Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007136.1 Corchorus capsularis cultivar CVL-1 contig07157, 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: 77414
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:4775 original size:19 final size:18
Alignment explanation
Indices: 4738--4812 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
4728 TCTAAATAAA
4738 TTCAATAATTCATATATT
1 TTCAATAATTCATATATT
4756 TTCAATCAATTCAT-TGA-T
1 TTCAAT-AATTCATAT-ATT
* * * *
4774 TT-ATTAATTTA-AGATA
1 TTCAATAATTCATATATT
*
4790 TTCATTAATTCATATATT
1 TTCAATAATTCATATATT
4808 TTCAA
1 TTCAA
4813 CCAATTGATA
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
15 1 0.02
16 7 0.16
17 10 0.23
18 17 0.40
19 8 0.19
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (18 bp):
TTCAATAATTCATATATT
Found at i:5945 original size:368 final size:369
Alignment explanation
Indices: 5263--5993 Score: 1446
Period size: 368 Copynumber: 2.0 Consensus size: 369
5253 TTCTTATAGA
5263 AACCTTTTTATGATACATTATTATTAAATTTATTATTTATTACAACTTTTATCCACATAGCATAT
1 AACCTTTTTATGATACATTATTATTAAATTTATTATTTATTACAACTTTTATCCACATAGCATAT
5328 AATGACACAACATTAAACAATTTGCAACTTTTTCAATATTAATCGTAACTTATTCAAAGTCAAAA
66 AATGACACAACATTAAACAATTTGCAACTTTTTCAATATTAATCGTAACTTATTCAAAGTCAAAA
5393 TTGTTATTAATTTAAATAACGAGACTTTCAGAGTTAGAGATATACATATATTTTACACCATAATG
131 TTGTTATTAATTTAAATAACGAGACTTTCAGAGTTAGAGATATACATATATTTTACACCATAATG
*
5458 AGAATTTTGATACCACAAGACTTCTTTAAAGTTGTTTCCAACTGCACCAAATTATTTTTAAACTT
196 AGAATTTTGATACCACAAGACTTCTTTAAAGTTGTTTCCAACTCCACCAAATTATTTTTAAACTT
5523 CTCTACAAATGGATAAGTTTTTTAGCTATTCAAATATTAAGGAAAACACAATACTTATGCGCTCA
261 CTCTACAAATGGATAAGTTTTTTAGCTATTCAAATATTAAGGAAAACACAATACTTATGCGCTCA
5588 AAGAGTTATATTGCATAAAAATAACTTTATCTACAAAATTAAGG
326 AAGAGTTATATTGCATAAAAATAACTTTATCTACAAAATTAAGG
5632 AACC-TTTTATGATACATTATTATTAAATTTATTATTTATTACAACTTTTATCCACATAGCATAT
1 AACCTTTTTATGATACATTATTATTAAATTTATTATTTATTACAACTTTTATCCACATAGCATAT
5696 AATGACACAACATTAAACAATTTGCAACTTTTTCAATATTAATCGTAACTTATTCAAAGTCAAAA
66 AATGACACAACATTAAACAATTTGCAACTTTTTCAATATTAATCGTAACTTATTCAAAGTCAAAA
5761 TTGTTATTAATTTAAATAACGAGACTTTCAGAGTTAGAGATATACATATATTTTACACCATAATG
131 TTGTTATTAATTTAAATAACGAGACTTTCAGAGTTAGAGATATACATATATTTTACACCATAATG
5826 AGAATTTTGATACCACAAGACTTCTTTAAAGTTGTTTCCAACTCCACCAAATTATTTTTAAACTT
196 AGAATTTTGATACCACAAGACTTCTTTAAAGTTGTTTCCAACTCCACCAAATTATTTTTAAACTT
5891 CTCTACAAATGGATAAGTTTTTTAGCTATTCAAATATTAAGGAAAACACAATACTTATGCGCTCA
261 CTCTACAAATGGATAAGTTTTTTAGCTATTCAAATATTAAGGAAAACACAATACTTATGCGCTCA
5956 AAGAGTTATATTGCATAAAAATAACTTTATCTACAAAA
326 AAGAGTTATATTGCATAAAAATAACTTTATCTACAAAA
5994 GTAACCGAAT
Statistics
Matches: 361, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
368 357 0.99
369 4 0.01
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (369 bp):
AACCTTTTTATGATACATTATTATTAAATTTATTATTTATTACAACTTTTATCCACATAGCATAT
AATGACACAACATTAAACAATTTGCAACTTTTTCAATATTAATCGTAACTTATTCAAAGTCAAAA
TTGTTATTAATTTAAATAACGAGACTTTCAGAGTTAGAGATATACATATATTTTACACCATAATG
AGAATTTTGATACCACAAGACTTCTTTAAAGTTGTTTCCAACTCCACCAAATTATTTTTAAACTT
CTCTACAAATGGATAAGTTTTTTAGCTATTCAAATATTAAGGAAAACACAATACTTATGCGCTCA
AAGAGTTATATTGCATAAAAATAACTTTATCTACAAAATTAAGG
Found at i:19382 original size:36 final size:37
Alignment explanation
Indices: 19303--19382 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 37
19293 CTCTTTTTAG
* *
19303 ATTAAGT-TCTTTATTGACTCTACTTAACTACCCTGG
