Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014423.1 Corchorus olitorius cultivar O-4 contig14456, 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: 75852
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:979 original size:12 final size:11
Alignment explanation
Indices: 960--989 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
950 CTTCTTCAGG
960 AAAAAAAATAA
1 AAAAAAAATAA
971 AATAAAAAATAA
1 AA-AAAAAATAA
983 AAAAAAA
1 AAAAAAA
990 GAAAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:5195 original size:18 final size:18
Alignment explanation
Indices: 5172--5225 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
5162 ATAGGTTTTG
5172 GCAGAGGTAATTTTGATC
1 GCAGAGGTAATTTTGATC
* *
5190 GCAGAGGCAACTTTGATC
1 GCAGAGGTAATTTTGATC
* * *
5208 GAAAAGGTAATATTGATC
1 GCAGAGGTAATTTTGATC
5226 AAACTCGCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (18 bp):
GCAGAGGTAATTTTGATC
Found at i:6901 original size:9 final size:9
Alignment explanation
Indices: 6887--6912 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6877 GTTGATAATG
6887 CTTTTGATT
1 CTTTTGATT
6896 CTTTTGATT
1 CTTTTGATT
6905 CTTTTGAT
1 CTTTTGAT
6913 GATAGTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (9 bp):
CTTTTGATT
Found at i:10181 original size:94 final size:95
Alignment explanation
Indices: 10044--10229 Score: 293
Period size: 94 Copynumber: 2.0 Consensus size: 95
10034 AATTTGAATT
* * * *
10044 ATCATTAAATTCTAATTTACACCCTACCACACTTAATTAAATTTTTATATTTTATTAATTACCTT
1 ATCATCAAATCCTAATTTACACCCTACCACACCTAATTAAATTTTTATATTTGATTAATTACCTT
** * *
10109 AATTTAATCTTAACGTCAGTTAAGAAAATC
66 AACCTAATCTTAACCTCAATTAAGAAAATC
10139 ATCATCAAATCCTAATTTACACCC-ACCACACCTAATTAAATTTTTATATTTGATTAATTACCTT
1 ATCATCAAATCCTAATTTACACCCTACCACACCTAATTAAATTTTTATATTTGATTAATTACCTT
10203 AACCTAATCTTAACCTCAATTAAGAAA
66 AACCTAATCTTAACCTCAATTAAGAAA
10230 GTTGAACAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 61 0.73
95 22 0.27
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.39
Consensus pattern (95 bp):
ATCATCAAATCCTAATTTACACCCTACCACACCTAATTAAATTTTTATATTTGATTAATTACCTT
AACCTAATCTTAACCTCAATTAAGAAAATC
Found at i:11161 original size:31 final size:30
Alignment explanation
Indices: 11123--11222 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 30
11113 TTTAATTTGG
*
11123 CAAATAAGGGCCTAACATTATCGAAAATGTT
1 CAAATAAGGGCCTAAC-TTATCGAAAATGCT
* * * ** *
11154 CAAATAAGGGTCCGATCTT-T-TAATTTGGT
1 CAAATAAGGG-CCTAACTTATCGAAAATGCT
11183 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAAC-TTATCGAAAATGCT
11214 CAAATAAGG
1 CAAATAAGG
11223 ACCCGGCATC
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 4 0.08
29 17 0.32
30 2 0.04
31 26 0.49
32 4 0.08
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (30 bp):
CAAATAAGGGCCTAACTTATCGAAAATGCT
Found at i:11210 original size:60 final size:60
Alignment explanation
Indices: 11060--11227 Score: 241
Period size: 60 Copynumber: 2.8 Consensus size: 60
11050 GGCTAATTGC
*
11060 TCAAATAAGGGCCTAACGTT-TCTCAAAATGCTTGACAAATAAGGGCCCGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTATC-GAAAATG-TT--CAAATAAGGGCCCGATCTTTTAATTTGG
* *
11123 -CAAATAAGGGCCTAACATTATCGAAAATGTTCAAATAAGGGTCCGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTATCGAAAATGTTCAAATAAGGGCCCGATCTTTTAATTTGG
