Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008810.1 Corchorus capsularis cultivar CVL-1 contig08831, 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: 15164
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Found at i:2849 original size:70 final size:71
Alignment explanation
Indices: 2688--2849 Score: 157
Period size: 70 Copynumber: 2.3 Consensus size: 71
2678 AGTGTGATTA
* * ** * * *
2688 AGAAGAATTAAGAAAAGAAAGTATAGTCAAGATCCTAATTTGGATAATTAAGAAGAGTAAAGTCT
1 AGAAGAATTAAGAAAAGAAAGCACAAACAAGATCCTAATTTGGAGAATCAAGAAGAGTAAAGTCA
2753 TAATTC
66 TAATTC
* * *** * * * *
2759 TG-GGTAATTAAGAGGGGAAAGCACAAACAAGGTCTTAATTTGG-GAATCAAGAATAGTAAATTC
1 AGAAG-AATTAAGAAAAGAAAGCACAAACAAGATCCTAATTTGGAGAATCAAGAAGAGTAAAGTC
2822 ATAATTC
65 ATAATTC
2829 AGAAGAATTAAGAAAAGAAAG
1 AGAAGAATTAAGAAAAGAAAG
2850 TCCAGTCAAG
Statistics
Matches: 68, Mismatches: 21, Indels: 5
0.72 0.22 0.05
Matches are distributed among these distances:
70 37 0.54
71 31 0.46
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (71 bp):
AGAAGAATTAAGAAAAGAAAGCACAAACAAGATCCTAATTTGGAGAATCAAGAAGAGTAAAGTCA
TAATTC
Found at i:2860 original size:70 final size:70
Alignment explanation
Indices: 2688--2916 Score: 178
Period size: 71 Copynumber: 3.2 Consensus size: 70
2678 AGTGTGATTA
** * * * *
2688 AGAAGAATTAAGAAAAGAAAGTATAGTCAAGATCCTAATTTGGATAATTAAGAAGAGTAAAGTCT
1 AGAAGAATTAAGAAAAGAAAGTCCAGTCAAGGTCCTAATTTGG-GAATCAAGAAGAGTAAAGTCA
2753 TAATTC
65 TAATTC
* * *** ** * * *
2759 TG-GGTAATTAAGAGGGGAAAG-CACAAACAAGGTCTTAATTTGGGAATCAAGAATAGTAAATTC
1 AGAAG-AATTAAGAAAAGAAAGTC-CAGTCAAGGTCCTAATTTGGGAATCAAGAAGAGTAAAGTC
2822 ATAATTC
64 ATAATTC
* * **
2829 AGAAGAATTAAGAAAAGAAAGTCCAGTCAAGGCCCTAATTTGGGTAATTAAGGAAG-GTAGCGTC
1 AGAAGAATTAAGAAAAGAAAGTCCAGTCAAGGTCCTAATTTGGG-AATCAA-GAAGAGTAAAGTC
*
2893 TTAATTC
64 ATAATTC
*
2900 A-AGGCAATTAAGAAAAG
1 AGAAG-AATTAAGAAAAG
2917 TATGCATAGT
Statistics
Matches: 119, Mismatches: 32, Indels: 14
0.72 0.19 0.08
Matches are distributed among these distances:
70 56 0.47
71 60 0.50
72 3 0.03
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (70 bp):
AGAAGAATTAAGAAAAGAAAGTCCAGTCAAGGTCCTAATTTGGGAATCAAGAAGAGTAAAGTCAT
AATTC
Found at i:2979 original size:40 final size:40
Alignment explanation
Indices: 2931--3081 Score: 185
Period size: 40 Copynumber: 3.8 Consensus size: 40
2921 CATAGTTGAG
* *
2931 GACTTAATTCATAGAAATCAAGTAAAAACAGTAGTCAAAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAATAGTCAAAA
2971 GACTTAATTCATAGAAATTAAGTAAAAACAATAGTCAAAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAATAGTCAAAA
* ** * * *
3011 GACTTAATTCATAAAAATTAAGTGGAAGCAACAGTTAAAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAATAGTCAAAA
* * * * *
3051 GGCTTAATTTATTGCAATTAAGTAAGAACAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAA
3082 AAGAAAGTTT
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (40 bp):
GACTTAATTCATAGAAATTAAGTAAAAACAATAGTCAAAA
Found at i:3149 original size:24 final size:24
Alignment explanation
Indices: 3108--3159 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
3098 ATTTCAAGGA
*
3108 AATTAGGTAAAAGAAGACAGATTT
1 AATTAGGTAAAAGAAGACAGACTT
* *
3132 AATTAGGT-GAAGATAGACTGACTT
1 AATTAGGTAAAAGA-AGACAGACTT
3156 AATT
1 AATT
3160 TCAAGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (24 bp):
