Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011348.1 Corchorus capsularis cultivar CVL-1 contig11369, 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: 84923
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:7755 original size:41 final size:42
Alignment explanation
Indices: 7710--7802 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
7700 GGCCGAGCAT
*
7710 GGCCGGGCAGGCGGTGCAAGT-GCGCGGCTGTGGCTTGGCAG
1 GGCCGGGCAGGCGGAGCAAGTGGCGCGGCTGTGGCTTGGCAG
7751 GGCCGGGCAGGCGGAGCAAGTGGCGCGGCTGTGGCTTGGCAG
1 GGCCGGGCAGGCGGAGCAAGTGGCGCGGCTGTGGCTTGGCAG
7793 GGCCGGGCAG
1 GGCCGGGCAG
7803 TCTTGGCCGG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 20 0.40
42 30 0.60
ACGTcount: A:0.11, C:0.25, G:0.53, T:0.12
Consensus pattern (42 bp):
GGCCGGGCAGGCGGAGCAAGTGGCGCGGCTGTGGCTTGGCAG
Found at i:11446 original size:13 final size:13
Alignment explanation
Indices: 11428--11462 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
11418 AATCTAAATC
*
11428 TAAAGCAGATTAA
1 TAAAGCAAATTAA
11441 TAAAGCAAATTAA
1 TAAAGCAAATTAA
11454 TAAAGCAAA
1 TAAAGCAAA
11463 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:20593 original size:15 final size:15
Alignment explanation
Indices: 20573--20603 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20563 ATGCCATGTG
20573 GGACTTAGTTGCCAT
1 GGACTTAGTTGCCAT
*
20588 GGACTTGGTTGCCAT
1 GGACTTAGTTGCCAT
20603 G
1 G
20604 AGCCATGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.32
Consensus pattern (15 bp):
GGACTTAGTTGCCAT
Found at i:20625 original size:24 final size:24
Alignment explanation
Indices: 20588--20676 Score: 151
Period size: 24 Copynumber: 3.7 Consensus size: 24
20578 TAGTTGCCAT
*
20588 GGACTTGGTTGCCATGAGCCATGG
1 GGACTTGGTCGCCATGAGCCATGG
*
20612 GGAGTTGGTCGCCATGAGCCATGG
1 GGACTTGGTCGCCATGAGCCATGG
20636 GGACTTGGTCGCCATGAGCCATGG
1 GGACTTGGTCGCCATGAGCCATGG
*
20660 GGACTTGGTTGCCATGA
1 GGACTTGGTCGCCATGA
20677 TATGGCATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.17, C:0.21, G:0.38, T:0.24
Consensus pattern (24 bp):
GGACTTGGTCGCCATGAGCCATGG
Found at i:22287 original size:26 final size:25
Alignment explanation
Indices: 22254--22302 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
22244 TGTCCCTCTG
* *
22254 AAAAAAAATGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGAGTTAGTAACCTC
*
22279 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAA-AAAAAGAGAGTTAGTAACC
22303 CCTTAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.18
Consensus pattern (25 bp):
AAAAAAAAAGAGAGTTAGTAACCTC
Found at i:28377 original size:91 final size:92
Alignment explanation
Indices: 28256--28429 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 92
28246 GCGCAGACTC
* ** *
28256 CTTATGCTAGGAAAGTGGCTTCTGTCGGCAATCATGCCTCTGCTGAGAAGACACATT-TTGCTAG
1 CTTATGCTAGGAAAATGGCTTCTGTCGGCAATCATGCCTCAACTAAGAAGACACATTGTTGCTAG
28320 TAAGCTTGCTTCTGCTGATGAAATCAA
66 TAAGCTTGCTTCTGCTGATGAAATCAA
* * * * * * *
28347 CTTATGTTGGGAAAATGTCTTCTG-CTGGCAATTATGCCTCAACTAAGAAGACACCTTGTTGTTG
1 CTTATGCTAGGAAAATGGCTTCTGTC-GGCAATCATGCCTCAACTAAGAAGACACATTGTTGCTA
28411 GTAAGCTTGCTTCTGCTGA
65 GTAAGCTTGCTTCTGCTGA
28430 GGAGAAACCA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
