Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012996.1 Corchorus olitorius cultivar O-4 contig13029, 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: 34321
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:6512 original size:11 final size:11
Alignment explanation
Indices: 6496--6520 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6486 TCATCTTTTA
6496 TTTTTCTCTAG
1 TTTTTCTCTAG
6507 TTTTTCTCTAG
1 TTTTTCTCTAG
6518 TTT
1 TTT
6521 AAGAAGAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTCTCTAG
Found at i:13023 original size:21 final size:21
Alignment explanation
Indices: 12997--13097 Score: 148
Period size: 21 Copynumber: 4.8 Consensus size: 21
12987 TGTTTTTGCT
* *
12997 CAAATTTTGATAGTCAAACCC
1 CAAAGTTTGATGGTCAAACCC
*
13018 CAAATTTTGATGGTCAAACCC
1 CAAAGTTTGATGGTCAAACCC
13039 CAAAGTTTGATGGTCAAACCC
1 CAAAGTTTGATGGTCAAACCC
* *
13060 CAAAGCTTGATGGACAAACCC
1 CAAAGTTTGATGGTCAAACCC
*
13081 CAAAGTTTGATAGTCAA
1 CAAAGTTTGATGGTCAA
13098 CCCATGTTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.25
Consensus pattern (21 bp):
CAAAGTTTGATGGTCAAACCC
Found at i:13185 original size:71 final size:71
Alignment explanation
Indices: 13066--13203 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 71
13056 ACCCCAAAGC
* * *
13066 TTGATGGACAAACCCCAAAGTTTGATAGTCAACCCATGTTAAATCTTATCAATTGAAGCACCCAC
1 TTGATGGACAAACCCCAAAGATTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
13131 CATATA
66 CATATA
* *
13137 TTGATGGTCAAACCCCGAAGATTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
1 TTGATGGACAAACCCCAAAGATTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
13202 CA
66 CA
13204 CATTTTTGCC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (71 bp):
TTGATGGACAAACCCCAAAGATTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
CATATA
Found at i:13318 original size:101 final size:101
Alignment explanation
Indices: 13137--13473 Score: 557
Period size: 101 Copynumber: 3.3 Consensus size: 101
13127 CCACCATATA
* *
13137 TTGATGGTCAAACCCCGAAGATTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
1 TTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
* * *
13202 CACATTTTTGCCCAAAATTATGTTTTTGCTCAAATT
66 CACATTTTTGCCCAAAAATGTGTTTTTGCCCAAATT
* * * *
13238 TTTATAGTCAAACCCCAAAGTTTGATAGTCAACCCATGTTAAACCTTATCAATTGAACCACCCAC
1 TTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
* *
13303 CATATTTTTGCCCAAAACTGTGTTTTTGCCCAAATT
66 CACATTTTTGCCCAAAAATGTGTTTTTGCCCAAATT
*
13339 TTGATGGTCAAACCCCAAAGTTTAATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
1 TTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
*
13404 CACATTTTTGCCCAAAAATGTATTTTTGCCCAAATT
66 CACATTTTTGCCCAAAAATGTGTTTTTGCCCAAATT
13440 TTGATGGTCAAACCCCAAAGTTTGATAGTCAAAC
1 TTGATGGTCAAACCCCAAAGTTTGATAGTCAAAC
13474 TCCAAATTTT
Statistics
Matches: 217, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 217 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (101 bp):
TTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCAC
CACATTTTTGCCCAAAAATGTGTTTTTGCCCAAATT
Found at i:13357 original size:21 final size:21
Alignment explanation
Indices: 13331--13373 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13321 TGTGTTTTTG
* * *
13331 CCCAAATTTTGATGGTCAAAC
1 CCCAAAGTTTAATAGTCAAAC
13352 CCCAAAGTTTAATAGTCAAAC
1 CCCAAAGTTTAATAGTCAAAC
13373 C
1 C
13374 ATGTTAAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (21 bp):
CCCAAAGTTTAATAGTCAAAC
Found at i:13458 original size:21 final size:21
Alignment explanation
Indices: 13432--13558 Score: 139
Period size: 21 Copynumber: 6.0 Consensus size: 21
