Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013243.1 Corchorus capsularis cultivar CVL-1 contig13264, 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: 126594
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3035 original size:15 final size:15
Alignment explanation
Indices: 3012--3041 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3002 AGTTGAGTCT
*
3012 TGTCGGATCCCAATC
1 TGTCCGATCCCAATC
3027 TGTCCGATCCCAATC
1 TGTCCGATCCCAATC
3042 GGGTTAGGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.27
Consensus pattern (15 bp):
TGTCCGATCCCAATC
Found at i:15985 original size:2 final size:2
Alignment explanation
Indices: 15978--16007 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15968 ATATTTATCA
15978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16008 TTCAGAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26163 original size:34 final size:34
Alignment explanation
Indices: 26120--26184 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
26110 TTCCTTTCTG
26120 TTTTATTCATACATTGTTATTCTGATATTGGTTT
1 TTTTATTCATACATTGTTATTCTGATATTGGTTT
* *
26154 TTTTGTTCATACATTGTTATTCTGATGTTGG
1 TTTTATTCATACATTGTTATTCTGATATTGG
26185 CCTTAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.57
Consensus pattern (34 bp):
TTTTATTCATACATTGTTATTCTGATATTGGTTT
Found at i:30453 original size:18 final size:18
Alignment explanation
Indices: 30430--30482 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
30420 CTGCATATTA
30430 CCCTGTTTCCTCTGTTTC
1 CCCTGTTTCCTCTGTTTC
*
30448 CCCTGTTTCCCCTGTTTC
1 CCCTGTTTCCTCTGTTTC
*
30466 CCCTGTTTTCTCTGTTT
1 CCCTGTTTCCTCTGTTT
30483 TCTTGGAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.00, C:0.38, G:0.11, T:0.51
Consensus pattern (18 bp):
CCCTGTTTCCTCTGTTTC
Found at i:30471 original size:27 final size:27
Alignment explanation
Indices: 30430--30482 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
30420 CTGCATATTA
*
30430 CCCTGTTTCCTCTGTTTCCCCTGTTTC
1 CCCTGTTTCCCCTGTTTCCCCTGTTTC
* *
30457 CCCTGTTTCCCCTGTTTTCTCTGTTT
1 CCCTGTTTCCCCTGTTTCCCCTGTTT
30483 TCTTGGAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.00, C:0.38, G:0.11, T:0.51
Consensus pattern (27 bp):
CCCTGTTTCCCCTGTTTCCCCTGTTTC
Found at i:30485 original size:9 final size:9
Alignment explanation
Indices: 30430--30473 Score: 79
Period size: 9 Copynumber: 4.9 Consensus size: 9
30420 CTGCATATTA
30430 CCCTGTTTC
1 CCCTGTTTC
*
30439 CTCTGTTTC
1 CCCTGTTTC
30448 CCCTGTTTC
1 CCCTGTTTC
30457 CCCTGTTTC
1 CCCTGTTTC
30466 CCCTGTTT
1 CCCTGTTT
30474 TCTCTGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.00, C:0.41, G:0.11, T:0.48
Consensus pattern (9 bp):
CCCTGTTTC
Found at i:32125 original size:13 final size:13
Alignment explanation
Indices: 32109--32134 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32099 AATTATTCAT
32109 TCATTAATTTAAA
1 TCATTAATTTAAA
32122 TCATTAATTTAAA
1 TCATTAATTTAAA
32135 GTGTGACAGA
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:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TCATTAATTTAAA
Found at i:34028 original size:32 final size:32
Alignment explanation
Indices: 33987--34050 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
33977 CTACTAGGTC
33987 TTTTCCAGTTTTGGTATTTTTGAATATGAACA
1 TTTTCCAGTTTTGGTATTTTTGAATATGAACA
34019 TTTTCCAGTTTTGGTATTTTTGAATATGAACA
1 TTTTCCAGTTTTGGTATTTTTGAATATGAACA
34051 AAACATCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (32 bp):
TTTTCCAGTTTTGGTATTTTTGAATATGAACA
Found at i:44926 original size:24 final size:24
Alignment explanation
Indices: 44899--44945 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
44889 AATATTTTAT
