Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020079.1 Corchorus olitorius cultivar O-4 contig20112, 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: 15949
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:2906 original size:47 final size:47
Alignment explanation
Indices: 2853--3935 Score: 604
Period size: 47 Copynumber: 22.2 Consensus size: 47
2843 GAGTAAAAGT
2853 AAAAGAA-ACAAAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
1 AAAAGAAGA-AAAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
*
2900 AAAAGAAGAAAAGGATAGTTTAATTCCAGGTAATTAAACTAAATAGC
1 AAAAGAAGAAAAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * * *
2947 AAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGATTAAATAGC
1 AAAAGAAGAAAAGGATAGTTTAATTCTAGGTAATTAAAC-------TAAATAGC
* * * *
3001 AAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGATTAAATAGC
1 AAAAGAAGAAAAGGATAGTTTAATTCTAGGTAATTAAAC-------TAAATAGC
* * *
3055 AAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACTAAATAGT
1 AAAAGAAGAAAAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * * *
3102 GAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACTAAATAGT
1 AAAAGAAGAAAAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * * * * * *
3149 GAAAGAAGAAGAGGTTAGTTTAATTATGGGCGATTGAACTAAAGATTAAATAGC
1 AAAAGAAGAAAAGGATAGTTTAATTCT-AG-G--T-AA-TTAA-ACTAAATAGC
* * * * **
3203 AAAAGAAGAAGAGGTTAGTCTAATTC-AGAGCAATTAAACTAAAGAGTAAA
1 AAAAGAAGAAAAGGATAGTTTAATTCTAG-GTAATTAAACT-AA-A-TAGC
* ** *
3253 AGAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAGTTAAATAGT
1 A-AA--AG---AAGAA-AAG-GA-TAGTTTAATTCTAGGTAATTAAACTAAATAGC
*
3309 AAAAGAAG--AAGGTATTAGTTTAATTCTAGGTAATTAAACTAAAGGGTA-A
1 AAAAGAAGAAAAGG-A-TAGTTTAATTCTAGGTAATTAAACTAAA---TAGC
* * *
3358 AAGAAGAAGTACACAGAGGCTAGTTTAATTCTAGGTCATTAAACTAAAGAGC
1 AA-AAGAAG-A-A-A-AGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * * * * * *
3410 AAGAGAGGAAGAA-AACAGTTTAATTCTGGGTAATTAAACTAAAAAGT
1 AAAAGAAGAA-AAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * ** * * *
3457 AAGAGGAGAAAAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGC
1 AAAAGAAGAAAAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * *
3504 AAAAGAAGAAGAA-AAGAGTTTAATTC-AGAGTAATTAAACTAAAAAGC
1 AAAAGAAGAA-AAGGATAGTTTAATTCTAG-GTAATTAAACTAAATAGC
* * * * *
3551 AAGAGAAGAAGAA-AACT-GTTTAATTCTGGGTAATTAAACTAAAAAGT
1 AAAAGAAGAA-AAGGA-TAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * * * * *
3598 AAGAGGAGAAAA-AAGAGTTTAATTCTGGGTAATTAAACTAAAGAGC
1 AAAAGAAGAAAAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * *
3644 AAAAGAAGAAGAA-AAGAGTTTAATTC-AGAGTAATTAAACTAAAAAGC
1 AAAAGAAGAA-AAGGATAGTTTAATTCTAG-GTAATTAAACTAAATAGC
* * * *
3691 AAGAGAAGAAGAA-AACAGTTTAATTC-AGAGTAATTAAACTAAAGAGC
1 AAAAGAAGAA-AAGGATAGTTTAATTCTAG-GTAATTAAACTAAATAGC
** * * * *
3738 AAGTGAAGAAGAA-AACAGTTTAATTCTGGGTAATTAAACTAAAGAGC
1 AAAAGAAGAA-AAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * * * * * * **
3785 AAGAGAAGAAGAA-AACATTTTAATTCTGGGTAACTAAACTAAAAATT
1 AAAAGAAGAA-AAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * * ** *
