Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009136.1 Corchorus capsularis cultivar CVL-1 contig09157, 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: 76790
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:16207 original size:156 final size:155
Alignment explanation
Indices: 15625--16189 Score: 617
Period size: 156 Copynumber: 3.6 Consensus size: 155
15615 CTTGGCTAAG
* * * *
15625 TTTCATCTCAAACGGACTTA-AGATGAAAAACTTATGCAAGTTTTTCAGTTAATGACATTTTGGG
1 TTTCAGCTCAAACGGACTTAGA-ATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGGG
* * *
15689 GTGAGAAACC-ACTTCACCATGATAGG-GAGTTCGGTTTTACTTAGAATTTTTTCCATAAGT-TT
65 GTGAGAAACCTAGTTCACCATGA-AGGAGAGCTAGGTTTTACTTAGAATTTTTTCCAT-AGTCTT
* *
15751 GTGGATATAATCTAAGTCTCTTGGCCCAAA
128 ATGGATATAATCTAAGTCTCGTGG--CAAA
* * * *
15781 TTTCATCTCAAACAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGG
1 TTTCAGCTCAAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGGGG
** * * ** *
15846 TGAG-AAGTTGGTTCACTACCAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTCTTATG
66 TGAGAAACCTAGTTCACCATGAAGGAGAGCTAGGTTTTACTTAGAATTTTTTCCATAGTCTTATG
* * *
15910 GAGATAATATAAGCCTACGGGTGG-AAA
131 GATATAATCTAAGTCT-C--GTGGCAAA
* * ** * * *
15937 -ATCAGC-CTTATTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGATAGTTTAGG
1 TTTCAGCTC-AAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGGG
* * * * * *
16000 GAGAGAAACCAAGTTCACCATAAAGGGGAGGTCA-GTTTTACTTGGAATTTTTTCCATAGTCTTA
65 GTGAGAAACCTAGTTCACCATGAAGGAGAGCT-AGGTTTTACTTAGAATTTTTTCCATAGTCTTA
* *
16064 AGGATATAGTCTAAGTCTCGTGGCAAA
129 TGGATATAATCTAAGTCTCGTGGCAAA
16091 GTTTCAGCTCAAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGGG
1 -TTTCAGCTCAAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGGG
*
16156 GTGTGAAACCTAGTTCACCATGAAGGAGAGCTAG
65 GTGAGAAACCTAGTTCACCATGAAGGAGAGCTAG
16190 AACCAAGCCA
Statistics
Matches: 336, Mismatches: 58, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
153 4 0.01
154 4 0.01
155 66 0.20
156 256 0.76
157 3 0.01
159 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (155 bp):
TTTCAGCTCAAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGGGG
TGAGAAACCTAGTTCACCATGAAGGAGAGCTAGGTTTTACTTAGAATTTTTTCCATAGTCTTATG
GATATAATCTAAGTCTCGTGGCAAA
Found at i:28665 original size:17 final size:17
Alignment explanation
Indices: 28643--28689 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
28633 AGGTGATCTA
28643 AGATCACCAGTGATTTT
1 AGATCACCAGTGATTTT
*
28660 -GCATCACCGGTGATTTT
1 AG-ATCACCAGTGATTTT
28677 AGATCACCAGTGA
1 AGATCACCAGTGA
28690 CTTGGGGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (17 bp):
AGATCACCAGTGATTTT
Found at i:36060 original size:49 final size:51
Alignment explanation
Indices: 35995--36094 Score: 143
Period size: 49 Copynumber: 2.0 Consensus size: 51
35985 TATTTATTTG
*
35995 TTTGTTTGTTTGTTAGATAG-AATTTATTAA-A-CTTAATTTAAGGTAATTA
1 TTTGTTTGTTTATTAGATAGTAATTTATTAACACCTT-ATTTAAGGTAATTA
*
36044 TTTGTTTGTTTATTAGATAGTAGTTTATTAACTACCTTATTTAAGGTAATT
1 TTTGTTTGTTTATTAGATAGTAATTTATTAAC-ACCTTATTTAAGGTAATT
36095 TCTTAGTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
49 19 0.42
50 9 0.20
52 14 0.31
53 3 0.07
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (51 bp):
TTTGTTTGTTTATTAGATAGTAATTTATTAACACCTTATTTAAGGTAATTA
Found at i:41495 original size:11 final size:11
Alignment explanation
Indices: 41481--41518 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
41471 ATTCATAACA
41481 AATTTATAATT
1 AATTTATAATT
41492 AATTTATAATT
1 AATTTATAATT
41503 -ATTTGATAATT
1 AATTT-ATAATT
*
41514 TATTT
1 AATTT