13422 TGTATTTTTG
* *
13432 CCCAAATTTTGATGGTCAAAC
1 CCCAAAGTTTGATAGTCAAAC
13453 CCCAAAGTTTGATAGTCAAAC
1 CCCAAAGTTTGATAGTCAAAC
* *
13474 TCCAAATTTTGAT-GCTCAAAC
1 CCCAAAGTTTGATAG-TCAAAC
* * * *
13495 GCCAAATTTTGATTGTCTAAC
1 CCCAAAGTTTGATAGTCAAAC
** *
13516 CCCAAAGTTCAATAGCCAAAC
1 CCCAAAGTTTGATAGTCAAAC
13537 CCCAAAGTTTGATAGTCAAAC
1 CCCAAAGTTTGATAGTCAAAC
13558 C
1 C
13559 ATGTTAAACT
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 1 0.01
21 86 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (21 bp):
CCCAAAGTTTGATAGTCAAAC
Found at i:13480 original size:42 final size:42
Alignment explanation
Indices: 13432--13558 Score: 155
Period size: 42 Copynumber: 3.0 Consensus size: 42
13422 TGTATTTTTG
13432 CCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAAC
1 CCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAAC
* * * * * *
13474 TCCAAATTTTGATGCTCAAACGCCAAATTTTGATTGTCTAAC
1 CCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAAC
* ** * *
13516 CCCAAAGTTCAATAGCCAAACCCCAAAGTTTGATAGTCAAAC
1 CCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAAC
13558 C
1 C
13559 ATGTTAAACT
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (42 bp):
CCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAAC
Found at i:13517 original size:63 final size:63
Alignment explanation
Indices: 13433--13557 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
13423 GTATTTTTGC
** * * *
13433 CCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACTCCAAATTTTGAT-GCTCAAACG
1 CCAAATTTTGATGGTCAAACCCCAAAGTTCAATAGCCAAACCCCAAAGTTTGATAG-TCAAACG
* *
13496 CCAAATTTTGATTGTCTAACCCCAAAGTTCAATAGCCAAACCCCAAAGTTTGATAGTCAAAC
1 CCAAATTTTGATGGTCAAACCCCAAAGTTCAATAGCCAAACCCCAAAGTTTGATAGTCAAAC
13558 CATGTTAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 53 0.98
64 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (63 bp):
CCAAATTTTGATGGTCAAACCCCAAAGTTCAATAGCCAAACCCCAAAGTTTGATAGTCAAACG
Found at i:13643 original size:21 final size:21
Alignment explanation
Indices: 13617--13864 Score: 226
Period size: 21 Copynumber: 12.0 Consensus size: 21
13607 TATATTTTGG
* *
13617 CCCAAATTTTGATGGTCAAAC
1 CCCAAAATTTGATAGTCAAAC
* *
13638 CCCAAATTTTGATGGTCAAAC
1 CCCAAAATTTGATAGTCAAAC
*
13659 CCCAAAGTTTGATAGTCAAA-
1 CCCAAAATTTGATAGTCAAAC
*
13679 CCCAAAATTTGATGGTC-AAC
1 CCCAAAATTTGATAGTCAAAC
* *
13699 CCCTAAAGTTTGATAGTTAAAC
1 CCC-AAAATTTGATAGTCAAAC
*
13721 CCCAAAATTTGATAGTGAAAC
1 CCCAAAATTTGATAGTCAAAC
** *
13742 CGTTTTAAACCTTT--T--T-AAAC
1 C---CCAAA-ATTTGATAGTCAAAC
* *
13762 CCCAAATTTTGATGGTCAAAC
1 CCCAAAATTTGATAGTCAAAC
*
13783 CCCAAAGTTTGATAGTCAAA-
1 CCCAAAATTTGATAGTCAAAC
*
13803 CCCAAAATTTGATGGTC-AAC
1 CCCAAAATTTGATAGTCAAAC
*
13823 CCCTAAAGTTTGATAGTCAAAC
1 CCC-AAAATTTGATAGTCAAAC
13845 CCCAAAATTTGATAGTCAAA
1 CCCAAAATTTGATAGTCAAA
13865 ACCATTTGAT
Statistics
Matches: 190, Mismatches: 22, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.02
17 3 0.02
18 1 0.01
19 4 0.02
20 42 0.22
21 118 0.62
22 12 0.06
23 1 0.01
24 3 0.02
25 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (21 bp):
CCCAAAATTTGATAGTCAAAC
Found at i:13694 original size:62 final size:62
Alignment explanation
Indices: 13617--13864 Score: 292
Period size: 62 Copynumber: 4.0 Consensus size: 62
13607 TATATTTTGG
* * * *
13617 CCCAAATTTTGATGGTCAAACCCC-AAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAA
1 CCCAAAATTTGATGGTC-AACCCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAA
* *
13679 CCCAAAATTTGATGGTCAACCCCTAAAGTTTGATAGTTAAACCCCAAAATTTGATAGTGAAA
1 CCCAAAATTTGATGGTCAACCCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAA
* * * * * *
13741 CCGTTTTAAACCTTT--T--TAAACCCC-AAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCA
1 CC----CAAA-ATTTGATGGTCAACCCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCA
13801 AA
61 AA
13803 CCCAAAATTTGATGGTCAACCCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAA
1 CCCAAAATTTGATGGTCAACCCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAA
13865 ACCATTTGAT
Statistics
Matches: 155, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
57 3 0.02
58 3 0.02
59 1 0.01
61 13 0.08
62 121 0.78
63 7 0.05
65 1 0.01
66 3 0.02
67 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (62 bp):
CCCAAAATTTGATGGTCAACCCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAA
Found at i:13791 original size:124 final size:124
Alignment explanation
Indices: 13634--13860 Score: 445
Period size: 124 Copynumber: 1.8 Consensus size: 124
13624 TTTGATGGTC
13634 AAACCCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCAAAATTTGATGGTCAAC
1 AAACCCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCAAAATTTGATGGTCAAC
*
13699 CCCTAAAGTTTGATAGTTAAACCCCAAAATTTGATAGTGAAACCGTTTTAAACCTTTTT
66 CCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTGAAACCGTTTTAAACCTTTTT
13758 AAACCCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCAAAATTTGATGGTCAAC
1 AAACCCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCAAAATTTGATGGTCAAC
13823 CCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGT
66 CCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGT
13861 CAAAACCATT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 102 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (124 bp):
AAACCCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCAAAATTTGATGGTCAAC
CCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTGAAACCGTTTTAAACCTTTTT
Found at i:13884 original size:16 final size:17
Alignment explanation
Indices: 13851--13887 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
13841 AAACCCCAAA
13851 ATTTGATAGTCAAAACC
1 ATTTGATAGTCAAAACC
*
13868 ATTTGATAGT-GAAACC
1 ATTTGATAGTCAAAACC
13884 ATTT
1 ATTT
13888 TAAACCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (17 bp):
ATTTGATAGTCAAAACC
Found at i:13937 original size:21 final size:21
Alignment explanation
Indices: 13912--13959 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
13902 ATTTGATTGT
13912 CAAACCCCAAAGTTCAATAGC
1 CAAACCCCAAAGTTCAATAGC
*
13933 CAAACCCCAAAGTTCGATAGC
1 CAAACCCCAAAGTTCAATAGC
13954 CAAACC
1 CAAACC
13960 ATGTTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.35, G:0.10, T:0.12
Consensus pattern (21 bp):
CAAACCCCAAAGTTCAATAGC
Found at i:14044 original size:21 final size:21
Alignment explanation
Indices: 14018--14143 Score: 148
Period size: 21 Copynumber: 6.0 Consensus size: 21
14008 TATATTTTGG
*
14018 CCCAAATTTTGATGGTCAAAC
1 CCCAAATTTTGATAGTCAAAC
*
14039 CCCAAATTTTGATGGTCAAAC
1 CCCAAATTTTGATAGTCAAAC
*
14060 CCCAAAATTTGATAGTCAAA-
1 CCCAAATTTTGATAGTCAAAC
* *
14080 CCAAAATTTTGATGGTC-AAC
1 CCCAAATTTTGATAGTCAAAC
*
14100 CCCTAAAGTTTGATAGTCAAAC
1 CCC-AAATTTTGATAGTCAAAC
* * *
14122 TCCAAAATTTGATAGTGAAAC
1 CCCAAATTTTGATAGTCAAAC
14143 C
1 C
14144 ATTTTAAACC
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 16 0.18
21 67 0.74
22 5 0.06
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (21 bp):
CCCAAATTTTGATAGTCAAAC
Found at i:14095 original size:62 final size:62
Alignment explanation
Indices: 14021--14144 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
14011 ATTTTGGCCC
* *