44899 TAAATAAGAATATATATATATATG
1 TAAATAAGAATATATATATATATG
44923 TAAATAAGAATATATATATATAT
1 TAAATAAGAATATATATATATAT
44946 ATGTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
TAAATAAGAATATATATATATATG
Found at i:44943 original size:84 final size:82
Alignment explanation
Indices: 44849--45005 Score: 192
Period size: 84 Copynumber: 1.9 Consensus size: 82
44839 TTATATATAT
* * *
44849 TATATATATATCCA-AAAATCATTTTTATTTTAATATGTAAAATATTTTATTAAATAAG-AATAT
1 TATATATATATACATAAAA--A-TTTTATTTTAATATATAAAATATGTTATT-AATAAGTAATAT
44912 ATATATATATGTAAATAAGAA
62 ATATATATATGTAAATAAGAA
* * *
44933 TATATATATATATATGTAAAAATTTTATTTTAATATATAATATATGTTATTAATATGTAATATAT
1 TATATATATATACA--TAAAAATTTTATTTTAATATATAAAATATGTTATTAATAAGTAATATAT
44998 ATATATAT
64 ATATATAT
45006 ATATGTGTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
83 5 0.08
84 53 0.84
85 1 0.02
87 4 0.06
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (82 bp):
TATATATATATACATAAAAATTTTATTTTAATATATAAAATATGTTATTAATAAGTAATATATAT
ATATATGTAAATAAGAA
Found at i:46192 original size:12 final size:12
Alignment explanation
Indices: 46175--46203 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
46165 TATTCAATAA
46175 TAATAAACATTT
1 TAATAAACATTT
46187 TAAT-AACATTT
1 TAATAAACATTT
46198 TAATAA
1 TAATAA
46204 TAAAATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAAACATTT
Found at i:48450 original size:31 final size:29
Alignment explanation
Indices: 48412--48517 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 29
48402 CTGACGCCAT
*
48412 ACCCTTATTTGAGCATTTTCGATAATGTTAG
1 ACCCTTATTTGAGCATTTT-GA-AAAGTTAG
** *
48443 ACCCTTATTTG-GTCAAATT-AAAAGATCAG
1 ACCCTTATTTGAG-CATTTTGAAAAG-TTAG
* *
48472 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 ACCCTTATTTGAGCATTTT-G-AAAAGTTAG
48503 ACCCTTATTTGAGCA
1 ACCCTTATTTGAGCA
48518 ATTAACATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 3 0.05
29 18 0.31
30 2 0.03
31 32 0.54
32 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (29 bp):
ACCCTTATTTGAGCATTTTGAAAAGTTAG
Found at i:48694 original size:22 final size:23
Alignment explanation
Indices: 48674--48805 Score: 78
Period size: 22 Copynumber: 6.0 Consensus size: 23
48664 TTATAATAAT
48674 TACACTATAAAATTTTGATAA-C
1 TACACTATAAAATTTTGATAACC
* * ** *
48696 TACATTGTGGAATTTTGATAACA
1 TACACTATAAAATTTTGATAACC
* * *
48719 TGC-TTATAAAATTTTAATAA-C
1 TACACTATAAAATTTTGATAACC
* * *
48740 TTCATTATGAAATTTTGATAACC
1 TACACTATAAAATTTTGATAACC
* ** *
48763 -ACAC-ATGAAATTTCAATAAGC
1 TACACTATAAAATTTTGATAACC
*
48784 T-CTCTATAAAATTTTGATAACC
1 TACACTATAAAATTTTGATAACC
48806 ATACTATGAT
Statistics
Matches: 81, Mismatches: 24, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
21 18 0.22
22 60 0.74
23 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (23 bp):
TACACTATAAAATTTTGATAACC
Found at i:52527 original size:6 final size:6
Alignment explanation
Indices: 52516--52593 Score: 138
Period size: 6 Copynumber: 13.0 Consensus size: 6
52506 GACTAACCAG
* *
52516 AGCGAC AGCGAC TGCGAC TGCGAC AGCGAC AGCGAC AGCGAC AGCGAC
1 AGCGAC AGCGAC AGCGAC AGCGAC AGCGAC AGCGAC AGCGAC AGCGAC
52564 AGCGAC AGCGAC AGCGAC AGCGAC AGCGAC
1 AGCGAC AGCGAC AGCGAC AGCGAC AGCGAC
52594 GGTGGGGAAG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.31, C:0.33, G:0.33, T:0.03
Consensus pattern (6 bp):
AGCGAC
Found at i:55747 original size:29 final size:29
Alignment explanation
Indices: 55711--55778 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
55701 TTGGGAACAT
* ** *
55711 GGCTTATTTGGTTTTTTTAAGAGTTCGGG
1 GGCTTATTTGGTTGTAATAAAAGTTCGGG
*
55740 GGCTTATTTAGTTGTAATAAAAGTTCGGG
1 GGCTTATTTGGTTGTAATAAAAGTTCGGG
*
55769 GGTTTATTTG
