Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019393.1 Corchorus olitorius cultivar O-4 contig19426, 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: 107150
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3436 original size:31 final size:31
Alignment explanation
Indices: 3391--3452 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
3381 GCGCTGCTTA
* *
3391 AAACTTGTGCACTCTAATTGGTTGGAAAGAT
1 AAACTTATGCACTCTAATTGGATGGAAAGAT
*
3422 AAACTTATGTACTCTAATTGGATGGAAAGAT
1 AAACTTATGCACTCTAATTGGATGGAAAGAT
3453 TGACGGCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (31 bp):
AAACTTATGCACTCTAATTGGATGGAAAGAT
Found at i:6847 original size:3 final size:3
Alignment explanation
Indices: 6832--6867 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
6822 ATTCCCCCAG
*
6832 AGA AGA TGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
6868 TGATGATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:8155 original size:12 final size:12
Alignment explanation
Indices: 8138--8165 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
8128 ACAAATAGTA
8138 AAAATCCCAATT
1 AAAATCCCAATT
8150 AAAATCCCAATT
1 AAAATCCCAATT
8162 AAAA
1 AAAA
8166 CCAGGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATCCCAATT
Found at i:8854 original size:22 final size:22
Alignment explanation
Indices: 8829--8875 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
8819 CGGAACTGAT
8829 CAAATCATAACACATGAACATG
1 CAAATCATAACACATGAACATG
* *
8851 CAAATTATAAGACATGAACATG
1 CAAATCATAACACATGAACATG
8873 CAA
1 CAA
8876 CTAGACACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (22 bp):
CAAATCATAACACATGAACATG
Found at i:23109 original size:17 final size:17
Alignment explanation
Indices: 23077--23111 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
23067 ATAATTATAT
* *
23077 TATTAATAATTTAGAAA
1 TATTAATAAATCAGAAA
23094 TATTAATAAATCAGAAA
1 TATTAATAAATCAGAAA
23111 T
1 T
23112 TATAAAAGCC
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:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (17 bp):
TATTAATAAATCAGAAA
Found at i:24201 original size:9 final size:9
Alignment explanation
Indices: 24187--24222 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
24177 TAAGTAAATG
24187 ATTGATGAT
1 ATTGATGAT
*
24196 ATTGATGGT
1 ATTGATGAT
24205 GATTGATGAT
1 -ATTGATGAT
24215 ATTGATGA
1 ATTGATGA
24223 ATGAAATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.42
Consensus pattern (9 bp):
ATTGATGAT
Found at i:24209 original size:19 final size:19
Alignment explanation
Indices: 24185--24221 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
24175 GTTAAGTAAA
24185 TGATTGATGATATTGATGG
1 TGATTGATGATATTGATGG
24204 TGATTGATGATATTGATG
1 TGATTGATGATATTGATG
24222 AATGAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TGATTGATGATATTGATGG
Found at i:27416 original size:18 final size:18
Alignment explanation
Indices: 27378--27419 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
27368 TTGTTAATAC
* **
27378 AAACTGCCAAAATCGCCA
1 AAACCGCCAAAATCGAAA
27396 AAACCGCCAAAATCGAAA
