Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012175.1 Corchorus capsularis cultivar CVL-1 contig12196, 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: 69002
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:235 original size:29 final size:31
Alignment explanation
Indices: 179--260 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 31
169 GCTCAGTTAA
* * * *
179 CTCCACTTCAGGGACTAAATTGCATATTTT-
1 CTCCACTTGAGAGACCAATTTGCATATTTTC
* *
209 TTTCACTTGAGAGACCAATTTGC-TATTTTC
1 CTCCACTTGAGAGACCAATTTGCATATTTTC
*
239 GCTCCACTTGAGGGACCAATTT
1 -CTCCACTTGAGAGACCAATTT
261 TGTACTTTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 6 0.15
30 17 0.41
31 18 0.44
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (31 bp):
CTCCACTTGAGAGACCAATTTGCATATTTTC
Found at i:2388 original size:20 final size:20
Alignment explanation
Indices: 2355--2402 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2345 CTCAATCCTC
2355 AATTCTTC--TTCTTGAAAT
1 AATTCTTCAATTCTTGAAAT
2373 AATTCTTCAATTCTTGAAAT
1 AATTCTTCAATTCTTGAAAT
*
2393 TATT-TTCAAT
1 AATTCTTCAAT
2403 AAATCTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 8 0.30
19 6 0.22
20 13 0.48
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (20 bp):
AATTCTTCAATTCTTGAAAT
Found at i:26624 original size:33 final size:33
Alignment explanation
Indices: 26564--26671 Score: 130
Period size: 33 Copynumber: 3.3 Consensus size: 33
26554 GCTGCGCAAC
** *
26564 ACCGGCCACGCGACTTGGAGATACCCGGCCATC-
1 ACCGGCCACGCGACTTGGCCATGCCCGGCCA-CA
26597 ACCGGCCACGCGA-TATGGCCATGCCCGGCCACA
1 ACCGGCCACGCGACT-TGGCCATGCCCGGCCACA
** *
26630 ACCGGCCACATGACTCGGCCATGCCCGGCCACA
1 ACCGGCCACGCGACTTGGCCATGCCCGGCCACA
26663 ACCGGCCAC
1 ACCGGCCAC
26672 ATGATCCTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
32 2 0.03
33 63 0.95
34 1 0.02
ACGTcount: A:0.21, C:0.44, G:0.26, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGCCATGCCCGGCCACA
Found at i:26634 original size:10 final size:10
Alignment explanation
Indices: 26621--26672 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
26611 ATGGCCATGC
26621 CCGGCCACAA
1 CCGGCCACAA
26631 CCGGCCACATGA
1 CCGGCCACA--A
***
26643 CTCGGCCATGC
1 C-CGGCCACAA
26654 CCGGCCACAA
1 CCGGCCACAA
26664 CCGGCCACA
1 CCGGCCACA
26673 TGATCCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 2 0.06
13 6 0.18
ACGTcount: A:0.23, C:0.48, G:0.23, T:0.06
Consensus pattern (10 bp):
CCGGCCACAA
Found at i:29877 original size:100 final size:100
Alignment explanation
Indices: 29704--29901 Score: 360
Period size: 100 Copynumber: 2.0 Consensus size: 100
29694 AGTCTATATG
*
29704 AAAAGAAAGGATGATGTGTAATACACAAATTTATTAAACTATATACTCATGAAAAAAATAGTAAG
1 AAAAGAAAGGATGATGGGTAATACACAAATTTATTAAACTATATACTCATGAAAAAAATAGTAAG
29769 ATTAACAACATCACATGAAACCAAAAGATTGAATT
66 ATTAACAACATCACATGAAACCAAAAGATTGAATT
* * *
29804 AAAAGGAAGGATGATGGGTAATACACAAATTTATTAAACTATTTGCTCATGAAAAAAATAGTAAG
1 AAAAGAAAGGATGATGGGTAATACACAAATTTATTAAACTATATACTCATGAAAAAAATAGTAAG
29869 ATTAACAACATCACATGAAACCAAAAGATTGAA
66 ATTAACAACATCACATGAAACCAAAAGATTGAA
