Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014829.1 Corchorus capsularis cultivar CVL-1 contig14850, 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: 45160
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:558 original size:33 final size:32
Alignment explanation
Indices: 447--559 Score: 120
Period size: 33 Copynumber: 3.4 Consensus size: 32
437 TAGACAAAGG
* *
447 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGG-TGTGGCCGGACATGTCC-AT
** * * *
480 GTCGTTTGGCCTGTTGTAGCCGGCCATGTCCAT
1 GTCGCGTGGCC-GGTGTGGCCGGACATGTCCAT
513 GTCGCGTGGCCGGTGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTG-TGGCCGGACATGTCCAT
546 GTCGCGTGGCCGGT
1 GTCGCGTGGCCGGT
560 CTTGTGGCCG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
32 4 0.06
33 61 0.92
34 1 0.02
ACGTcount: A:0.08, C:0.27, G:0.41, T:0.24
Consensus pattern (32 bp):
GTCGCGTGGCCGGTGTGGCCGGACATGTCCAT
Found at i:1219 original size:12 final size:13
Alignment explanation
Indices: 1195--1219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1185 ATTTAAAAGG
1195 AAAAACGGAAAAA
1 AAAAACGGAAAAA
1208 AAAAACGGAAAA
1 AAAAACGGAAAA
1220 TTAATTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAACGGAAAAA
Found at i:1248 original size:51 final size:52
Alignment explanation
Indices: 1193--1310 Score: 143
Period size: 51 Copynumber: 2.3 Consensus size: 52
1183 TTATTTAAAA
1193 GGAAAAACGGAAAAAAAAAACGGAA-AATTAA-TTTTTTTTAAAAGAAAAATC
1 GGAAAAACGGAAAAAAAAAACGGAATAA-TAATTTTTTTTTAAAAGAAAAATC
* ** ** **
1244 GG-AAACCCTAAATTAAAAACGGAATAATAATTTTTTTTTTTAAGAAAAATC
1 GGAAAAACGGAAAAAAAAAACGGAATAATAATTTTTTTTTAAAAGAAAAATC
1295 GGAAAAACGGAAAAAA
1 GGAAAAACGGAAAAAA
1311 CTTTTTTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
50 20 0.38
51 24 0.46
52 8 0.15
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.24
Consensus pattern (52 bp):
GGAAAAACGGAAAAAAAAAACGGAATAATAATTTTTTTTTAAAAGAAAAATC
Found at i:5000 original size:33 final size:33
Alignment explanation
Indices: 4963--5035 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
4953 ATTAGCATCC
* *
4963 AAAACATATTTTGTTTCATCACAAACAACACCT
1 AAAACATATTTAGTGTCATCACAAACAACACCT
* * *
4996 AAAACAGATTTAGTGTCATCGCAAACAACATCT
1 AAAACATATTTAGTGTCATCACAAACAACACCT
5029 AAAACAT
1 AAAACAT
5036 TCTTTGCAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26
Consensus pattern (33 bp):
AAAACATATTTAGTGTCATCACAAACAACACCT
Found at i:10270 original size:47 final size:47
Alignment explanation
Indices: 10196--10878 Score: 455
Period size: 47 Copynumber: 15.0 Consensus size: 47
10186 ACTTTATCTT
* * *
10196 ATTCCCACTTTGCCCTT-CCCAGTCGGAAGGTGTTATTTAGTTGTCAA
1 ATTCCCAGTTTGCCCTTCCCCA-CCGGAAGGTGTTGTTTAGTTGTCAA
* * * * *
10243 ATTCCCAATTTACCCTTCCCCACCGGAAGGTGTTGTCTAGTT-ACCA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTCAA
* * *
10289 ATTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTGTCGAA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTC-AA
*
10337 A-TCCCAGTTTGCCCTTCCCCACCGGTA-G-G-TG-TT-GTT-T-AA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTCAA
* * * *