3832 AAGAGAAGAAGAA-AAGAGTTTAATTCCGGGTAATTAAACTAAATAGT
1 AAAAGAAGAA-AAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
* * * * *
3879 AAAAGAGGAAGAA-AAGAGTTTAACTC-AGGGTAATTAAACTAAAGAGC
1 AAAAGAAGAA-AAGGATAGTTTAATTCTA-GGTAATTAAACTAAATAGC
*
3926 AAGAGAAGAA
1 AAAAGAAGAA
3936 GAAAACAGTT
Statistics
Matches: 889, Mismatches: 97, Indels: 100
0.82 0.09 0.09
Matches are distributed among these distances:
46 45 0.05
47 591 0.66
48 12 0.01
49 8 0.01
50 15 0.02
51 8 0.01
52 6 0.01
53 7 0.01
54 157 0.18
55 3 0.00
56 11 0.01
57 3 0.00
58 3 0.00
59 18 0.02
60 2 0.00
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (47 bp):
AAAAGAAGAAAAGGATAGTTTAATTCTAGGTAATTAAACTAAATAGC
Found at i:2982 original size:94 final size:93
Alignment explanation
Indices: 2867--3959 Score: 747
Period size: 94 Copynumber: 11.2 Consensus size: 93
2857 GAAACAAAGG
* * *
2867 ATAGTTTAATTCTAGGTAATTAAACTAAATAGCAAAAGAAGAAAAGGATAGTTTAATTCCAGGTA
1 ATAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAAAA-AATAGTTTAATTCTAGGTA
**
2932 ATTAAACTAAATAGCAAAAGAAGAAGAGG
65 ATTAAACTAAATAGCAAAAGAAGAAGAAA
* * ***
2961 TTAGTTTAATTCTGGGCAATTAAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTTAGTTTAATT
1 ATAGTTTAATTCTGGGTAATTAAAC-------TAAATAGCAAAAGAAGAA-AAAATAGTTTAATT
* * **
3026 CTGGGCAATTAAACTAAAGATTAAATAGCAAAAGAAGAAGAGG
58 CTAGGTAATTAAAC-------TAAATAGCAAAAGAAGAAGAAA
* * ** ***
3069 TTAGTTTAATTCTAGGTAATTAAACTAAATAGTGAAAGAAGAAGAGGTTAGTTTAATTCTAGGTA
1 ATAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAA-AAAATAGTTTAATTCTAGGTA
** **
3134 ATTAAACTAAATAGTGAAAGAAGAAGAGG
65 ATTAAACTAAATAGCAAAAGAAGAAGAAA
* * * * *** *
3163 TTAGTTTAATTATGGGCGATTGAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTTAGTCTAATT
1 ATAGTTTAATTCT-GG-G--T-AA-TTAA-ACTAAATAGCAAAAGAAGAA-AAAATAGTTTAATT
* **
3228 C-AGAGCAATTAAACTAAAGAGTAAAAGAAGTAGTAAAAGAAGAAGA
58 CTAG-GTAATTAAACT-AA-A-TAGCA-AA--AG---AAGAAGAA-A
** ** * ** *
3274 GATTAGTTTAATTCCAGGTAATTAAGTTAAATAGTAAAAGAAGAAGGTATTAGTTTAATTCTAGG
1 -A-TAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAA-AAAATAGTTTAATTCTAGG
** *
3339 TAATTAAACTAAAGGGTAAAAGAAGAAGTACACA
63 TAATTAAACTAAATAGCAAAAGAAGAAG-A-A-A
* * * * * * *
3373 GAGGCTAGTTTAATTCTAGGTCATTAAACTAAAGAGCAAGAGAGGAAGAAAACAGTTTAATTCTG
1 -A---TAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAA-AAAATAGTTTAATTCTA
* * * * *
3438 GGTAATTAAACTAAAAAGTAAGAGGAGAAAAAA
61 GGTAATTAAACTAAATAGCAAAAGAAGAAGAAA
* * *
3471 AGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAAAAGAGTTTAATTC-AGAGT
1 ATAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAA-AAAATAGTTTAATTCTAG-GT
* *
3535 AATTAAACTAAAAAGCAAGAGAAGAAGAAA
64 AATTAAACTAAATAGCAAAAGAAGAAGAAA
* * * * * *
3565 ACT-GTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGGAGAAAAAAGAGTTTAATTCTGGGTA
1 A-TAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAAAAAATAGTTTAATTCTAGGTA
*
3629 ATTAAACTAAAGAGCAAAAGAAGAAGAAA
65 ATTAAACTAAATAGCAAAAGAAGAAGAAA
* * * * * *
3658 AGAGTTTAATTCAGAGTAATTAAACTAAAAAGCAAGAGAAGAAGAAAACAGTTTAATTC-AGAGT
1 ATAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAA-AAAATAGTTTAATTCTAG-GT
* **
