Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018451.1 Corchorus olitorius cultivar O-4 contig18484, 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: 39398
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:777 original size:22 final size:22
Alignment explanation
Indices: 753--993 Score: 195
Period size: 22 Copynumber: 10.8 Consensus size: 22
743 ATAAGCACAC
*
753 TATGAAATTTTGATAATCTTCC-
1 TATGAAATTTTGATAA-CCTCCT
* *
775 TATGAAATTTTAATAACCTCCA
1 TATGAAATTTTGATAACCTCCT
* * *
797 TAT-AAGATTTTGATAATCGCCC
1 TATGAA-ATTTTGATAACCTCCT
* ****
819 TATGAGATTTTGATAACCAGAG
1 TATGAAATTTTGATAACCTCCT
841 TATGAAATTTT-AGTAACCTCCT
1 TATGAAATTTTGA-TAACCTCCT
* *
863 TGTGAAATTTTGACAACCTTCC-
1 TATGAAATTTTGATAACC-TCCT
* *
885 CATG-AATTTCGATAACCTCCT
1 TATGAAATTTTGATAACCTCCT
* *
906 TATAAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCT
*
928 TATGAAATTTTGATAACATCCT
1 TATGAAATTTTGATAACCTCCT
*
950 TATGAAATTTTATTTTAATAACCTCCT
1 TATG-AA----ATTTTGATAACCTCCT
977 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
994 ATCCCATGGA
Statistics
Matches: 173, Mismatches: 33, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
20 3 0.02
21 20 0.12
22 123 0.71
23 7 0.04
26 2 0.01
27 18 0.10
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCT
Found at i:954 original size:109 final size:110
Alignment explanation
Indices: 755--961 Score: 265
Period size: 109 Copynumber: 1.9 Consensus size: 110
745 AAGCACACTA
* * * * * * *
755 TGAAATTTTGATAATCTTCCTATGAAATTTTAATAACCTCCATATAAGATTTTGATAATCGCCCT
1 TGAAATTTTGACAACCTTCCCATGAAATTTCAATAACCTCCATATAAAATTTTGATAACCGCCAT
* *
820 ATGAGATTTTGATAACCAGAGTATGAAATTTTAGTAACCTCCTTG
66 ATGAAATTTTGATAACCACAGTATGAAATTTTAGTAACCTCCTTG
* * *
865 TGAAATTTTGACAACCTTCCCATG-AATTTCGATAACCTCCTTATAAAATTTTGATAACCTCCAT
1 TGAAATTTTGACAACCTTCCCATGAAATTTCAATAACCTCCATATAAAATTTTGATAACCGCCAT
**
929 ATGAAATTTTGATAA-CATCCTTATGAAATTTTA
66 ATGAAATTTTGATAACCA-CAGTATGAAATTTTA
962 TTTTAATAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
108 2 0.02
109 59 0.72
110 21 0.26
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (110 bp):
TGAAATTTTGACAACCTTCCCATGAAATTTCAATAACCTCCATATAAAATTTTGATAACCGCCAT
ATGAAATTTTGATAACCACAGTATGAAATTTTAGTAACCTCCTTG
Found at i:976 original size:27 final size:27
Alignment explanation
Indices: 934--987 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
924 TCCATATGAA
*
934 ATTTTGATAACATCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
*
961 ATTTTAATAACCTCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
988 GATAACATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (27 bp):
ATTTTAATAACATCCTTATGAAATTTT
Found at i:1046 original size:114 final size:114
Alignment explanation
Indices: 847--1058 Score: 263
Period size: 114 Copynumber: 1.9 Consensus size: 114
837 AGAGTATGAA
* * *
847 ATTTTAGTAACCTCCTTGTGAAATTTTGACAACCTTCCCATGAATTTCGATAACCTCCTTATAAA
1 ATTTTAATAACCTCCTTATGAAATTTTGACAACCATCCCATGAATTTCGATAACCTCCTTATAAA
* * *
