Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021452.1 Corchorus olitorius cultivar O-4 contig21485, 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: 70332
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:7666 original size:4 final size:4
Alignment explanation
Indices: 7649--7682 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
7639 TTATTATGCG
7649 ATTT ATTAT ATTT ATTT ATTT ATTT ATTT -TTT AT
1 ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT AT
7683 GATTTATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 21 0.75
5 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:7714 original size:60 final size:57
Alignment explanation
Indices: 7616--7729 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 57
7606 GTGAAGATTA
* * *
7616 TATTTTTTATGTTATATGACAAATTATTATGCGATTTATTATATTTATTTATTTATT
1 TATTTTTTATGTTATATGACAAATTAATATACGATTTATTACATTTATTTATTTATT
*
7673 TATTTTTTATGATTTATGATTACAAATTAATATACGATTTATTACATTTATTTATTT
1 TATTTTTTATG--TTAT-ATGACAAATTAATATACGATTTATTACATTTATTTATTT
7730 GTTTCTTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 11 0.22
59 4 0.08
60 35 0.70
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (57 bp):
TATTTTTTATGTTATATGACAAATTAATATACGATTTATTACATTTATTTATTTATT
Found at i:8460 original size:19 final size:19
Alignment explanation
Indices: 8413--8462 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
8403 TATACATACA
8413 GTAAGTGAGTATGGCCTTT
1 GTAAGTGAGTATGGCCTTT
* *
8432 GTAGGAGAGTATGGCCTTT
1 GTAAGTGAGTATGGCCTTT
*
8451 TTAAGTGAGTAT
1 GTAAGTGAGTAT
8463 TGTATTGGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (19 bp):
GTAAGTGAGTATGGCCTTT
Found at i:8491 original size:32 final size:32
Alignment explanation
Indices: 8455--8525 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
8445 GCCTTTTTAA
* *
8455 GTGAGTATTGTATT-GGATGAGTGTTGTATTGG
1 GTGAGTATTGTATTGGGA-GAATGTTGTATTAG
8487 GTGAGTATTGTATTGGGAGAATGTTGTATTAG
1 GTGAGTATTGTATTGGGAGAATGTTGTATTAG
8519 GTGAGTA
1 GTGAGTA
8526 GGGTAGGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 33 0.92
33 3 0.08
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.41
Consensus pattern (32 bp):
GTGAGTATTGTATTGGGAGAATGTTGTATTAG
Found at i:8503 original size:16 final size:16
Alignment explanation
Indices: 8455--8525 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
8445 GCCTTTTTAA
8455 GTGAGTATTGTATTGG
1 GTGAGTATTGTATTGG
* *
8471 ATGAGTGTTGTATTGG
1 GTGAGTATTGTATTGG
8487 GTGAGTATTGTATTGG
1 GTGAGTATTGTATTGG
* * * *
8503 GAGAATGTTGTATTAG
1 GTGAGTATTGTATTGG
8519 GTGAGTA
1 GTGAGTA
8526 GGGTAGGAAC
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.41
Consensus pattern (16 bp):
GTGAGTATTGTATTGG
Found at i:10174 original size:22 final size:22
Alignment explanation
Indices: 10129--10181 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
10119 TGCTTTCTGA
**
10129 TTAATTGTTTTCTTTAATTTTC
1 TTAATTGTTTTCTTTAATAGTC
*
10151 TTGATTGTTTTC-TTAGATAGTC
1 TTAATTGTTTTCTTTA-ATAGTC
10173 TTAATTGTT
1 TTAATTGTT
10182 AGTTTGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62
Consensus pattern (22 bp):
TTAATTGTTTTCTTTAATAGTC
Found at i:17535 original size:11 final size:11
Alignment explanation
Indices: 17519--17543 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17509 AGAAAATTGT
