Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020543.1 Corchorus olitorius cultivar O-4 contig20576, 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: 9189
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:305 original size:35 final size:35
Alignment explanation
Indices: 212--756 Score: 392
Period size: 35 Copynumber: 15.3 Consensus size: 35
202 TTGCTGAAGA
* *
212 TTTAATTCAGTTGATCCAGGGCGATCTTTCCTTCCA-
1 TTTATTTCAGTTGATCCAGGGCGAT-TTTTCTT-CAG
*
248 TTTATTTCAGCTGATCCAGGGCGATTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAG
* * * * *
283 TTCATTTTAATTGATCCAGGGCGATCTTTCCTCA-
1 TTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAG
* *
317 ATTACTTCAGTTGATCCAGGGCGATCTTTAT-TTCAG
1 TTTATTTCAGTTGATCCAGGGCGAT-TTT-TCTTCAG
* * ** *
353 TTTATTTCAGTTGACCCAGGGCGGTCCTTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAG
* * * *
388 TTCATTTTAATGGATCCAGGGCGATCTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGAT-TTTTCTTCAG
* * * * *
424 CTTA---C--TTGACCCAGGGCGGTCTTTCTCCAG
1 TTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAG
* *
454 TTTATTTCAGTTGATCTAGTTGATCCAGGGTGATCTTTCTTCAG
1 ----TTT-A-TT--TC-AGTTGATCCAGGGCGATTTTTCTTCAG
** * * * * * * *
498 AATATGTCAGTTGACCCAGGGTGGTCTCTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAG
* * * * *
533 TTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAG
* * * *
568 TTTACTTCAATTGATCCAGGGCGATCTTTTCTACAA
1 TTTATTTCAGTTGATCCAGGGCGAT-TTTTCTTCAG
*
604 TCTA-TTCAGTTGATCCAGGGCGATCTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGAT-TTTTCTTCAG
* *
639 TTTATTTTAGTTGATCCAGGGCGATCTTTCTTC-G
1 TTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAG
* * *
673 ATTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAA
1 -TTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAG
709 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTGT-AG
1 TTTATTTCAGTTGATCCAGGGCGAT-TTTTCT-TCAG
745 TTTATTTCAGTT
1 TTTATTTCAGTT
757 TACCGCAAAT
Statistics
Matches: 407, Mismatches: 76, Indels: 52
0.76 0.14 0.10
Matches are distributed among these distances:
30 8 0.02
31 12 0.03
34 26 0.06
35 231 0.57
36 104 0.26
37 1 0.00
38 1 0.00
39 1 0.00
40 1 0.00
41 1 0.00
44 21 0.05
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (35 bp):
TTTATTTCAGTTGATCCAGGGCGATTTTTCTTCAG
Found at i:344 original size:105 final size:104
Alignment explanation
Indices: 217--737 Score: 464
Period size: 105 Copynumber: 4.9 Consensus size: 104
207 GAAGATTTAA
* *
217 TTCAGTTGATCCAGGGCGATCTTTCCTTCCATTTATTTCAGCTGATCCAGGGCGATTTTTCTTCA
1 TTCAGTTGATCCAGGGCGATCTTT-CTTCCATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * * *
282 GTTCATTTTAATTGATCCAGGGCGATCTTTCCTCAATTAC
65 ATTCATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTAC
* * * * *
322 TTCAGTTGATCCAGGGCGATCTTTATTTCAGTTTATTTCAGTTGACCCAGGGCGGTCCTTCTTCA