AATTAGGTAAAAGAAGACAGACTT
Found at i:3185 original size:35 final size:35
Alignment explanation
Indices: 3132--4343 Score: 1070
Period size: 35 Copynumber: 33.5 Consensus size: 35
3122 AGACAGATTT
* * *
3132 AATTAGGTGAAGATAGACTGACTTAATTTCAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
*
3167 AATTAGGTAAAGAAAGACTGACTTAATTTCAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
3202 AATTAGGTAAA-AGAAGACT-G----ATTT------
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGA
* * * *
3226 AATTAGGTGAAGATAGACTGACTTATTTTCAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
* *
3261 AATTAGGTAAAGAAAGAATGACTTAATTTCAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
3296 AATTAGGTAAA-AGAAGACT-G----ATTT------
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGA
* *
3320 AATTAGGTAAAGAAAGACTGACTTAATGTCAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
**
3355 AATTAGGTAAA-AGAAGACTAACTTAATTTCAAGGA
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGA
* *
3390 AATTACGTAAAGAAAGACTGACTTAATTTCAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
*
3425 AATTAGGTAAA-AGAAGACTGACTTAATTTCAAGGA
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGA
*
3460 AATTAGGTAAA-AGAAGACTGACTTAATTTCAAGAAAGAA
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAG---G-A
*
3499 AATTAGGTAAAGAAAGACTGACTTAATTTCAAGAAATGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAG----GA
* *
3538 AATTAGGTAAAGATAGACTGACTTAATTTCAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
* *
3573 AATTAAGTAAAGATAGACTGGCTTAATTTCAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
* *
3608 AATTAAGTAAA-AAAGGCTGGCTTAATTTCAAAAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
* * *
3646 AATTAGGTAAAAAGAAGAATGGTTTAATTTCAAGGA
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGA
* *
3682 AATTAAGTAAA-AAAGACTAGCTTAATTTCAAAAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
3720 AATTAGGTAAA-AAAGACTGGCTTAATTTCAAGAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
*
3758 AATTAGGTAAA-AAAGACTGGCATAATTTCAAGAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
* * * *
3796 AATTAGGTAAAAAGAAGACAGTCTTAATTTCAAAGA
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGA
* *
3832 AATTAGGTAAAGATAGACTGGCTTAATTTCAAGAAAGGG
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
3871 AATTAGGTAAA-AAAGACTGGCTTAATTTCAGGAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
*
3909 AATTAGGTAAA-AAAGACTGGTTTAATTTCAAGAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
*
3947 AATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGA
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGA
*
3983 AATTAGGTAAAGATAGACTGGCTTAATTTCAAGAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
*
4022 AATTAGGTAAAGAGAAGACTGGTTTAATTTCAGGAAAGGA
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTC----AAGGA
* * *
4062 AATTAGGTAAAAAAAGATTGGTTTAATTTCAAGAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
*
4101 AATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGA
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGA
* *
4137 AATTAGGTAACGATAGACTGGCTTAATTTCAAGAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
**
4176 AATTAGGTAAAGAAAAGACTAACTTAATTTCAAGAAAGGA