1 ATTAAGTCTCTTTATTGACGCTACTTAACTACCCTGA
*
19339 ATTAAGTCT-TTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTCTCTTTATTGACGCTACTTAACTACCCTGA
19375 ATTAAGTC
1 ATTAAGTC
19383 CCTAACTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 39 0.98
37 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (37 bp):
ATTAAGTCTCTTTATTGACGCTACTTAACTACCCTGA
Found at i:19415 original size:37 final size:36
Alignment explanation
Indices: 19374--19612 Score: 153
Period size: 41 Copynumber: 6.2 Consensus size: 36
19364 AATTACCCTG
*
19374 AATTAAGTCCCTAACTTGACTTAATTTCCTTCCTTCA
1 AATTAAGTCCCTAACTT-ACTTAATTTCCTTCCTTGA
* * * *
19411 AATTAAGTCCTTAACTCTACTTAATTCCCTTCTTTGG
1 AATTAAGTCCCTAACT-TACTTAATTTCCTTCCTTGA
*
19448 AATCAAGT-CCT-A--TACTTAATTTCCTTCCTTGA
1 AATTAAGTCCCTAACTTACTTAATTTCCTTCCTTGA
*
19480 AATTAAGTCCTTTGCTCTACCTTACTTAATTTCCTTCCTTGA
1 AATTAAGT-C----C-CTAACTTACTTAATTTCCTTCCTTGA
** * * *
19522 AATTAAGTTTATGCTATAATTCACCTAATTTCCTTCCTTAA
1 AATTAAG--T-CCCTA-ACTT-ACTTAATTTCCTTCCTTGA
* * *
19563 AATTAAGTCTGTGCTATAATTCACCTAATTTCCTTCCTTGA
1 AATTAAGTC---CCTA-ACTT-ACTTAATTTCCTTCCTTGA
19604 AATTAAGTC
1 AATTAAGTC
19613 TGTGCTTTTC
Statistics
Matches: 163, Mismatches: 21, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
32 24 0.15
35 1 0.01
36 2 0.01
37 37 0.23
38 2 0.01
39 6 0.04
40 2 0.01
41 61 0.37
42 27 0.17
44 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.42
Consensus pattern (36 bp):
AATTAAGTCCCTAACTTACTTAATTTCCTTCCTTGA
Found at i:19464 original size:32 final size:32
Alignment explanation
Indices: 19392--19490 Score: 90
Period size: 32 Copynumber: 2.9 Consensus size: 32
19382 CCCTAACTTG
* * *
19392 ACTTAATTTCCTTCCTTCAAATTAAGTCCTTAACTCT
1 ACTTAATTCCCTTCCTTGAAATCAAGTCC-T-A---T
* *
19429 ACTTAATTCCCTTCTTTGGAATCAAGTCCTAT
1 ACTTAATTCCCTTCCTTGAAATCAAGTCCTAT
* *
19461 ACTTAATTTCCTTCCTTGAAATTAAGTCCT
1 ACTTAATTCCCTTCCTTGAAATCAAGTCCT
19491 TTGCTCTACC
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
32 27 0.51
35 1 0.02
36 1 0.02
37 24 0.45
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.42
Consensus pattern (32 bp):
ACTTAATTCCCTTCCTTGAAATCAAGTCCTAT
Found at i:19612 original size:41 final size:41
Alignment explanation
Indices: 19464--19618 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
19454 GTCCTATACT
* * * *
19464 TAATTTCCTTCCTTGAAATTAAGTCCTTTGCTCTACCTT-ACT
1 TAATTTCCTTCCTTGAAATTAAGT-CTGTGCTATA-ATTCACC
* *
19506 TAATTTCCTTCCTTGAAATTAAGTTTATGCTATAATTCACC
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTATAATTCACC
*
19547 TAATTTCCTTCCTTAAAATTAAGTCTGTGCTATAATTCACC
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTATAATTCACC
19588 TAATTTCCTTCCTTGAAATTAAGTCTGTGCT
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCT
19619 TTTCCTTACT
Statistics
Matches: 103, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
40 2 0.02
41 77 0.75
42 24 0.23
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Consensus pattern (41 bp):
TAATTTCCTTCCTTGAAATTAAGTCTGTGCTATAATTCACC
Found at i:19633 original size:41 final size:40
Alignment explanation
Indices: 19455--19633 Score: 196
Period size: 41 Copynumber: 4.3 Consensus size: 40
19445 TGGAATCAAG
* *
19455 TCCTATACTTAATTTCCTTCCTTGAAATTAAGTCCTTTGCTC
1 TCCT-TACTTAATTTCCTTCCTTGAAATTAAGT-CTGTGCTA
* *
19497 TACCTTACTTAATTTCCTTCCTTGAAATTAAGTTTATGCTA
1 T-CCTTACTTAATTTCCTTCCTTGAAATTAAGTCTGTGCTA