29902 GAATAAGAGG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 94 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (100 bp):
AAAAGAAAGGATGATGGGTAATACACAAATTTATTAAACTATATACTCATGAAAAAAATAGTAAG
ATTAACAACATCACATGAAACCAAAAGATTGAATT
Found at i:30111 original size:15 final size:16
Alignment explanation
Indices: 30088--30120 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
30078 AGATTTTAAG
30088 TTAAATGTTC-TTCCT
1 TTAAATGTTCTTTCCT
*
30103 TTAATTGTTCTTTCCT
1 TTAAATGTTCTTTCCT
30119 TT
1 TT
30121 TTCATTGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.61
Consensus pattern (16 bp):
TTAAATGTTCTTTCCT
Found at i:30296 original size:31 final size:32
Alignment explanation
Indices: 30247--30311 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 32
30237 TCTAGACTGT
30247 ATATATATTTATTTATTAAATAATATCAGACA
1 ATATATATTTATTTATTAAATAATATCAGACA
*
30279 ATATATATTT-TTTATTAAATAATGTCAGACA
1 ATATATATTTATTTATTAAATAATATCAGACA
30310 AT
1 AT
30312 TGAAATCTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 22 0.69
32 10 0.31
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (32 bp):
ATATATATTTATTTATTAAATAATATCAGACA
Found at i:30877 original size:128 final size:128
Alignment explanation
Indices: 30646--30893 Score: 417
Period size: 128 Copynumber: 1.9 Consensus size: 128
30636 GCAAATGAAA
30646 GGCAGCAAGAAAACAAAGGAAATAATATTATTTTCAGCTAATTTCCTACAGTTTATACTTTATAC
1 GGCAGCAAGAAAACAAAGGAAATAATATTATTTTCAGCTAATTTCCTACAGTTTATACTTTATAC
30711 ATCTAGAACATATACTTATTAGTTTTTGTTAGTAGTTATTAGTTTATTACACAAACAGAAAGG
66 ATCTAGAACATATACTTATTAGTTTTTGTTAGTAGTTATTAGTTTATTACACAAACAGAAAGG
* *
30774 GGCAGCAAGAAAACAAAGGAAATAATTTTATTTTCAGCTAATTTCCTAC-GATTTATACTTTGTA
1 GGCAGCAAGAAAACAAAGGAAATAATATTATTTTCAGCTAATTTCCTACAG-TTTATACTTTATA
* * * * *
30838 CATCTATAACGTGTAGTTATTAGTTTTTGTTAGTTGTTATTAGTTTATTACACAAA
65 CATCTAGAACATATACTTATTAGTTTTTGTTAGTAGTTATTAGTTTATTACACAAA
30894 TAGAGAAACA
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
127 1 0.01
128 111 0.99
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (128 bp):
GGCAGCAAGAAAACAAAGGAAATAATATTATTTTCAGCTAATTTCCTACAGTTTATACTTTATAC
ATCTAGAACATATACTTATTAGTTTTTGTTAGTAGTTATTAGTTTATTACACAAACAGAAAGG
Found at i:34023 original size:32 final size:32
Alignment explanation
Indices: 33982--34047 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
33972 TTTAGACTGT
*
33982 ATATATATTTATTAATTAAAC-GATGTCAGACA
1 ATATATATTTATTAATT-AACTAATGTCAGACA
*
34014 ATATATATTTATTTATTAACTAATGTCAGACA
1 ATATATATTTATTAATTAACTAATGTCAGACA
34046 AT
1 AT
34048 TGAAATCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 3 0.10
32 28 0.90
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (32 bp):
ATATATATTTATTAATTAACTAATGTCAGACA
Found at i:36886 original size:32 final size:32
Alignment explanation
Indices: 36845--36910 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
36835 TCTAGACTGT
*
36845 ATATATATTTATTTATTAAATAATGTCAGACA
1 ATATATATTTATTTATTAAATAATGTCACACA
* *
36877 ATATATATTTTTTTATTAACTAATGTCACACA
1 ATATATATTTATTTATTAAATAATGTCACACA
36909 AT
1 AT
36911 TGATATCTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (32 bp):