17519 TTGTTTTTGGA
1 TTGTTTTTGGA
17530 TTGTTTTTGGA
1 TTGTTTTTGGA
17541 TTG
1 TTG
17544 ATTATTCCCC
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:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:17727 original size:31 final size:31
Alignment explanation
Indices: 17692--17763 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
17682 TTTTTAATAA
17692 TGTTTGATTTATTGATTGAGTTATAGCATGT
1 TGTTTGATTTATTGATTGAGTTATAGCATGT
17723 TGTTTGATTTATTGATTGAGTTATAGCATGT
1 TGTTTGATTTATTGATTGAGTTATAGCATGT
*
17754 TTTTTGATTT
1 TGTTTGATTT
17764 CTTAGAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.56
Consensus pattern (31 bp):
TGTTTGATTTATTGATTGAGTTATAGCATGT
Found at i:18523 original size:15 final size:16
Alignment explanation
Indices: 18494--18523 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18484 GTGTGAATTC
18494 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
18510 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
18524 TAAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:20147 original size:22 final size:22
Alignment explanation
Indices: 20102--20154 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
20092 TGCTTTCTGA
**
20102 TTAATTGTTTTCTTTAATTTTC
1 TTAATTGTTTTCTTTAATAGTC
*
20124 TTGATTGTTTTC-TTAGATAGTC
1 TTAATTGTTTTCTTTA-ATAGTC
20146 TTAATTGTT
1 TTAATTGTT
20155 AGTTTGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62
Consensus pattern (22 bp):
TTAATTGTTTTCTTTAATAGTC
Found at i:26444 original size:27 final size:28
Alignment explanation
Indices: 26414--26480 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
26404 AACCTAGAGA
*
26414 ACTAACTTTGAATGGGA-AACTGACTTG
1 ACTAACTTTGAATGGGAGAACTAACTTG
**
26441 ACTAGGTTTGAAT-GGAGAACTAACTTG
1 ACTAACTTTGAATGGGAGAACTAACTTG
*
26468 ACTGAC-TTGAATG
1 ACTAACTTTGAATG
26481 ATCCTTGACA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (28 bp):
ACTAACTTTGAATGGGAGAACTAACTTG
Found at i:30257 original size:21 final size:21
Alignment explanation
Indices: 30233--30273 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30223 TTGAAGCACT
30233 ATTGGATAC-AAGTGGTACTAA
1 ATTGGAT-CTAAGTGGTACTAA
30254 ATTGGATCTAAGTGGTACTA
1 ATTGGATCTAAGTGGTACTA
30274 GGGTTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (21 bp):
ATTGGATCTAAGTGGTACTAA
Found at i:34154 original size:17 final size:17
Alignment explanation
Indices: 34128--34162 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34118 GAGAACATGA
*
34128 TTTGAGAAAAAACCTTT
1 TTTGAAAAAAAACCTTT
*
34145 TTTGAAAAAACACCTTT
1 TTTGAAAAAAAACCTTT
34162 T
1 T
34163 ATTACCTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (17 bp):
TTTGAAAAAAAACCTTT
Found at i:37522 original size:25 final size:24
Alignment explanation
Indices: 37473--37523 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
37463 ACATCATTTG
*
37473 GTGCAAAAGAAATGTAAATGCAGA
1 GTGCAAAAGAAATGTAAAAGCAGA
*
37497 GTGCAAAAAGAAATGTAAAAGTAGA
1 GTGC-AAAAGAAATGTAAAAGCAGA
37522 GT
1 GT
37524 AAAACCACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.51, C:0.06, G:0.25, T:0.18
Consensus pattern (24 bp):
GTGCAAAAGAAATGTAAAAGCAGA
Found at i:37707 original size:35 final size:35
Alignment explanation
Indices: 37664--37736 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
37654 TGAATGCAAT
*
