Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005672.1 Corchorus capsularis cultivar CVL-1 contig05690, 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: 2458
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Found at i:132 original size:39 final size:39
Alignment explanation
Indices: 11--375 Score: 249
Period size: 39 Copynumber: 9.4 Consensus size: 39
1 AGTAATTAAG
* * *
11 TAATTAAGAGTCAAAATG--ATAGTAACCAGT-AATTAA
1 TAATTAAGAGTCAAAAAGAAATAGTAATCAGTAAATTGA
*
47 GTAATTAAGAGTC--AAAGTAATAGTAATCAGTAAAATTGA
1 -TAATTAAGAGTCAAAAAGAAATAGTAATCAGT-AAATTGA
*
86 TAATTAAGAGTCAAAAAGAAATATTAATCAGTAAATTGA
1 TAATTAAGAGTCAAAAAGAAATAGTAATCAGTAAATTGA
* *
125 TAATTAAGAGTAAAAAAGAAATAGTAATCAGTAAATCGA
1 TAATTAAGAGTCAAAAAGAAATAGTAATCAGTAAATTGA
* *
164 TAATTAAGAGTC--AAGGTAATAGTAATCAGTAAATT-A
1 TAATTAAGAGTCAAAAAGAAATAGTAATCAGTAAATTGA
** * * *
200 GTAATTAAGCA-AAAAAAAAAAAGAGATTAACCAGTAAAATTGA
1 -TAATTAAG-AGTCAAAAAGAAATAG--TAATCAGT-AAATTGA
* * * * *
243 TAATTAAGAGTC--AAAGTAATAATAGTCGGCAAAATTGA
1 TAATTAAGAGTCAAAAAGAAATAGTAATCAG-TAAATTGA
* * *
281 TAATTAAGGGTCAAGATAAGAGAT--TAATCTGTAAAGTCTG-
1 TAATTAAGAGTCAA-A-AAGAAATAGTAATCAGTAAA-T-TGA
* *
321 TAATTAAAGAGTCAAGGTAA-AAATAGTAATCAGTAAA-TCA
1 TAATT-AAGAGTCAA--AAAGAAATAGTAATCAGTAAATTGA
*
361 GTAATTAAGAATCAA
1 -TAATTAAGAGTCAA
376 GGGATTAATC
Statistics
Matches: 259, Mismatches: 41, Indels: 53
0.73 0.12 0.15
Matches are distributed among these distances:
35 3 0.01
36 1 0.00
37 51 0.20
38 35 0.14
39 69 0.27
40 44 0.17
41 26 0.10
42 29 0.11
43 1 0.00
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (39 bp):
TAATTAAGAGTCAAAAAGAAATAGTAATCAGTAAATTGA
Found at i:138 original size:18 final size:18
Alignment explanation
Indices: 79--138 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
69 GTAATCAGTA
79 AAATTGATAATTAAGAGT
1 AAATTGATAATTAAGAGT
** * *
97 CAAAAAGAAATATTAATCAGT
1 -AAATTGATA-ATTAA-GAGT
118 AAATTGATAATTAAGAGT
1 AAATTGATAATTAAGAGT
136 AAA
1 AAA
139 AAAGAAATAG
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
18 6 0.19
19 11 0.35
20 11 0.35
21 3 0.10
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.28
Consensus pattern (18 bp):
AAATTGATAATTAAGAGT
Found at i:262 original size:79 final size:77
Alignment explanation
Indices: 11--288 Score: 244
Period size: 79 Copynumber: 3.6 Consensus size: 77
1 AGTAATTAAG
* * * * ** ** *
11 TAATTAAGAGTCAAAATGATAGTAACCAGT-AATTAAGTAATTAAGAG--TCAAAGTAATAGTAA
1 TAATTAAGAGTCAAAGTAATAGTAATCAGTAAATTGA-TAATTAAGAGAAAAAAAAAAAGAGTAA
*
73 TCAGTAAAATTGA
65 CCAGTAAAATTGA
* * * * *
86 TAATTAAGAGTCAAAAAGAAATATTAATCAGTAAATTGATAATTAAGAGTAAAAAAGAAATAGTA
1 TAATTAAGAGTC--AAAGTAATAGTAATCAGTAAATTGATAATTAAGAGAAAAAAAAAAAGAGTA
* *
151 ATCAGT-AAATCGA
64 ACCAGTAAAATTGA
*
164 TAATTAAGAGTCAAGGTAATAGTAATCAGTAAATT-AGTAATTAAGCA-AAAAAAAAAAAGAGAT