ATATATATTTATTTATTAAATAATGTCACACA
Found at i:38091 original size:15 final size:16
Alignment explanation
Indices: 38068--38100 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
38058 ACATTTGAAG
38068 TTAAATGTTC-TTCCT
1 TTAAATGTTCTTTCCT
*
38083 TTAATTGTTCTTTCCT
1 TTAAATGTTCTTTCCT
38099 TT
1 TT
38101 TTCATTGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.61
Consensus pattern (16 bp):
TTAAATGTTCTTTCCT
Found at i:38269 original size:32 final size:32
Alignment explanation
Indices: 38227--38289 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
38217 TTCTAGATTG
* *
38227 TATATATATTTATTAAATAATGTCAGACAATA
1 TATATATATTTATGAAATAATGTCAAACAATA
* *
38259 TATATTTATTTATGAACTAATGTCAAACAAT
1 TATATATATTTATGAAATAATGTCAAACAAT
38290 TGAACATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (32 bp):
TATATATATTTATGAAATAATGTCAAACAATA
Found at i:40096 original size:18 final size:18
Alignment explanation
Indices: 40073--40125 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
40063 CAACGCACGA
40073 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
*
40091 GCCAT-C-G-CA-TA--G
1 GCCATCCGGCCACAACCG
40103 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
40121 GCCAT
1 GCCAT
40126 TTGATCCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 6 0.22
13 1 0.04
14 2 0.07
15 4 0.15
16 2 0.07
17 1 0.04
18 11 0.41
ACGTcount: A:0.23, C:0.45, G:0.23, T:0.09
Consensus pattern (18 bp):
GCCATCCGGCCACAACCG
Found at i:50974 original size:27 final size:27
Alignment explanation
Indices: 50938--50997 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
50928 AAAGTAATTT
* *
50938 TTTATGAGAAAAGAAATTAATAAGTAG
1 TTTATAAGAAAAGAAACTAATAAGTAG
* *
50965 TTTATAAGAAAAGAGACTGATAAGTAG
1 TTTATAAGAAAAGAAACTAATAAGTAG
*
50992 TATATA
1 TTTATA
50998 CCCAAAGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.50, C:0.02, G:0.18, T:0.30
Consensus pattern (27 bp):
TTTATAAGAAAAGAAACTAATAAGTAG
Found at i:57381 original size:25 final size:25
Alignment explanation
Indices: 57347--57401 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
57337 AACGAAATTT
57347 TCTTCCCCAAATTCATCGGTGATCA
1 TCTTCCCCAAATTCATCGGTGATCA
* *
57372 TCTTCCCCAAATTCATTGGTGATTA
1 TCTTCCCCAAATTCATCGGTGATCA
57397 TCTTC
1 TCTTC
57402 AACTTGGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.38
Consensus pattern (25 bp):
TCTTCCCCAAATTCATCGGTGATCA
Found at i:61197 original size:264 final size:264
Alignment explanation
Indices: 60696--61208 Score: 884
Period size: 264 Copynumber: 1.9 Consensus size: 264
60686 GGGCCGGGTT
* *
60696 AACAAGAATTCCAGTCACAAATAACAAAAAGCAAAATCACACAAATTTAATATGGCAAAAAATAA
1 AACAAGAATTCCAGGCACAAATAACAAAAAGCAAAATCACACAAATTTAATATGGAAAAAAATAA
* *
60761 AAAGAGATTTTATCTATTATAATAACTAAGACAGTAAAACCCCATCAATTTGCAATATCAAATGC
66 AAAGAGATTTTATCTATTATAATAACTAAGACAATAAAACCCCATCAATTTACAATATCAAATGC
*
60826 TATAGTATTTTTGGTTTTTTTTTTTGGGGGGGGGGGGGTTGTTTTTAAATAGACCAGGTTAAAAT
131 TATAGTA-------TTTTTTTTTTGGGGGGGGGGGGGGTTGTTTTTAAATAGACCAGGTTAAAAT
* *
60891 TAAGGAGGGCATAAGGAGATGTATAAAAACCTTGAAACTTTTTTAATTTTTTTTTATTAGTTTTA
