGATCAGGACCTTTA
GCGACGCTCTTTACAAAAACGCAGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTTCAAAAACGC
CGCTATAGCTCAAGACATTTAGCGACGCTTTATTACAAAAAC
Found at i:31008 original size:14 final size:14
Alignment explanation
Indices: 30985--31014 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30975 AAATCTTGTT
30985 AAATTACAAGTTCA
1 AAATTACAAGTTCA
*
30999 AAATTTCAAGTTCA
1 AAATTACAAGTTCA
31013 AA
1 AA
31015 TAGTGCAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (14 bp):
AAATTACAAGTTCA
Found at i:36424 original size:41 final size:41
Alignment explanation
Indices: 36366--36683 Score: 442
Period size: 41 Copynumber: 7.8 Consensus size: 41
36356 NNNNNNNTAA
* * *
36366 TAGCGGCACTTCTACAAAAACGCCGCTAAAGACCAGAGCAT
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCAT
* **
36407 TAGCGGCG-TTTTCACAAAAGCGCCGCTAAAGAATAGAGCAT
1 TAGCGGCGCTTTTC-CAAAAACGCCGCTAAAGACCAGAGCAT
* * *
36448 TAGTGGCGCTTTCCCAAAAACGCCGCTAAAGACCAGACCAT
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCAT
*
36489 TAGCGGCGCTTTTCCAAAAACGCCGCTGAAGACCAGAGCAT
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCAT
*
36530 TAACGGCGC-TTTCTCAAAAACGCCGCTAAAGACCAGAGCAT
1 TAGCGGCGCTTTTC-CAAAAACGCCGCTAAAGACCAGAGCAT
36571 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCAT
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCAT
* *
36612 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGATCTT
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCAT
* * ** *
36653 TAGTGGCACTTTTTGAAAAACGCCACTAAAG
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAG
36684 CCCCGAAAAC
Statistics
Matches: 247, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
40 7 0.03
41 232 0.94
42 8 0.03
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.19
Consensus pattern (41 bp):
TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCAT
Found at i:36846 original size:40 final size:40
Alignment explanation
Indices: 36741--36856 Score: 105
Period size: 40 Copynumber: 2.9 Consensus size: 40
36731 CGCTTTTTGG
* *
36741 AAAA-CGCCGCTAATTCTCATTTTTAGCGGC-GTTTTCTA
1 AAAAGCGCCGCTAATACTGATTTTTAGCGGCGGTTTTCTA
* * * *
36779 AAAAGTGCCGCTAATACCCGATCTTTAGTGGCGGTATTT-T-
1 AAAAGCGCCGCTAATA-CTGATTTTTAGCGGCGGT-TTTCTA
* *
36819 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTT
1 AAAAGCGCCGCTAATAC-TGATTTTTAGCGGCGGTTTT
36857 TATACAAACG
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
38 4 0.07
39 13 0.21
40 38 0.62
41 3 0.05
42 3 0.05
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (40 bp):
AAAAGCGCCGCTAATACTGATTTTTAGCGGCGGTTTTCTA
Found at i:41181 original size:21 final size:21
Alignment explanation
Indices: 41155--41195 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41145 AACTTAAAAC
* *
41155 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCCGCAGCGAGAGAAGT
41176 AGAGGCCGCAGCGAGAGAAG
1 AGAGGCCGCAGCGAGAGAAG
41196 CAGTGAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.49, T:0.02
Consensus pattern (21 bp):
AGAGGCCGCAGCGAGAGAAGT
Found at i:41682 original size:43 final size:43
Alignment explanation
Indices: 41635--41749 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
41625 ATCATATAGT
*
41635 GGCGTTTCTGAAAT-AAGCGCCGCTAAAGCACACTACTTTTAGC
1 GGCGTTTCT-AAATAAAGCGCCGCTAAAGAACACTACTTTTAGC
* * **
41678 GGCGTTTGTAGATAAAGCGCCGCTAAAGAACTTTACTTTTAGC
1 GGCGTTTCTAAATAAAGCGCCGCTAAAGAACACTACTTTTAGC
*
41721 GGCGTTT-T-ATTCACAAGCGCCGCTAAAGA
1 GGCGTTTCTAAAT-A-AAGCGCCGCTAAAGA
41750 TGATGGTCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.02
42 5 0.08
43 56 0.90
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (43 bp):
GGCGTTTCTAAATAAAGCGCCGCTAAAGAACACTACTTTTAGC
Found at i:41832 original size:42 final size:42
Alignment explanation
Indices: 41648--41997 Score: 366
Period size: 43 Copynumber: 8.2 Consensus size: 42
41638 GTTTCTGAAA
* * ***
41648 TAAGCGCCGCTAAAGCACACT-A-CTTTTAGCGGCGTTTGTAGA
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTTC
* * *
41690 TAAAGCGCCGCTAAAGAACTTTA-CTTTTAGCGGCGTTTTATTC
1 T-AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTTC
* ** * *
41733 ACAAGCGCCGCTAAAGATGATGGTCTTTAGCGGCGTTTTTTGC
1 -TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * * * *
41776 ACAAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTTTC
1 -TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
*
41819 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * *
41861 TAAGCACCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-C
* *
41904 TAAGCGCCGCTAAAGAACACGATCTTTAGTGGC-TTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
41945 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCTG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TC
41988 TAAGCGCCGC
1 TAAGCGCCGC
41998 AAAAAGTTAG
Statistics
Matches: 263, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
41 31 0.12
42 88 0.33
43 143 0.54
44 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:41897 original size:84 final size:83
Alignment explanation
Indices: 41692--41997 Score: 362
Period size: 84 Copynumber: 3.6 Consensus size: 83
41682 TTTGTAGATA
* * * * * ** *
41692 AAGCGCCGCTAAAGAACTTTA-CTTTTAGCGGCGTTTTATTCACAAGCGCCGCTAAAGATGATGG
1 AAGCGCCGCTAAAGATCATGATC-TTTAGCGGCGTTTTTTTC-TAAGCGCCGCTAAAGAACATGA
* *
41756 TCTTTAGCGGCGTTTTTTGCAC
64 TCTTTAGCGGC-TTTTTTTC-T
* * *
41778 AAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
41843 TTTAGCGGCTTTTTTTTCT
66 TTTAGCGGC-TTTTTTTCT
* * *
41862 AAGCACCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACACGAT
1 AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTT-CTAAGCGCCGCTAAAGAACATGAT
*
41927 CTTTAGTGGCTTTTTTTCT
65 CTTTAGCGGCTTTTTTTCT
* * *
41946 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCTGTAAGCGCCGC
1 AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTT-TCTAAGCGCCGC
41998 AAAAAGTTAG
Statistics
Matches: 192, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
84 90 0.47
85 69 0.36
86 32 0.17
87 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (83 bp):
AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCTTTTTTTCT
Found at i:42391 original size:19 final size:20
Alignment explanation
Indices: 42367--42404 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
42357 AAATTACAAT
42367 ATTTTTATAACTTT-TTTTC
1 ATTTTTATAACTTTATTTTC
*
42386 ATTTTTATATCTTTATTTT
1 ATTTTTATAACTTTATTTT
42405 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTATAACTTTATTTTC
Done.