912 ATTTTGATAACCTCCATATGAAATTTTGATAACATCCTTATGAAATTTT
66 ATTTTAACAACATCCATATGAAATTTTGATAACATCCTTATGAAATTTT
*
961 ATTTTAATAACCTCCTTATGAAATTTTGATAA-CATCCCATGGAATTGT-GATAA-CTACAC-TA
1 ATTTTAATAACCTCCTTATGAAATTTTGACAACCATCCCAT-GAATT-TCGATAACCT-C-CTTA
* *
1022 TAAAATTTTAACATCATACC-TATGAAATTTTGGTAAC
62 TAAAATTTTAACAACAT-CCATATGAAATTTTGATAAC
1059 CACACTAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
113 9 0.11
114 71 0.85
115 4 0.05
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (114 bp):
ATTTTAATAACCTCCTTATGAAATTTTGACAACCATCCCATGAATTTCGATAACCTCCTTATAAA
ATTTTAACAACATCCATATGAAATTTTGATAACATCCTTATGAAATTTT
Found at i:1119 original size:21 final size:21
Alignment explanation
Indices: 1046--1166 Score: 102
Period size: 21 Copynumber: 5.6 Consensus size: 21
1036 CATACCTATG
** *
1046 AAATTTTGGTAACCACACTA-
1 AAATTTTAATAACCACACAAT
* * *
1066 AAATTTTGAGAACCACACTAT
1 AAATTTTAATAACCACACAAT
1087 AAATTTTAATAACCACACAAT
1 AAATTTTAATAACCACACAAT
* *
1108 AAATTTTTATAACTTC-CAAAATTAT
1 AAATTTTAATAAC--CAC-ACA--AT
1133 AAATTTTAATAACCACACAAT
1 AAATTTTAATAACCACACAAT
*
1154 AAATTTTTATAAC
1 AAATTTTAATAAC
1167 TTCCAAAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
20 18 0.21
21 44 0.52
22 1 0.01
23 6 0.07
24 1 0.01
25 14 0.17
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (21 bp):
AAATTTTAATAACCACACAAT
Found at i:1135 original size:25 final size:25
Alignment explanation
Indices: 1106--1177 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
1096 TAACCACACA
1106 ATAAATTTTTATAACTTCCAAAATT
1 ATAAATTTTTATAACTTCCAAAATT
* *
1131 ATAAATTTTAATAA---CCACACA--
1 ATAAATTTTTATAACTTCCA-AAATT
1152 ATAAATTTTTATAACTTCCAAAATT
1 ATAAATTTTTATAACTTCCAAAATT
1177 A
1 A
1178 AAACATAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
21 13 0.35
22 3 0.08
23 4 0.11
24 3 0.08
25 14 0.38
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAAATTTTTATAACTTCCAAAATT
Found at i:1136 original size:46 final size:46
Alignment explanation
Indices: 1084--1177 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1074 AGAACCACAC
1084 TATAAATTTTAATAACCACACAATAAATTTTTATAACTTCCAAAAT
1 TATAAATTTTAATAACCACACAATAAATTTTTATAACTTCCAAAAT
1130 TATAAATTTTAATAACCACACAATAAATTTTTATAACTTCCAAAAT
1 TATAAATTTTAATAACCACACAATAAATTTTTATAACTTCCAAAAT
1176 TA
1 TA
1178 AAACATAGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (46 bp):
TATAAATTTTAATAACCACACAATAAATTTTTATAACTTCCAAAAT
Found at i:6782 original size:13 final size:14
Alignment explanation
Indices: 6764--6793 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6754 GTAGATATGT
6764 AGTTTGTTTT-TTA
1 AGTTTGTTTTGTTA
6777 AGTTTGTTTTGTTA
1 AGTTTGTTTTGTTA
6791 AGT
1 AGT
6794 CAGTTTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.20, T:0.63
Consensus pattern (14 bp):
AGTTTGTTTTGTTA
Found at i:9494 original size:42 final size:42
Alignment explanation
Indices: 9447--9530 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
9437 TGCACATCCT
9447 CTCCATGATCTCCATTGTGCTCTTCAAAACCATGATAAGTCC