189 TAAGGAGGGCAGAAGGAGATGTATAAAAACCTTGAAACTTTTTTAATGTTTTTTTATTAGTTTTA
60956 GCTTTCATTTG
254 GCTTTCATTTG
60967 AACAAGAATTCCAGGCACAAATAACAAAAAGCAAAATCACACAAATTTAAATATGGAAAAAAATA
1 AACAAGAATTCCAGGCACAAATAACAAAAAGCAAAATCACACAAATTT-AATATGGAAAAAAATA
61032 AAAAGAGATTTTATCTATTATAATAACTAAGACAATAAAACCCCATCAATTTACAATATCAAATG
65 AAAAGAGATTTTATCTATTATAATAACTAAGACAATAAAACCCCATCAATTTACAATATCAAATG
61097 CTATAGTA-TTTTTTTTTGGGGGGGGGGGGGGTTGTTTTTAAATAGACCAGGTTAAAATTAAGGA
130 CTATAGTATTTTTTTTTTGGGGGGGGGGGGGGTTGTTTTTAAATAGACCAGGTTAAAATTAAGGA
61161 GGGCAGAAGGAGATGTATAAAAACCTTGAAACTTTTTTAATGTTTTTT
195 GGGCAGAAGGAGATGTATAAAAACCTTGAAACTTTTTTAATGTTTTTT
61209 GATAGGAACA
Statistics
Matches: 234, Mismatches: 7, Indels: 9
0.94 0.03 0.04
Matches are distributed among these distances:
264 101 0.43
271 47 0.20
272 86 0.37
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (264 bp):
AACAAGAATTCCAGGCACAAATAACAAAAAGCAAAATCACACAAATTTAATATGGAAAAAAATAA
AAAGAGATTTTATCTATTATAATAACTAAGACAATAAAACCCCATCAATTTACAATATCAAATGC
TATAGTATTTTTTTTTTGGGGGGGGGGGGGGTTGTTTTTAAATAGACCAGGTTAAAATTAAGGAG
GGCAGAAGGAGATGTATAAAAACCTTGAAACTTTTTTAATGTTTTTTTATTAGTTTTAGCTTTCA
TTTG
Found at i:66889 original size:23 final size:23
Alignment explanation
Indices: 66861--66940 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
66851 CCTCGCTACG
66861 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
66884 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
* * *
66907 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
66929 AAATCTTGATAA
1 AAATTTTGATAA
66941 CTACAAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:66939 original size:45 final size:45
Alignment explanation
Indices: 66834--66940 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
66824 GATACTCACA
* *
66834 CTATGAAATTGTGAT-AACCTCGCTACGAAATTTTGATAAATCTTC
1 CTATGAAATT-TGATAAACCTCCCTACAAAATTTTGATAAATCTTC
* * *
66879 CTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACT-TTC
1 CTATGAAA-TTTGATAAACCTCCCTACAAAATTTTGATAAATCTTC
*
66924 TTATGAAATCTTGATAA
1 CTATGAAAT-TTGATAA
66941 CTACAAATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
44 1 0.02
45 27 0.52
46 24 0.46
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (45 bp):
CTATGAAATTTGATAAACCTCCCTACAAAATTTTGATAAATCTTC
Found at i:67568 original size:22 final size:22
Alignment explanation
Indices: 66569--67568 Score: 165
Period size: 22 Copynumber: 44.9 Consensus size: 22
66559 TATGATCACA
*
66569 TTATGAAATTTTGATAACCTTC
1 TTATGAAATTTTGATAACCATC
* * * *
66591 CTATAAAATTTTAATAACGATAC
1 TTATGAAATTTTGATAACCAT-C
* * * *
66614 -TAT-AGAATTTCGAGAACCTTT
1 TTATGA-AATTTTGATAACCATC
* ** **
66635 TTAT-AATTTTTTTTAACTTTC
1 TTATGAAATTTTGATAACCATC
* *
66656 TTATGAAATTTTGTTAACCTTC
1 TTATGAAATTTTGATAACCATC
* * *
66678 CTAAGGAATTTTGA-AGACC-TC
1 TTATGAAATTTTGATA-ACCATC
* *
66699 AATATGAAATTTTGATAACCAAC
1 -TTATGAAATTTTGATAACCATC
* * * *
66722 ACTATGAGATGTTGATAACCTTC
1 -TTATGAAATTTTGATAACCATC
* *
66745 TATATGATATATTGATAACCA-C
1 T-TATGAAATTTTGATAACCATC
* * * *
66767 GTTATGAAAATTTAAAAACCTTC
