Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022794.1 Corchorus olitorius cultivar O-4 contig22827, 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: 92708
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2357 original size:67 final size:67
Alignment explanation
Indices: 2258--2403 Score: 172
Period size: 67 Copynumber: 2.2 Consensus size: 67
2248 TAATTTTGGA
* * * * * *
2258 GGTTATCAAAA--TTCATTGTGTGGTTACTAAAATTTTATAGCGT-GGTTCTCAAAATTTTATAG
1 GGTTATCAAAATTTTCATAGTGAGGTTACCAAAATTTCATAG-GTAGGATATCAAAATTTTATAG
2320 TGT
65 TGT
* *
2323 GGTTATCAAAATTTTTATAGTGAGGTTACCAAAATTTCATAGGTAGGATATTAAAATTTTATAGT
1 GGTTATCAAAATTTTCATAGTGAGGTTACCAAAATTTCATAGGTAGGATATCAAAATTTTATAGT
2388 GT
66 GT
* *
2390 AGTTATCACAATTT
1 GGTTATCAAAATTT
2404 CATGGGATGT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 11 0.16
66 2 0.03
67 55 0.81
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (67 bp):
GGTTATCAAAATTTTCATAGTGAGGTTACCAAAATTTCATAGGTAGGATATCAAAATTTTATAGT
GT
Found at i:2445 original size:67 final size:67
Alignment explanation
Indices: 2308--2448 Score: 151
Period size: 67 Copynumber: 2.1 Consensus size: 67
2298 CGTGGTTCTC
* * * * *
2308 AAAATTTTATAGTGTGGTTATCAAAATTTTTATAGTGAGGTTACCAAAATTTCATAGGTAGGATA
1 AAAATTTTATAGTGTAGTTATCAAAATTTTCATAGGGAGGTTACAAAAATTTCATAGGTAGGAAA
*
2373 TT
66 AT
* * * **
2375 AAAATTTTATAGTGTAGTTATCACAA-TTTCAT-GGGATGTTATAAAAATTTCATGAGGTTATTA
1 AAAATTTTATAGTGTAGTTATCAAAATTTTCATAGGGAGGTTACAAAAATTTCAT-AGG-TAGGA
2438 AAAT
64 AAAT
2442 AAAATTT
1 AAAATTT
2449 CATATGGATG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
65 17 0.28
66 8 0.13
67 36 0.59
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (67 bp):
AAAATTTTATAGTGTAGTTATCAAAATTTTCATAGGGAGGTTACAAAAATTTCATAGGTAGGAAA
AT
Found at i:2546 original size:22 final size:22
Alignment explanation
Indices: 2255--2650 Score: 179
Period size: 22 Copynumber: 18.0 Consensus size: 22
2245 TTTTAATTTT
*
2255 GGAGGTTATCAAAA-TTCATTG
1 GGAGGTTATCAAAATTTCATAG
* * *
2276 TGTGGTTA-CTAAAATTTTATAG
1 GGAGGTTATC-AAAATTTCATAG
* * * *
2298 CGTGGTTCTCAAAATTTTATAG
1 GGAGGTTATCAAAATTTCATAG
* * *
2320 TGTGGTTATCAAAATTTTTATAG
1 GGAGGTTATCAAAA-TTTCATAG
* *
2343 TGAGGTTACCAAAATTTCATAG
1 GGAGGTTATCAAAATTTCATAG
* * * *
2365 GTAGGATATTAAAATTTTATAG
1 GGAGGTTATCAAAATTTCATAG
* *
2387 TGTA-GTTATCACAATTTCAT-G
1 -GGAGGTTATCAAAATTTCATAG
* *
2408 GGATGTTATAAAAATTTCAT--
1 GGAGGTTATCAAAATTTCATAG
* *
2428 -GAGGTTATTAAAATAAAATTTCATAT
1 GGAGGTTA-T----CAAAATTTCATAG
* * * *
2454 GGATGTTACCAAAATCTCATAT
1 GGAGGTTATCAAAATTTCATAG
** *
2476 AAAGGTTATCAAAATTTCATAT
1 GGAGGTTATCAAAATTTCATAG
** *
2498 AAAGGTTATCGAAA-TTCAT-G
1 GGAGGTTATCAAAATTTCATAG
*
2518 GGAAGGTTATCAAAATTTCACAG
1 GG-AGGTTATCAAAATTTCATAG
* *
2541 GGAGGTTA-CTGAAATTTCATACT
1 GGAGGTTATC-AAAATTTCATA-G
*
2564 GCA-GTTATCAAAATTTCATAG
1 GGAGGTTATCAAAATTTCATAG
** *
2585 GGACACTAAT-AAAATTTCATA-
1 GGA-GGTTATCAAAATTTCATAG
* * * *
2606 GGATGATTATCGAAATTTTATAT
1 GGA-GGTTATCAAAATTTCATAG
*
2629 TGAGGTTATCAAAATTTCATAG
1 GGAGGTTATCAAAATTTCATAG
2651 TATGCTTATA
Statistics
