Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011283.1 Corchorus olitorius cultivar O-4 contig11316, 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: 32992
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:3096 original size:24 final size:25
Alignment explanation
Indices: 3050--3097 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3040 ATTGGAGTAT
*
3050 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
3075 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
3098 TATTGTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:3685 original size:31 final size:31
Alignment explanation
Indices: 3647--3708 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3637 CCAGCATCTG
3647 CCTTTGTCTGTTGTCTCACCTCAAGTCAGTT
1 CCTTTGTCTGTTGTCTCACCTCAAGTCAGTT
3678 CCTTTGTCTGTTGTCTCACCTCAAGTCAGTT
1 CCTTTGTCTGTTGTCTCACCTCAAGTCAGTT
3709 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.13, C:0.29, G:0.16, T:0.42
Consensus pattern (31 bp):
CCTTTGTCTGTTGTCTCACCTCAAGTCAGTT
Found at i:8612 original size:21 final size:21
Alignment explanation
Indices: 8586--8695 Score: 148
Period size: 21 Copynumber: 5.2 Consensus size: 21
8576 TACATACATG
* **
8586 GTCAAACCACAAAGGATGATA
1 GTCAAACCCCAAAGTTTGATA
*
8607 GTCAAACCCCAAATTTTGATA
1 GTCAAACCCCAAAGTTTGATA
* * *
8628 GTTAAACCCCATAGTTTGAAA
1 GTCAAACCCCAAAGTTTGATA
8649 GTCAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAAGTTTGATA
*
8670 GTCAAACCCCAAATTTTGATA
1 GTCAAACCCCAAAGTTTGATA
8691 GTCAA
1 GTCAA
8696 CACGTTAAAC
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.25
Consensus pattern (21 bp):
GTCAAACCCCAAAGTTTGATA
Found at i:9580 original size:15 final size:14
Alignment explanation
Indices: 9548--9606 Score: 70
Period size: 15 Copynumber: 4.2 Consensus size: 14
9538 TAATATTACC
9548 ATAGTCTATGTT-AT
1 ATAGTCTAT-TTAAT
9562 ATAGTCTATTTGAAT
1 ATAGTCTATTT-AAT
9577 ATAGTCTATTTGAAT
1 ATAGTCTATTT-AAT
9592 AT-GT-TATTTAAT
1 ATAGTCTATTTAAT
9604 ATA
1 ATA
9607 TGAGAAACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.12
13 7 0.17
14 11 0.26
15 19 0.45
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (14 bp):
ATAGTCTATTTAAT
Found at i:9867 original size:10 final size:10
Alignment explanation
Indices: 9825--9867 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
9815 TTGTATATTA
9825 AATAAAATAT
1 AATAAAATAT
9835 AATAAGGAATAT
1 AATAA--AATAT
*
9847 AAGAAAATAT
1 AATAAAATAT
*
9857 AATAAATTAT
1 AATAAAATAT
9867 A
1 A
9868 GAGTAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 19 0.68
12 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (10 bp):
AATAAAATAT
Found at i:9965 original size:23 final size:24
Alignment explanation
Indices: 9921--9966 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
9911 AACATGTGAT
*
9921 CCCACAAAGAGAGAAAATGGTGGGG
1 CCCACAAAGAGAG-AAAGGGTGGGG
9946 CCCACAAAGAGAG-AAGGGTGG
1 CCCACAAAGAGAGAAAGGGTGG
9967 TTGGATGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
25 13 0.65
ACGTcount: A:0.39, C:0.17, G:0.37, T:0.07
Consensus pattern (24 bp):
CCCACAAAGAGAGAAAGGGTGGGG
Found at i:10259 original size:37 final size:37
Alignment explanation
Indices: 10204--10280 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
10194 ATAATGTGAT
*
10204 TATTTATGAATCAAGAGTTGTCTTGTGAAAAGACATG
1 TATTCATGAATCAAGAGTTGTCTTGTGAAAAGACATG
*
10241 TATTCATGAATTAAGAGTTGTCTTGTGAAAAGACATG
1 TATTCATGAATCAAGAGTTGTCTTGTGAAAAGACATG
10278 TAT
1 TAT