1 AATTAGGTAAAG-AAAGACTGGCTTAATTTC----AAGGA
4216 AATTAGGTAAA-AAAGACTGGCTTAATTTCATGAAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGA
*
4254 AATTAGGTAAACAAAAGACTGGCTTAATTTCAAGGA
1 AATTAGGTAAA-GAAAGACTGGCTTAATTTCAAGGA
*
4290 AATTAGGTAAAGATAGACTGGCTTAATTTCAAGGA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
*
4325 AATTAGGCAAAGAAAGACT
1 AATTAGGTAAAGAAAGACT
4344 AAGGCACAAG
Statistics
Matches: 1033, Mismatches: 78, Indels: 132
0.83 0.06 0.11
Matches are distributed among these distances:
24 32 0.03
25 2 0.00
29 6 0.01
30 8 0.01
34 34 0.03
35 356 0.34
36 81 0.08
38 210 0.20
39 153 0.15
40 151 0.15
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.26
Consensus pattern (35 bp):
AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGA
Found at i:3230 original size:59 final size:59
Alignment explanation
Indices: 3167--3288 Score: 183
Period size: 59 Copynumber: 2.1 Consensus size: 59
3157 ATTTCAAGGA
* *
3167 AATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAA-AGAAGACTGATTT
1 AATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAGA-AAGAATGACTT
* * *
3226 AATTAGGTGAAGATAGACTGACTTATTTTCAAGGAAATTAGGTAAAGAAAGAATGACTT
1 AATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAGAAAGAATGACTT
3285 AATT
1 AATT
3289 TCAAGGAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 56 0.98
60 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (59 bp):
AATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAGAAAGAATGACTT
Found at i:3242 original size:94 final size:94
Alignment explanation
Indices: 3081--3526 Score: 569
Period size: 94 Copynumber: 4.6 Consensus size: 94
3071 AGTAAGAACA
** * *
3081 AAAGAAAGTTTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACAGATTTAATTAGGTGAAGAT
1 AAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTTAATTAGGTAAAGAT
3146 AGACTGACTTAATTTCAAGGAAATTAGGT
66 AGACTGACTTAATTTCAAGGAAATTAGGT
*
3175 AAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTTAATTAGGTGAAGAT
1 AAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTTAATTAGGTAAAGAT
*
3240 AGACTGACTTATTTTCAAGGAAATTAGGT
66 AGACTGACTTAATTTCAAGGAAATTAGGT
* *
3269 AAAGAAAGAATGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTTAATTAGGTAAAGAA
1 AAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTTAATTAGGTAAAGAT
*
3334 AGACTGACTTAATGTCAAGGAAATTAGGT
66 AGACTGACTTAATTTCAAGGAAATTAGGT
* *
3363 AAA-AGAAGACTAACTTAATTTCAAGGAAATTACGT-AAAGAAAGACTGACTTAATTTCAAGGAA
1 AAAGA-AAGACTGACTTAATTTCAAGGAAATTAGGTAAAAG-AAGACTG-----ATTT------A
3426 ATTAGGTAAAAGA-AGACTGACTTAATTTCAAGGAAATTAGGT
53 ATTAGGT-AAAGATAGACTGACTTAATTTCAAGGAAATTAGGT
*
3468 AAA-AGAAGACTGACTTAATTTCAAGAAAGAAAATTAGGT-AAAGAAAGACTGACTTAATT
1 AAAGA-AAGACTGACTTAATTTCAAG---G-AAATTAGGTAAAAG-AAGACTGATTTAATT
3527 TCAAGAAATG
Statistics
Matches: 318, Mismatches: 16, Indels: 32
0.87 0.04 0.09
Matches are distributed among these distances:
93 5 0.02
94 216 0.68
98 4 0.01
99 4 0.01
104 3 0.01
105 60 0.19
106 5 0.02
108 1 0.00
109 20 0.06
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.27
Consensus pattern (94 bp):
AAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTTAATTAGGTAAAGAT
AGACTGACTTAATTTCAAGGAAATTAGGT
Found at i:3324 original size:59 final size:59
Alignment explanation
Indices: 3261--3452 Score: 240