Matches: 290, Mismatches: 61, Indels: 47
0.73 0.15 0.12
Matches are distributed among these distances:
19 6 0.02
20 4 0.01
21 50 0.17
22 179 0.62
23 35 0.12
24 10 0.03
27 6 0.02
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
GGAGGTTATCAAAATTTCATAG
Found at i:2781 original size:22 final size:22
Alignment explanation
Indices: 2749--2830 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
2739 TTTCATAGAA
*
2749 GTTAACAAAATTTTATGGGGAG
1 GTTATCAAAATTTTATGGGGAG
*
2771 GTTATCGAAATTTTA-GAGGGAG
1 GTTATCAAAATTTTATG-GGGAG
* * * * *
2793 ATTATCAAAATTTCATAGTGTG
1 GTTATCAAAATTTTATGGGGAG
2815 GTTATCAAAATTTTAT
1 GTTATCAAAATTTTAT
2831 AATGTGGTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTTATGGGGAG
Found at i:2836 original size:22 final size:22
Alignment explanation
Indices: 2794--2838 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2784 TAGAGGGAGA
*
2794 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAATGTGG
*
2816 TTATCAAAATTTTATAATGTGG
1 TTATCAAAATTTCATAATGTGG
2838 T
1 T
2839 ATTTCAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGTGG
Found at i:2910 original size:22 final size:22
Alignment explanation
Indices: 2860--2932 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
2850 AGAGGTTGTC
*
2860 AAATTTTACAGGG-AGTGTAACAA
1 AAATTTTATAGGGAAGT-TAAC-A
2883 AAATTTTATAGGGAAGTTAACA
1 AAATTTTATAGGGAAGTTAACA
* * *
2905 AAATTTCATATGGAGGTTAACA
1 AAATTTTATAGGGAAGTTAACA
2927 AAATTT
1 AAATTT
2933 CATATGGAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
22 26 0.58
23 16 0.36
24 3 0.07
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (22 bp):
AAATTTTATAGGGAAGTTAACA
Found at i:2953 original size:22 final size:22
Alignment explanation
Indices: 2877--2944 Score: 100
Period size: 22 Copynumber: 3.0 Consensus size: 22
2867 ACAGGGAGTG
* * *
2877 TAACAAAAATTTTATAGGGAAGT
1 TAAC-AAAATTTCATATGGAGGT
2900 TAACAAAATTTCATATGGAGGT
1 TAACAAAATTTCATATGGAGGT
2922 TAACAAAATTTCATATGGAGGT
1 TAACAAAATTTCATATGGAGGT
2944 T
1 T
2945 CTCGAAATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 38 0.90
23 4 0.10
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (22 bp):
TAACAAAATTTCATATGGAGGT
Found at i:11044 original size:39 final size:39
Alignment explanation
Indices: 11001--11125 Score: 121
Period size: 39 Copynumber: 3.3 Consensus size: 39
10991 TATCTTCAGC
11001 TGATGAAGAAGACTCTATGAACTGTTCTTCACCAGATGG
1 TGATGAAGAAGACTCTATGAACTGTTCTTCACCAGATGG
** * * * * * *
11040 TGATGGTGAAGATTCTGTAAACTGATCTT---CAGCTGA
1 TGATGAAGAAGACTCTATGAACTGTTCTTCACCAGATGG
* **
11076 TGATGAAGAAGACTCGATGAACTGTTCTTCACTTGATGG
1 TGATGAAGAAGACTCTATGAACTGTTCTTCACCAGATGG
*
11115 TGATGGAGAAG
1 TGATGAAGAAG
11126 GTACTCCAAG
Statistics
Matches: 63, Mismatches: 20, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
36 27 0.43
39 36 0.57
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (39 bp):
TGATGAAGAAGACTCTATGAACTGTTCTTCACCAGATGG
Found at i:11068 original size:72 final size:73
Alignment explanation
Indices: 10981--11125 Score: 211
Period size: 75 Copynumber: 2.0 Consensus size: 73
10971 TGAAGAAGGG
* * *
