Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022605.1 Corchorus olitorius cultivar O-4 contig22638, 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: 3853
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Found at i:2952 original size:24 final size:24
Alignment explanation
Indices: 2923--2979 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
2913 AGTTTAAAAA
*
2923 AAATAGGTATAGA-AATAAATAAAT
1 AAATAGGTACAGAGAAT-AATAAAT
* * *
2947 AAATAGATACAGAGAATAGTAGAT
1 AAATAGGTACAGAGAATAATAAAT
2971 AAATAGGTA
1 AAATAGGTA
2980 GCTAAAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.58, C:0.02, G:0.18, T:0.23
Consensus pattern (24 bp):
AAATAGGTACAGAGAATAATAAAT
Found at i:3009 original size:4 final size:4
Alignment explanation
Indices: 3000--3225 Score: 111
Period size: 4 Copynumber: 58.5 Consensus size: 4
2990 AGATAATAAT
* ** * *
3000 AATA AATA AATA GAT- AATA GCTA AATT AATA AAGA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * *
3046 AGTA AATA AATA GAT- AACA ATTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * * *
3092 AGTA AATA AATA GAT- AATA ATTA AATT AATA AATA AATA GATA ATAGTT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-A-TA
* * * *
3141 AA-A AATA AATA AAAA AATA AAT- AGTA AATA AATA GATA ATAGTT AA-A
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-A-TA AATA
*
3188 AATA AATA AA-A AA-A AATA AAT- AATG AATA AAT- AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
3226 AAAAATCTTT
Statistics
Matches: 163, Mismatches: 40, Indels: 38
0.68 0.17 0.16
Matches are distributed among these distances:
3 31 0.19
4 120 0.74
5 8 0.05
6 4 0.02
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:3029 original size:27 final size:27
Alignment explanation
Indices: 2999--3187 Score: 114
Period size: 23 Copynumber: 7.7 Consensus size: 27
2989 AAGATAATAA
2999 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAATAGATAAATAG-TAAAT
* *
3026 TAATAAAGAAAAAGATAAATAGT--A-
1 TAATAAATAAATAGATAAATAGTAAAT
* *
3050 -AATAAATAGATA-A-CAAT--TAAAT
1 TAATAAATAAATAGATAAATAGTAAAT
*
3072 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAATAGATAAATAGTAAAT
*
3096 -AATAAATAGATA-AT-AAT--TAAAT
1 TAATAAATAAATAGATAAATAGTAAAT
3118 TAATAAATAAATAGAT-AATAGTTAAA-
1 TAATAAATAAATAGATAAATAG-TAAAT
* *
3144 -AATAAATAAAAAAATAAATAGTAAAT
1 TAATAAATAAATAGATAAATAGTAAAT
* * *
3170 AAATAGAT-AATAGTTAAA
1 TAATAAATAAATAGATAAA
3188 AATAAATAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 41
0.68 0.10 0.22
Matches are distributed among these distances:
19 2 0.02
21 8 0.06
22 3 0.02
23 40 0.32
24 6 0.05
25 22 0.18
26 12 0.10
27 26 0.21
28 5 0.04
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.27
Consensus pattern (27 bp):
TAATAAATAAATAGATAAATAGTAAAT
Found at i:3059 original size:46 final size:46
Alignment explanation
Indices: 2982--3152 Score: 222
Period size: 46 Copynumber: 3.7 Consensus size: 46
2972 AATAGGTAGC
* **
2982 TAAAG-AAAAGATAATAATAATAAATAAATAGATAATAGCTAAATTAA
1 TAAAGAAAAAGAT-A-AATAGTAAATAAATAGATAATAATTAAATTAA
*
3029 TAAAGAAAAAGATAAATAGTAAATAAATAGATAACAATTAAATTAA
1 TAAAGAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
*
3075 TAAATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
1 TAAAGAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
* * * *
3121 TAAATAAATAGAT-AATAGTTAA-AAATAAATAA
1 TAAAGAAAAAGATAAATAGTAAATAAATAGATAA
3153 AAAAATAAAT
Statistics
Matches: 114, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
44 9 0.08
45 8 0.07
46 84 0.74
47 6 0.05
48 7 0.06
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (46 bp):
TAAAGAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
Found at i:3089 original size:12 final size:11
Alignment explanation
Indices: 3027--3230 Score: 90