* *
11182 TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGACCCG
1 TCAAATAAGGGCCTAACGTTATCGAAAATGTTCAAATAAGGGCCCG
11228 GCATCGAAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
59 27 0.28
60 41 0.43
61 2 0.02
62 24 0.25
63 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTATCGAAAATGTTCAAATAAGGGCCCGATCTTTTAATTTGG
Found at i:11343 original size:60 final size:60
Alignment explanation
Indices: 11268--11489 Score: 347
Period size: 60 Copynumber: 3.7 Consensus size: 60
11258 TGACAACAAG
* *
11268 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTGGCA-AACGTTAAGCCCTTATTTGACCAAATTAAAAGATCAGA
* * *
11328 CACTTATTTGAGCATTTTGGCAAACGTTAAGCCCTTATTTGGCCAAATTAAAAGATCAAA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAAGCCCTTATTTGACCAAATTAAAAGATCAGA
* *
11388 CCCTTATTTGAGCATTTTGGCAAACATTAAGCCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAAGCCCTTATTTGACCAAATTAAAAGATCAGA
* *
11448 CCCTTATTTGAGCATTTTGGCAAACGTTAGGTCCTTATTTGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAAGCCCTTATTTGA
11490 GTAATTAGCC
Statistics
Matches: 149, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
60 148 0.99
61 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAAGCCCTTATTTGACCAAATTAAAAGATCAGA
Found at i:11368 original size:31 final size:29
Alignment explanation
Indices: 11265--11490 Score: 111
Period size: 31 Copynumber: 7.5 Consensus size: 29
11255 AACTGACAAC
11265 AAGCCCTTATTTGAGCATTTTCGATAACGTT
1 AAGCCCTTATTTGAGCATTTT-GA-AACGTT
* * ** * *
11296 AGGCCCTTATTTGACCAAATT-AAAAGAT
1 AAGCCCTTATTTGAGCATTTTGAAACGTT
* *
11324 CAGACACTTATTTGAGCATTTTGGCAAACGTT
1 AAG-CCCTTATTTGAGCATTTT-G-AAACGTT
** * *
11356 AAGCCCTTATTTG-GCCAAATT-AAAAGATC
1 AAGCCCTTATTTGAG-CATTTTGAAACG-TT
* *
11385 AAACCCTTATTTGAGCATTTTGGCAAACATT
1 AAGCCCTTATTTGAGCATTTT-G-AAACGTT
** * *
11416 AAGCCCTTATTTG-GCCAAATT-AAAAGAT
1 AAGCCCTTATTTGAG-CATTTTGAAACGTT
*
11444 CAGACCCTTATTTGAGCATTTTGGCAAACGTT
1 AAG-CCCTTATTTGAGCATTTT-G-AAACGTT
* *
11476 AGGTCCTTATTTGAG
1 AAGCCCTTATTTGAG
11491 TAATTAGCCA
Statistics
Matches: 139, Mismatches: 40, Indels: 32
0.66 0.19 0.15
Matches are distributed among these distances:
28 15 0.11
29 46 0.33
30 4 0.03
31 58 0.42
32 16 0.12
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (29 bp):
AAGCCCTTATTTGAGCATTTTGAAACGTT
Found at i:11395 original size:29 final size:29
Alignment explanation
Indices: 11359--11457 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
11349 AAACGTTAAG
11359 CCCTTATTTGGCCAAATTAAAAGATCAAA
1 CCCTTATTTGGCCAAATTAAAAGATCAAA
** * * * *
11388 CCCTTATTTGAG-CATTTTGGCAAACATTAAG
1 CCCTTATTTG-GCCAAATT--AAAAGATCAAA
*
11419 CCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGGCCAAATTAAAAGATCAAA
11448 CCCTTATTTG
1 CCCTTATTTG
11458 AGCATTTTGG
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
29 30 0.57
30 2 0.04
31 21 0.40
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCAAA
Found at i:12110 original size:42 final size:41
Alignment explanation
Indices: 12050--12141 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 41
12040 TCAAATCTAG
* *
12050 CAAATCCAACAACGAGGAATAACAAGTCTTCAGCCATTTCTCT
1 CAAATCC-ACAACGAGGAATAACAAGCCTTC-GCCATTCCTCT