1 GGCTTATTTG
55779 ACGGTTTGGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.46
Consensus pattern (29 bp):
GGCTTATTTGGTTGTAATAAAAGTTCGGG
Found at i:58012 original size:39 final size:39
Alignment explanation
Indices: 57958--58041 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
57948 AATCCAATCC
57958 CCTTTGATTAACTCCAAACAATCCCGAATCAAAGTGTAA
1 CCTTTGATTAACTCCAAACAATCCCGAATCAAAGTGTAA
57997 CCTTTGATTAACTCCAAACAATCCCGAATCAAAGTGTAA
1 CCTTTGATTAACTCCAAACAATCCCGAATCAAAGTGTAA
58036 CCTTTG
1 CCTTTG
58042 GAGTTATAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (39 bp):
CCTTTGATTAACTCCAAACAATCCCGAATCAAAGTGTAA
Found at i:63391 original size:4 final size:4
Alignment explanation
Indices: 63377--63410 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
63367 AATTATTATC
*
63377 TTTA TTTTA TTTA TTTA TTCA TTTA TTTA TTTA T
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
63411 ATAAAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:77722 original size:16 final size:17
Alignment explanation
Indices: 77674--77719 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
77664 TTATGAAGAG
77674 AAGAGAAATTTTCTTCA
1 AAGAGAAATTTTCTTCA
*
77691 AAAAGAAAATTTTCTTCA
1 AAGAG-AAATTTTCTTCA
77709 AAGAGAAATTT
1 AAGAGAAATTT
77720 CTTGTGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (17 bp):
AAGAGAAATTTTCTTCA
Found at i:91095 original size:84 final size:84
Alignment explanation
Indices: 90954--91290 Score: 584
Period size: 84 Copynumber: 4.0 Consensus size: 84
90944 AATCTGATCT
* * *
90954 ATCACCACCTAGGAAAAGTAGAACTCGACATGACACACCGCCAGCCAGAGAAGATGCTGATTTAT
1 ATCACCACCTAGGAAAACTAGAACCCGACATGACACACCACCAGCCAGAGAAGATGCTGATTTAT
91019 CACCTCCTCGTAGGAAGGC
66 CACCTCCTCGTAGGAAGGC
* *
91038 ATCACCACCTAGGAAAACTAGAACTCGACATGACACACCGCCAGCCAGAGAAGATGCTGATTTAT
1 ATCACCACCTAGGAAAACTAGAACCCGACATGACACACCACCAGCCAGAGAAGATGCTGATTTAT
91103 CACCTCCTCGTAGGAAGGC
66 CACCTCCTCGTAGGAAGGC
* * *
91122 ATCGCCACCTAGGAAAACTAGGACCCGGCATGACACACCACCAGCCAGAGAAGATGCTGATTTAT
1 ATCACCACCTAGGAAAACTAGAACCCGACATGACACACCACCAGCCAGAGAAGATGCTGATTTAT
91187 CACCTCCTCGTAGGAAGGC
66 CACCTCCTCGTAGGAAGGC
* *
91206 ATCGCCACCTAGGAAAACTAGGACCCGACATGACACACCACCAGCCAGAGAAGATGCTGATTTAT
1 ATCACCACCTAGGAAAACTAGAACCCGACATGACACACCACCAGCCAGAGAAGATGCTGATTTAT
91271 CACCTCCTCGTAGGAAGGC
66 CACCTCCTCGTAGGAAGGC
91290 A
1 A
91291 GCTCAGACTG
Statistics
Matches: 246, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 246 1.00
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (84 bp):
ATCACCACCTAGGAAAACTAGAACCCGACATGACACACCACCAGCCAGAGAAGATGCTGATTTAT
CACCTCCTCGTAGGAAGGC
Found at i:92433 original size:24 final size:24
Alignment explanation
Indices: 92406--92454 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
92396 GTTTTGAGAG
*
92406 AGCAGTGACTAATAGTTAGCTATT
1 AGCAGCGACTAATAGTTAGCTATT
92430 AGCAGCGACTAATAGTTAGCTATT
1 AGCAGCGACTAATAGTTAGCTATT
92454 A
1 A
92455 TGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (24 bp):
AGCAGCGACTAATAGTTAGCTATT
Found at i:95380 original size:15 final size:15
Alignment explanation
Indices: 95362--95401 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
95352 TTTCATGACA
*
95362 ATGATCATCATCATC
1 ATGATCATCACCATC
*
95377 ATGATGATCACCATC
1 ATGATCATCACCATC
*
95392 ATCATCATCA
1 ATGATCATCA
95402 ACCCTCCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (15 bp):
ATGATCATCACCATC
Found at i:95383 original size:18 final size:18
Alignment explanation
Indices: 95362--95396 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
95352 TTTCATGACA
*
95362 ATGATCATCATCATCATG
1 ATGATCACCATCATCATG
95380 ATGATCACCATCATCAT
1 ATGATCACCATCATCAT