1 CTCCATGATCTCCATTGTGCTCTTCAAAACCATGATAAGTCC
*
9489 CTCCATGATCTCCATTGTGCTCTTCAAGACCATGATAAGTCC
1 CTCCATGATCTCCATTGTGCTCTTCAAAACCATGATAAGTCC
9531 TTGGCGCATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (42 bp):
CTCCATGATCTCCATTGTGCTCTTCAAAACCATGATAAGTCC
Found at i:11291 original size:9 final size:9
Alignment explanation
Indices: 11279--11303 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11269 TTATTATATA
11279 TATATATGT
1 TATATATGT
11288 TATATATGT
1 TATATATGT
11297 TATATAT
1 TATATAT
11304 TATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (9 bp):
TATATATGT
Found at i:11564 original size:42 final size:43
Alignment explanation
Indices: 11513--11606 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
11503 AGTGCATTAT
*
11513 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
11554 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
11599 CTAATATT
1 CTAATATT
11607 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:12444 original size:3 final size:3
Alignment explanation
Indices: 12436--12519 Score: 168
Period size: 3 Copynumber: 28.0 Consensus size: 3
12426 TATAGTATAT
12436 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12484 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12520 TATAGCATTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13520 original size:67 final size:67
Alignment explanation
Indices: 13315--13523 Score: 172
Period size: 67 Copynumber: 3.1 Consensus size: 67
13305 AGTTGCAAAA
13315 ATGGAAAGACATAAGAAAAGGTGTAAGTAGCAAAAAAGCATTGTCAATATAAATAGGGGAAATTA
1 ATGGAAAGACATAAGAAAAGGTGTAAGTAGCAAAAAAGCATTGTCAATATAAATAGGGGAAATTA
13380 TC
66 TC
* * * *
13382 ATGGAAAG---TAATG--GAGGTGT-TGATACCCTAATTTCAACAAGCATTG--AATAATAATAA
1 ATGGAAAGACATAA-GAAAAGGTGTAAG-TA-GC-AA----AA-AAGCATTGTCAAT-ATAA-AT
* *
13439 AGTTGCAAA--A--
55 AG-GGGAAATTATC
13449 ATGGAAAGACATAAGAAAAGGTGTAAGTAGCAAAAAAGCATTGTCAATATAAATAGGGGAAATTA
1 ATGGAAAGACATAAGAAAAGGTGTAAGTAGCAAAAAAGCATTGTCAATATAAATAGGGGAAATTA
13514 TC
66 TC
13516 ATGGAAAG
1 ATGGAAAG
13524 TAATGGAGGT
Statistics
Matches: 106, Mismatches: 12, Indels: 48
0.64 0.07 0.29
Matches are distributed among these distances:
62 1 0.01
63 12 0.11
64 15 0.14
65 10 0.09
66 3 0.03
67 24 0.23
68 3 0.03
69 10 0.09
70 15 0.14
71 12 0.11
72 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (67 bp):
ATGGAAAGACATAAGAAAAGGTGTAAGTAGCAAAAAAGCATTGTCAATATAAATAGGGGAAATTA
TC
Found at i:13521 original size:134 final size:134
Alignment explanation
Indices: 13281--13545 Score: 503
Period size: 134 Copynumber: 2.0 Consensus size: 134
13271 TTTTCTTTTG
* *
13281 TCAACAATCATTGAATAATGATAAAGTTGCAAAAATGGAAAGACATAAGAAAAGGTGTAAGTAGC
1 TCAACAAGCATTGAATAATAATAAAGTTGCAAAAATGGAAAGACATAAGAAAAGGTGTAAGTAGC
13346 AAAAAAGCATTGTCAATATAAATAGGGGAAATTATCATGGAAAGTAATGGAGGTGTTGATACCCT
66 AAAAAAGCATTGTCAATATAAATAGGGGAAATTATCATGGAAAGTAATGGAGGTGTTGATACCCT
13411 AATT
131 AATT
13415 TCAACAAGCATTGAATAATAATAAAGTTGCAAAAATGGAAAGACATAAGAAAAGGTGTAAGTAGC