1 TTCAGTTGATCCAGGGCGATCTTTCTTCCA-TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * * *
387 ATTCATTTTAATGGATCCAGGGCGATCTTTTCTTC-A--GC
65 ATTCATTTCAGTTGATCCAGGGCGATC-TTTCTTCAATTAC
* * * *
425 TT-ACTTGACCCAGGGCGGTCTTTC-TCCAGTTTATTTCAGTTGATCTAGTTGATCCAGGGTGAT
1 TTCAGTTGATCCAGGGCGATCTTTCTTCC-----ATTT-A-TT--TC-AGTTGATCCAGGGCGAT
* * * * * * *
488 CTTTCTTCAGAAT-ATGTCAGTTGACCCAGGGTGGTCTCTCTTCAATTTAT
56 CTTTCTTCA-ATTCATTTCAGTTGATCCAGGGCGATCTTTCTTCAA-TTAC
* * * * * * *
538 TTCAGTTGACCCAGGGTGGTCTTTCTTCAATTTACTTCAATTGATCCAGGGCGATCTTTTCTACA
1 TTCAGTTGATCCAGGGCGATCTTTCTTCCATTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCA
* *
603 A-TC-TATTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTAT
65 ATTCAT-TTCAGTTGATCCAGGGCGATC-TTTCTTCA-ATTAC
* * *
644 TTTAGTTGATCCAGGGCGATCTTTCTTCGATTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAA
1 TTCAGTTGATCCAGGGCGATCTTTCTTCCATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAA
*
709 TTTATTTCAGTTGATCCAGGGCGATCTTT
66 TTCATTTCAGTTGATCCAGGGCGATCTTT
738 TCTGTAGTTT
Statistics
Matches: 336, Mismatches: 54, Indels: 52
0.76 0.12 0.12
Matches are distributed among these distances:
101 2 0.01
102 18 0.05
103 3 0.01
104 6 0.02
105 127 0.38
106 98 0.29
107 3 0.01
108 1 0.00
109 9 0.03
110 43 0.13
111 2 0.01
113 2 0.01
114 20 0.06
115 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.40
Consensus pattern (104 bp):
TTCAGTTGATCCAGGGCGATCTTTCTTCCATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAA
TTCATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTAC
Found at i:388 original size:70 final size:69
Alignment explanation
Indices: 212--737 Score: 454
Period size: 70 Copynumber: 7.4 Consensus size: 69
202 TTGCTGAAGA
* * *
212 TTTAATTCAGTTGATCCAGGGCGATCTTTCCTTCCATTTATTTCAGCTGATCCAGGGCGAT-TTT
1 TTTATTTCAGTTGATCCAGGGCGATCTTT-CTT-CAATTATTTCAGTTGATCCAGGGCGATCTTT
276 TCTTCAG
64 T-TTCAG
* * * * *
283 TTCATTTTAATTGATCCAGGGCGATCTTTCCTCAATTACTTCAGTTGATCCAGGGCGATCTTTAT
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTATTTCAGTTGATCCAGGGCGATCTTT-T
348 TTCAG
65 TTCAG
* * * * * *
353 TTTATTTCAGTTGACCCAGGGCGGTCCTTCTTCAATTCATTTTAATGGATCCAGGGCGATCTTTT
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATT-ATTTCAGTTGATCCAGGGCGATCTTTT
418 CTTCAG
65 -TTCAG
* * * *
424 CTTA---C--TTGACCCAGGGCGGTCTTTCTCCAGTTTATTTCAGTTGATCTAGTTGATCCAGGG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA----A-TT-A-TT--TC-AGTTGATCCAGGG
* *
484 TGATCTTTCTTCAG
56 CGATCTTTTTTCAG
** * * * * * * * * *
498 AATATGTCAGTTGACCCAGGGTGGTCTCTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTC
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAA-TTATTTCAGTTGATCCAGGGCGATCTTTT
*
563 TTCAA
65 TTCAG
* * *
568 TTTACTTCAATTGATCCAGGGCGATCTTTTCTACAATCTA-TTCAGTTGATCCAGGGCGATCTTT
1 TTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAAT-TATTTCAGTTGATCCAGGGCGATCTTT