10376 TTTCCCGGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTA-----CAT
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTCAA
* * *
10418 TTTCCCGGTTTGCCCTTCCCCACCGGAA-G-G-TGTTTAGTTGTCAT
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTCAA
* * * ** * *
10462 TTTCCAAGTTCGCCCTTCCCCACCTTAAGGTGTTGTCTA--AGTCTACA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTC-A-A
* * * * * * *
10509 TTTCCCAGTTTTCCCTTCCCCACCAGAATGTGTTGGTTAGTTGACAT
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTCAA
* ** * *
10556 TTTCATAGTTTGCCCTT-CCCAGTCGAAAGGTGTTGTTTA-----C--
1 ATTCCCAGTTTGCCCTTCCCCA-CCGGAAGGTGTTGTTTAGTTGTCAA
* * *
10596 ATT-CCTGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTTAGTGGTCAT
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAG-T--T-GTCAA
*
10646 ATT-CCAGTTTGCCCTTCCCCACCAGAAGGTGTTGTTTAAGTT-T-ACA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT-AGTTGTCA-A
* * * * *
10692 ATTCCAAATTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTGGTCAT
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTCAA
*
10739 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA--AGTCTATA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTC-A-A
* * * *
10786 ATTCCCAATTTTCCCTTCCCCAACGGAAGGTGTTGTTTAGTTTTGTC-T
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAG--TTGTCAA
* * *** * *
10834 TTTCCCAATTTGCCCTTCCCGGTCAGAAGGTGTTGTTTAATTGTC
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTC
10879 TTATTCCAAA
Statistics
Matches: 507, Mismatches: 83, Indels: 93
0.74 0.12 0.14
Matches are distributed among these distances:
39 33 0.07
40 30 0.06
41 3 0.01
42 33 0.07
43 4 0.01
44 30 0.06
45 9 0.02
46 60 0.12
47 220 0.43
48 43 0.08
49 2 0.00
50 35 0.07
51 5 0.01
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (47 bp):
ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGTCAA
Found at i:10679 original size:136 final size:139
Alignment explanation
Indices: 10513--10777 Score: 333
Period size: 136 Copynumber: 1.9 Consensus size: 139
10503 TCTACATTTC
* * * * *
10513 CCAGTTTTCCCTTCCCCACCAGAATGTGTTGGTT-AGTTGACATTTTCATAGTTTGCCCTT-CCC
1 CCAGTTTGCCCTTCCCCACCAGAAGGTGTTGGTTAAGTTGACAATTCCA-AATTTGCCCTTCCCC
* *
10576 AGTCGAAAGGTGTTGTTTA-C-ATT-CCTGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTTA
65 A-ACGAAAGGTGTTGTTTAGCAATTCCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTTA
10638 GTGGTCATATT
129 GTGGTCATATT
* *
10649 CCAGTTTGCCCTTCCCCACCAGAAGGTGTTGTTTAAGTTTACAATTCCAAATTTGCCCTTCCCCA
1 CCAGTTTGCCCTTCCCCACCAGAAGGTGTTGGTTAAGTTGACAATTCCAAATTTGCCCTTCCCCA
* *
10714 ACGGAAGGTGTTGTTTAGTGGTCATATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
66 ACGAAAGGTGTTGTTTA---G-CA-ATTCCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTA
10778 AGTCTATAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
136 56 0.52
137 15 0.14
141 1 0.01
143 3 0.03
144 33 0.31
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (139 bp):
CCAGTTTGCCCTTCCCCACCAGAAGGTGTTGGTTAAGTTGACAATTCCAAATTTGCCCTTCCCCA
ACGAAAGGTGTTGTTTAGCAATTCCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTTAGT
GGTCATATT
Found at i:10751 original size:183 final size:179