3722 AATTAAACTAAAGAGCAAGTGAAGAAGAAA
64 AATTAAACTAAATAGCAAAAGAAGAAGAAA
* * * * * *
3752 ACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACATTTTAATTCTGGGTA
1 ATAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAA-AAAATAGTTTAATTCTAGGTA
* * ** *
3817 ACTAAACTAAAAATTAAGAGAAGAAGAAA
65 ATTAAACTAAATAGCAAAAGAAGAAGAAA
* * * * * *
3846 AGAGTTTAATTCCGGGTAATTAAACTAAATAGTAAAAGAGGAAGAAAAGAGTTTAACTC-AGGGT
1 ATAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAA-AAAATAGTTTAATTCTA-GGT
* *
3910 AATTAAACTAAAGAGCAAGAGAAGAAGAAA
64 AATTAAACTAAATAGCAAAAGAAGAAGAAA
* *
3940 ACAGTTTGATTCTGGGTAAT
1 ATAGTTTAATTCTGGGTAAT
3960 CAAGCTAAGC
Statistics
Matches: 831, Mismatches: 120, Indels: 96
0.79 0.11 0.09
Matches are distributed among these distances:
93 84 0.10
94 394 0.47
95 2 0.00
96 1 0.00
97 7 0.01
98 3 0.00
99 7 0.01
100 8 0.01
101 197 0.24
102 5 0.01
103 2 0.00
104 3 0.00
105 4 0.00
106 40 0.05
107 7 0.01
108 47 0.06
109 1 0.00
110 7 0.01
111 1 0.00
112 1 0.00
113 10 0.01
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.24
Consensus pattern (93 bp):
ATAGTTTAATTCTGGGTAATTAAACTAAATAGCAAAAGAAGAAAAAATAGTTTAATTCTAGGTAA
TTAAACTAAATAGCAAAAGAAGAAGAAA
Found at i:3001 original size:54 final size:54
Alignment explanation
Indices: 2939--3407 Score: 430
Period size: 54 Copynumber: 9.0 Consensus size: 54
2929 GTAATTAAAC
2939 TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
1 TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
2993 TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
1 TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
* *
3047 TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACT-AA-A-
1 TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
* * *
3098 T-AGT-G--AAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACT-AA-A-
1 TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
* * * *
3145 T-AGT-G--AAAGAAGAAGAGGTTAGTTTAATTATGGGCGATTGAACTAAAGAT
1 TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
* * *
3195 TAAATAGCAAAAGAAGAAGAGGTTAGTCTAATTCAGAGCAATTAAACTAAAGAGT
1 TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGA-T
* * * ** *
3250 AAAAGAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTC----CAGGT-AA-TTAAG-T
1 --TA-AA-TAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
* * * * **
3301 TAAATAGTAAAAGAAGAAG-GTATTAGTTTAATTCTAGGTAATTAAACTAAAGGG
1 TAAATAGCAAAAGAAGAAGAG-GTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
* * * *
3355 TAAA-AG-AAGAAGTACACAGAGGCTAGTTTAATTCTAGGTC-ATTAAACTAAAGA
1 TAAATAGCAA-AAGAAGA-AGAGGTTAGTTTAATTCT-GGGCAATTAAACTAAAGA
3408 GCAAGAGAGG
Statistics
Matches: 355, Mismatches: 36, Indels: 48
0.81 0.08 0.11
Matches are distributed among these distances:
46 1 0.00
47 109 0.31
48 4 0.01
49 3 0.01
50 3 0.01
51 6 0.02
52 6 0.02
53 17 0.05
54 170 0.48
55 6 0.02
57 1 0.00
58 2 0.01
59 27 0.08
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.26
Consensus pattern (54 bp):
TAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGAT
Found at i:3199 original size:202 final size:202
Alignment explanation
Indices: 2824--3366 Score: 750