632 TCTTCAG
64 T-TTCAG
* * * *
639 TTTATTTTAGTTGATCCAGGGCGATCTTTCTTCGATTTATTTCAGTTGATCCAGGGCGGTCTTTC
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTC-AATTATTTCAGTTGATCCAGGGCGATCTTTT
*
704 TTCAA
65 TTCAG
709 TTTATTTCAGTTGATCCAGGGCGATCTTT
1 TTTATTTCAGTTGATCCAGGGCGATCTTT
738 TCTGTAGTTT
Statistics
Matches: 373, Mismatches: 59, Indels: 47
0.78 0.12 0.10
Matches are distributed among these distances:
66 22 0.06
68 1 0.00
69 24 0.06
70 146 0.39
71 123 0.33
72 2 0.01
73 2 0.01
74 9 0.02
75 22 0.06
77 1 0.00
79 21 0.06
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (69 bp):
TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTATTTCAGTTGATCCAGGGCGATCTTTTT
TCAG
Found at i:539 original size:180 final size:174
Alignment explanation
Indices: 263--731 Score: 538
Period size: 180 Copynumber: 2.6 Consensus size: 174
253 TTCAGCTGAT
* * *
263 CCAGGGCGAT-TTTTCTTCAGTTCATTTTAATTGATCCAGGGCGATCTTTCCTCA-ATTACTTCA
1 CCAGGGCGATCTTTTCTTCAGTTTATTTTAGTTGATCCAGGGCGATCTTTCTTCAGATTA-TTCA
* * *
326 GTTGATCCAGGGCGATCTTTATTTCAGTTTATTTCAGTTGACCCAGGGCGGTCCTTCTTCAATTC
65 GTTGATCCAGGGCGGTCTTT-CTTCAATTTATTTCAGTTGACCCAGGGCGGTCCTTCTTCAATTC
* * *
391 ATTTTAATGGATCCAGGGCGATCTTTTCTTC-AGC-TT-ACTTGAC
129 ACTTCAATGGATCCAGGGCGATCTTTTCTACAAGCATTCACTTGAC
* * *
434 CCAGGGCGGTC-TTTCTCCAGTTTATTTCAGTTGATCTAGTTGATCCAGGGTGATCTTTCTTCAG
1 CCAGGGCGATCTTTTCTTCAG----TTT-A-TT--T-TAGTTGATCCAGGGCGATCTTTCTTCAG
* * * * * *
498 AATATGTCAGTTGACCCAGGGTGGTCTCTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTC
57 ATTAT-TCAGTTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGACCCAGGGCGGTCCTTC
* * * * *
563 TTCAATTTACTTCAATTGATCCAGGGCGATCTTTTCTACAATCTATTCAGTTGAT
121 TTCAATTCACTTCAATGGATCCAGGGCGATCTTTTCTACAAGC-ATTCACTTGAC
618 CCAGGGCGATCTTTTCTTCAGTTTATTTTAGTTGATCCAGGGCGATCTTTCTTC-GATTTATTTC
1 CCAGGGCGATCTTTTCTTCAGTTTATTTTAGTTGATCCAGGGCGATCTTTCTTCAGA-TTA-TTC
*
682 AGTTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGATCCAGGGCG
64 AGTTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGACCCAGGGCG
732 ATCTTTTCTG
Statistics
Matches: 247, Mismatches: 32, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
171 17 0.07
175 4 0.02
176 75 0.30
177 4 0.02
179 3 0.01
180 92 0.37
181 27 0.11
183 2 0.01
184 15 0.06
185 8 0.03
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.40
Consensus pattern (174 bp):
CCAGGGCGATCTTTTCTTCAGTTTATTTTAGTTGATCCAGGGCGATCTTTCTTCAGATTATTCAG
TTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGACCCAGGGCGGTCCTTCTTCAATTCAC
TTCAATGGATCCAGGGCGATCTTTTCTACAAGCATTCACTTGAC
Found at i:677 original size:106 final size:105
Alignment explanation
Indices: 473--756 Score: 349
Period size: 106 Copynumber: 2.7 Consensus size: 105
463 GTTGATCTAG
* * * * * *
473 TTGATCCAGGGTGATCTTTCTTCAGA-ATATGTCAGTTGACCCAGGGTGGTC-TCTCTTCAATTT