10981 TCTGTAAGCTTATCTTCAGC-TGATGAAGAAGACTCTATGAACTGTTCTTCACCAGATGGTGATG
1 TCTGTAAACTGATCTTCAGCATGATGAAGAAGACTCGATGAACTGTTCTTCACCAGATGGTGATG
*
11045 GTGAAGAT
66 GAGAAGAT
**
11053 TCTGTAAACTGATCTTCAGCTGATGATGAAGAAGACTCGATGAACTGTTCTTCACTTGATGGTGA
1 TCTGTAAACTGATCTTCAGC--ATGATGAAGAAGACTCGATGAACTGTTCTTCACCAGATGGTGA
11118 TGGAGAAG
64 TGGAGAAG
11126 GTACTCCAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
72 18 0.28
75 46 0.72
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (73 bp):
TCTGTAAACTGATCTTCAGCATGATGAAGAAGACTCGATGAACTGTTCTTCACCAGATGGTGATG
GAGAAGAT
Found at i:11083 original size:33 final size:33
Alignment explanation
Indices: 10941--11084 Score: 90
Period size: 33 Copynumber: 4.2 Consensus size: 33
10931 ATTGACCGGG
* * *
10941 AGAAGATACTATAAACTGACCTTGAGCTGATGA
1 AGAAGATTCTATAAACTGATCTTCAGCTGATGA
** * * *
10974 AGAAGGGTCTGTAAGCTTATCTTCAGCTGATGA
1 AGAAGATTCTATAAACTGATCTTCAGCTGATGA
* * * * *
11007 AGAAGACTCTATGAACTGTTCTTCACCAGATGGTGATGG
1 AGAAGATTCTATAAACTGATCTT---C--A-GCTGATGA
* *
11046 TGAAGATTCTGTAAACTGATCTTCAGCTGATGA
1 AGAAGATTCTATAAACTGATCTTCAGCTGATGA
*
11079 TGAAGA
1 AGAAGA
11085 AGACTCGATG
Statistics
Matches: 81, Mismatches: 24, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
33 53 0.65
34 1 0.01
36 2 0.02
38 1 0.01
39 24 0.30
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (33 bp):
AGAAGATTCTATAAACTGATCTTCAGCTGATGA
Found at i:11113 original size:36 final size:36
Alignment explanation
Indices: 11001--11113 Score: 102
Period size: 36 Copynumber: 3.1 Consensus size: 36
10991 TATCTTCAGC
* *
11001 TGATGAAGAAGACTCTATGAACTGTTCTTCACCAGATGG
1 TGATGAAGAAGACTCGATGAACTGTTCTTCACC---TGA
** * * * *
11040 TGATGGTGAAGATTCTG-TAAACTGATCTTCAGCTGA
1 TGATGAAGAAGACTC-GATGAACTGTTCTTCACCTGA
*
11076 TGATGAAGAAGACTCGATGAACTGTTCTTCACTTGA
1 TGATGAAGAAGACTCGATGAACTGTTCTTCACCTGA
11112 TG
1 TG
11114 GTGATGGAGA
Statistics
Matches: 57, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
35 1 0.02
36 31 0.54
39 25 0.44
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (36 bp):
TGATGAAGAAGACTCGATGAACTGTTCTTCACCTGA
Found at i:11140 original size:75 final size:75
Alignment explanation
Indices: 10986--11150 Score: 201
Period size: 75 Copynumber: 2.2 Consensus size: 75
10976 AAGGGTCTGT
* * *
10986 AAGCTTATCTTCAGC---TGATGAAGAAGACTCTATGAACTGTTCTTCACCAGATGGTGATGGTG
1 AAGCTGATCTTCAGCTGATGATGAAGAAGACTCGATGAACTGTTCTTCACCAGATGGTGATGGAG
* **
11048 AAGATTCTGT
66 AAGATACTCC
* **
11058 AAACTGATCTTCAGCTGATGATGAAGAAGACTCGATGAACTGTTCTTCACTTGATGGTGATGGAG
1 AAGCTGATCTTCAGCTGATGATGAAGAAGACTCGATGAACTGTTCTTCACCAGATGGTGATGGAG
*
11123 AAGGTACTCC
66 AAGATACTCC
* *
11133 AAGCTGATTTTGAGCTGA
1 AAGCTGATCTTCAGCTGA
11151 CAGAGAAGAA
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
72 13 0.17
75 64 0.83
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (75 bp):
AAGCTGATCTTCAGCTGATGATGAAGAAGACTCGATGAACTGTTCTTCACCAGATGGTGATGGAG
AAGATACTCC
Found at i:20875 original size:44 final size:44
Alignment explanation
Indices: 20812--20903 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