Alignment explanation
Indices: 10243--10873 Score: 576
Period size: 183 Copynumber: 3.5 Consensus size: 179
10233 TAGTTGTCAA
* * * * **
10243 ATTCCCAATTTACCCTTCCCCACCGGAAGGTGTTGTCTAG-TTACCA-ATTCCCAATTTGCCCTT
1 ATTCCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTTTGTCATATTCCCAATTTGCCCTT
* * * * *
10306 CCTCATCGGAAGGTGTTGTTT-AGTTGT-CGAAATCCCAGTTTGCCCTTCCCCACCGGTAGGTGT
66 CCCCACCAGAAGGTGTTGTTTAAGTT-TAC-AATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGT
*
10369 TGTTTA----ATTTCCCGGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAC
129 TGTTTAGTGCATTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAC
* * * *
10416 ATTTTCCCGGTTTGCCCTTCCCCACCGGAA-G-G-TGTTTAG-TTGTCAT-TTTCCAAGTTCGCC
1 A--TTCCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTTTGTCATATTCCCAA-TTTGCC
** * * * * * *
10476 CTTCCCCACCTTAAGGTGTTGTCTAAGTCTACATTTCCCAGTTTTCCCTTCCCCACCAGAATGTG
63 CTTCCCCACCAGAAGGTGTTGTTTAAGTTTACAATTCCCAGTTTGCCCTTCCCCACCGGAAGGTG
* ** *
10541 TTGGTTAGTTGACATTTTCATAGTTTGCCCTT-CCCAGTCGAAAGGTGTTGTTTAC
128 TTGTTTAG-TG-CA-TTTCCCAGTTTGCCCTTCCCCA-TCGGAAGGTGTTGTTTAC
* *
10596 ATT-CCTGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTTAGTGGTCATATT-CCAGTTTGCC
1 ATTCCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTT--T-GTCATATTCCCAATTTGCC
* * *
10659 CTTCCCCACCAGAAGGTGTTGTTTAAGTTTACAATTCCAAATTTGCCCTTCCCCAACGGAAGGTG
63 CTTCCCCACCAGAAGGTGTTGTTTAAGTTTACAATTCCCAGTTTGCCCTTCCCCACCGGAAGGTG
*
10724 TTGTTTAGTGGTCATATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTC
128 TTGTTTAGT-G-CAT-TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-A--C
* * *
10782 TATAATTCCCAATTTTCCCTTCCCCAACGGAAGGTGTTGTTTAGTTTTGTC-TTTTCCCAATTTG
1 ----ATTCCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAG-TTTGTCATATTCCCAATTTG
***
10846 CCCTTCCCGGTCAGAAGGTGTTGTTTAA
61 CCCTTCCCCACCAGAAGGTGTTGTTTAA
10874 TTGTCTTATT
Statistics
Matches: 369, Mismatches: 54, Indels: 54
0.77 0.11 0.11
Matches are distributed among these distances:
172 16 0.04
173 60 0.16
174 5 0.01
175 24 0.07
177 22 0.06
178 3 0.01
179 6 0.02
180 39 0.11
181 1 0.00
182 2 0.01
183 98 0.27
184 13 0.04
185 2 0.01
186 1 0.00
188 3 0.01
189 35 0.09
190 4 0.01
191 33 0.09
192 2 0.01
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (179 bp):
ATTCCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTTTAGTTTGTCATATTCCCAATTTGCCCTT
CCCCACCAGAAGGTGTTGTTTAAGTTTACAATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
TTTAGTGCATTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAC
Found at i:10898 original size:48 final size:49
Alignment explanation
Indices: 10877--11208 Score: 377
Period size: 49 Copynumber: 6.8 Consensus size: 49
10867 TGTTTAATTG
* *
10877 TCTTATTCCAAAAATGACCCTTCCCGGTCGGAAGGTCACAGTTTTCTTG
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTC
* * * *
10926 TCTTATTCCTAAAATGCCCCTTCTCGGTCGGAAGGTAACAGTTTTATTC
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTC
* * * *
10975 TCTAATTCCAAAAATGCTCCTT-CTGGTCGGAAAGTCACAGTTTTCTTC
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTC
* *