1 TTGATCCAGGGCGATCTTTCTTCA-ATATAT-TCAGTTGATCCAGGGCGATCTTTTCTTCAGTTT
* *
536 ATTTCAGTTGACCCAGGGTGGTCTTTCTTCAATTTACTTCAA
64 ATTTCAGTTGACCCAGGGCGATCTTTCTTCAATTTACTTCAA
* *
578 TTGATCCAGGGCGATCTTTTCTACAATCTATTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTA
1 TTGATCCAGGGCGATC-TTTCTTCAATATATTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTA
* * * * *
643 TTTTAGTTGATCCAGGGCGATCTTTCTTCGATTTATTTCAG
65 TTTCAGTTGACCCAGGGCGATCTTTCTTCAATTTACTTCAA
* *
684 TTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTGT-AGTTT
1 TTGATCCAGGGCGATCTTTCTTCAATATA-TTCAGTTGATCCAGGGCGATCTTTTCT-TCAGTTT
748 ATTTCAGTT
64 ATTTCAGTT
757 TACCGCAAAT
Statistics
Matches: 155, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
105 44 0.28
106 110 0.71
107 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.42
Consensus pattern (105 bp):
TTGATCCAGGGCGATCTTTCTTCAATATATTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTAT
TTCAGTTGACCCAGGGCGATCTTTCTTCAATTTACTTCAA
Found at i:1270 original size:30 final size:30
Alignment explanation
Indices: 1229--1516 Score: 414
Period size: 30 Copynumber: 9.6 Consensus size: 30
1219 TTATGATTCA
* * * *
1229 ATTTCAATCCTGTTTGAGGACCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
* *
1259 ATTTTAATCCTGGTTGAGGATCGTTACTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
* *
1289 ATTTTTGATCCTGGTTGAGGATCATTACTTT
1 A-TTTTAATCCTGGTTGAGGATCATTGCTTT
*
1320 ATTTTAATCCTGGTTGAGGATCACTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
1350 ATTTTAATCCTGGTTAAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
1380 ATTTTAATCCTGGTTGAGGATCGTTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
1410 ATTTTAATCCTGGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
1440 ATTTTAATCCTGGTTGAGGATCGTTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
* * * *
1470 ATTTTAATCATGGTTGAGGATCGTTTCCTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
1500 ATTTTAATACTGGTTGA
1 ATTTTAATCCTGGTTGA
1517 AGCTTTCTTA
Statistics
Matches: 235, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
30 207 0.88
31 28 0.12
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (30 bp):
ATTTTAATCCTGGTTGAGGATCATTGCTTT
Found at i:1593 original size:30 final size:30
Alignment explanation
Indices: 1552--1675 Score: 160
Period size: 30 Copynumber: 4.1 Consensus size: 30
1542 ATTGCTTTCC
1552 AGGATCATTGCTTTATTTTAATCCTGGTTG
1 AGGATCATTGCTTTATTTTAATCCTGGTTG
*
1582 AGGATCGTTGCTTTATTTTAATCCTGGTTG
1 AGGATCATTGCTTTATTTTAATCCTGGTTG
* * *
1612 AGGATCATTGCATTATTTTAATCCTAGTTT
1 AGGATCATTGCTTTATTTTAATCCTGGTTG
* * * *
1642 AAGATCATTGCCATT-TTTCAATCCTGGTTT
1 AGGATCATTG-CTTTATTTTAATCCTGGTTG
1672 AGGA
1 AGGA
1676 CTATTTGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
30 80 0.95
31 4 0.05
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.44
Consensus pattern (30 bp):
AGGATCATTGCTTTATTTTAATCCTGGTTG