1 AAACCGCCAAAATCGAAA
27414 AAACCG
1 AAACCG
27420 ACCGAATCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.31, G:0.12, T:0.07
Consensus pattern (18 bp):
AAACCGCCAAAATCGAAA
Found at i:34639 original size:51 final size:55
Alignment explanation
Indices: 34584--34687 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 55
34574 GACCAACAAA
*
34584 TTCAAGAGGTTTTCTAT-TT-T-AGT-ATTAGATTATCAAGGATAACAACACGTG
1 TTCAAGAGGTTTTCTATATTATAAGTAATTAGATTATCAAAGATAACAACACGTG
*
34635 TTCAAGAGGTTTTCTATATTATAATTAGATTAGATTATCAAAGATAACAACAC
1 TTCAAGAGGTTTTCTATATTATAAGTA-ATTAGATTATCAAAGATAACAACAC
34688 ATGGGGTTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
51 17 0.37
52 2 0.04
53 1 0.02
54 2 0.04
56 24 0.52
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (55 bp):
TTCAAGAGGTTTTCTATATTATAAGTAATTAGATTATCAAAGATAACAACACGTG
Found at i:39906 original size:3 final size:3
Alignment explanation
Indices: 39898--39923 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39888 TTGATTTTTT
39898 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
39924 AGGTACTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40191 original size:2 final size:2
Alignment explanation
Indices: 40184--40228 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
40174 GCAACCTATA
40184 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
40226 AC A
1 AC A
40229 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40233 original size:2 final size:2
Alignment explanation
Indices: 40228--40258 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40218 ACACACACAC
40228 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40259 CAACAAGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:43877 original size:21 final size:22
Alignment explanation
Indices: 43853--43893 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
43843 GTGTATAATA
*
43853 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
43874 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
43894 CAAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:44550 original size:16 final size:16
Alignment explanation
Indices: 44529--44563 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
44519 CGACCACATT
44529 GAACTCCTACTAATTC
1 GAACTCCTACTAATTC
*
44545 GAACTCCTACTATTTC
1 GAACTCCTACTAATTC
44561 GAA
1 GAA
44564 TTCAAGTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (16 bp):
GAACTCCTACTAATTC
Found at i:48570 original size:22 final size:22
Alignment explanation
Indices: 48545--48595 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
48535 CCTCCATATG
*
48545 AAATTTTGTTAAATTCCCTATA
1 AAATTTTGTCAAATTCCCTATA
**
48567 AAATTTTGTCACGTTCCCTATA
1 AAATTTTGTCAAATTCCCTATA
48589 AAATTTT
1 AAATTTT
48596 AATAATTACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (22 bp):
AAATTTTGTCAAATTCCCTATA
Found at i:48614 original size:22 final size:22
Alignment explanation
Indices: 48589--48886 Score: 155
Period size: 22 Copynumber: 13.6 Consensus size: 22
48579 GTTCCCTATA
* **
48589 AAATTTTAATAATTACCTAATG
1 AAATTTTGATAACCACCTAATG
*