Period size: 59 Copynumber: 3.1 Consensus size: 59
3251 TTTTCAAGGA
*
3261 AATTAGGTAAAGAAAGAATGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTT
1 AATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTT
* *
3320 AATTAGGTAAAGAAAGACTGACTTAATGTCAAGGAAATTAGGTAAAAGAAGACTAACTTAATTT
1 AATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAG----AC-TGATTT
* *
3384 CAAGGAAATTACGTAAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACTT
1 ------AATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTT
3449 AATT
1 AATT
3453 TCAAGGAAAT
Statistics
Matches: 115, Mismatches: 7, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
59 53 0.46
63 2 0.02
64 5 0.04
65 4 0.03
66 2 0.02
70 49 0.43
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (59 bp):
AATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATTT
Found at i:3328 original size:24 final size:24
Alignment explanation
Indices: 3296--3346 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
3286 ATTTCAAGGA
*
3296 AATTAGGTAAA-AGAAGACTGATTT
1 AATTAGGTAAAGA-AAGACTGACTT
3320 AATTAGGTAAAGAAAGACTGACTT
1 AATTAGGTAAAGAAAGACTGACTT
3344 AAT
1 AAT
3347 GTCAAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (24 bp):
AATTAGGTAAAGAAAGACTGACTT
Found at i:3576 original size:74 final size:72
Alignment explanation
Indices: 3320--4331 Score: 1049
Period size: 75 Copynumber: 13.6 Consensus size: 72
3310 AGACTGATTT
* * **
3320 AATTAGGTAAAGAAAGACTGACTTAATGTC-AAGGAAATTAGGT-AAAAGAAGACTAACTTAATT
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATT
3383 TCAAGGA
66 TCAAGGA
* * *
3390 AATTACGTAAAGAAAGACTGACTTAATTTC-AAGGAAATTAGGT-AAAAGAAGACTGACTTAATT
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATT
3453 TCAAGGA
66 TCAAGGA
* * * *
3460 AATTAGGTAAA-AGAAGACTGACTTAATTTCAAGAAAGAAAATTAGGTAAAGA-AAGACTGACTT
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAAAAGAAGACTGGCTT
3523 AATTTCAAGAAATGA
62 AATTTCAAG----GA
* * *
3538 AATTAGGTAAAGATAGACTGACTTAATTTC-AAGGAAATTAAGT--AAAGATAGACTGGCTTAAT
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAAGGAAATTAGGTAAAAAGA-AGACTGGCTTAAT
3600 TTCAAGGA
65 TTCAAGGA
* * * *
3608 AATTAAGTAAA-AAAGGCTGGCTTAATTTCAAAAAAGGAAATTAGGTAAAAAGAAGAATGGTTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAAAAGAAGACTGGCTTA
3672 ATTTCAAGGA
63 ATTTCAAGGA
* *
3682 AATTAAGTAAA-AAAGACTAGCTTAATTTCAAAAAAGGAAATTAGGT-AAAA-AAGACTGGCTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAAAAGAAGACTGGCTTA
3744 ATTTCAAGAAAGGA
63 ATTTC----AAGGA
* * *
3758 AATTAGGTAAA-AAAGACTGGCATAATTTCAAGAAAGGAAATTAGGTAAAAAGAAGACAGTCTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAAAAGAAGACTGGCTTA
*
3822 ATTTCAAAGA
63 ATTTCAAGGA
* *
3832 AATTAGGTAAAGATAGACTGGCTTAATTTCAAGAAAGGGAATTAGGT-AAAA-AAGACTGGCTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAAAAGAAGACTGGCTTA
3895 ATTTCAGGAAAGGA
63 ATTTC----AAGGA
*
3909 AATTAGGTAAA-AAAGACTGGTTTAATTTCAAGAAAGGAAATTAGGTAAAAAGAAGACTGGCTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAAAAGAAGACTGGCTTA
3973 ATTTCAAGGA
63 ATTTCAAGGA
* * *
3983 AATTAGGTAAAGATAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAGAAGACTGGTTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAAAAGAAGACTGGCTTA
4048 ATTTCAGGAAAGGA
63 ATTTC----AAGGA
* * *