** * *
19538 TAATTCACCTAATTTCCTTCCTTAAAATTAAGTCTGTGCTA
1 TCCTT-ACTTAATTTCCTTCCTTGAAATTAAGTCTGTGCTA
** * *
19579 TAATTCACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTT
1 TCCTT-ACTTAATTTCCTTCCTTGAAATTAAGTCTGTGC-TA
19621 TCCTTACTTAATT
1 TCCTTACTTAATT
19634 ACCATGAATT
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.02
41 82 0.68
42 33 0.28
43 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.45
Consensus pattern (40 bp):
TCCTTACTTAATTTCCTTCCTTGAAATTAAGTCTGTGCTA
Found at i:19662 original size:41 final size:39
Alignment explanation
Indices: 19623--19761 Score: 187
Period size: 37 Copynumber: 3.6 Consensus size: 39
19613 TGTGCTTTTC
* *
19623 CTTACTTAATTACCATGAATTAAGTCCTTTGACTAC-TT
1 CTTACTTAATTACCATGAATTAAGTTCTTTGACTGCTTT
*
19661 -TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTTT
1 CTTACTTAATTACCATGAATTAAGTTCTTTGACTGCTTT
19699 C--ACTTAATTACCATGAATTAAGTTCTTTGACTGCTTTT
1 CTTACTTAATTACCATGAATTAAGTTCTTTGACTGC-TTT
* *
19737 ACTTTCTTAATTACCCTGAATTAAG
1 -CTTACTTAATTACCATGAATTAAG
19762 ACTCTATTCT
Statistics
Matches: 89, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
37 64 0.72
38 5 0.06
39 1 0.01
41 19 0.21
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.44
Consensus pattern (39 bp):
CTTACTTAATTACCATGAATTAAGTTCTTTGACTGCTTT
Found at i:19670 original size:37 final size:37
Alignment explanation
Indices: 19624--19740 Score: 198
Period size: 37 Copynumber: 3.2 Consensus size: 37
19614 GTGCTTTTCC
* *
19624 TTACTTAATTACCATGAATTAAGTCCTTTGACTACTT
1 TTACTTAATTACCATGAATTAAGTTCTTTGACTGCTT
*
19661 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
1 TTACTTAATTACCATGAATTAAGTTCTTTGACTGCTT
*
19698 TCACTTAATTACCATGAATTAAGTTCTTTGACTGCTT
1 TTACTTAATTACCATGAATTAAGTTCTTTGACTGCTT
19735 TTACTT
1 TTACTT
19741 TCTTAATTAC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.45
Consensus pattern (37 bp):
TTACTTAATTACCATGAATTAAGTTCTTTGACTGCTT
Found at i:19820 original size:71 final size:71
Alignment explanation
Indices: 19739--20062 Score: 515
Period size: 71 Copynumber: 4.6 Consensus size: 71
19729 CTGCTTTTAC
* * **
19739 TTTCTTAATTACCCTGAATTAAGACTCTATTCTTCTTAACCGCCCAACCTAGGACCTTGACTGTA
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
19804 CTTTCT
66 CTTTCT
* **
19810 TTTCTCAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAAGTTAGGACCTTGACTGTA
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
19875 CTTTCT
66 CTTTCT
* * * *
19881 TTTCTTACTTACCCTGAATTAAGTCTTTATTCTTCTTAATTGTCCAACCTAGGACCTTGACTGTA
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
*
19946 TTTTCT
66 CTTTCT
* *
19952 TTTCTCAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACTTAGGACCTTGACTGTA
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
20017 CTTTCT
66 CTTTCT
20023 TTTCTTAATTACCCTGAATCAAGAC-TTATTCTTCTTAATT
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATT
20063 ACCTTTATGT
Statistics
Matches: 230, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
70 15 0.07
71 215 0.93
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (71 bp):
TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
CTTTCT
Found at i:22326 original size:40 final size:40
Alignment explanation
Indices: 22274--22407 Score: 259
Period size: 40 Copynumber: 3.4 Consensus size: 40
22264 TCTTCAATTG
*
22274 TCTTCAAATCTTCAAAATATCTTCAATAACGAACTTCGCA
1 TCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCA
22314 TCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCA
1 TCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCA
22354 TCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCA
1 TCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCA
22394 TCTTCAAATCTTCA
1 TCTTCAAATCTTCA
22408 TTCTAAATGG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 93 1.00
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (40 bp):
TCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCA
Found at i:22358 original size:21 final size:21
Alignment explanation
Indices: 22332--22400 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
22322 TCTTCAAAAT
22332 ATCTTCAATCACGAACTTCGC
1 ATCTTCAATCACGAACTTCGC
* **
22353 ATCTTCAAATCTTC-AAAAT---
1 ATCTTC-AATC-ACGAACTTCGC
22372 ATCTTCAATCACGAACTTCGC
1 ATCTTCAATCACGAACTTCGC
22393 ATCTTCAA
1 ATCTTCAA
22401 ATCTTCATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 6 0.17
21 14 0.39
22 7 0.19
23 1 0.03
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (21 bp):
ATCTTCAATCACGAACTTCGC
Found at i:26738 original size:18 final size:18
Alignment explanation
Indices: 26700--26738 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
26690 TTAAGTGCTT
*
26700 AATTCTTCTTTACTAAGC
1 AATTCTTCTTTACTAACC
* *
26718 AATTTTTCTTTATTAACC
1 AATTCTTCTTTACTAACC
26736 AAT
1 AAT
26739 GTAAATATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.49
Consensus pattern (18 bp):
AATTCTTCTTTACTAACC
Found at i:27081 original size:22 final size:22
Alignment explanation
Indices: 27048--27231 Score: 158
Period size: 22 Copynumber: 8.4 Consensus size: 22
27038 ATTTGAAACC
* *
27048 GCCCAGAGACGCTTAAAAGTTT
1 GCCCTGAGACGCTTAAAAGTCT
* *
27070 GCGCTGAGACGCTTGAAAGTCT
1 GCCCTGAGACGCTTAAAAGTCT
* *
27092 ACCCTGAGACGCTTCAAAGTCT
1 GCCCTGAGACGCTTAAAAGTCT
**
27114 GCCCTGAGACATTTAAAAGTCT
1 GCCCTGAGACGCTTAAAAGTCT
* **
27136 -TCCTGAGACGCTTTGAAGTCT
1 GCCCTGAGACGCTTAAAAGTCT
* * *
27157 ACCCTGAGA-GGTCTGAAAGTCT
1 GCCCTGAGACGCT-TAAAAGTCT
*
27179 ACCCTGAGACGCTTGAAAA-TCT
1 GCCCTGAGACGCTT-AAAAGTCT
* * * *
27201 GCCCTGAGACACTTGAAGGACT
1 GCCCTGAGACGCTTAAAAGTCT
27223 GCCCTGAGA
1 GCCCTGAGA
27232 AGCTGAAGAA
Statistics
Matches: 130, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
21 20 0.15
22 105 0.81
23 5 0.04
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (22 bp):
GCCCTGAGACGCTTAAAAGTCT
Found at i:27102 original size:44 final size:44
Alignment explanation
Indices: 27053--27231 Score: 184
Period size: 44 Copynumber: 4.1 Consensus size: 44
27043 AAACCGCCCA
* * *
27053 GAGACGCTTAAAAGTTTGCGCTGAGACGCTTGAAAGTCTACCCT
1 GAGACGCTTAAAAGTCTGCCCTGAGACACTTGAAAGTCTACCCT
* * * *
27097 GAGACGCTTCAAAGTCTGCCCTGAGACATTTAAAAGTCT-TCCT
1 GAGACGCTTAAAAGTCTGCCCTGAGACACTTGAAAGTCTACCCT
** * **
27140 GAGACGCTTTGAAGTCTACCCTGAGA-GGTCTGAAAGTCTACCCT
1 GAGACGCTTAAAAGTCTGCCCTGAGACACT-TGAAAGTCTACCCT
* * *
27184 GAGACGCTTGAAAA-TCTGCCCTGAGACACTTGAAGGACTGCCCT
1 GAGACGCTT-AAAAGTCTGCCCTGAGACACTTGAAAGTCTACCCT
27228 GAGA
1 GAGA
27232 AGCTGAAGAA
Statistics
Matches: 109, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.01
43 34 0.31
44 71 0.65
45 3 0.03
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (44 bp):
GAGACGCTTAAAAGTCTGCCCTGAGACACTTGAAAGTCTACCCT
Found at i:27157 original size:65 final size:66
Alignment explanation
Indices: 27060--27188 Score: 176
Period size: 65 Copynumber: 2.0 Consensus size: 66