Period size: 202 Copynumber: 2.7 Consensus size: 202
2814 AAAGTTTAAA
* * * * * *
2824 TCAGAACAGTTAAATTAAAGAGTAAA-AGTAAAAGAA-ACAAAGGATAGTTTAATTCTAGGTAAT
1 TCAGAGCAATTAAACTAAAGATTAAATAGTAAAAGAAGA-AGAGGTTAGTTTAATTCTAGGTAAT
* * * * *
2887 TAAACTAAATAGCAAAAGAAGAAAAGGATAGTTTAATTCCAGGTAATTAAACTAAATAGCAAAAG
65 TAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAG
*
2952 AAGAAGAGGTTAGTTTAATTCTGGGCAATTAAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTT
130 AAGAAGAGGTTAGTTTAATTATGGGCAATTAAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTT
*
3017 AGTTTAAT
195 AGTCTAAT
* * *
3025 TCTGGGCAATTAAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATT
1 TCAGAGCAATTAAACTAAAGATTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATT
* *
3090 AAACTAAATAGTGAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTGAAAGA
66 AAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGA
* *
3155 AGAAGAGGTTAGTTTAATTATGGGCGATTGAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTTA
131 AGAAGAGGTTAGTTTAATTATGGGCAATTAAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTTA
3220 GTCTAAT
196 GTCTAAT
* * *
3227 TCAGAGCAATTAAACTAAAGAGTAAAAGAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCCAGG
1 TCAGAGCAATTAAACTAAAGA-T--TA-AA-TAGTAAAAGAAGAAGAGGTTAGTTTAATTCTAGG
** * **
3292 TAATTAAGTTAAATAGTAAAAGAAGAAG-GTATTAGTTTAATTCTAGGTAATTAAACTAAAGGGT
61 TAATTAAACTAAATAGTAAAAGAAGAAGAG-GTTAGTTTAATTCTAGGTAATTAAACTAAATAGT
3356 AAAAGAAGAAG
125 AAAAGAAGAAG
3367 TACACAGAGG
Statistics
Matches: 301, Mismatches: 33, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
201 20 0.07
202 178 0.59
203 2 0.01
205 1 0.00
206 3 0.01
207 97 0.32
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (202 bp):
TCAGAGCAATTAAACTAAAGATTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATT
AAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGA
AGAAGAGGTTAGTTTAATTATGGGCAATTAAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTTA
GTCTAAT
Found at i:3268 original size:59 final size:59
Alignment explanation
Indices: 3203--3316 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
3193 ATTAAATAGC
*
3203 AAAAGAAGAAGAGGTTAGTCTAATT-CAGAGCAATTAAACTAAAGAGTAAAAGAAGTAGT
1 AAAAGAAGAAGAGATTAGTCTAATTCCAG-GCAATTAAACTAAAGAGTAAAAGAAGTAGT
* * ** *
3262 AAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAGTTAAATAGTAAAAGAAG
1 AAAAGAAGAAGAGATTAGTCTAATTCCAGGCAATTAAACTAAAGAGTAAAAGAAG
3317 AAGGTATTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 45 0.94
60 3 0.06
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.23
Consensus pattern (59 bp):
AAAAGAAGAAGAGATTAGTCTAATTCCAGGCAATTAAACTAAAGAGTAAAAGAAGTAGT
Found at i:3401 original size:160 final size:160
Alignment explanation
Indices: 3098--3408 Score: 380
Period size: 160 Copynumber: 1.9 Consensus size: 160
3088 TTAAACTAAA
* * * * *
3098 TAGTGAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTGAAAGAAGAAGAGG
1 TAGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGA
* * * * * *
3163 TTAGTTTAATTATGGGCGATTGAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTTAGTCTAATT
66 TTAGTTTAATTATAGGCAATTAAACTAAAGAGTAAATAGCAAAAGAACAAGAGGCTAGTCTAATT
3228 CAGAGCAATTAAACTAAAGAGTAAAAGAAG
131 CAGAGCAATTAAACTAAAGAGTAAAAGAAG
**
3258 TAGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAGTTAAATAGTAAAAGAAGAAG-GT
1 TAGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAATAGTAAAAGAAGAAGAG-
* * * * *
3322 ATTAGTTTAATTCTAGGTAATTAAACTAAAGGGTAAA-AG-AAGAAGTACACAGAGGCTAGTTTA
65 ATTAGTTTAATTATAGGCAATTAAACTAAAGAGTAAATAGCAA-AAGAACA-AGAGGCTAGTCTA
3385 ATTCTAG-GTC-ATTAAACTAAAGAG
128 ATTC-AGAG-CAATTAAACTAAAGAG
3409 CAAGAGAGGA
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
158 2 0.02
159 8 0.06
160 115 0.90
161 3 0.02
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (160 bp):
TAGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGA
TTAGTTTAATTATAGGCAATTAAACTAAAGAGTAAATAGCAAAAGAACAAGAGGCTAGTCTAATT
CAGAGCAATTAAACTAAAGAGTAAAAGAAG
Found at i:3582 original size:141 final size:141
Alignment explanation
Indices: 2869--3951 Score: 894
Period size: 141 Copynumber: 7.4 Consensus size: 141
2859 AACAAAGGAT
* * * *
2869 AGTTTAATTCTAGGTAATTAAACTAAATAGCAAAAGAAGAA-AAGGATAGTTTAATTCCAGGTAA
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAAGAAGAGTTTAATT-CAGGTAA
* * *** * * *
2933 TTAAACTAAATAGCAAAAGAAGAAG-AGGTTAGTTTAATTCTGGGCAATTAAACTAAAGATTAAA
65 TTAAACTAAAAAGCAAGAGAAGAAGAAAACT-GTTTAATTCTGGGTAATTAAACTAAATAGT--A
* *
2997 TAGCAAAAGAAGAAGAGG
127 -AG-AGAAGAAGAA-AAG
* ** *
3015 TTAGTTTAATTCTGGGCAATTAAACTAAAGATTAAATAGCAAAAGAAGAAGAGGTTAGTTTAATT
1 --AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAA-AG---AAGAAGAAGAAG--AGTTTAATT
* * *** *
3080 CTAGGTAATTAAACTAAATAGTGAA-AGAAGAAG-AGGTTAGTTTAATTCTAGGTAATTAAACTA
58 C-AGGTAATTAAACTAAAAAG-CAAGAGAAGAAGAAAACT-GTTTAATTCTGGGTAATTAAACTA
****
3143 AATAGTGAA-AGAAGAAGAGGTT
120 AATAGT-AAGAGAAGAAGAAAAG
* ** * **
3165 AGTTTAATTATGGGCGATTGAACTAAAGATTAAATAGCAA-AAGAAGAAGAGGTTAGTCTAATTC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAA-AG-AAGAAGAAGAAGA-G-T--T-TAATTC
* * **
3229 AGAGCAATTAAACTAAAGAGTAAAAG-AAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGT
59 AG-GTAATTAAACT----A--AAAAGCAAG-AG---AAGAAGAA-A-ACT-GTTTAATTCTGGGT
** * ** **
3293 AATTAAGTTAAATAGTAAAAGAAGAAGGTATT
110 AATTAAACTAAATAGTAAGAGAAGAAGAAAAG
* * * *
3325 AGTTTAATTCTAGGTAATTAAACTAAAGGGTAAAAGAAGAAGTACACAGAGGCTAGTTTAATTCT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAG---A-AGAAG--AGTTTAATTC-
* * * * *
3390 AGGTCATTAAACTAAAGAGCAAGAGAGGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAAA
59 AGGTAATTAAACTAAAAAGCAAGAGAAGAAGAAAACTGTTTAATTCTGGGTAATTAAACTAAATA
* *
3455 GTAAGAGGAGAAAAAAAG
124 GTAAGAGAAGAAGAAAAG
3473 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAA-AAGAGTTTAATTCAGAGTAA
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAAGAAGAGTTTAATTCAG-GTAA
*
3537 TTAAACTAAAAAGCAAGAGAAGAAGAAAACTGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGA
65 TTAAACTAAAAAGCAAGAGAAGAAGAAAACTGTTTAATTCTGGGTAATTAAACTAAATAGTAAGA
*
3602 GGAGAA-AAAAG
130 GAAGAAGAAAAG
3613 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAA-AAGAGTTTAATTCAGAGTAA