48611 AAATTTTGATAACCACCTTATG
1 AAATTTTGATAACCACCTAATG
* *
48633 AAATTTTGATAACCTCCCAATG
1 AAATTTTGATAACCACCTAATG
* * * *
48655 AAATGTTGGTAAACGCACATTATG
1 AAATTTTGAT-AAC-CACCTAATG
* * *
48679 AAATTTTGATAACCTTCC-GATA
1 AAATTTTGATAACC-ACCTAATG
* * * * * *
48701 AAATATCGGTAATCACATTATG
1 AAATTTTGATAACCACCTAATG
* ** *
48723 AAATTTTGATAAACATATCATG
1 AAATTTTGATAACCACCTAATG
* *
48745 AAATTGTGAT-ACCTCACT-ATG
1 AAATTTTGATAACCAC-CTAATG
* *
48766 AAAATTTT-ATAAACCTCCCT-ATA
1 -AAATTTTGAT-AACC-ACCTAATG
* *
48789 AAATTTTGATAACCTCC-ATTTG
1 AAATTTTGATAACCACCTA-ATG
*
48811 AAATTTTGAT-A--ACCTCATG
1 AAATTTTGATAACCACCTAATG
* *
48830 AAATTTTGAAAACCACCTCATG
1 AAATTTTGATAACCACCTAATG
* *
48852 AAATTTTGATAACCATCTTATG
1 AAATTTTGATAACCACCTAATG
48874 AAATTTTGATAAC
1 AAATTTTGATAAC
48887 ATCCCTATAA
Statistics
Matches: 209, Mismatches: 51, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.06
20 1 0.00
21 11 0.05
22 154 0.74
23 16 0.08
24 14 0.07
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCACCTAATG
Found at i:48637 original size:44 final size:44
Alignment explanation
Indices: 48589--48886 Score: 179
Period size: 44 Copynumber: 6.8 Consensus size: 44
48579 GTTCCCTATA
* *
48589 AAATTTTAATAATTACCTAATGAAATTTTGATAACCACCTTATG
1 AAATTTTGATAACTACCTAATGAAATTTTGATAACCACCTTATG
* * * *
48633 AAATTTTGATAACCT-CCCAATGAAATGTTGGTAAACGCACATTATG
1 AAATTTTGATAA-CTACCTAATGAAATTTTGAT-AAC-CACCTTATG
* * * * * * * *
48679 AAATTTTGATAACCTTCC-GATAAAATATCGGTAATCACATTATG
1 AAATTTTGATAA-CTACCTAATGAAATTTTGATAACCACCTTATG
* * *
48723 AAATTTTGATAAACATA--TCATGAAATTGTGAT-ACCTCAC-TATG
1 AAATTTTGAT-AAC-TACCTAATGAAATTTTGATAACCAC-CTTATG
* * *
48766 AAAATTTT-ATAAACCTCCCT-ATAAAATTTTGATAACCTCCATT-TG
1 -AAATTTTGAT-AA-CTACCTAATGAAATTTTGATAACCACC-TTATG
* * *
48811 AAATTTTGAT-A--ACCTCATGAAATTTTGAAAACCACCTCATG
1 AAATTTTGATAACTACCTAATGAAATTTTGATAACCACCTTATG
* * *
48852 AAATTTTGATAACCATCTTATGAAATTTTGATAAC
1 AAATTTTGATAACTACCTAATGAAATTTTGATAAC
48887 ATCCCTATAA
Statistics
Matches: 201, Mismatches: 32, Indels: 42
0.73 0.12 0.15
Matches are distributed among these distances:
40 4 0.02
41 29 0.14
42 1 0.00
43 14 0.07
44 98 0.49
45 19 0.09
46 34 0.17
47 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (44 bp):
AAATTTTGATAACTACCTAATGAAATTTTGATAACCACCTTATG
Found at i:48851 original size:107 final size:107
Alignment explanation
Indices: 48720--48912 Score: 261
Period size: 107 Copynumber: 1.8 Consensus size: 107
48710 TAATCACATT
* *
48720 ATGAAATTTTGATAAACATATCATGAAATTGTGAT-ACC-TCACTATGAAAATTTT-ATAAACCT
1 ATGAAATTTTGATAAACACATCATGAAATTGTGATAACCATC-CTATG-AAATTTTGAT-AACAT
48782 CCCTATAAA-ATTTTGATAACCTCCATTTGAAATTTTGATAACCTC
63 CCCTATAAACATTTT-ATAACCTCCATTTGAAATTTTGATAACCTC
* * *
48827 ATGAAATTTTGA-AAACCACCTCATGAAATTTTGATAACCATCTTATGAAATTTTGATAACATCC
1 ATGAAATTTTGATAAA-CACATCATGAAATTGTGATAACCATCCTATGAAATTTTGATAACATCC
48891 CTATAAACATTTTATAACCTCC
65 CTATAAACATTTTATAACCTCC
48913 CCATAAAATT
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
106 3 0.04
107 57 0.75
108 14 0.18
109 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (107 bp):