Found at i:2097 original size:27 final size:28
Alignment explanation
Indices: 2067--2147 Score: 103
Period size: 27 Copynumber: 2.9 Consensus size: 28
2057 AAGTCATCTG
2067 GGGGCATTTTGGTCATTTTTAATTC-CA
1 GGGGCATTTTGGTCATTTTTAATTCTCA
*
2094 GGGGCATTTTGGTCATTTTT-TTTACTTCA
1 GGGGCATTTTGGTCATTTTTAATT-C-TCA
* *
2123 GGGGCACTTTAGTCATTTTTAATTC
1 GGGGCATTTTGGTCATTTTTAATTC
2148 ATTACTAGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.04
27 21 0.46
29 21 0.46
30 2 0.04
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTTAATTCTCA
Found at i:2124 original size:29 final size:30
Alignment explanation
Indices: 2067--2142 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 30
2057 AAGTCATCTG
2067 GGGGCATTTTGGTCA---TTTTTAATTCCA
1 GGGGCATTTTGGTCATTTTTTTTAATTCCA
*
2094 GGGGCATTTTGGTCATTTTTTTTACTT-CA
1 GGGGCATTTTGGTCATTTTTTTTAATTCCA
* *
2123 GGGGCACTTTAGTCATTTTT
1 GGGGCATTTTGGTCATTTTT
2143 AATTCATTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 15 0.35
29 20 0.47
30 8 0.19
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.47
Consensus pattern (30 bp):
GGGGCATTTTGGTCATTTTTTTTAATTCCA
Found at i:2685 original size:12 final size:13
Alignment explanation
Indices: 2655--2687 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2645 TCTCTCAATG
2655 TCATTTCTTCTTA
1 TCATTTCTTCTTA
2668 TCATTTCTTCTT-
1 TCATTTCTTCTTA
2680 TCATTTCT
1 TCATTTCT
2688 CACAGCTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (13 bp):
TCATTTCTTCTTA
Found at i:8827 original size:40 final size:39
Alignment explanation
Indices: 8800--9189 Score: 334
Period size: 40 Copynumber: 9.7 Consensus size: 39
8790 CTCCCGATGA
*
8800 GGAAAGGCAAATTGAGAATTTAGACAACACTTTCCGGTGG
1 GGAAAGGCAAACTGAGAATTTAGACAACACTTTCCGGT-G
*
8840 GGAAAGGCAAACTAAGAATTTAGACAACACTTTCCGGTG
1 GGAAAGGCAAACTGAGAATTTAGACAACACTTTCCGGTG
*
8879 GAGAAAGGCAAACTGGGAATTTAGACAACAAC-TTCCGGTGG
1 G-GAAAGGCAAACTGAGAATTTAGACAAC-ACTTTCCGGT-G
* *
8920 GGAATGGCAAACT-AGGTATTTAGACAACACTTTCCGGTAG
1 GGAAAGGCAAACTGA-GAATTTAGACAACACTTTCCGGT-G
* * * * *
8960 GGAAGGGCAAACTGTGTATTTACACAACACCTTCCGGTG
1 GGAAAGGCAAACTGAGAATTTAGACAACACTTTCCGGTG
* ** * * * *
8999 GGGAAGGGGAATTGGGGTATTTAGACAACACCTTCCGGTGG
1 GGAAAGGCAAACT-GAGAATTTAGACAACACTTTCCGGT-G
* * * * *
9040 GGAAGGGCAAACCGAGTATTTATACAACACCTTTCCAGTG
1 GGAAAGGCAAACTGAGAATTTAGACAACA-CTTTCCGGTG
* * * * *
9080 CGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGG
1 -GGAAAGGCAAACTGAGAATTTAGACAACACTTTCCGGT-G
* * * * *
9121 GGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGG
1 GGAAAGGCAAACTGAGAATTTAGACAACACTTTCCGGT-G
* * * *
9161 GGAAGGGCAAACTGGGTATTTAAACAACA
1 GGAAAGGCAAACTGAGAATTTAGACAACA
Statistics
Matches: 305, Mismatches: 34, Indels: 22
0.84 0.09 0.06
Matches are distributed among these distances:
39 13 0.04
40 246 0.81
41 46 0.15
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (39 bp):