37664 TAAATACATGCAATGCCAAGCAAAGAAAATCAAAA
1 TAAATACATGCAATGCCAAGCAAAAAAAATCAAAA
37699 TAAATACATGCAATGCCAAGCAAAAAAAATCAAAA
1 TAAATACATGCAATGCCAAGCAAAAAAAATCAAAA
37734 TAA
1 TAA
37737 TGCATGAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.15
Consensus pattern (35 bp):
TAAATACATGCAATGCCAAGCAAAAAAAATCAAAA
Found at i:38129 original size:28 final size:28
Alignment explanation
Indices: 38084--38212 Score: 161
Period size: 28 Copynumber: 4.6 Consensus size: 28
38074 AGTACTTGAG
* *
38084 ATGACCCAAATGCCCCCTGGATGTGCAAA
1 ATGACCAAAATG-CCCCTGGATATGCAAA
38113 ATGACCAAAATGCCCCTGGATATGCAAA
1 ATGACCAAAATGCCCCTGGATATGCAAA
* *
38141 ATGGCCAAAATGCCCCTGGATGTGCAAA
1 ATGACCAAAATGCCCCTGGATATGCAAA
* *
38169 ATGACCAAAGTGCCCTTGG-TCATGCAAA
1 ATGACCAAAATGCCCCTGGAT-ATGCAAA
* *
38197 ATTATCAAAATGCCCC
1 ATGACCAAAATGCCCC
38213 CTTAAGTGAC
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
27 1 0.01
28 75 0.86
29 11 0.13
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (28 bp):
ATGACCAAAATGCCCCTGGATATGCAAA
Found at i:38175 original size:56 final size:56
Alignment explanation
Indices: 38084--38212 Score: 179
Period size: 56 Copynumber: 2.3 Consensus size: 56
38074 AGTACTTGAG
*
38084 ATGACCCAAATGCCCCCTGGATGTGCAAAATGACCAAAATGCCCCTGGAT-ATGCAAA
1 ATGACCAAAATG-CCCCTGGATGTGCAAAATGACCAAAATGCCCCTGG-TCATGCAAA
* * *
38141 ATGGCCAAAATGCCCCTGGATGTGCAAAATGACCAAAGTGCCCTTGGTCATGCAAA
1 ATGACCAAAATGCCCCTGGATGTGCAAAATGACCAAAATGCCCCTGGTCATGCAAA
* *
38197 ATTATCAAAATGCCCC
1 ATGACCAAAATGCCCC
38213 CTTAAGTGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
55 1 0.02
56 53 0.83
57 10 0.16
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (56 bp):
ATGACCAAAATGCCCCTGGATGTGCAAAATGACCAAAATGCCCCTGGTCATGCAAA
Found at i:41129 original size:7 final size:7
Alignment explanation
Indices: 41117--41158 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
41107 TCTACTTCTC
41117 ATATTAT
1 ATATTAT
41124 ATATTAT
1 ATATTAT
41131 ATATTAT
1 ATATTAT
41138 ATATTAT
1 ATATTAT
41145 ATATTAT
1 ATATTAT
*
41152 ATGTTAT
1 ATATTAT
41159 TTTAGATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:41177 original size:6 final size:7
Alignment explanation
Indices: 41119--41203 Score: 57
Period size: 7 Copynumber: 11.9 Consensus size: 7
41109 TACTTCTCAT
*
41119 ATTATAT
1 ATTATAG
*
41126 ATTATAT
1 ATTATAG
*
41133 ATTATAT
1 ATTATAG
*
41140 ATTATAT
1 ATTATAG
41147 ATTATATG
1 ATTATA-G
*
41155 TTATTTTAG
1 --ATTATAG
41164 ATTATAG
1 ATTATAG
41171 A-TATAG
1 ATTATAG
41177 ATTATAG
1 ATTATAG
*
41184 ATATTTAG
1 AT-TATAG
*
41192 ATAATA-
1 ATTATAG
41198 ATTATA
1 ATTATA
41204 CTAGCGCTAG
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
6 11 0.17
7 43 0.65
8 6 0.09
9 1 0.02
10 5 0.08
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (7 bp):
ATTATAG
Found at i:41179 original size:13 final size:13
Alignment explanation
Indices: 41161--41187 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41151 TATGTTATTT
41161 TAGATTATAGATA
1 TAGATTATAGATA
41174 TAGATTATAGATA
1 TAGATTATAGATA
41187 T
1 T
41188 TTAGATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (13 bp):
TAGATTATAGATA
Found at i:41203 original size:28 final size:31
Alignment explanation
Indices: 41140--41203 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 31
41130 TATATTATAT