ATGAAATTTTGATAAACACATCATGAAATTGTGATAACCATCCTATGAAATTTTGATAACATCCC
TATAAACATTTTATAACCTCCATTTGAAATTTTGATAACCTC
Found at i:48922 original size:44 final size:43
Alignment explanation
Indices: 48545--48924 Score: 129
Period size: 44 Copynumber: 8.7 Consensus size: 43
48535 CCTCCATATG
* ** * *
48545 AAATTTTGTTAAATTCCCTATAAAATTTTG-TCACGTTCCCTATA
1 AAATTTTGATAACCTCCC-ATAAAATTTTGATAAC-ATCCCTATA
* * * * * *
48589 AAATTTTAATAA-TTACCTAATGAAATTTTGATAACCA-CCTTATG
1 AAATTTTGATAACCT-CC-CATAAAATTTTGATAA-CATCCCTATA
* * * *
48633 AAATTTTGATAACCTCCCAATGAAATGTTGGTAA-A-CGCACATTATG
1 AAATTTTGATAACCTCCC-ATAAAATTTTGATAACATC-C-C--TATA
* * * * ** *
48679 AAATTTTGATAACCTTCCGATAAAATATCGGTAATCA-CATTATG
1 AAATTTTGATAACC-TCCCATAAAATTTTGATAA-CATCCCTATA
* ** * * * *
48723 AAATTTTGATAAACATATCATGAAATTGTGAT-ACCTCACTATGA
1 AAATTTTGAT-AACCTCCCATAAAATTTTGATAACATCCCTAT-A
* * * *
48767 AAATTTT-ATAAACCTCCCTATAAAATTTTGATAACCTCCATTTG
1 AAATTTTGAT-AACCTCCC-ATAAAATTTTGATAACATCCCTATA
* * *
48811 AAATTTTGATAACCT--CATGAAATTTTGA-AA-ACCACCTCATG
1 AAATTTTGATAACCTCCCATAAAATTTTGATAACATC-CCT-ATA
** *
48852 AAATTTTGATAACCATCTTATGAAATTTTGATAACATCCCTATA
1 AAATTTTGATAACC-TCCCATAAAATTTTGATAACATCCCTATA
48896 AACATTTT-ATAACCTCCCCATAAAATTTT
1 AA-ATTTTGATAACCT-CCCATAAAATTTT
48925 ATTAACCTCC
Statistics
Matches: 256, Mismatches: 52, Indels: 56
0.70 0.14 0.15
Matches are distributed among these distances:
39 1 0.00
40 4 0.02
41 27 0.11
42 5 0.02
43 18 0.07
44 138 0.54
45 25 0.10
46 33 0.13
47 3 0.01
48 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.36
Consensus pattern (43 bp):
AAATTTTGATAACCTCCCATAAAATTTTGATAACATCCCTATA
Found at i:48930 original size:22 final size:21
Alignment explanation
Indices: 48766--48934 Score: 94
Period size: 22 Copynumber: 7.8 Consensus size: 21
48756 CCTCACTATG
*
48766 AAAATTTTATAAACCTCCCTAT
1 AAAATTTTAT-AACCTCCCCAT
***
48788 AAAATTTTGATAACCTCCATTT
1 AAAATTTT-ATAACCTCCCCAT
*
48810 GAAATTTTGATAACCT---CAT
1 AAAATTTT-ATAACCTCCCCAT
* * * *
48829 GAAATTTTGAAAACCACCTCAT
1 AAAATTTT-ATAACCTCCCCAT
* **
48851 GAAATTTTGATAACCAT-CTTAT
1 AAAATTTT-ATAACC-TCCCCAT
* * *
48873 GAAATTTTGATAACATCCCTAT
1 AAAATTTT-ATAACCTCCCCAT
48895 AAACATTTTATAACCTCCCCAT
1 AAA-ATTTTATAACCTCCCCAT
48917 AAAATTTTATTAACCTCC
1 AAAATTTTA-TAACCTCC
48935 TACGGATTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.12
21 7 0.06
22 95 0.77
23 7 0.06
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAATTTTATAACCTCCCCAT
Found at i:49153 original size:22 final size:21
Alignment explanation
Indices: 49099--49154 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
49089 GAGAACCACT
*
49099 CTATCAAATTTTATTAATCTCA
1 CTAT-AAATTTTATAAATCTCA
49121 CTATAAATTTTGATAAAT-TCA
1 CTATAAATTTT-ATAAATCTCA
*
49142 TTATGAAATTTTA
1 CTAT-AAATTTTA
49155 GTTACCACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (21 bp):
CTATAAATTTTATAAATCTCA
Found at i:49236 original size:22 final size:22
Alignment explanation
Indices: 49208--49348 Score: 110
Period size: 22 Copynumber: 6.5 Consensus size: 22
49198 CCATATTATA
