Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007649.1 Corchorus capsularis cultivar CVL-1 contig07670, 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: 67338
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:218 original size:14 final size:15
Alignment explanation
Indices: 188--222 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
178 ACAATTCTAG
188 AACATTTATTATTAT
1 AACATTTATTATTAT
*
203 AACATTTA-TGTTAT
1 AACATTTATTATTAT
217 AACATT
1 AACATT
223 GAATTTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (15 bp):
AACATTTATTATTAT
Found at i:5188 original size:30 final size:30
Alignment explanation
Indices: 5152--5214 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
5142 TGTCTTCAAG
*
5152 TCCATGATAAGTCCTT-GGCGCATCATTCCC
1 TCCATGATAAG-CCTTGGGCACATCATTCCC
5182 TCCATGATAAGCCTTGGGCACATCATTCCC
1 TCCATGATAAGCCTTGGGCACATCATTCCC
5212 TCC
1 TCC
5215 CCCTTGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCACATCATTCCC
Found at i:8067 original size:70 final size:70
Alignment explanation
Indices: 7986--8125 Score: 244
Period size: 70 Copynumber: 2.0 Consensus size: 70
7976 TCTAATTTCA
* *
7986 ATTTGAAGCTTTTGGTTTGTTTCGGATTGGATTCATTTTGATTAATATTAGTAAGTTTTGGGATT
1 ATTTGAAGCTTTTGGTTTGTTTCGGATTGGATTCATTTTGATTAATATGAGAAAGTTTTGGGATT
8051 TCAGG
66 TCAGG
* *
8056 ATTTGAAGCTTTTGGTTTGTTTCGGATTGGATTCGTTTTGATTAATATGAGAAAGTTTTGGTATT
1 ATTTGAAGCTTTTGGTTTGTTTCGGATTGGATTCATTTTGATTAATATGAGAAAGTTTTGGGATT
8121 TCAGG
66 TCAGG
8126 TTTCAGAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.21, C:0.06, G:0.25, T:0.48
Consensus pattern (70 bp):
ATTTGAAGCTTTTGGTTTGTTTCGGATTGGATTCATTTTGATTAATATGAGAAAGTTTTGGGATT
TCAGG
Found at i:33413 original size:12 final size:12
Alignment explanation
Indices: 33396--33420 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33386 AAGACTGCTA
33396 CATCAGGAATTG
1 CATCAGGAATTG
33408 CATCAGGAATTG
1 CATCAGGAATTG
33420 C
1 C
33421 CAACTTCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (12 bp):
CATCAGGAATTG
Found at i:36348 original size:24 final size:24
Alignment explanation
Indices: 36312--36427 Score: 205
Period size: 24 Copynumber: 4.8 Consensus size: 24
36302 TATATATAGC
36312 GGCGTCCCAGACGCCGCTATTTAGA
1 GGCGT-CCAGACGCCGCTATTTAGA
*
36337 GGCGTCCAGACGCCGCAATTTAGA
1 GGCGTCCAGACGCCGCTATTTAGA
36361 GGCGTCCAGACGCCGCTATTTAGA
1 GGCGTCCAGACGCCGCTATTTAGA
36385 GGCGTCCAGACGCCGCTATTTAGA
1 GGCGTCCAGACGCCGCTATTTAGA
*
36409 GGCGTCCAAACGCCGCTAT
1 GGCGTCCAGACGCCGCTAT
36428 ATTACAGTGT
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
24 83 0.94
25 5 0.06
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.19
Consensus pattern (24 bp):
GGCGTCCAGACGCCGCTATTTAGA
Found at i:36931 original size:14 final size:16
Alignment explanation
Indices: 36914--36955 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
36904 AAAAAGAAAG
36914 TATAAAATTTCAG-A-