10281 CTATTTAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (37 bp):
TATTCATGAATCAAGAGTTGTCTTGTGAAAAGACATG
Found at i:10326 original size:41 final size:41
Alignment explanation
Indices: 10269--10348 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
10259 TGTCTTGTGA
10269 AAAGACATGTATCTATTTAATGTTGTCTTTATCCAAAAGGG
1 AAAGACATGTATCTATTTAATGTTGTCTTTATCCAAAAGGG
*
10310 AAAGACATGTATCTATTTAATGTTGTCTTTATCTAAAAG
1 AAAGACATGTATCTATTTAATGTTGTCTTTATCCAAAAG
10349 ACATGTACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (41 bp):
AAAGACATGTATCTATTTAATGTTGTCTTTATCCAAAAGGG
Found at i:10421 original size:18 final size:18
Alignment explanation
Indices: 10398--10433 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10388 TTCATCAACT
10398 ATATAAAGGATCTTTATA
1 ATATAAAGGATCTTTATA
10416 ATATAAAGGATCTTTATA
1 ATATAAAGGATCTTTATA
10434 TTGCTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
ATATAAAGGATCTTTATA
Found at i:15125 original size:37 final size:37
Alignment explanation
Indices: 15070--15146 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
15060 ATAATGTGAT
*
15070 TATTTATGAATCAAGAGTTGTCTTGTGAAAAGACATG
1 TATTCATGAATCAAGAGTTGTCTTGTGAAAAGACATG
* *
15107 TATTCATGAATCAAGAGTTGTCTTGTGAAAATATATG
1 TATTCATGAATCAAGAGTTGTCTTGTGAAAAGACATG
15144 TAT
1 TAT
15147 CTATTTAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (37 bp):
TATTCATGAATCAAGAGTTGTCTTGTGAAAAGACATG
Found at i:18212 original size:5 final size:5
Alignment explanation
Indices: 18202--18283 Score: 85
Period size: 5 Copynumber: 16.4 Consensus size: 5
18192 TTAGTCGTGT
* * * * * *
18202 ACACG ACACG ACATG AC-CTG ACACG ACACG ACCCG ATATG CCACA ACACG
1 ACACG ACACG ACACG ACAC-G ACACG ACACG ACACG ACACG ACACG ACACG
*
18252 ACACG ATACG ACACG ACACG ACACG ACACG AC
1 ACACG ACACG ACACG ACACG ACACG ACACG AC
18284 TAACACGATT
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
5 60 0.98
6 1 0.02
ACGTcount: A:0.38, C:0.38, G:0.18, T:0.06
Consensus pattern (5 bp):
ACACG
Found at i:21934 original size:17 final size:17
Alignment explanation
Indices: 21881--21935 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
21871 ATCACCCCCC
*
21881 AGATCACTAGTGATCTAA
1 AGATCACCAGTGATC-AA
21899 A-ATCACCAGTGATGC-A
1 AGATCACCAGTGAT-CAA
*
21915 AGATCACCGGTGATCAA
1 AGATCACCAGTGATCAA
21932 AGAT
1 AGAT
21936 TACATGGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 3 0.09
17 27 0.84
18 2 0.06
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (17 bp):
AGATCACCAGTGATCAA
Found at i:24131 original size:20 final size:20
Alignment explanation
Indices: 24108--24159 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
24098 AAAGTGCTAT
24108 AACGGCTAGAAAAGAGCTCC
1 AACGGCTAGAAAAGAGCTCC
24128 AACGGCTAGAAAAGAGCTCC
1 AACGGCTAGAAAAGAGCTCC
24148 AACGGCTAGAAA
1 AACGGCTAGAAA
24160 CTTGTGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (20 bp):
AACGGCTAGAAAAGAGCTCC
Found at i:25336 original size:26 final size:26
Alignment explanation
Indices: 25307--25370 Score: 65
Period size: 31 Copynumber: 2.3 Consensus size: 26
25297 AAAGATTAAA
* *
25307 AATAATTGAAGGACTAAATTGCATTG
1 AATAATTGAAGGACTAAATTACATGG
25333 AATAGAATGTTTGAAGGACTAAATTACATGG
1 AAT--AA---TTGAAGGACTAAATTACATGG
25364 AATAATT
1 AATAATT
25371 AAAATGTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
26 5 0.16
28 2 0.06
29 2 0.06
31 22 0.71
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (26 bp):
AATAATTGAAGGACTAAATTACATGG