1 TCAACAAGCATTGAATAATAATAAAGTTGCAAAAATGGAAAGACATAAGAAAAGGTGTAAGTAGC
*
13480 AAAAAAGCATTGTCAATATAAATAGGGGAAATTATCATGGAAAGTAATGGAGGTGTTGATATCCT
66 AAAAAAGCATTGTCAATATAAATAGGGGAAATTATCATGGAAAGTAATGGAGGTGTTGATACCCT
13545 A
131 A
13546 TTTGGGTAAA
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 128 1.00
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (134 bp):
TCAACAAGCATTGAATAATAATAAAGTTGCAAAAATGGAAAGACATAAGAAAAGGTGTAAGTAGC
AAAAAAGCATTGTCAATATAAATAGGGGAAATTATCATGGAAAGTAATGGAGGTGTTGATACCCT
AATT
Found at i:13983 original size:23 final size:20
Alignment explanation
Indices: 13963--14006 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
13953 GAAATAATCA
13963 TATAAAATAATAATAACTAAT
1 TATAAAA-AATAATAACTAAT
* *
13984 TTTTAAAAATAATAACTAAT
1 TATAAAAAATAATAACTAAT
14004 TAT
1 TAT
14007 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAAAAAATAATAACTAAT
Found at i:13996 original size:20 final size:20
Alignment explanation
Indices: 13971--14009 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13961 CATATAAAAT
*
13971 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
13991 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
14010 TTTAAAAAAA
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:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:14162 original size:54 final size:54
Alignment explanation
Indices: 14046--14152 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 54
14036 ACATGGCTAG
* * * *
14046 TCGCGAGCCGTGGTCGCTCGTGACTAAGCCATGGCTCGGTCGCGAGTGGCTTGA
1 TCGCGAGCCGTGGTCGCTCGCGACCAAGCCATGGCTCGATCGCGAGCGGCTTGA
* * *
14100 TCGCGAGCCTTGGTCGCTCGCGACCAAGCCATGGCTTGATCGCGCGCGGCTTG
1 TCGCGAGCCGTGGTCGCTCGCGACCAAGCCATGGCTCGATCGCGAGCGGCTTG
14153 TGACTGAGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.12, C:0.31, G:0.36, T:0.21
Consensus pattern (54 bp):
TCGCGAGCCGTGGTCGCTCGCGACCAAGCCATGGCTCGATCGCGAGCGGCTTGA
Found at i:14331 original size:17 final size:18
Alignment explanation
Indices: 14306--14352 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
14296 ATTGAGGTTT
*
14306 GAAAGTTTGAA-AATTGA
1 GAAAATTTGAAGAATTGA
14323 GAAAATTTGAGAGAATTGA
1 GAAAATTTGA-AGAATTGA
*
14342 -AAATTTTGAAG
1 GAAAATTTGAAG
14353 TTTGAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (18 bp):
GAAAATTTGAAGAATTGA
Found at i:21680 original size:7 final size:6
Alignment explanation
Indices: 21671--21713 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
21661 CGTTTTCGTT
*
21671 TTTTTG TTTTTTG TTTTTG -TTTTG TTTTTG -TTTTG CTTTTG TT
1 TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
21714 ACGTTGTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
5 10 0.30
6 17 0.52
7 6 0.18
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:21695 original size:11 final size:11
Alignment explanation
Indices: 21662--21713 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
21652 GTTTGGCATC
*
21662 GTTTTCGTTTT
1 GTTTTTGTTTT
21673 -TTTGTT-TTTT
1 GTTT-TTGTTTT
21683 GTTTTTGTTTT
1 GTTTTTGTTTT
21694 GTTTTTGTTTT
1 GTTTTTGTTTT