1 TATAAAATTTCAGAAC
36928 TATAGAAA-TTCAGAAC
1 TATA-AAATTTCAGAAC
36944 TATAAAATTTCA
1 TATAAAATTTCA
36956 TGTAAGTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 8 0.33
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (16 bp):
TATAAAATTTCAGAAC
Found at i:37871 original size:13 final size:13
Alignment explanation
Indices: 37853--37878 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37843 TGATATTTGG
37853 AAACAAGCCCTGA
1 AAACAAGCCCTGA
37866 AAACAAGCCCTGA
1 AAACAAGCCCTGA
37879 TATTTGGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (13 bp):
AAACAAGCCCTGA
Found at i:40188 original size:17 final size:18
Alignment explanation
Indices: 40157--40192 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40147 GGGTCTCTGG
*
40157 TCTTTATTTCCTTTTTCT
1 TCTTTATTTCATTTTTCT
40175 TCTTT-TTTCATTTTTCT
1 TCTTTATTTCATTTTTCT
40192 T
1 T
40193 TTTCCTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (18 bp):
TCTTTATTTCATTTTTCT
Found at i:44632 original size:54 final size:54
Alignment explanation
Indices: 44426--44630 Score: 297
Period size: 54 Copynumber: 3.8 Consensus size: 54
44416 CTGCTTTCGT
* * * *
44426 CCTTTGAGTAGGAATT-TTTGAGGTGTCGTGTGCCAATTTTTGCCTTTTGTTTTC
1 CCTTTGAGTGGGAATTCTTGGA-GTGTCGTGCGCCAAATTTTGCCTTTTGTTTTC
*
44480 CCTTTGAGTGGGAATTCTTGGAGTGTCGTGCGCCAAATTTTGCCTTTTATTTTC
1 CCTTTGAGTGGGAATTCTTGGAGTGTCGTGCGCCAAATTTTGCCTTTTGTTTTC
* * *
44534 GCTTTAAGTGGGAATTCTTGGAGTGTCGTGCGCCAAATTTTGCTTTTTGTTTTC
1 CCTTTGAGTGGGAATTCTTGGAGTGTCGTGCGCCAAATTTTGCCTTTTGTTTTC
*
44588 CCTTGGAGTGGGAATTCTTAGG-GTGTCGTGCGCCAAATTTTGC
1 CCTTTGAGTGGGAATTCTT-GGAGTGTCGTGCGCCAAATTTTGC
44631 TTCTTCTTTT
Statistics
Matches: 137, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
54 131 0.96
55 6 0.04
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.42
Consensus pattern (54 bp):
CCTTTGAGTGGGAATTCTTGGAGTGTCGTGCGCCAAATTTTGCCTTTTGTTTTC
Found at i:44976 original size:50 final size:52
Alignment explanation
Indices: 44888--45093 Score: 159
Period size: 58 Copynumber: 3.8 Consensus size: 52
44878 GTCCTTTGTC
* *
44888 TGCCTCCTTCCCATTT-TATGTTGTCGCGCGCCATTTTGC-AA-TTTTTGATT
1 TGCCTCCTTCCC-TTTCTATGTTGTCGCACGCCACTTTGCAAATTTTTTGATT
* * *
44938 TGCCTCCTTCCCTTTCTATGTTGTCACATGCCAGTTTGCAATTGAGAATTTTTTGATT
1 TGCCTCCTTCCCTTTCTATGTTGTCGCACGCCACTTTGC-----A-AATTTTTTGATT
* * * *
44996 TGCCTCCTTCCATTTCTATGTTGTCGCACGCCACTTTGCGATTGGGAGTCTTTTG-TC
1 TGCCTCCTTCCCTTTCTATGTTGTCGCACGCCACTTTGC-A-----AATTTTTTGATT
** *
45053 TGCCTCCTTCCCACTCTATGTTGTTGCACGCCACTTTGCAA
1 TGCCTCCTTCCCTTTCTATGTTGTCGCACGCCACTTTGCAA
45094 TTGAGAATTT
Statistics
Matches: 128, Mismatches: 15, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
49 3 0.02
50 31 0.24
51 1 0.01
54 2 0.02
56 1 0.01
57 38 0.30
58 52 0.41
ACGTcount: A:0.14, C:0.28, G:0.17, T:0.42
Consensus pattern (52 bp):
TGCCTCCTTCCCTTTCTATGTTGTCGCACGCCACTTTGCAAATTTTTTGATT
Found at i:44999 original size:58 final size:58