27050 CCAGAGACGC
*
27060 TTAAAAGTTTGCGCTGAGACGCTTGAAAGTCTACCCTGAGACGCT-TCAAAGTCTGCCCTGAGAC
1 TTAAAAGTTTGCGCTGAGACGCTTGAAAGTCTACCCTGAGA-GCTCTCAAAGTCTACCCTGAGAC
27124 AT
65 AT
* *
27126 TTAAAAGTCTT-C-CTGAGACGCTTTG-AAGTCTACCCTGAGAGGTCTGAAAGTCTACCCTGAGA
1 TTAAAAGT-TTGCGCTGAGACGC-TTGAAAGTCTACCCTGAGAGCTCTCAAAGTCTACCCTGAGA
27188 C
64 C
27189 GCTTGAAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
64 2 0.04
65 41 0.72
66 12 0.21
67 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.26
Consensus pattern (66 bp):
TTAAAAGTTTGCGCTGAGACGCTTGAAAGTCTACCCTGAGAGCTCTCAAAGTCTACCCTGAGACA
T
Found at i:39634 original size:129 final size:128
Alignment explanation
Indices: 39399--39635 Score: 411
Period size: 129 Copynumber: 1.8 Consensus size: 128
39389 TTTAATGGTG
39399 TGGAGTCCCTCCACAATTTGGTAGGAACTTCCACAAGCCAAAAGCCGTGACATTTACAATTCTGT
1 TGGAGTCCCTCCACAATTTGGTAGGAACTTCCACAAGCCAAAAGCCGTGACATTTACAATTCTGT
*
39464 GAATAATCAGGGTTCTTGCCTTTATACAATTGATGCAAATGAACGTTATGACAAGTTATAACA
66 GAATAATCAGGGTTCTTACCTTTATACAATTGATGCAAATGAACGTTATGACAAGTTATAACA
* * *
39527 TGGAGTCCCTCCACAATTTGGTAGGAATTTCCATAAGCCAAAAGCCGTGACCATTTACGATTCTG
1 TGGAGTCCCTCCACAATTTGGTAGGAACTTCCACAAGCCAAAAGCCGTGA-CATTTACAATTCTG
* *
39592 TGAATAATCAGGGTTCTTACCTTTATGCAATTGATGCGAATGAA
65 TGAATAATCAGGGTTCTTACCTTTATACAATTGATGCAAATGAA
39636 TGTCAAGTTA
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
128 48 0.47
129 54 0.53
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (128 bp):
TGGAGTCCCTCCACAATTTGGTAGGAACTTCCACAAGCCAAAAGCCGTGACATTTACAATTCTGT
GAATAATCAGGGTTCTTACCTTTATACAATTGATGCAAATGAACGTTATGACAAGTTATAACA
Found at i:41041 original size:36 final size:37
Alignment explanation
Indices: 40962--41041 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 37
40952 CTCTTTTTAG
* *
40962 ATTAAGT-TCTTTATTGACTCCACTTAACTACCCTGG
1 ATTAAGTCTCTTTATTGACGCCACTTAACTACCCTGA
* *
40998 ATTAAGTCT-TTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTCTCTTTATTGACGCCACTTAACTACCCTGA
41034 ATTAAGTC
1 ATTAAGTC
41042 CCTAACTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 38 0.97
37 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (37 bp):
ATTAAGTCTCTTTATTGACGCCACTTAACTACCCTGA
Found at i:41083 original size:32 final size:32
Alignment explanation
Indices: 41047--41150 Score: 120
Period size: 32 Copynumber: 3.1 Consensus size: 32
41037 AAGTCCCTAA
41047 CTTAACTTAATTTCCTTCCTTGAAATTAAGTC
1 CTTAACTTAATTTCCTTCCTTGAAATTAAGTC
* * *
41079 CTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
1 CTT-A----ACTTAATTTCCTTCCTTGAAATTAAGTC
41116 CTCT-ACTTAATTTCCTTCCTTGAAATTAAGTC
1 CT-TAACTTAATTTCCTTCCTTGAAATTAAGTC
41148 CTT
1 CTT
41151 TTTTTCTACC
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
31 1 0.02
32 30 0.50
33 1 0.02
37 27 0.45
38 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.07, T:0.42
Consensus pattern (32 bp):
CTTAACTTAATTTCCTTCCTTGAAATTAAGTC
Found at i:41085 original size:37 final size:37
Alignment explanation
Indices: 41033--41272 Score: 165
Period size: 41 Copynumber: 6.2 Consensus size: 37
41023 AATTACCCTG
*
41033 AATTAAGTCC-CTAACTTAACTTAATTTCCTTCCTTGA
1 AATTAAGTCCTATAACTT-ACTTAATTTCCTTCCTTGA
* *
41070 AATTAAGTCCT-TAACTCTACTTAATTCCCTTCCTTGG
1 AATTAAGTCCTATAACT-TACTTAATTTCCTTCCTTGA
*
41107 AATCAAGTCC--T--C-TACTTAATTTCCTTCCTTGA
1 AATTAAGTCCTATAACTTACTTAATTTCCTTCCTTGA
* *
41139 AATTAAGTCCTTTTTTTCTACCTTACTTAATTTCCTTCCTTGA
