Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014569.1 Corchorus olitorius cultivar O-4 contig14602, 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: 146328
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:16739 original size:288 final size:288
Alignment explanation
Indices: 16223--16799 Score: 1109
Period size: 288 Copynumber: 2.0 Consensus size: 288
16213 AGCAGGTAAT
*
16223 GTTAGAAAATTTCTAAAAACAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGGTTTCTCAAATA
1 GTTAGAAAATTTCTAAAAACAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGCTTTCTCAAATA
16288 CAATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTC
66 CAATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTC
*
16353 AGAGAGAAGTAGAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTTTATATACTTG
131 AGAGAGAAGTACAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTTTATATACTTG
16418 ATCAACATACATGTCTCTTCATATAGACATAACTTTATGATCATTACATGTCTTTCCAAATAGAC
196 ATCAACATACATGTCTCTTCATATAGACATAACTTTATGATCATTACATGTCTTTCCAAATAGAC
16483 ATAACTTTATGAATAATTATGCCATAAA
261 ATAACTTTATGAATAATTATGCCATAAA
16511 GTTAGAAAATTTCTAAAAACAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGCTTTCTCAAATA
1 GTTAGAAAATTTCTAAAAACAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGCTTTCTCAAATA
16576 CAATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTC
66 CAATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTC
16641 AGAGAGAAGTACAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTTTATATACTTG
131 AGAGAGAAGTACAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTTTATATACTTG
* *
16706 ATCAACATACATGTCTTTTCATATAGACATAACTTTATGATCATTGCATGTCTTTCCAAATAGAC
196 ATCAACATACATGTCTCTTCATATAGACATAACTTTATGATCATTACATGTCTTTCCAAATAGAC
*
16771 ATAACTTTATGAATAATTATGTCATAAA
261 ATAACTTTATGAATAATTATGCCATAAA
16799 G
1 G
16800 ATACCTTTTA
Statistics
Matches: 284, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
288 284 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (288 bp):
GTTAGAAAATTTCTAAAAACAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGCTTTCTCAAATA
CAATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAGAACATTC
AGAGAGAAGTACAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTTTATATACTTG
ATCAACATACATGTCTCTTCATATAGACATAACTTTATGATCATTACATGTCTTTCCAAATAGAC
ATAACTTTATGAATAATTATGCCATAAA
Found at i:19357 original size:199 final size:197
Alignment explanation
Indices: 19017--19419 Score: 743
Period size: 199 Copynumber: 2.0 Consensus size: 197
19007 AGGAATATTG
*
19017 TATTTGAATTGTTAGAAAATTTCTAAAACCAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGCT
1 TATTTGAATTGTTAGAAAATTTCTAAAAACAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGCT
*
19082 TTCTCAAATACAATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAACCACTT
66 TTCTCAAATACAATATTGCCTAACTATTTTAAACAAGTCGTATTTGGGATACAACAAAACCACTT
*
19147 GAGAACATTCAGAGAGAAGTAGAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTT
131 GAGAACATTC--AGAGAAGTACAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTT
19212 TATA
194 TATA
19216 TATTTGAATTGTTAGAAAATTTCTAAAAACAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGCT
1 TATTTGAATTGTTAGAAAATTTCTAAAAACAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGCT
*
19281 TTCTCAAATACAATATTGCCTAACTATTTTAAACAAGTCGTATTTGGGATACAACAAAGCCACTT
66 TTCTCAAATACAATATTGCCTAACTATTTTAAACAAGTCGTATTTGGGATACAACAAAACCACTT
19346 GAGAACATTCAGAGAAGTACAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTTTA
131 GAGAACATTCAGAGAAGTACAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTTTA
19411 TA
196 TA
*
19413 TACTTGA
1 TATTTGA
19420 TCAACATACA
Statistics
Matches: 199, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
197 62 0.31
199 137 0.69
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (197 bp):
TATTTGAATTGTTAGAAAATTTCTAAAAACAAGAAAAGAGAAACAAGACTTTGAGGCGCCAAGCT
TTCTCAAATACAATATTGCCTAACTATTTTAAACAAGTCGTATTTGGGATACAACAAAACCACTT
GAGAACATTCAGAGAAGTACAATAATTGGTTATGTCTCTTAAATGTTTATGTGGAAGGCTCTTTA
TA
Found at i:22181 original size:19 final size:19
Alignment explanation
Indices: 22157--22193 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22147 TTTGTACCCA
*
22157 AAACGGTGATGAAACGGTC
1 AAACGGTAATGAAACGGTC
22176 AAACGGTAATGAAACGGT
1 AAACGGTAATGAAACGGT
22194 TACAGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.30, T:0.16
Consensus pattern (19 bp):
AAACGGTAATGAAACGGTC
Found at i:23079 original size:9 final size:9
Alignment explanation
Indices: 23065--23093 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
23055 ATACATATTT
23065 AAAAAATAA
1 AAAAAATAA
23074 AAAAAAT-A
1 AAAAAATAA
23082 AAAAAATAA
1 AAAAAATAA
23091 AAA
1 AAA
23094 GTTTTTCCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:29322 original size:34 final size:34
Alignment explanation
Indices: 29275--29346 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
29265 AACAAACACT
*
29275 AAATATTTATTTAAGTTCATTCGTTTATCTTATC
1 AAATATTTATTTAAGTTCATTCATTTATCTTATC
*
29309 AAATATTTGTTTAAGTTCATTCATTTATCTTATC
1 AAATATTTATTTAAGTTCATTCATTTATCTTATC
29343 AAAT
1 AAAT
29347 GAACATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (34 bp):
AAATATTTATTTAAGTTCATTCATTTATCTTATC
Found at i:33199 original size:53 final size:53
Alignment explanation
Indices: 33140--33244 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
33130 AACCAAGCAA
* *
33140 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAGCTTTCACCAGCAAAATAT
1 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACCAACAAAATAT
*
33193 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACTAACAAAATA
1 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACCAACAAAATA
33245 ATATACTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (53 bp):
ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACCAACAAAATAT
Found at i:38203 original size:31 final size:31
Alignment explanation
Indices: 38168--38231 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
38158 AGAGTTTGTC
38168 TTTATTTTCTTA-TTTAGGTTAGTATTAGGCT
1 TTTATTTTCTTATTTTA-GTTAGTATTAGGCT
*
38199 TTTATTTTCTTATTTTAGTTAGTATTGGGCT
1 TTTATTTTCTTATTTTAGTTAGTATTAGGCT
38230 TT
1 TT
38232 ATGGGCAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.17, C:0.06, G:0.16, T:0.61
Consensus pattern (31 bp):
TTTATTTTCTTATTTTAGTTAGTATTAGGCT
Found at i:41321 original size:29 final size:29
Alignment explanation
Indices: 41289--41357 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
41279 CATTTAGCAT
41289 CAAATTGAGC-AATTTTAATAATTTGATAC
1 CAAATTGAGCTAATTTTAA-AATTTGATAC
* ** * *
41318 CAAATTGATCTTTTTTTCAAATTTGGTAC
1 CAAATTGAGCTAATTTTAAAATTTGATAC
41347 CAAATTGAGCT
1 CAAATTGAGCT
41358 TTTAGCCCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (29 bp):
CAAATTGAGCTAATTTTAAAATTTGATAC
Found at i:41450 original size:13 final size:13
Alignment explanation
Indices: 41428--41461 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
41418 CCTCGTTATT
41428 AAAA-AAAAAAAA
1 AAAACAAAAAAAA
*
41440 AAAACAAAAAACA
1 AAAACAAAAAAAA