49208 AAATTTTGATAATCACACTATG
1 AAATTTTGATAATCACACTATG
* * *
49230 AAATTTTGATAATCTCCCTCTG
1 AAATTTTGATAATCACACTATG
* * * * *
49252 AAATTTCGATAACCTCCCCATG
1 AAATTTTGATAATCACACTATG
* * *
49274 AGATTTTGTTAA-C-CTCTATG
1 AAATTTTGATAATCACACTATG
* * *
49294 AAATTGTGATTATTACACTATG
1 AAATTTTGATAATCACACTATG
*
49316 AAATTTTGGTAA-CGACACT-TG
1 AAATTTTGATAATC-ACACTATG
49337 AAATTTTGATAA
1 AAATTTTGATAA
49349 ACTCACTCTA
Statistics
Matches: 93, Mismatches: 23, Indels: 7
0.76 0.19 0.06
Matches are distributed among these distances:
20 13 0.14
21 14 0.15
22 66 0.71
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAATCACACTATG
Found at i:49280 original size:66 final size:66
Alignment explanation
Indices: 49208--49621 Score: 261
Period size: 66 Copynumber: 6.2 Consensus size: 66
49198 CCATATTATA
* *
49208 AAATTTTGATAATCACACTATGAAATTTTGATAATCTCCCTCTGAAATTTCGATAACCTCCCCAT
1 AAATTTTGATAATCACACTATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCCCCAT
49273 G
66 G
* * * * * * * ** * *
49274 AGATTTTGTTAA-C-CTCTATGAAATTGTGATTAT-TACACTATGAAATTTTGGTAA-CGACACT
1 AAATTTTGATAATCACACTATGAAATTTTGATAATCT-CCCTATGAAATTTTGATAACCTCCCCA
49335 TG
65 TG
* * * * *
49337 AAATTTTGATAAACTCACTCTATCTCACTATGCAATTTTTATAAGCACACTATGAAATTTTGATA
1 AAATTTTGAT--A---A-TC-A---CACTATGAAATTTTGATAATCTCCCTATGAAATTTTGATA
* * *
49402 ATCTTCCTATG
56 ACCTCCCCATG
* * * *
49413 AAATTTTGATAACCTC-CA-TATAAAATTTTGATAATCGCCCTATGAAATTTTGTTAACCTCCCT
1 AAATTTTGATAA--TCACACTATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCCCC
49476 ATG
64 ATG
* * * * * * *
49479 AAATTTTGATAACCAGAGTATGAAATTTT-AGTAATCCCCCTGTGAAATTCTGATAACCTTCCCA
1 AAATTTTGATAATCACACTATGAAATTTTGA-TAATCTCCCTATGAAATTTTGATAACCTCCCCA
49543 TG
65 TG
* * * * * * * **
49545 -AATTTCGATAACCTC-CTTATGAAATTTTAATAACCTCCATATGAAATTTTGATAACATCCTTA
1 AAATTTTGATAATCACAC-TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCCCCA
49608 TG
65 TG
49610 AAATTTTGATAA
1 AAATTTTGATAA
49622 CATCCCATGA
Statistics
Matches: 266, Mismatches: 60, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
63 14 0.05
64 33 0.12
65 53 0.20
66 111 0.42
67 2 0.01
68 1 0.00
70 1 0.00
71 1 0.00
72 3 0.01
74 1 0.00
75 32 0.12
76 14 0.05
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (66 bp):
AAATTTTGATAATCACACTATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCCCCAT
G
Found at i:49411 original size:22 final size:21
Alignment explanation
Indices: 49386--49778 Score: 260
Period size: 22 Copynumber: 18.0 Consensus size: 21
49376 TATAAGCACA
*
49386 CTATGAAATTTTGATAATCTTC
1 CTATGAAATTTTGATAA-CCTC
49408 CTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACCTC
*
49429 CATATAAAATTTTGATAATCGC-C
1 C-TATGAAATTTTGATAA-C-CTC
*
49452 CTATGAAATTTTGTTAACCTCC
1 CTATGAAATTTTGATAACCT-C
**
49474 CTATGAAATTTTGATAACCAGA
1 CTATGAAATTTTGATAACC-TC
* *
49496 GTATGAAATTTT-AGTAATCCCC
1 CTATGAAATTTTGA-TAA-CCTC
* *
49518 CTGTGAAATTCTGATAACCTTC
1 CTATGAAATTTTGATAACC-TC
* *
49540 CCATG-AATTTCGATAACCTC
1 CTATGAAATTTTGATAACCTC
*
49560 CTTATGAAATTTTAATAACCTC
1 C-TATGAAATTTTGATAACCTC
*
49582 CATATGAAATTTTGATAACATC
