Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017301.1 Corchorus olitorius cultivar O-4 contig17334, 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: 33877
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:275 original size:32 final size:32
Alignment explanation
Indices: 239--417 Score: 270
Period size: 32 Copynumber: 5.5 Consensus size: 32
229 GTGTGAATAG
239 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
271 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
*
303 AAAACGCCCTTATTTAGCGGCGTCTATAAAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
* *
335 AAAAACGCCCTTATTTAGCGGCGTCTACAGACC
1 -AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
* *
368 AAAACACCCTTATTTAGCGGCGTCT-TAAAATC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAA-C
400 AAAACGCCGCTATATTTA
1 AAAACGCC-CT-TATTTA
418 ACTGCTTTTA
Statistics
Matches: 134, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
31 2 0.01
32 95 0.71
33 31 0.23
34 6 0.04
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
Found at i:350 original size:97 final size:99
Alignment explanation
Indices: 239--417 Score: 292
Period size: 97 Copynumber: 1.8 Consensus size: 99
229 GTGTGAATAG
* * *
239 AAAACGCCCTTATTTAGCGGCGTCTATAGAACAAAACGCCCTTATTTAGCGGCGTCTATAGAA-C
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAACAAAACACCCTTATTTAGCGGCGTCT-TAAAATC
303 AAAACGCC-CT-TATTTAGCGGCGTCTATAAAACA
65 AAAACGCCGCTATATTTAGCGGCGTCTATAAAACA
*
336 AAAACGCCCTTATTTAGCGGCGTCTACAGACCAAAACACCCTTATTTAGCGGCGTCTTAAAATCA
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAACAAAACACCCTTATTTAGCGGCGTCTTAAAATCA
401 AAACGCCGCTATATTTA
66 AAACGCCGCTATATTTA
418 ACTGCTTTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
96 4 0.05
97 63 0.84
98 2 0.03
99 6 0.08
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (99 bp):
AAAACGCCCTTATTTAGCGGCGTCTACAGAACAAAACACCCTTATTTAGCGGCGTCTTAAAATCA
AAACGCCGCTATATTTAGCGGCGTCTATAAAACA
Found at i:378 original size:65 final size:64
Alignment explanation
Indices: 239--417 Score: 279
Period size: 65 Copynumber: 2.8 Consensus size: 64
229 GTGTGAATAG
* *
239 AAAACGCCCTTATTTAGCGGCGTCTATAGAACAAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAAAACAAAACGCCCTTATTTAGCGGCGTCTACAGAAC
*
303 AAAACGCCCTTATTTAGCGGCGTCTATAAAACAAAAACGCCCTTATTTAGCGGCGTCTACAGACC
1 AAAACGCCCTTATTTAGCGGCGTCTATAAAAC-AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
*
368 AAAACACCCTTATTTAGCGGCGTCT-TAAAATCAAAACGCCGCTATATTTA
1 AAAACGCCCTTATTTAGCGGCGTCTATAAAA-CAAAACGCC-CT-TATTTA
418 ACTGCTTTTA
Statistics
Matches: 107, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
64 44 0.41
65 57 0.53
66 6 0.06
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (64 bp):
AAAACGCCCTTATTTAGCGGCGTCTATAAAACAAAACGCCCTTATTTAGCGGCGTCTACAGAAC
Found at i:1335 original size:13 final size:13
Alignment explanation
Indices: 1310--1350 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1300 TTTTTTCAAA
1310 AAAAATGGTTTTTC
1 AAAAATGG-TTTTC
1324 AAAAATGGTTTTC
1 AAAAATGGTTTTC
* *
1337 AAAATTTGTTTTC
1 AAAAATGGTTTTC
1350 A
1 A
1351 CGAGGATGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (13 bp):
AAAAATGGTTTTC
Found at i:2899 original size:35 final size:35
Alignment explanation
Indices: 2853--3256 Score: 468
Period size: 35 Copynumber: 11.5 Consensus size: 35
2843 CTAAAGATTT
* *
2853 ATTTCTGCTGACCCAGGGTGGTCTTTCTTCAATTC
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
* * *
2888 ATTTCAGCTGACCTAGGGCGGTCTTTCTTCAATTC
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
*
2923 ATTTCAGCTGACCCAAGGTGGTCTTTCTTCAGTTC
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
* * * *
2958 ATTTCAGTTGACCCAGGGCGATCTTTCTTCAATTC
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
*
2993 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTA
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
* * * *
3028 ATTTCAGTTGACCCAGGGCGATCTTTCTTCAATTC
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
*
3063 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTA
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
* * * * *
3098 ATTTCAGTTGACCCAGGGTGGTCCTTATTTAGTTT