41453 AAAACAAAA
1 AAAACAAAA
41462 TTTTCGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAA
Found at i:43805 original size:147 final size:150
Alignment explanation
Indices: 43615--43946 Score: 509
Period size: 147 Copynumber: 2.2 Consensus size: 150
43605 ATAATATAAT
*
43615 TATAAAAATATCGAATTTAATT-AATAAAAATAGAGTTTTTAGTAGAATAAAACTGTAAAAGTTT
1 TATAAAAATATTGAATTTAATTAAAT-AAAATAGAGTTTTTAGTAGAATAAAACTGTAAAAGTTT
*
43679 AACA-G-TGGCATTTAAGAAATAATATTAAAAAAAT-TTTAATATATCTAAGTTTTTAATCAAAA
65 AA-ATGATGGCATTTAAGAAATAATATTAAAAAAATGTCTAATATATCTAAGTTTTTAATCAAAA
43741 TAGTAAAATGGTAA-AAAAAAG
129 TAGTAAAATGGTAATAAAAAAG
* *
43762 -ATAGAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATTAAACTGTAAAAGTTT
1 TATAAAAATATTGAATTTAATTAAAT-AAAATAGAGTTTTTAGTAGAATAAAACTGTAAAAGTTT
* *
43826 AAATGATGGCATTTAAGCAATAATATTAAAAAAATGTCTAATATATCTTAGTTTTTAATCAAAAT
65 AAATGATGGCATTTAAGAAATAATATTAAAAAAATGTCTAATATATCTAAGTTTTTAATCAAAAT
43891 AGTAAAATGGTAATAAAAAAG
130 AGTAAAATGGTAATAAAAAAG
43912 TTATAAAAATATT-AGATTTAATTAAATAAAA-AGAG
1 -TATAAAAATATTGA-ATTTAATTAAATAAAATAGAG
43947 GAGAGATCAA
Statistics
Matches: 169, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
146 20 0.12
147 43 0.25
148 28 0.17
149 40 0.24
150 11 0.07
151 5 0.03
152 22 0.13
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (150 bp):
TATAAAAATATTGAATTTAATTAAATAAAATAGAGTTTTTAGTAGAATAAAACTGTAAAAGTTTA
AATGATGGCATTTAAGAAATAATATTAAAAAAATGTCTAATATATCTAAGTTTTTAATCAAAATA
GTAAAATGGTAATAAAAAAG
Found at i:44934 original size:22 final size:20
Alignment explanation
Indices: 44901--44970 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 20
44891 CAAACATGTT
44901 TCTTTTCTCAGATCTATTTGA
1 TCTTTTCTCAGATCT-TTTGA
44922 TCTTTTGCTCAGATCTTTCTGA
1 TCTTTT-CTCAGATCTTT-TGA
*
44944 TCTTTCACTTC-GATCTCTTTGA
1 TCTTT-TC-TCAGATCT-TTTGA
44966 TCTTT
1 TCTTT
44971 CTTTGATCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
21 8 0.19
22 31 0.72
23 4 0.09
ACGTcount: A:0.14, C:0.23, G:0.10, T:0.53
Consensus pattern (20 bp):
TCTTTTCTCAGATCTTTTGA
Found at i:50334 original size:28 final size:28
Alignment explanation
Indices: 50288--50342 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
50278 GTTTATATTG
50288 AGAGGGAAATTACTAAAACTTTTGACTT
1 AGAGGGAAATTACTAAAACTTTTGACTT
* * *
50316 AGAGGGAGATTGCTGAAACTTTTGACT
1 AGAGGGAAATTACTAAAACTTTTGACT
50343 CTGTACTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (28 bp):
AGAGGGAAATTACTAAAACTTTTGACTT
Found at i:50511 original size:14 final size:14
Alignment explanation
Indices: 50474--50512 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
50464 ATATATAAGA
50474 TAAAATATGTATGC
1 TAAAATATGTATGC
50488 TACAAAAATATGTATGC
1 T---AAAATATGTATGC
50505 TAAAATAT
1 TAAAATAT
50513 AATTATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.36
17 14 0.64
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (14 bp):
TAAAATATGTATGC
Found at i:64021 original size:13 final size:13
Alignment explanation
Indices: 64003--64028 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63993 TGTTTCTTAT
64003 AATAAAAGCCAAC
1 AATAAAAGCCAAC
64016 AATAAAAGCCAAC
1 AATAAAAGCCAAC
64029 GCGTTAAATC
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:0.62, C:0.23, G:0.08, T:0.08
Consensus pattern (13 bp):
AATAAAAGCCAAC
Found at i:69687 original size:45 final size:45
Alignment explanation
Indices: 69602--69698 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
69592 AACAACAATT
* * * * *