Found at i:29741 original size:7 final size:7
Alignment explanation
Indices: 29731--30154 Score: 731
Period size: 7 Copynumber: 60.4 Consensus size: 7
29721 TTTTGAGCCA
29731 TGAATTT
1 TGAATTT
29738 TGAATTT
1 TGAATTT
29745 TGAATTTT
1 TGAA-TTT
*
29753 TGAGTTT
1 TGAATTT
*
29760 TGAGTTT
1 TGAATTT
*
29767 TGAGTTT
1 TGAATTT
*
29774 TGAGTTT
1 TGAATTT
*
29781 TGAGTTT
1 TGAATTT
*
29788 TGAGTTT
1 TGAATTT
*
29795 TGAGTTT
1 TGAATTT
*
29802 TGAGTTT
1 TGAATTT
*
29809 TGAGTTT
1 TGAATTT
*
29816 TGAGTTT
1 TGAATTT
*
29823 TGAGTTT
1 TGAATTT
29830 TGAATTT
1 TGAATTT
29837 TGAATTT
1 TGAATTT
29844 TGAATTT
1 TGAATTT
29851 TGAATTT
1 TGAATTT
29858 TGAATTT
1 TGAATTT
29865 TGAATTT
1 TGAATTT
29872 TGAATTT
1 TGAATTT
29879 TGAATTT
1 TGAATTT
29886 TGAATTT
1 TGAATTT
29893 TGAATTT
1 TGAATTT
29900 TGAATTT
1 TGAATTT
29907 TGAATTT
1 TGAATTT
29914 TGAATTT
1 TGAATTT
29921 TGAATTT
1 TGAATTT
29928 TGAATTT
1 TGAATTT
29935 TGAATTT
1 TGAATTT
29942 TGAATTT
1 TGAATTT
29949 TGAATTT
1 TGAATTT
29956 TGAATTT
1 TGAATTT
29963 TGAATTT
1 TGAATTT
*
29970 TGAACTT
1 TGAATTT
29977 TGAATTT
1 TGAATTT
29984 TGAATTT
1 TGAATTT
29991 TGAATTT
1 TGAATTT
29998 TGAATTT
1 TGAATTT
30005 TGAATTT
1 TGAATTT
30012 TGAATTT
1 TGAATTT
30019 TGAATTT
1 TGAATTT
30026 TGAATTT
1 TGAATTT
30033 TGAATTT
1 TGAATTT
30040 TGAATTT
1 TGAATTT
30047 TGAATTT
1 TGAATTT
30054 TGAATTT
1 TGAATTT
30061 TGAATTT
1 TGAATTT
30068 TGAATTT
1 TGAATTT
30075 TGAATTT
1 TGAATTT
30082 TGAATTT
1 TGAATTT
30089 TGAATTT
1 TGAATTT
30096 TGAATTT
1 TGAATTT
30103 TGAATTT
1 TGAATTT
30110 TGAATTT
1 TGAATTT
30117 TGAATTT
1 TGAATTT
30124 TGAATTT
1 TGAATTT
30131 TGAATTT
1 TGAATTT
30138 TGAATTT
1 TGAATTT
30145 TGAATTT
1 TGAATTT
30152 TGA
1 TGA
30155 GCAATGAAAT
Statistics
Matches: 412, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
7 406 0.99
8 6 0.01
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (7 bp):
TGAATTT
Found at i:30337 original size:33 final size:33
Alignment explanation
Indices: 30290--30367 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
30280 AGAAACTGTG
* * * *
30290 GATTTTGAATTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
30323 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
30356 AATTTTGAACTT
1 GATTTTGAACTT
30368 CTTAATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:30586 original size:54 final size:53
Alignment explanation
Indices: 30472--30729 Score: 317
Period size: 54 Copynumber: 4.8 Consensus size: 53
30462 TGATCATCGT
* * * * * * *
30472 AAACTTCT-TGGAATGACCACACTAGATCAACTT-AGATTAACTTAGATTTTTGA
1 AAACTTCTAT-GAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACTTCT-A
* * *
30525 AAACTTCTATGGAAA-ACCACACAGGGTCGTCTGAAGATCAACTTAGACTTCTA
1 AAACTTCTAT-GAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACTTCTA
*
30578 AAAGCTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGA-TCTCTG
1 AAA-CTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACT-TCTA
*
30632 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACTTCTA
*
30685 AAAGCTTCTATGAAAGACCACATTGGGTCATCTTAAGATCAACTT
1 AAA-CTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTT
30730 TCTAGAGAGA
Statistics
Matches: 181, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
53 79 0.44
54 102 0.56
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (53 bp):
AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACTTCTA
Found at i:30586 original size:107 final size:107
Alignment explanation
Indices: 30486--30729 Score: 330