11023 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCATAGTTTTCTCC
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTC
* * * * *
11072 TCTTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTA
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTC-TTC
* *
11122 TTTGTTTTCC-AAAATGCCCCTTCCCGGTCGGAAGGTC-CTTA-TTTTCTT-
1 TCT-TATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCAC--AGTTTTCTTC
* * *
11170 TAAATTTTTCCAAAAATGCCCTTTCCCGGTCGGAAGGTC
1 T--CTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTC
11209 CTCGTTTTCT
Statistics
Matches: 241, Mismatches: 34, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
48 42 0.17
49 134 0.56
50 60 0.25
51 5 0.02
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.36
Consensus pattern (49 bp):
TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTC
Found at i:10941 original size:49 final size:48
Alignment explanation
Indices: 10846--11317 Score: 373
Period size: 49 Copynumber: 9.6 Consensus size: 48
10836 TCCCAATTTG
* *** ** *
10846 CCCTTCCCGGTCAGAAGGTGTTGTTTAATTGTCTTATTCCAAAAATGA
1 CCCTTCCCGGTCGGAAGGTCCAGTTTTCTTGTCTTATTCCAAAAATGC
*
10894 CCCTTCCCGGTCGGAAGGTCACAGTTTTCTTGTCTTATTCCTAAAATGC
1 CCCTTCCCGGTCGGAAGGTC-CAGTTTTCTTGTCTTATTCCAAAAATGC
* * * * *
10943 CCCTTCTCGGTCGGAAGGTAACAGTTTTATTCTCTAATTCCAAAAATGC
1 CCCTTCCCGGTCGGAAGGT-CCAGTTTTCTTGTCTTATTCCAAAAATGC
* * * *
10992 TCCTT-CTGGTCGGAAAGTCACAGTTTTCTTCTCTTATTCCAAAAATGC
1 CCCTTCCCGGTCGGAAGGTC-CAGTTTTCTTGTCTTATTCCAAAAATGC
* **
11040 CCCTTCCCGGTCGGAAGGTCATAGTTTTCTCCTCTTATTCCAAAAATGC
1 CCCTTCCCGGTCGGAAGGTC-CAGTTTTCTTGTCTTATTCCAAAAATGC
* * * * * *
11089 CCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTATTTGTTTTCC-AAAATGC
1 CCCTTCCCGGTCGGAAGGT-CCAGTTTTC-TTGTCT-TATTCCAAAAATGC
* *
11139 CCCTTCCCGGTCGGAAGGTCCTTA-TTTTCTT-TAAATTTTTCCAAAAATGC
1 CCCTTCCCGGTCGGAAGGTCC--AGTTTTCTTGT--CTTATTCCAAAAATGC
* * * *
11189 CCTTTCCCGGTCGGAAGGTCCTCGTTTTCTTTGT-TTGTTTACC-AAAATGT
1 CCCTTCCCGGTCGGAAGGTCC-AGTTTTC-TTGTCTT-ATT-CCAAAAATGC
** * * * *
11239 CCCTTCCTAGTCGGAAGATCCTTGTTTTCTTTGT-TTGTGTCCCAAAATGC
1 CCCTTCCCGGTCGGAAGGTCC-AGTTTTC-TTGTCTTAT-TCCAAAAATGC
* *
11289 CCTTTCCCGGTCGGAAGGTCCAATTTTCT
1 CCCTTCCCGGTCGGAAGGTCCAGTTTTCT
11318 CTTCACATTT
Statistics
Matches: 351, Mismatches: 54, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
48 60 0.17
49 151 0.43
50 130 0.37
51 9 0.03
52 1 0.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.37
Consensus pattern (48 bp):
CCCTTCCCGGTCGGAAGGTCCAGTTTTCTTGTCTTATTCCAAAAATGC
Found at i:11003 original size:97 final size:96
Alignment explanation
Indices: 10881--11157 Score: 349
Period size: 97 Copynumber: 2.8 Consensus size: 96
10871 TAATTGTCTT
* *
10881 ATTCCAAAAATGACCCTTCCCGGTCGGAAGGTCACAGTTTTCTTGTCTTATTCCTAAAATGCCCC
1 ATTCCAAAAATG-CCCTTCCTGGTCGGAAGGTCACAGTTTTCTTATCTTATTCC-AAAATGCCCC
* *
10946 TTCTCGGTCGGAAGGTAACAGTTTTATTCTCTA
64 TTCCCGGTCGGAAGGTAACAGTTTTATCCTCTA
* *
10979 ATTCCAAAAATGCTCCTT-CTGGTCGGAAAGTCACAGTTTTCTTCTCTTATTCCAAAAATGCCCC
1 ATTCCAAAAATGC-CCTTCCTGGTCGGAAGGTCACAGTTTTCTTATCTTATTCC-AAAATGCCCC
* * * *
11043 TTCCCGGTCGGAAGGTCATAGTTTTCTCCTCTT