1 C-TATGAAATTTTGATAACCTC
*
49604 CTTATGAAATTTTGATAACATC
1 C-TATGAAATTTTGATAACCTC
* * *
49626 CCATGAACTTGTGATAA-CTAC
1 CTATGAAATTTTGATAACCT-C
* * *
49647 ACTATAAAATTTTAATATCCTAC
1 -CTATGAAATTTTGATAACCT-C
* * * *
49670 CTATTAAAGTTGGGTAACCTC
1 CTATGAAATTTTGATAACCTC
* *
49691 ACTATAAAATTTTGATAACCAC
1 -CTATGAAATTTTGATAACCTC
* * *
49713 ACAATAAAATTTTGA-AAACTAC
1 -CTATGAAATTTTGATAACCT-C
* *
49735 ACTATAAAATTTT-AGTAACCAC
1 -CTATGAAATTTTGA-TAACCTC
*
49757 ACAATG-AATTTTGATAACCTC
1 -CTATGAAATTTTGATAACCTC
49778 C
1 C
49779 AAAATTAAAA
Statistics
Matches: 296, Mismatches: 55, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
20 6 0.02
21 53 0.18
22 223 0.75
23 13 0.04
24 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:49777 original size:87 final size:85
Alignment explanation
Indices: 49566--49778 Score: 205
Period size: 87 Copynumber: 2.4 Consensus size: 85
49556 CCTCCTTATG
* * * * *
49566 AAATTTTAATAACCTCCATATGAAATTTTGATAACATCCTTATGAAATTTTGATAACATCCCATG
1 AAATTTTAATAACCACCA-ATG-AATTTTGATAACCTCCTTATAAAATTTTGATAACATCCAATA
* *
49631 AACTTGTGATAACTACACTATA
64 AAATTGTGAAAACTACACTATA
* * * * * *
49653 AAATTTTAATATCCTACCTATTAAAGTTGGGTAACCTCAC-TATAAAATTTTGATAACCA-CACA
1 AAATTTTAATAACC-ACC-AATGAATTTTGATAACCTC-CTTATAAAATTTTGATAA-CATC-CA
*
49716 ATAAAATTTTGAAAACTACACTATA
61 ATAAAATTGTGAAAACTACACTATA
*
49741 AAATTTTAGTAACCACACAATGAATTTTGATAACCTCC
1 AAATTTTAATAACCAC-CAATGAATTTTGATAACCTCC
49779 AAAATTAAAA
Statistics
Matches: 99, Mismatches: 21, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
86 1 0.01
87 56 0.57
88 41 0.41
89 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.34
Consensus pattern (85 bp):
AAATTTTAATAACCACCAATGAATTTTGATAACCTCCTTATAAAATTTTGATAACATCCAATAAA
ATTGTGAAAACTACACTATA
Found at i:58098 original size:31 final size:31
Alignment explanation
Indices: 58060--58118 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
58050 AATATGACTG
*
58060 AAATCTCAATTTGGTACCAAACCTTTTAAGA
1 AAATCTCAACTTGGTACCAAACCTTTTAAGA
*
58091 AAATCTCAACTTGGTACGAAACCTTTTA
1 AAATCTCAACTTGGTACCAAACCTTTTA
58119 TTTCGTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.32
Consensus pattern (31 bp):
AAATCTCAACTTGGTACCAAACCTTTTAAGA
Found at i:59837 original size:24 final size:24
Alignment explanation
Indices: 59828--59875 Score: 82
Period size: 22 Copynumber: 2.1 Consensus size: 24
59818 TATATATATA
59828 TGTACATATATATATAGTTAAAAT
1 TGTACATATATATATAGTTAAAAT
59852 TGTAC--ATATATATAGTTAAAAT
1 TGTACATATATATATAGTTAAAAT
59874 TG
1 TG
59876 GTAATGCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.79
24 5 0.21
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (24 bp):
TGTACATATATATATAGTTAAAAT
Found at i:59862 original size:2 final size:2
Alignment explanation
Indices: 59805--59843 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
59795 AAACTTGTGG
* *
59805 AT AT AT AT AT AT AT AT AT AT AT AT GT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59844 GTTAAAATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:68844 original size:28 final size:28