69602 AATATTAGCTTTATTTTGATGAATTATATAGAGATTGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACACAAAAATGGAGGAGTAG
* *
69647 AATATTAGTTTTATTTTGATGAATTACCCAAAAATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACACAAAAATGGAGGAGTAG
69692 AAT-TTAG
1 AATATTAG
69699 GTAATGCACT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 4 0.09
45 41 0.91
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACACAAAAATGGAGGAGTAG
Found at i:74697 original size:1 final size:1
Alignment explanation
Indices: 74650--74685 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
74640 AGTAATATTG
74650 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
74686 CTGGCTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:85559 original size:2 final size:2
Alignment explanation
Indices: 85552--85585 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
85542 TTTGCTTCTT
85552 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
85586 CCCCAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:90086 original size:2 final size:2
Alignment explanation
Indices: 90079--90131 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
90069 GTGTGAGCTT
*
90079 GA GA GA GA GA GA AA GA -A GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
90120 GA GA GA GA GA GA
1 GA GA GA GA GA GA
90132 AGGTGAGGCT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:92066 original size:34 final size:34
Alignment explanation
Indices: 92005--92071 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
91995 ACAACGATCA
**
92005 ATTTAGTCCCTCTATTTACAGGTTTGGATCAATT
1 ATTTAGTCCCTCTATTTACAGAATTGGATCAATT
*
92039 ATTTAGTCCCTCTATTTGC-GAAATTGGATCAAT
1 ATTTAGTCCCTCTATTTACAG-AATTGGATCAAT
92072 CGAGTCCGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (34 bp):
ATTTAGTCCCTCTATTTACAGAATTGGATCAATT
Found at i:93614 original size:27 final size:27
Alignment explanation
Indices: 93558--93614 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
93548 ACGGGATAAA
* * *
93558 GAGGTTGAGGCTGCTCGGATGTATGGG
1 GAGGCTGAGGCTGCTCGGATCTATAGG
*
93585 GAGGCTGAGGCTGCTCGGATCTATATG
1 GAGGCTGAGGCTGCTCGGATCTATAGG
93612 GAG
1 GAG
93615 AGGGAGCCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.44, T:0.25
Consensus pattern (27 bp):
GAGGCTGAGGCTGCTCGGATCTATAGG
Found at i:93938 original size:20 final size:20
Alignment explanation
Indices: 93898--93939 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
93888 TATTATGTGA
**
93898 TATTATAAATTGAAATGAAT
1 TATTATAAATTGAAAAAAAT
93918 TATTATAAATTGAAAAAAAT
1 TATTATAAATTGAAAAAAAT
93938 TA
1 TA
93940 AATAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
TATTATAAATTGAAAAAAAT
Found at i:95819 original size:55 final size:56
Alignment explanation
Indices: 95741--95856 Score: 225
Period size: 55 Copynumber: 2.1 Consensus size: 56
95731 TTATTATGGA
95741 TGTTTATGTTCTTTTTTTGGATTTTTATGGAATATACTTATGGATATTTATTGTAC
1 TGTTTATGTTCTTTTTTTGGATTTTTATGGAATATACTTATGGATATTTATTGTAC
95797 TGTTTATG-TCTTTTTTTGGATTTTTATGGAATATACTTATGGATATTTATTGTAC
1 TGTTTATGTTCTTTTTTTGGATTTTTATGGAATATACTTATGGATATTTATTGTAC
95852 TGTTT
1 TGTTT
95857 CTCCTAATAC
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 52 0.87
56 8 0.13
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.58
Consensus pattern (56 bp):
TGTTTATGTTCTTTTTTTGGATTTTTATGGAATATACTTATGGATATTTATTGTAC
Found at i:96000 original size:32 final size:33
Alignment explanation
Indices: 95941--96007 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 33
95931 TATAAAATCA
95941 ATACTACACCAGGACATTTTTTTTTGAGCCTCCC
1 ATACTACACCAGGACA-TTTTTTTTGAGCCTCCC