4062 AATTAGGTAAAAAAAGATTGGTTTAATTTCAAGAAAGGAAATTAGGTAAAAAGAAGACTGGCTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAAAAGAAGACTGGCTTA
4127 ATTTCAAGGA
63 ATTTCAAGGA
* * **
4137 AATTAGGTAACGATAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAA-AAGACTAACTT
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAA-AAGAAGACTGGCTT
4201 AATTTCAAGAAAGGA
62 AATTTC----AAGGA
4216 AATTAGGTAAA-AAAGACTGGCTTAATTTCATGAAAGGAAATTAGGTAAACAA-AAGACTGGCTT
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC---AAAGGAAATTAGGTAAA-AAGAAGACTGGCTT
4279 AATTTCAAGGA
62 AATTTCAAGGA
*
4290 AATTAGGTAAAGATAGACTGGCTTAATTTC-AAGGAAATTAGG
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAAGGAAATTAGG
4332 CAAAGAAAGA
Statistics
Matches: 837, Mismatches: 62, Indels: 85
0.85 0.06 0.09
Matches are distributed among these distances:
69 16 0.02
70 106 0.13
71 12 0.01
72 17 0.02
73 32 0.04
74 175 0.21
75 176 0.21
76 81 0.10
77 23 0.03
78 114 0.14
79 85 0.10
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (72 bp):
AATTAGGTAAAGAAAGACTGGCTTAATTTCAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATT
TCAAGGA
Found at i:3583 original size:113 final size:112
Alignment explanation
Indices: 3320--4343 Score: 1153
Period size: 113 Copynumber: 9.2 Consensus size: 112
3310 AGACTGATTT
* * **
3320 AATTAGGTAAAGAAAGACTGACTTAATGTCAAGGAAATTAGGTAAAAGAAGACTAACTTAATTTC
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTC
* *
3385 AAG---GAAATTACGTAAAGAAAGACTGACTTAATTTC----AAGGA
66 AAGAAAGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGA
* *
3425 AATTAGGTAAA-AGAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACTTAATTT
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTT
* *
3489 CAAGAAAGAAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGAAATGA
65 CAAGAAAG-AAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGA
* * *
3538 AATTAGGTAAAGATAGACTGACTTAATTTCAAGGAAATTAAGT-AAAGATAGACTGGCTTAATTT
1 AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGA-AGACTGGCTTAATTT
* * *
3602 CAAG---GAAATTAAGTAAA-AAAGGCTGGCTTAATTTCAAAAAAGGA
65 CAAGAAAGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGA
* * * * *
3646 AATTAGGTAAAAAGAAGAATGGTTTAATTTCAAGGAAATTAAGTAAAA-AAGACTAGCTTAATTT
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTT
*
3710 CAAAAAAGGAAATTAGGTAAA-AAAGACTGGCTTAATTTCAAGAAAGGA
65 CAAGAAA-GAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGA
* * *
3758 AATTAGGTAAA-AAAGACTGGCATAATTTCAAGAAAGGAAATTAGGTAAAAAGAAGACAGTCTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGAAATTAGGT-AAAAGAAGACTGGCTTA
* *
3822 ATTTC---AAAGAAATTAGGTAAAGATAGACTGGCTTAATTTCAAGAAAGGG
61 ATTTCAAGAAAGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGA
*
3871 AATTAGGTAAA-AAAGACTGGCTTAATTTCAGGAAAGGAAATTAGGTAAAA-AAGACTGGTTTAA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGAAATTAGGTAAAAGAAGACTGGCTTAA
*
3934 TTTCAAGAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATTTC----AAGGA
62 TTTCAAGAAA-GAAATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGAAAGGA
* *
3983 AATTAGGTAAAGATAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAGAAGACTGGTTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGAAATTAGGTAAA-AGAAGACTGGCTTA
* * * *
4048 ATTTCAGGAAAGGAAATTAGGTAAAAAAAGATTGGTTTAATTTCAAGAAAGGA