64 TTCCCGGTCGGAAGGTAACAGTTTTATCCTCTA
* * * * *
11076 ATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTATTTGTTTTCCAAAATGCCC
1 ATTCCAAAAATG-CCCTTCCTGGTCGGAAGGTCACAGTTTTC-TTATCT-TATTCCAAAATGCCC
11141 CTTCCCGGTCGGAAGGT
63 CTTCCCGGTCGGAAGGT
11158 CCTTATTTTC
Statistics
Matches: 157, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
97 86 0.55
98 36 0.23
99 30 0.19
100 5 0.03
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (96 bp):
ATTCCAAAAATGCCCTTCCTGGTCGGAAGGTCACAGTTTTCTTATCTTATTCCAAAATGCCCCTT
CCCGGTCGGAAGGTAACAGTTTTATCCTCTA
Found at i:11155 original size:50 final size:50
Alignment explanation
Indices: 10877--11309 Score: 366
Period size: 50 Copynumber: 8.8 Consensus size: 50
10867 TGTTTAATTG
* * * *
10877 TCTTATTCCAAAAATGACCCTTCCCGGTCGGAAGGTCACAGTTTTC-TTG
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTC
* * ** * *
10926 TCTTATTCCTAAAATGCCCCTTCTCGGTCGGAAGGTAACAGTTTT-ATTC
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTC
* * * * * *
10975 TCTAATTCCAAAAATGCTCCTT-CTGGTCGGAAAGTCACAGTTTTC-TTC
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTC
* *
11023 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGT-CATAGTTTTC-TCC
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCT-GTTTTCTTTC
* * *
11072 TCTTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTA
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTC
* * * * *
11122 TTTGTTTTCC-AAAATGCCCCTTCCCGGTCGGAAGGTCCTTATTTTCTTTA
1 TCT-TATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTC
** * * *
11172 AATTTTTCCAAAAATGCCCTTTCCCGGTCGGAAGGT-CCTCGTTTTCTTTG
1 TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCT-GTTTTCTTTC
* * ** * * *
11222 T-TTGTTTACC-AAAATGTCCCTTCCTAGTCGGAAGATCCTTGTTTTCTTTG
1 TCTT-ATT-CCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTC
* * *
11272 T-TTGTGTCCCAAAATGCCCTTTCCCGGTCGGAAGGTCC
1 TCTTAT-TCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC
11310 AATTTTCTCT
Statistics
Matches: 320, Mismatches: 50, Indels: 27
0.81 0.13 0.07
Matches are distributed among these distances:
48 41 0.13
49 134 0.42
50 136 0.43
51 9 0.03
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (50 bp):
TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTC
Found at i:14159 original size:940 final size:939
Alignment explanation
Indices: 12342--14218 Score: 3107
Period size: 940 Copynumber: 2.0 Consensus size: 939
12332 ATTACCAATA
*
12342 GATACGAATCTAGTTCTATTAGATTCAAATCCACCTTTGAGACCTGCCAAAGATCAATTTGACAA
1 GATACGAATCTAGTTCTATTAGATTCAAATCCACCTTTGAGACCTGCCAAAGATCAACTTGACAA
*
12407 CTTCAACTTCTAGACTTGTCTATAGATCGATAATCCTAACCTAGCCTTCTTCTTCGTTCGTCGCC
66 CTTCAACTTCTAGACTTGTCTATAGATCGATAATCCTAACCTAGCCTTCTTCTTCATTCGTCGCC
* *
12472 TTGGGATGGATAATTAAACCTGCAATTATCAACCTAAGATCACAAGATTCACAAACAATTAACCA
131 TTGAGATGGATAATTAAACATGCAATTATCAACCTAAGATCACAAGATTCACAAACAATTAACCA
* * * *
12537 TTCAGAACCTAATTCTTTGCTATGACTCTACAAGACTGAAGAACACTAAAGTTTGCTCAAACTAG
196 ATCACAACCTAATTCTTTGCTAGGACTCTACAAGACTGAAGAACACTAAAGTATGCTCAAACTAG
* *
12602 AACAATGAAGCTAAGATAATCAATTTGGTGACAAACCTCAAATTTGTATTGAAAACTTAACTTAT