41519 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:41717 original size:16 final size:17
Alignment explanation
Indices: 41696--41729 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
41686 GAAACATAGA
*
41696 AATTAATCAC-TATAAT
1 AATTAATAACTTATAAT
41712 AATTAATAACTTATAAT
1 AATTAATAACTTATAAT
41729 A
1 A
41730 TAAGATAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAATAACTTATAAT
Found at i:61483 original size:2 final size:2
Alignment explanation
Indices: 61476--61500 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61466 AAATAAGGGG
61476 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
61501 CATGATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61704 original size:2 final size:2
Alignment explanation
Indices: 61697--61727 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
61687 AAATAAGGGG
61697 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61728 CATGATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61752 original size:227 final size:223
Alignment explanation
Indices: 61380--61806 Score: 714
Period size: 227 Copynumber: 1.9 Consensus size: 223
61370 GTCTAATTAT
61380 TAATATCTTTGTTAAGATGGCTCAATTTAGAACCCAATTTTTTTCAATTTGACCAATCAAGATTT
1 TAATATCTTTGTTAAGATGGCTCAATTTAGAACCCAATTTTTTTCAATTTGACCAATCAAGATTT
* *
61445 AGTATGTTCCAATTTTGGCTCAAATAAGGGGTATATATATATATATATATATATATCATGATTAT
66 AGTA-GTTCCAATTTCGACTCAAATAAGGGGTATATATATATATATATATATATATCATGATTAT
61510 TAACCATCGAGTCGACATGTGACACTAAAAAATGTGTTATATATATATCATGTTATCATGTCCTT
130 TAACCATCGAGTCGACATGTGACACTAAAAAATGTGTTATATATATATCATGTTATCATGTCCTT
61575 ATTTGAACAGAAACAATAGCGCATGTAAC
195 ATTTGAACAGAAACAATAGCGCATGTAAC
* **
61604 TAATATCTTTGTTAAGATGGCTCAATTTAGAACCCAA-TTTTTTCAATTTGACGAATCGGGATTT
1 TAATATCTTTGTTAAGATGGCTCAATTTAGAACCCAATTTTTTTCAATTTGACCAATCAAGATTT
61668 AGTA-TTCCAATTTCGACTCAAATAAGGGGTATATATATATATATATATATATATATATATCATG
66 AGTAGTTCCAATTTCGACTCAAATAAGGGG------TATATATATATATATATATATATATCATG
*
61732 ATTATTAACCATCGAGTCGACATGTGACACTAAAAAATGTGTTTTATATATATCATGTTATCATG
125 ATTATTAACCATCGAGTCGACATGTGACACTAAAAAATGTGTTATATATATATCATGTTATCATG
*
61797 TCTTTATTTG
190 TCCTTATTTG
61807 TACCGAATCA
Statistics
Matches: 190, Mismatches: 7, Indels: 9
0.92 0.03 0.04
Matches are distributed among these distances:
221 23 0.12
223 28 0.15
224 37 0.19
227 102 0.54
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (223 bp):
TAATATCTTTGTTAAGATGGCTCAATTTAGAACCCAATTTTTTTCAATTTGACCAATCAAGATTT
AGTAGTTCCAATTTCGACTCAAATAAGGGGTATATATATATATATATATATATATCATGATTATT
AACCATCGAGTCGACATGTGACACTAAAAAATGTGTTATATATATATCATGTTATCATGTCCTTA
TTTGAACAGAAACAATAGCGCATGTAAC
Found at i:73614 original size:45 final size:44
Alignment explanation
Indices: 73558--73660 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 44
73548 TCACACTGTG
* *
73558 AAATTGTGATAACCTCACC-ACGAAATTTTGATAAATCTT-CCTATA
1 AAATTTTGATAACCTC-CCTACAAAATTTTGAT-AA-CTTGCCTATA
* *
73603 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTGCTTATA
1 AAATTTTGAT-AACCTCCCTACAAAATTTTGATAACTTGCCTATA
*
73648 AAATCTTGATAAC
1 AAATTTTGATAAC
73661 TACAAATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
44 6 0.12
45 27 0.54
46 17 0.34
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAACCTCCCTACAAAATTTTGATAACTTGCCTATA
Found at i:73650 original size:22 final size:22
Alignment explanation
Indices: 73580--73659 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 22
73570 CCTCACCACG
73580 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAA-CTTCCTATA
*
73603 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAA-CTTCCTATA
*