* * *
41140 ATTATATATTATATGTTATTTTAGATTATAG
1 ATTATAGATTATATGATATTTTAGATAATAG
41171 A-TATAGATTATA-GATA-TTTAGATAATA-
1 ATTATAGATTATATGATATTTTAGATAATAG
41198 ATTATA
1 ATTATA
41204 CTAGCGCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.03
28 14 0.48
29 3 0.10
30 10 0.34
31 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (31 bp):
ATTATAGATTATATGATATTTTAGATAATAG
Found at i:44286 original size:22 final size:22
Alignment explanation
Indices: 44261--44310 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
44251 ACCACCTAAA
* *
44261 GCCACCACTACCATCGCCTCCG
1 GCCACCACTACCACCGCCGCCG
*
44283 GCCACCACTGCCACCGCCGCCG
1 GCCACCACTACCACCGCCGCCG
44305 GCCACC
1 GCCACC
44311 TTTCCGGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.58, G:0.18, T:0.08
Consensus pattern (22 bp):
GCCACCACTACCACCGCCGCCG
Found at i:46079 original size:22 final size:22
Alignment explanation
Indices: 46011--46080 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
46001 CTTTTAGTAA
46011 TTAAATATATATTATTTATTTATT
1 TTAAA-ATATATTATTTATTTA-T
* * *
46035 TTGAACT-CATTATTTA-TTAT
1 TTAAAATATATTATTTATTTAT
*
46055 TTAAAATATATTTTTTATTTAT
1 TTAAAATATATTATTTATTTAT
46077 TTAA
1 TTAA
46081 TAGTATATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
20 6 0.16
21 10 0.27
22 16 0.43
23 1 0.03
24 4 0.11
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (22 bp):
TTAAAATATATTATTTATTTAT
Found at i:47094 original size:14 final size:15
Alignment explanation
Indices: 47060--47097 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
47050 TGAACAAATC
* *
47060 AAATTTTAATTTTTG
1 AAATTGTAAATTTTG
47075 AAATTGTAAATTTT-
1 AAATTGTAAATTTTG
47089 AAATTGTAA
1 AAATTGTAA
47098 TCTGTTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (15 bp):
AAATTGTAAATTTTG
Found at i:52039 original size:16 final size:16
Alignment explanation
Indices: 52018--52053 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
52008 ATTAGTGGTG
52018 GAATACATTCGGATTT
1 GAATACATTCGGATTT
52034 GAATACATTCGGATTT
1 GAATACATTCGGATTT
52050 GAAT
1 GAAT
52054 CTCCATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (16 bp):
GAATACATTCGGATTT
Found at i:56906 original size:51 final size:51
Alignment explanation
Indices: 56839--57005 Score: 185
Period size: 51 Copynumber: 3.5 Consensus size: 51
56829 TACCCAATTA
56839 GCCCTTCCCCATCGGAAGGTGTTGTCCAGAGTTACCTGCTTTTCCTAGTTT
1 GCCCTTCCCCATCGGAAGGTGTTGTCCAGAGTTACCTGCTTTTCCTAGTTT
* * * * *
56890 GCCCTTCCTCACCGGAAGGTGTTGT------TTA--AG---TTCCCAATTT
1 GCCCTTCCCCATCGGAAGGTGTTGTCCAGAGTTACCTGCTTTTCCTAGTTT
* *
56930 GCCCTTCCCCATCGGGAGGTGTTGTCCAGAGTTGCCTGCTTTTCCTAGTTT
1 GCCCTTCCCCATCGGAAGGTGTTGTCCAGAGTTACCTGCTTTTCCTAGTTT
*
56981 GCCCTTCCTCATCGGAAGGTGTTGT
1 GCCCTTCCCCATCGGAAGGTGTTGT
57006 TTAGATCGAC
Statistics
Matches: 91, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
40 30 0.33
43 1 0.01
45 3 0.03
46 2 0.02
48 1 0.01
51 54 0.59
ACGTcount: A:0.13, C:0.29, G:0.23, T:0.35
Consensus pattern (51 bp):
GCCCTTCCCCATCGGAAGGTGTTGTCCAGAGTTACCTGCTTTTCCTAGTTT
Found at i:56986 original size:91 final size:91
Alignment explanation
Indices: 56831--57008 Score: 320
Period size: 91 Copynumber: 2.0 Consensus size: 91
56821 GTCTGCTTTA
56831 CCCAATTAGCCCTTCCCCATCGGAAGGTGTTGTCCAGAGTTACCTGCTTTTCCTAGTTTGCCCTT