261 AACAATGAAGCTAAGATAATCAATTGGGTGACAAACCTCAAATTTGTAATGAAAACTTAACTTAT
12667 GTTTACAAGAGGGTACTGAAGCCCTTATATAGTGGTAAAGGACATCCTAACCCTAATCCTAAAAG
326 GTTTACAAGAGGGTACTGAAGCCCTTATATAGTGGTAAAGGACATCCTAACCCTAATCCTAAAAG
* *
12732 GATATGGGCAACTATAAAGTCTAACAACCCCCAAAAATAAAAATAAACTTAAAACACAATAATTA
391 GATATGGGCAACTATAAAGCCTAACAACCCCCAAAAATAAAAATAAACTAAAAACACAATAATTA
* * * *
12797 AAATAAATCCGCAGGCTACCCGCCCCTAGGTGACCCCTACCCGGTCCTGCGCGCCCTCAGGATGT
456 AAATAAATCCACAAGCTACCCGCACCTAGGTGACCCCTACCCGGCCCTGCGCGCCCTCAGGATGT
* * * *
12862 TTAAGGCCTTTTTTGATGCTACCCGGCCTTGGGTACCCCCTACCCGCCCCTGGGCACCACCGAAA
521 TTAAGGCCTTTTATGATGCTACCCGGCCCTAGGTACCCCCTACCCGCCCCTGGCCACCACCGAAA
*
12927 ACTTCAATTATACTTTAAAAATAAGCAAAGTGATGAACTTATAATTGATTGGTAATTTCTTGCTC
586 ACTTCAATTAGACTTTAAAAATAAGCAAAGTGATGAACTTATAATTGATTGGTAATTTCTTGCTC
* * *
12992 AAATCATCATCAAAGCTCTTCAATTGAACTTCAATAGTCTTCATGTCATCAAAATGAGTTTGAAC
651 AAATCATCATCAAAACTCTTCAATTGAACTTCAATAGTCTTCATGTCATCAAAATGAGCTCGAAC
** * *
13057 AAGGCCCATGAGTACAACCTTGAATCTCTTAGCTCTTGCTCTTGTCATTGGACTAATAGGTATCT
716 AAGGCCCATGAGTACAACCTTGAATCTCTTAGCTCTTGCTCTTGTCATCAGACCAATAGGCATCT
*
13122 TCAATGGATCAAATGGCATCTTCTTGGTGCTTGGAACATGTTGTGCGATATCACCATCATCTTCA
781 TCAATGGATCAAATGGCATCTTCTTGGTGCTTGGAACATGTTGTGCGATATCACCAGCATCTTCA
* *
13187 TACTTGTCCATGCTTCCTTGCAGTCCATACACA-CCATCTCCATCATCTTCATTGTGCACTTGAA
846 TACTTGTCCATGCTTCCTTGCAGCCCATACACATCC-TCTCCATCATCTTCATTGTGCACTTCAA
13251 GTCCATGATAAGCTCTTGGCGCATCAGTTT
910 GTCCATGATAAGCTCTTGGCGCATCAGTTT
* * *
13281 GATACGAATCTAGTTGTGTTAGATTCAAATCCACCTTTGAGACCTGCCAAAGATCAGCTTGACAA
1 GATACGAATCTAGTTCTATTAGATTCAAATCCACCTTTGAGACCTGCCAAAGATCAACTTGACAA
* * *
13346 CTTCAACTTCTAGATTTGTTTGTAGATCGATAATCCTAACCTAGCCTTCTTCTTCATTCGTCGCC
66 CTTCAACTTCTAGACTTGTCTATAGATCGATAATCCTAACCTAGCCTTCTTCTTCATTCGTCGCC
* * *
13411 TTGAGATGGATAATTAAACATGCAATTATTAACCTAAGATCACAAGATTTACAAACAATTAAGCA
131 TTGAGATGGATAATTAAACATGCAATTATCAACCTAAGATCACAAGATTCACAAACAATTAACCA
* * *
13476 ATCACAACCTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCT-AAGTATGCTCAAACTAG
196 ATCACAACCTAATTCTTTGCTAGGACTCTACAAGACTGAAGAACACTAAAGTATGCTCAAACTAG
* *
13540 AACAATGAAGCTAAGGTAATCAATTGGGTGAGTAAACCTCAAATCTT-TAATGAAAACTTAACTT
261 AACAATGAAGCTAAGATAATCAATTGGGTGA-CAAACCTCAAAT-TTGTAATGAAAACTTAACTT
** *
13604 ATGTTTACAAGAGGGTGTTGAAGCCCTTATATAGTGGTAAGGGACATCCTAACCCTAATCCTAAA
324 ATGTTTACAAGAGGGTACTGAAGCCCTTATATAGTGGTAAAGGACATCCTAACCCTAATCCTAAA
* * *
13669 AGGATATGGGCAGCTATAAAGCCTAACAA-GCCCAAAAATAAAAATAAACTAAAAAAACGCAATA
389 AGGATATGGGCAACTATAAAGCCTAACAACCCCCAAAAATAAAAATAAACT--AAAAACACAATA
* *
13733 ATTAAAATAATTCCACAAGCTACCCGCACCT-GGCTGACCCCTACCCGGCCCTGGGCGCCCTCAG
452 ATTAAAATAAATCCACAAGCTACCCGCACCTAGG-TGACCCCTACCCGGCCCTGCGCGCCCTCAG
13797 GATGTTTAAGGCCTTTTATGATGCTACCCGGCCCTAGGTACCCCCTACCCGCCCCTGGCCACCAC
516 GATGTTTAAGGCCTTTTATGATGCTACCCGGCCCTAGGTACCCCCTACCCGCCCCTGGCCACCAC
* ** *
13862 CGGAAACTTCAATTAGGTTTTAAAAATAAGCAAAGTGATGAACTTGTAATTGATTGGTAATTTCT
581 CGAAAACTTCAATTAGACTTTAAAAATAAGCAAAGTGATGAACTTATAATTGATTGGTAATTTCT
13927 TGCTCAAATCATCATCAAAACTCTTCAATTGAACTTCAATAGTCTTCATGTCATCAAAATGAGCT
646 TGCTCAAATCATCATCAAAACTCTTCAATTGAACTTCAATAGTCTTCATGTCATCAAAATGAGCT