Period size: 107 Copynumber: 2.3 Consensus size: 107
30476 TTCTTGGAAT
* * *
30486 GACCACACTAGATCAACTT-AGATTAACTTAGATTTTTGAAAACTTCTATGGAAA-ACCACACAG
1 GACCACACTAGATCAACTTAAGATCAACTTAGATCTCTG-AAACTTCTAT-GAAAGACCACACAG
* *
30549 GGTCGTCTGAAGATCAACTTAGACTTCTAAAAGCTTCTATGAAA
64 GGTCATCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAA
* * * *
30593 GACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAACTTCTATGAAAGACCACACTGGG
1 GACCACACTAGATCAACTTAAGATCAACTTAGATCTCTGAAACTTCTATGAAAGACCACACAGGG
*
30658 TCATCTTAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAA
66 TCATCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAA
* * * *
30700 GACCACATTGGGTCATCTTAAGATCAACTT
1 GACCACACTAGATCAACTTAAGATCAACTT
30730 TCTAGAGAGA
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
106 4 0.03
107 104 0.84
108 16 0.13
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (107 bp):
GACCACACTAGATCAACTTAAGATCAACTTAGATCTCTGAAACTTCTATGAAAGACCACACAGGG
TCATCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAA
Found at i:30882 original size:37 final size:37
Alignment explanation
Indices: 30829--31221 Score: 276
Period size: 37 Copynumber: 10.6 Consensus size: 37
30819 AAACTGGGAT
* * * *
30829 TTTGAAGAGACACCTAAACAGGTACCTTAAATAAGGA
1 TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
* * * * ** *
30866 TTTAATAAGAAACCTAAACATGAATTTTGAACAA-GA
1 TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
* *
30902 TTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
1 -TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
* * * * *
30940 TTTGATAAGAAACCTAAACAAGAATCTTGAACAAGG-
1 TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
* * * * *
30976 TTTGATGAGATAGCTAAAAAGGGACTTTAAACAAGGT
1 TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
* * * *
31013 TTTGATGAGACATCC-AAACAAGGACCTTGAACAAGGT
1 TTTGATGAGA-AACCTAAACAGGGACCTTAAACAAGGA
* * *
31050 TTTGATGAGACACCTAAATAGGGACCTTAAATAAGGA
1 TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
* * * * * *
31087 TTTAATAAGAAAGCTAAACCGAGATCTTAAACAA-GA
1 TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
* * *
31123 TTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGA
1 -TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
* * * * * * *
31161 TTTAATAAGACACCTAAATAGGAATCTTGAACAA-GA
1 TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
*
31197 TTTTGATGA-AACACGTAAACAGGGA
1 -TTTGATGAGAA-ACCTAAACAGGGA
31222 TCTTGAACCA
Statistics
Matches: 268, Mismatches: 79, Indels: 18
0.73 0.22 0.05
Matches are distributed among these distances:
36 36 0.13
37 227 0.85
38 5 0.02
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (37 bp):
TTTGATGAGAAACCTAAACAGGGACCTTAAACAAGGA
Found at i:30913 original size:74 final size:74
Alignment explanation
Indices: 30826--31221 Score: 501
Period size: 74 Copynumber: 5.4 Consensus size: 74
30816 CCTAAACTGG
* * *
30826 GATTTTGAAGAGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAAGAAT
*
30891 TTTGAACAA
66 CTTGAACAA
*
30900 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAAGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAAGAAT
30965 CTTGAACAA
66 CTTGAACAA
* * * * * * * * * * *
30974 G-GTTTGATGAGATAGCTAAAAAGGGACTTTAAACAAGGTTTTGATGAGACATCC-AAACAAGGA
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGA-AACCTAAACAAGAA
*
31037 CCTTGAACAA
65 TCTTGAACAA
* * * *
31047 GGTTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTAATAAGAAAGCTAAAC-CGAGA