1 -TTATGAAATTTTGATAACCATC
* * *
66790 ATATG-AATTGTTAGTTATCACA-C
1 TTATGAAATT-TT-GATAAC-CATC
*
66813 -TCTGAAATTTTGAT-ACTCA-C
1 TTATGAAATTTTGATAAC-CATC
* *
66833 ACTATGAAATTGTGATAACC-TC
1 -TTATGAAATTTTGATAACCATC
* * * *
66855 GCTACGAAATTTTGATAAATCTTC
1 -TTATGAAATTTTGAT-AACCATC
* *
66879 CTATAAAATTTTGATAAACC-TCC
1 TTATGAAATTTTGAT-AACCAT-C
* * **
66902 CTATAAAATTTTGATAACTTTC
1 TTATGAAATTTTGATAACCATC
*
66924 TTATGAAATCTTGAT-A--A-C
1 TTATGAAATTTTGATAACCATC
*
66942 -TA-CAAATTTTGATAA-CATCC
1 TTATGAAATTTTGATAACCAT-C
* * *
66962 CT-TG-ATTTATTAATAACC-TC
1 TTATGAAATT-TTGATAACCATC
* *
66982 ATTTTGAAAATTTGATAACC-TC
1 -TTATGAAATTTTGATAACCATC
*
67004 TTTATGAAATTTTAATAACC-TC
1 -TTATGAAATTTTGATAACCATC
* * * *
67026 TTTATAAAATTTTGTTGACC-CC
1 -TTATGAAATTTTGATAACCATC
* * *
67048 TCTATGAAATTCTGATAATCATA
1 T-TATGAAATTTTGATAACCATC
*
67071 TTATGTAATTTTGATAA-CATCGC
1 TTATGAAATTTTGATAACCAT--C
*
67094 TT-TAAAATTTTGATAACAACA-C
1 TTATGAAATTTTGATAAC--CATC
* *
67116 -TATGAAATTTTGATAATCTTC
1 TTATGAAATTTTGATAACCATC
*
67137 CTAT-AAATTTTGATAATCCGATC
1 TTATGAAATTTTGATAA-CC-ATC
* *
67160 TCTATGAAATTTCGATAATCA-C
1 T-TATGAAATTTTGATAACCATC
* *
67182 TCTATGAGA-TTTGATAACCTTC
1 T-TATGAAATTTTGATAACCATC
* *
67204 -TATCAAATTTTGGT-A-C-TCC
1 TTATGAAATTTTGATAACCAT-C
** *
67223 TTATGAAATTGAGACTTTTTTAACCTTC
1 TTATGAAA-T-----TTTGATAACCATC
* *
67251 ATATGAAATTTTGATAACCACACC
1 TTATGAAATTTTGATAA-C-CATC
67275 TTA--AAATTTTGATAACC-TCC
1 TTATGAAATTTTGATAACCAT-C
* *
67295 TAATGAAATTTTGTTAACCA-C
1 TTATGAAATTTTGATAACCATC
*
67316 AGTATGAAATTCTT-ATAACC-TGAC
1 -TTATGAAATT-TTGATAACCAT--C
* *
67340 ATTTTGATAATCTCTTTGATAACC-TT
1 -TTATGA-AA--T-TTTGATAACCATC
* * *
67366 TCTATAAAATTGTGATAATTAACCACC
1 T-TATGAAATT-T--TGA-TAACCATC
** *
67393 TTATGAAATTTCAATAACCAAC
1 TTATGAAATTTTGATAACCATC
* * *
67415 CTAAGAAATTTTAATAACCTGATC
1 TTATGAAATTTTGATAACC--ATC
* * * *
67439 CTCTGAAATTTTGGTAGCTACA-C
1 TTATGAAATTTTGATAAC--CATC
*
67462 -TATGAAATTTTGATAA-CTTCC
1 TTATGAAATTTTGATAACCAT-C
* *
67483 ATATAAAATTTTCG-TAACCA-C
1 TTATGAAATTTT-GATAACCATC
*
67504 ATTATGGAATTTTGATAACC-TCC
1 -TTATGAAATTTTGATAACCAT-C
* * *
67527 TCATGAAATTATAATAACCATC
1 TTATGAAATTTTGATAACCATC
67549 TTATGAAATTTTGATAACCA
1 TTATGAAATTTTGATAACCA
67569 CATAGAGACA
Statistics
Matches: 716, Mismatches: 165, Indels: 194
0.67 0.15 0.18
Matches are distributed among these distances:
16 9 0.01
17 3 0.00
18 3 0.00
19 3 0.00
20 26 0.04
21 69 0.10
22 399 0.56
23 105 0.15
24 33 0.05
25 21 0.03
26 21 0.03
27 6 0.01
28 17 0.02
29 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCATC
Found at i:68481 original size:31 final size:32
Alignment explanation
Indices: 68454--68515 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
68444 AGAAATATGT
*
68454 TTTTTAAAA-AAGGGTACAAT-TGAAAATATA
1 TTTTTAAAATAAGGGTACAATCGGAAAATATA
68484 TTTTTAAAATAAGGGTACAATCGGAAAATATA
1 TTTTTAAAATAAGGGTACAATCGGAAAATATA
68516 AAATTTCCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 9 0.31
31 11 0.38
32 9 0.31
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (32 bp):
TTTTTAAAATAAGGGTACAATCGGAAAATATA
Done.