14021 AAATTTTGATGGTCAAACCCC-AAATTTTGATGGTCAAACCCCAAAATTTGATAGTCAAACCA
1 AAATTTTGATGGTC-AACCCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAACCA
* *
14083 AAATTTTGATGGTCAACCCCTAAAGTTTGATAGTCAAACTCCAAAATTTGATAGTGAAACCA
1 AAATTTTGATGGTCAACCCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAACCA
14145 TTTTAAACCT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
61 6 0.11
62 51 0.89
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (62 bp):
AAATTTTGATGGTCAACCCCTAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAACCA
Found at i:14112 original size:41 final size:42
Alignment explanation
Indices: 14018--14131 Score: 160
Period size: 41 Copynumber: 2.7 Consensus size: 42
14008 TATATTTTGG
* * *
14018 CCCAAATTTTGATGGTCAAACCCCAAATTTTGATGGTCAAAC
1 CCCAAAATTTGATAGTCAAACCCAAAATTTTGATGGTCAAAC
14060 CCCAAAATTTGATAGTCAAA-CCAAAATTTTGATGGTC-AAC
1 CCCAAAATTTGATAGTCAAACCCAAAATTTTGATGGTCAAAC
*
14100 CCCTAAAGTTTGATAGTCAAACTCCAAAATTT
1 CCC-AAAATTTGATAGTCAAAC-CCAAAATTT
14132 GATAGTGAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
40 6 0.09
41 32 0.49
42 18 0.28
43 9 0.14
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (42 bp):
CCCAAAATTTGATAGTCAAACCCAAAATTTTGATGGTCAAAC
Found at i:14418 original size:15 final size:15
Alignment explanation
Indices: 14398--14428 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
14388 TAAACAACTA
14398 ATAATATTACTATAT
1 ATAATATTACTATAT
14413 ATAATATTACTATAT
1 ATAATATTACTATAT
14428 A
1 A
14429 GTCTACTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATATTACTATAT
Found at i:14510 original size:20 final size:19
Alignment explanation
Indices: 14486--14532 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
14476 ATCCTATATA
*
14486 CAATATATTTAATATTACTAT
1 CAATATA-TTAAT-TTACAAT
14507 -AATAGTATTAATTTACAAT
1 CAATA-TATTAATTTACAAT
14526 CAATATA
1 CAATATA
14533 ATATTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 8 0.35
20 13 0.57
21 2 0.09
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (19 bp):
CAATATATTAATTTACAAT
Found at i:27689 original size:40 final size:40
Alignment explanation
Indices: 27633--27711 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
27623 ATGACCTGAT
*
27633 TGATGCGCCAAGGACTCATCATGGTCTTGAAGATGCTAGC
1 TGATGCGCCAAGGACTCATCATGGTCATGAAGATGCTAGC
27673 TGATGCGCCACA-GACTCATCATGGTCATGAAGATGCTAG
1 TGATGCGCCA-AGGACTCATCATGGTCATGAAGATGCTAG
27712 GAGATCATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TGATGCGCCAAGGACTCATCATGGTCATGAAGATGCTAGC
Found at i:27742 original size:21 final size:21
Alignment explanation
Indices: 27716--27763 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
27706 TGCTAGGAGA
27716 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
27737 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
27758 TCATTG
1 TCATTG
27764 TGACACGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:28998 original size:154 final size:154
Alignment explanation
Indices: 28718--29646 Score: 1547
Period size: 154 Copynumber: 6.0 Consensus size: 154
28708 ACCCCGTATC
** *
28718 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCTATTT-GCAACCCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG
* * * * *
28782 CTTTTCTTTCCAATGTTTATGACCTAACTATACTCATTTTGGTAAGATTAGTCCACTTTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
28847 TTTAGCTCATTTGGAACACTTGTT
131 TTTAGCTCATTTGGAACACTTGTT
**
28871 ATTTTGGGCAC-ATCAAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT
1 ATTTTGGGC-CTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT
28935 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