* * *
13992 CGAACAAGGCCCATGAGTGCATCCTTGAATCTTTTAGCTCTTGCTCTTGTCATCAGACCAATAGG
711 CGAACAAGGCCCATGAGTACAACCTTGAATCTCTTAGCTCTTGCTCTTGTCATCAGACCAATAGG
14057 CATCTTCAATGGATCAAATGGCATCTTCTTGGTGCTTGGAACATGTTGTGCGATATCACCAGCAT
776 CATCTTCAATGGATCAAATGGCATCTTCTTGGTGCTTGGAACATGTTGTGCGATATCACCAGCAT
* *
14122 CTTCATGCTTGTCCATGCTTCCTTGCAGCCCATACACATCCTCTCCATGATCTTCATTGTGCACT
841 CTTCATACTTGTCCATGCTTCCTTGCAGCCCATACACATCCTCTCCATCATCTTCATTGTGCACT
14187 TCAAGTCCATGATAAGCTCTTGGCGCATCAGT
906 TCAAGTCCATGATAAGCTCTTGGCGCATCAGT
14219 ACCTCCAATA
Statistics
Matches: 870, Mismatches: 62, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
938 65 0.07
939 341 0.39
940 462 0.53
941 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (939 bp):
GATACGAATCTAGTTCTATTAGATTCAAATCCACCTTTGAGACCTGCCAAAGATCAACTTGACAA
CTTCAACTTCTAGACTTGTCTATAGATCGATAATCCTAACCTAGCCTTCTTCTTCATTCGTCGCC
TTGAGATGGATAATTAAACATGCAATTATCAACCTAAGATCACAAGATTCACAAACAATTAACCA
ATCACAACCTAATTCTTTGCTAGGACTCTACAAGACTGAAGAACACTAAAGTATGCTCAAACTAG
AACAATGAAGCTAAGATAATCAATTGGGTGACAAACCTCAAATTTGTAATGAAAACTTAACTTAT
GTTTACAAGAGGGTACTGAAGCCCTTATATAGTGGTAAAGGACATCCTAACCCTAATCCTAAAAG
GATATGGGCAACTATAAAGCCTAACAACCCCCAAAAATAAAAATAAACTAAAAACACAATAATTA
AAATAAATCCACAAGCTACCCGCACCTAGGTGACCCCTACCCGGCCCTGCGCGCCCTCAGGATGT
TTAAGGCCTTTTATGATGCTACCCGGCCCTAGGTACCCCCTACCCGCCCCTGGCCACCACCGAAA
ACTTCAATTAGACTTTAAAAATAAGCAAAGTGATGAACTTATAATTGATTGGTAATTTCTTGCTC
AAATCATCATCAAAACTCTTCAATTGAACTTCAATAGTCTTCATGTCATCAAAATGAGCTCGAAC
AAGGCCCATGAGTACAACCTTGAATCTCTTAGCTCTTGCTCTTGTCATCAGACCAATAGGCATCT
TCAATGGATCAAATGGCATCTTCTTGGTGCTTGGAACATGTTGTGCGATATCACCAGCATCTTCA
TACTTGTCCATGCTTCCTTGCAGCCCATACACATCCTCTCCATCATCTTCATTGTGCACTTCAAG
TCCATGATAAGCTCTTGGCGCATCAGTTT
Found at i:18082 original size:20 final size:22
Alignment explanation
Indices: 18057--18098 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18047 CAAATTCATT
18057 AATCC-ATCTTT-TAAAACCCA
1 AATCCAATCTTTCTAAAACCCA
*
18077 AATCCAATCTTTCTAAAGCCCA
1 AATCCAATCTTTCTAAAACCCA
18099 TTTTATTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.29
Consensus pattern (22 bp):
AATCCAATCTTTCTAAAACCCA
Found at i:20961 original size:18 final size:16
Alignment explanation
Indices: 20938--20975 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 16
20928 TAAAAAGGTT
20938 TTCAAAATTCCAAAAAAA
1 TTCAAAATT-C-AAAAAA
20956 TTCAAAATTCAAAAAA
1 TTCAAAATTCAAAAAA
20972 TTCA
1 TTCA
20976 TTCAAGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 1 0.05
18 9 0.45
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (16 bp):
TTCAAAATTCAAAAAA
Found at i:37845 original size:70 final size:70
Alignment explanation
Indices: 37765--38139 Score: 472
Period size: 70 Copynumber: 5.4 Consensus size: 70
37755 AATGCTTTGA
* * * * *
37765 CTTTTCCATAAGTCAAACTCGTTTCCACACAAGCCAGTTCAAGCTTTGATTCCATCCAAGCATTC
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCTTTGGTTCCATCCAAGCATTC
*
37830 AAGGA
66 AAGGG
* * * *
37835 CTTTTCCATAAGTCAAATTCGTTTCCACACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTC
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCTTTGGTTCCATCCAAGCATTC
37900 AAGGG
66 AAGGG
* * * * *
37905 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAG-TCTAGCCTTGGTTCCATCCAAGCA-GC
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCTTTGGTTCCATCCAAGCATTC
*
37968 AGGGG
66 AAGGG
* * *
37973 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGCTTCCACCCAAGCATTC
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCTTTGGTTCCATCCAAGCATTC
38038 AAGGG
66 AAGGG
* * * * *
38043 CTTTTCCAAAAGCCAAACTCGCTTCCATACGAGACAG-TCTAGCCTTGGTTCCATCCAAGCA-GC
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCTTTGGTTCCATCCAAGCATTC
38106 -AGCGG
66 AAG-GG
* *
38111 CTTTTCCACAAGCCAAACTCTTTTCCATA
1 CTTTTCCATAAGCCAAACTCGTTTCCATA
38140 AGTCAGGTTC
Statistics
Matches: 267, Mismatches: 35, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
67 2 0.01
68 68 0.25
69 62 0.23
70 135 0.51
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (70 bp):
CTTTTCCATAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCTTTGGTTCCATCCAAGCATTC
AAGGG
Found at i:37995 original size:138 final size:138
Alignment explanation
Indices: 37765--38137 Score: 530
Period size: 138 Copynumber: 2.7 Consensus size: 138
37755 AATGCTTTGA
* * * * * * * * *
37765 CTTTTCCATAAGTCAAACTCGTTTCCACACAAGCCAGTTCAAGCTTTGATTCCATCCAAGCATTC
1 CTTTTCCAAAAGCCAAACTCGTTTCCATACGAGACAG-TCTAGCCTTGGTTCCATCCAAGCA-GC
* * * * * *
37830 AAGGACTTTTCCATAAGTCAAATTCGTTTCCACACGAGTCAGTTCAAGCTTTGGTTCCATCCAAG
64 AGGGGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGTTCAAGCTTTGCTTCCACCCAAG
37895 CATTCAAGGG
129 CATTCAAGGG
* *
37905 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTCTAGCCTTGGTTCCATCCAAGCAGCAG
1 CTTTTCCAAAAGCCAAACTCGTTTCCATACGAGACAGTCTAGCCTTGGTTCCATCCAAGCAGCAG
*
37970 GGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGCTTCCACCCAAGCA
66 GGGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGTTCAAGCTTTGCTTCCACCCAAGCA
38035 TTCAAGGG
131 TTCAAGGG
*
38043 CTTTTCCAAAAGCCAAACTCGCTTCCATACGAGACAGTCTAGCCTTGGTTCCATCCAAGCAGCAG
1 CTTTTCCAAAAGCCAAACTCGTTTCCATACGAGACAGTCTAGCCTTGGTTCCATCCAAGCAGCAG
* * *
38108 CGGCTTTTCCACAAGCCAAACTCTTTTCCA
66 GGGCTTTTCCATAAGCCAAACTCGTTTCCA
38138 TAAGTCAGGT
Statistics
Matches: 210, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
138 158 0.75
139 21 0.10
140 31 0.15
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (138 bp):
CTTTTCCAAAAGCCAAACTCGTTTCCATACGAGACAGTCTAGCCTTGGTTCCATCCAAGCAGCAG
GGGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGTTCAAGCTTTGCTTCCACCCAAGCA
TTCAAGGG
Found at i:38475 original size:6 final size:6
Alignment explanation
Indices: 38464--38490 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38454 AAAGCAAAGC
38464 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
38491 GCAGAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:44668 original size:6 final size:6
Alignment explanation
Indices: 44657--44683 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
44647 AAAGTAAAGC
44657 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
44684 GCAGAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Done.