1 CCCAATTAGCCCTTCCCCATCGGAAGGTGTTGTCCAGAGTTACCTGCTTTTCCTAGTTTGCCCTT
56896 CCTCACCGGAAGGTGTTGTTTAAGTT
66 CCTCACCGGAAGGTGTTGTTTAAGTT
* * *
56922 CCCAATTTGCCCTTCCCCATCGGGAGGTGTTGTCCAGAGTTGCCTGCTTTTCCTAGTTTGCCCTT
1 CCCAATTAGCCCTTCCCCATCGGAAGGTGTTGTCCAGAGTTACCTGCTTTTCCTAGTTTGCCCTT
*
56987 CCTCATCGGAAGGTGTTGTTTA
66 CCTCACCGGAAGGTGTTGTTTA
57009 GATCGACTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.15, C:0.29, G:0.22, T:0.35
Consensus pattern (91 bp):
CCCAATTAGCCCTTCCCCATCGGAAGGTGTTGTCCAGAGTTACCTGCTTTTCCTAGTTTGCCCTT
CCTCACCGGAAGGTGTTGTTTAAGTT
Found at i:57075 original size:41 final size:41
Alignment explanation
Indices: 57024--57123 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 41
57014 ACTTTACCCG
* * *
57024 ATTTGCCCTTCCTTATTGAAAGGTTTTGTCAGCATTTACCA
1 ATTTCCCCTTCCTTATCGAAAGGTATTGTCAGCATTTACCA
* * *
57065 TTTTCCCCTTCCTTGTCGGAAGGTATTGTCAGCATTTACCA
1 ATTTCCCCTTCCTTATCGAAAGGTATTGTCAGCATTTACCA
* *
57106 ATTTGCCCTTCCTCATCG
1 ATTTCCCCTTCCTTATCG
57124 GGAGGTGTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (41 bp):
ATTTCCCCTTCCTTATCGAAAGGTATTGTCAGCATTTACCA
Found at i:60313 original size:5 final size:5
Alignment explanation
Indices: 60299--60383 Score: 110
Period size: 5 Copynumber: 18.0 Consensus size: 5
60289 AGCCAGCTTG
*
60299 CAAAG CAAAA -AAAA -AAAA CAAAA -AAAA CAAAA CAAAA -AACAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAA-AA CAAAA
60346 CAAAA CAAAA CAAAA CAAAA CAAAA C--AA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
60384 AAAGAGTGGA
Statistics
Matches: 73, Mismatches: 1, Indels: 12
0.85 0.01 0.14
Matches are distributed among these distances:
3 3 0.04
4 14 0.19
5 54 0.74
6 2 0.03
ACGTcount: A:0.81, C:0.18, G:0.01, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:64472 original size:7 final size:7
Alignment explanation
Indices: 64455--64487 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
64445 CTTCCGTAAA
64455 AAAAAAT
1 AAAAAAT
64462 -AAAAAT
1 AAAAAAT
64468 AAAAAAAT
1 -AAAAAAT
64476 AAAAAAT
1 AAAAAAT
64483 AAAAA
1 AAAAA
64488 GCCAGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 12 0.50
8 6 0.25
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:64473 original size:14 final size:15
Alignment explanation
Indices: 64454--64487 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
64444 CCTTCCGTAA
64454 AAAAAAAT-AAAAAT
1 AAAAAAATAAAAAAT
64468 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
64483 AAAAA
1 AAAAA
64488 GCCAGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:64473 original size:15 final size:16
Alignment explanation
Indices: 64453--64487 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
64443 ACCTTCCGTA
64453 AAAAAAAAT-AAAAAT
1 AAAAAAAATAAAAAAT
64468 -AAAAAAATAAAAAAT
1 AAAAAAAATAAAAAAT
64483 AAAAA
1 AAAAA
64488 GCCAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.44
15 6 0.33
16 4 0.22
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAAAAAATAAAAAAT
Found at i:68123 original size:19 final size:18
Alignment explanation
Indices: 68099--68134 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
68089 TGAAGACTTA
68099 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
68118 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
68135 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.