65 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
*
29000 TTTTAGCTCATTTGGAACACATGTT
130 TTTTAGCTCATTTGGAACACTTGTT
* ** * * *
29025 ATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTGGGCAACCTTCGATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG
29090 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
29155 TTTAGCTCATTTGGAACACTTGTT
131 TTTAGCTCATTTGGAACACTTGTT
29179 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG
* *
29244 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTGTGAAGGT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
*
29309 TTTAGCTCATTTGGAACACTTATT
131 TTTAGCTCATTTGGAACACTTGTT
* * *
29333 ATTTTGGGCCTATCGAGGCCCATTAGTTCAGTTTTGAATTGTCTTCGATTTGGCAACCCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG
*
29398 CCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
* * *
29463 TCTAGCTCATTTGGATCAGTTGTT
131 TTTAGCTCATTTGGAACACTTGTT
*
29487 ATTTTGGGCCAATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG
* *
29552 TTTTTTTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
* *
29617 TTTAGCTCATTTGGAACGCTTTTT
131 TTTAGCTCATTTGGAACACTTGTT
29641 ATTTTG
1 ATTTTG
29647 TGACACGGGA
Statistics
Matches: 722, Mismatches: 51, Indels: 5
0.93 0.07 0.01
Matches are distributed among these distances:
153 45 0.06
154 677 0.94
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG
CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
TTTAGCTCATTTGGAACACTTGTT
Found at i:31807 original size:153 final size:154
Alignment explanation
Indices: 31133--33445 Score: 3404
Period size: 154 Copynumber: 15.1 Consensus size: 154
31123 TATAATCATT
* *
31133 TTGTTTATAGCCTAACTATAATCATTTTGGTGAGATTAGTCCAATGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
*
31198 AGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
66 -GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
*
31263 GGAACCCTCAATGCTTTTCTTTCCA
130 GCAACCCTCAATGCTTTTCTTTCCA
** * * * * *
31288 AAGTTTATGACCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGAGGTTTTTAACTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
**
31353 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGG
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* *
31418 CAAGCCTCATTGCTTTTCTTTCCA
131 CAACCCTCAATGCTTTTCTTTCCA
* *
31442 TTGTTTATGCCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
* * ** *
31507 GGAACACTT-TTCATTTT-GGCCTATAGGGGCCCATTAATGACGTTTTGAATCGTCTTCGACTT-
66 GGAACACTTGTT-ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
31569 GCAACCCTCAATGCTTTTCTTTCCA
130 GCAACCCTCAATGCTTTTCTTTCCA
*
31594 TTGTTTATGGCCT-ACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
31658 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
31723 CAACCCTCAATGC-TTTCTTTCCA
131 CAACCCTCAATGCTTTTCTTTCCA
*
31746 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGTTTAGTCCACTGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
** *
31811 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTGTGAATCGTCTTCGATTTGG
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
*
31876 CGACCCTCAATGCTTTTCTTTCCA
131 CAACCCTCAATGCTTTTCTTTCCA
* *
31900 TTGTTTATGCCCTAACTATAATCATCTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA-TT
* * *
31965 TGGAACACTTTTTATTTTGGGCCTATCGGGGCCCGTTAGTTCCGTTTTGAATTGTCTTCGATTTG
65 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
* *
32030 GCAACCCTCATTGTTTTTCTTTCCA
130 GCAACCCTCAATGCTTTTCTTTCCA
* * *
32055 TTGTTTATGCCCTAACTATAATGATTTGGGT-AGGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGA-GATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * * ** *
