Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016561.1 Corchorus olitorius cultivar O-4 contig16594, 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: 58083
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:10731 original size:14 final size:13
Alignment explanation
Indices: 10712--10750 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
10702 AAATTATAAA
10712 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
10725 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
10739 ATTTAAAAAATT
1 ATTTAAAAAATT
10751 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:10952 original size:122 final size:128
Alignment explanation
Indices: 10733--10988 Score: 389
Period size: 122 Copynumber: 2.0 Consensus size: 128
10723 TTCATTTAAG
10733 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTTAAATAAAATAGCAAAATGGTAAAAAT
1 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTTAAATAAAATAGCAAAATGGTAAAAAT
*
10798 AAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTAT
66 ---ACA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTAT
10863 AA
127 AA
* *
10865 AAATATATTT-AAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT
1 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTTAAATAAAATAGCAAAATGGTAAAAAT
* *
10928 -CA-TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAA
66 ACAGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAA
10987 AA
1 AA
10989 GTTTAAACAA
Statistics
Matches: 119, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
122 53 0.45
123 2 0.02
124 2 0.02
126 1 0.01
130 30 0.25
131 21 0.18
132 10 0.08
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (128 bp):
AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTTAAATAAAATAGCAAAATGGTAAAAAT
ACAGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAA
Found at i:12114 original size:41 final size:40
Alignment explanation
Indices: 12054--12135 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
12044 AACATGTGAA
*
12054 TCCTTAAAAAAAAATCGACCATGGAACTTTGAAATGAAAT
1 TCCTTAAAAAAAAATCGACCATAGAACTTTGAAATGAAAT
** *
12094 TCCTTAACAAAACGATCGACCATATAACTTTGAAATGAAAT
1 TCCTTAA-AAAAAAATCGACCATAGAACTTTGAAATGAAAT
12135 T
1 T
12136 AATGTAGTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 7 0.19
41 30 0.81
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (40 bp):
TCCTTAAAAAAAAATCGACCATAGAACTTTGAAATGAAAT
Found at i:12312 original size:14 final size:14
Alignment explanation
Indices: 12293--12339 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
12283 TTTGACCTCA
12293 TAATAATAATTCTC
1 TAATAATAATTCTC
12307 TAATAA-AA-----
1 TAATAATAATTCTC
12315 TAATAATAATTCTC
1 TAATAATAATTCTC
12329 TAATAATAATT
1 TAATAATAATT
12340 AATCACAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
8 6 0.22
9 2 0.07
13 2 0.07
14 17 0.63
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATAATAATTCTC
Found at i:12320 original size:22 final size:22
Alignment explanation
Indices: 12292--12334 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
12282 TTTTGACCTC
12292 ATAATAATAATTCTCTAATAAA
1 ATAATAATAATTCTCTAATAAA
12314 ATAATAATAATTCTCTAATAA
1 ATAATAATAATTCTCTAATAA
12335 TAATTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAATAATAATTCTCTAATAAA
Found at i:21760 original size:5 final size:5
Alignment explanation
Indices: 21750--21784 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
21740 ATCTCAATCT
21750 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTT
21785 GCTCCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:28333 original size:21 final size:21
Alignment explanation
Indices: 28304--28376 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
28294 GGCCCGACTC
*
28304 TTTGTGGGTTTCGAAGATAAAT
1 TTTGAGGGTTTC-AAGATAAAT
28326 TTTG-GGGTTTCAA-A-AAA-
1 TTTGAGGGTTTCAAGATAAAT
***
28343 AAAGAGGGTTTCAAAGATAAAT