Alignment explanation
Indices: 44929--45118 Score: 258
Period size: 57 Copynumber: 3.3 Consensus size: 58
44919 CATTTTGCAA
* * *
44929 TTTTTGATTTGCCTCCTTCCCTTTCTATGTTGTCACATGCCAGTTTGCAATTGAGAAT
1 TTTTTGATTTGCCTCCTTCCCTTTCTATGTTGTCGCACGCCACTTTGCAATTGAGAAT
* * * *
44987 TTTTTGATTTGCCTCCTTCCATTTCTATGTTGTCGCACGCCACTTTGCGATTGGGAGT
1 TTTTTGATTTGCCTCCTTCCCTTTCTATGTTGTCGCACGCCACTTTGCAATTGAGAAT
* * ** *
45045 CTTTTG-TCTGCCTCCTTCCCACTCTATGTTGTTGCACGCCACTTTGCAATTGAGAAT
1 TTTTTGATTTGCCTCCTTCCCTTTCTATGTTGTCGCACGCCACTTTGCAATTGAGAAT
45102 TTTTT-ATTTGCCTCCTT
1 TTTTTGATTTGCCTCCTT
45119 ATTTTGTATT
Statistics
Matches: 113, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
57 57 0.50
58 56 0.50
ACGTcount: A:0.14, C:0.25, G:0.16, T:0.44
Consensus pattern (58 bp):
TTTTTGATTTGCCTCCTTCCCTTTCTATGTTGTCGCACGCCACTTTGCAATTGAGAAT
Found at i:45082 original size:57 final size:58
Alignment explanation
Indices: 44930--45118 Score: 222
Period size: 58 Copynumber: 3.3 Consensus size: 58
44920 ATTTTGCAAT
* * * * * *
44930 TTTTGATTTGCCTCCTTCCCTTTCTATGTTGTCACATGCCAGTTTGCAATTGAGAATT
1 TTTTGATCTGCCTCCTTCCCATTCTATGTTGTCGCACGCCACTTTGCAATTGAGAATC
* * * *
44988 TTTTGATTTGCCTCCTT-CCATTTCTATGTTGTCGCACGCCACTTTGCGATTGGGAGTC
1 TTTTGATCTGCCTCCTTCCCA-TTCTATGTTGTCGCACGCCACTTTGCAATTGAGAATC
* *
45046 TTTTG-TCTGCCTCCTTCCCACTCTATGTTGTTGCACGCCACTTTGCAATTGAGAAT-
1 TTTTGATCTGCCTCCTTCCCATTCTATGTTGTCGCACGCCACTTTGCAATTGAGAATC
* *
45102 TTTTTATTTGCCTCCTT
1 TTTTGATCTGCCTCCTT
45119 ATTTTGTATT
Statistics
Matches: 112, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
56 4 0.04
57 53 0.47
58 55 0.49
ACGTcount: A:0.14, C:0.25, G:0.16, T:0.44
Consensus pattern (58 bp):
TTTTGATCTGCCTCCTTCCCATTCTATGTTGTCGCACGCCACTTTGCAATTGAGAATC
Found at i:45217 original size:45 final size:45
Alignment explanation
Indices: 45180--45497 Score: 512
Period size: 45 Copynumber: 7.1 Consensus size: 45
45170 TGTCGCTCGT
* *
45180 CACATTTTGACCAAGAGTCTTTGATTTGTTGTACTTGTTGTACGC
1 CACATTTTGACCGAGAGTCTTTGATTTGTTGTACTTGTCGTACGC
*
45225 CACATTTTGACCGAGAGTCTTTGATTTGTTGTACTTGTCGTACAC
1 CACATTTTGACCGAGAGTCTTTGATTTGTTGTACTTGTCGTACGC
45270 CACATTTTGACCGAGAGTCTTTGATTTGTTGGT-CTTGTCGTACGC
1 CACATTTTGACCGAGAGTCTTTGATTTGTT-GTACTTGTCGTACGC
* * * *
45315 TACATTTTGACCGAGTGTCTTTGATTTGTTTTGCTTGTCGTACGC
1 CACATTTTGACCGAGAGTCTTTGATTTGTTGTACTTGTCGTACGC
* * *
45360 CACATTTTGACCGAGAGTCTTTGATTTGTTTTGCTTGTCATACGC
1 CACATTTTGACCGAGAGTCTTTGATTTGTTGTACTTGTCGTACGC
*
45405 CACATTTTGTCCGAGAGTCTTTGATTTGTTGTACTTGTCGTACGC
1 CACATTTTGACCGAGAGTCTTTGATTTGTTGTACTTGTCGTACGC
*
45450 CACATTTTGACCAAGAGTCTTTGATTTGTTGTACTTGTCGTACGC
1 CACATTTTGACCGAGAGTCTTTGATTTGTTGTACTTGTCGTACGC
45495 CAC
1 CAC
45498 GTAATAGTTA
Statistics
Matches: 255, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
44 1 0.00
45 252 0.99
46 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.42