95397 CATCAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (18 bp):
ATGATCACCATCATCATG
Found at i:95889 original size:6 final size:6
Alignment explanation
Indices: 95878--95911 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
95868 AGGGTGAGTT
95878 TTTTTG TTTTTG TTTTTG TTTTTTG TTTTT- TTTT
1 TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTT
95912 GTTACTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.15
6 17 0.63
7 6 0.22
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:95895 original size:12 final size:12
Alignment explanation
Indices: 95878--95911 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
95868 AGGGTGAGTT
95878 TTTTTGTTTTTG
1 TTTTTGTTTTTG
95890 TTTTTGTTTTTTG
1 TTTTTG-TTTTTG
95903 TTTTT-TTTT
1 TTTTTGTTTT
95912 GTTACTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 6 0.29
13 11 0.52
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTTTTGTTTTTG
Found at i:102363 original size:41 final size:41
Alignment explanation
Indices: 102300--102380 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
102290 ACTTGACCCT
* *
102300 CCTAATAATTAAGAAAATAAATTAAATTCAGGTTTAGCCCC
1 CCTAATAATTAAGAAAAGAAATTAAATCCAGGTTTAGCCCC
**
102341 CCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGAAAAGAAATTAAATCCAGGTTTAGCCC
102381 TAATTATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (41 bp):
CCTAATAATTAAGAAAAGAAATTAAATCCAGGTTTAGCCCC
Found at i:102745 original size:15 final size:17
Alignment explanation
Indices: 102719--102751 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
102709 CGGCATGTGA
102719 GTTTAGTTTGTA-ATTT
1 GTTTAGTTTGTATATTT
102735 GTTTA-TTTGTATATTT
1 GTTTAGTTTGTATATTT
102751 G
1 G
102752 GTAGGTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (17 bp):
GTTTAGTTTGTATATTT
Found at i:106783 original size:41 final size:41
Alignment explanation
Indices: 106731--106918 Score: 225
Period size: 41 Copynumber: 4.5 Consensus size: 41
106721 AGGGTCGAAT
*
106731 GACTTGGTCTTGAATTGATAATTTAATTCAAGGGTCTTGAC
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTTGAC
106772 GACTTGATCTTGAATTGAATTGATAATTTAATTCAAGGGTCTTGAC
1 GACTTGATC-----TTGAATTGATAATTTAATTCAAGGGTCTTGAC
* * * *
106818 GACCTGATCTTGAATTGATGACTTAATTCAAGGGT-TTCGAT
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTT-GAC
** * *
106859 GACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTTGAC
*
106900 GACTTGTTCTTGAATTGAT
1 GACTTGATCTTGAATTGAT
106919 GATAATATGG
Statistics
Matches: 126, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
40 2 0.02
41 83 0.66
42 1 0.01
46 40 0.32
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (41 bp):
GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTTGAC
Found at i:106807 original size:46 final size:46
Alignment explanation
Indices: 106740--106924 Score: 200
Period size: 46 Copynumber: 4.3 Consensus size: 46
106730 TGACTTGGTC
106740 TTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGATCTTGAA
1 TTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGATCTTGAA
*
106786 TTGAATTGATAATTTAATTCAAGGGTCTTGACGACCTGATCTTGAA
1 TTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGATCTTGAA
* *
106832 TTG-A-TG---ACTTAATTCAAGGGT-TT--CGA--TGA-C-TCAA
1 TTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGATCTTGAA
* * *
106866 TCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAA
1 --TTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGATCTTGAA
106914 TTG-A-TGATAAT
1 TTGAATTGATAAT
106925 ATGGCTCAAG
Statistics
Matches: 117, Mismatches: 8, Indels: 30
0.75 0.05 0.19
Matches are distributed among these distances:
34 3 0.03
35 1 0.01
36 6 0.05
37 1 0.01
38 5 0.04
40 2 0.02
41 28 0.24
42 1 0.01