Alignment explanation
Indices: 68813--68866 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
68803 ATGTTTCAAA
*
68813 TTTTAGTAGGGTTAAAATCTTGGGTCAT
1 TTTTAGTAGGGATAAAATCTTGGGTCAT
**
68841 TTTTTTTAGGGATAAAATCTTGGGTC
1 TTTTAGTAGGGATAAAATCTTGGGTC
68867 TTGTTGTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (28 bp):
TTTTAGTAGGGATAAAATCTTGGGTCAT
Found at i:74540 original size:107 final size:107
Alignment explanation
Indices: 74354--74620 Score: 351
Period size: 107 Copynumber: 2.5 Consensus size: 107
74344 TTTTTGCCAG
* * *
74354 AACTAATTTCACTAAGTTTAGTGTCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAA
1 AACTAATTTCACTAAGTTTAGGGCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAA
*
74419 ATTAATAATTTATTGTTATAAAAATTT-ATAAATAAAATACAA
66 ATTAATAATTTATTGTTAT-AAAATTTAAGAAATAAAATACAA
* **
74461 AACTAATTTCACTAAATTTAGGGCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATG
1 AACTAATTTCACTAAGTTTAGGGCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAA
** * * *
74526 ATTAATAATTTATTGTTATAGGATTTAAGAAATATAATATAT
66 ATTAATAATTTATTGTTATAAAATTTAAGAAATAAAATACAA
* * ** *
74568 AACTAA-TTCACTAAGTTTA-GCCCCAATTAAAATTAAAATTTTATTTTAAGGGT
1 AACTAATTTCACTAAGTTTAGGGCCAAATTAAAATTTTATTTTTATTTTAAGGGT
74621 TAGAAAAATT
Statistics
Matches: 141, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
105 29 0.21
106 17 0.12
107 95 0.67
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (107 bp):
AACTAATTTCACTAAGTTTAGGGCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAA
ATTAATAATTTATTGTTATAAAATTTAAGAAATAAAATACAA
Found at i:76232 original size:53 final size:54
Alignment explanation
Indices: 76110--76236 Score: 211
Period size: 54 Copynumber: 2.4 Consensus size: 54
76100 CATAATTACT
* * * *
76110 TTGTTAATTTGTCTTTATATCATTAAATCATTTGTAATTTTATTTTTATATGAG
1 TTGTAAATTTGTCATTACATCATTAAATCACTTGTAATTTTATTTTTATATGAG
76164 TTGTAAATTTGTCATTACATCATTAAATCACTTGTAATTTTA-TTTTATATGAG
1 TTGTAAATTTGTCATTACATCATTAAATCACTTGTAATTTTATTTTTATATGAG
76217 TTGTAAATTTGTCATTACAT
1 TTGTAAATTTGTCATTACAT
76237 GCAATTAATG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
53 31 0.45
54 38 0.55
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (54 bp):
TTGTAAATTTGTCATTACATCATTAAATCACTTGTAATTTTATTTTTATATGAG
Found at i:76257 original size:54 final size:53
Alignment explanation
Indices: 76110--76265 Score: 199
Period size: 54 Copynumber: 2.9 Consensus size: 53
76100 CATAATTACT
* * * * *
76110 TTGTTAATTTGTCTTTATATCATTAAATCATTTGTAATTTTATTTTTATATGAG
1 TTGTAAATTTGTCATTACATCATTAAATCACTTGAAATTTTA-TTTTATATGAG
*
76164 TTGTAAATTTGTCATTACATCATTAAATCACTTGTAATTTTATTTTATATGAG
1 TTGTAAATTTGTCATTACATCATTAAATCACTTGAAATTTTATTTTATATGAG
*
76217 TTGTAAATTTGTCATTACATGCAATT-AATGACTTGAAATTTGT-TTTTAT
1 TTGTAAATTTGTCATTACAT-C-ATTAAATCACTTGAAATTT-TATTTTAT
76266 CTCATTTAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
53 31 0.33
54 58 0.62
55 4 0.04
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (53 bp):
TTGTAAATTTGTCATTACATCATTAAATCACTTGAAATTTTATTTTATATGAG
Found at i:82562 original size:42 final size:42