*
12093 CAAATCCACAACGAGGAATAACAAGCCTTCGGCATTCCTCT
1 CAAATCCACAACGAGGAATAACAAGCCTTCGCCATTCCTCT
12134 CAAATCCA
1 CAAATCCA
12142 TTTCATCGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 17 0.37
42 22 0.48
43 7 0.15
ACGTcount: A:0.37, C:0.30, G:0.12, T:0.21
Consensus pattern (41 bp):
CAAATCCACAACGAGGAATAACAAGCCTTCGCCATTCCTCT
Found at i:15384 original size:53 final size:47
Alignment explanation
Indices: 15282--15405 Score: 196
Period size: 47 Copynumber: 2.7 Consensus size: 47
15272 ACTCGAGGAA
*
15282 AGGTAGAGGGCGATAAAAAAATCAACTCCGCCAAGATGCTGATGCAG
1 AGGTAGAGGGCGATAAAAAAATCAACTCCGCCAAGATACTGATGCAG
*
15329 AGGTAGAGGGCGATAAAAAAATCAATTCCGCCAAGATACTGATGCAG
1 AGGTAGAGGGCGATAAAAAAATCAACTCCGCCAAGATACTGATGCAG
* * *
15376 AAGTAGAGGGCGAT-AAATAATCAACCCCGC
1 AGGTAGAGGGCGATAAAAAAATCAACTCCGC
15406 GAAAGGTAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 13 0.18
47 58 0.82
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (47 bp):
AGGTAGAGGGCGATAAAAAAATCAACTCCGCCAAGATACTGATGCAG
Found at i:15510 original size:57 final size:56
Alignment explanation
Indices: 15407--15524 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 56
15397 CAACCCCGCG
* * *
15407 AAAGGTAGAGGGTGATCAAAAAATGATAAACCCCGCCATTCTACAAAACTGAAGCA
1 AAAGGTAAAGGGTGATAAAAAAATGATAAACCCCGCCATTCCACAAAACTGAAGCA
* *
15463 AAAGGTAAAGGGTGATAAAAAAAATGA-AACACCCTGCCATTCCACAAAGCTGAAGCA
1 AAAGGTAAAGGGTGAT-AAAAAAATGATAA-ACCCCGCCATTCCACAAAACTGAAGCA
15520 AAAGG
1 AAAGG
15525 GAGCCTCAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
56 17 0.31
57 38 0.69
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (56 bp):
AAAGGTAAAGGGTGATAAAAAAATGATAAACCCCGCCATTCCACAAAACTGAAGCA
Found at i:18200 original size:42 final size:42
Alignment explanation
Indices: 18140--18232 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
18130 TCAAATCTAG
*
18140 CAAATCCGACAACGAGGAATAACAAGCCTTCGGCCATTTCTCT
1 CAAATCC-ACAACGAGGAATAACAAGCCTTCGGCCATTCCTCT
18183 CAAATCCACAACGAGGAATAACAAGCCTTCGGCCATTCCTCT
1 CAAATCCACAACGAGGAATAACAAGCCTTCGGCCATTCCTCT
18225 CAAATCCA
1 CAAATCCA
18233 TTTCATCGAG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 42 0.86
43 7 0.14
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.19
Consensus pattern (42 bp):
CAAATCCACAACGAGGAATAACAAGCCTTCGGCCATTCCTCT
Found at i:18579 original size:25 final size:25
Alignment explanation
Indices: 18531--18580 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
18521 TATTTATAAA
* *
18531 TTTTATTTGTAACTTACTTCTTTTC
1 TTTTACTTGTAACTGACTTCTTTTC
*
18556 TTTTACTTGTAACGTGACTTTTTTT
1 TTTTACTTGTAAC-TGACTTCTTTT
18581 TTAATAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTTACTTGTAACTGACTTCTTTTC
Found at i:22432 original size:35 final size:35
Alignment explanation
Indices: 22386--22459 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
22376 TAGAATTGTA
*
22386 GAAACAAGATTACACGTTGTAAAAACAAGGGTGAT
1 GAAACAAGATTACACCTTGTAAAAACAAGGGTGAT
22421 GAAACAAGATTACACCTTGTAAAAACAAGGGTGAT
1 GAAACAAGATTACACCTTGTAAAAACAAGGGTGAT
22456 GAAA
1 GAAA
22460 AGTAAAAGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (35 bp):
GAAACAAGATTACACCTTGTAAAAACAAGGGTGAT
Found at i:32803 original size:13 final size:13
Alignment explanation