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAAGA-A
*
31111 TCTTAAACAA
65 TCTTGAACAA
* * * *
31121 GATTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTAATAAGACACCTAAATAGGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAAGAAT
31186 CTTGAACAA
66 CTTGAACAA
* *
31195 GATTTTGATGAAACACGTAAACAGGGA
1 GATTTTGATGAGACACCTAAACAGGGA
31222 TCTTGAACCA
Statistics
Matches: 277, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
73 61 0.22
74 214 0.77
75 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (74 bp):
GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAAGAAT
CTTGAACAA
Found at i:31096 original size:147 final size:148
Alignment explanation
Indices: 30829--31221 Score: 479
Period size: 147 Copynumber: 2.7 Consensus size: 148
30819 AAACTGGGAT
* * * * * * * **
30829 TTTGAAGAGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAATTTT
1 TTTGATGAGACACCTAAAAAGGGACCTTAAACAAGGATTTAATAAGACACCTAAAAAGGAACCTT
*
30894 GAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAAC
66 GAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAAC
*
30959 A-AGAATCTTGAACAAG-G
131 AGAG-ATCTTAAACAAGAG
* * * * * *
30976 TTTGATGAGATAGCTAAAAAGGGACTTTAAACAAGGTTTTGATGAGACATCC-AAACAAGG-ACC
1 TTTGATGAGACACCTAAAAAGGGACCTTAAACAAGGATTTAATAAGACA-CCTAAA-AAGGAACC
* * *
31039 TTGAACAAGGTTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTAATAAGAAAGCTAA
64 TTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAA
* *
31104 ACCGAGATCTTAAACAAGAT
129 ACAGAGATCTTAAACAAGAG
* * * *
31124 TTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTAATAAGACACCTAAATAGGAATCTT
1 TTTGATGAGACACCTAAAAAGGGACCTTAAACAAGGATTTAATAAGACACCTAAAAAGGAACCTT
* *
31189 GAACAAGATTTTGATGAAACACGTAAACAGGGA
66 GAACAAGATTTTGATGAGACACCTAAACAGGGA
31222 TCTTGAACCA
Statistics
Matches: 204, Mismatches: 36, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
147 121 0.59
148 83 0.41
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (148 bp):
TTTGATGAGACACCTAAAAAGGGACCTTAAACAAGGATTTAATAAGACACCTAAAAAGGAACCTT
GAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAAC
AGAGATCTTAAACAAGAG
Found at i:31216 original size:111 final size:109
Alignment explanation
Indices: 30895--31242 Score: 387
Period size: 111 Copynumber: 3.1 Consensus size: 109
30885 ATGAATTTTG
* *
30895 AACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACA
1 AACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAATA
* * * *
30960 AGAATCTTGAACAAGGTTTGATGAGATAGCTAAAAAGGGA-CTTTA
66 GGAATCTTGAACAAGATTTGATGA-AAAGCTAAACAGGGATC-TTA
* * * * * *
31005 AACAAGGTTTTGATGAGACATCC-AAACAAGGACCTTGAACAAGGTTTTGATGAGACACCTAAAT
1 AACAAGATTTTGATGAGACA-CCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAAT
* * * * * * * *
31069 AGGGACCTTAAATAAGGATTTAATAAGAAAGCTAAACCGAGATCTTA
65 AGGAATCTTGAACAA-GATTTGATGA-AAAGCTAAACAGGGATCTTA
* *
31116 AACAAGATTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTAATAAGACACCTAAATA
1 AACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAATA
*
31181 GGAATCTTGAACAAGATTTTGATGAAACA-CGTAAACAGGGATCTTG
66 GGAATCTTGAACAAGA-TTTGATGAAA-AGC-TAAACAGGGATCTTA
*
31227 AACCAGATTTTGATGA
1 AACAAGATTTTGATGA
31243 AACTGAATTT
Statistics
Matches: 193, Mismatches: 38, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
110 70 0.36
111 122 0.63
112 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (109 bp):
AACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAATA
GGAATCTTGAACAAGATTTGATGAAAAGCTAAACAGGGATCTTA
Found at i:32139 original size:87 final size:87
Alignment explanation
Indices: 31993--32162 Score: 250
Period size: 87 Copynumber: 2.0 Consensus size: 87
31983 TGATTGATGC
* * * *
31993 CCCAAACCTTCTTCCAATTTGGTCATGTATTGATATTCCCAACTCAACTGATGGTTCTGGATCAG
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAACTGATGGTTCTGGATCAA
32058 CTTCCCACCTTAAGAAATATTT
66 CTTCCCACCTTAAGAAATATTT
* * *
32080 CCCAAATCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCAA
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAACTGATGGTTCTGGATCAA
* * *
32145 TTTCTCATCTTAAGAAAT
66 CTTCCCACCTTAAGAAAT
32163 GTTCAAACAT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (87 bp):
CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAACTGATGGTTCTGGATCAA
CTTCCCACCTTAAGAAATATTT
Found at i:32308 original size:4 final size:4
Alignment explanation
Indices: 32295--32367 Score: 52
Period size: 4 Copynumber: 18.8 Consensus size: 4
32285 TCCTTTTGAT
32295 TTTC -TTC TTTC TTTC TTTC ATTT- TTTC TTTCAC TTT- TTTC TTTGC
1 TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTT--C TTTC TTTC TTT-C
32340 TTTC TCTT- TTT- TTTC TTT- TTT- TTTC TTT
1 TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTT
32368 TAGATTTGCT
Statistics
Matches: 59, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
3 20 0.34
4 26 0.44
5 9 0.15
6 4 0.07
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:32323 original size:12 final size:12
Alignment explanation
Indices: 32294--32337 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
32284 TTCCTTTTGA
32294 TTTTC-TTC-TT
1 TTTTCTTTCATT
32304 TCTTTCTTTCATT
1 T-TTTCTTTCATT
32317 TTTTCTTTCACTT
1 TTTTCTTTCA-TT
32330 TTTTCTTT
1 TTTTCTTT
32338 GCTTTCTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.03
11 4 0.13
12 12 0.40
13 13 0.43
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTCTTTCATT
Found at i:32333 original size:13 final size:13
Alignment explanation
Indices: 32301--32337 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
32291 TGATTTTCTT
32301 CTTTCTTTCTTTCA
1 CTTT-TTTCTTTCA
32315 -TTTTTTCTTTCA
1 CTTTTTTCTTTCA
32327 CTTTTTTCTTT
1 CTTTTTTCTTT
32338 GCTTTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTTTTTCTTTCA
Found at i:32335 original size:29 final size:26
Alignment explanation
Indices: 32294--32367 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 26
32284 TTCCTTTTGA
*
32294 TTTTCTTCTTTCTTTCTTTCAT-TTTT
1 TTTTCTTTTTTCTTTCTTTC-TCTTTT
32320 TCTTTCACTTTTTTCTTTGCTTTCTCTTTT
1 T-TTT--CTTTTTTCTTT-CTTTCTCTTTT
32350 TTTTCTTTTTT-TTTCTTT
1 TTTTCTTTTTTCTTTCTTT
32368 TAGATTTGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
25 4 0.10
26 4 0.10
27 10 0.24
29 14 0.33
30 10 0.24
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (26 bp):
TTTTCTTTTTTCTTTCTTTCTCTTTT
Found at i:32342 original size:12 final size:11
Alignment explanation
Indices: 32294--32367 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 11
32284 TTCCTTTTGA
32294 TTTTC-TTCTT
1 TTTTCTTTCTT
32304 TCTTTCTTTCATT
1 T-TTTCTTTC-TT
32317 TTTTCTTTCACTT
1 TTTTCTTT--CTT
32330 TTTTCTTTGC-T
1 TTTTCTTT-CTT
*
32341 TTCTC-TT-TT
1 TTTTCTTTCTT
32350 TTTTCTTT-TT
1 TTTTCTTTCTT
32360 TTTTCTTT
1 TTTTCTTT
32368 TAGATTTGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
9 5 0.09
10 15 0.28
11 9 0.17
12 11 0.20
13 13 0.24
14 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (11 bp):
TTTTCTTTCTT
Done.