Period size: 11 Copynumber: 18.1 Consensus size: 11
3017 TAGCTAAATT
*
3027 AATAAAGAAAA
1 AATAAATAAAA
**
3038 AGATAAATAGTA
1 A-ATAAATAAAA
* *
3050 AATAAATAGAT
1 AATAAATAAAA
* * *
3061 AACAATTAAATT
1 AATAAATAAA-A
3073 AATAAATAAAA
1 AATAAATAAAA
**
3084 AGATAAATAGTA
1 A-ATAAATAAAA
* *
3096 AATAAATAGAT
1 AATAAATAAAA
* *
3107 AATAATTAAATT
1 AATAAATAAA-A
3119 AATAAATAAATA
1 AATAAATAAA-A
* *
3131 GATAATAGTTAAA
1 AATAA-A-TAAAA
3144 AATAAATAAAAA
1 AATAAAT-AAAA
**
3156 AATAAATAGTA
1 AATAAATAAAA
* *
3167 AATAAATAGAT
1 AATAAATAAAA
* *
3178 AAT-AGTTAAA
1 AATAAATAAAA
3188 AATAAATAAAA
1 AATAAATAAAA
*
3199 AA-AAATAAAT
1 AATAAATAAAA
* *
3209 AATGAATAAAT
1 AATAAATAAAA
3220 AATAAA-AAAA
1 AATAAATAAAA
3230 A
1 A
3231 TCTTTTTGGT
Statistics
Matches: 147, Mismatches: 37, Indels: 19
0.72 0.18 0.09
Matches are distributed among these distances:
10 19 0.13
11 67 0.46
12 52 0.35
13 6 0.04
14 3 0.02
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:3171 original size:44 final size:44
Alignment explanation
Indices: 3021--3224 Score: 189
Period size: 46 Copynumber: 4.5 Consensus size: 44
3011 AGATAATAGC
* * * * * *
3021 TAAATTAATAAAGAAAAAGATAAATAGTAAATAAATAGAT-AACAAT
1 TAAA-TAATAAATAAATAGAT-AATAGTTAA-AAATAAATAAAAAAA
* * * * *
3067 TAAATTAATAAATAAAAAGATAAATAGTAAATAAATAGAT-AATAAT
1 TAAA-TAATAAATAAATAGAT-AATAGTTAA-AAATAAATAAAAAAA
3113 TAAATTAATAAATAAATAGATAATAGTTAAAAATAAATAAAAAAA
1 TAAA-TAATAAATAAATAGATAATAGTTAAAAATAAATAAAAAAA
*
3158 TAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAAAAA
1 TAAATAATAAATAAATAGATAATAGTTAAAAATAAAT--AAAAAAA
*
3204 TAAATAATGAATAAATA-ATAA
1 TAAATAATAAATAAATAGATAA
3225 AAAAAATCTT
Statistics
Matches: 145, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
44 39 0.27
45 20 0.14
46 86 0.59
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.26
Consensus pattern (44 bp):
TAAATAATAAATAAATAGATAATAGTTAAAAATAAATAAAAAAA
Found at i:3223 original size:7 final size:7
Alignment explanation
Indices: 3067--3225 Score: 66
Period size: 7 Copynumber: 22.6 Consensus size: 7
3057 AGATAACAAT
3067 TAAATTAA
1 TAAA-TAA
3075 TAAATAA
1 TAAATAA
*
3082 -AAA-GA
1 TAAATAA
*
3087 TAAATAG
1 TAAATAA
3094 TAAATAAA
1 TAAAT-AA
*
3102 TAGATAA
1 TAAATAA
*
3109 TAATTAAA
1 TAAAT-AA
*
3117 TTAATAAA
1 TAAAT-AA
3125 TAAATAGA
1 TAAATA-A
*
3133 T-AATAGT
1 TAAATA-A
3140 TAAA-AA
1 TAAATAA
3146 TAAATAA
1 TAAATAA
3153 -AAA-AA
1 TAAATAA
*
3158 TAAATAG
1 TAAATAA
3165 TAAATAAA
1 TAAAT-AA
*
3173 TAGATAA
1 TAAATAA
**
3180 TAGTTAA
1 TAAATAA
3187 -AAATAAA
1 TAAAT-AA
3194 TAAA-AA
1 TAAATAA
*
3200 AAAATAA
1 TAAATAA
3207 -ATAATGAA
1 TA-AAT-AA
3215 TAAATAA
1 TAAATAA
3222 TAAA
1 TAAA
3226 AAAAATCTTT
Statistics
Matches: 116, Mismatches: 19, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
5 3 0.03
6 24 0.21
7 50 0.43
8 38 0.33
9 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (7 bp):
TAAATAA
Found at i:3227 original size:71 final size:72
Alignment explanation
Indices: 3068--3228 Score: 195
Period size: 71 Copynumber: 2.2 Consensus size: 72
3058 GATAACAATT
* *
3068 AAATTAATAAATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAATAAATAAATAGA
1 AAATAAAT-AATAAAAA-ATAAATAGTAAATAAATAGATAATAATTAAA-TAATAAATAAATAAA
* **
3133 TAATAGTTAA
63 AAATAAATAA
*
3143 AAATAAAT-A-AAAAAATAAATAGTAAATAAATAGATAATAGTTAAA-AATAAATAAA-AAAAAA
1 AAATAAATAATAAAAAATAAATAGTAAATAAATAGATAATAATTAAATAATAAATAAATAAAAAA
3204 TAAATAA
66 TAAATAA
*
3211 TGAATAAATAATAAAAAA
1 -AAATAAATAATAAAAAA
3229 AATCTTTTTG
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
68 9 0.12
69 17 0.22
70 1 0.01
71 36 0.47
72 5 0.07
73 1 0.01
75 7 0.09
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (72 bp):
AAATAAATAATAAAAAATAAATAGTAAATAAATAGATAATAATTAAATAATAAATAAATAAAAAA
TAAATAA
Done.