Indices: 32785--32811 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32775 GCCTACTCTG
32785 TCTCCAATATCAC
1 TCTCCAATATCAC
32798 TCTCCAATATCAC
1 TCTCCAATATCAC
32811 T
1 T
32812 GCAAACCAAT
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:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (13 bp):
TCTCCAATATCAC
Found at i:35917 original size:77 final size:74
Alignment explanation
Indices: 35831--36225 Score: 466
Period size: 77 Copynumber: 5.1 Consensus size: 74
35821 TATATGCCTT
** * *
35831 ATTTATTTTTTACGGGGACATAAGTTCTTGCGTTCGACCATTGCGATGAAACGGTTCTCAAGGGA
1 ATTTATTTTTTACGGGGACACCAGTT-TTG-GTTCGACCGTTGTGATGAAACGG-TCTCAAGGGA
*
35896 GACGTTCATTTC
63 GACGTTCGTTTC
* * * **
35908 ATTTATTTTTATACGGGGACACCATTTTTGGTGCTCGACCGTTGTGGTGAAACGATCTTGAGGGA
1 ATTTATTTTT-TACGGGGACACCAGTTTTGGT--TCGACCGTTGTGATGAAACGGTCTCAAGGGA
*
35973 GACGTTCATTTC
63 GACGTTCGTTTC
* *
35985 ATTCATTGTTATACGGGGACACCAGTTTTGGTGTTCGACCGTTGTGATGAAACGGTCTCAAGGGA
1 ATTTATT-TTTTACGGGGACACCAGTTTT-G-GTTCGACCGTTGTGATGAAACGGTCTCAAGGGA
36050 GACGTTCGTTTC
63 GACGTTCGTTTC
* * *
36062 ATTCATTGTTATACGGGGACACCAGTTTTGGTGTTCGACCGTTGTGATGAAACGGTCTCCAGGGA
1 ATTTATT-TTTTACGGGGACACCAGTTTT-G-GTTCGACCGTTGTGATGAAACGGTCTCAAGGGA
36127 GACGTTCGTTTC
63 GACGTTCGTTTC
* * * *
36139 ATTTATTTTTATACAGGGACACCATTTTTGGTGCTCGACCGTTGTGATGAAACGGTCTCCAGGGT
1 ATTTATTTTT-TACGGGGACACCAGTTTTGGT--TCGACCGTTGTGATGAAACGGTCTCAAGGGA
36204 GACGTTCGTTTC
63 GACGTTCGTTTC
*
36216 ATTTAGTTTT
1 ATTTATTTTT
36226 CAATTTCTAA
Statistics
Matches: 285, Mismatches: 24, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
75 2 0.01
76 5 0.02
77 243 0.85
78 33 0.12
79 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (74 bp):
ATTTATTTTTTACGGGGACACCAGTTTTGGTTCGACCGTTGTGATGAAACGGTCTCAAGGGAGAC
GTTCGTTTC
Found at i:36126 original size:154 final size:154
Alignment explanation
Indices: 35862--36218 Score: 534
Period size: 154 Copynumber: 2.3 Consensus size: 154
35852 AAGTTCTTGC
* * * * *
35862 GTTCGACCATTGCGATGAAACGGTTCTCAAGGGAGACGTTCATTTCATTTATTTTTATACGGGGA
1 GTTCGACCGTTGTGATGAAACGG-TCTCAAGGGAGACGTTCGTTTCATTCATTGTTATACGGGGA
* * **
35927 CACCATTTTTGGTGCTCGACCGTTGTGGTGAAACGATCTTGAGGGAGACGTTCATTTCATTCATT
65 CACCAGTTTTGGTGCTCGACCGTTGTGATGAAACGATCTCCAGGGAGACGTTCATTTCATTCATT
*
35992 GTTATACGGGGACACCAGTTTTGGT
130 GTTATACAGGGACACCAGTTTTGGT
36017 GTTCGACCGTTGTGATGAAACGGTCTCAAGGGAGACGTTCGTTTCATTCATTGTTATACGGGGAC
1 GTTCGACCGTTGTGATGAAACGGTCTCAAGGGAGACGTTCGTTTCATTCATTGTTATACGGGGAC
* * * * *
36082 ACCAGTTTTGGTGTTCGACCGTTGTGATGAAACGGTCTCCAGGGAGACGTTCGTTTCATTTATTT
66 ACCAGTTTTGGTGCTCGACCGTTGTGATGAAACGATCTCCAGGGAGACGTTCATTTCATTCATTG
*
36147 TTATACAGGGACACCATTTTTGGT
131 TTATACAGGGACACCAGTTTTGGT
* * *
36171 GCTCGACCGTTGTGATGAAACGGTCTCCAGGGTGACGTTCGTTTCATT
1 GTTCGACCGTTGTGATGAAACGGTCTCAAGGGAGACGTTCGTTTCATT
36219 TAGTTTTCAA
Statistics
Matches: 183, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
154 162 0.89
155 21 0.11
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.34
Consensus pattern (154 bp):
GTTCGACCGTTGTGATGAAACGGTCTCAAGGGAGACGTTCGTTTCATTCATTGTTATACGGGGAC
ACCAGTTTTGGTGCTCGACCGTTGTGATGAAACGATCTCCAGGGAGACGTTCATTTCATTCATTG
TTATACAGGGACACCAGTTTTGGT
Found at i:43969 original size:226 final size:226