*
21705 GCTTTTGTT
1 GTTTTTGTT
21714 ACGTTGTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 9 0.25
11 27 0.75
ACGTcount: A:0.00, C:0.04, G:0.17, T:0.79
Consensus pattern (11 bp):
GTTTTTGTTTT
Found at i:21700 original size:17 final size:17
Alignment explanation
Indices: 21672--21713 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
21662 GTTTTCGTTT
21672 TTTTGTTTTTTGTTTTTG-
1 TTTTG-TTTTTG-TTTTGC
21690 TTTTGTTTTTGTTTTGC
1 TTTTGTTTTTGTTTTGC
21707 TTTTGTT
1 TTTTGTT
21714 ACGTTGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (17 bp):
TTTTGTTTTTGTTTTGC
Found at i:31512 original size:28 final size:29
Alignment explanation
Indices: 31460--31533 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
31450 TACCCAGAAA
*
31460 AATCCCTTATGTTTTGCTTTTGGGACAAAAT
1 AATCCCTTATG-TTT-CTTTCGGGACAAAAT
*
31491 AATCCCTTATGTTT-TTTCGGGACAAATT
1 AATCCCTTATGTTTCTTTCGGGACAAAAT
* *
31519 AATTCCTTACGTTTC
1 AATCCCTTATGTTTC
31534 AATAATGATC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 24 0.63
30 3 0.08
31 11 0.29
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (29 bp):
AATCCCTTATGTTTCTTTCGGGACAAAAT
Found at i:31715 original size:31 final size:31
Alignment explanation
Indices: 31680--31772 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
31670 GACTAATTTG
*
31680 TCCCAAAAAAAAAACATAAGGGATTTTTTTA
1 TCCCAAAAGAAAAACATAAGGGATTTTTTTA
* *
31711 TCCCAAAAGAAAAACAAAAGGGATTTTTTTG
1 TCCCAAAAGAAAAACATAAGGGATTTTTTTA
*
31742 TCCCAAAAGAAAAACATTAGGGATTTTTTTA
1 TCCCAAAAGAAAAACATAAGGGATTTTTTTA
31773 GTATTTAGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (31 bp):
TCCCAAAAGAAAAACATAAGGGATTTTTTTA
Found at i:32147 original size:125 final size:125
Alignment explanation
Indices: 31923--32162 Score: 313
Period size: 125 Copynumber: 1.9 Consensus size: 125
31913 ATTCCCTAAA
* *
31923 AAAATGGTAAAGATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAATTTTTGG
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAATTTTTAG
* * *
31988 TAAAAAAAACTGTAAAAGTTTAAAAAATGTCATTTAAGAAATATATTTAATTAAAATAGT
66 TAAAAAAAACTGTAAAAGTATAAAAAATGACATTTAAAAAATATATTTAATTAAAATAGT
* * *
32048 AAAATGGTAAAAATAAAATAGTTATAAATATATT-AGATTTGATTAAATAAAAATAGAGTTTTTA
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTGA-ATTTAATTAAATAAAAATAGAATTTTT-
* * ** * * *
32112 ATTGAGTAAAATTTTCAAAGTAT-AAAAATGACATTTAAAAAATATATTTAA
64 AGTAAAAAAAACTGTAAAAGTATAAAAAATGACATTTAAAAAATATATTTAA
32163 AAAATAAGGG
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
124 1 0.01
125 83 0.85
126 14 0.14
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.35
Consensus pattern (125 bp):
AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAATTTTTAG
TAAAAAAAACTGTAAAAGTATAAAAAATGACATTTAAAAAATATATTTAATTAAAATAGT
Found at i:32152 original size:14 final size:13
Alignment explanation
Indices: 32135--32168 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
32125 TTCAAAGTAT
32135 AAAAATGACATTTA
1 AAAAAT-ACATTTA
*
32149 AAAAATATATTTA
1 AAAAATACATTTA