61 ATTTCAAGAAA-GAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGA
* *
4101 AATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGAAATTAGGT-AACGATAGACTGGCTTAATT
1 AATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGA-AGACTGGCTTAATT
**
4165 TCAAGAAAGGAAATTAGGTAAAGAAAAGACTAACTTAATTTCAAGAAAGGA
64 TCAAGAAA-GAAATTAGGTAAAG-AAAGACTGGCTTAATTTCAAGAAAGGA
*
4216 AATTAGGTAAA-AAAGACTGGCTTAATTTCATGAAAGGAAATTAGGTAAACAAAAGACTGGCTTA
1 AATTAGGTAAAGAAAGACTGGCTTAATTTC----AAGGAAATTAGGTAAA-AGAAGACTGGCTTA
*
4280 ATTTCAAG---GAAATTAGGTAAAGATAGACTGGCTTAATTTC----AAGGA
61 ATTTCAAGAAAGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGA
*
4325 AATTAGGCAAAGAAAGACT
1 AATTAGGTAAAGAAAGACT
4344 AAGGCACAAG
Statistics
Matches: 813, Mismatches: 60, Indels: 87
0.85 0.06 0.09
Matches are distributed among these distances:
104 1 0.00
105 64 0.08
108 53 0.07
109 83 0.10
110 25 0.03
111 15 0.02
112 85 0.10
113 203 0.25
114 83 0.10
115 103 0.13
116 30 0.04
117 13 0.02
118 38 0.05
119 17 0.02
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (112 bp):
AATTAGGTAAAGAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTC
AAGAAAGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGA
Found at i:4434 original size:36 final size:33
Alignment explanation
Indices: 4382--4487 Score: 148
Period size: 32 Copynumber: 3.2 Consensus size: 33
4372 AATTAAGAAG
4382 AAGAA-AAG-GACTTAATTCAGGGTAATTAAGT
1 AAGAATAAGTGACTTAATTCAGGGTAATTAAGT
*
4413 AGAGTTAATAAGTGGCTTAATTCAGGGTAATTAAGT
1 A-AG--AATAAGTGACTTAATTCAGGGTAATTAAGT
4449 -AGAATAAGTGACTTAATTCAGGGTAATTAAGT
1 AAGAATAAGTGACTTAATTCAGGGTAATTAAGT
4481 AA-AATAA
1 AAGAATAA
4488 AAGAACTTGA
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
31 1 0.01
32 36 0.54
33 1 0.01
34 4 0.06
35 3 0.04
36 22 0.33
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (33 bp):
AAGAATAAGTGACTTAATTCAGGGTAATTAAGT
Found at i:6490 original size:82 final size:82
Alignment explanation
Indices: 6397--6562 Score: 314
Period size: 82 Copynumber: 2.0 Consensus size: 82
6387 TTTTTAACAG
*
6397 TTTATCAGATTTAAAAGATGCCTCTTAACCGAAAAATGATATCCGAACCAAAAAAATTAACACTT
1 TTTATCAGATTTAAAAGATGCCTCTTAACCGAAAAATGATATCCGAACCAAAAAAATTAACACAT
6462 AGAAAAATTCAAAGTCA
66 AGAAAAATTCAAAGTCA
*
6479 TTTATCAGATTTAAAAGATGCCTCTTAACCGAAAAATGATATCCGAACCAAAAAGATTAACACAT
1 TTTATCAGATTTAAAAGATGCCTCTTAACCGAAAAATGATATCCGAACCAAAAAAATTAACACAT
6544 AGAAAAATTCAAAGTCA
66 AGAAAAATTCAAAGTCA
6561 TT
1 TT
6563 AAGAGCCCAA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (82 bp):
TTTATCAGATTTAAAAGATGCCTCTTAACCGAAAAATGATATCCGAACCAAAAAAATTAACACAT
AGAAAAATTCAAAGTCA
Found at i:6688 original size:20 final size:20
Alignment explanation
Indices: 6663--6702 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6653 AGTACGATAT
6663 CAAGTCCAAATGACTTGAAA
1 CAAGTCCAAATGACTTGAAA
6683 CAAGTCCAAATGACTTGAAA
1 CAAGTCCAAATGACTTGAAA
6703 ACCACCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (20 bp):
CAAGTCCAAATGACTTGAAA
Found at i:7538 original size:6 final size:6
Alignment explanation
Indices: 7529--7560 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
7519 AAAAAATAAG
7529 TATCTA TATCTA TATCTA TATCTA TA-CTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TAT