Alignment explanation
Indices: 43565--43972 Score: 654
Period size: 226 Copynumber: 1.8 Consensus size: 226
43555 TTTTTAGTTA
* *
43565 CCAGGGAAATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGCCACATTTTGGCTTTTTTTGGT
1 CCAGGGAAATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGCCACATTTTGACCTTTTTTGGT
* *
43630 CTTTTCTCACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTTCCCCCTTCCTTTTCCTACTA
66 ATTTTCTCACTTTTCGGATGACTAAAAACCCCCTCTATGAGTTTTCCCCCTTCCTTTTCCTACTA
* *
43695 CCCTTTTGTGTAATAACTCATTTTACTTCCTTAATTGTTTTGAATTAATGTTCCCCCCCCCCCCA
131 CCCTTTTGTGTAATAACCCATTTCACTTCCTTAATTGTTTTGAATTAATGTTCCCCCCCCCCCCA
43760 ATTTCCTTTTTTCCTCTCACCAACTCAGTAC
196 ATTTCCTTTTTTCCTCTCACCAACTCAGTAC
* * *
43791 CCAGGGTAGTTACTAAAAGGCCAAATTGAGGATTAATGTGGTGCCACCTTTTGACCTTTTTTGGT
1 CCAGGGAAATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGCCACATTTTGACCTTTTTTGGT
* *
43856 ATTTTCTCACTTTTCGGATGACTAAAAACCCCCTCTATGAGTTTTCCCCCTTCCTTTTTCTGCTA
66 ATTTTCTCACTTTTCGGATGACTAAAAACCCCCTCTATGAGTTTTCCCCCTTCCTTTTCCTACTA
** * * * * *
43921 CTTTTTTTTGTAATTACCCATTTCCCTTCCTTATTTGTTTTTAATTAATGTT
131 CCCTTTTGTGTAATAACCCATTTCACTTCCTTAATTGTTTTGAATTAATGTT
43973 TATGGCTTTT
Statistics
Matches: 164, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
226 164 1.00
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (226 bp):
CCAGGGAAATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGCCACATTTTGACCTTTTTTGGT
ATTTTCTCACTTTTCGGATGACTAAAAACCCCCTCTATGAGTTTTCCCCCTTCCTTTTCCTACTA
CCCTTTTGTGTAATAACCCATTTCACTTCCTTAATTGTTTTGAATTAATGTTCCCCCCCCCCCCA
ATTTCCTTTTTTCCTCTCACCAACTCAGTAC
Found at i:45094 original size:60 final size:60
Alignment explanation
Indices: 44958--45095 Score: 204
Period size: 60 Copynumber: 2.3 Consensus size: 60
44948 AATGTTTGCC
* * * * *
44958 AAAATGTTCAAATAAGCGCCCGATCTTTTAATTTGGCCAAATACGGGCCTAACGGTATCG
1 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGACCAAATAAGGGACTAACGGTATCG
* * *
45018 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGACCAAATAAGTGACTAACGTTATTG
1 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGACCAAATAAGGGACTAACGGTATCG
45078 AAAATGCTCAAATAAGGG
1 AAAATGCTCAAATAAGGG
45096 TCTGGTGTCG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGACCAAATAAGGGACTAACGGTATCG
Found at i:45238 original size:60 final size:60
Alignment explanation
Indices: 45146--45303 Score: 196
Period size: 60 Copynumber: 2.6 Consensus size: 60
45136 CAGACCCTTA
* *
45146 TTATTTGAGCATTTTCAATCATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGCTC
1 TTATTTGAGCATTTTCAATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGCCC
* * * *
45206 TTATTTGAGCATTTTCGATAACT-TTAGGCCCTTATTTGGTCAAATTAAAAGCTCGGGCCC
1 TTATTTGAGCATTTTCAATAA-TGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGCCC
**
45266 TTATTTGAATATTTTGACAA-AA-GTTAGGCCCTTATTTG
1 TTATTTGAGCATTTT--CAATAATGTTAGGCCCTTATTTG
45304 AACAATTAGC
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
60 80 0.94
61 3 0.04
62 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (60 bp):
TTATTTGAGCATTTTCAATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGCCC
Found at i:46130 original size:35 final size:37
Alignment explanation
Indices: 46064--46133 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 37