20802 CATTAAAATT
* * *
20812 GCTTACTCAAATAACAATTATACATAAGTAACTGAGGAGGAATG
1 GCTTACTCAAATAACAATTATACAAAAGCAACTGACGAGGAATG
20856 GCTTACTCAAATAACAATTATACAAAAGCAACTGACGAGGAATG
1 GCTTACTCAAATAACAATTATACAAAAGCAACTGACGAGGAATG
20900 GCTT
1 GCTT
20904 TGTCCAAAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (44 bp):
GCTTACTCAAATAACAATTATACAAAAGCAACTGACGAGGAATG
Found at i:30203 original size:29 final size:29
Alignment explanation
Indices: 30158--30224 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
30148 TAGTCTGAGG
* *
30158 GGGCAAAACGTCTCAAAATTGAAGTTCAA
1 GGGCAAAACATCCCAAAATTGAAGTTCAA
* *
30187 GGGCAAAACATCCCAAAATTGAAGTTTAT
1 GGGCAAAACATCCCAAAATTGAAGTTCAA
30216 GGGCAAAAC
1 GGGCAAAAC
30225 GTCCAAAGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (29 bp):
GGGCAAAACATCCCAAAATTGAAGTTCAA
Found at i:35154 original size:85 final size:85
Alignment explanation
Indices: 35004--35169 Score: 237
Period size: 85 Copynumber: 2.0 Consensus size: 85
34994 AGGATTTTCA
* * * *
35004 TTCTATGAATTCTATTTCAATCATTATATGTTGATTTTGTAACGTTATAGAATATATATGTTTTT
1 TTCTATAAATTCTATTTAAATCATTATATGTTGATTTTGTAACGTTAAAGAATATAAATGTTTTT
35069 CATTAAATGAAATTAATTTAG
66 CATT-AATGAAATTAATTTAG
* *
35090 TTCTATAAATTCTATTTAAATCATTATGT-TTGATTTTTTAACGTTACAAG-ATATAAATGTTTT
1 TTCTATAAATTCTATTTAAATCATTATATGTTGATTTTGTAACGTTA-AAGAATATAAATGTTTT
*
35153 TCATTAATGGAATTAAT
65 TCATTAATGAAATTAAT
35170 ATAGGGTATT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
84 11 0.15
85 33 0.46
86 28 0.39
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (85 bp):
TTCTATAAATTCTATTTAAATCATTATATGTTGATTTTGTAACGTTAAAGAATATAAATGTTTTT
CATTAATGAAATTAATTTAG
Found at i:36764 original size:2 final size:2
Alignment explanation
Indices: 36757--36792 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
36747 ATTTAAGAGC
36757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36793 TAAAGTCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37833 original size:31 final size:31
Alignment explanation
Indices: 37795--37867 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
37785 TGTCAAATAT
*
37795 ATATAACGTTTGTTGCGGCAAGCAATTAAGG
1 ATATAACGTTTGTTACGGCAAGCAATTAAGG
* ****
37826 ATATAACGTTTTTTATTTTAAGCAATTAAGG
1 ATATAACGTTTGTTACGGCAAGCAATTAAGG
37857 ATATAACGTTT
1 ATATAACGTTT
37868 TCAATTTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (31 bp):
ATATAACGTTTGTTACGGCAAGCAATTAAGG
Found at i:37868 original size:31 final size:31
Alignment explanation
Indices: 37813--37891 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
37803 TTTGTTGCGG
**
37813 CAAGCAATTAAGGATATAACGTTTTTTATTT
1 CAAGCAATTAAGGATATAACGTTTTCAATTT
*
37844 TAAGCAATTAAGGATATAACGTTTTCAATTT
1 CAAGCAATTAAGGATATAACGTTTTCAATTT
37875 CAAGCAATTAAGGATAT
1 CAAGCAATTAAGGATAT
37892 TGTCAGTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCAATTT
Found at i:38044 original size:31 final size:29
Alignment explanation
Indices: 38001--38067 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
37991 TCTAACTGAC
*
38001 TATACCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCG-TTTT-GTAACGT