7561 ATATTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:11863 original size:14 final size:14
Alignment explanation
Indices: 11844--11875 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
11834 ACTGTACTAG
11844 TGTATATATATATA
1 TGTATATATATATA
*
11858 TGTATATATATGTA
1 TGTATATATATATA
11872 TGTA
1 TGTA
11876 CCTCATCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
TGTATATATATATA
Found at i:13391 original size:2 final size:2
Alignment explanation
Indices: 13378--13417 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
13368 TTGTATGAAT
* *
13378 TA TA TT TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13418 GTGCACTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:14178 original size:20 final size:20
Alignment explanation
Indices: 14153--14197 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
14143 AGTGGATAAA
14153 AATCCTCTCCCCTCATTTTC
1 AATCCTCTCCCCTCATTTTC
14173 AATCCTCTCCCCTCATTTTC
1 AATCCTCTCCCCTCATTTTC
*
14193 TATCC
1 AATCC
14198 CCCATTGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.40
Consensus pattern (20 bp):
AATCCTCTCCCCTCATTTTC
Found at i:14661 original size:145 final size:144
Alignment explanation
Indices: 14474--14769 Score: 529
Period size: 145 Copynumber: 2.0 Consensus size: 144
14464 TAATTAGTAT
* *
14474 TTATAATGTGAGCCTATGAGTTTGTCTAACGAGTTGATTCGGAGACAAATTCAGTTTTTTAAAAA
1 TTATAATGTGAGCCTACGAGTTTGTCTAACGAGTTGACTCGGAGACAAATTCAGTTTTTTAAAAA
14539 TTCAAAACAAAATAAAAACTACTCATCTTAAATAAAACTACCAATATAATATTTAAAACTACCAA
66 TTCAAAACAAAATAAAAACTACTCATCTTAAATAAAACTACCAATATAATATTTAAAACTACCAA
14604 ATATTAGAAGACTAA
131 ATATTAGAAGA-TAA
* *
14619 TTATAATGTGAGCCTCCGAGTTTGTCTCACGAGTTGACTCGGAGACAAATTCAGTTTTTTAAAAA
1 TTATAATGTGAGCCTACGAGTTTGTCTAACGAGTTGACTCGGAGACAAATTCAGTTTTTTAAAAA
*
14684 TTCAAAACAAAATAAAAACTACTCATCTTAAATAAAACTACCAATATAATATTTAAAACTACCCA
66 TTCAAAACAAAATAAAAACTACTCATCTTAAATAAAACTACCAATATAATATTTAAAACTACCAA
14749 ATATTAGAAGATAA
131 ATATTAGAAGATAA
*
14763 ATATAAT
1 TTATAAT
14770 ATTTAAATTT
Statistics
Matches: 145, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
144 9 0.06
145 136 0.94
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (144 bp):
TTATAATGTGAGCCTACGAGTTTGTCTAACGAGTTGACTCGGAGACAAATTCAGTTTTTTAAAAA
TTCAAAACAAAATAAAAACTACTCATCTTAAATAAAACTACCAATATAATATTTAAAACTACCAA
ATATTAGAAGATAA
Found at i:15018 original size:23 final size:23
Alignment explanation
Indices: 14990--15040 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 23
14980 TATAATATAT
14990 ATATATAATATCAATATCAATATCA
1 ATATAT-ATAT-AATATCAATATCA
*
15015 ATATATATATAATATCAATATGA
1 ATATATATATAATATCAATATCA
15038 ATA
1 ATA
15041 GGTACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 15 0.60
24 4 0.16
25 6 0.24
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (23 bp):
ATATATATATAATATCAATATCA
Found at i:15034 original size:6 final size:6
Alignment explanation
Indices: 14992--15040 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
14982 TAATATATAT
*
14992 ATAT-A ATATCA ATATCA ATATCA ATAT-A TATAT-A ATATCA ATATGA
1 ATATCA ATATCA ATATCA ATATCA ATATCA -ATATCA ATATCA ATATCA
15038 ATA
1 ATA
15041 GGTACTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
5 9 0.22
6 31 0.77
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (6 bp):
ATATCA
Done.