*
95975 ATACTACCCCAGGACA-TTTTTTTGAGCCTCCC
1 ATACTACACCAGGACATTTTTTTTGAGCCTCCC
96007 A
1 A
96008 ATCTTGTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 17 0.53
34 15 0.47
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (33 bp):
ATACTACACCAGGACATTTTTTTTGAGCCTCCC
Found at i:96772 original size:24 final size:24
Alignment explanation
Indices: 96740--96798 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
96730 TGACGATGAG
96740 CTACGGCCACGCCCACTGGAGGTA
1 CTACGGCCACGCCCACTGGAGGTA
*
96764 CTACGGCCACGCCCAGTGGAGGTA
1 CTACGGCCACGCCCACTGGAGGTA
96788 CTACGGCCACG
1 CTACGGCCACG
96799 ACCCCTCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.20, C:0.37, G:0.31, T:0.12
Consensus pattern (24 bp):
CTACGGCCACGCCCACTGGAGGTA
Found at i:99031 original size:33 final size:32
Alignment explanation
Indices: 98994--99088 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 32
98984 CCGCCCTGCT
* *
98994 AGGGCGGCGTGGCTATGACCATGCCGCCCAAGG
1 AGGGCGCCGTGGC-ATGACCATGCCGCCCAAGA
*
99027 AGGGCGCCATGGACAT-AGCCATGCCGCCCAAGA
1 AGGGCGCCGTGG-CATGA-CCATGCCGCCCAAGA
* *
99060 AGGGCGCCGTGGCCAAGTCCATGCCGCCC
1 AGGGCGCCGTGG-CATGACCATGCCGCCC
99089 TCGGTGGGCG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
32 1 0.02
33 50 0.96
34 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.35, T:0.11
Consensus pattern (32 bp):
AGGGCGCCGTGGCATGACCATGCCGCCCAAGA
Found at i:99098 original size:33 final size:33
Alignment explanation
Indices: 99012--99106 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
99002 GTGGCTATGA
99012 CCATGCCGCCCAAGGAGGGCGCCATGGACATAG
1 CCATGCCGCCCAAGGAGGGCGCCATGGACATAG
* * *
99045 CCATGCCGCCCAAGAAGGGCGCCGTGGCCA-AG
1 CCATGCCGCCCAAGGAGGGCGCCATGGACATAG
** * *
99077 TCCATGCCGCCCTCGGTGGGCGGCATGGAC
1 -CCATGCCGCCCAAGGAGGGCGCCATGGAC
99107 TTGGCCGCGC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 2 0.04
33 49 0.96
ACGTcount: A:0.19, C:0.36, G:0.35, T:0.11
Consensus pattern (33 bp):
CCATGCCGCCCAAGGAGGGCGCCATGGACATAG
Found at i:99119 original size:66 final size:66
Alignment explanation
Indices: 98994--99131 Score: 150
Period size: 66 Copynumber: 2.1 Consensus size: 66
98984 CCGCCCTGCT
* * * *
98994 AGGGCGGCGTGGCTATGACCATGCCGCCCAAGGAGGGCGCCATGGACATAGCCATGCCGCCCAAG
1 AGGGCGCCGTGGCCAAGACCATGCCGCCCAAGGAGGGCGCCATGGACATAGCCACGCCGCCCAAG
99059 A
66 A
* ** * * * * * *
99060 AGGGCGCCGTGGCCAAGTCCATGCCGCCCTCGGTGGGCGGCATGGACTTGGCCGCGCCGCCCTAG
1 AGGGCGCCGTGGCCAAGACCATGCCGCCCAAGGAGGGCGCCATGGACATAGCCACGCCGCCCAAG
*
99125 C
66 A
99126 AGGGCG
1 AGGGCG
99132 GCACCGACCA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.17, C:0.34, G:0.38, T:0.12
Consensus pattern (66 bp):
AGGGCGCCGTGGCCAAGACCATGCCGCCCAAGGAGGGCGCCATGGACATAGCCACGCCGCCCAAG
A
Found at i:100989 original size:49 final size:48
Alignment explanation
Indices: 100907--101037 Score: 158
Period size: 49 Copynumber: 2.7 Consensus size: 48
100897 AGCGTGCCAA
* * *
100907 TCAATTTTGTTCAGAAATTGA-TAAAAGGATGCGAGGAAAAGTAAATA-T
1 TCAATTTTGTGCAAAAATTGAGAAAAAGG-TGCGAGGAAAAGTAAA-AGT
*
100955 TCAATTTTGATGCAAAAATTGAGAAAAAGGTGCGAGGAAAATTAAAAGT
1 TCAATTTTG-TGCAAAAATTGAGAAAAAGGTGCGAGGAAAAGTAAAAGT
*
101004 TCAATTTTGTTGTAAAAATTGAGAAAAAGAGTGC
1 TCAATTTTG-TGCAAAAATTGAGAAAAAG-GTGC
101038 AGTAAAAATG
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
48 10 0.14
49 53 0.73
50 10 0.14
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.28
Consensus pattern (48 bp):
TCAATTTTGTGCAAAAATTGAGAAAAAGGTGCGAGGAAAAGTAAAAGT