32119 TGGAACACTTTTTATTTTGGGCCTATAGGGACCCATTAGTGACGTTTTGAATCCTCTTCGATTT-
65 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
32183 GCAACCCTCAATGAC-TTTCTTTCCA
130 GCAACCCTCAATG-CTTTTCTTTCCA
* * *
32208 TTGTTTATGCCCTAACTATAATCATTTTGCTGAGATTAGTCCACTGTG-AGGTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
** *
32272 GGAACACTT-TTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATTGTCTTCGATTT-G
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
32335 CAACCCTCAATGCTTTTCTTTCCA
131 CAACCCTCAATGCTTTTCTTTCCA
* *
32359 TTGTATATGGCTTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
* **
32424 GGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGG
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* *
32489 CGACCCTCAATGCTCTTCTTTCCA
131 CAACCCTCAATGCTTTTCTTTCCA
* * * *
32513 TTGTTTATGGCCTAACTATAATCATTGTGGTGATATTAGTCCACTGTGAAGTTTATAGTTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
* *** *
32578 GGAACACTTTTTATTTT-GGCCTATCGGGGCCCATTAGTAATGTTTTGAATCCTCTTCGATTT-G
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
*
32641 CAACCCTCAATGCCTTTCTTTCCA
131 CAACCCTCAATGCTTTTCTTTCCA
* *
32665 TTGTTTATGGCCTAACTATAATAATTTTGGTGAGACTAGTCCACTGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
*
32730 GGAACTCTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGT-CGTTTTGAATCGTCTTCGATTTG
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCCGTTTTGAATCGTCTTCGATTTG
* *
32794 AG-AAACCTCAATGGTTTTCTTTCCA
130 -GCAACCCTCAATGCTTTTCTTTCCA
* *** *
32819 TTGTTTATGGCCTAACTA-ATATCATTTTCGTGAGATTAGTCCAAACTGAAGTTTTTAACTCATT
1 TTGTTTATGGCCTAACTATA-ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * * * * *
32883 TGGAACAATTGTTATTTTGGGCATATCGGGGACCATTAGTGT-CGTTCTAAATCGTCTTCAATTT
65 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCCGTTTTGAATCGTCTTCGATTT
* * *
32947 GGGAAACCTCAATGCTTTTATTTCCA
129 GGCAACCCTCAATGCTTTTCTTTCCA
*
32973 TTGTTTATGGCCTAACTATAATCATTTTTAGTGTAGATTAGTCCACTGTGAAGTTTTTTAGCTCT
1 TTGTTTATGGCCTAACTATAATCA-TTTTGGTG-AGATTAGTCCACTGTGAAG-TTTTTAGCTC-
*
33038 ATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
62 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
*
33103 TTGGCAAACCTCAATGCTTTTCTTTCCA
127 TTGGCAACCCTCAATGCTTTTCTTTCCA
* * * *
33131 TTGTTTATGGACTAACTACAATCATTTTGATGAGATTAGTGCACTGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
* * * *
33196 GGAACACTTCTTATTTTGGGCCTATCGGGGCCCATTAGTGCCGTTTTGAATCGTCTTCGA-CTGC
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* * *
33260 CAAACCTCAACGCTTTTCCTTCCA
131 CAACCCTCAATGCTTTTCTTTCCA
* *
33284 TTGTTTATGGCCT-ACTATAATCATTTTGGTGAGATTAATCCACTGTGAAGTTTTTATCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
*** *
33348 GGAACACTTGTTATTTTGGGCCTATCGACACCCATTAGTTCCGTTTTGAATCGTCTTCGATCTGG
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
*
33413 CAACCCTCAATGCTTTACTTTCCA
131 CAACCCTCAATGCTTTTCTTTCCA
*
33437 ATGTTTATG
1 TTGTTTATG
33446 ACCTGATTGA
Statistics
Matches: 1960, Mismatches: 171, Indels: 56
0.90 0.08 0.03
Matches are distributed among these distances:
150 1 0.00
151 179 0.09
152 345 0.18
153 445 0.23
154 621 0.32
155 215 0.11
156 34 0.02
157 16 0.01
158 104 0.05
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
CAACCCTCAATGCTTTTCTTTCCA
Found at i:32298 original size:613 final size:612
Alignment explanation
Indices: 31133--33445 Score: 3414
Period size: 613 Copynumber: 3.8 Consensus size: 612
31123 TATAATCATT
* *
31133 TTGTTTATAGCCTAACTATAATCATTTTGGTGAGATTAGTCCAATGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