Consensus pattern (45 bp):
CACATTTTGACCGAGAGTCTTTGATTTGTTGTACTTGTCGTACGC
Found at i:45781 original size:150 final size:150
Alignment explanation
Indices: 45543--45878 Score: 654
Period size: 150 Copynumber: 2.2 Consensus size: 150
45533 CGTGTCGTAT
*
45543 GCCATATTGTAGTTGGAACTTCATTTTGCTTTTCATCATTTTTTGTTGAGCGCTGCATGACAGAT
1 GCCATATTGTAGTTGGAACTTCATTTTGCTTTTCATCATTTTTTGTCGAGCGCTGCATGACAGAT
45608 ATGGCTCCACTCCCTTCTTTTGCTCTTTGCCGAATGCCTCATTGTAGATAGGACTTGAATTCTTT
66 ATGGCTCCACTCCCTTCTTTTGCTCTTTGCCGAATGCCTCATTGTAGATAGGACTTGAATTCTTT
45673 CTTCCACTTTTTGGTCGAGC
131 CTTCCACTTTTTGGTCGAGC
45693 GCCATATTGTAGTTGGAACTTCATTTTGCTTTTCATCATTTTTTGTCGAGCGCTGCATGACAGAT
1 GCCATATTGTAGTTGGAACTTCATTTTGCTTTTCATCATTTTTTGTCGAGCGCTGCATGACAGAT
*
45758 ATGGCTCCACTCCCTTCTTTTGCTCTTTGTCGAATGCCTCATTGTAGATAGGACTTGAATTCTTT
66 ATGGCTCCACTCCCTTCTTTTGCTCTTTGCCGAATGCCTCATTGTAGATAGGACTTGAATTCTTT
45823 CTTCCACTTTTTGGTCGAGC
131 CTTCCACTTTTTGGTCGAGC
45843 GCCATATTGTAGTTGGAACTTCATTTTGCTTTTCAT
1 GCCATATTGTAGTTGGAACTTCATTTTGCTTTTCAT
45879 TTTTGTCGTT
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 184 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (150 bp):
GCCATATTGTAGTTGGAACTTCATTTTGCTTTTCATCATTTTTTGTCGAGCGCTGCATGACAGAT
ATGGCTCCACTCCCTTCTTTTGCTCTTTGCCGAATGCCTCATTGTAGATAGGACTTGAATTCTTT
CTTCCACTTTTTGGTCGAGC
Found at i:45852 original size:50 final size:50
Alignment explanation
Indices: 45648--45854 Score: 122
Period size: 49 Copynumber: 4.1 Consensus size: 50
45638 CGAATGCCTC
45648 ATTGTAGATAGGACTTGAATTCTTTCTTCCACTTTTTGGTCGAGCGCCAT
1 ATTGTAGATAGGACTTGAATTCTTTCTTCCACTTTTTGGTCGAGCGCCAT
* * * * * ***
45698 ATTGTAG-TTGGAACTT-CATT-TTGCTTTTCATCATTTTTTGTCGAGCGCTGC
1 ATTGTAGATAGG-ACTTGAATTCTTTC-TTCCA-C-TTTTTGGTCGAGCGCCAT
* ** * * * *** * **
45749 A-TGACAGATATGG-CTCCACTCCCTTCTTTTGCTCTTT-GTCGAATGCC-T
1 ATTG-TAGATA-GGACTTGAATTCTTTCTTCCACTTTTTGGTCGAGCGCCAT
45797 CATTGTAGATAGGACTTGAATTCTTTCTTCCACTTTTTGGTCGAGCGCCAT
1 -ATTGTAGATAGGACTTGAATTCTTTCTTCCACTTTTTGGTCGAGCGCCAT
45848 ATTGTAG
1 ATTGTAG
45855 TTGGAACTTC
Statistics
Matches: 108, Mismatches: 35, Indels: 28
0.63 0.20 0.16
Matches are distributed among these distances:
48 5 0.05
49 38 0.35
50 35 0.32
51 21 0.19
52 5 0.05
53 4 0.04
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.41
Consensus pattern (50 bp):
ATTGTAGATAGGACTTGAATTCTTTCTTCCACTTTTTGGTCGAGCGCCAT
Found at i:47340 original size:98 final size:98
Alignment explanation
Indices: 47171--47630 Score: 715
Period size: 98 Copynumber: 4.7 Consensus size: 98
47161 CGAGCCCATC
* * * * * *
47171 TTTTTCGCCATCTTGGGCTTTCTTCACTTGCTCTCAAGGAGCATTCTCCATTTGGCACTCCACGA
1 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
* * *
47236 GCGTCCTACGCTTCACGTTTGGCGAGCGTCATG
66 GCGTCCTCCGCTTCGCATTTGGCGAGCGTCATG
* *
47269 TTTTTCTCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCCCGACCA
1 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