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
* * * *
3133 ATTTCAG-TCGATCCAGGGCGATCATTTCTTTAGTTC
1 ATTTCAGCT-GACCCAGGGTGGTC-TTTCTTCAGTTC
* * * *
3169 ATTTCAGTTGACCTAGGGCGGTCTTTCTTCAATTC
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
* * *
3204 ATTTCAGCTGACCTAGGGTGGTTTTTTCTTCAGTTT
1 ATTTCAGCTGACCCAGGGTGG-TCTTTCTTCAGTTC
*
3240 ATTTCAAGTTGACCCAG
1 ATTTC-AGCTGACCCAG
3257 AGCGGTTGTC
Statistics
Matches: 314, Mismatches: 50, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
34 1 0.00
35 260 0.83
36 43 0.14
37 10 0.03
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (35 bp):
ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTC
Found at i:2970 original size:70 final size:70
Alignment explanation
Indices: 2853--3262 Score: 561
Period size: 70 Copynumber: 5.8 Consensus size: 70
2843 CTAAAGATTT
* * * *
2853 ATTTCTGCTGACCCAGGGTGGTCTTTCTTCAATTCATTTCAGCTGACCTAGGGCGGTCTTTCTTC
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTC
2918 AATTC
66 AATTC
* *
2923 ATTTCAGCTGACCCAAGGTGGTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCGATCTTTCTTC
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTC
2988 AATTC
66 AATTC
* *
2993 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTAATTTCAGTTGACCCAGGGCGATCTTTCTTC
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTC
3058 AATTC
66 AATTC
* * * * *
3063 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTAATTTCAGTTGACCCAGGGTGGTCCTTATTT
1 ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTC
* *
3128 AGTTT
66 AATTC
* * * * *
3133 ATTTCAG-TCGATCCAGGGCGATCATTTCTTTAGTTCATTTCAGTTGACCTAGGGCGGTCTTTCT
1 ATTTCAGCT-GACCCAGGGTGGTC-TTTCTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTCT
3197 TCAATTC
64 TCAATTC
* * * *
3204 ATTTCAGCTGACCTAGGGTGGTTTTTTCTTCAGTTTATTTCAAGTTGACCCAGAGCGGT
1 ATTTCAGCTGACCCAGGGTGG-TCTTTCTTCAGTTCATTTC-AGTTGACCCAGGGCGGT
3263 TGTCGTAACG
Statistics
Matches: 299, Mismatches: 36, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
69 1 0.00
70 213 0.71
71 68 0.23
72 17 0.06
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.39
Consensus pattern (70 bp):
ATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTC
AATTC
Found at i:3040 original size:105 final size:105
Alignment explanation
Indices: 2861--3256 Score: 531
Period size: 105 Copynumber: 3.7 Consensus size: 105
2851 TTATTTCTGC
* * * * *
2861 TGACCCAGGGTGGTCTTTCTTCAATTCATTTCAGCTGACCTAGGGCGGTCTTTCTTCAATTCATT
1 TGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTTATT
* * * *
2926 TCAGCTGACCCAAGGTGGTCTTTCTTCAGTTCATTTCAGT
66 TCAGTTGACCCAGGGCGATCTTTCTTCAGTTCATTTCAGT
* *
2966 TGACCCAGGGCGATCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTAATT
1 TGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTTATT
* *
3031 TCAGTTGACCCAGGGCGATCTTTCTTCAATTCATTTCAGC
66 TCAGTTGACCCAGGGCGATCTTTCTTCAGTTCATTTCAGT
* * * * * * *
3071 TGACCCAGGGTGGTCTTTCTTCAGTTAATTTCAGTTGACCCAGGGTGGTCCTTATTTAGTTTATT
1 TGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTTATT
* * *
3136 TCAGTCGATCCAGGGCGATCATTTCTTTAGTTCATTTCAGT
66 TCAGTTGACCCAGGGCGATC-TTTCTTCAGTTCATTTCAGT
* * *
3177 TGACCTAGGGCGGTCTTTCTTCAATTCATTTCAGCTGACCTAGGGTGGTTTTTTCTTCAGTTTAT
1 TGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGG-TCTTTCTTCAGTTTAT
3242 TTCAAGTTGACCCAG
65 TTC-AGTTGACCCAG
3257 AGCGGTTGTC
Statistics
Matches: 250, Mismatches: 38, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
105 167 0.67
106 59 0.24
107 15 0.06
108 9 0.04
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (105 bp):
TGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTTATT
TCAGTTGACCCAGGGCGATCTTTCTTCAGTTCATTTCAGT
Found at i:3668 original size:24 final size:24
Alignment explanation
Indices: 3641--3689 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3631 AAATAAAATA
* *
3641 ATAAAAAAATAAATAGCTATAGAG
1 ATAAAAAAATAAATAGATACAGAG
* *
3665 ATAAATAGATAAATAGATACAGAG
1 ATAAAAAAATAAATAGATACAGAG
3689 A
1 A
3690 ATAATAGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.61, C:0.04, G:0.14, T:0.20
Consensus pattern (24 bp):
ATAAAAAAATAAATAGATACAGAG
Found at i:3676 original size:8 final size:8
Alignment explanation
Indices: 3636--3704 Score: 52