*
31198 AGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
66 -GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
** * *
31263 G-GAACCCTCAATGCTTTTCTTTCCAAAGTTTATGACCTAACTATAATCATTTTGGTAAGATTAG
130 GCG-ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* * * *
31327 TCCACTTTGAGGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
194 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGT
** * *
31392 TTTGTTTTGAATCGTCTTCGATTTGGCAAGCCTCATTGCTTTTCTTTCCATTGTTTATGCCCTAA
259 TCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGCCCTAA
*
31457 CTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT-TTCAT
324 CTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT-AT
* * *
31521 TTT-GGCCTATAGGGGCCCATTAATGACGTTTTGAATCGTCTTCGACTTGCAACCCTCAATGCTT
388 TTTGGGCCTATAGGGACCCATTAGTGACGTTTTGAATCGTCTTCGATTTGCAACCCTCAATGC-T
* *
31585 TTCTTTCCATTGTTTATGGCCT-ACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
452 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGCTGAGATTAGTCCACTGTG-AGTTTTT
31649 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
516 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT-CGTTTTGAATCGTCT
31714 TCGATTTGGCAACCCTCAATGC-TTTCTTTCCA
580 TCGATTTGGCAACCCTCAATGCTTTTCTTTCCA
*
31746 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGTTTAGTCCACTGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
** *
31811 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTGTGAATCGTCTTCGATTTGG
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* *
31876 CGACCCTCAATGCTTTTCTTTCCATTGTTTATGCCCTAACTATAATCATCTTGGTGAGATTAGTC
131 CGACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
*
31941 CACTGTGAAGTTTTTAGCTCATTTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCGTTAGTT
196 CACTGTGAAGTTTTTAGCTCA-TTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTT
* * *
32006 CCGTTTTGAATTGTCTTCGATTTGGCAACCCTCATTGTTTTTCTTTCCATTGTTTATGCCCTAAC
260 CCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGCCCTAAC
* * *
32071 TATAATGATTTGGGT-AGGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATT
325 TATAATCATTTTGGTGA-GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
*
32135 TTGGGCCTATAGGGACCCATTAGTGACGTTTTGAATCCTCTTCGATTTGCAACCCTCAATGACTT
389 TTGGGCCTATAGGGACCCATTAGTGACGTTTTGAATCGTCTTCGATTTGCAACCCTCAATG-CTT
* *
32200 TCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAGGTTTTAG
453 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAGTTTTTAG
* *
32265 CTCATTTGGAACACTT-TTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATTGTCTTC
518 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCGTTTTGAATCGTCTTC
32329 GATTT-GCAACCCTCAATGCTTTTCTTTCCA
582 GATTTGGCAACCCTCAATGCTTTTCTTTCCA
* *
32359 TTGTATATGGCTTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
1 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
* **
32424 GGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGG
66 GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* * *
32489 CGACCCTCAATGCTCTTCTTTCCATTGTTTATGGCCTAACTATAATCATTGTGGTGATATTAGTC
131 CGACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* * **
32554 CACTGTGAAGTTTATAGTTCATTTGGAACACTTTTTATTTT-GGCCTATCGGGGCCCATTAGTAA
196 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTC
* * * *
32618 TGTTTTGAATCCTCTTCGATTT-GCAACCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACT
261 CGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGCCCTAACT
* * *
32682 ATAATAATTTTGGTGAGACTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACTCTTGTTATTTT
326 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
* * * * * *
32747 GGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATCGTCTTCGATTTGAGAAACCTCAATGGTTTT
391 GGGCCTATAGGGACCCATTAGTGACGTTTTGAATCGTCTTCGATTTG-CAACCCTCAAT-GCTTT
*
32812 CTTTCCATTGTTTATGGCCTAACTA-ATATCATTTT-CGTGAGATTAGTCCAAACTG-AAGTTTT
454 CTTTCCATTGTTTATGGCCTAACTATA-ATCATTTTGC-TGAGATTAGTCC--ACTGTGAGTTTT
* * * * * *
32874 TAACTCATTTGGAACAATTGTTATTTTGGGCATATCGGGGACCATTAGTGTCGTTCTAAATCGTC
515 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCGTTTTGAATCGTC
* * * *
32939 TTCAATTTGGGAAACCTCAATGCTTTTATTTCCA
579 TTCGATTTGGCAACCCTCAATGCTTTTCTTTCCA
*
32973 TTGTTTATGGCCTAACTATAATCATTTTTAGTGTAGATTAGTCCACTGTGAAGTTTTTTAGCTCT
1 TTGTTTATGGCCTAACTATAATCA-TTTTGGTG-AGATTAGTCCACTGTGAAG-TTTTTAGCTC-
*
33038 ATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
62 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
* * * * *
33103 TTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTACAATCATTTTGATGAGATT
127 TTGGCGACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
* *
33168 AGTGCACTGTGAAGTTTTTAGCTCATTTGGAACACTTCTTATTTTGGGCCTATCGGGGCCCATTA
192 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTA
* * * * * * *
33233 GTGCCGTTTTGAATCGTCTTCGA-CTGCCAAACCTCAACGCTTTTCCTTCCATTGTTTATGGCCT
257 GTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGCCCT
* *
33297 -ACTATAATCATTTTGGTGAGATTAATCCACTGTGAAGTTTTTATCTCATTTGGAACACTTGTTA
322 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* ** ** *
33361 TTTTGGGCCTATCGACACCCATTAGTTCCGTTTTGAATCGTCTTCGATCTGGCAACCCTCAATGC
387 TTTTGGGCCTATAGGGACCCATTAGTGACGTTTTGAATCGTCTTCGAT-TTGCAACCCTCAATGC
*
33426 TTTACTTTCCAATGTTTATG
451 TTT-CTTTCCATTGTTTATG
33446 ACCTGATTGA
Statistics
Matches: 1544, Mismatches: 130, Indels: 47
0.90 0.08 0.03
Matches are distributed among these distances:
610 141 0.09
611 96 0.06
612 195 0.13
613 534 0.35
614 146 0.09
615 40 0.03
616 19 0.01
617 14 0.01
618 286 0.19
619 73 0.05
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (612 bp):
TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
GGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGG
CGACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
CACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTC
CGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGCCCTAACT
ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
GGGCCTATAGGGACCCATTAGTGACGTTTTGAATCGTCTTCGATTTGCAACCCTCAATGCTTTCT
TTCCATTGTTTATGGCCTAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAGTTTTTAGCTC
ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCGTTTTGAATCGTCTTCGATT
TGGCAACCCTCAATGCTTTTCTTTCCA
Found at i:33509 original size:40 final size:40
Alignment explanation
Indices: 33453--33531 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
33443 ATGACCTGAT
33453 TGATGCGCCAAGGACTCATCATGGTCTTGAAGATGCTAGC
1 TGATGCGCCAAGGACTCATCATGGTCTTGAAGATGCTAGC
33493 TGATGCGCCACA-GACTCATCATGGTCTTGAAGATGCTAG
1 TGATGCGCCA-AGGACTCATCATGGTCTTGAAGATGCTAG
33532 GAGATCATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 37 0.97
41 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TGATGCGCCAAGGACTCATCATGGTCTTGAAGATGCTAGC
Found at i:33577 original size:21 final size:21
Alignment explanation
Indices: 33536--33580 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33526 TGCTAGGAGA
*
33536 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGATCCAAGC
*
33557 TCATTGGAG-AAGGATCTAAGC
1 TCATTGGAGCAA-GATCCAAGC
33578 TCA
1 TCA
33581 CTGTGACACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATTGGAGCAAGATCCAAGC
Done.