90 1 0.01
91 46 0.66
92 23 0.33
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (92 bp):
CTTATGCTAGGAAAATGGCTTCTGTCGGCAATCATGCCTCAACTAAGAAGACACATTGTTGCTAG
TAAGCTTGCTTCTGCTGATGAAATCAA
Found at i:29170 original size:36 final size:36
Alignment explanation
Indices: 29120--29195 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
29110 AGAAAAGACC
* * *
29120 AGAAAACGTTTTCTGCTGGCAGTCATGCCTAC-GCTG
1 AGAAAACATCTTCTGCTAGCAGTCATGCCT-CTGCTG
29156 AGAAAACATCTTCTGCTAGCAGTCATGCCTCTGCTG
1 AGAAAACATCTTCTGCTAGCAGTCATGCCTCTGCTG
29192 AGAA
1 AGAA
29196 TACGTCTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 1 0.03
36 35 0.97
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (36 bp):
AGAAAACATCTTCTGCTAGCAGTCATGCCTCTGCTG
Found at i:30229 original size:19 final size:19
Alignment explanation
Indices: 30205--30270 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
30195 TGGTAGAGAC
30205 TTTTTTTCTTCTTCTTTCT
1 TTTTTTTCTTCTTCTTTCT
30224 TTTTTTT-TTCTTTCTTT-T
1 TTTTTTTCTTC-TTCTTTCT
*
30242 GTTTCTCTTTCTT-TTTTTTGCT
1 -TTT-T-TTTCTTCTTCTTT-CT
30264 TTTTTTT
1 TTTTTTT
30271 AGTGGTTTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
18 4 0.10
19 19 0.49
20 7 0.18
21 6 0.15
22 3 0.08
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTTTCTTCTTCTTTCT
Found at i:30234 original size:15 final size:15
Alignment explanation
Indices: 30206--30260 Score: 74
Period size: 15 Copynumber: 3.5 Consensus size: 15
30196 GGTAGAGACT
30206 TTTTTTCTTCTTCTTTC
1 TTTTTT-TT-TTCTTTC
30223 TTTTTTTTTTCTTTC
1 TTTTTTTTTTCTTTC
* *
30238 TTTTGTTTCTCTTTC
1 TTTTTTTTTTCTTTC
30253 TTTTTTTT
1 TTTTTTTT
30261 GCTTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
15 27 0.77
16 2 0.06
17 6 0.17
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTCTTTC
Found at i:37325 original size:4 final size:4
Alignment explanation
Indices: 37316--37340 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
37306 TTATCAGCTT
37316 TTTG TTTG TTTG TTTG TTTG TTTG T
1 TTTG TTTG TTTG TTTG TTTG TTTG T
37341 GAGAAAGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:37749 original size:38 final size:38
Alignment explanation
Indices: 37706--37854 Score: 173
Period size: 38 Copynumber: 4.0 Consensus size: 38
37696 TTCCTTCTCT
* *
37706 ATATTAGCTAAGAGGTTTAATAGGCTACATCTTCTTTG
1 ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
* *
37744 ATATTAGCTAAGGGGTTTTATAGGCTGCATCTTCTTTC
1 ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
* * * * *
37782 ATATTAGCTCAGGGGTATTGATA--TTTC--CTT-TTTT
1 ATATTAGCTAAGGGGT-TTTATAGGCTACATCTTCTTTG
37816 ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
1 ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
37854 A
1 A
37855 GGTTCTCTAG
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
33 5 0.05
34 18 0.20
35 5 0.05
37 5 0.05
38 53 0.58
39 5 0.05
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.43
Consensus pattern (38 bp):
ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
Found at i:40176 original size:11 final size:11
Alignment explanation
Indices: 40156--40189 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40146 TCTGTTTTTT
40156 GTTTTTGTTTC
1 GTTTTTGTTTC
* *
40167 GTTTTCGTTTT
1 GTTTTTGTTTC
