Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015802.1 Corchorus olitorius cultivar O-4 contig15835, 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: 11722
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Found at i:3129 original size:13 final size:13
Alignment explanation
Indices: 3111--3135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3101 ACAGCAAGTA
3111 AGGAACTAAAAAC
1 AGGAACTAAAAAC
3124 AGGAACTAAAAA
1 AGGAACTAAAAA
3136 AACAGTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.12, G:0.16, T:0.08
Consensus pattern (13 bp):
AGGAACTAAAAAC
Found at i:3138 original size:15 final size:15
Alignment explanation
Indices: 3118--3174 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
3108 GTAAGGAACT
3118 AAAAACAGGAACTAA
1 AAAAACAGGAACTAA
*
3133 AAAAACA-G--TTAA
1 AAAAACAGGAACTAA
* * *
3145 ACAAATAGGAACTCA
1 AAAAACAGGAACTAA
3160 AAAAACAGGAACTAA
1 AAAAACAGGAACTAA
3175 TGAACTAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
12 8 0.26
13 1 0.03
14 1 0.03
15 21 0.68
ACGTcount: A:0.63, C:0.14, G:0.12, T:0.11
Consensus pattern (15 bp):
AAAAACAGGAACTAA
Found at i:3143 original size:60 final size:63
Alignment explanation
Indices: 3059--3210 Score: 202
Period size: 64 Copynumber: 2.4 Consensus size: 63
3049 TAAAACAGTT
* * *
3059 AAACAGGGACTCAAAAAAACAGTTAAAGAAATA-GAACTC-AAAACAGCAAGTAAGGAACT-AA
1 AAACAGGAACT-AAAAAAACAGTTAAACAAATAGGAACTCAAAAACAGCAACTAAGGAACTAAA
* *
3120 AAACAGGAACTAAAAAAACAGTTAAACAAATAGGAACTCAAAAAACAGGAACTAATGAACTAAA
1 AAACAGGAACTAAAAAAACAGTTAAACAAATAGGAACTC-AAAAACAGCAACTAAGGAACTAAA
* *
3184 AAACAGCAACTTAAAAAACAGTTAAAC
1 AAACAGGAACTAAAAAAACAGTTAAAC
3211 CAGCAGGAAC
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
60 20 0.25
61 16 0.20
63 17 0.21
64 27 0.34
ACGTcount: A:0.59, C:0.15, G:0.13, T:0.12
Consensus pattern (63 bp):
AAACAGGAACTAAAAAAACAGTTAAACAAATAGGAACTCAAAAACAGCAACTAAGGAACTAAA
Found at i:3185 original size:22 final size:23
Alignment explanation
Indices: 3153--3256 Score: 79
Period size: 22 Copynumber: 4.4 Consensus size: 23
3143 AAACAAATAG
3153 GAACTCAAAAAACAGGAAC-TAAT
1 GAACT-AAAAAACAGGAACTTAAT
* *
3176 GAACTAAAAAACAGCAACTTAAA
1 GAACTAAAAAACAGGAACTTAAT
* * *
3199 AAACAGTTAAACCAGCAGGAACTTAAT
1 GAAC---TAAA-AAACAGGAACTTAAT
* *
3226 -TACTCAAAAACAGGAAC-TAAT
1 GAACTAAAAAACAGGAACTTAAT
3247 GAACTAAAAA
1 GAACTAAAAA
3257 CAACAACTAA
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
21 4 0.06
22 27 0.44
23 14 0.23
26 6 0.10
27 11 0.18
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (23 bp):
GAACTAAAAAACAGGAACTTAAT
Found at i:3240 original size:71 final size:72
Alignment explanation
Indices: 3155--3427 Score: 380
Period size: 71 Copynumber: 3.8 Consensus size: 72
3145 ACAAATAGGA
*
3155 ACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTTAAAAAACAGTTAAACCAGCAGGAA
1 ACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAACCAGCAGGAA
*
3220 CTTAATT
66 CTCAATT
*
3227 ACTC-AAAAACAGGAACTAATGAACT-AAAAACAACAACT-AAAAAACAGTTAAACTTAAACTAG
1 ACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAAC-----C-AG
*
3289 CAGG-A-TGCAGA-A
60 CAGGAACT-CA-ATT
3301 ACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAACCAGCAGGAA
1 ACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAACCAGCAGGAA
3366 CTCAATT
66 CTCAATT
*
3373 ACTC-AAAAACAGGAACTAATGAACTAAAAAATAGCAACTAAAAAAACAGTTAAAC
1 ACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAAC
3428 TTAAACCAGC
Statistics
Matches: 181, Mismatches: 6, Indels: 29
0.84 0.03 0.13
Matches are distributed among these distances:
69 15 0.08
70 12 0.07
71 78 0.43
72 12 0.07
73 2 0.01
74 7 0.04
75 28 0.15
76 12 0.07
77 15 0.08
ACGTcount: A:0.56, C:0.18, G:0.11, T:0.15
Consensus pattern (72 bp):
ACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAACCAGCAGGAA
CTCAATT
Found at i:3315 original size:146 final size:148
Alignment explanation
Indices: 3154--3457 Score: 542
Period size: 146 Copynumber: 2.1 Consensus size: 148
3144 AACAAATAGG
*
3154 AACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTTAAAAAACAGTTAAACCAGCAGGA
1 AACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAACCAGCAGGA
*
3219 ACTTAATTACTCAAAAACAGGAACTAATGAACTAAAAACA-A-CAACT-AAAAAACAGTTAAACT
66 ACTCAATTACTCAAAAACAGGAACTAATGAACTAAAAA-ATAGCAACTAAAAAAACAGTTAAACT
*
3281 TAAACTAGCAGGATGCAGA
130 TAAACCAGCAGGATGCAGA
3300 AACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAACCAGCAGGA
1 AACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAACCAGCAGGA
3365 ACTCAATTACTCAAAAACAGGAACTAATGAACTAAAAAATAGCAACTAAAAAAACAGTTAAACTT
66 ACTCAATTACTCAAAAACAGGAACTAATGAACTAAAAAATAGCAACTAAAAAAACAGTTAAACTT
*
3430 AAACCAGCAGGATGCAGG
131 AAACCAGCAGGATGCAGA
3448 AACTCAAAAA
1 AACTCAAAAA
3458 CAAGATCTAC
Statistics
Matches: 151, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
145 1 0.01
146 102 0.68
147 5 0.03
148 43 0.28
ACGTcount: A:0.55, C:0.18, G:0.12, T:0.15
Consensus pattern (148 bp):
AACTCAAAAAACAGGAACTAATGAACTAAAAAACAGCAACTAAAAAAACAGTTAAACCAGCAGGA
ACTCAATTACTCAAAAACAGGAACTAATGAACTAAAAAATAGCAACTAAAAAAACAGTTAAACTT
AAACCAGCAGGATGCAGA
Found at i:3330 original size:22 final size:22
Alignment explanation
Indices: 3300--3413 Score: 77
Period size: 22 Copynumber: 4.9 Consensus size: 22
3290 AGGATGCAGA
3300 AACTCAAAAAACAGGAACTAATG
1 AACT-AAAAAACAGGAACTAATG
* **
3323 AACTAAAAAACAGCAACTAAAAA
1 AACTAAAAAACAGGAACT-AATG
* *
3346 AACAGTTAAACCAGCAGGAACTCAAT-
1 AAC---TAAA-AAACAGGAACT-AATG
* *
3372 TACTCAAAAACAGGAACTAATG
1 AACTAAAAAACAGGAACTAATG
* *
3394 AACTAAAAAATAGCAACTAA
1 AACTAAAAAACAGGAACTAA
3414 AAAAACAGTT
Statistics
Matches: 69, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
21 3 0.04
22 38 0.55
23 12 0.17
26 6 0.09
27 10 0.14
ACGTcount: A:0.57, C:0.18, G:0.11, T:0.14
Consensus pattern (22 bp):
AACTAAAAAACAGGAACTAATG
Found at i:6265 original size:28 final size:29
Alignment explanation
Indices: 6230--6285 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
6220 GTCAAAATTA
6230 AAACAGTAAATACAGTATGG-AAATACAT
1 AAACAGTAAATACAGTATGGAAAATACAT
6258 AAACAGTAAATACAGTATGGAAAATACA
1 AAACAGTAAATACAGTATGGAAAATACA
6286 GTATACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (29 bp):
AAACAGTAAATACAGTATGGAAAATACAT
Found at i:6338 original size:13 final size:13
Alignment explanation
Indices: 6322--6346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6312 ATATATAGTT
6322 ATACAATATCAGC
1 ATACAATATCAGC
6335 ATACAATATCAG
1 ATACAATATCAG
6347 AAACAGAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
ATACAATATCAGC
Found at i:8122 original size:7 final size:7
Alignment explanation
Indices: 8110--8134 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8100 AATTACAAAT
8110 GATTGGG
1 GATTGGG
8117 GATTGGG
1 GATTGGG
8124 GATTGGG
1 GATTGGG
8131 GATT
1 GATT
8135 TTCGGATAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (7 bp):
GATTGGG
Done.