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAAGAAGAGTTTAATTCAG-GTAA
* * * * * *
3677 TTAAACTAAAAAGCAAGAGAAGAAGAAAACAGTTTAATTCAGAGTAATTAAACTAAAGAGCAAGT
65 TTAAACTAAAAAGCAAGAGAAGAAGAAAACTGTTTAATTCTGGGTAATTAAACTAAATAGTAAGA
*
3742 GAAGAAGAAAAC
130 GAAGAAGAAAAG
* * * *
3754 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAA-AACATTTTAATTCTGGGTAA
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAAGAAGAGTTTAATTC-AGGTAA
* ** ** * *
3818 CTAAACTAAAAATTAAGAGAAGAAGAAAAGAGTTTAATTCCGGGTAATTAAACTAAATAGTAAAA
65 TTAAACTAAAAAGCAAGAGAAGAAGAAAACTGTTTAATTCTGGGTAATTAAACTAAATAGTAAGA
*
3883 GAGGAAGAAAAG
130 GAAGAAGAAAAG
* * * * *
3895 AGTTTAACTCAGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAA-AACAGTTTGATTC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAAGAAGAGTTTAATTC
3952 TGGGTAATCA
Statistics
Matches: 797, Mismatches: 96, Indels: 91
0.81 0.10 0.09
Matches are distributed among these distances:
140 135 0.17
141 261 0.33
142 1 0.00
143 3 0.00
144 2 0.00
145 10 0.01
146 2 0.00
147 3 0.00
148 152 0.19
149 3 0.00
150 1 0.00
151 15 0.02
152 8 0.01
153 4 0.01
154 14 0.02
155 71 0.09
156 3 0.00
157 6 0.01
158 3 0.00
159 7 0.01
160 82 0.10
161 3 0.00
162 1 0.00
163 5 0.01
164 1 0.00
165 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (141 bp):
AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAAGAAGAGTTTAATTCAGGTAAT
TAAACTAAAAAGCAAGAGAAGAAGAAAACTGTTTAATTCTGGGTAATTAAACTAAATAGTAAGAG
AAGAAGAAAAG
Found at i:3937 original size:47 final size:47
Alignment explanation
Indices: 3379--3959 Score: 786
Period size: 47 Copynumber: 12.4 Consensus size: 47
3369 CACAGAGGCT
* * *
3379 AGTTTAATTCTAGGTCATTAAACTAAAGAGCAAGAGAGGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* * * * *
3426 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGGAGAAAAAAAG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* *
3473 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAAAAG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* * *
3520 AGTTTAATTCAGAGTAATTAAACTAAAAAGCAAGAGAAGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* * * * *
3567 TGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGGAGAA-AAAAG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* *
3613 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGAAAAG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* * *
3660 AGTTTAATTCAGAGTAATTAAACTAAAAAGCAAGAGAAGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* * *
3707 AGTTTAATTCAGAGTAATTAAACTAAAGAGCAAGTGAAGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
3754 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* * * ** *
3801 ATTTTAATTCTGGGTAACTAAACTAAAAATTAAGAGAAGAAGAAAAG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* * * * * *
3848 AGTTTAATTCCGGGTAATTAAACTAAATAGTAAAAGAGGAAGAAAAG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
* *
3895 AGTTTAACTCAGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
*
3942 AGTTTGATTCTGGGTAAT
1 AGTTTAATTCTGGGTAAT
3960 CAAGCTAAGC
Statistics
Matches: 471, Mismatches: 62, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
46 40 0.08
47 431 0.92