40178 GTTTTTGTTTC
1 GTTTTTGTTTC
40189 G
1 G
40190 CTGTCAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.09, G:0.21, T:0.71
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:50962 original size:4 final size:4
Alignment explanation
Indices: 50953--50979 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
50943 ATAAAACATA
50953 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
50980 ATATAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:51755 original size:10 final size:10
Alignment explanation
Indices: 51742--51770 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
51732 CTCTTCTTCT
51742 TCTTTCTCTC
1 TCTTTCTCTC
51752 TCTTTCTCTC
1 TCTTTCTCTC
51762 TCTTTCTCT
1 TCTTTCTCT
51771 TTCACTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TCTTTCTCTC
Found at i:51758 original size:20 final size:19
Alignment explanation
Indices: 51731--51770 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
51721 TTCAATTCCT
51731 TCTCTTCT-TCTTCTTTCTC
1 TCTCTTCTCTC-TCTTTCTC
51750 TCTCTTTCTCTCTCTTTCTC
1 TCTC-TTCTCTCTCTTTCTC
51770 T
1 T
51771 TTCACTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 13 0.68
21 2 0.11
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
TCTCTTCTCTCTCTTTCTC
Found at i:55455 original size:60 final size:61
Alignment explanation
Indices: 55382--55585 Score: 187
Period size: 60 Copynumber: 3.5 Consensus size: 61
55372 CTAATTGTTC
* *
55382 AAATAGG-TCCCTAATCTATGCAAAAATGCTCAATTTAGGG-CTTATGTTTTTAATTTGATT
1 AAATAGGATCCCTAATCTATGCAAAAATGCTCAATTTAGGGTC-AATGCTTTTAATTTGATT
* * *
55442 AAATAGGAT-CCTAATGTATTCAAAAATGCTCAATTTAGGGTCAATGCTTTTAATTTGGTT
1 AAATAGGATCCCTAATCTATGCAAAAATGCTCAATTTAGGGTCAATGCTTTTAATTTGATT
* * * ** * * *
55502 AAATAGGA-CCC-AA--TGTG--AAAATGTTCAATTGAGGACCCATACTTTTAATTTGTTT
1 AAATAGGATCCCTAATCTATGCAAAAATGCTCAATTTAGGGTCAATGCTTTTAATTTGATT
*
55557 AAATATGA-CCCTAA-CGTATGCAAAAATGC
1 AAATAGGATCCCTAATC-TATGCAAAAATGC
55586 ACAAATAAAG
Statistics
Matches: 119, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
55 41 0.34
56 2 0.02
57 2 0.02
58 3 0.03
59 2 0.02
60 67 0.56
61 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (61 bp):
AAATAGGATCCCTAATCTATGCAAAAATGCTCAATTTAGGGTCAATGCTTTTAATTTGATT
Found at i:56653 original size:31 final size:31
Alignment explanation
Indices: 56612--56691 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
56602 TTTTAATTGT
56612 AACCTTATATCCTGAATTGCATTTTCAGGCA
1 AACCTTATATCCTGAATTGCATTTTCAGGCA
* * *
56643 AACCTCATATCGTGAATTGCATTTTTAGGCA
1 AACCTTATATCCTGAATTGCATTTTCAGGCA
*
56674 AACCTTATACCCTGAATT
1 AACCTTATATCCTGAATT
56692 ATTTTAAAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (31 bp):
AACCTTATATCCTGAATTGCATTTTCAGGCA
Found at i:57643 original size:48 final size:48
Alignment explanation
Indices: 57580--57677 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
57570 TGTAGAAAGG
57580 GAGAAAGAGCATCTTCAATACAAAAATTCAGAAATGGAGAAAGAGAAA
1 GAGAAAGAGCATCTTCAATACAAAAATTCAGAAATGGAGAAAGAGAAA
** *
57628 GAGAAAGAGGGTCTTCAATACAAAAATTCATAAATGGAGAAAGAGAAA
1 GAGAAAGAGCATCTTCAATACAAAAATTCAGAAATGGAGAAAGAGAAA
57676 GA
1 GA
57678 TATGGAAAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.53, C:0.09, G:0.22, T:0.15