1 AATTAAGTCC------TATAACTTACTTAATTTCCTTCCTTGA
* *
41182 AATTAAGTCTATGCTATAA-TTCACCTAATTTCCTTCATTGA
1 AATTAAGTC----CTATAACTT-ACTTAATTTCCTTCCTTGA
* *
41223 AATTAAGTTTGTGCTATAA-TTCACCTAATTTCCTTCCTTGA
1 AATTAA----GTCCTATAACTT-ACTTAATTTCCTTCCTTGA
41264 AATTAAGTC
1 AATTAAGTC
41273 TGTGCTTTTC
Statistics
Matches: 168, Mismatches: 13, Indels: 44
0.75 0.06 0.20
Matches are distributed among these distances:
32 27 0.16
34 1 0.01
36 1 0.01
37 43 0.26
38 1 0.01
40 3 0.02
41 59 0.35
42 1 0.01
43 29 0.17
45 2 0.01
47 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (37 bp):
AATTAAGTCCTATAACTTACTTAATTTCCTTCCTTGA
Found at i:41223 original size:41 final size:41
Alignment explanation
Indices: 41166--41278 Score: 199
Period size: 41 Copynumber: 2.8 Consensus size: 41
41156 CTACCTTACT
*
41166 TAATTTCCTTCCTTGAAATTAAGTCTATGCTATAATTCACC
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTATAATTCACC
* *
41207 TAATTTCCTTCATTGAAATTAAGTTTGTGCTATAATTCACC
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTATAATTCACC
41248 TAATTTCCTTCCTTGAAATTAAGTCTGTGCT
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCT
41279 TTTCCTTACT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.43
Consensus pattern (41 bp):
TAATTTCCTTCCTTGAAATTAAGTCTGTGCTATAATTCACC
Found at i:41293 original size:41 final size:40
Alignment explanation
Indices: 41114--41293 Score: 173
Period size: 41 Copynumber: 4.3 Consensus size: 40
41104 TGGAATCAAG
* *
41114 TCCTCTACTTAATTTCCTTCCTTGAAATTAAGTCCTTTTTTTCTA
1 TCCT-TACTTAATTTCCTTCCTTGAAATTAAGT-C---TGTGCTA
*
41159 -CCTTACTTAATTTCCTTCCTTGAAATTAAGTCTATGCTA
1 TCCTTACTTAATTTCCTTCCTTGAAATTAAGTCTGTGCTA
** * * *
41198 TAATTCACCTAATTTCCTTCATTGAAATTAAGTTTGTGCTA
1 TCCTT-ACTTAATTTCCTTCCTTGAAATTAAGTCTGTGCTA
** * *
41239 TAATTCACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTT
1 TCCTT-ACTTAATTTCCTTCCTTGAAATTAAGTCTGTGC-TA
41281 TCCTTACTTAATT
1 TCCTTACTTAATT
41294 ACCATGAATT
Statistics
Matches: 118, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 5 0.04
40 2 0.02
41 75 0.64
42 5 0.04
43 28 0.24
44 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (40 bp):
TCCTTACTTAATTTCCTTCCTTGAAATTAAGTCTGTGCTA
Found at i:41330 original size:37 final size:37
Alignment explanation
Indices: 41284--41610 Score: 440
Period size: 37 Copynumber: 8.6 Consensus size: 37
41274 GTGCTTTTCC
* * *
41284 TTACTTAATTACCATGAATTAAGTCCTTTGACTACTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
*
41321 TTACTTAATTACCCTAAATTAAGTTCTTTGACTGCTCT
1 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCT-T
* * *
41359 TT-CTTAATTTCCATGAATTAAGTTCTTTGACTACTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
*
41395 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
*
41432 ATACTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
* * *
41469 TTACTTAATTACCCGGAATTAAGTTCTTTAACTACTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
41506 TTACTTTCTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
1 TTA----CTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
* *
41547 TCACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
41584 TTACTTTCTTAATTACCCTGAATTAAG
1 TTA----CTTAATTACCCTGAATTAAG
41611 ACTATATTCT
Statistics
Matches: 256, Mismatches: 24, Indels: 16
0.86 0.08 0.05
Matches are distributed among these distances:
36 3 0.01
37 197 0.77
38 3 0.01
41 53 0.21