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.22
Consensus pattern (47 bp):
AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
Found at i:4001 original size:22 final size:22
Alignment explanation
Indices: 3970--4207 Score: 263
Period size: 22 Copynumber: 11.1 Consensus size: 22
3960 CAAGCTAAGC
3970 AGTAAAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
* *
3992 AGTAATAGAAAGAGTAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
*
4014 AGTAATAGAAAGAGTAATCAG-
1 AGTAAAAGAAAGAGTAATCAGA
* *
4035 AGTAAAAGGAAGAGTAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
**
4057 AGCCAAAGAAAGAGTAATCAG-
1 AGTAAAAGAAAGAGTAATCAGA
* * *
4078 AGTAAAAGGAAGAATAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
**
4100 AGGCAAAGAAAGAGTAATCAG-
1 AGTAAAAGAAAGAGTAATCAGA
* * *
4121 AGTAAAAGGAAGAATAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
** *
4143 AGCCAAAGAAATAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
*
4165 AG---AAGAAAGAGTAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
4184 AGTAAAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
4206 AG
1 AG
4208 ATTAGAGTAA
Statistics
Matches: 176, Mismatches: 34, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
19 17 0.10
21 50 0.28
22 109 0.62
ACGTcount: A:0.58, C:0.07, G:0.22, T:0.13
Consensus pattern (22 bp):
AGTAAAAGAAAGAGTAATCAGA
Found at i:4009 original size:12 final size:12
Alignment explanation
Indices: 3970--4031 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
3960 CAAGCTAAGC
*
3970 AGTAAAAGAAAG
1 AGTAATAGAAAG
3982 AGTAATCAG--A-
1 AGTAAT-AGAAAG
3992 AGTAATAGAAAG
1 AGTAATAGAAAG
*
4004 AGTAAT-CAAA-
1 AGTAATAGAAAG
4014 AGTAATAGAAAG
1 AGTAATAGAAAG
4026 AGTAAT
1 AGTAAT
4032 CAGAGTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
9 2 0.05
10 12 0.29
11 8 0.20
12 17 0.41
13 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.18
Consensus pattern (12 bp):
AGTAATAGAAAG
Found at i:4019 original size:10 final size:11
Alignment explanation
Indices: 3978--4033 Score: 53
Period size: 10 Copynumber: 5.1 Consensus size: 11
3968 GCAGTAAAAG
3978 AAAGAGTAATC
1 AAAGAGTAATC
* *
3989 AGA-AGTAATAG
1 AAAGAGTAAT-C
4000 AAAGAGTAATC
1 AAAGAGTAATC
*
4011 AAA-AGTAATAG
1 AAAGAGTAAT-C
4022 AAAGAGTAATC
1 AAAGAGTAATC
4033 A
1 A
4034 GAGTAAAAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
10 12 0.34
11 11 0.31
12 12 0.34
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18
Consensus pattern (11 bp):
AAAGAGTAATC
Found at i:4053 original size:43 final size:42
Alignment explanation
Indices: 3974--4205 Score: 315
Period size: 43 Copynumber: 5.4 Consensus size: 42
3964 CTAAGCAGTA
* * *
3974 AAAGAAAGAGTAATCAGAAGTAATAGAAAGAGTAATCAAAAGT
1 AAAGAAAGAGTAATCAG-AGTAAAAGGAAGAGTAATCAAAAGC
4017 AATAGAAAGAGTAATCAGAGTAAAAGGAAGAGTAATCAAAAGCC
1 AA-AGAAAGAGTAATCAGAGTAAAAGGAAGAGTAATCAAAAG-C
*
4061 AAAGAAAGAGTAATCAGAGTAAAAGGAAGAATAATCAAAAGGC
1 AAAGAAAGAGTAATCAGAGTAAAAGGAAGAGTAATCAAAA-GC
*
4104 AAAGAAAGAGTAATCAGAGTAAAAGGAAGAATAATCAAAAGCC
1 AAAGAAAGAGTAATCAGAGTAAAAGGAAGAGTAATCAAAAG-C
* * * *
4147 AAAGAAATAGTAATCAGA--AGAAGAAAGAGTAATCAAAAGTA