Consensus pattern (48 bp):
GAGAAAGAGCATCTTCAATACAAAAATTCAGAAATGGAGAAAGAGAAA
Found at i:58769 original size:29 final size:29
Alignment explanation
Indices: 58717--58777 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
58707 ACCCTTCACA
* * *
58717 AAACAAGTCAATTAAATTATTTAAATAGT
1 AAACAAGTCAATCAAACTAGTTAAATAGT
*
58746 AAACAAGTCAATCAAACTAGTTAAATATT
1 AAACAAGTCAATCAAACTAGTTAAATAGT
58775 AAA
1 AAA
58778 TACAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.30
Consensus pattern (29 bp):
AAACAAGTCAATCAAACTAGTTAAATAGT
Found at i:61925 original size:16 final size:13
Alignment explanation
Indices: 61894--61918 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61884 TATCATTATT
61894 ATTATTATTTAAA
1 ATTATTATTTAAA
61907 ATTATTATTTAA
1 ATTATTATTTAA
61919 CTAAATTCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTATTTAAA
Found at i:62838 original size:29 final size:26
Alignment explanation
Indices: 62787--62850 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 26
62777 ATAAATATGT
*
62787 GATTAATGAGAATGATTCATCTTACTATA
1 GATTTATG-GAATGATTCATCTT-CT-TA
*
62816 GATGTTATGGAATGTTTCATCTTCTTA
1 GAT-TTATGGAATGATTCATCTTCTTA
62843 GATTTATG
1 GATTTATG
62851 ATGATGTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 5 0.16
27 5 0.16
28 2 0.06
29 16 0.50
30 4 0.12
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (26 bp):
GATTTATGGAATGATTCATCTTCTTA
Found at i:62965 original size:30 final size:30
Alignment explanation
Indices: 62929--62994 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
62919 CTCTATATCC
* *
62929 TCTTGTCTCTATCATACTTCAATCGTTTTT
1 TCTTGTCTCTATCATACTTCAATCATTTGT
62959 TCTTGTCTCTATCATACTTCAATCATTTGT
1 TCTTGTCTCTATCATACTTCAATCATTTGT
62989 TCTTGT
1 TCTTGT
62995 TCTTTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.17, C:0.23, G:0.08, T:0.53
Consensus pattern (30 bp):
TCTTGTCTCTATCATACTTCAATCATTTGT
Found at i:63207 original size:33 final size:34
Alignment explanation
Indices: 63170--63233 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
63160 TCAACATGCA
*
63170 TGATCTCCTTCTTCTACCTTT-CTTTATCATACG
1 TGATCTCCTCCTTCTACCTTTGCTTTATCATACG
*
63203 TGATCTCCTCCTTCTACCTTTGTTTTATCAT
1 TGATCTCCTCCTTCTACCTTTGCTTTATCAT
63234 TGAAATTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 20 0.71
34 8 0.29
ACGTcount: A:0.14, C:0.30, G:0.06, T:0.50
Consensus pattern (34 bp):
TGATCTCCTCCTTCTACCTTTGCTTTATCATACG
Found at i:67323 original size:21 final size:21
Alignment explanation
Indices: 67297--67350 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
67287 TGAAGGCTTA
67297 CCCAGGCGCGGGTTACCCTTG
1 CCCAGGCGCGGGTTACCCTTG
67318 CCCAGGCGCGGGTTACCCTTG
1 CCCAGGCGCGGGTTACCCTTG
67339 CCCAGGCGCGGG
1 CCCAGGCGCGGG
67351 CTACACCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.09, C:0.39, G:0.37, T:0.15
Consensus pattern (21 bp):
CCCAGGCGCGGGTTACCCTTG
Found at i:74621 original size:33 final size:33
Alignment explanation
Indices: 74543--74647 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
74533 TGCAAAAGAG
* *
74543 TGTTTTAGATGTTGTTTGCGATGATACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGACACTAAATC
** *
74576 TAATTT-GAGTGTTGTTTGCGATGACACTAAATT
1 TGTTTTAG-GTGTTGTTTGCGATGACACTAAATC