46054 TTCAAGACTA
* ***
46064 TTTTTTCAGACTTTTTCTTCTTCTTCTTAAAATCTTT
1 TTTTTTCAGACTTTTTCTACTTCTAAATAAAATCTTT
46101 TTTTTTCAGAC-TTTT-TACTTCTAAATAAAATCT
1 TTTTTTCAGACTTTTTCTACTTCTAAATAAAATCT
46134 GTAGTTCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 14 0.48
36 4 0.14
37 11 0.38
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (37 bp):
TTTTTTCAGACTTTTTCTACTTCTAAATAAAATCTTT
Found at i:46193 original size:33 final size:33
Alignment explanation
Indices: 46151--46214 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
46141 ACAAATGTAA
*
46151 TTGTTTTTATTAAT-AACCTCTTTTGTAGACTCT
1 TTGTTTTTATTAATAAATCTC-TTTGTAGACTCT
*
46184 TTGTTTTTATTAGTAAATCTCTTTGTAGACT
1 TTGTTTTTATTAATAAATCTCTTTGTAGACT
46215 TTTTATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.22, C:0.12, G:0.11, T:0.55
Consensus pattern (33 bp):
TTGTTTTTATTAATAAATCTCTTTGTAGACTCT
Found at i:46907 original size:23 final size:23
Alignment explanation
Indices: 46881--46927 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
46871 TCAAAGGTTG
46881 ACAAGTATCCCATTTCAGAATTA
1 ACAAGTATCCCATTTCAGAATTA
*
46904 ACAAGTATCCCATTTCAGAGTTA
1 ACAAGTATCCCATTTCAGAATTA
46927 A
1 A
46928 TTAGATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (23 bp):
ACAAGTATCCCATTTCAGAATTA
Found at i:52961 original size:60 final size:60
Alignment explanation
Indices: 52852--52964 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
52842 AATTGTAACA
* * *
52852 ATTTTGATAGTTTAGGGGTGAAAGTTTCAATTTAAAAGTTCAAGGGGGGAAATTGTCTTG
1 ATTTTGATAGTTTAGGGGTAAAAGTTTCAAATTAAAACTTCAAGGGGGGAAATTGTCTTG
* *
52912 ATTTTGATAGTTTAGGGGTAAAAGTTTCAAATTAAGACTT-TAGGAGGGGAAAT
1 ATTTTGATAGTTTAGGGGTAAAAGTTTCAAATTAAAACTTCAAGG-GGGGAAAT
52965 GTCCGTTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (60 bp):
ATTTTGATAGTTTAGGGGTAAAAGTTTCAAATTAAAACTTCAAGGGGGGAAATTGTCTTG
Found at i:69042 original size:30 final size:30
Alignment explanation
Indices: 69008--69067 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
68998 TAATTCTTCC
*
69008 TCTTCAGATAATTCTTCAATG-GTCTTCAAA
1 TCTTCAAATAA-TCTTCAATGAGTCTTCAAA
*
69038 TCTTCAAATTATCTTCAATGAGTCTTCAAA
1 TCTTCAAATAATCTTCAATGAGTCTTCAAA
69068 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (30 bp):
TCTTCAAATAATCTTCAATGAGTCTTCAAA
Found at i:69560 original size:12 final size:13
Alignment explanation
Indices: 69533--69562 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
69523 TTGGTGGAAC
69533 AAAATTGAGAGCA
1 AAAATTGAGAGCA
69546 AAAATTGAGAG-A
1 AAAATTGAGAGCA
69558 AAAAT
1 AAAAT
69563 AGCAGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (13 bp):
AAAATTGAGAGCA
Found at i:70021 original size:26 final size:26
Alignment explanation
Indices: 69985--70038 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
69975 TGTGAGACCT
69985 TTGGGTTATGGTTTAATTAATTTAGG
1 TTGGGTTATGGTTTAATTAATTTAGG
70011 TTGGGTTATGGTTTAATTAATTTAGG
1 TTGGGTTATGGTTTAATTAATTTAGG
70037 TT
1 TT
70039 TTTAATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (26 bp):
TTGGGTTATGGTTTAATTAATTTAGG
Found at i:70446 original size:4 final size:4
Alignment explanation
Indices: 70410--70609 Score: 106
Period size: 4 Copynumber: 53.0 Consensus size: 4
70400 AGACCAAAAA
* * *