1 AAAGAAAGAGTAATCAGAGTAAAAGGAAGAGTAATCAAAAG-C
4188 AAAGAAAGAGTAATCAGA
1 AAAGAAAGAGTAATCAGA
4206 AGATTAGAGT
Statistics
Matches: 174, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
41 35 0.20
42 1 0.01
43 120 0.69
44 18 0.10
ACGTcount: A:0.58, C:0.07, G:0.22, T:0.13
Consensus pattern (42 bp):
AAAGAAAGAGTAATCAGAGTAAAAGGAAGAGTAATCAAAAGC
Found at i:4120 original size:86 final size:86
Alignment explanation
Indices: 3974--4205 Score: 351
Period size: 86 Copynumber: 2.7 Consensus size: 86
3964 CTAAGCAGTA
* * *
3974 AAAGAAAGAGTAATCAGAAGTAATAGAAAGAGTAATCAAAAGTAATAGAAAGAGTAATCAGAGTA
1 AAAGAAAGAGTAATCAG-AGTAAAAGAAAGAGTAATCAAAAGGAAAAGAAAGAGTAATCAGAGTA
*
4039 AAAGGAAGAGTAATCAAAAGCC
65 AAAGGAAGAATAATCAAAAGCC
* * *
4061 AAAGAAAGAGTAATCAGAGTAAAAGGAAGAATAATCAAAAGGCAAAGAAAGAGTAATCAGAGTAA
1 AAAGAAAGAGTAATCAGAGTAAAAGAAAGAGTAATCAAAAGGAAAAGAAAGAGTAATCAGAGTAA
4126 AAGGAAGAATAATCAAAAGCC
66 AAGGAAGAATAATCAAAAGCC
* * *
4147 AAAGAAATAGTAATCAGA--AGAAGAAAGAGTAATCAAAAGTAAAAGAAAGAGTAATCAGA
1 AAAGAAAGAGTAATCAGAGTAAAAGAAAGAGTAATCAAAAGGAAAAGAAAGAGTAATCAGA
4206 AGATTAGAGT
Statistics
Matches: 132, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
84 36 0.27
86 79 0.60
87 17 0.13
ACGTcount: A:0.58, C:0.07, G:0.22, T:0.13
Consensus pattern (86 bp):
AAAGAAAGAGTAATCAGAGTAAAAGAAAGAGTAATCAAAAGGAAAAGAAAGAGTAATCAGAGTAA
AAGGAAGAATAATCAAAAGCC
Found at i:4234 original size:47 final size:44
Alignment explanation
Indices: 4181--4281 Score: 132
Period size: 47 Copynumber: 2.2 Consensus size: 44
4171 AAGAGTAATC
4181 AAAAGTAAAAGAAAGAGTAATCAGAAGATTAGAG-TAATTAAGCTA
1 AAAAGTAAAAGAAAGAGTAATCAGAAG--TAGAGTTAATTAAGCTA
* * *
4226 AATGAAGTAAAAGCAAGAGTAATTAGTAGTAGAGTTAATTAAGCTA
1 AA--AAGTAAAAGAAAGAGTAATCAGAAGTAGAGTTAATTAAGCTA
4272 AAAAGTAAAA
1 AAAAGTAAAA
4282 AGTAATAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
44 8 0.16
45 7 0.14
46 13 0.26
47 22 0.44
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (44 bp):
AAAAGTAAAAGAAAGAGTAATCAGAAGTAGAGTTAATTAAGCTA
Found at i:12329 original size:18 final size:18
Alignment explanation
Indices: 12306--12341 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12296 GATTTCCCCA
12306 CTCTGTTTCATTCCACTT
1 CTCTGTTTCATTCCACTT
12324 CTCTGTTTCATTCCACTT
1 CTCTGTTTCATTCCACTT
12342 GATATCTTCC
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:0.11, C:0.33, G:0.06, T:0.50
Consensus pattern (18 bp):
CTCTGTTTCATTCCACTT
Found at i:14646 original size:2 final size:2
Alignment explanation
Indices: 14639--14683 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
14629 TAGAAAGCTG
14639 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14680 TA TA
1 TA TA
14684 GAGAGAGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15203 original size:23 final size:23
Alignment explanation
Indices: 15159--15203 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
15149 TTTTCCATTA
* *
15159 CTAACATTAAAAAGGGGGAAAAT
1 CTAACATTAAAAAGAGGAAAAAT
*
15182 CTAACATTATAAAGAGGAAAAA
1 CTAACATTAAAAAGAGGAAAAA
15204 AAAAAAGAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (23 bp):
CTAACATTAAAAAGAGGAAAAAT
Done.