* * * *
74609 TGTTTTAGGTGTTGTTTGTGATGAAACAAAACC
1 TGTTTTAGGTGTTGTTTGCGATGACACTAAATC
74642 TGTTTT
1 TGTTTT
74648 GGATGCTAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 1 0.02
33 56 0.97
34 1 0.02
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.45
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGACACTAAATC
Found at i:75093 original size:30 final size:30
Alignment explanation
Indices: 75057--75119 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
75047 TCTTGAAAGG
*
75057 GGAGGGAATGATGCGCCTAA-AGCTTATCAT
1 GGAGGGAATGATGCGCC-AAGAACTTATCAT
75087 GGAGGGAATGATGCGCCAAGAACTTATCAT
1 GGAGGGAATGATGCGCCAAGAACTTATCAT
75117 GGA
1 GGA
75120 CTTGAAGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.21
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGAACTTATCAT
Found at i:76710 original size:18 final size:18
Alignment explanation
Indices: 76681--76724 Score: 79
Period size: 19 Copynumber: 2.4 Consensus size: 18
76671 TTTCCTTTAG
76681 TTTTGTTTTTTTTTTCGT
1 TTTTGTTTTTTTTTTCGT
76699 ATTTTGTTTTTTTTTTCGT
1 -TTTTGTTTTTTTTTTCGT
76718 TTTTGTT
1 TTTTGTT
76725 GATTTTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.02, C:0.05, G:0.11, T:0.82
Consensus pattern (18 bp):
TTTTGTTTTTTTTTTCGT
Found at i:76730 original size:18 final size:19
Alignment explanation
Indices: 76690--76730 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
76680 GTTTTGTTTT
**
76690 TTTTTTCGTATTTTGTTTT
1 TTTTTTCGTATTTTGTTGA
76709 TTTTTTCGT-TTTTGTTGA
1 TTTTTTCGTATTTTGTTGA
76727 TTTT
1 TTTT
76731 CTTAACTCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.05, C:0.05, G:0.12, T:0.78
Consensus pattern (19 bp):
TTTTTTCGTATTTTGTTGA
Found at i:76730 original size:19 final size:19
Alignment explanation
Indices: 76681--76730 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
76671 TTTCCTTTAG
*
76681 TTTTGTTTTTTTTTTCGTA
1 TTTTGTTATTTTTTTCGTA
*
76700 TTTTGTTTTTTTTTTCGT-
1 TTTTGTTATTTTTTTCGTA
76718 TTTTGTTGATTTT
1 TTTTGTT-ATTTT
76731 CTTAACTCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.04, C:0.04, G:0.12, T:0.80
Consensus pattern (19 bp):
TTTTGTTATTTTTTTCGTA
Found at i:77786 original size:40 final size:41
Alignment explanation
Indices: 77708--77789 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
77698 ATTCGAAGAA
77708 GCTCTTGCACAAACCCACCACAAAAACAACAAGGGCATTGGC
1 GCTCTTGCACAAACCCA-CACAAAAACAACAAGGGCATTGGC
* ** *
77750 GCTCTTGCACAAACCCA-TCGGAAACAACAATGGCATTGGC
1 GCTCTTGCACAAACCCACACAAAAACAACAAGGGCATTGGC
77790 TTTACTAGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 19 0.53
42 17 0.47
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (41 bp):
GCTCTTGCACAAACCCACACAAAAACAACAAGGGCATTGGC
Found at i:78910 original size:25 final size:25
Alignment explanation
Indices: 78881--78937 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
78871 TGCAACCACC
*
78881 AAGAAAATTCAAAAAAGAAGAA-GA
1 AAGAAAATTCAAAAAAAAAGAACGA
*
78905 AGAGAAAATTGAAAAAAAAAGAACGA
1 A-AGAAAATTCAAAAAAAAAGAACGA
78931 AAGAAAA
1 AAGAAAA
78938 AAAGACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.03
25 25 0.86
26 3 0.10
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (25 bp):
AAGAAAATTCAAAAAAAAAGAACGA
Done.