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (37 bp):
TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTT
Found at i:41553 original size:78 final size:78
Alignment explanation
Indices: 41275--41610 Score: 490
Period size: 74 Copynumber: 4.4 Consensus size: 78
41265 ATTAAGTCTG
* * * * *
41275 TGCTTTTCCTTACTTAATTACCATGAATTAAGTCCTTTGACTACTTTTACTTAATTACCCTAAAT
1 TGCTTTTACTTTCTTAATTACCCTGAATTAAGTTCTTTGACTACTTTTACTTAATTACCCTGAAT
*
41340 TAAGTTCTTTGAC
66 TAAGTTCTTTAAC
* *
41353 TGC---T-CTTTCTTAATTTCCATGAATTAAGTTCTTTGACTACTTTTACTTAATTACCCTGAAT
1 TGCTTTTACTTTCTTAATTACCCTGAATTAAGTTCTTTGACTACTTTTACTTAATTACCCTGAAT
41414 TAAGTTCTTTAAC
66 TAAGTTCTTTAAC
* * *
41427 TGC--TTA--TACTTAATTACCCTGAATTAAGTTCTTTGACTGCTTTTACTTAATTACCCGGAAT
1 TGCTTTTACTTTCTTAATTACCCTGAATTAAGTTCTTTGACTACTTTTACTTAATTACCCTGAAT
41488 TAAGTTCTTTAAC
66 TAAGTTCTTTAAC
* * *
41501 TACTTTTACTTTCTTAATTACCCTGAATTAAGTTCTTTGACTGCTTTCACTTAATTACCCTGAAT
1 TGCTTTTACTTTCTTAATTACCCTGAATTAAGTTCTTTGACTACTTTTACTTAATTACCCTGAAT
41566 TAAGTTCTTTAAC
66 TAAGTTCTTTAAC
41579 TGCTTTTACTTTCTTAATTACCCTGAATTAAG
1 TGCTTTTACTTTCTTAATTACCCTGAATTAAG
41611 ACTATATTCT
Statistics
Matches: 237, Mismatches: 15, Indels: 12
0.90 0.06 0.05
Matches are distributed among these distances:
74 133 0.56
75 2 0.01
76 3 0.01
78 99 0.42
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.46
Consensus pattern (78 bp):
TGCTTTTACTTTCTTAATTACCCTGAATTAAGTTCTTTGACTACTTTTACTTAATTACCCTGAAT
TAAGTTCTTTAAC
Found at i:41669 original size:71 final size:71
Alignment explanation
Indices: 41588--41911 Score: 524
Period size: 71 Copynumber: 4.6 Consensus size: 71
41578 CTGCTTTTAC
* * **
41588 TTTCTTAATTACCCTGAATTAAGACTATATTCTTCTTAACCGCCCAACCTAGGACCTTGACTGTA
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
41653 CTTTCT
66 CTTTCT
* * *
41659 TTTCTCAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACTTAGGACCTTGAATGTA
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
41724 CTTTCT
66 CTTTCT
* *
41730 TTTCTTAATTACCCTGAATTAAGTC-TTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
*
41794 TTTTCT
66 CTTTCT
* * *
41800 TTTCTCAATTACCCTGAATCAAGACTTTATTCTTCTTCATTGCCCAACTTAGGACCTTGACTGTA
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
41865 CTTTCT
66 CTTTCT
41871 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATT
1 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATT
41912 ACCTTTATGT
Statistics
Matches: 231, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
70 64 0.28
71 167 0.72
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (71 bp):
TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
CTTTCT
Found at i:41780 original size:141 final size:141
Alignment explanation
Indices: 41588--41911 Score: 567
Period size: 141 Copynumber: 2.3 Consensus size: 141
41578 CTGCTTTTAC
**
41588 TTTCTTAATTACCCTGAATTAAGACTATATTCTTCTTAACCGCCCAACCTAGGACCTTGACTGTA
1 TTTCTTAATTACCCTGAATTAAGACT-TATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTA
41653 CTTTCTTTTCTCAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACTTAGGACCTTG
65 CTTTCTTTTCTCAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACTTAGGACCTTG
41718 AATGTACTTTCT
130 AATGTACTTTCT
* *
41730 TTTCTTAATTACCCTGAATTAAGTCTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTAT
1 TTTCTTAATTACCCTGAATTAAGACTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTAC
*