44 11 0.09
45 2 0.02
46 53 0.45
47 1 0.01
48 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (46 bp):
TTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGATCTTGAA
Found at i:107237 original size:16 final size:16
Alignment explanation
Indices: 107216--107249 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
107206 TGAAGATCAT
*
107216 TTCAGAGCTTTTCTGC
1 TTCAGAGCTATTCTGC
107232 TTCAGAGCTATTCTGC
1 TTCAGAGCTATTCTGC
107248 TT
1 TT
107250 TCTGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (16 bp):
TTCAGAGCTATTCTGC
Found at i:108830 original size:16 final size:16
Alignment explanation
Indices: 108809--108842 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
108799 ACAATTCAGA
108809 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
108825 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
108841 AA
1 AA
108843 CTATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:109235 original size:45 final size:45
Alignment explanation
Indices: 109186--109310 Score: 109
Period size: 45 Copynumber: 3.1 Consensus size: 45
109176 GAATCAAATC
109186 AAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATT
1 AAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATT
** * *
109231 AAATTATCAA---ATTCAAGACCAA---GTC---A----T--ATC
1 AAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATT
109261 AAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATT
1 AAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATT
109306 AAATT
1 AAATT
109311 ATCAAATTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 30
0.60 0.08 0.32
Matches are distributed among these distances:
30 10 0.18
32 1 0.02
33 11 0.19
36 4 0.07
39 4 0.07
42 11 0.19
43 1 0.02
45 15 0.26
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.27
Consensus pattern (45 bp):
AAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATT
Found at i:109267 original size:75 final size:75
Alignment explanation
Indices: 109183--109332 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
109173 CTCGAATCAA
109183 ATCAAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAAATTCAAG
1 ATCAAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAAATTCAAG
109248 ACCAAGTCAT
66 ACCAAGTCAT
109258 ATCAAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAAATTCAAG
1 ATCAAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAAATTCAAG
109323 ACCAAGTCAT
66 ACCAAGTCAT
109333 TCGACCCTTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.27
Consensus pattern (75 bp):
ATCAAATTCCCAAGTCATTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAAATTCAAG
ACCAAGTCAT
Found at i:118955 original size:16 final size:17
Alignment explanation
Indices: 118934--118966 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
118924 TCTAGTCAAA
*
118934 TCGGGTT-GGGCGGGTT
1 TCGGGTTCGGACGGGTT
118950 TCGGGTTCGGACGGGTT
1 TCGGGTTCGGACGGGTT
118967 GGCCGGGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.03, C:0.15, G:0.52, T:0.30
Consensus pattern (17 bp):
TCGGGTTCGGACGGGTT
Found at i:124570 original size:58 final size:58
Alignment explanation
Indices: 124500--124619 Score: 240
Period size: 58 Copynumber: 2.1 Consensus size: 58
124490 TCAAAGCCTC
124500 TATATCGCGTGACAAAGAAATGAGGTGGAGCCATGGAAATGAAAAGCAAGGCAAAATT
1 TATATCGCGTGACAAAGAAATGAGGTGGAGCCATGGAAATGAAAAGCAAGGCAAAATT
124558 TATATCGCGTGACAAAGAAATGAGGTGGAGCCATGGAAATGAAAAGCAAGGCAAAATT
1 TATATCGCGTGACAAAGAAATGAGGTGGAGCCATGGAAATGAAAAGCAAGGCAAAATT
124616 TATA
1 TATA
124620 GACACTTTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.43, C:0.12, G:0.27, T:0.18
Consensus pattern (58 bp):
TATATCGCGTGACAAAGAAATGAGGTGGAGCCATGGAAATGAAAAGCAAGGCAAAATT
Done.