*
38032 TATATCCTTAATTGCTTGTTTTGTAACGT
1 TATATCCTTAATTGCTCGTTTTGTAACGT
*
38061 TACATCC
1 TATATCC
38068 CAAATTTCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (29 bp):
TATATCCTTAATTGCTCGTTTTGTAACGT
Found at i:38067 original size:29 final size:31
Alignment explanation
Indices: 38006--38067 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
37996 CTGACTATAC
*
38006 CCTTAATTGCTCGCTTTTCGTAACGTTATAT
1 CCTTAATTGCTCGCTTTTCGTAACGTTACAT
*
38037 CCTTAATTGCTTG-TTTT-GTAACGTTACAT
1 CCTTAATTGCTCGCTTTTCGTAACGTTACAT
38066 CC
1 CC
38068 CAAATTTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 13 0.45
30 4 0.14
31 12 0.41
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (31 bp):
CCTTAATTGCTCGCTTTTCGTAACGTTACAT
Found at i:39252 original size:31 final size:31
Alignment explanation
Indices: 39214--39381 Score: 118
Period size: 31 Copynumber: 5.5 Consensus size: 31
39204 TACAGCTAAT
39214 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * **
39245 TGCTCAAATAAGGGCATGATC-TTT-T-AATT
1 TGCTCAAATAAGGGCCT-AACGTTTGTCAAAA
* *
39274 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * * **
39305 TGCTCAAATAAGGGTCTGATC-TTT-T-GATT
1 TGCTCAAATAAGGGCCT-AACGTTTGTCAAAA
* *
39334 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
*
39365 TGCTCAAATAAGTGCCT
1 TGCTCAAATAAGGGCCT
39382 GGCATCGAAA
Statistics
Matches: 100, Mismatches: 25, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
28 2 0.02
29 35 0.35
30 9 0.09
31 51 0.51
32 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
Found at i:39285 original size:60 final size:60
Alignment explanation
Indices: 39218--39376 Score: 275
Period size: 60 Copynumber: 2.6 Consensus size: 60
39208 GCTAATTGCT
* *
39218 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGG-CATGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTC-TGATCTTTTAATTTGGC
*
39278 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTGATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
39338 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAG
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAG
39377 TGCCTGGCAT
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
Found at i:39347 original size:29 final size:28
Alignment explanation
Indices: 39249--39348 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 28
39239 TCAAAATGCT
*
39249 CAAATAAGGGCATGATCTTTTAATTTGGC
1 CAAATAAGGGC-TGATCTTTTGATTTGGC
* * **
39278 CAAATAAGGGCCTAAT-GTTTGCCAAAAT-GC
1 CAAATAAGGG-CTGATCTTTTG---ATTTGGC
39308 TCAAATAAGGGTCTGATCTTTTGATTTGGC
1 -CAAATAAGGG-CTGATCTTTTGATTTGGC
39338 CAAATAAGGGC
1 CAAATAAGGGC
39349 CTAATGTTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
28 4 0.07
29 25 0.46
30 5 0.09
31 16 0.30
32 4 0.07
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (28 bp):
CAAATAAGGGCTGATCTTTTGATTTGGC
Found at i:39500 original size:60 final size:60
Alignment explanation
Indices: 39421--39583 Score: 231
Period size: 60 Copynumber: 2.7 Consensus size: 60
39411 ACTGATGCCA
* * * *
39421 GGCCCTTATTTGAGTATTTTGGCAAACGTTAGGCCCTTATTTGGCTAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACCG
*
39481 GGCCCTTATTTAAGCATTTT--CAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACCG
1 GGCCCTTATTTGAGCATTTTGGC-A-AACGTTAGGCCCTTATTTGGCCAAATTAAAAAACCG
* *
39541 GGTCCTTATTTGAGCATTTTGGCAAACGTTAGGCTCTTATTTG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
39584 AGTAATTAGC
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 87 0.96
61 1 0.01
62 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACCG
Found at i:40799 original size:30 final size:29
Alignment explanation
Indices: 40726--40801 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
40716 ATTTGTAGTG
*
40726 TTTGGATGTTTTGCCCCCTGAACTTCAAT
1 TTTGGATGTTTTACCCCCTGAACTTCAAT
* ** *
40755 TTTGAACATTTTACCCCCTGAATTTCAAT
1 TTTGGATGTTTTACCCCCTGAACTTCAAT
40784 TTTGGGATGTTTTACCCC
1 TTT-GGATGTTTTACCCC
40802 TTCAGCCTAA
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:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTGGATGTTTTACCCCCTGAACTTCAAT
Found at i:48196 original size:108 final size:104
Alignment explanation
Indices: 48027--48285 Score: 387
Period size: 108 Copynumber: 2.5 Consensus size: 104
48017 TAGCCTTAAC
48027 TTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATA
1 TTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATA
48092 ATTTATTATTATAGGGTTTTAGAAATAAAAATACAAAACTAA
66 A--TATTATTATAGGGTTTTAGAAAT-AAAATACAAAACTAA
* *
48134 TTTCACTAGGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAA-TTCTATAATTAA
1 -TTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTC-AAAATTAA
* * *
48198 TAATATTGTTATAGGGTTTTAGAAATAAAATATATAACTAA
64 TAATATTATTATAGGGTTTTAGAAATAAAATACAAAACTAA
** *
48239 TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
48286 TAGAAAAATT
Statistics
Matches: 141, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
103 30 0.21
104 13 0.09
105 13 0.09
106 22 0.16
107 3 0.02
108 60 0.43
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (104 bp):
TTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATA
ATATTATTATAGGGTTTTAGAAATAAAATACAAAACTAA
Found at i:50259 original size:17 final size:17
Alignment explanation
Indices: 50237--50284 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
50227 ATCACCCCCC
*
50237 AGATCACTAGTGAT-CTA
1 AGATCACCAGTGATGC-A
50254 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
*
50271 AGATCACCGGTGAT
1 AGATCACCAGTGAT
50285 CAAATATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 27 0.96
18 1 0.04
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:59002 original size:16 final size:19
Alignment explanation
Indices: 58966--59003 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
58956 TTTCCCAGAC
58966 TTTCTTCTTCTTCTTCTTT
1 TTTCTTCTTCTTCTTCTTT
58985 TTTCTTC-TCTT-TT-TTT
1 TTTCTTCTTCTTCTTCTTT
59001 TTT
1 TTT
59004 TAATATGCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
18 4 0.21
19 7 0.37
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCTTCTTCTTCTTCTTT
Found at i:61868 original size:19 final size:20
Alignment explanation
Indices: 61844--61882 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