41795 TTTCTTTTCTCAATTACCCTGAATCAAGACTTTATTCTTCTTCATTGCCCAACTTAGGACCTTGA
66 TTTCTTTTCTCAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACTTAGGACCTTGA
*
41860 CTGTACTTTCT
131 ATGTACTTTCT
*
41871 TTTCTTAATTACCCTGAATCAAGACTTTATTCTTCTTAATT
1 TTTCTTAATTACCCTGAATTAAGAC-TTATTCTTCTTAATT
41912 ACCTTTATGT
Statistics
Matches: 173, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
141 133 0.77
142 40 0.23
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (141 bp):
TTTCTTAATTACCCTGAATTAAGACTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTAC
TTTCTTTTCTCAATTACCCTGAATCAAGACTTTATTCTTCTTAATTGCCCAACTTAGGACCTTGA
ATGTACTTTCT
Found at i:42607 original size:21 final size:21
Alignment explanation
Indices: 42574--42618 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42564 TATAAAAACA
* *
42574 CAGCTCCTATCTTTTTCTTCG
1 CAGCTCCTATCTTCTACTTCG
* *
42595 CAGCTTCTGTCTTCTACTTCG
1 CAGCTCCTATCTTCTACTTCG
42616 CAG
1 CAG
42619 AACCCTAACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.33, G:0.13, T:0.42
Consensus pattern (21 bp):
CAGCTCCTATCTTCTACTTCG
Found at i:46827 original size:36 final size:36
Alignment explanation
Indices: 46679--46830 Score: 107
Period size: 36 Copynumber: 4.3 Consensus size: 36
46669 TAAAATAAGT
* *
46679 AACTGAAGAACGACCACCCTTGATCATTCCGGAA-TG
1 AACTGAAGAACGACCACCCTCGATCATT-CTGAACTG
* * * *
46715 AACTAAAGAACGACCACCCTCGATCGTTCCG-ACTCA
1 AACTGAAGAACGACCACCCTCGATCATTCTGAACT-G
** * ** * * * *
46751 AACTGGGGAA-GACCGCCCAGGGTTA-ACTGAAAT-
1 AACTGAAGAACGACCACCCTCGATCATTCTGAACTG
46784 AAGCTGAAGAACGACCACCCTCGATCATTCTGAACTG
1 AA-CTGAAGAACGACCACCCTCGATCATTCTGAACTG
46821 AACTGAAGAA
1 AACTGAAGAA
46831 TAGACCAACA
Statistics
Matches: 83, Mismatches: 26, Indels: 14
0.67 0.21 0.11
Matches are distributed among these distances:
33 2 0.02
34 9 0.11
35 24 0.29
36 46 0.55
37 2 0.02
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (36 bp):
AACTGAAGAACGACCACCCTCGATCATTCTGAACTG
Found at i:49604 original size:18 final size:18
Alignment explanation
Indices: 49566--49604 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
49556 TTAAGTGCTT
*
49566 AATTCTTCTTTACTAAGC
1 AATTCTTCTTTACTAACC
* *
49584 AATTTTTCTTTATTAACC
1 AATTCTTCTTTACTAACC
49602 AAT
1 AAT
49605 GTAAATATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.49
Consensus pattern (18 bp):
AATTCTTCTTTACTAACC
Found at i:63614 original size:12 final size:12
Alignment explanation
Indices: 63597--63625 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
63587 TTAAGATCAT
63597 ATATAACATAAC
1 ATATAACATAAC
63609 ATATAACATAAC
1 ATATAACATAAC
63621 ATATA
1 ATATA
63626 TTAAAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (12 bp):
ATATAACATAAC
Found at i:73568 original size:17 final size:17
Alignment explanation
Indices: 73535--73569 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
73525 AATTTTATTA
* *
73535 TTTTATTGTTTATTTAT
1 TTTTATTGTTCACTTAT
73552 TTTTATTGTTCACTTAT
1 TTTTATTGTTCACTTAT
73569 T
1 T
73570 CACAAAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTTATTGTTCACTTAT
Found at i:75019 original size:17 final size:17
Alignment explanation
Indices: 74997--75036 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
74987 TGCATTTTAG
74997 TATTTACCATATTATTT
1 TATTTACCATATTATTT
75014 TATTTACCATATTATTT
1 TATTTACCATATTATTT
*
75031 TCTTTA
1 TATTTA
75037 GTTTAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTACCATATTATTT
Done.