*
47334 GCGTCCTCCCCTTCGCATTTGGCGAGCGTCATG
66 GCGTCCTCCGCTTCGCATTTGGCGAGCGTCATG
47367 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
1 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
* * * *
47432 TCGTCCTCCTCTTCGCATTTGGAGACCGTCATG
66 GCGTCCTCCGCTTCGCATTTGGCGAGCGTCATG
* * * *
47465 TTTTTCGCTATCTCGAGCATT-TTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTAGACTA
1 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
*
47529 GCGTCCTCCGCTTCGCATTTGGCAAGCGTCATG
66 GCGTCCTCCGCTTCGCATTTGGCGAGCGTCATG
*
47562 TTTTTCGCCATCTCAGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
1 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
47627 GCGT
66 GCGT
47631 TTTCCTCTCC
Statistics
Matches: 329, Mismatches: 32, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
97 87 0.26
98 242 0.74
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (98 bp):
TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
GCGTCCTCCGCTTCGCATTTGGCGAGCGTCATG
Found at i:47545 original size:195 final size:196
Alignment explanation
Indices: 47171--47630 Score: 715
Period size: 195 Copynumber: 2.4 Consensus size: 196
47161 CGAGCCCATC
* * * * * *
47171 TTTTTCGCCATCTTGGGCTTTCTTCACTTGCTCTCAAGGAGCATTCTCCATTTGGCACTCCACGA
1 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
* * * * *
47236 GCGTCCTACGCTTCACGTTTGGCGAGCGTCATGTTTTTCTCCATCTCGGGCATTCTTCATTTGCT
66 GCGTCCTACGCTTCACATTTGGAGACCGTCATGTTTTTCGCCATCTCGAGCATTCTTCATTTGCT
* *
47301 CTCAAGGAGCATTCTCCATTTGGCGCCCGACCAGCGTCCTCCCCTTCGCATTTGGCGAGCGTCAT
131 CTCAAGGAGCATTCTCCATTTGGCGCCAGACCAGCGTCCTCCCCTTCGCATTTGGCAAGCGTCAT
47366 G
196 G
47367 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
1 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
* * * * *
47432 TCGTCCTCCTCTTCGCATTTGGAGACCGTCATGTTTTTCGCTATCTCGAGCATT-TTCATTTGCT
66 GCGTCCTACGCTTCACATTTGGAGACCGTCATGTTTTTCGCCATCTCGAGCATTCTTCATTTGCT
* * *
47496 CTCAAGGAGCATTCTCCATTTGGCGCTAGACTAGCGTCCTCCGCTTCGCATTTGGCAAGCGTCAT
131 CTCAAGGAGCATTCTCCATTTGGCGCCAGACCAGCGTCCTCCCCTTCGCATTTGGCAAGCGTCAT
47561 G
196 G
*
47562 TTTTTCGCCATCTCAGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
1 TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
47627 GCGT
66 GCGT
47631 TTTCCTCTCC
Statistics
Matches: 241, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
195 138 0.57
196 103 0.43
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (196 bp):
TTTTTCGCCATCTCGGGCATTCTTCATTTGCTCTCAAGGAGCATTCTCCATTTGGCGCTCGACCA
GCGTCCTACGCTTCACATTTGGAGACCGTCATGTTTTTCGCCATCTCGAGCATTCTTCATTTGCT
CTCAAGGAGCATTCTCCATTTGGCGCCAGACCAGCGTCCTCCCCTTCGCATTTGGCAAGCGTCAT
G
Found at i:47706 original size:21 final size:21
Alignment explanation
Indices: 47666--47706 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47656 CTCTAGTAGG
* *
47666 GAGCATTCTTCTTTGTTTGGA
1 GAGCATTCTTCTCTGCTTGGA
47687 GAGCATTCTTCTCTGCTTGG
1 GAGCATTCTTCTCTGCTTGG