Period size: 8 Copynumber: 8.8 Consensus size: 8
3626 TAAAAAAATA
3636 AAATA-AT
1 AAATAGAT
* *
3643 AAAAAAAT
1 AAATAGAT
*
3651 AAATAGCT
1 AAATAGAT
* *
3659 ATAGAGAT
1 AAATAGAT
3667 AAATAGAT
1 AAATAGAT
3675 AAATAGAT
1 AAATAGAT
* *
3683 ACAGAGA-
1 AAATAGAT
3690 ATAATAGAT
1 A-AATAGAT
3699 AAATAG
1 AAATAG
3705 GTAGCTAAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
7 5 0.11
8 40 0.87
9 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.22
Consensus pattern (8 bp):
AAATAGAT
Found at i:3695 original size:24 final size:24
Alignment explanation
Indices: 3649--3704 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
3639 TAATAAAAAA
* *
3649 ATAAATAGCTATAGAGATAAATAG
1 ATAAATAGATACAGAGATAAATAG
3673 ATAAATAGATACAGAGA-ATAATAG
1 ATAAATAGATACAGAGATA-AATAG
3697 ATAAATAG
1 ATAAATAG
3705 GTAGCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.23
Consensus pattern (24 bp):
ATAAATAGATACAGAGATAAATAG
Found at i:3825 original size:43 final size:44
Alignment explanation
Indices: 3723--3855 Score: 189
Period size: 43 Copynumber: 3.0 Consensus size: 44
3713 AAAGGATAAT
* * * * *
3723 AATAATAAATAAATAGGTAATAGCTAAATTAATAAGTAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTGAA--AATAAATAAAAAGATA
3769 AATAGTAAA-AAATAGATAATAGTTGAAAATAAAT-AAAAGATA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAAGATA
3811 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAAGATA
3855 A
1 A
3856 TAAAGAGTGA
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
42 17 0.21
43 31 0.39
44 9 0.11
45 15 0.19
46 8 0.10
ACGTcount: A:0.63, C:0.01, G:0.11, T:0.25
Consensus pattern (44 bp):
AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAAGATA
Found at i:3833 original size:18 final size:19
Alignment explanation
Indices: 3759--3834 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 19
3749 AATTAATAAG
*
3759 TAAAAAGATAAATAGTAAA
1 TAAATAGATAAATAGTAAA
3778 -AAATAGAT-AATAGTTGAAAA
1 TAAATAGATAAATAG-T--AAA
3798 TAAATAAAAGATAAATAGTAAA
1 TAAAT---AGATAAATAGTAAA
3820 TAAATAGAT-AATAGT
1 TAAATAGATAAATAGT
3835 TGAAAATAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 17
0.73 0.02 0.26
Matches are distributed among these distances:
17 5 0.10
18 14 0.29
19 4 0.08
20 3 0.06
21 4 0.08
22 8 0.17
24 5 0.10
25 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (19 bp):
TAAATAGATAAATAGTAAA
Found at i:5055 original size:35 final size:35
Alignment explanation
Indices: 5001--5639 Score: 657
Period size: 35 Copynumber: 17.9 Consensus size: 35
4991 GGTCTTTCTT
*
5001 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGTG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
* * * * *
5036 GTCCTTATTCAGTTTATTTCAGTCGATCCAGGGCG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
*
5071 ATCTTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
1 GTC-TTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
* * * * *
5107 GTCTTTCTTCAATTCATTTCAGCTGACCTAAGGTG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
*
5142 GTCTTTTCTTCAGTTTATTTCAAGTTGACCCAGGGCG
1 GTC-TTTCTTCAGTTCATTTC-AGTTGACCCAGGGCG
* *
5179 GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGCG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
* * *
5214 GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
* * *
5249 GTCTTTCCTTTAGTTTATTTCAAGTTGACCCAGGGCA
1 GTCTTT-CTTCAGTTCATTTC-AGTTGACCCAGGGCG
* * *
5286 GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
*
5321 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGTG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
* * * * *
5356 GTCCTTATTCAGTTTATTTCAGTCGATCCAGGGCG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
*
5391 ATCTTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
1 GTC-TTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
* * * *
5427 GTCTTTCTTCAATTCATTTCAGCTGGCCCAGGGTG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
*
5462 GTCTGTTCTTCAGTTTATTTCAAGTTGACCCAGGGCG
1 GTCT-TTCTTCAGTTCATTTC-AGTTGACCCAGGGCG
* * * *
5499 GTCTTTCTTCAATTTAATTCAGTTGATCCAGGGCG
1 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
* * * * * ** *
5534 ATCTTTTCTTCGGTTTATGTCAGGTGGATACAAGGCG