73626 AAATTTTGAT-AACTTGCTTATA
1 AAATTTTGATAAACTT-CCTATA
*
73648 AAATCTTGATAA
1 AAATTTTGATAA
73660 CTACAAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
21 2 0.04
22 16 0.32
23 32 0.64
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAAACTTCCTATA
Found at i:73692 original size:22 final size:22
Alignment explanation
Indices: 73664--73849 Score: 108
Period size: 22 Copynumber: 8.7 Consensus size: 22
73654 TGATAACTAC
73664 AAATTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCATTATG
* * **
73686 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCATTATG
73708 AAATTTTGAT---CTACATATATG
1 AAATTTTGATAACCT-CAT-TATG
73729 AAATTTTGATAACCCTC-TTATG
1 AAATTTTGATAA-CCTCATTATG
* * *
73751 AAATTTTGA-AAACTAAATTATA
1 AAATTTTGATAACCT-CATTATG
* * *
73773 AAATTTTGATTA-CTCCATAATA
1 AAATTTTGATAACCT-CATTATG
* * *
73795 AAAGTTTAATAACCT--TCAT-
1 AAATTTTGATAACCTCATTATG
*
73814 -AA-TTTGATAACCAT-ACTATG
1 AAATTTTGATAACC-TCATTATG
73834 AAATTTTGATAACCTC
1 AAATTTTGATAACCTC
73850 CCCAGAAATA
Statistics
Matches: 127, Mismatches: 21, Indels: 32
0.71 0.12 0.18
Matches are distributed among these distances:
17 9 0.07
18 3 0.02
19 4 0.03
20 6 0.05
21 19 0.15
22 79 0.62
23 4 0.03
24 1 0.01
25 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCATTATG
Found at i:73717 original size:60 final size:63
Alignment explanation
Indices: 73603--73764 Score: 145
Period size: 60 Copynumber: 2.6 Consensus size: 63
73593 TCTTCCTATA
* * * * *
73603 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTGCTTATAAAATCTTGA-TA-A-CTA-C
1 AAATTTTGAT-AACCT-CTTATGAAATTTTGATAACTTCCCTATAAAATCTTGACTACATATATC
* * *
73664 AAATTTTGATAACCTCATTATGAAATTTTGTTAA-TCTCCCTATGAAATTTTGATCTACATATAT
1 AAATTTTGATAACCTC-TTATGAAATTTTGATAACT-TCCCTATAAAATCTTGA-CTACATATAT
*
73728 G
63 C
*
73729 AAATTTTGATAACCCTCTTATGAAATTTTGAAAACT
1 AAATTTTGATAA-CCTCTTATGAAATTTTGATAACT
73765 AAATTATAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
59 2 0.02
60 32 0.40
61 10 0.12
62 2 0.02
63 1 0.01
64 2 0.02
65 27 0.33
66 5 0.06
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (63 bp):
AAATTTTGATAACCTCTTATGAAATTTTGATAACTTCCCTATAAAATCTTGACTACATATATC
Found at i:73913 original size:22 final size:22
Alignment explanation
Indices: 73888--74010 Score: 108
Period size: 22 Copynumber: 5.6 Consensus size: 22
73878 AATCACATTT
73888 TGAAATTTTGATAGCCTCTTTA
1 TGAAATTTTGATAGCCTCTTTA
73910 TGAAATTTTGATAGCCTCTTTA
1 TGAAATTTTGATAGCCTCTTTA
* * *
73932 TAAAATTTTG-TTGACCCCTTTA
1 TGAAATTTTGATAG-CCTCTTTA
** * *
73954 TGAAATTCTT-ATAATCACATTA
1 TGAAATT-TTGATAGCCTCTTTA
* * *
73976 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAGCCTC-TTTA
73998 TGAAATTTTGATA
1 TGAAATTTTGATA
74011 ACAACGCTAT
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
21 4 0.05
22 73 0.89
23 5 0.06
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (22 bp):
TGAAATTTTGATAGCCTCTTTA
Found at i:73914 original size:44 final size:44
Alignment explanation
Indices: 73864--74006 Score: 114
Period size: 44 Copynumber: 3.2 Consensus size: 44
73854 GAAATACCAC
73864 TATGAAATTTTTGTAATCACATTTTGAAATTTTGATAGCCTCTT
1 TATGAAATTTTTGTAATCACATTTTGAAATTTTGATAGCCTCTT
** * * * *
73908 TATGAAA-TTTTGATAGCCTC-TTTATAAAATTTTG-TTGACCCCTT
1 TATGAAATTTTTG-TAATCACATTT-TGAAATTTTGATAG-CCTCTT
* * * * * *
73952 TATGAAATTCTTATAATCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTTGTAATCACATTTTGAAATTTTGATAGCCTC-TT
73997 T-TGAAATTTT
1 TATGAAATTTT
74007 GATAACAACG
Statistics
Matches: 73, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
43 10 0.14
44 55 0.75
45 8 0.11