1 TTTGAGGGTTTC-AAGATAAAT
28365 TTTG-GGGTTTCA
1 TTTGAGGGTTTCA
28377 GATTTGTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
17 1 0.03
18 10 0.25
19 3 0.08
20 4 0.10
21 17 0.43
22 5 0.12
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (21 bp):
TTTGAGGGTTTCAAGATAAAT
Found at i:29946 original size:3 final size:3
Alignment explanation
Indices: 29940--29973 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
29930 TTCTTCTTCT
29940 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
29974 GAGTATTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:30195 original size:57 final size:57
Alignment explanation
Indices: 30090--30207 Score: 182
Period size: 57 Copynumber: 2.1 Consensus size: 57
30080 ATCACAATGG
*
30090 AAACATATACAATACTACAAATATTGCATCATATCTCTGCTTTAAAAAAATGTAGAA
1 AAACATATACAATACTACAAATATTGCATCACATCTCTGCTTTAAAAAAATGTAGAA
* * * *
30147 AAACATGTACACTACTACACATATTGCATCACATCTTTGCATTTAAAAAAATGTAGAA
1 AAACATATACAATACTACAAATATTGCATCACATCTCTGC-TTTAAAAAAATGTAGAA
30205 AAA
1 AAA
30208 AAATATACTG
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 35 0.64
58 20 0.36
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.29
Consensus pattern (57 bp):
AAACATATACAATACTACAAATATTGCATCACATCTCTGCTTTAAAAAAATGTAGAA
Found at i:31156 original size:33 final size:33
Alignment explanation
Indices: 31091--31156 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
31081 TTTATCTTGA
* * *
31091 GACCACCATAACAATCCGGGTCTTTTGGTTTGC
1 GACCACCATAACAATCCGGATCATTTGCTTTGC
*
31124 GACCACCATGACTAA-CCGGATCATTTGCTTTGC
1 GACCACCATAAC-AATCCGGATCATTTGCTTTGC
31157 AAGAAGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (33 bp):
GACCACCATAACAATCCGGATCATTTGCTTTGC
Found at i:31521 original size:161 final size:162
Alignment explanation
Indices: 31314--31641 Score: 568
Period size: 164 Copynumber: 2.0 Consensus size: 162
31304 AGGGTTTATT
31314 ATGAAATGTGTAACTGTAACAACAATAAAAACATATAATCATATCATATGATCATAATTACAA-T
1 ATGAAATGTGTAACTGTAACAACAATAAAAACATATAATCATATCATATGATCATAATTACAATT
*
31378 TTAAATAATTAATTGAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTGGAATGTAACGT
66 TTAAATAATTAATTGAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTAGAATGTAACGT
31443 ACATGTAAACATCAAATGACAATTAATATAGA
131 ACATGTAAACATCAAATGACAATTAATATAGA
* * *
31475 ATGAAATGTGTAACTGTAACCAGAATAAAAGCATATAATCATATCATATGATCATAATTACAATT
1 ATGAAATGTGTAACTGTAACAACAATAAAAACATATAATCATATCATATGATCATAATTACAA--
31540 TTTTAAATAATTAATTGAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTAGAATGTAAC
64 TTTTAAATAATTAATTGAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTAGAATGTAAC
* * *
31605 GTACATGTAAATATCCAATGACAATTCATATAGA
129 GTACATGTAAACATCAAATGACAATTAATATAGA
31639 ATG
1 ATG
31642 TAATTTTTTG
Statistics
Matches: 157, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
161 60 0.38
164 97 0.62
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (162 bp):
ATGAAATGTGTAACTGTAACAACAATAAAAACATATAATCATATCATATGATCATAATTACAATT
TTAAATAATTAATTGAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTAGAATGTAACGT
ACATGTAAACATCAAATGACAATTAATATAGA
Found at i:33281 original size:121 final size:122
Alignment explanation
Indices: 33134--33375 Score: 405
Period size: 124 Copynumber: 2.0 Consensus size: 122
33124 GTCATACATG
33134 ATTTGGTGAGTCAGATTTGTGGTACTTAGAG-CTTTAGTTCAATAAGACTGCTATTATGTCTTTC
1 ATTTGGTGAGTCAGATTTGTGGTACTTAGAGTCTTTAGTTCAATAAGACTGCTATTATGTCTTTC
* * * *
33198 AAGTAAGATAGACTATAAGCATGCTTAACTAAGTGTTTTTTAGGCCTTTTTGACAAA
66 AAGTAAGATAGACTATAAACATGCTTAACAAAGTGTATTCTAGGCCTTTTTGACAAA
33255 ATTTGGTGAGTCAGATTTGTGGTACTTAGAGCTTCTTTAGTTCAATAAGACTGCTATTATGTCTT
1 ATTTGGTGAGTCAGATTTGTGGTACTTAGAG--TCTTTAGTTCAATAAGACTGCTATTATGTCTT
* *
33320 TCAATTAAGATAGGCTATAAACATGCTTAACAAAGTGTATTCTAGGCCTTTTTGAC
64 TCAAGTAAGATAGACTATAAACATGCTTAACAAAGTGTATTCTAGGCCTTTTTGAC