47707 GGAGTGAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (21 bp):
GAGCATTCTTCTCTGCTTGGA
Found at i:48684 original size:57 final size:57
Alignment explanation
Indices: 48583--48819 Score: 350
Period size: 57 Copynumber: 4.2 Consensus size: 57
48573 TCCTCCAGTT
* * * * * * *
48583 TTTTGG-CGATCGCCGCATGTTCTGCTTTCTTCTTTAATCATTTCGGCTTAGATGCGA
1 TTTTGGTCGACCGCCACATTTTCTTCTTT-TTCCTTAATCGTTTCGGCTTAGATGCAA
*
48640 TTTTGGTCGACCGCCACATTTTCTTCTTTTTCCTTAATCGTTTCGACTTAGATGCAA
1 TTTTGGTCGACCGCCACATTTTCTTCTTTTTCCTTAATCGTTTCGGCTTAGATGCAA
* **
48697 TTTTGGTCGACCGCCACATTTTTTTCTTTTTCCTTAATCGTTTCGGCTTAGAAACAA
1 TTTTGGTCGACCGCCACATTTTCTTCTTTTTCCTTAATCGTTTCGGCTTAGATGCAA
*
48754 TTTTGGTCGACCACCACATTTTCTTCTTTTTCCTTAATCGTTTCGGCTTAGATGCAA
1 TTTTGGTCGACCGCCACATTTTCTTCTTTTTCCTTAATCGTTTCGGCTTAGATGCAA
48811 TTTTGGTCG
1 TTTTGGTCG
48820 TTCGACGCTT
Statistics
Matches: 163, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
57 145 0.89
58 18 0.11
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.44
Consensus pattern (57 bp):
TTTTGGTCGACCGCCACATTTTCTTCTTTTTCCTTAATCGTTTCGGCTTAGATGCAA
Found at i:49983 original size:26 final size:26
Alignment explanation
Indices: 49943--49992 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
49933 CCTTGTACGG
49943 GTCGTACGTGCGAGGTCACATGTGAA
1 GTCGTACGTGCGAGGTCACATGTGAA
49969 GTCGTACGTTG-GAGGTCACATGTG
1 GTCGTACG-TGCGAGGTCACATGTG
49993 GGGTGCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.26
Consensus pattern (26 bp):
GTCGTACGTGCGAGGTCACATGTGAA
Found at i:57092 original size:21 final size:21
Alignment explanation
Indices: 57064--57114 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
57054 AGAAGAGATC
57064 AGAAAAGAAAGCAA-AGAAAA
1 AGAAAAGAAAGCAAGAGAAAA
*
57084 AGAATAAGAAAGCAAGGGAAAA
1 AGAA-AAGAAAGCAAGAGAAAA
57106 A-AAAAGAAA
1 AGAAAAGAAA
57115 AAAAAATGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.36
21 12 0.43
22 6 0.21
ACGTcount: A:0.73, C:0.04, G:0.22, T:0.02
Consensus pattern (21 bp):
AGAAAAGAAAGCAAGAGAAAA
Found at i:57355 original size:21 final size:20
Alignment explanation
Indices: 57323--57373 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
57313 TTTTTTTTTT
57323 GAAAAA-AAAAAAGGAAAAA
1 GAAAAAGAAAAAAGGAAAAA
* *
57342 GAACAAAGAAAAAATGAAGAA
1 GAA-AAAGAAAAAAGGAAAAA
*
57363 GAAAATGAAAA
1 GAAAAAGAAAA
57374 GAAAGTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 10 0.37
21 14 0.52
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (20 bp):
GAAAAAGAAAAAAGGAAAAA
Found at i:59795 original size:22 final size:23
Alignment explanation
Indices: 59767--59810 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
59757 CGTTTTTTCT
59767 AAAAAAAAAA-GTTTGCGATTTG
1 AAAAAAAAAAGGTTTGCGATTTG
59789 AAAAAAAAAAGGTTTGCGATTT
1 AAAAAAAAAAGGTTTGCGATTT
59811 TTAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (23 bp):
AAAAAAAAAAGGTTTGCGATTTG
Done.