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.46
Consensus pattern (44 bp):
TATGAAATTTTTGTAATCACATTTTGAAATTTTGATAGCCTCTT
Found at i:74011 original size:22 final size:22
Alignment explanation
Indices: 73974--74079 Score: 99
Period size: 22 Copynumber: 4.7 Consensus size: 22
73964 ATAATCACAT
* *
73974 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACATCGC
* *
73996 TTTGAAATTTTGATAACAACGC
1 TATGAAATTTTGATAACATCGC
*
74018 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAA-CATCGC
*
74040 TAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAA--C-ATCGC
*
74064 TATGAAATTTCGATAA
1 TATGAAATTTTGATAA
74080 TCACTCTTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
21 12 0.17
22 38 0.55
23 4 0.06
24 4 0.06
25 11 0.16
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACATCGC
Found at i:74026 original size:88 final size:88
Alignment explanation
Indices: 73864--74029 Score: 208
Period size: 88 Copynumber: 1.9 Consensus size: 88
73854 GAAATACCAC
* * * * * * ** *
73864 TATGAAATTTTTGTAATCACATTTTGAAATTTTGATAGCCTCTTTATGAAATTTTGATAGCCTCT
1 TATGAAATTCTTATAATCACATTATGAAATTTTGATAACCTCCTTATGAAATTTTGATAACAACG
*
73929 TTATAAAATTTTGTTGACCCCTT
66 CTATAAAATTTTGTTGACCCCTT
*
73952 TATGAAATTCTTATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAAC
1 TATGAAATTCTTATAATCACATTATGAAATTTTGATAACCTC-CTTATGAAATTTTGATAACAAC
*
74016 GCTATGAAATTTTG
65 GCTATAAAATTTTG
74030 ATAATCTTCC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
88 63 0.97
89 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (88 bp):
TATGAAATTCTTATAATCACATTATGAAATTTTGATAACCTCCTTATGAAATTTTGATAACAACG
CTATAAAATTTTGTTGACCCCTT
Found at i:74071 original size:25 final size:23
Alignment explanation
Indices: 73952--74081 Score: 98
Period size: 22 Copynumber: 5.8 Consensus size: 23
73942 TTGACCCCTT
73952 TATGAAATTCTT-ATAATCACAT--
1 TATGAAATT-TTGATAATC-CATCC
*
73974 TATGTAATTTTGATAA-CC-TCGC
1 TATGAAATTTTGATAATCCATC-C
* *
73996 TTTGAAATTTTGATAA--CAACGC
1 TATGAAATTTTGATAATCCATC-C
*
74018 TATGAAATTTTGATAAT-CTTCC
1 TATGAAATTTTGATAATCCATCC
74040 TAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAATCC-ATC-C
*
74064 TATGAAATTTCGATAATC
1 TATGAAATTTTGATAATC
74082 ACTCTTTGAG
Statistics
Matches: 89, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 17 0.19
22 49 0.55
23 4 0.04
24 4 0.04
25 13 0.15
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (23 bp):
TATGAAATTTTGATAATCCATCC
Found at i:74203 original size:44 final size:43
Alignment explanation
Indices: 74148--74253 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 43
74138 ACTTTTATAA
* * *
74148 CTATAAAATTTTGATAACCTCCCCATGAAA-TATTAGTAACCTC-
1 CTATGAAATTTTGATAACCACACCATGAAATTA-TA-TAACCTCG
* *
74191 CTAATGAAATTTTGTTAACCACACTATGAAATTCATATAACCTCG
1 CT-ATGAAATTTTGATAACCACACCATGAAATT-ATATAACCTCG
*
74236 CTATGACATTTTGATAAC
1 CTATGAAATTTTGATAAC
74254 ATCTTTGATA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
43 2 0.04
44 44 0.85
45 5 0.10
46 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCACACCATGAAATTATATAACCTCG
Found at i:74209 original size:22 final size:20
Alignment explanation
Indices: 74148--74253 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 20
74138 ACTTTTATAA
*
74148 CTATAAAATTTTGATAACCTCC
1 CTATGAAATTTTG-TAACCT-C
* *
74170 CCATGAAATATTAGTAACCTC
1 CTATGAAAT-TTTGTAACCTC
*
74191 CTAATGAAATTTTGTTAACCAC
1 CT-ATGAAATTTTG-TAACCTC
* *
74213 ACTATGAAATTCATATAACCTC
1 -CTATGAAATT-TTGTAACCTC
*
74235 GCTATGACATTTTGATAAC
1 -CTATGAAATTTTG-TAAC
74254 ATCTTTGATA
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
21 6 0.09
22 53 0.82