70410 TATT T-TT TA-T TATT TATT CA-C TATT TATC TATT TATT TATT T-TT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
* * * * *
70454 AACTAT TATC TATT TATT TA-C TATT TATT TA-T T-TT TATT TTTT TAAT
1 TA-T-T TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
* * *
70501 TA-T TATC TACT TATT TA-T TATT TATCT T-TT TATT TA-T T-TT TAAT
1 TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TATT TATT TATT
* * * * **
70545 TA-T TATC TATT TATT TA-C TATT TATT TTTT TATT TATT AATT TAGC
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
*
70591 TA-T TATC TATT TATT TATT
1 TATT TATT TATT TATT TATT
70610 ATTATTATCC
Statistics
Matches: 145, Mismatches: 33, Indels: 36
0.68 0.15 0.17
Matches are distributed among these distances:
3 34 0.23
4 105 0.72
5 4 0.03
6 2 0.01
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.68
Consensus pattern (4 bp):
TATT
Found at i:70469 original size:44 final size:44
Alignment explanation
Indices: 70416--70612 Score: 245
Period size: 44 Copynumber: 4.5 Consensus size: 44
70406 AAAATATTTT
*
70416 TTAT-TATTTATTCACTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
* * *
70459 TTATCTATTTATTTACTATTTATTTATTT-TTATTTTTTTAATTA
1 TTATCTATTTATTTACTATTTATCTATTTATT-TATTTTTAACTA
* * * *
70503 TTATCTACTTATTTATTATTTATCTTTTTATTTATTTTTAATTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
* * *
70547 TTATCTATTTATTTACTATTTATTTTTTTATTTATTAATTTAGCTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATT--TTTAACTA
*
70593 TTATCTATTTATTTATTATT
1 TTATCTATTTATTTACTATT
70613 ATTATCCTTT
Statistics
Matches: 134, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
43 6 0.04
44 101 0.75
45 2 0.01
46 25 0.19
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.67
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
Found at i:70561 original size:88 final size:90
Alignment explanation
Indices: 70431--70612 Score: 278
Period size: 88 Copynumber: 2.0 Consensus size: 90
70421 ATTTATTCAC
*
70431 TATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTA-TTTATT-TTTATTT
1 TATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTATTTTATTATTTATTA
* *
70494 TTTTAATTATTATCTACTTATTTAT
66 ATTTAACTATTATCTACTTATTTAT
* * *
70519 TATTTATCTTTTTATTTATTTTTAATTATTATCTATTTATTTACTATTTATTTTTTTATTTATTA
1 TATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTATTTTATTATTTATTA
* *
70584 ATTTAGCTATTATCTATTTATTTAT
66 ATTTAACTATTATCTACTTATTTAT
70609 TATT
1 TATT
70613 ATTATCCTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 48 0.57
89 5 0.06
90 31 0.37
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.68
Consensus pattern (90 bp):
TATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTATTTTATTATTTATTA
ATTTAACTATTATCTACTTATTTAT
Found at i:74805 original size:21 final size:21
Alignment explanation
Indices: 74781--74837 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
74771 ATTCAACATC
74781 TGAGGCAGGCACAAGAAGAAA
1 TGAGGCAGGCACAAGAAGAAA
* ** * * *
74802 TGAGACATTCGCAAAAAGAGA
1 TGAGGCAGGCACAAGAAGAAA
*
74823 TGAGGCAGGAACAAG
1 TGAGGCAGGCACAAG
74838 GTGTTATAAA
Statistics
Matches: 24, Mismatches: 12, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.32, T:0.09
Consensus pattern (21 bp):
TGAGGCAGGCACAAGAAGAAA
Done.