33376 CATTGACATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
121 31 0.28
124 81 0.72
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (122 bp):
ATTTGGTGAGTCAGATTTGTGGTACTTAGAGTCTTTAGTTCAATAAGACTGCTATTATGTCTTTC
AAGTAAGATAGACTATAAACATGCTTAACAAAGTGTATTCTAGGCCTTTTTGACAAA
Found at i:33804 original size:68 final size:71
Alignment explanation
Indices: 33670--33813 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 71
33660 TGATGATGAT
* *
33670 AAAATTTTTCTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTCATTTCT
1 AAAATTTTTCTTCTAAAGGTTGCTCTCAAACAC---ATTCTTATAGATGCGTATCATTCATTTCT
33735 TGACAATGC
63 TGACAATGC
*
33744 AAAA-TTTT-TTCTAAAGGTTGCTCTCAAACAC-TTCTTATAGATGCGTATCATTCTTTTCTTGA
1 AAAATTTTTCTTCTAAAGGTTGCTCTCAAACACATTCTTATAGATGCGTATCATTCATTTCTTGA
33806 CAATGC
66 CAATGC
33812 AA
1 AA
33814 TTTTAGTTCC
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
68 36 0.54
72 23 0.34
73 4 0.06
74 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (71 bp):
AAAATTTTTCTTCTAAAGGTTGCTCTCAAACACATTCTTATAGATGCGTATCATTCATTTCTTGA
CAATGC
Found at i:34613 original size:2 final size:2
Alignment explanation
Indices: 34606--34633 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34596 AAGAATACAT
34606 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
34634 GAGCGTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:35568 original size:18 final size:18
Alignment explanation
Indices: 35541--35575 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35531 GGAAGTCAAC
35541 GATTTCTTATTAATTGTT
1 GATTTCTTATTAATTGTT
* *
35559 GATTTTTTATTGATTGT
1 GATTTCTTATTAATTGT
35576 AAATATGTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (18 bp):
GATTTCTTATTAATTGTT
Found at i:38075 original size:30 final size:27
Alignment explanation
Indices: 38021--38084 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 27
38011 GGGGTGCGGG
*
38021 TTTCTTTTTTATTTTTGCTTTTCCTTC
1 TTTCTTTTTCATTTTTGCTTTTCCTTC
38048 TTTCTTTATTCATCTTTTGCTTTTTCCTTC
1 TTTCTTT-TTCAT-TTTTGC-TTTTCCTTC
38078 TTTCTTT
1 TTTCTTT
38085 GTTTCACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 7 0.21
28 4 0.12
29 6 0.18
30 16 0.48
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (27 bp):
TTTCTTTTTCATTTTTGCTTTTCCTTC
Found at i:40433 original size:34 final size:35
Alignment explanation
Indices: 40372--40447 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
40362 AATGTAATTA
*
40372 TTTTTATTAGTAAACCTCTTTTGTAGACTCTTTAT
1 TTTTTATTAGTAAACCTCTTTTCTAGACTCTTTAT
40407 TTTTTATTAGTAAACCTC-TTTCTAGACTCTTTAT
1 TTTTTATTAGTAAACCTCTTTTCTAGACTCTTTAT
40441 TTGTTTA
1 TT-TTTA
40448 GACTTTTTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 17 0.44
35 22 0.56
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.55
Consensus pattern (35 bp):
TTTTTATTAGTAAACCTCTTTTCTAGACTCTTTAT
Found at i:44064 original size:2 final size:2
Alignment explanation
Indices: 44057--44089 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
44047 TTGACGCTCA
*
44057 TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
44090 ATACACACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:44856 original size:74 final size:74
Alignment explanation
Indices: 44770--44910 Score: 189
Period size: 74 Copynumber: 1.9 Consensus size: 74
44760 ATTAATTATT
44770 TATATATTATAATCATATTATATATGAT-T-AATT-ATAAAAAAAACCAAACATATAATTATATA
1 TATATATTATAATCATATTATATAT-ATATAAATTAAT-AAAAAAA-CAAACATATAATTATATA
44832 TATATAACAAAA
63 TATATAACAAAA
* * * *
44844 TATATATTATAATTATATTATATATATAATAAATTAATTATAAAACAAATATATAATTATATATA
1 TATATATTATAATCATATTATATATAT-ATAAATTAATAAAAAAACAAACATATAATTATATATA
44909 TA
65 TA
44911 AATATTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
73 2 0.03
74 24 0.41
75 22 0.37
76 9 0.15
77 2 0.03
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (74 bp):