GGAAAGGCAAACTGAGAATTTAGACAACACTTTCCGGTG
Found at i:8916 original size:80 final size:80
Alignment explanation
Indices: 8800--9189 Score: 458
Period size: 80 Copynumber: 4.9 Consensus size: 80
8790 CTCCCGATGA
* * * * * *
8800 GGAAAGGCAAATTGAGAATTTAGACAACACTTTCCGGTGGGGAAAGGCAAACTAAGAATTTAGAC
1 GGAAGGGCAAACTGAGTATTTAGACAACACCTTCCGGTGGGGAAAGGCAAACTAGGTATTTAGAC
*
8865 AACACTTTCCGGTGG
66 AACACCTTCCGGTGG
* * * * * *
8880 AGAAAGGCAAACTGGGAATTTAGACAACAACTTCCGGTGGGGAATGGCAAACTAGGTATTTAGAC
1 GGAAGGGCAAACTGAGTATTTAGACAACACCTTCCGGTGGGGAAAGGCAAACTAGGTATTTAGAC
* *
8945 AACACTTTCCGGTAG
66 AACACCTTCCGGTGG
* * ** * *
8960 GGAAGGGCAAACTGTGTATTTACACAACACCTTCCGGTGGGG-AAGGGGAATTGGGGTATTTAGA
1 GGAAGGGCAAACTGAGTATTTAGACAACACCTTCCGGTGGGGAAAGGCAAACT-AGGTATTTAGA
9024 CAACACCTTCCGGTGG
65 CAACACCTTCCGGTGG
* * * * * * *
9040 GGAAGGGCAAACCGAGTATTTATACAACACCTTTCCAGTGCGGAAGGGCAAACTGGGTATTTAAA
1 GGAAGGGCAAACTGAGTATTTAGACAACACC-TTCCGGTGGGGAAAGGCAAACTAGGTATTTAGA
9105 CAACACCTTCCGGTGG
65 CAACACCTTCCGGTGG
* * * * *
9121 GGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
1 GGAAGGGCAAACTGAGTATTTAGACAACACCTTCCGGTGGGGAAAGGCAAACTAGGTATTTAGAC
9186 AACA
66 AACA
Statistics
Matches: 270, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
79 6 0.02
80 195 0.72
81 63 0.23
82 6 0.02
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (80 bp):
GGAAGGGCAAACTGAGTATTTAGACAACACCTTCCGGTGGGGAAAGGCAAACTAGGTATTTAGAC
AACACCTTCCGGTGG
Found at i:9123 original size:121 final size:118
Alignment explanation
Indices: 8817--9189 Score: 469
Period size: 121 Copynumber: 3.1 Consensus size: 118
8807 CAAATTGAGA
* * * * *
8817 ATTTAGACAACACTTTCCGGTGGGGAAAGGCAAACTAAGAATTTAGACAACACTTTCCGGTGGAG
1 ATTTAGACAACACTTTCCGGT-GGGAAGGGCAAACTGAGTATTTAAACAACACCTTCCGGTGG-G
* * * * * *
8882 AAAGGCAAACTGGGAATTTAGACAACAACTTCCGGTGGGGAATGGCAAA-CTAGGT
64 GAAGGGAAACTGGGTATTTAGACAACACCTTCCGGTGGGGAAGGGCAAACCGA-GT
* *
8937 ATTTAGACAACACTTTCCGGTAGGGAAGGGCAAACTGTGTATTTACACAACACCTTCCGGTGGGG
1 ATTTAGACAACACTTTCCGGT-GGGAAGGGCAAACTGAGTATTTAAACAACACCTTCCGGTGGGG
* *
9002 AAGGGGAATTGGGGTATTTAGACAACACCTTCCGGTGGGGAAGGGCAAACCGAGT
65 AAGGGAAACT-GGGTATTTAGACAACACCTTCCGGTGGGGAAGGGCAAACCGAGT
* * *
9057 ATTTATACAACACCTTTCCAGTGCGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGGG
1 ATTTAGACAACA-CTTTCCGGTG-GGAAGGGCAAACTGAGTATTTAAACAACACCTTCCGGTGGG
* * *
9122 GAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGT
64 GAAGGG-AAACTGGGTATTTAGACAACACCTTCCGGTGGGGAAGGGCAAACCGAGT
*
9178 ATTTAAACAACA
1 ATTTAGACAACA
Statistics
Matches: 223, Mismatches: 25, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
119 8 0.04
120 105 0.47
121 107 0.48
122 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (118 bp):
ATTTAGACAACACTTTCCGGTGGGAAGGGCAAACTGAGTATTTAAACAACACCTTCCGGTGGGGA
AGGGAAACTGGGTATTTAGACAACACCTTCCGGTGGGGAAGGGCAAACCGAGT
Done.