32162 AAAAATA
1 AAAAATA
32169 AGGGTAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (13 bp):
AAAAATACATTTA
Found at i:32795 original size:31 final size:31
Alignment explanation
Indices: 32759--32866 Score: 171
Period size: 31 Copynumber: 3.5 Consensus size: 31
32749 ACTAAATACT
* *
32759 AAAAAAATTCTCTTATATTTTTCTTTTGGGAC
1 AAAAAAA-TCCCTTATGTTTTTCTTTTGGGAC
32791 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
32822 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
**
32853 AAATCAATCCCTTA
1 AAAAAAATCCCTTA
32867 CTGGCGCGGA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
31 65 0.90
32 7 0.10
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:33045 original size:31 final size:29
Alignment explanation
Indices: 32979--33058 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
32969 CTCATTTTTG
* * *
32979 AAACGTAAGGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
33008 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
33039 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
33059 GATTTTTAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:35758 original size:440 final size:438
Alignment explanation
Indices: 34921--35842 Score: 1488
Period size: 440 Copynumber: 2.1 Consensus size: 438
34911 GCATTAAATG
* * * *
34921 GTCCAACCCATAATTCTGAGGGATTAAATAGCATAAAGCATAAAAAACTGAGGTTCATTTGATAA
1 GTCCAACCCAAAATTATGAGGGACTAAATAGCATAAAGCATAAAAAACTGAGGATCATTTGATAA
* * *
34986 ATAATCCAGCAAAAAAATTATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTTGAACCCTCC
66 ATAATCCAGCAAAAAAAATATTTGTTTATGGAAACCAAACATAAAAATTCCCTCTTGAACCCTCA
* *
35051 ACGAAACTCATTAATCAAATTCAACTTTGAGCTCCTTAACGAAAGTCGTAGATCACACAATAACC
131 ACAAAACTCATTAATCAAATTCAACTTTGAGCTCCTTAACGAAAGCCGTAGATCACACAATAACC
35116 TTTTAACCGACACTTGAATAACCTCAATCGAACAAGTGGACCAAAAATTATACGATATCAAATAG
196 TTTTAACCGACACTTGAATAACCTCAATCGAACAAGTGGACCAAAAATTATACGATATCAAATAG
* * *
35181 ACTGATAATCAAGACCACAAAATTTCAAAAACATTTTTTAAAATCAAAACATTAAAATTGGCTTT
261 ACCGACAATCAAAACCACAAAATTTCAAAAACATTTTTTAAAATCAAAACATTAAAATTGGCTTT
* *
35246 TGAGTCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTAAATCACCTTGAT
326 TGAGTCCTTCATGGAAGTTGTAGATCATGAAAATACCTTTTAATAGACACTTAAATAACCTTGAT
*
35311 CGGACAAGCAAAACAAAAAATAAAAGAATTAAAGCTGAAACGTTCAGTC
391 CGGACAAGC-AAACAAAAAATAAAAGAATTAAAGCCGAAACGTTCAGTC
* ** *
35360 GTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCTGAGGATCATTTGTTA
1 GTCCAACCCA-AAATTATGAGGGACTAAATAGCATAAAGCATAAAAAACTGAGGATCATTTGATA
* **
35425 AATAATCTAGCAAAAAAAATATTTGTTTATGGAAACCAAACATAAAAATTCGTTCTTGAACCCTC
65 AATAATCCAGCAAAAAAAATATTTGTTTATGGAAACCAAACATAAAAATTCCCTCTTGAACCCTC
* *
35490 AACAAAACTCATTAATCAAATTCAGCTTTGAGGC-CTTTAACGAAAGCCGTAGATCACACAATAA
130 AACAAAACTCATTAATCAAATTCAACTTTGA-GCTCCTTAACGAAAGCCGTAGATCACACAATAA
* * * *
35554 CCTTTTAACCGACACTTGAATAAGCTCAATCGGACAAGTGGAGCAAAAATTATACGATATCATAT
194 CCTTTTAACCGACACTTGAATAACCTCAATCGAACAAGTGGACCAAAAATTATACGATATCAAAT
*
35619 AGACCGACAATCAAAACCACAAAATTTCAAAAGCATTTTTTAAAATCAAAACATTAAAATTGGCT