23 6 0.09
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (20 bp):
CTATGAAATTTTGTAACCTC
Found at i:74320 original size:22 final size:22
Alignment explanation
Indices: 74288--74352 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
74278 TTGTGATAAT
*
74288 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTCAA
* *
74310 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTCAA
*
74332 TAACCTGATCCTATGAAATTT
1 TAACC--AACCTATGAAATTT
74353 TGGTAACCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 24 0.67
24 12 0.33
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTCAA
Found at i:74360 original size:46 final size:44
Alignment explanation
Indices: 74295--74470 Score: 162
Period size: 44 Copynumber: 4.0 Consensus size: 44
74285 AATTAACCAC
*** * *
74295 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCACA-CTATGAAATTTTGATAACCT--T
*
74341 CCTATGAAATTTTGGTAACCACAATATGAAATTTTGATAA-CTT
1 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
*
74384 CCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-T
1 CC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
* ** * *
74428 CCTCATGAAATTATAATAACTATC-TTATGAAATTTTGATAACC
1 CCT-ATGAAATTTTGGTAACCA-CACTATGAAATTTTGATAACC
74471 ACATAGAGAC
Statistics
Matches: 111, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
43 4 0.04
44 70 0.63
45 4 0.04
46 32 0.29
47 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
Found at i:74371 original size:22 final size:22
Alignment explanation
Indices: 74343--74473 Score: 113
Period size: 22 Copynumber: 6.0 Consensus size: 22
74333 AACCTGATCC
*
74343 TATGAAATTTTGGTAACCACAA
1 TATGAAATTTTGATAACCACAA
** *
74365 TATGAAATTTTGATAACTTCCA
1 TATGAAATTTTGATAACCACAA
* *
74387 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCACAA
* * *
74409 TATGGAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCACAA
* * * *
74430 TCATGAAATTATAATAACTATC-T
1 T-ATGAAATTTTGATAACCA-CAA
74453 TATGAAATTTTGATAACCACA
1 TATGAAATTTTGATAACCACA
74474 TAGAGACAAG
Statistics
Matches: 85, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
21 3 0.04
22 80 0.94
23 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAA
Found at i:74542 original size:13 final size:13
Alignment explanation
Indices: 74524--74548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74514 ATTATGATTA
74524 AAAAAATAATTTT
1 AAAAAATAATTTT
74537 AAAAAATAATTT
1 AAAAAATAATTT
74549 AATAAGGAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAAATAATTTT
Found at i:74578 original size:19 final size:18
Alignment explanation
Indices: 74549--74585 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
74539 AAAATAATTT
74549 AATAAGGAATAATTAAAA
1 AATAAGGAATAATTAAAA
74567 AATAATGGAATAATTAAAA
1 AATAA-GGAATAATTAAAA
74586 TATTATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (18 bp):
AATAAGGAATAATTAAAA
Found at i:74711 original size:2 final size:2
Alignment explanation
Indices: 74704--74737 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
74694 TTCGTACTTT
74704 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
74738 TAATACTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:74803 original size:26 final size:26
Alignment explanation
Indices: 74768--74821 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
74758 TTCAAATTTC
* *
74768 TTTGTGTTTGGTAA-TACATTGAACTT
1 TTTGTATTTGATAATTACATTGAA-TT
74794 TTTGTATTTGATAATTACATTGAATT
1 TTTGTATTTGATAATTACATTGAATT
74820 TT
1 TT
74822 AGTTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.54
Consensus pattern (26 bp):
TTTGTATTTGATAATTACATTGAATT
Done.