TATATATTATAATCATATTATATATATATAAATTAATAAAAAAACAAACATATAATTATATATAT
ATAACAAAA
Found at i:44866 original size:20 final size:20
Alignment explanation
Indices: 44843--44911 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
44833 ATATAACAAA
*
44843 ATATATATTAT-AATTATATT
1 ATATATATAATAAATTA-ATT
44863 ATATATATAATAAATTAATT
1 ATATATATAATAAATTAATT
* * *
44883 ATA-AAACAA-ATATATAATT
1 ATATATATAATAAAT-TAATT
44902 ATATATATAA
1 ATATATATAA
44912 ATATTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 3 0.08
19 12 0.30
20 20 0.50
21 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATATAATAAATTAATT
Found at i:44911 original size:25 final size:25
Alignment explanation
Indices: 44809--44912 Score: 81
Period size: 25 Copynumber: 4.1 Consensus size: 25
44799 AATTATAAAA
*
44809 AAAACCAAACATATAATTATATATAT
1 AAAA-CAAATATATAATTATATATAT
*
44835 ATAACAAA-ATATATATTATA-ATTAT
1 AAAACAAATATATA-ATTATATA-TAT
** * *
44860 ATTATATATATAATAAATTA-AT-TAT
1 AAAACAAATAT-AT-AATTATATATAT
44885 AAAACAAATATATAATTATATATAT
1 AAAACAAATATATAATTATATATAT
44910 AAA
1 AAA
44913 TATTAAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
23 5 0.08
24 10 0.16
25 34 0.55
26 6 0.10
27 6 0.10
28 1 0.02
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAACAAATATATAATTATATATAT
Found at i:48336 original size:43 final size:44
Alignment explanation
Indices: 48283--48365 Score: 150
Period size: 43 Copynumber: 1.9 Consensus size: 44
48273 TATTATTTTG
*
48283 TTTGTTTGGTAAGTAGGTTAATTAAATTAATTTT-GTTTGTTTA
1 TTTGTTTGGTAAGTAAGTTAATTAAATTAATTTTAGTTTGTTTA
48326 TTTGTTTGGTAAGTAAGTTAATTAAATTAATTTTAGTTTG
1 TTTGTTTGGTAAGTAAGTTAATTAAATTAATTTTAGTTTG
48366 GATTGAATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
43 33 0.87
44 5 0.13
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (44 bp):
TTTGTTTGGTAAGTAAGTTAATTAAATTAATTTTAGTTTGTTTA
Found at i:49833 original size:21 final size:24
Alignment explanation
Indices: 49804--49854 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
49794 TTTTGAACTC
49804 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
49827 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
49850 ATTAT
1 ATTAT
49855 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:49849 original size:25 final size:25
Alignment explanation
Indices: 49804--49852 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
49794 TTTTGAACTC
*
49804 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
49829 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
49853 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:55903 original size:3 final size:3
Alignment explanation
Indices: 55895--55930 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
55885 ATATATATAT
55895 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55931 TATTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:57366 original size:22 final size:22
Alignment explanation
Indices: 57316--57366 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
57306 TTCATAGGAA
*
57316 AGTTTATTAAAATTTCATAATT
1 AGTTTATTAAAATTTCATAATG
* *
57338 AGGTTATTAAAGTTTCAT-ATGG
1 AGTTTATTAAAATTTCATAAT-G
57360 AGTTTAT
1 AGTTTAT
57367 CACATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (22 bp):
AGTTTATTAAAATTTCATAATG
Found at i:57379 original size:22 final size:22
Alignment explanation
Indices: 57354--57439 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 22
57344 TTAAAGTTTC
* * *
57354 ATATGGAGTTTATCACATTTTT
1 ATATGGAGATTATCAAAATTTT
*
57376 ATATGTA-ATTATCAAAATTTT
1 ATATGGAGATTATCAAAATTTT
* * *
57397 ATATGGTGGTTATCAAAATTTA
1 ATATGGAGATTATCAAAATTTT
*
57419 ATA-GGATAATTATCAAAATTT
1 ATATGGA-GATTATCAAAATTT
57440 CATAAAAATA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 18 0.35
22 33 0.65
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (22 bp):
ATATGGAGATTATCAAAATTTT
Done.