259 AGACCGACAATCAAAACCACAAAATTTCAAAAACATTTTTTAAAATCAAAACATTAAAATTGGCT
*
35684 TTTGAGTTCCTT-ATGGAAGTTGTAGATCATGAAAATACCTTTTAATAGACACTTGAATAACCTT
324 TTTGAG-TCCTTCATGGAAGTTGTAGATCATGAAAATACCTTTTAATAGACACTTAAATAACCTT
* *
35748 GATCGGACAAGCAAACAAAAAATAGAAGAATTAAAGCCGAAACGTTTAGTC
388 GATCGGACAAGCAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTCAGTC
*
35799 GTCTAACCCATAAATTATGAGGGACTAAATAGCATAAAGCATAA
1 GTCCAACCCA-AAATTATGAGGGACTAAATAGCATAAAGCATAA
35843 GTATATGAAT
Statistics
Matches: 446, Mismatches: 34, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
439 87 0.20
440 352 0.79
441 7 0.02
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (438 bp):
GTCCAACCCAAAATTATGAGGGACTAAATAGCATAAAGCATAAAAAACTGAGGATCATTTGATAA
ATAATCCAGCAAAAAAAATATTTGTTTATGGAAACCAAACATAAAAATTCCCTCTTGAACCCTCA
ACAAAACTCATTAATCAAATTCAACTTTGAGCTCCTTAACGAAAGCCGTAGATCACACAATAACC
TTTTAACCGACACTTGAATAACCTCAATCGAACAAGTGGACCAAAAATTATACGATATCAAATAG
ACCGACAATCAAAACCACAAAATTTCAAAAACATTTTTTAAAATCAAAACATTAAAATTGGCTTT
TGAGTCCTTCATGGAAGTTGTAGATCATGAAAATACCTTTTAATAGACACTTAAATAACCTTGAT
CGGACAAGCAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTCAGTC
Found at i:37134 original size:20 final size:20
Alignment explanation
Indices: 37106--37144 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
37096 GAAAGGAAAA
*
37106 GAAAGAAAAGAAAAAGGAAG
1 GAAAAAAAAGAAAAAGGAAG
*
37126 GAAAAAAAAGAAGAAGGAA
1 GAAAAAAAAGAAAAAGGAA
37145 ATTAAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAGAAAAAGGAAG
Found at i:37141 original size:16 final size:16
Alignment explanation
Indices: 37102--37145 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
37092 AATAGAAAGG
*
37102 AAAAGAAAGAAAAGAA
1 AAAAGAAGGAAAAGAA
*
37118 AAAGGAAGGAAAA-AA
1 AAAAGAAGGAAAAGAA
37133 AAGAAGAAGGAAA
1 AA-AAGAAGGAAA
37146 TTAAAGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAAAGAAGGAAAAGAA
Found at i:37145 original size:27 final size:28
Alignment explanation
Indices: 37076--37145 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
37066 AAAAAGGGAG
* *
37076 AAAAAAAGACG-AGAAAAATAGAAAGGA
1 AAAAAAAGAAGAAGGAAAATAGAAAGGA
* *
37103 AAAGAAAGAA-AA-GAAAA-AGGAAGGA
1 AAAAAAAGAAGAAGGAAAATAGAAAGGA
37128 AAAAAAAGAAGAAGGAAA
1 AAAAAAAGAAGAAGGAAA
37146 TTAAAGATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 16 0.46
26 6 0.17
27 13 0.37
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (28 bp):
AAAAAAAGAAGAAGGAAAATAGAAAGGA
Found at i:37277 original size:27 final size:27
Alignment explanation
Indices: 37209--37278 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
37199 TTACTATTTT
*
37209 ACCCTTTGATGGA-TAAAGTACTAAATC
1 ACCCTTTGAT-GATTAAAGTACGAAATC
* * *
37236 ACCC-TTAAGTTATTAAATTACGAAATC
1 ACCCTTTGA-TGATTAAAGTACGAAATC
37263 ACCCTTTGATGATTAA
1 ACCCTTTGATGATTAA
37279 TTTTAAGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 4 0.12
27 27 0.79
28 3 0.09
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (27 bp):
ACCCTTTGATGATTAAAGTACGAAATC
Done.