61834 CTGACGTGGT
61844 AATACCACGTCGGA-CAAAA
1 AATACCACGTCGGACCAAAA
*
61863 AATACCACGTTGGACCAAAA
1 AATACCACGTCGGACCAAAA
61883 TGCCATGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (20 bp):
AATACCACGTCGGACCAAAA
Found at i:62017 original size:31 final size:30
Alignment explanation
Indices: 61938--62021 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
61928 AAGTAACTTC
* * * *
61938 AAATTGCAAGGTCAAGGGGTAAAATGTCGA
1 AAATTACAAGTTCAAGGGGCAAAATGTCCA
*
61968 AAATTA-AAGTTCAGGGGGCAAAATG-CCA
1 AAATTACAAGTTCAAGGGGCAAAATGTCCA
61996 AAATCATACAAGTTCAAGGGGCAAAA
1 AAAT--TACAAGTTCAAGGGGCAAAA
62022 AGGGCATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.13
29 16 0.36
30 7 0.16
31 16 0.36
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (30 bp):
AAATTACAAGTTCAAGGGGCAAAATGTCCA
Found at i:77780 original size:123 final size:127
Alignment explanation
Indices: 77531--77782 Score: 377
Period size: 131 Copynumber: 2.0 Consensus size: 127
77521 TAAGAAATAA
*
77531 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAATAAAATAG
1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-
* *
77596 ATATAAGGATATTAGTTTTAATTAAATAAAAATAGAGCTTTTAGTTGAGTAAAACTGTAAAAGTA
62 ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGTA
77661 T
127 T
*
77662 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAGATAGTAAAATGGTAAAAAT-T-ATA-
1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAATAT
* * *
77724 AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTTAGTGAAACTATAAAAGT
66 AAGGATATTAGATTTAATTAAATAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGT
77783 TTAAACAATG
Statistics
Matches: 114, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
123 52 0.46
124 2 0.02
125 3 0.03
127 1 0.01
131 56 0.49
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAATAT
AAGGATATTAGATTTAATTAAATAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGTAT
Found at i:81292 original size:43 final size:43
Alignment explanation
Indices: 81229--81402 Score: 321
Period size: 43 Copynumber: 4.0 Consensus size: 43
81219 ACCCGACTAA
* * *
81229 TCCAGAATCGAGACTCTCTACACTAATCCAGAATCGAGACGTG
1 TCCAGAATCGAGATTTTCTACACTAATCTAGAATCGAGACGTG
81272 TCCAGAATCGAGATTTTCTACACTAATCTAGAATCGAGACGTG
1 TCCAGAATCGAGATTTTCTACACTAATCTAGAATCGAGACGTG
81315 TCCAGAATCGAGATTTTCTACACTAATCTAGAATCGAGACGTG
1 TCCAGAATCGAGATTTTCTACACTAATCTAGAATCGAGACGTG
81358 TCCAGAATCGAGATTTTCTACACTAATCTAGAATCGAGACGTG
1 TCCAGAATCGAGATTTTCTACACTAATCTAGAATCGAGACGTG
81401 TC
1 TC
81403 GAATCCAAAA
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 128 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (43 bp):
TCCAGAATCGAGATTTTCTACACTAATCTAGAATCGAGACGTG
Found at i:85979 original size:16 final size:19
Alignment explanation
Indices: 85940--85979 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
85930 GGTTTTGTCC
85940 TTATTTCACAAATTCTCTA
1 TTATTTCACAAATTCTCTA
*
85959 TTATTTCACAAATTCTATA
1 TTATTTCACAAATTCTCTA
85978 TT
1 TT
85980 CAATTCATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTTCACAAATTCTCTA
Done.