1 TAATTAAGAGTCAAAGTAATAGTAATCAGTAAATTGA-TAATTAAG-AGAAAAAAAAAAAGAG--
227 TAACCAGTAAAATTGA
62 TAACCAGTAAAATTGA
* * * *
243 TAATTAAGAGTCAAAGTAATAATAGTCGGCAAAATTGATAATTAAG
1 TAATTAAGAGTCAAAGTAATAGTAATCAG-TAAATTGATAATTAAG
289 GGTCAAGATA
Statistics
Matches: 168, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
75 13 0.08
76 39 0.23
77 24 0.14
78 30 0.18
79 48 0.29
80 13 0.08
81 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.26
Consensus pattern (77 bp):
TAATTAAGAGTCAAAGTAATAGTAATCAGTAAATTGATAATTAAGAGAAAAAAAAAAAGAGTAAC
CAGTAAAATTGA
Found at i:527 original size:18 final size:19
Alignment explanation
Indices: 504--544 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
494 AATCAAATGG
*
504 TAAGAGT-AGAAAGGGTAT
1 TAAGAGTGAAAAAGGGTAT
*
522 TAAGAGTGAAAAATGGTAT
1 TAAGAGTGAAAAAGGGTAT
541 TAAG
1 TAAG
545 TAAAAAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.24
Consensus pattern (19 bp):
TAAGAGTGAAAAAGGGTAT
Found at i:555 original size:44 final size:44
Alignment explanation
Indices: 505--634 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 44
495 ATCAAATGGT
*
505 AAGAGTAGAAAGGGTATTAAGAGTGAAAAATGGTATTAAGTAAA
1 AAGAGTAAAAAGGGTATTAAGAGTGAAAAATGGTATTAAGTAAA
* * * *
549 AAGAGTAAAAATGGTA--AAAAGAGACAAAATGGTATCATAGTAAA
1 AAGAGTAAAAAGGGTATTAAGAGTGA-AAAATGGTATTA-AGTAAA
* *
593 AAGAGTAAAAAGGAT-TTGAAGAGTAAAAAAAATGGTATTAAG
1 AAGAGTAAAAAGGGTATT-AAGAGT--GAAAAATGGTATTAAG
635 AGTAAAAATG
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
42 6 0.09
43 11 0.16
44 33 0.49
46 6 0.09
47 11 0.16
48 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.21
Consensus pattern (44 bp):
AAGAGTAAAAAGGGTATTAAGAGTGAAAAATGGTATTAAGTAAA
Found at i:567 original size:18 final size:18
Alignment explanation
Indices: 544--582 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
534 ATGGTATTAA
544 GTAAAAAGAGTA-AAAATG
1 GTAAAAAGAG-ACAAAATG
562 GTAAAAAGAGACAAAATG
1 GTAAAAAGAGACAAAATG
580 GTA
1 GTA
583 TCATAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.59, C:0.03, G:0.23, T:0.15
Consensus pattern (18 bp):
GTAAAAAGAGACAAAATG
Found at i:2202 original size:15 final size:15
Alignment explanation
Indices: 2182--2216 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2172 GAAACAGGGG
*
2182 ATTAAAAAGAAATCA
1 ATTAAAAAGAAAGCA
2197 ATT-AAAAGAAAGCA
1 ATTAAAAAGAAAGCA
2211 ATTAAA
1 ATTAAA
2217 CTAAAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.20
Consensus pattern (15 bp):
ATTAAAAAGAAAGCA
Found at i:2250 original size:6 final size:6
Alignment explanation
Indices: 2234--2270 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
2224 CTAAGCAAAG
*
2234 TAAAT- TAAATC TAAATC TAAATC TAAATC TGAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
2271 TAGCAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (6 bp):
TAAATC
Done.