Alignment explanation
Indices: 82503--82583 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
82493 GCTAAGTCTT
* *
82503 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACCCAACTAAAATCATA
*
82545 GAAAATTCTTTGTAAATTAAGAAATACCCAACTAAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACCCAACTAAAATC
82584 CTGATCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.28
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACCCAACTAAAATCATA
Found at i:84587 original size:20 final size:20
Alignment explanation
Indices: 84559--84596 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
84549 AAGGTGCAAC
84559 ATCTGCAAACCAAACGGGTG
1 ATCTGCAAACCAAACGGGTG
*
84579 ATCTTCAAACCAAACGGG
1 ATCTGCAAACCAAACGGG
84597 GTGGAATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCTGCAAACCAAACGGGTG
Found at i:85181 original size:29 final size:29
Alignment explanation
Indices: 85148--85223 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
85138 ACTTGTAGCG
* *
85148 TTTGGACGTTTTGCCCTATGAACTTCAAT
1 TTTGGACATTTTGCCCCATGAACTTCAAT
* * *
85177 TTTGGATATTTTACCCCCTGAACTTCAAT
1 TTTGGACATTTTGCCCCATGAACTTCAAT
*
85206 TTTGGGACTTTTTGCCCC
1 TTT-GGACATTTTGCCCC
85224 TTCAAGTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 27 0.71
30 11 0.29
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCATGAACTTCAAT
Found at i:90502 original size:21 final size:21
Alignment explanation
Indices: 90452--90509 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
90442 TTCACTAGTG
90452 AGTTTGGTATTATTGA-T--T
1 AGTTTGGTATTATTGACTGCT
90470 -GTTATGG-A-TATTGACTGCT
1 AGTT-TGGTATTATTGACTGCT
90489 AGTTTGGTATTATTGACTGCT
1 AGTTTGGTATTATTGACTGCT
90510 CTTTTTCTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
16 6 0.18
17 5 0.15
18 3 0.09
19 4 0.12
20 4 0.12
21 11 0.33
ACGTcount: A:0.21, C:0.07, G:0.24, T:0.48
Consensus pattern (21 bp):
AGTTTGGTATTATTGACTGCT
Found at i:96321 original size:2 final size:2
Alignment explanation
Indices: 96314--96347 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
96304 CAAATGAATA
96314 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
96348 TAAGTTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:104994 original size:27 final size:27
Alignment explanation
Indices: 104955--105006 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
104945 TTTTGTTTTT
**
104955 TTTTTTTTTACAAAATAATCACTTATG
1 TTTTTTTAGACAAAATAATCACTTATG
* *
104982 TTTTTTTAGACAAATTAATCCCTTA
1 TTTTTTTAGACAAAATAATCACTTA
105007 CATTTCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (27 bp):
TTTTTTTAGACAAAATAATCACTTATG
Found at i:104996 original size:26 final size:26
Alignment explanation
Indices: 104957--105006 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
104947 TTGTTTTTTT
104957 TTTTTTTACAAAA-TAATCACTTATG
1 TTTTTTTACAAAATTAATCACTTATG
* *
104982 TTTTTTTAGACAAATTAATCCCTTA
1 TTTTTTTACA-AAATTAATCACTTA
105007 CATTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 3 0.14
27 9 0.43
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (26 bp):
TTTTTTTACAAAATTAATCACTTATG
Done.