Found at i:104063 original size:6 final size:6
Alignment explanation
Indices: 104052--104116 Score: 130
Period size: 6 Copynumber: 10.8 Consensus size: 6
104042 CCTAGTATAC
104052 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
104100 ATTAAA ATTAAA ATTAA
1 ATTAAA ATTAAA ATTAA
104117 GGTGTAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTAAA
Found at i:104296 original size:2 final size:2
Alignment explanation
Indices: 104243--104281 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
104233 AATGATCAAC
*
104243 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
104282 CTATGTAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:129550 original size:91 final size:91
Alignment explanation
Indices: 129396--129577 Score: 348
Period size: 91 Copynumber: 2.0 Consensus size: 91
129386 AAACCCTAGT
129396 GGGAGCTACAAAATTAACCCAGCTATCTAGAATTAATGCACTATATTTCAAAAATAAACCAACTC
1 GGGAGCTACAAAATTAACCCAGCTATCTAGAATTAATGCACTATATTTCAAAAATAAACCAACTC
129461 ATACAATAAGT-CACACAATAACCCA
66 ATACAATAAGTCCACACAATAACCCA
129486 GGGAGCTACAAAATTAACCCAGCTATGCTAGAATTAATGCACTATATTTCAAAAATAAACCAACT
1 GGGAGCTACAAAATTAACCCAGCTAT-CTAGAATTAATGCACTATATTTCAAAAATAAACCAACT
129551 CATACAATAAGTCCACACAATAACCCA
65 CATACAATAAGTCCACACAATAACCCA
129578 AAACCCTATT
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
90 26 0.29
91 50 0.56
92 14 0.16
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (91 bp):
GGGAGCTACAAAATTAACCCAGCTATCTAGAATTAATGCACTATATTTCAAAAATAAACCAACTC
ATACAATAAGTCCACACAATAACCCA
Found at i:131814 original size:18 final size:18
Alignment explanation
Indices: 131787--131821 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
131777 CTGGATTTAT
*
131787 ACAATATTTTAATATAAA
1 ACAATATTTTAAGATAAA
*
131805 ACAATTTTTTAAGATAA
1 ACAATATTTTAAGATAA
131822 TTTAAATGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (18 bp):
ACAATATTTTAAGATAAA
Found at i:135949 original size:18 final size:19
Alignment explanation
Indices: 135923--135961 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
135913 TTAAAATTAA
*
135923 TAATTAGTTATTATT-TTT
1 TAATCAGTTATTATTATTT
135941 TAATCAGTTATTATTATTT
1 TAATCAGTTATTATTATTT
135960 TA
1 TA
135962 TATGATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TAATCAGTTATTATTATTT
Found at i:139599 original size:27 final size:26
Alignment explanation
Indices: 139553--139604 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
139543 TTTTACTGTT
139553 TTTTTAAAAATTAATAATTAGTTATTA
1 TTTTTAAAAATTAATAATTA-TTATTA
* *
139580 TTTTTAAAAATTAGTTATTATTATT
1 TTTTTAAAAATTAATAATTATTATT
139605 TTATATGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TTTTTAAAAATTAATAATTATTATTA
Found at i:139615 original size:23 final size:20
Alignment explanation
Indices: 139563--139601 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
139553 TTTTTAAAAA
*
139563 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
139583 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
139602 ATTTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Found at i:140139 original size:30 final size:29
Alignment explanation
Indices: 140103--140170 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
140093 CAGCAGAAGA
*
140103 GCTTATTTGGCCAAAATTGATAGTTCAGGG
1 GCTTATTTGGCCAAAATTGA-AATTCAGGG
** * *
140133 GCTTATTTGGTGAAAATTGAAATTTATGG
1 GCTTATTTGGCCAAAATTGAAATTCAGGG
140162 GCTTATTTG
1 GCTTATTTG
140171 ACTGTTGGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.40
Consensus pattern (29 bp):
GCTTATTTGGCCAAAATTGAAATTCAGGG
Done.