1 GTC-TTTCTTCAGTTCATTTCA-GTTGACCCAGGGCG
* * *
5571 ATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
1 GTC-TTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
* * * * * *
5607 ATCTTTATTTAATATTATTTCAGTTGATCCAGG
1 GTCTTTCTTCAGT-TCATTTCAGTTGACCCAGG
5640 TTGATTTCAG
Statistics
Matches: 510, Mismatches: 83, Indels: 21
0.83 0.14 0.03
Matches are distributed among these distances:
35 246 0.48
36 185 0.36
37 79 0.15
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (35 bp):
GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
Found at i:5206 original size:107 final size:106
Alignment explanation
Indices: 5001--5639 Score: 780
Period size: 107 Copynumber: 6.0 Consensus size: 106
4991 GGTCTTTCTT
* * * * * *
5001 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGTGGTC-CTTATTCAGTTTATTTCAGTCGATCC
1 GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGACCC
*
5065 AGGGCGATCTTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
66 AGGGCGATC-TTTCTTCAATTCATTTCAGTTGACCCAGGGCG
* *
5107 GTCTTTCTTCAATTCATTTCAGCTGACCTAAGGTGGTCTTTTCTTCAGTTTATTTCAAGTTGACC
1 GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTC-AGTTGACC
* *
5172 CAGGGCGGTCTTTCTTCAATTCATTTCAGCTGACCCAGGGCG
65 CAGGGCGATCTTTCTTCAATTCATTTCAGTTGACCCAGGGCG
* *
5214 GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTCCTTTAGTTTATTTCAAGTTGACC
1 GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTC-AGTTGACC
* *
5279 CAGGGC-AGTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTG
65 CAGGGCGA-TCTTTCTTCAATTCATTTCAGTTGACCCAGGGCG
* * * * * *
5321 GTCTTTCTTCAGTTCATTTCAGTTGACCCAGGGTGGTC-CTTATTCAGTTTATTTCAGTCGATCC
1 GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGACCC
*
5385 AGGGCGATCTTTTCTTCAGTTCATTTCAGTTGACCCAGGGCG
66 AGGGCGATC-TTTCTTCAATTCATTTCAGTTGACCCAGGGCG
* *
5427 GTCTTTCTTCAATTCATTTCAGCTGGCCCAGGGTGGTCTGTTCTTCAGTTTATTTCAAGTTGACC
1 GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTC-AGTTGACC
* * * *
5492 CAGGGCGGTCTTTCTTCAATTTAATTCAGTTGATCCAGGGCG
65 CAGGGCGATCTTTCTTCAATTCATTTCAGTTGACCCAGGGCG
* ** * * * ** * * * *
5534 ATCTTTTCTTCGGTTTATGTCAGGTGGATACAAGGCGATCTTTTCTTCAGTTTATTTCAGTTGAT
1 GTC-TTTCTTCAATTCATTTCAGCT-GACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGAC
* * * *
5599 CCAGGGCGATCTTTATTTAATATTATTTCAGTTGATCCAGG
64 CCAGGGCGATCTTTCTTCAAT-TCATTTCAGTTGACCCAGG
5640 TTGATTTCAG
Statistics
Matches: 465, Mismatches: 58, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
105 14 0.03
106 112 0.24
107 226 0.49
108 70 0.15
109 43 0.09
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (106 bp):
GTCTTTCTTCAATTCATTTCAGCTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGACCC
AGGGCGATCTTTCTTCAATTCATTTCAGTTGACCCAGGGCG
Found at i:13600 original size:29 final size:29
Alignment explanation
Indices: 13559--13629 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
13549 GAATCTCAAA
13559 CAAA-CAATCAATTAGGGTTAATTGCAAC
1 CAAATCAATCAATTAGGGTTAATTGCAAC
13587 CAAATCAATCAATTAGGGTTAATTGCAAC
1 CAAATCAATCAATTAGGGTTAATTGCAAC
13616 CAAATCAATCAATT
1 CAAATCAATCAATT
13630 GCAAAAAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 4 0.10
29 38 0.90
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (29 bp):
CAAATCAATCAATTAGGGTTAATTGCAAC
Found at i:13844 original size:10 final size:11
Alignment explanation
Indices: 13828--13865 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13818 TGGTCGACAA
13828 ATTTTTTTTAT
1 ATTTTTTTTAT
13839 -TTTTTTTTAT
1 ATTTTTTTTAT
**
13849 ATTTTTGATAT
1 ATTTTTTTTAT
13860 ATTTTT
1 ATTTTT
13866 CGATTAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (11 bp):
ATTTTTTTTAT
Found at i:16784 original size:154 final size:154
Alignment explanation
Indices: 16512--17309 Score: 1382
Period size: 154 Copynumber: 5.2 Consensus size: 154
16502 TCCATTAAGA
* *
16512 ACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCCTTCCATTGTATATGGCCTAAC
1 ACGTTTTGAATCGACTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATATGGCCTAAC
* *
16577 TATAATCATTTTGGTGAGATTAGTCTACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
*
16642 TGGGCCTATCGGGGCCCATTAGTT
131 TGGGCCTATCGGGGCCCATTAGTG
* *
16666 CCGTTTTGAATCGACTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 ACGTTTTGAATCGACTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATATGGCCTAAC
*
16731 TATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
16796 TGAGCCTATCGGGGCCCATTAGGG
131 TGGGCCTATCGGGGCCCATTAGTG
* *
16820 ACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATATGGCGTAAC
1 ACGTTTTGAATCGACTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATATGGCCTAAC
*
16885 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
16950 TGGGCCTATCGGGGCCCATTAGTG
131 TGGGCCTATCGGGGCCCATTAGTG
*
16974 ACGTTTTGAATCGACTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCT-AC
1 ACGTTTTGAATCGACTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATATGGCCTAAC
*
17038 TATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
17103 TGAGCCTATCGGGGCCCATTAGGG
131 TGGGCCTATCGGGGCCCATTAGTG
*
17127 ACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATATGGCCTAAC
1 ACGTTTTGAATCGACTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATATGGCCTAAC
*
17192 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACATTTGTTATTT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
17257 TGGGCCTATCGGGGCCTATTAGTT
131 TGGGCCTATCGGGGCCCATTAGTG
* *
17281 CCATTTTGAATCGACTTCGATTTGGCAAC
1 ACGTTTTGAATCGACTTCGATTTGGCAAC
17310 TTGCCCTAGC
Statistics
Matches: 607, Mismatches: 36, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
153 147 0.24
154 460 0.76
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (154 bp):
ACGTTTTGAATCGACTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATATGGCCTAAC
TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
TGGGCCTATCGGGGCCCATTAGTG
Found at i:17194 original size:307 final size:308
Alignment explanation
Indices: 16503--17309 Score: 1508
Period size: 307 Copynumber: 2.6 Consensus size: 308
16493 GGGTATATGT
* * *
16503 CCATTAAGAACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCCTTCCATTGTATA
1 CCATTAGGGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATA
*
16568 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCTACTGTGAAGTTTTTAGCTCATTCGGAACAC
66 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACAC
16633 TTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAACCCT
131 TTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAACCCT
16698 CAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTG
196 CAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTG
16763 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGC
261 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGC
16811 CCATTAGGGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATA
1 CCATTAGGGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATA
*
16876 TGGCGTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACAC
66 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACAC
**
16941 TTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAACCCT
131 TTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAACCCT
17006 CAATGCTTTTCTTTCCATTGTTTATGGCCT-ACTATAATCATTTTGGTGAGATTAGTCCACTTTG
196 CAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTG
17070 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGC
261 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGC
17118 CCATTAGGGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATA
1 CCATTAGGGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATA
* *
17183 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAT
66 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACAC
* *
17248 TTGTTATTTTGGGCCTATCGGGGCCTATTAGTTCCATTTTGAATCGACTTCGATTTGGCAAC
131 TTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAC
17310 TTGCCCTAGC
Statistics
Matches: 485, Mismatches: 14, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
307 267 0.55
308 218 0.45
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (308 bp):
CCATTAGGGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTATA
TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACAC
TTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAACCCT
CAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTG
AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGC
Done.